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# Introduction Bats and toothed whales have independently evolved a sophisticated biosonar system, allowing both clades to diversify and occupy many different niches. Toothed whales constitute a morphologically and ecologically diverse group of predators, inhabiting every ocean and several large, freshwater river systems. Some species forage on deep-sea squid at mesopelagic depths (e.g. sperm whales), others prey on large schools of fish sparsely distributed in oceanic habitats (e.g. dusky dolphins) or on individual shrimp and fish encountered in shallow river systems inhabited by several species of river dolphins, including Irrawaddy and Ganges river dolphins. While the biosonar signals of many marine toothed whales have been studied in detail, we know little about the polyphyletic assembly of true river dolphins and how the biosonar of these old lineages have evolved to their freshwater habitat. Toothed whale biosonar signals have been studied in captivity over the last 60 years and increasingly also in the wild. Studies of captive animals have contributed greatly towards our understanding of the biosonar performance including dynamic biosonar control. Studies of free-ranging animals complement laboratory studies by revealing how animals use echolocation in the wild, where the natural habitat may have physical characteristics very different from captive settings. Four different types of odontocete biosonar signals have been identified: Sperm whales produce highly directional echolocation signals characterized by low centroid frequency and very high peak-to-peak source level (SL) exceeding 235 dB<sub>pp</sub> re 1 µPa @1 m, which enables them to echolocate deep-sea squid or other prey at relatively long range. Whistling delphinids use very short, broadband clicks with centroid frequencies above 60–80 kHz, and peak-to-peak SL of 210–228 dB. Beaked whales produce frequency- modulated clicks centered around 45 kHz. Peak-to-peak source levels are slightly lower than delphinid clicks, but due to their much longer duration, they contain comparable amounts of energy. Lastly, a polyphyletic assemblage of porpoises, six non-whistling delphinids of the Cephalorhynchus and Lagenorhynchus families, pygmy sperm whales (*Kogia sp.*), and the Franciscana dolphin (*Pontoporia franciscana*) all use Narrow Band High Frequency (NBHF) clicks where energy is concentrated in a narrow frequency band around 130 kHz. These animals seem to produce nearly as directional biosonar signals as delphinids, but at lower source levels. Despite the many studies quantifying sonar parameters for free-living, marine toothed whales, much less variation in signal type or biosonar parameters has been found compared to bats, especially among delphinids. However, most of the delphinids studied to date forage in habitats that may differ less acoustically than is the case for the different bat guilds. Instead it seems that an inverse scaling of frequency with body mass to achieve a similar directionality may be a major driving force across the toothed whale suborder. However, it is unclear how these selective pressures for high amplitude, high source level biosonar signals can be extrapolated to the acoustically complex, relatively shallow and turbid environments inhabited by river dolphins. To address this question, we studied two species of toothed whales that co-occur in waterways of the Sundarbans mangrove forest of Bangladesh. Irrawaddy dolphins (*Orcaella brevirostris*) are freshwater cetaceans living in shallow coastal waters, generally associated with freshwater inputs, as well as far upstream in three large, Indo-Pacific river systems. The extent of their inland range in the Sundarbans varies with seasonal freshwater regimes and may be influenced by the distribution of Ganges river dolphins. Ganges river dolphins (*Platanista gangetica gangetica*) are obligate freshwater dolphins found in the Ganges, Brahmaputra and Karnaphuli river systems where they exhibit a peculiar, side-swimming form of locomotion. The extent of their downstream range in the Sundarbans is also determined by seasonally dynamic freshwater flows, with the Ganges river dolphin favouring low salinity, high turbidity and moderate depth. Both Irrawaddy dolphins and Ganges river dolphins have relatively small bodies comparable to small marine delphinids and porpoises. In the Sundarbans, they inhabit geomorphically complex areas with extremely variable depth, salinity and turbidity in contrast to the more stable characteristics of marine environments. Given the complex acoustic environment and high amount of clutter and reverberation, it may be hypothesized that Irrawaddy dolphins and Ganges river dolphins employ echolocation signals characterized by low-amplitude, high frequency sonar signals emitted at high repetition rates like small bat species hunting in cluttered habitats. In this study, we quantify the biosonar source parameters of Ganges river dolphins and Irrawaddy dolphins to test this hypothesis. We show that these animals use consistently lower source levels and higher repetition rates than oceanic delphinids, possibly limited by high amounts of clutter and reverberation. We demonstrate that Ganges river dolphins have a slightly broader beamwidth than other toothed whales due to their very low centroid frequency but that they achieve a higher directionality than expected from a direct scaling with centroid frequency and size, possibly by using a novel set of bony plates in the forehead. We conclude this study by discussing means to use acoustics to help better understand the conservation needs of these highly endangered freshwater toothed whales. # Materials and Methods ## Study Area Recordings were obtained in the waterways of the Bangladesh part of the Sundarban mangrove forest where recording depths varied from 6.5 to 23 m, (mean 12.94 m). Recordings took place during daylight hours between the 4<sup>th</sup> and16<sup>th</sup> of February 2010 from a 12 m long, wooden research boat. All research was conducted under a research permit issued to the Bangladesh Cetacean Diversity Project of the Wildlife Conservation Society by the Ministry of Environment and Forest, Government of Bangladesh. ## Recording Equipment A vertical array of four Reson TC4034 spherical hydrophones (Reson A/S, Slangerup, Denmark) was formed by mounting hydrophones in a Perspex rod (4 cm diameter, hollow) with 0.75 m spacing. The first hydrophone was positioned at 2 m depth while the last hydrophone was at 4.25 m depth. A buoy was attached to the top of the array, and a 4 kg weight was fixed to the bottom to help maintain the array vertical in the water. Signals were amplified 60 dB by a custom-made amplifier and filter box (1 kHz 1-pole high-pass and 200 kHz 4-pole low-pass filter), then digitized by two synchronized National Instruments USB-6251 A/D converters (National Instruments, Texas, USA) at a sampling rate of 500 kHz per channel and a resolution of 16 bits. The calibrated clip level of the recording chain was 174 dB re µPa (peak), and the frequency response of the recording chain was flat (±2 dB) from 2–180 kHz. ## Data Collection Ganges river dolphins were recorded while foraging or resting at the convergences of channels. Irrawaddy dolphins were recorded during different behaviors (travelling, foraging, and socializing). The boat engine was turned off and the array was lowered into the water once the animals were within about 100 m of the vessel. Data acquisition was initiated and terminated manually and files were stored approximately every minute. Start and end time, position and depth were recorded for every recording event, as well as group composition and behavior. ## Click Analysis Signal analysis was carried out with custom-written routines in Matlab 7.5 (The Mathworks, Inc., Natwick, MA, USA). Each click series (also referred to in the literature as a click train) was examined visually and discarded if more than one animal was present to avoid underestimating interclick intervals. Echolocation clicks were then located on the third hydrophone using an automated click detector with a variable detection threshold chosen during visual inspection of waveforms to exceed the background noise level and detect individual click series. Each click was further analyzed only if detected on all four channels. ## Acoustic Localization Source location relative to the hydrophones was obtained through acoustic localization techniques based on time-of-arrival differences of the same click on the four receivers. To find the time of arrival differences, the signal recorded on the top hydrophone was cross-correlated with the signals recorded on the other hydrophones, excluding surface reflections. A sound speed of 1500 m/s was measured in each recording habitat by emitting pulses with a portable echosounder (Speedtech, Virginia, USA) at the position of the top hydrophone and cross-correlating to find the time-of-arrival at the remaining hydrophones at known distances. For each pair of hydrophones, the time-of-arrival difference can be explained by the equation for a single hyperbola in the two-dimensional plane of the array. Using four receivers, equations for three independent hyperbolas can be generated, and the position of the sound source found by solving the three equations with a least-squares method. Acoustic localization with this array was calibrated in Aarhus Harbour, Denmark, using artificial clicks (2 cycles at 70 kHz) generated by an omnidirectional HS70 hydrophone (Sonar Products) connected to a waveform generator (model 33220A, Agilent Technologies, California, USA). Pulses were emitted from a depth of 2 m and at distances from 5 m to 40 m from the array. Speed of sound during this calibration was calculated using the Leroy equation from measured temperature and salinity values. ## Source Parameter Estimation The interclick interval (ICI) was defined as the time between each click and the previous. Received levels were calculated as peak-peak (pp) and root-mean-square (rms) sound pressure levels within a time window given by the −10 dB end points relative to the peak of the amplitude envelope. The temporal duration of clicks was defined as the length of the −10 dB time window. The energy flux density was calculated for each click as the sum of squared sound pressure values within the −10 dB analysis window. Subsequently, the click power spectrum was calculated as the squared Fast Fourier Transform of a 32-point window centred on the peak envelope of each signal. The power spectrum was then normalized and interpolated with a factor of 100 using a low-pass interpolation. Peak frequency, centroid frequency (defined as the frequency separating the power spectrum into two halves of equal energy) and signal bandwidth (−3 dB power and −10 dB power) was calculated from this power spectrum. Source levels (SL) were defined as the back-calculated sound pressure level 1 m from the source on the acoustic axis, and calculated from received levels by compensating for the transmission loss (dB re. 1 m), estimated as the combination of spherical spreading and frequency- dependent absorption (taken at the centroid frequency of the received click) over the range from the source coordinates to the receiver. ## On-axis Criteria Off-axis signals are subjected to distortion. This means that it is essential to quantify the signal on or as close as possible to the acoustic axis when investigating source parameters of highly directional biosonar signals. With a linear array, the vertical angle of incidence can be estimated, but the horizontal angle of incidence is unknown. To maximize the likelihood of analyzing on-axis clicks, we selected only the highest-amplitude click in a longer click sequences (scans) with clicks of increasing and decreasing amplitude. These scans are most likely associated with the acoustic beam of the animal passing across the axis of the array. Assuming the animal maintains the same source level and directionality, the click with the highest amplitude has the highest likelihood of being on-axis in the horizontal plane. The criteria used to determine if the click was on axis is similar to that described in previous studies with similar arrays, : (1) the click could be localized; (2) the click had the highest received level in a scan (and thus assumed to be on- axis in the horizontal plane); and (3) the highest received level was recorded on one of the two central hydrophones, allowing for estimation of the angle of incidence in the vertical plane. ## Implications for Passive Acoustic Monitoring To evaluate the use of sound source parameters for passive acoustic monitoring studies without the potential for identifying on-axis clicks, a set of click series with only one clicking animal was identified. Each of these click series was passed through an automatic click detector (described above) to find accurate inter-click intervals for the two species. Subsequently, the power spectrum of each click was analyzed to find the centroid frequency. # Results Irrawaddy dolphins were recorded on 16 different occasions during a total of 9 hours, 58 minutes of recordings. The median group size encountered during recordings of Irrawaddy dolphins was 3 animals. During recordings, this species was observed while foraging and travelling. Ganges river dolphins (median group size 4 animals) were recorded in two different occasions and a total of 57 minutes of recordings were obtained from these encounters. In both recording occasions, the Ganges river dolphins were located in channel convergences. The hydrophone localization calibration indicated that clicks within 40 m were localized with a resulting error in the transmission loss estimates of less than 3 dB, which was deemed acceptable in accordance with previous studies. Consequently, only clicks recorded within a 40 m range of the hydrophone array were used for the analysis of the source parameters. A total of 15 Irrawaddy dolphin and 29 Ganges river dolphin clicks met the on- axis criteria and were recorded within the localization range of 40 meters. Only one click from each scan was used for analysis, and all recording areas were well separated to prevent recording the same groups of animals repeatedly. Clicks for both species were broadband transients similar to those of marine, whistling delphinids. Mean click duration ± SD was 13.4±3.0 µs for Irrawaddy dolphins and 21.7±2.2 µs for Ganges river dolphins, and Q ratios (defined as the ratio of centroid frequency to RMS bandwidth) was 3.2±0.3 (mean±SD) for Irrawaddy dolphins and 3.1±0.3 for Ganges river dolphins. Ganges river dolphin click source levels were significantly lower than the source levels of Irrawaddy dolphin clicks (Kruskal-Wallis: p\<0.0001). Peak-to- peak source levels (mean±SD) were 194.5±3.6 dB re 1 µPa at 1 m for Irrawaddy dolphins and 183.3±3.4 dB re 1 µPa at 1 m for Ganges river dolphins. For both species, these source levels are significantly lower (Kruskal-Wallis: p\<0.0001) than source levels produced by a marine delphinid, the Indopacific Bottlenose dolphin (*Tursiops aduncus*) recorded in a 5–8 m shallow bay (mean peak-to-peak source levels ± SD of 205±7 dB re 1 µPa at 1 m) and lower than published source levels from most other free-ranging toothed whales with the exception of some species producing narrow-band high-frequency clicks. Similarly, the mean source energy flux density was 136.3 dB re 1 µPa<sup>2</sup>\*s at 1 m for Irrawaddy dolphins and 126.6 dB re 1 µPa<sup>2</sup>\*s at 1 m for Ganges river dolphins. There was no significant relationship between the recording range and the source levels for either species (Kruskal-Wallis: p = 0.46 for Ganges river dolphins and p = 0.45 for Irrawaddy dolphins). The centroid frequency (mean±SD) for Irrawaddy dolphins was 94.6±9.7 kHz, with −3 dB bandwidth of 64.4±15.8 kHz. Ganges river dolphins had a significantly lower centroid frequency (mean±SD) of 61.4±4.9 kHz (Kruskal-Wallis: p\<0.001) and correspondingly also a significantly lower −3 dB bandwidth of 43.8±7.1 dB (Kruskal-Wallis: p\<0.001). Interclick intervals were measured for both species for all on-axis clicks. The ICI values for on-axis clicks were higher than ICI values measured across entire click series. Interclick intervals (mean±SD) for Irrawaddy dolphin on-axis clicks was 44.8±24.6 ms and for Ganges river dolphin on-axis clicks it was 35.0±18.4 ms. In addition, the ICI was measured for entire click series with good signal-to-noise-ratio (SNR) and only one clicking animal at a time. A total of 923 clicks across 41 click series were analyzed for the ICI values of Irrawaddy dolphins and 614 clicks across 25 click series for Ganges river dolphins. For the entire click series, ICI (mean±SD) for Irrawaddy dolphins was 33.5±13.5 ms, and for Ganges river dolphins it was 29.9±9.0 ms. To test the potential for species discrimination in passive acoustic monitoring, probability density functions for Ganges river dolphin and Irrawaddy dolphin centroid frequencies were calculated using means and standard deviations from this paper, and assuming a normal distribution. In addition, a normalized probability density function for the Yangtze finless porpoise species (*Neophocaena phocaenoides asiaeorientialis*) was calculated using peak frequency (comparable to centroid frequency for narrowband high frequency species) and standard deviations from Li et al.. An estimated best separation criterion of 72.5 kHz provided a theoretical 98.7% correct classification of Ganges river dolphin clicks and 98.9% correct classification of Irrawaddy dolphin clicks, whereas an estimated best separation criterion of 112.35 kHz provided 97.2% correct classification of Irrawaddy dolphins and 96.7% correct classification of finless porpoises. For off-axis clicks, spectral distortion increases low-frequency energy so centroid frequency estimates decrease. This meant that the classification of Irrawaddy dolphins decreased to 72.7% (N = 971) with the remainder being misclassified as Ganges river dolphins. Ganges river dolphins, in contrast, were successfully classified 99.2% of the time (N = 641). # Discussion The study of toothed whale biosonar signals has developed rapidly during the last decade. Most studies have focused on marine delphinids and have revealed consistent high amplitude, highly directional echolocation signals from these species. Here, we recorded two small toothed whale species inhabiting areas that are more acoustically complex compared to the open ocean environments of many delphinids to better understand the evolutionary factors shaping different biosonar parameters of echolocating toothed whales. Both species produce broadband echolocation clicks characterized by a short duration and a low Q ratio of centroid frequency to RMS bandwidth of around 3. A short, broadband echolocation click is characteristic of all whistling delphinids, as well as sperm whales. The family platanistidae is an ancient evolutionary lineage that diverged not long after physeteridae. Its use of short, broadband clicks corroborates the hypothesis that the echolocation signal evolved by the shared ancestor of toothed whales was a short, broadband click that gradually evolved towards higher frequencies as greater high-frequency hearing sensitivity co-evolved with the capacity for high-frequency sound production. Echolocating toothed whales normally wait until the echo from a potential target has been received before producing a new click, meaning that the interclick interval between clicks exceeds the two-way travel time plus a processing lag time. When animals are searching, the interclick interval may also reflect the limits of their environment, such as the back wall of a pool or for a deep- diving animal, the altitude above the sea floor where the animal is operating. The interclick interval is therefore often taken as a maximum estimate of the acoustic search range of an echolocating animal. The two animals studied here both had higher click repetition rates compared to Indo-Pacific bottlenose dolphins (*Tursiops aduncus*) and even higher click repetition rates than coastal harbor porpoises \[mean ICI: 80.5 ms, 47\] and riverine Yangtze finless porpoises \[mean ICI: 60.4 ms, 47\]. This indicates that both Irrawaddy dolphins and Ganges river dolphins were searching for prey within a shorter range than most other studied odontocetes. Concurrent with the higher repetition rates, the two species also produced echolocation signals with much lower source level compared to similar sized marine delphinids. Irrawaddy dolphins (mean source levels ± SD of 194.7±4 dB re 1 µPa pp at 1 m) and Ganges river dolphins (183.6±3.5 dB re 1 µPa pp at 1 m) echolocate at more than 10 dB to 20 dB (respectively) lower source levels than other small, oceanic delphinids such as free-ranging pygmy killer whales (*Feresa attenuata*), bottlenose dolphins (*Tursiops sp.*), white-beaked dolphins (*Lagenorhynchus albirostris*), spinner (*Stenella longirostris*) and spotted dolphins (*Stenella attenuata*), and dusky dolphins (*Lagenorhynchus obscurus*, max 210 dB pp). Common to these species is that they often forage in an environment where background noise is the limiting factor that determines how far away the faint echoes from prey organisms can be detected. In a noise- limited echolocation scenario, the echo-to-noise ratio increases proportionally with the source level so that a greater detection range can be achieved by increasing the amplitude of the outgoing signals. For many of these exclusively marine species, the detection range of sparse, patchily distributed prey is a crucial parameter for survival. Selection for a long detection range would therefore promote the evolution of high-amplitude echolocation signals within the constraints provided by the size of the animal, principally the dimensions, composition and biomechanics of the sound-generating nasal structures. The overall body size of many oceanic delphinids is larger than the animals studied here, and it is possible that this size difference could account for the lower source levels of our animals. Indeed, large echolocating animals tend to produce echolocation clicks at high source levels and scaling of source level with body size might explain the low source levels produced by small species such as dusky dolphins. However, Ganges river dolphins are about the same size as dusky dolphins and spinner dolphins and produce similar biosonar clicks (as characterized by short duration and low Q) but with a maximum measured source level of 191 dB re 1 uPa (pp), about 20 dB lower than the maximum measured source levels for the dusky dolphins. Irrawaddy dolphins are larger than both dusky dolphins and Ganges river dolphins yet produce source levels on average nearly 10 dB lower than dusky dolphins. Porpoises and other NBHF species have also been thought particularly adapted to coastal environments, and these species are mostly similar in size or smaller than the Ganges river dolphin. The longer duration of NBHF signals compared to broadband delphinid signals means that it is most appropriate to compare the click energy flux density between species. Source levels of porpoises are comparable to the two species recorded here, with source energy flux density (SL<sub>EFD</sub>)for harbor porpoises (*Phocoena phocoena*) (mean SL<sub>EFD</sub>: 137 dB re 1 µPa<sup>2</sup>\*s) similar to the source energy flux density of Irrawaddy dolphin clicks; Peale’s dolphins (*Lagenorhynchus australis*) with somewhat intermediate source levels (mean SL<sub>EFD</sub>: 133 dB re 1 µPa<sup>2</sup>\*s); and Commerson’s dolphins (*Cephalorhynchus commersonii*) with source levels as low as Ganges river dolphin (mean SL<sub>EFD</sub>: 125 dB re 1 µPa<sup>2</sup>\*s). However, while porpoises and other NBHF species resemble the two study species here both in size and source level, they echolocate at much higher peak and centroid frequencies around 130 kHz. These species have seemingly undergone evolutionary selection for a high-pass filtered biosonar signal, possibly to avoid predation from other toothed whales such as killer whales (*Orcinus orca*). Ganges river dolphins diverged out early in the evolution of *odontoceti*, and it is unlikely that these animals ever risked predation by killer whales. However, the NBHF signal type is a subsequently derived biosonar signal that comes at the cost of a smaller bandwidth and thereby presumably less information about the acoustic environment and it does not help explain why the two species in this study produce source levels below those of oceanic delphinids. One important challenge that these animals face is the task of locating and catching food in an acoustic habitat with high reverberation and clutter levels. Several studies have shown how close proximity to clutter or to the bottom may interfere with the detection of targets. Reverberation from the bottom will necessarily depend on signal frequency, grazing angle, bottom sediment type, and especially depth. The two species here both forage for sparse prey through relatively shallow environments (10–15 m in the Sundarbans). While it is difficult to quantify both underwater clutter and reverberation, it is reasonable to assume that a shallow, restricted river habitat provides more challenging acoustic conditions than the open ocean. Unlike a noise-limited situation, higher source levels do not help detect targets in either reverberation or clutter limited conditions, as the backscattered echo from clutter or bottom will be just as much greater as the echo from potential targets. In addition, forward masking of the outgoing click may play an increasingly important role for toothed whales echolocating at very close range. Consequently, we argue that the acoustic properties of the shallow-water habitat might have favored the use of clicks with relatively low source levels in Irrawaddy and Ganges river dolphins. If reverberation can play an important role in shaping the source levels of echolocating toothed whales, this might also explain the lower source levels found for the Indo-pacific bottlenose dolphins (*Tursiops aduncus*) in a shallow coastal habitat, compared to deep-water common bottlenose dolphins (*Tursiops truncatus*). While common bottlenose dolphins are capable of detecting a metal target on a sandy bottom at up to 70 m range despite the clutter caused by the environment, the typical prey of Irrawaddy dolphins and Ganges river dolphins constitute small fish and shrimp. The low target strength and varied bottom composition in shallow water may prove to be a more complex discrimination task for the animals than detecting high target strength, metal objects. While quantitative measurements of prey target strength and reverberation in different river habitats are needed to support this, we hypothesize that both Irrawaddy dolphins and Ganges river dolphins gain an advantage by using low source level clicks for detecting and discriminating small prey items in shallow-water, cluttered environments. This is not unknown among echolocating animals. Brinkløv et al. demonstrated that the long-legged bat (*Macrophyllum macrophyllum*) gradually decreased the source levels of its echolocation calls when operating in three increasingly cluttered environments. Clutter-imposed constraints from such habitats may have resulted in microchiropteran bats having specialized into guilds inhabiting different foraging niches, with longer detection range seemingly favored for open space foragers compared to bats hunting within dense vegetation. This situation may be paralleled for source levels of toothed whales: Oceanic delphinids use high source levels to find prey at long range in open areas; Irrawaddy dolphins utilize coastal habitats and venture upriver while using intermediate source levels for echolocation; and Ganges river dolphins, which diverged early from the remaining toothed whales and evolved in a spatially restricted freshwater habitat, received little advantage from long- range echolocation and use the lowest measured source levels best suited for echolocating prey at short range. It therefore seems that the selective pressures that have favored the evolution of high frequency, high source level biosonar signals in marine toothed whales cannot be extrapolated to the complex acoustic habitats of freshwater cetaceans. A central component in the high source levels of toothed whales is the production of a narrow echolocation beam through partial collimation of the acoustic energy. Evolution appears to have favored toothed whales with a high directionality index that seems to be remarkably similar across species, with horizontal −3 dB (half-power) beamwidths reported between 13.1 degrees for a harbor porpoise to 6.5 degrees for a beluga (*Delphinapterus leucas*) and 6.2 degrees for a false killer whale (*Pseudorca crassidens*). Large odontocetes (such as sperm whales or beaked whales) can achieve a certain directionality with lower frequencies than smaller whales (such as porpoises or small delphinids) , and this might explain the overall negative correlation between biosonar frequency and body size in toothed whales. From this relationship between body size and frequency, we would predict a relatively high centroid frequency of around 80–100 kHz for the moderately sized Irrawaddy dolphins and a higher centroid frequency of around 80–120 kHz for the small Ganges river dolphins. While Irrawaddy dolphins produced clicks with a relatively high centroid frequency (mean of 92 kHz), the Ganges river dolphins produced clicks with a surprisingly low centroid frequency (a mean±SD of 61.4±4.9 kHz) compared to their body size. Other toothed whales of similar size use biosonar centroid frequencies of around 70–85 kHz (Pygmy killer whales), 80 kHz (Hawaiian spotted dolphins and spinner dolphins), 90–100 kHz (Dusky dolphins) and around 130 kHz for the many NBHF species. The measured centroid frequency and the small size of the Ganges river dolphin would predict approximately half the directionality (6 dB smaller DI) and consequently a much broader beamwidth compared to delphinids and porpoises. Using equations derived from Au et al. and Madsen and Wahlberg (2007), the Ganges river dolphin should have a symmetric −3 dB beamwidth of some 20 degrees and a directionality index (DI) of some 19 dB. This prediction conflicts with findings reported in the only paper investigating the directionality of Ganges river dolphins: Bahl et al. reported that the −3 dB beamwidths of the Ganges river dolphins were in the order of 10 degrees in the horizontal plane and 14 degrees in the vertical plane. We find a similar, but slightly higher value, when fitting the data from Bahl et al. (2007) with a piston that best describes the variation in the data. The data indicate a single-lobed sound beam like all other toothed whales studied so far rather than the peculiar, double-lobed sound beam reported in the early literature. The best-fitting piston model provides a composite beamwidth of 14.5 degrees in the horizontal plane. Such a half power beamwidth corresponds to a DI of 22 dB which is comparable to or slightly lower than the half power beamwidth of harbor porpoises, but around 3 dB (50%) better directionality index than predicted from the low frequency clicks and the small head size of the Ganges river dolphin. Thus, somehow Ganges river dolphins seem to generate a beam directionality that, albeit slightly lower than most toothed whales, is comparable to that of similar sized toothed whales operating almost an octave higher in frequency. The reason for this apparent discrepancy might well lie in the unusual head anatomy of this species: Ganges river dolphins possess two unusual bony maxillary crests that project anteriorly over the facial region and virtually encircle the melon. They are asymmetrical and skewed to the left, and their ventral surfaces are dominated by a thin network of air sacs that seem to have grown dorsally from the pterygoid air sinus system. Purves and Pilleri and Pilleri and colleagues proposed that the crests might function in directing the sound from the melon. It is thus possible that these air-filled bony crests could help provide a better directionality than expected from scaling, and hence explain why Ganges river dolphins can produce clicks at centroid frequencies about an octave below what should be predicted from their size and still achieve a sufficient directionality. These findings support the notion that one of the evolutionary drivers for the echolocation click frequency in toothed whales is indeed directionality. The estimated beamwidth of Ganges river dolphins is still in the broad end of measured toothed whale biosonar beams. While this might be considered a more primitive condition, a slightly wider beam combined with the greater short-range maneuverability of these animals (a consequence of having completely free cervical vertebrae), may facilitate the capture of highly maneuverable prey items at close range throughout a shallow, cluttered rivers habitat. The significant difference in frequency content for these two species might be useful for acoustic species recognition such as seen in songbirds and other animals, and arguably also for some sympatric delphinids. Passive acoustic monitoring efforts may exploit such differences to locate critical species- specific hotspots for these endangered species. The three toothed whale species typically found in the coastal and river areas of the Sundarban National Forest include *Platanista gangetica gangetica*, *Orcaella brevirostris* and *Neophocaena phocaenoides*. The on-axis biosonar centroid frequencies of these species are well separated, and spectral parameters may be a promising way of both detecting and discriminating these animals acoustically. However, because biosonar signals are somewhat distorted when recorded off the acoustic axis, signals recorded away from the acoustic axis will have a lower frequency emphasis ( B and C). Applying the centroid frequency criteria that best separates on-axis clicks to a long series of clicks that would resemble what a passive acoustic monitor could record, results in clicks from Ganges river dolphins classified correctly nearly all the time (99.2% correct classification) whereas clicks from Irrawaddy dolphins were classified less successfully (72.7% correct classification). This results in some Irrawaddy dolphin clicks being incorrectly classified as Ganges river dolphins. The same degree of spectral distortion does not happen with NBHF clicks, whereby passive acoustic monitoring would be able to detect the presence of both finless porpoises and Irrawaddy dolphins reliably. Other criteria would be necessary to reliably classify Ganges river dolphins and discriminate such detections from off-axis Irrawaddy dolphins. One way of doing this would be to shift the separation criteria slightly upwards, and to use only the maximum centroid frequency for a series of clicks. For this dataset, reliable discrimination would be achieved based on the maximum frequency of 11–15 clicks and evaluated using a separation criterion of 74 kHz. In addition to spectral species discrimination, source levels presented here would be essential for estimating the detection function of an acoustic monitoring system, providing the basis for quantifying abundance of these threatened freshwater species. Acoustic monitoring has proven to be a powerful method for determining range, seasonality, and abundance of animals, and may prove essential for understanding the population parameters of cryptic, aquatic animals such as beaked whales, or finless porpoises. Freshwater dolphins all face significant extinction risks, primarily due to habitat loss and fisheries interactions, which led to the recent functional extinction of the Baiji (*Lipotes vexillifer*). Robust acoustic discrimination mechanisms that allows for monitoring of Irrawaddy dolphins and Ganges river dolphins could be especially helpful for managing protected areas such as the three new wildlife sanctuaries that were established by the Government of Bangladesh in the Sundarbans for the conservation of both species and provide better information that can help prevent a continued decline or extinction of these two threatened freshwater species. ## Conclusion Irrawaddy dolphins and Ganges river dolphins within the river systems of the Sundarban mangrove forest use high repetition rate, low source level echolocation clicks compared to marine species of similar size. Whereas obligate marine delphinids use high source level echolocation signals, Irrawaddy dolphins, inhabiting coastal and upriver habitats, produce lower source levels, with mean source levels of 194.7 dB (max 203 dB) re 1 µPa<sub>pp</sub> and Ganges river dolphins, living exclusively in a shallow river habitat, produce even lower source levels of 183.6 dB (max 191) re 1 µPa<sub>pp</sub>. The ultimate cause of these low source levels may be a relaxed selection for long- range echolocation inhabiting restricted, shallow, geomorphically complex river systems, with limits on echolocation range imposed by reverberation and clutter. Interestingly, the centroid frequency of the clicks used by Ganges river dolphins is almost an octave lower than expected from their size. The unusual, air-filled bony maxillary crests found in this species may compensate in part for this lower frequency by providing a larger effective baffle and hence a more directional sound beam than the biosonar frequency and head size would predict. The beamwidth of Ganges river dolphins is still wider than most other toothed whales, and it is possible that this may facilitate capture of highly maneuverable prey items in shallow water. Acoustic discrimination between freshwater odontocetes may facilitate acoustic monitoring efforts and may help prevent a continued decline of these two threatened freshwater species. This study was made possible through the logistical and field support of the Bangladesh Cetacean Diversity Project of the Wildlife Conservation Society. The study was conducted under a research permit issued by the Ministry of Environment and Forest, Government of Bangladesh. E. Fordyce, A. Galatius, J. Ososky, J. Mead, and C. Potter kindly provided pictures and helpful discussions of internal skull morphology. J. S. Jensen and N. U. Kristiansen provided technical support and K. Beedholm assisted with invaluable discussions and technical help. Finally, three anonymous reviewers offered helpful comments and constructive feedback to improve on the manuscript. [^1]: The authors have declared that no competing interests exist. [^2]: Conceived and designed the experiments: FHJ AR PTM. Performed the experiments: FHJ AR RMM BDS. Analyzed the data: FHJ AR. Contributed reagents/materials/analysis tools: PTM VMJ. Wrote the paper: FHJ AR RMM BDS VMJ PTM.
# Introduction *P. marneffei* is considered an indicator pathogen for AIDS. It mainly exits endemically in area of South East Asia that causes fever, lymphadenopathy, hepatosplenomegaly and cutaneous lesions. *P. marneffei* has the unique feature among the species of *Penicillium* of being thermally dimorphic for diagnosis, it grows as a mycelium at 25°C, and a soluble red pigment is produced, whereas, at 37°C, it grows as a yeast form. The clinical features of *P. marneffei* in AIDS patients have been well described, and like other opportunistic pathogens, the infection of *P. marneffei* would exacerbate deterioration of the immune response and accelerate AIDS disease progression, while the mechanism remains elusive. Dendritic cells (DCs) play pivotal roles in host defense by initiating innate immunity and bridging adaptive immunity. DCs are widely distributed in the sub- mucosa, yet have been believed to be involved in HIV-1 infection and transmission. The migration property of DCs has been hijacked by HIV-1 for viral dissemination to CD4<sup>+</sup> T cells by a process that is known as *trans*-infection. The formation of DC-T-cell conjunction, or so-called virological synapses, at which numerous intact viral particles and viral receptors can be recruited, appears to be required for efficient viral transfer. Upon activation by stimuli, such as the bacterial product LPS (lipopolysaccharide), DCs could uptake much more viruses and recruit significantly amounts of viral particles on the virological synapses for enhancement of HIV-1 *trans*-infection. DCs express HIV-1 receptors and can serve as targets for productive HIV-1 replication. Persistent infection of HIV-1 may generate the potential long-lived viral reservoirs in DCs. DCs appear to take vital roles in HIV-1 infection and viral pathogenesis, and a better understanding of the interactions between HIV-1 and DCs would facilitate the elucidation of AIDS pathogenesis. We hence isolated *P. marneffei* from the cutaneous lesions of AIDS patients and analyzed its effects on HIV-1-dendritic cells interaction. We found that MDDCs could be activated by both dimorphic forms of *P. marneffei* for significantly promoting HIV-1 *trans*-infection of CD4<sup>+</sup> T cells, and the *Candida albicans* (*C. albicans*), which has been proved to possess the similar capacity, was used as control. Increased expression of intercellular adhesion molecule 1 (ICAM-1) was observed on fungus-activated MDDCs, and the tighter DC- T-cell conjunction recruited significant amounts of virus particles for viral transfer. We also found that *P. marneffei*-activated MDDCs efficiently activated resting CD4<sup>+</sup> T cells through cell-cell contact and thereby could result in more susceptible targets for viral infection. Our findings demonstrate that DC function and its interaction with HIV-1 have been modulated by opportunistic pathogens such as *P. marneffei* for viral dissemination and infection amplification, highlighting the importance of understanding DC-HIV-1 interaction for viral immunopathogenesis elucidation. # Results ## P. marneffei stimulation promotes the activation of MDDCs In current study, the *C. albican* which has been described previously for induce DC activation was used as a control. *P. marneffe* and *C. albicans* were isolated separately from the skin lesions or the tongues of AIDS patients and cultured in Sabouraud agar plates. *P. marneffei* has the unique feature among the species of *Penicillium* of being thermally dimorphic, it grows as a mycelium at 25°C, similar to *Aspergillus* spp, and a soluble red pigment is produced (PMm-i and-ii), whereas, at 37°C, it grows as a yeast form (PMy). *C. albicans* was identified with sub-inoculation in CHROMagar Candida (, CA-ii), in Corn Tween agar (CA-iii) and with the API 20C AUX yeast identification system. These fungi were sub-cultured for amplification and harvested for heat inactivation. To investigate the potential activation of DCs by fungi, MDDCs were incubated separately with heat-inactivated *C. albicans*, PMy and PMm at a ratio of 1∶10 of DCs to fungi. The phenotypes of MDDCs were examined by immunostaining of cell surface markers; MDDCs showed high level of CD11c expression and were measured for CD83, CD86 and HLA-DR expression levels. Fungal stimulation significantly increased CD83, CD86 and HLA-DR expression compared with medium-treated cells, indicating of fungus-induced MDDCs activation, whereas surface expression of a C-type lectin, DC-SIGN (DC-specific intercellular adhesion molecule 3-grabbing nonintegrin), was decreased in fungus-treated MDDCs. These data suggest that stimulation of *P. marneffei* promotes DCs activation. ## HIV-1 infection of P. marneffei-activated MDDCs is blocked To examine the effects of the stimulation of *P. marneffei* on HIV-1 infection of MDDCs, fungus-treated MDDCs were inoculated with single-cycle, luciferase reporter HIV-Luc/JRFL (CCR5-tropic), and HIV-1 infection was measured by detecting the luciferase activity in cell lysates at 3-9 days post-infection. HIV-1 infection was fully blocked in all fungus-treated MDDCs compared with medium-treated controls, and the detected luciferase activities decreased by at least 75% at 5, 7 and 9 days post-infection. The *C. albicans*, which has been shown to inhibit HIV-1 replication in DCs, was used as a control. These data suggest that HIV-1 infection in MDDCs is blocked after the stimulation of *P. marneffei*. ## P. marneffei stimulation promotes DC-mediated HIV-1 transmission to CD4<sup>+</sup> T cells To determine the capacity for DC-mediated HIV-1 transmission after *P. marneffei* stimulation, MDDCs were treated with heat-inactivated fungi as above and GFP-containing HIV-1 VLPs were used to measure viral transmission efficiency using flow cytometry. HIV-1 VLP-loaded MDDCs were co-cultured with human CD4<sup>+</sup> T-cell line Hut/CCR5 for 30 min, Hut/CCR5 cells with the CD11c<sup>-</sup> staining were gated, and Gag-GFP-associated cells were quantified. The level of GFP association on Hut/CCR5 cells increased from 11% in medium-treated controls to 27–30% in fungus-activated MDDCs, the MFI values showed an over 2-fold increase. Thus, the fungus, including *P. marneffei* and the *C. albicans* control, can promote MDDC-mediated HIV-1 transfer to CD4<sup>+</sup> T cells. Viral *trans* infection was also quantified by using the DC-T-cell co-culture system as described previously. Pseudotyped single-cycle, luciferase reporter HIV-1 was used. Hut/CCR5 and activated autologous primary CD4 <sup>+</sup> T cells were used as the target cells. Differently treated MDDCs loaded HIV- luc/JRFL or HIV-luc/NL4-3 were co-cultured with target cells for 3 days, and HIV-1 infection was monitored by measuring luciferase activity. Fungus- stimulated MDDCs significantly enhanced the capacity to mediate HIV-luc/JRFL or HIV-luc/NL4-3 *trans* infection of HutCCR5 cells, there was a 4.8- to 6.5-fold increase in luciferase activity, when activated primary CD4<sup>+</sup> T cells were used as target, fungus-stimulated MDDCs enhanced HIV-luc/NL4-3 *trans-*infection of primary CD4<sup>+</sup> T cells approximately 2-3- fold. *C. albicans*, having been shown previously to promote DC-mediated HIV-1 transmission, was used as a positive control. Together, these results indicate that MDDCs stimulated by PMm and PMy enhanced their capacity to mediate HIV-1 *trans* infection of CD4<sup>+</sup> T cells. ## Enhanced endocytosis and altered intracellular trafficking of HIV-1 in fungus-activated MDDCs LPS-activated DCs potently enhance HIV-1 *trans* infection and the endocytosis of large amounts of viruses, and the harboring of intact viruses in non- classical multiple vesicular bodies might provide viruses with a means to escape from intracellular proteolysis. To investigate whether fungal stimulation similarly affect on viral endocytosis, fungus-stimulated MDDCs were pulsed with HIV-1 VLPs for 2 h. Trypsin was used to strip cell-surface-bound virus particles, and the internalized viral particles were quantified by detection of Gag-GFP by flow cytometry. Numerous viruses were internalized by fungus- stimulated MDDCs. Gag-GFP was demonstrated in 53.5–57.3% of MDDCs stimulated by *C. albicans*, PMy or PMm, compared with 15.9% in medium-treated immature MDDCs, and the calculated MFI of GFP also exhibited a two-fold increase relative to that in medium-treated controls. The majority of MDDCs-associated viruses could not be removed by trypsin digestion. Blocking with anti-DC-SIGN antibodies before VLP pulsing did not inhibit viral uptake, suggesting a DC-SIGN- independent endocytosis process. By contrast, as shown previously, immature MDDCs bind HIV-1 mainly through surface-expressed DC-SIGN, which can be easily removed by trypsin treatment. To better understand intracellular trafficking in fungus-stimulated DCs, HIV-1 VLP-pulsed MDDCs were visualized by confocal microscopy with immunostaining. Fewer viruses were evenly distributed on the surface or were internalized in medium-treated immature MDDCs, whereas many viral particles were endocytosed and concentrated into the CD81<sup>+</sup> DC-SIGN<sup>-</sup> compartments in fungus-treated MDDCs. These results are consistent with previous observations that LPS-stimulated MDDCs sequester intact HIV-1 in a specialized and tetraspanin CD81<sup>+</sup> compartments. These data suggest that the stimulation by PMy, PMm or *C. albicans* largely promotes HIV-1 endocytosis and sequestration within the tetraspanin CD81<sup>+</sup> compartments of fungus- activated DCs. ## Fungus-activated MDDCs increase ICAM-1 expression, and facilitate DC-T cell contact formation and viral concentration in virological synapses The virological synapses have been demonstrated to provide the most efficient route for HIV-1 transfers between contacting cells. The ICAM-1-LFA-1 interaction has been proved to be involved in the formation of DC-T-cell conjunction and contribute to efficient HIV-1 transfer. To investigate further the mechanism by which fungal treatment enhances viral transfer, ICAM-1 expression on the cell surface was measured. Stimulation with heat-killed PMy, PMm and *C. albicans* enhanced ICAM-1 expression on MDDCs by 2.4- to 2.6-fold, which indicates the potential for tighter cell conjunction formation. The formation of virological synapses was visualized by confocal microscopy, and Hut/CCR5 or activated primary CD4<sup>+</sup> T cells were used as target cells. Many viral particles were efficiently concentrated at the fungus-stimulated DC-T cell contact sites to form virological synapses. In more detailed analysis of the staining, the tetraspanin molecule of CD81 was recruited to the contact sites, which suggests a potential role of CD81 in HIV-1 trafficking. Taken together, these data demonstrated that the enhanced ICAM-1 expression and virological synapses account for increased HIV-1 *trans*-infection mediated by fungus-stimulated MDDCs. ## Fungi facilitate DC-induced activation of resting CD4 <sup>+</sup> T cells and promote viral infection by providing more permissive cell targets DCs can efficiently active naïve T cell, and the activated T cells can provide more permissive targets for robust viral infection. To examine the potential effects of fungi on DC-induced CD4<sup>+</sup> T cell activation and HIV-1 infection of T cells, MDDCs were pulsed with heat-killed fungi or control medium for 2 h. After washing, MDDCs were co-cultured with allogeneic resting CD4<sup>+</sup> T cells for an additional 48 h. T-cell activation was monitored by detection of CD69 expression in gated CD3<sup>+</sup> cells. Overall, fungus- pulsed MDDCs facilitated T-cell activation. In the presence of fungi-pulsed MDDCs, CD69 was expressed on the surface of around 12% of T cells, compared with 4.8% of T cells cultured with MDDCs without fungi. In order to demonstrate the DC-T cell direct contact is requirement for efficient T activation, the transwell plates with an insert membrane size of 0.4 µm were used to separate the MDDCs from T cells. As expected, much less or non- activation of resting T cells was observed. Direct stimulation with heat-killed fungi alone induced very little, transient expression of CD69 on resting T cells, or no expression at all, which demonstrated the need for DCs for activation of resting T cells. We investigated whether fungus-loaded MDDCs can facilitate T-cell susceptibility to HIV-1 infection. T cells co-cultured with fungi-loaded MDDCs were purified and plused with pseudotyped sing-cycle HIV-Luc/NL4-3 reporter virus, and viral infection was detected 5 days later by measuring luciferase activity in cell lysates. HIV-1 infection was significantly enhanced in primary CD4<sup>+</sup> T cells activated by fungus-pulsed MDDCs compared with control MDDCs without fungi. Moreover, direct cell-cell contact was required for initiating T-cell susceptibility to viral infection. Direct treatment of heat-killed fungi did not induce susceptibility of resting T cells to HIV-1 infection. PHA-activated CD4<sup>+</sup> T cells were used as a positive control, which displayed around 30% cells expressed CD69 expression and supported efficient HIV-1 infection in treated T cells. These data suggest that fungus-pulsed DCs facilitate the activation of resting T cells and activate more permissive T cells targets for robust HIV-1 replication. # Discussion Microbial translocation has been proposed as the cause of systemic immune activation in chronic HIV-1 infection ; however, it has not been extensively studied how these co-pathogens speed up deterioration of the immune response. DCs appear to be the common targets for HIV-1 invasion and translocation of other opportunistic pathogens at the mucosa. The functional compromise of DCs by HIV-1 infection is associated with immunosuppression and lack of control of microbial translocation. Given the pivotal roles of DCs in host immunity and viral pathogenesis, the interactions of DCs with HIV-1 have been preferentially targeted for exploiting the potential effects of opportunistic pathogens. DCs treated with opportunistic pathogens, such as *Malaria hemozoin*, *Mycobacterium tuberculosis*, and *C. albicans*, impairs degradative processing and MHC-II presentation of HIV-1 antigens to CD4<sup>+</sup> T cells, and alters cytokine secretion, the enhanced DC-mediated viral *trans* infection was also observed during certain opportunistic infections. In those published studies, the synthetic *hemozoin* products, the *M. tuberculosis* cell wall, or the heal- killed *M. tuberculosis* or *C. albicans* laboratory strains was used. Here, the effects of *P. marneffei* on HIV-1-DC interactions were investigated. The difference is that the used *P. marneffei and the C. albicans* were directly isolated from AIDS patients. Our results demonstrated that both thermally dimorphic forms of *P. marneffei* activated DCs and promoted DC-mediated HIV-1 *trans*-infection of CD4<sup>+</sup> T cells. Moreover, *P. marneffei* -stimulated DCs could further activate resting CD4<sup>+</sup> T cells to induce more susceptible targets for HIV-1 infection. Our results have also shed light on the detailed mechanisms for the enhancement of viral spread. We demonstrated that heat-killed *P. marneffei*, along with *C. albicans*, promote viral uptake in MDDCs, altered viral intracellular sequestration, and importantly, facilitated MDDC-T cell contact by increasing ICAM-1 expression and efficiently concentrating HIV-1 particles in virological synapses. DC activation and altered viral intracellular trafficking are associated with enhanced viral spread. Upregulation of HLA-DR, costimulatory molecules CD83 and CD86, and intercellular molecules on fungus-activated DCs, in general, would encourage DC-T cell conjugate formation. We and other groups have previously reported that increased ICAM-1 expression on DCs correlates with promoted viral transfer, due to stronger DC-T cell interactions through ICAM-1 binding to T-cell-expressed LFA-1. Fungus-stimulated DCs accelerate viral uptake and sequestrate intact viral particles in non-conventional, non-lysosomal tetraspanin CD81<sup>+</sup> compartments. The harboring of intact virus into the non-classical multiple vesicular bodies might provide virus a means to escape from the cellular proteolysis. Upon encountering with CD4<sup>+</sup> T cells, more viruses were recruited on the DC-T cell contacted sites. High levels of endocytosis and altered intracellular trafficking of HIV-1 appear to account for enhanced viral transmission mediated by fungus-activated DCs. *P. marneffe*-stimulated DCs were less permissive for productive infection, which is consistent with previous reports of LPS and *malaria hemozoin* treatment. However, it remains to be clarified which fungal component(s) is responsible for HIV-1 restriction and the underlying mechanisms. LPS-matured DCs show dis-association of the susceptibility for HIV-1 infection with the capacity for mediating HIV-1 *trans* infection. Post-entry restriction of HIV-1 infection in LPS-induced mature DCs has been noted, and inhibition on the levels of reverse transcription and post-integration have been further identified by using real time PCR quantification of viral DNA and integration. Reduced gene expression, such as for co-receptor CCR5, has been reported to be responsible for impaired productive infection of HIV-1 in *malaria-hemozoin-*treated DCs. Higher levels of APOBEC3G and APOBEC3F (for “apolipoprotein B mRNA-editing enzyme, catalytic polypeptide-like 3G and 3F”) also have been shown to mediate the post-entry block of HIV replication in DCs and LPS can upregulate the expression of APOBEC3G/F,. The antiretroviral protein, namely SAMHD1 (SAM domain HD domain-containing protein 1), has been recently identified to inhibit the early step of HIV-1 replication in dendritic- and myeloid cells. It might be possible that fungus-treated DCs increased the expression of these HIV-1 restriction factors and therefore become more resistant to HIV-1 infection. DCs activate resting T cells and can provide more permissive targets for HIV-1 infection. We found that the stimulation of *P. marneffe* significantly accelerated DC-induced activation of resting CD4<sup>+</sup> T cells, which indicates the pivotal importance of DC-driven T-cell activation for the high level of viremia and exacerbation of T-cell depletion in the late stage of HIV-1 infection. It would be interesting to confirm these *in vitro* observations in HIV-1-infected individuals. Our findings revealed that DC function and its interaction with HIV-1 have been modulated by opportunistic pathogens for viral dissemination. Enhanced HIV-1 spread by DCs can target activated CD4<sup>+</sup> T cells, which could further accelerate T-cell depletion and immunosuppression, leading to the lack of control of both viral and fungal pathogens. Our results highlight the importance of studying DC-HIV-1 interactions for understanding viral pathogenesis, and might provide a new insight into the interventions against HIV-1 infection and spread. # Materials and Methods ## Ethics statement and fungi isolation and identification This study was reviewed and approved by the Medical Ethics Review Committee of Yunnan Province, Kunming, China. Written informed consent was provided by study participants and/or their legal guardians. Fungi were isolated from skin lesions or tongue of AIDS patients and cultured on Sabouraud agar plates. Fungus species were identified, sub-cultured for amplification, then harvested and killed by boiling for 1 hr. Fungal cell counts were determined under a light microscope and diluted at 1×10<sup>8</sup>/ml in PBS. MDDCs were stimulated with fungi for 48 hrs at a 1∶10 ratio of cells. ## Cell culture Human peripheral blood mononuclear cells (PBMCs) from healthy donors were provided by the Blood Center of Shanghai, Shanghai, China. CD14<sup>+</sup> monocytes and resting CD4<sup>+</sup> T cells were purified from PBMCs using magnetic beads (BD Biosciences) as described before. CD14<sup>+</sup> monocytes were cultured with granulocyte-macrophage colony-stimulating factor and interleukin (IL)-4 for 6 days to generate the immature DCs. Resting CD4<sup>+</sup> T cells were activated with 5 µg/ml of phytohemagglutinin-P (PHA-P) (Sigma-Aldrich) for 48 h in the presence of 20 IU/ml of recombinant IL-2 (R&D). The human embryonic kidney cell lines HEK293T and the CD4<sup>+</sup> T-cell line Hut/CCR5 (kind gifts from Dr. Vineet KewalRamani, National Cancer Institute, USA) have been described previously. ## HIV-1 or virus-like particle stocks Pseudotyped single-cycle HIV-1 stocks were generated by using calcium phosphate- mediated co-transfection of HEK293T cells with the plasmid pLAI-Δ-env-Luc and expression plasmids of either JRFL (R5-tropic) or NL4-3 (X4-tropic) envelope glycoproteins as described previously. Virus like particles (VLPs), HIV-1-Gag- GFP/JRFL, were generated by cotransfection of HEK293T cells with a plasmid encoding HIV-Gag-GFP and with an expression plasmid of JRFL (kind gifts from Dr. Vineet KewalRamani, National Cancer Institute, USA). Harvested supernatants of transfected cells that contained HIV-1 particles were filtered and titrated with p24<sup>gag</sup> capture ELISA. ## Flow cytometry Cells were stained with specific monoclonal antibodies (McAbs) or isotype- matched IgG controls. McAbs against the following human molecules were used for staining (clone numbers and resources are given in parentheses), Phycoerythrin (PE)-conjugated CD3 (UCHT1; eBioscience), PerCP-cy5.5-CD3 (OKT3, eBioscience), PE-CD11c (3.9; eBioscience), APC-Alexa Fluor750-CD11c (B-ly6; BD Pharmingen), PE-ICAM-1(CD54) (HA58;eBioscience), PE-CD69 (FN50; eBioscience), PE-CD83 (HB15e;eBioscience), PE-CD86 (IT2.2; eBioscience), PE-DC-SIGN (eB-h209; eBioscience), and APC-cy7-HLA-DR (LN3; eBioscience). Stained cells were detected with an LSRII flow cytometer (BD Pharmingen) and analyzed with FlowJo 7.6.1 software. ## HIV infection and transmission assays The luciferase reporter system was adopted for assay of HIV-1 infection and transmission as previously described. In brief, MDDCs were pulsed with 5 ng p24<sup>gag</sup> amounts of pseudotyped HIV-luc/JRFL or HIV-luc/HXB2 for 2 h, and cells were washed for culture or for co-culture with CD4<sup>+</sup> T cells. Hut/CCR5 or PHA-P-activated primary CD4<sup>+</sup> T cells were used as targets. Cells were harvested after 3 days post-infection, and the cell lysates were measured for luciferase activity with a commercially available kit (Promega). DC-mediated HIV-1 transmission also was detected by flow cytometry. HIV-1 VLP (HIV-Gag-GFP/JRFL) was used, and after 1-h co-culture of virus-loaded MDDCs with Hut/CCR5 cells, the T cells were distinguished based on CD11c<sup>-</sup> staining from the mixed cell culture, and the numbers of Gag-GFP associated with T cells were measured. ## HIV-1 binding and internalization assay HIV-1 binding and internalization were quantified by flow cytometry using the VLPs (HIV-Gag-GFP/JRFL). MDDCs were incubated with 40 ng p24<sup>gag</sup> amounts of viruses for 2 h at 37°C and washed. The numbers of Gag-GFP associated with MDDCs were quantified by flow cytometry, and mean fluorescence intensity (MFI) was calculated. When indicated, anti- human DC-SIGN specific McAbs (10 µg/ml) (120507; Abcam) were used for pre-incubation with MDDCs before viral pulsing, or 5 min treatment with 0.25% trypsin (without EDTA) was used after viral-loading to remove surface-bound HIV-1. ## T-cells activation assay and viral infection Various fungus-stimulated MDDCs or heat-killed fungi species were used to coculture with or treat allergenic resting CD4<sup>+</sup> T cells for 48 h at the same ratio of cells. The T cells were gated based on CD3-positive populations, and the activation was monitored by detecting the transient expression of CD69 by flow cytometry. For viral infection, the activated T cells from DC-T cell co-cultures were purified by magnetic beads and then challenged with 5 ng p24<sup>gag</sup> amounts of HIV-1/NL-43 for 2 h. After washing, the cells were further cultured for 5 days, and HIV-1 infection was detected with luciferase activity assay as mentioned above. Transwell culture plates with a membrane size of 0.4 µm were used to separate MDDCs and T cells. ## Confocal microscopy and image analysis HIV-1 intracellular trafficking and the formation of virological synapses were observed by confocal microscopy. MDDCs were pulsed with HIV-1 VLPs, or virus- loaded MDDCs were co-cultured with CD4<sup>+</sup> T cells for 30 min. Cells were seeded on the poly-L-lysine coated microscope slides and fixed with 4% paraformaldehyde (Sigma-Aldrich) for 1 h at 4°C. Cells were immunostained with anti-CD81 McAbs (M38; Abcam), anti-DC-SIGN McAbs (120507; R&D system), or anti- βactin (AC-15, Sigma), followed by staining with Alexa-Fluor 555-labeled goat anti-mouse IgG (Invitrogen). Nuclei were stained indicated with DAPI. Slides were mounted with Fluorescent Mounting Medium (Dako) and observed using a laser scanning confocal microscope (Leica SP5). ## Statistical analysis Statistical analysis was performed using paired *t* test with the SigmaStat program. We thank Dr. Vineet KewalRamani for generous reagents. [^1]: Conceived and designed the experiments: YQ KL JW. Performed the experiments: YQ YL WL RT QG. Analyzed the data: YQ YZ KL JW. Contributed reagents/materials/analysis tools: YL SL HL DZ LW. Wrote the paper: LW JW. [^2]: The authors have declared that no competing interests exist.
# Introduction ## Background The SARS-CoV-2 (COVID-19) pandemic is posing major challenges for health care systems across the world. Throughout the pandemic, the primary goal has been to protect the population from infection and provide medical care for infected persons. In the first peak of infections in spring 2020, the German federal government, in consultation with the federal states, enacted containment measures for the general public, including social distancing, the isolation of positive or suspected cases, a ban on admissions to nursing homes and a ban on visitation in hospitals, nursing homes and hospices. Although these were helpful strategies to reduce infection and mortality, by March 2021, more than 70,000 people had died from or with COVID-19 in Germany. Throughout the pandemic, people have continued to require end-of-life care for cancer and other advanced chronic diseases. However, in Germany as all over the world, adequate palliative care for the severely ill and dying (with and without COVID-19), and their loved ones, has not been available at all times and in all settings during the pandemic. This has caused psychological, social and spiritual distress for patients, thereby compromising their quality of life. Palliative care aims at maintaining patients’ quality of life. It can be provided on at least two levels: general and specialist. When administering palliative care, GPs maintain close contact with patients and their relatives. Frequently, they form significant and long-term relationships with patients, initiating and coordinating care and further treatment with other health care providers. Thus, in Germany, GPs represent a key provider of general palliative care, and the COVID-19 pandemic has served to underline their significance in this respect. ## Study aim This paper aims at describing GPs’ experiences, challenges and perspectives relating to general palliative care during the COVID-19 pandemic in Germany. # Materials and methods The present study, based on an online survey with GPs in Germany, is part of the German collaborative project "National Strategy for Palliative Care of Severely Ill and Dying People and their Relatives in Pandemics (PallPan) in Germany," led by the National Research Network of University Medicine on COVID-19. PallPan aims at developing and achieving consensus on a national strategy for the care of seriously ill, dying and deceased adults (with and without COVID-19) and their relatives during a pandemic. ## Pre-study Recent subjective field experiences were explored through two informal conversations with resident GPs in July and August 2020. The topics that emerged in these conversations were further discussed and explored in September 2020 within an online focus group involving three GPs, as well as telephone interviews with two GPs. The focus group and interviews were audio-recorded and transcribed verbatim. Main reported experiences and challenges were for instance limited home visits, restricted physical closeness to patients and less visits from relatives, less body-related therapies, and an increased isolation of patients. ## Survey development and pre-test Between September and November 2020, a standardized questionnaire was developed using the synthesized findings from our pre-study. The questionnaire was pre- tested by six GPs using the online survey tool Unipark, with special attention paid to the questionnaire’s structure and coherence, comprehensibility, technical aspects and duration. Information was collected on the following sections: 1. sociodemographic data on the study population; 2. patient contact; 3. telephone contact; 4. video consultation; 5. cooperation with other health care providers; 6. psychosocial aspects; and 7. needs and suggestions for managing end-of-life care in the context of a pandemic. The questionnaire used 4- and 5-point verbal rating scales (i.e. *totally agree*, *rather agree*, *rather disagree*, *fully disagree*) to determine the extent of (dis)agreement with the presented statements, which reflected subjective experiences, challenges and perspectives pertaining to end-of-life care during COVID-19. Free-text options were also provided to allow for respondents’ comments on their individual provided statements. ## Recruitment of the study population In November and December 2020, the information and invitation letter, including a direct, non-personalized link to the GP survey in Unipark, was sent to: 1. nine university institutes for general practice in seven federal states (Mecklenburg-Western Pomerania, Berlin, Lower Saxony, Hessen, North Rhine- Westphalia, Baden-Wuerttemberg, Bavaria), for distribution to their teaching and research networks; 2. three GP Associations in Lower Saxony and Bremen; 3. the German College of General Practitioners and Family Physicians; 4. the German Association for Palliative Medicine; and 5. the Competence and GP Training Center of Lower Saxony, for distribution to their members. The research team had no direct access to the distribution lists of the abovementioned parties and cannot quantify the number of GPs who were contacted. However, we estimate that the survey was distributed to at least 3,000 GPs. In the invitation letter, participants were asked to forward the letter to other interested parties, thereby triggering a snowball effect to maximize the study population. Each participant was asked to complete the questionnaire only once. Participation was completely anonymous. The survey was open from November 23 to December 18, 2020. ## Data analysis The SPSS 26 statistical software package was used to calculate descriptive statistics (mean value, standard deviation, minimum, maximum) and the absolute and percentage frequencies of the questionnaire data. Outliers were treated with the full dataset. Missing data are reported explicitly. The qualitative analysis of the pre-study data and free-text comments was based on content analysis (according to Kuckartz), using MAXQDA version 18. The main categories of the qualitative interview guide were used as the basis for the questionnaire content domains. ## Ethical requirements A written positive ethics vote (No. 9232_BO_K\_2020 of 24.07.2020) for the project was issued by the Ethics Committee of the Hannover Medical School. Prior to a subject’s participation in the online questionnaire, the participants had to confirm a check box that they have read and understood the written informed consent form concerning ethics and data protection and accept the regulations. Without this confirmation the participation was not possible. # Results ## Sociodemographic data on the study population The survey was completed by 410 GPs, comprising an approximately equal number of women and men. Their average age was 54 years (range 31–73 years), and they represented all 16 federal states in Germany. Approximately half of the GPs (51.5%) had completed additional training in palliative care. On average, they required 23 minutes to complete the questionnaire. Almost all of the GPs were experienced palliative care providers and reported that they had seen patients with COVID-19 in their practice. ## Experiences and challenges during the pandemic The following results for patient contact, telephone contact, video consultation, cooperation with other health care providers, psychosocial aspects, and needs and suggestions for end-of-life care in the context of a pandemic refer exclusively to GPs’ experiences caring for severely ill and dying patients during the first peak of the pandemic, in spring 2020. ### Patient contact The majority of respondents assessed the quality of their patients’ end-of-life care as consistent (61.5%), while 36.8% reported a decrease in quality relative to the pre-pandemic period. Of the GPs who made private home visits to severely ill and dying patients, 61.4% reported a consistent number of visits, 28.5% fewer home visits, and 9.1% more home visits (1.1% missing data) compared to the pre-pandemic situation. Similar results were found with respect to nursing home visits. The most frequently cited reason for reduced visits was restricted access. ### Telephone contact In total, 62.7% of the GPs reported increased telephone contact to replace personal contact with severely ill and dying patients. Of these, 36.2% indicated that the quality of end-of-life care worsened due to the lack of personal contact, because there were no physical examinations, communication was challenged and they were less able to provide emotional support. Similar problems were reported for telephone contact with relatives. ### Video consultation In total, 36.1% of the GPs offered video consultation in lieu of face-to-face contact with severely ill and dying patients and their relatives, which was generally only realized in individual cases by primary care physicians at private homes and nursing homes. Many GPs stated that video consultation was not used or requested by severely ill and dying patients. Their cited reasons for this included technical difficulties, lack of user competence on the part of the patient and poor quality of care. Video consultation was, however, used to support relatives of severely ill and dying patients. ### Cooperation with other health care providers The respondents rated their cooperation with other GPs, community nursing services and nursing homes as good. In contrast, they evaluated their cooperation with physio, occupational and other therapeutic professions, medical specialists, hospitals and health authorities as satisfactory, and thus slightly worse. Local health authorities, described as overburdened, were criticized primarily for their lack of accessibility. The GPs described nursing homes’ hygiene concepts as inconsistent. In the free- text fields, some GPs (n = 15) reported that they were challenged in their attempts to access nursing homes. The main reason for this was that nursing home stakeholders were uncertain of how to interpret and apply hygiene-related contact restrictions. In addition, the GPs also reported problems admitting severely ill patients to nursing homes. According to the GPs evaluation, many relatives could have been restricted (48.5%) or prohibited from visiting (33.4%) patients in nursing homes. The GPs perceived deterioration in the physical and mental health of patients in private homes and nursing homes as a consequence of this restricted contact. The GPs also perceived that relatives saying goodbye to their loved ones was only possible to a very limited extent (91.7%) or not at all (56.1%). ### Psychosocial aspects of severely ill and dying patients and their relatives The GPs observed an increased fear of loneliness among severely ill and dying patients in nursing homes (91.9%), private homes (87.3%) and hospitals (86.1%). With regard to the psychosocial burden on relatives, the majority of the GPs reported increased distress due to relatives’ reduced receipt of information about the patient (85.9%) and inability to support them with their physical presence (99.3%). ### Needs and suggestions for end-of-life care in the context of a pandemic The GPs identified social contact with relatives and face-to-face contact with physicians as the most important aspects of patient care. In total, 92.4% of the GPs (fully/rather) agreed that GPs should be involved in local crisis teams, and 79.5% (fully/rather) agreed that palliative care physicians should also be involved. These local crisis teams were imagined to improve the exchange between outpatient and inpatient care providers and facilitate efficient, decentralized coordination and decision making at the local level. # Discussion The present study administered a nationwide online survey to collect GPs’ experiences, challenges and perspectives with respect to caring for severely ill and dying patients and their relatives during the COVID-19 pandemic. Almost all of the participating GPs had treated patients with COVID-19 in their practice. Throughout the pandemic, despite many efforts to adapt their individual practice management, the GPs felt challenged in their ability to administer high quality palliative care. Of note, the GPs reported deterioration in patients’ physical and mental health in both private and nursing homes, due to contact restriction. This concerning trend has also been observed by the German Association for Palliative Medicine and other professional organizations. In the present study, the GPs reported an increased fear of loneliness in their patients, as well as greater psychological distress in patients’ relatives, due to an inability to support their loved ones in person or to say goodbye. Girum et al., in a systematic review of 22 studies, demonstrated that quarantine and isolation measures have been effective in controlling the spread of COVID-19. Thus, protective measures (e.g. social distancing) are recommended, especially for those at greater risk of infection. However, while these measures may be important for managing the wider spread of the pandemic, the present study and other research has highlighted their serious physical and psychological consequences for severely ill and dying patients. To prevent these negative consequences, the GPs in our study recommended that social contact be maintained for patients receiving palliative care. The long-term effects of contact restriction and isolation on vulnerable groups must be investigated in future studies. Germany’s Federal Government Commissioner for Long-Term Care and the Federal Minister of Health addressed this challenge in December 2020, proposing regulations for visitation to care facilities. They emphasized the central role of social relationships for residents and listed basic measures to enable relatives to safely visit during the pandemic, with as few restrictions as possible. In contrast, the German College of General Practitioners and Family Physicians advised, in its “Action Recommendation on the New Coronavirus,” reduced face-to- face contact between GPs and nursing home residents, where possible. A reduction in home visits across both private and nursing homes was confirmed by approximately one-third of our GP respondents. In the event of reduced home visits, the German College of General Practitioners and Family Physicians recommended that GPs should reduce personal patient contacts, but engage in telephone and video consultation. They also recommended that these methods be widely applied in GP practices, to ease pressure. Our survey showed that this occurred in almost two-thirds of our respondents’ practices, with the GPs increasing the frequency of their telephone consultations with patients relative to the pre-pandemic period. Saint-Lary et al. showed a similar trend for increased use of telephone communication with patients in their observational survey with French GPs. In the present study, video consultation was offered by slightly more than one- third of the GP practices, for individual treatment. In contrast, another study found that 81% of GPs in Norway offered video consultation and found it suitable for maintaining patients’ continuity of care. In our study, the GPs connected their minimal use of video consultation to their reservations about technical implementation, user competence and reduced quality of care (due to a lack of physical examination). Similar attitudes were found by Randhawa et al., in their qualitative study of 12 GPs in London. Hawley et al. and Lieneck et al. reported further barriers to the use of this technology, including uncertainty among patients, concerns over data protection and lack of access to mobile devices among older patients. While reservations towards video consultation should not exclude the expansion of digital communication in health care, they reveal the need for training, broader implementation in nursing homes and clarity around data protection. In its draft “Digital Care and Nursing Modernization Act” of January 20, 2021, the Federal Cabinet addressed some of the abovementioned technical and infrastructure issues. As further guidelines on digital communication are developed, they must consider the views and experiences of health care providers, patients and their relatives. Based on their research in Atlanta, Kuntz et al. see great potential for video communication with relatives of palliative care patients. Drawing on data from their online survey with 67 caregivers and 10 semi-structured telephone interviews, the authors evaluate digitally-mediated family meetings as feasible and efficient. In addition, they conclude that video meetings might allow relatives to understand both the health and the care of the patient and to express their thoughts and feelings. ## Limitations As we did not have access to the distribution lists used for our survey, we cannot comment on the response rate or non-responder characteristics, and we cannot fully exclude the possibility that some individual GPs participated in the survey more than once. Furthermore, due to the cross-sectional study design, we can only provide data related to changes over time during the pandemic. Since this survey was based on the GPs’ recall of their experiences, there is the potential for recall and confirmation bias. Finally, it can be assumed that, among the study participants, GPs with a particular interest in palliative care were disproportionately represented. Therefore these findings may not be fully representative of primary palliative care and end of life care provision by GPs across Germany. # Conclusion The present work provides insights into the nationwide pandemic management of a representative group of GPs in Germany. The findings may support the development of a national strategy for palliative care during a pandemic. We conclude that, during a pandemic, the preservation of face-to-face visits by relatives and the development of feasible and safe video communication should be prioritized. Finally, to address end-of-life care issues appropriately, GPs and palliative care specialists should be involved in COVID-19 task forces on the micro, meso, and macro levels of health care. We thank all of the GPs who participated in the survey. We also acknowledge Valerie Appleby’s excellent editorial scrutiny of the present research article. [^1]: The authors have declared that no competing interests exist.
# Introduction Diabetes mellitus is one of the most common chronic diseases worldwide, with an increasing incidence in most countries. There were more than 382 million people with diabetes mellitus in 2013 and this is forecasted to reach 592 million people by 2035.\[–\] Most of the deaths among patients with diabetes are not due to diabetes itself but due to the complications associated with it. This includes cardiovascular disease which can cause about 50% of the deaths among patients with diabetes. In Saudi Arabia, diabetes mellitus has become an overwhelming health problem with an overall prevalence among adults of approximately 23.7%. The complications that are usually associated with diabetes mellitus are due to macrovascular or microvascular disease.\[–\] The prevalence of these complications in Saudi Arabia is quite high. In one study done in that country, the prevalence of complications were: myocardial infarction (14.3%), retinopathy (16.7%), acute coronary syndrome (23.1%) and nephropathy (32.1%). Erectile dysfunction (ED) is a common association of diabetes and is caused by a neuropathy or vasculopathy.\[–\] ED is defined as “the persistent inability to attain and maintain an erection that is sufficient to permit satisfactory sexual performance”. There is some evidence that suggests that low testosterone might be involved in both the development of type 2 diabetes and the subsequent complication of ED. Several epidemiological studies have shown that both type 1 and type 2 diabetes are associated with higher risks of ED. Also, it has been recognized that ED can be found even in preclinical or newly diagnosed diabetes. The prevalence of ED among men with diabetes ranges from 35% to 90% depending on the method used to identify it. In Saudi Arabia, studies have shown that the overall prevalence of ED in men with diabetes range from 63.5% to 83%.\[–\] There is a threefold increased risk of ED in men with diabetes compared to men without diabetes. Furthermore, even after adjusting the risk of ED for age in men with diabetes, the risk is still double compared to those without the disease. Moreover, ED in men with diabetes occurs 10–15 years earlier than in men without diabetes. It has been shown that quality of life is reduced in men with diabetes who are suffering from ED. In addition, ED is considered a predictor for cardiovascular events and can be associated with silent myocardial ischemia among men with type 2 diabetes mellitus.\[–\] In addition to that, ED in people with diabetes can be the first sign of future cardiovascular events. The existence of ED in men with diabetes is a reason to screen for other diabetic complications caused by microangiopathy in target organs. Doctors can diagnose ED by several methods. A detailed medical history and physical examination can give a good idea about its causes or degree of severity. Obviously, the most important step to start with is to simply ask men with diabetes about this problem during a routine clinical review. The UK NICE guidelines for diabetes mellitus recommend that “Review the issue of erectile dysfunction with men annually”. Surprisingly, few doctors ask men with diabetes about ED and this problem is frequently overlooked. For example, in one study done in England only 9% of men with diabetes were asked by their physicians about ED. In another study done in the United states, physicians initiated the discussion about ED with only 18% of their patients with diabetes. On the other hand, very few studies have addressed the issue of the discussion of ED from the perspective of the patient with diabetes, for example, whether they are willing to be asked about ED by their physicians. For example, a study done in Taiwan showed that 56.6% of patients with diabetes wished to discuss ED with their physicians. The literature indicates that barriers that might prevent health professionals from asking about sexual problems such as ED include lack of time or knowledge, lack of training among physicians, false beliefs about sexuality, thinking that this is a job for another physician, patients not being ready to discuss these issues, believing it is not an important subject, fear of increasing patient anxiety and patients being too ill or too old to be asked. In the Middle East, the literature is lacking in studies on the proportion of men with diabetes who have been asked about ED or their willingness to discuss ED with their physicians. Also, in searching the literature, no studies were found that described the barriers faced by patients with type 2 diabetes to discuss ED with their physicians. This study was aimed primarily to find out the proportion of Saudi men with type 2 diabetes who have been asked about ED in the last year by their physicians in hospital-based primary care clinics in Riyadh. We also aimed to determine the willingness of Saudi men with type 2 diabetes to discuss ED with their physicians and the factors that either increase or reduce their willingness to discuss this issue. # Methods and materials ## Study design This study employed a cross-sectional survey using a quantitative self- administered questionnaire investigating the proportion of Saudi men with type 2 diabetes who have been asked by their physicians about ED in the last year, their willingness to discuss ED with their physicians, and the factors that may be related to their willingness to discuss ED with their physicians. ## Study site The study was conducted in hospital-based primary care clinics at King Khalid University Hospital, Riyadh, Saudi Arabia. These primary care clinics consist of 8–10 clinic sessions each day, led by approximately 40 staff specialized in family medicine. Each clinic has about 30 patients daily with the majority of the patients having diabetes. ## Eligibility criteria The participants were included in this project if they were married, adult (i.e. \> 18 years), diagnosed with type 2 diabetes mellitus, having at least one year of follow-up in the clinics, and could read and write Arabic. We excluded any participant with anatomical penile deformities, past history of spinal cord injury or past history of prostate diseases or prostate surgery. ## Patient enrolment Patients were approached at the reception desk after they completed their review with their physician and asked about the inclusion and exclusion criteria. Those who met our eligibility criteria were included in the study. The participants were informed about the study’s objectives. They were asked to enter the study and for those who accepted this request, written consent was obtained. Confidentiality of their information was assured. The data were collected by a family physician (the principle investigator) from July to September 2015 ## Instrument development The questionnaire consisted of 26 items divided into 4 sections. The first section of the questionnaire collected information about the socio-demographic background of the patients. The second section contained two questions, the first one regarding the proportion of patients with type 2 diabetes who have been asked about ED. The responses were either yes, no, or I can’t remember. The second section measured the degree of willingness to discuss ED by the patients with their physician (i.e. unwilling, slightly willing, moderately willing, and very willing). The third section consisted of self-reported statements about 11 barriers preventing patients from discussing ED with their physicians. The responses to these statements were recorded on a five point Likert scale ranging from strongly agree to strongly disagree. These statements were developed after reviewing the literature. The last section of the questionnaire comprised a brief survey to assess the presence of ED in respondents by using a validated Arabic translation of the Index of Erectile Function (IIEF-5) questionnaire. IIEF-5 is a well-known tool to screen for ED and it has been used extensively in previous studies. It comprises only five questions. Also, it categorizes ED according to its severity as follow: severe ED (1–7), moderate ED (8–11), mild to moderate ED (12–16), mild ED (17–21), and no ED (22–25). Apart from the last section of the questionnaire which was adopted from the previously validated Arabic version, the majority of the questionnaire was developed in English, translated by an accredited translator in Arabic, and then back-translated by another accredited translator into English. The mismatches between the two English versions, the original and back-translated versions, were discussed and resolved by the primary author and the translators. The questionnaire was pretested and piloted on 30 monolingual patients with type 2 diabetes to ensure the comprehensibility and readability of the final Arabic version. The participants in the pilot study were recruited from medical out- patient clinics to prevent contamination with the main sample for the current study. ## Sample size calculation A sample size calculation was based on a pilot study with 30 participants which showed that 15% of patients with type 2 diabetes had been asked about ED in the last year. So, a sample of 306 patients with type 2 diabetes was required to obtain a 95% confidence interval of +/- 4% around the prevalence estimate of 15%. Assuming 10% of questionnaires in the pilot study were incomplete or not returned, a total of 336 questionnaires was required. ## Statistical analysis Descriptive statistics were used to describe the study sample characteristics and the participants’ identified barriers to discussing ED with their physicians. To test the association between patients who were willing to discuss (i.e. very willing, moderately willing, and slightly willing) and unwilling to discuss ED with the physicians, and the participants’ socio-demographic and clinical characteristics, chi-square tests were used for categorical variables. In one variable (current occupation), we collapsed some groups together to meet the conditions of the Chi-square test. For continuous variables, the normality of the data was checked by the Kolmogorov-Smirnov test. For normally distributed data, an independent sample t test was used to compare means. For skewed data, the Mann-Whitney U test was used to compare medians. Chi-square tests were used to compare the association between the willingness to discuss ED with the physician and the different participants’ barriers, after removing the neutral response variable. The Fisher exact test was used to test the association between participants having ED and their willingness to discuss but were not yet asked by their physicians in the last year, as the conditions of the Chi-square test were not met. Multivariable logistic regression analyses were performed to predict the willingness to discuss ED with the physicians by using the participants’ barriers, socio-demographic and clinical characteristics as covariates. For the logistic regression analysis, participants’ willingness to discuss ED was categorized as a binary variable, comparing those who reported any degree of willingness (very willing, moderately willing, and slightly willing) with those who were unwilling. The data were analysed using the statistical software package IBM SPSS Statistics for Windows, Version 22.0 (IBM Crop., Armonk, NY, USA). A p-value of less than 0.05 was considered to be statistically significant for all analyses. ## Ethics The study protocol was reviewed and approved by the Monash University Human Research Ethics Committee and the Institutional Review Board of King Khalid University Hospital, Riyadh, Saudi Arabia, where the data were collected. The participants were informed about the study’s objectives and their permission to enter the study was requested. Written consent was obtained from the participants. Confidentiality of their information was assured. # Results ## Participants’ socio-demographic and clinical characteristics Out of the 336 distributed questionnaires, 309 were completed and returned. The response rate was therefore 92%. The median age of the respondents was 60 years and the median duration of diabetes among the respondents was 10 years, with over half (59.2%) on tablets alone as treatment for this condition. Few (9.7%) had been asked by their physicians about ED in the last year although most (84.8%) were willing to discuss this problem with them. The presence of ED among the respondents was 89% with one third of them (28.2%) suffering from severe ED. The remaining socio-demographic and clinical characteristics are shown in. ## Prevalence of identified participants’ barriers to discussing ED with their doctors shows the distribution of participants’ barriers to discussing ED with their physicians. The most prevalent barriers among these respondents were having sex is not important to me (49.5%) and the treatment is too expensive (24.6%). ## Willingness to discuss erectile dysfunction (ED) and participants’ socio-demographic and clinical characteristics shows the association between the willingness of respondents to discuss ED with their physicians, and the respondents” socio-demographic and clinical characteristics. The participants who were willing to discuss ED with their physicians were younger with the mean age being 59.3 compared to the mean age of 65 in unwilling participants (P\< 0.001). Participants with low monthly incomes (i.e. \<5000 SR) (53.2%) were unwilling to discuss ED with their physicians (P = 0.03). Also, among participants who have ED, those who were complaining of severe ED (63.1) were unwilling to discuss it with their physicians. There were no significant associations between a willingness to discuss ED with the physicians and the highest education level, location of residency, current occupation, smoking status, duration of diabetes, type of diabetes treatment, and presence of ED. Multivariable logistic regression analysis was used to predict the participants’ willingness to discuss ED by their socio-demographic and clinical characteristics. After adjusting for the educational level, location of residency, monthly income, current occupation, smoking status, duration of diabetes, type of diabetes treatment, presence of ED, two participants’ characteristics were associated with willingness to discuss ED with the physicians. These characteristics were age above 60 (OR = 0.25, 95% CI: 0.11–0.55), and having severe ED (OR = 0.26, 95% CI: 0.08–0.85). No significant association has been found between the participants’ willingness to discuss ED and the other socio-demographic and clinical characteristics. ## Participants’ willingness to discuss ED and identified barriers shows the comparison between participants’ willingness to discuss ED with their physicians and the identified barriers. Comparing the ‘unwilling’ participants to the ‘willing’ ones revealed that the barriers which provide the main obstacles to discussing ED with the doctors are: embarrassing my doctor (63.9%, P \< 0.001), ED is a personal issue (60.6%, P \< 0.001), too old now (59.4%, P \< 0.001), feeling embarrassed to talk about it (57.1%, P \< 0.001), too sick now to address ED issues (55.9%, P \< 0.001), no effective treatment is available (54.8%, P \< 0.001), and my doctor is too young to discuss my ED with him (54.8%, P \< 0.001). ## Predicting participants’ barriers to their willingness to discuss ED shows the multivariable logistic regression analysis which was used to predict the participants’ willingness to discuss ED by their identified barriers. After adjusting for the age and severity of ED as possible confounders, two participants’ barriers were associated with willingness to discuss ED with the physicians. These barriers were “it may embarrass my doctor” (OR = 0.04, 95% CI: 0.01–0.2), and “It is a personal issue” (OR = 0.05, 95% CI: 0.01–0.28). ## Participants who have not been asked about ED and their willingness to discuss it shows that among the respondents who have not yet been asked about ED in the last year by their physicians, 91% of them have ED and would be willing to discuss it with their physicians (P = 0.02). Even if they do not have ED, twice as many are willing to discuss this matter as unwilling. # Discussion This survey has shown that few (9.7%) patients with type 2 diabetes mellitus have been asked about ED in the past year by their physicians, in spite of the majority (84.8%) being willing to discuss it. Further, the presence of ED was high (89%) among these patients, with one third of them (28.2%) suffering from severe ED. In spite of guidelines recommending physicians to enquire about ED in patients with diabetes, this does not take place in most cases. Grant et al found that only 9% of the patients with diabetes have been asked about ED in their last diabetes review consultation. In addition, Perttula found that physicians discussed ED with just 18% of their patients who have diabetes. This is in spite of the prevalence of ED being high in these patients. Also, the low rate of asking about ED in patients who have diabetes by physicians who work in primary care settings is similar to what happens in specialty practices where patients are at high risk for ED, such as those seen by cardiologists. Nicolai et al found that only 16% of cardiologists admitted to discussing sexual function regularly with their patients. So, there is a wide gap between recommendations and what takes place in practice. A study done in Bulgaria has shown that this gap reflects, in part, physicians’ beliefs that patients with ED rarely share this problem with their physicians, Overall, a large majority of patients (84.8%) were willing to discuss this topic. Unfortunately, to date few studies have examined ED-related issues from the patient perspective. Jiann et al showed that 56.6% of patients with type 2 diabetes wished to discuss ED with their physicians while Lo et al found that 76.1% of patients with type 2 diabetes would want to receive treatment for ED from their physicians. However, most patients think that the discussion should be initiated by the physicians. At the same time, most physicians seem to assume that patients do not like to be asked about sexual problems. The study’s findings suggest that two main factors were associated with a willingness to discuss ED: age and severity of ED. The patients above 60 years were 70% less willing to discuss ED with their physicians compared to the patients less than 60 years old. In addition, the patients who do have severe ED were 75% less willing to discuss ED with their physicians compared to the patients who have mild ED. As mentioned above, we found that elderly people were less willing to discuss ED with their physicians compared to younger patients in spite of the majority of the elderly population remaining interested in sexual activity. This group needs to be given more attention by their physicians as they have a very high prevalence of ED. In addition to that, ED is often underreported and underdiagnosed in the older male population. It has been shown that physicians are not proactive in discussing and managing the sexual health of elderly people. In a study done by Harding and Manry in the United States among health care providers, it was found that only 28% of the surveyed health care providers would usually asses the sexual health of elderly patients. Also, a negative attitude has been found in a study done to examine American psychologists’ willingness to assess the sexual health of older adults. In addition to the age of patients with diabetes as a predictor for willingness to discuss ED, the level of ED severity plays a major role, with this study showing that patients who have diabetes with severe ED are less willing to discuss this with their physicians compared to those with mild ED. This is particularly important as the literature suggests that diabetes is associated with more severe forms of ED. Men with diabetes also require more aggressive therapy to treat ED. In a study done by Walsh et al. it was found that men with diabetes were likely to need more aggressive therapy, and most went on to second line therapy (i.e. penile prosthesis surgery) for ED as these patients were less responsive to first line therapy (oral agents). It is important to identify the group who have diabetes and suffer from severe ED to optimise diabetes control and treat the ED as best one can. This should lead to improvement in both their sexual function and depressive symptoms, as shown by the SUBITO-DE study, an Italian multicentre study. The main barriers contributing to an unwillingness to discuss ED were: embarrassing the doctor, ED is a personal issue, too old, too sick to address ED issues now, no effective treatment available, and the doctor is too young to discuss ED with. Jiann BP et al found that patients’ embarrassment and false beliefs about ED treatment being either ineffective or harmful accounted for three quarters of the reasons why patients with diabetes will not discuss ED with their physicians. Embarrassment was the key factor preventing this discussion according to Rutte et al. as also shown by Gott M and Hichliff S. Other studies have revealed the importance of other barriers including differences in patient characteristics, i.e. their age, lack of knowledge, and difference in their culture. These differences in patients’ barriers found by various studies can be explained by difference in customs, traditions, culture, and health systems. The study findings also suggest that most (91%) of the patients who have not yet been asked about ED in the last year actually have ED and are willing to discuss it. This is contrary to what has been reported by Smith et al. who found that sexually active men are more likely to discuss sex with their physicians. These discrepancies in findings might be related to differences in sociocultural factors including social norms and attitudes. The current study has several implications for clinical practice. Firstly, ED is a major problem among patients with type 2 diabetes and this is frequently ignored by physicians even though a majority of these patients are willing to discuss this problem. Physicians who are involved in treating these patients should initiate the discussion. Secondly, patients with diabetes who are older and suffer from severe ED are less likely to discuss ED with their physicians. Targeting this sub-group of patients through education and the building of better relationships between physicians and their patients should help. Thirdly, there are multiple barriers that prevent patients with type 2 diabetes discussing ED with their physicians which could be reduced by better patient education and the addressing of psychological factors. There are several limitations to this study. The sample was taken from one hospital and may therefore not be generalizable. Also, the patients were taken from primary care clinics affiliated to a teaching hospital so that they might have more severe diabetes, and be older than patients in other primary care clinics. In addition to that, and due to the nature of the study design, the results revealed associations and not necessarily causal relationships between a range of factors and willingness to discuss ED. However, we believe that our findings shed an important light on this very sensitive issue among patients with type 2 diabetes. Also, no comparable work has been done in this country, and so it is of importance within this health care system. # Conclusions ED is a highly prevalent condition among patients who have type 2 diabetes. Most of these patients are not asked about ED within the last year of attending a clinic, even though most are willing to discuss it with their physicians. Many patients’ barriers to discussing ED have been identified, including being older and suffering from more severe ED, with these patients being less willing to discuss this with their physicians. Further research is needed to explore the barriers which prevent physicians from discussing ED with their patients who have diabetes. # Supporting information [^1]: The authors have declared that no competing interests exist.
# Introduction Tuberculosis (TB) remains a global threat with an estimated 1.8 million deaths in 2015; approximately 14 percent attributed to multi-drug resistant (MDR-TB) and rifampicin resistant (RR-TB) tuberculosis. Advances in case detection and treatment regimens have dramatically reduced incidence and mortality; yet lengthy and complex treatment regimens continue to take a toll on treatment completion and success rates. Patients who default on TB treatment continue to contribute to the infectious disease burden of the community, increase their risk of developing MDR-TB, and are at an increased risk for TB-related mortality. According to the WHO 2016 report, Ukraine is among the top 20 highest drug- resistant TB burden countries in the world. National survey data estimate 25% of new incident cases and 58% of previously treated cases are MDR/RR-TB cases, resulting in approximately 22,000 cases per year. Driving these increasing MDR/RR-TB rates is an unchecked treatment default rate. Among the 2014 national TB cohort, treatment success was only 72% compared to 83% globally. Patient predictors for treatment default vary across Europe and Central Asia. In Spain, Cayla and colleagues found that immigrants, patients living alone, patients previously treated, and injection drug users (IDU) were at higher risk for default; whereas in Russia, the homeless, unemployed and alcoholics were at highest risk; in Moldova patients who were homeless, living alone, less educated, or living for extended periods outside the country were at risk; and in Estonia alcohol abuse, unemployment, MDR-TB, urban residence and previous incarceration increased risk. Timing of default was found to be heterogeneous across a large meta-analysis by Kruk and colleagues. In Uzbekistan, the first two-month intensive phase led to high rates of default, in Moldova the risky period was between intensive and continuation treatment, while data overall suggest that lengthy treatment during the continuation phase is the most likely period for defaulting. Strategies to improve treatment adherence and success center on directly observed therapy short-course (DOTS) with adaptations to different clinical service and social environments. DOTS has been implemented in clinical settings, through home visits by medical personnel, use of community volunteers, and DOTS by family members. Patient incentives are sometimes included to improve adherence, most commonly periodic food packages, transportation vouchers, and cash payments. However, evaluation of the impact of these strategies on treatment success remains inconclusive. The standard TB treatment for smear-positive patients in Ukraine covers 2–4 months of intensive inpatient therapy at the central TB dispensary. Once the patient tests smear-negative, (s)he is referred to a TB cabinet or polyclinic closest to their home for 2–5 months of outpatient continuation therapy. Directly observed therapy is the standard of care, requiring direct contact between patients and providers to administer the TB medication. According to the National TB Program (NTP), adherence to therapy is insufficiently controlled, with a 7.6% national default rate in 2010. In 2010, the Ukraine Red Cross Society (URCS), funded by the United States Agency for International Development (USAID), piloted a community-based social support program designed to improve TB treatment adherence during outpatient continuation therapy. URCS provided DOTS to a limited number of patients in their homes. Additionally, incentive food packages, psychological and career counseling, and/or vouchers for transportation or other necessities were provided periodically based on client needs. TB physicians managing patients’ continuation treatment at the outpatient facility made case-by-case referrals to URCS based on identification of the patient as high risk for defaulting on treatment according to established criteria for program inclusion. In 2011, the URCS program was suspended due to insufficient funds. By 2012, the program was again active and expanded to cover 10 oblasts in eastern and southern Ukraine with reported default rates ranging from 6.1–12.7%. This study measures the effect of the URCS social support program on the rate of treatment default among those at risk for defaulting during continuation therapy. Given the high rate of treatment default and the growing problem of treatment-resistant TB strains, identifying effective strategies for treatment adherence is critical. # Methods ## Study settings and sample population Three oblasts in Ukraine were purposively chosen for this study due to their high TB caseloads and high treatment default rates. In 2010, Dnipropetrovsk reported 1,077 TB cases and 12.4% default rate; Kharkiv reported 738 cases with 11.1% default; and Odessa reported 789 cases and 9.4% default rate. The study population was composed of patients receiving TB continuation treatment in these three oblasts in 2011 and 2012. Patients were classified as high-risk for TB treatment default per program criteria covering eleven self-reported risk factors: HIV positive, alcoholism, injection drug use (IDU), a contact to a TB case, a co-morbidity, homeless, unemployed, a health care worker, a migrant, a refugee or immigrant, an ex-prisoner, and room to record other risk factors that a provider might deem noteworthy. Low-risk patients did not report these risk factors with the exception of unemployment. Facility staff revealed that TB patients routinely report being unemployed. This is to avoid stigma in the workplace, as workplace TB screening is routinely undertaken after a case is diagnosed. Consequently, we considered a patient as low risk during sample selection if the only reported risk factor was unemployment. During data cleaning, minimal corrections were made for misclassification of risk status at time of data entry. All study patients completed TB intensive treatment, initiated TB continuation treatment, and had a TB treatment outcome recorded in their medical record. Five patient cohorts were sampled: high-risk (HR) patients enrolled in the URCS social support program January 1 –May 31, 2012 (henceforth 2012 HR- Intervention); high-risk patients not enrolled in the social support program in January 1 –May 31, 2012 (henceforth 2012 HR-Comparison); low-risk (LR) patients not enrolled in the social support program in January 1 –May 31, 2012 (henceforth 2012 LR-Comparison); high-risk patients not enrolled in the social support program in January 1 –May 31, 2011 (henceforth 2011 HR-Comparison); and low-risk patients not enrolled in the social support program in January 1 –May 31, 2011 (henceforth 2011 LR-Comparison). A cohort of 2012 HR-Intervention patients (n = 409) was randomly sampled from a complete listing of URCS enrollees, stratified and proportionate in size to the TB patient population by oblast. These patients served as the index cases. Each TB facility where an index case was receiving continuation therapy served as the facility match point to ensure controls experienced similar service environments to the randomly selected cases. In order to obtain a group of controls not exposed to the program, four patients from these facilities’ TB registries were matched to the index patient: one 2012 HR-Comparison patient; one 2012 LR-Comparison patient; one 2011 HR-Comparison patient; and one 2011 LR-Comparison patient. The primary comparison group for this analysis was the 2012 HR-Comparison cohort; however, additional cohorts were sampled to explore selection. The second matching variable was the start date for TB continuation treatment for the index case in order to control for seasonality of TB and services. Additional matching on sex and age was done if more than one match was eligible. Data from 1630 TB patients across the five cohorts were collected. Sampling weights were generated to account for sampling proportionate to the varying size of TB caseload per oblast and non-response. During data cleaning, minimal corrections were made for misclassification of risk status at time of data entry. Data entry misclassifications included: dropping cases who received the intervention in 2012 but had no reported risk factors (n = 12); reclassifying those whose only risk factor was unemployment from high risk to low risk (n = 16); and reclassifying another 33 cases as high risk based on a risk factor reported. A survey of 50 TB polyclinics and cabinets that provided continuation therapy to the study population was also completed to provide details on the referral and treatment practices at these facilities (see report for details). ## Data collection and definitions For each study patient, retrospective data were abstracted from TB medical records (national form TB01). The data abstracted included basic demographics, sex, age, employment status, urban or rural residence; and TB diagnosis, treatment, interruptions to intensive treatment and treatment outcomes. Standard WHO definitions were used for TB classification (e.g., first diagnosis, re- initiated treatment, treatment failure, relapse, and referral); for clinical TB (e.g., pulmonary or extra-pulmonary); for WHO diagnostic categories to indicate treatment regimens; and for treatment outcomes (e.g., success, death, treatment failure, treatment interrupted, and transferred). A patient’s outcome was successful if the full course of prescribed treatment was completed or follow-up testing indicated patient was cured. Treatment default included anyone who missed treatment for more than 60 consecutive days per WHO standards. Additional data from the TB records were abstracted from form TB01-01, the risk screening form used by providers to identify a patient’s risk for defaulting on treatment. For the 2012 HR-Intervention group, data on social support services received such as home visits, food packages, clothing, transport vouchers, monetary incentives, and counseling were abstracted from the URCS records and merged with the patient TB record. ## Data analysis Descriptive statistics were generated to compare demographics, TB disease characteristics, and reported risk factors for treatment default across the five cohorts. Logistic regression models with average marginal effects (AME) were estimated to test the study questions. All analyses used data weighted for sample selection; reported standard errors are clustered at the facility level. To validate risk factors predictive of treatment default, the social support program criteria risk factors were regressed on treatment default among patients receiving continuation therapy. Dichotomous variables for seven individual risk factors (HIV positive, alcoholic, IDU, contact to a case, co-morbidity, homeless, and unemployed) were included. Very few patients reported being a health care worker, migrant, refugee, or ex-prisoner; hence, these were combined with the unspecified risk factor as “other”. A dichotomous variable indicating the presence of more than one risk factor was also added. All risk factors were run simultaneously first (Model A). Next, we controlled for basic demographics and four dichotomous disease and treatment characteristics due to their hypothesized role in TB treatment adherence and outcome: first time TB diagnosis, pulmonary TB, WHO Category I and more than 2 interruptions in care during intensive therapy (Model B). To identify the salient risk factors for default in the absence of an intervention, this analysis was restricted to data from 2011 when the URCS program was not operating. To evaluate the impact of the social support program on treatment default, the second regression analysis was limited to the 2012 HR-Intervention and the 2012 HR-Comparison cohorts. Prior to estimating impact, balance between the intervention and comparison groups was examined. The final model estimated the impact of the social support program on treatment default, controlling for risk, disease status, and demographics. Analyses were produced using Stata SE version 13 (College Station, TX). This study was approved by the Office of Human Research Ethics at the University of North Carolina at Chapel Hill and the ethical review board of the F.H. Yanovskyi Institute of Phthisiology and Pulmonology, Academy of Medical Sciences of Ukraine. Both review committees waived the requirement for informed patient consent. Data collection was performed by the IFAK Institut in Ukraine. Data collectors had access to patient names in order to track patients from registry entries to patient records; however, names were not recorded on data collection tools nor reported to the researchers. # Results ## Study population The final dataset included 1,618 records from TB patients across the five cohorts: 2011 LR-Comparison (n = 308), 2011 HR-Comparison (n = 340), 2012 LR- Comparison (n = 262), 2012 HR-Comparison (n = 311), and 2012 HR-Intervention (n = 397). The study populations shared similar demographic profiles across risk cohorts and years. Approximately two-thirds of the patients were male in every risk group, just over three-quarters were under fifty years of age, and a large majority lived in urban areas. Over half of all patient cohorts were unemployed, ranging from 55–72%. Half of the study population received TB continuation treatment in Dnipropetrovsk (50.0%), with the remainder evenly divided between Kharkiv (25.4%) and Odessa (24.6%). Among the three HR cohorts, unemployment was the most common reported risk factor (48–62 percent), followed by alcoholism (34–44 percent), co-morbidities (33–36 percent) and being HIV-positive (21–47 percent). A majority (63–72 percent) reported between 2 and 3 factors putting them at risk for treatment default, while 3–7 percent reported four or more. Notably, the proportion of HR patients who reported injection drug use in their medical records was small, ranging from 5–12 percent. In discussions with facility staff, it was noted that information on IDU status and treatment is not routinely recorded in the TB charts nor shared across cabinets due to concerns of confidentiality. As expected over half of the LR patients reported no risk factors for treatment default, while the remaining reported unemployment. Overall, 81.1 percent of the TB patients were undergoing treatment for a first diagnosis, although among the HR cohorts, a higher percentage re-initiated treatment after earlier failure or relapse compared to the LR cohorts (7–12 percent versus 3–5 percent). Ninety-three percent of all cases were pulmonary TB, a majority was classified as WHO Category I (63.8 percent), and 81.3 percent reported only one or fewer interruptions in intensive treatment. TB treatment outcomes in 2011 were significantly different between the LR and HR cohorts on treatment adherence. Treatment default among the 2011 LR-Comparison cohort was 4.2 percent compared to 13.3 percent in the 2011 HR-Comparison cohort (p\<0.000); while 90.6 percent of the LR-Comparison cohort reported treatment success compared to only 74.3 percent of the HR cohort (p\<0.000). Similar differences were measured in 2012 when comparing the LR-Comparison and HR- Comparison on default, 4.6 percent and 10.6 percent (p\<0.006), and success, 87.0 percent and 69.8 percent (p\<0.000) respectively. The 2012 HR-Intervention cohort fared better than the 2012 HR-Comparison on default (1.3 and 10.6 respectively, p\<0.000) and on success (88.4 and 69.8 respectively, p\<0.000). However, comparisons between the 2012 LR-Comparison and the 2012 HR-Intervention on default (4.6 and 1.3 percent respectively) and success (87.0 and 88.4 percent respectively) found no statistical differences. Lastly, statistical differences were found between the 2011 HR-Comparison and the 2012 HR-Intervention cohorts for both treatment default and treatment success (p\<0.000); while no statistical differences were found between the 2011 HR-Comparison and 2012 HR- Comparison groups. These comparisons across cohorts highlight that the difference in outcomes between the 2012 HR and LR comparison cohorts is similar to the differences between the 2011 HR and LR cohorts. This supports the impact identification strategy employed in our evaluation of the program. ## Predicting treatment default The URCS social support program was designed to target those at highest risk of treatment default and provide support to improve treatment adherence. The official eligibility criteria for program support cover eleven risk factors. Among patients from 2011, only those who reported being an alcoholic (p = 0.002) or an IDU (p = 0.043) were more likely to default on TB continuation treatment, while a patient reporting a co-morbidity was less likely to default (p = 0.028). Additionally, those patients enrolled in continuation care who had two or more interruptions recorded during intensive treatment were more likely to default during outpatient treatment (p = 0.028). Estimated marginal effects predict that an individual’s probability of default increased by 0.08 (p = 0.017) if an alcohol abuser and by 0.05 (p = 0.043) if prior treatment interruptions were noted; yet one’s probability of default decreased by 0.06 (p = 0.043) if reporting a co-morbidity. ## Evaluating program impact Primary impact analyses were limited to the 2012 HR-Intervention and the 2012 HR-Comparison cohorts. Mean differences between the two groups were tested for 18 variables; seven (38 percent) were unbalanced at standard statistical levels (p\<0.05). Looking at the intervention group, a higher proportion of patients were alcoholics or unemployed, and were 18–29 years of age, while the comparison group had a higher proportion of persons with HIV, homeless, undergoing WHO treatment category 1, and who were male. All risk factors, disease characteristics, patient demographics and treatment oblast were controlled for in the final impact model. Measuring impact, results indicate that the HR patients receiving the social support program decreased their probability of treatment default by 0.101 (p\<0.000) compared to the comparison cohort. A second analysis, comparing outcomes for the 2012 HR-Intervention cohort to the 2011 HR-Comparison cohort, produced similar results. Five of 18 variables (28 percent) were not balanced between the cohorts. Controlling for all variables, the 2012 HR patients receiving the social support intervention were significantly less likely to default (p\<0.000) compared to the 2011 HR- Comparison cohort, and the probability of default decreased by 0.120 (p\<0.000) (data not shown). However, alcoholism remained a significant risk factor with the probability of default 0.069 (p\<0.014) higher among alcoholics compared to non-alcoholics. Additionally, the probability of default among those with more than two treatment interruptions during intensive care was higher at 0.047 (p = 0.017). # Discussion In 2012, TB patients receiving social support provided by URCS in Ukraine reduced their probability of defaulting on continuation treatment by 10 percentage points compared to high-risk patients who did not receive social support in 2012 or 2011. Treatment success rates for the high-risk patients receiving social support were comparable to the low-risk cohorts and significantly improved over the high-risk comparison cohorts. This result was found despite the heterogeneity of the patient population and the services provided. Although treatment oblast was not predictive of success or default in 2012, routine implementation of DOTS and social support varied by study oblast. According to reported practices in 2014, 89 percent of surveyed facilities in Dnipropetrovsk provided facility-based DOTS and a majority of these facilities required daily DOTS visits (83 percent). Among the sites offering home-based DOTS, half provided weekly or bi-weekly visits. In contrast, 88 percent of the facilities in Odessa provided home-based DOTS and the majority of home visits were daily. This increase in home-based services may reflect a growing recognition in Odessa that facility DOTS is insufficient to assure compliance. Variation across oblasts may reflect patient population needs or facility capacity. Further investigation into best practices for DOTS and social support in Ukraine is warranted. URCS was the only provider of social support in Kharkiv and Odessa in 2012 and the primary provider in Dnipropetrovsk. In 2011, only 23 percent of the facilities referred patients for social support, increasing to 94 percent by 2012. In all oblasts the primary point of referral was the city or raion TB physician. This is in keeping with URCS’ policy to only provide social support to smear-negative patients who successfully completed intensive TB treatment and initiated continuation treatment. This focus on continuation patients ignored patients who defaulted during intensive treatment, which could be substantial. In Russia, Jakubowiak et al. found that 44 percent of TB treatment defaulters exited treatment during the intensive regimen. In Moldova, the highest default rates were recorded during the first month of inpatient intensive treatment. Our data did not include patients who defaulted during inpatient treatment, however in 2011, patients with more than two treatment interruptions during inpatient care increased their probability of defaulting during outpatient care by 5 percentage points. This is similar to findings by Jakubowiak in Russia and Santha in India, where gaps in intensive treatment were associated with future treatment default. Prioritization for support services may benefit those who had difficulty during the intensive phase. Alcoholism was the one risk criteria predictive of defaulting among the 2011 cohorts, increasing the probability of default by 5 percentage points. Neither positive HIV status nor reported injection drug use were statistically associated with higher default rates. Under-reporting of these two risk factors may be one explanation for their lack of significance. In Ukraine, sharing of confidential patient information between service delivery clinics is limited. The risk factor information documented on a patient’s TB form is all self- reported and possibly under-reported due to fear of stigmatization. For example, a patient seeking HIV-related services may not report their status to the TB physician. Unless an infectious disease specialist is overseeing services for both TB and HIV patients, this case of co-infection may go undetected by the individual clinics, despite best practices of routine HIV screening among TB patients. According to the facility survey, only 32% of facilities providing DOTS also provided ART for persons living with HIV. For IDUs the challenge may be two-fold. First, the availability of drug-substitution therapy for IDUs in Ukraine is scarce; only 16% of the outpatient TB facilities reported offering this service. Without adequate substitution therapy, many IDUs may drop out of service during the intensive, inpatient TB treatment phase, excluding them from our sample. Second, the stigma for drug addiction may discourage IDUs from revealing this risk to their TB physician. In either scenario, the risk of default among IDUs may not be adequately reflected in our data. Patients with reported co-morbidities reduced their probability of defaulting by almost 6 percentage points in 2011, possibly due to additional support received from providers caring for the co-morbidities. For all other risk factors, no statistical associations were found with default. Whether this is due to the small numbers of patients with these other risks or because these factors do not increase one’s risk of default is undetermined in this study. Interestingly, almost 20% of the high-risk cohort receiving the intervention had an undetermined or “other” risk factor recorded. Provider interviews suggested that compliant patients in our study sites may have been referred to URCS as a reward for their adherence. If widespread, this preferential referral of adherent patients could create selection bias, affecting results. This is one of the limitations of retrospective data analysis, it is difficult to measure the fidelity of program implementation retrospectively. However, if there was widespread selective referral one would expect the 2012 HR-Comparison group to have reported a higher default rate than the 2011 HR-Comparison group. The comparability of the default rates among these two cohorts suggests that very little selection bias exists. In an era of declining health resources and increasing drug-resistant TB, refining and standardizing the referral criteria for additional social support may reduce the national default rate, but not without a cost. This study shows that social support is effective in reducing default rates but whether or not that means it should or can be scaled-up depends on the cost of wider implementation and the cost relative to other potential interventions that might also reduce default rates. # Conclusions This study demonstrates the positive impact of providing social support to those at-risk for treatment default. Targeting services to those who will most benefit is critical to reduce continuing TB transmission. Further research is recommended to differentiate the costs and benefits from home-based DOTS versus additional services offered through social support programs. Prospective cohort studies could refine targeting of programming, evaluate social support program fidelity, identify which populations respond best to select services, and what barriers might still exist to achieving better adherence. With that information, tailoring programs to most effectively reach and serve clients in a patient- centered approach may reap substantial rewards for Ukraine. Prioritizing support services for clients who struggle with alcohol or drug addictions or struggle with adherence to intensive inpatient treatment regimens, may improve treatment success. Identifying approaches to assure intensive treatment completion and flagging those upon completion for additional follow-up during continuation treatment, has the potential to further reduce program defaults and improve outcomes. MEASURE Evaluation is funded by the U.S. Agency for International Development (USAID) under Cooperative Agreement GHA-A-00-08-00003-00 and is implemented by the Carolina Population Center at the University of North Carolina at Chapel Hill, in association with The Palladium Group, ICF International; John Snow, Inc.; Management Sciences for Health, and Tulane University. We are grateful for the Carolina Population Center (R24 HD050924) for general support. We also thank the F.H. Yanovskyi Institute of Phthisiology and Pulmonology, Academy of Medical Sciences of Ukraine for their support in conducting this study in Ukraine. [^1]: The authors have read the journal's policy and have the following conflicts: Stephanie Mullen is employed by John Snow Inc. This affiliation does not alter our adherence to PLOS ONE policies on sharing data and materials. [^2]: Current address: Office of Family and Community Health Improvement, Washington Department of Health, Olympia, Washington, United States of America
# Introduction Ferulic acid (FA) is a phenolic substance and an important active ingredient that is common in various plants. It occurs at high concentrations in food ingredients such as coffee, grain hulls, vanilla beans, wheat bran, and rice bran. The FA molecule is a 4-hydroxy-3-methoxy cinnamic acid (C<sub>10</sub> H<sub>10</sub> O<sub>4</sub>), and FA exhibits various biological activities and physiological functions and has low toxicity. Importantly, FA has been shown to exhibit antioxidant and anti-inflammatory properties and is an effective modulator of multidrug resistance in cancer. FA can prevent acute liver injury due to sepsis by attenuating the inflammatory response, and it improves corticosterone-induced liver damage. Moreover, FA also improves corticosterone- induced depressive behaviour and oxidative stress in mice, and enhances the antibacterial activity of quinolone antibiotics. Geese is a nutritious and healthy food resource. the short reproductive periods, low hatchability, and high embryo mortality of geese. it is reported that the content of protein and trace elements in the meat of goose is higher than in other poultry products. So, geese breeding industry has broad prospects. Intestine plays a key supporting role in the growth of animals. and early growth and development of the gastrointestinal tract are critical to optimizing the growth of poultry. In the early stages of goose growth and development, a large amount of nutritional support is required. After the intestinal structure and function are damaged, it will affect the individual’s early nutritional absorption, causing irreversible damage to the body’s growth and development in the early stages. Lipopolysaccharide (LPS) is a pathogenic compound that occurs in the outer membrane of the cell wall of all gram-negative bacteria, and it can elicit multiple signaling events in the cell. LPS can act as a strong inflammatory mediator and is widely used in animal studies to simulate bacterial infection. Peng et al. studied inflammation in bovine endometrial epithelial cells caused by LPS and found that FA exerted an anti-inflammatory effect by inhibiting the release of cytokines. Chen et al. reported that 30 mg/kg FA increased the antioxidant capacity of the liver and repaired liver damage, reducing hepatocyte death due to LPS in blunt-nosed sea bream. Further, FA plays a positive role in reducing renal injury in HFD/STZ-induced DN mice by enhancing autophagy and inhibiting inflammation. However, to date, the effects of FA treatment in geese after triggering oxidative stress have not been studied, nor has the oxidative stress damage encountered during the development of the geese industry been addressed, which would lead to mortality in geese, and could adversely affect the development of the geese industry. In the present study, FA was added to the diets of Jilin white geese at different concentrations, and LPS was injected intraperitoneally at 14 and 21 days of age to investigate the effects of FA on the growth performance and intestinal antioxidant capacity of LPS-stressed Jilin white geese. Our findings show that FA can protect animals under oxidative stress conditions and provide a scientific basis for the implementation of FA as an antioxidant agent. # Materials and methods ## Experimental design This study was carried out in strict accordance with the recommendations of the Guide to Nursing and Use of Experimental Animals of Jilin Agricultural University. The study was verbal approval by the Experimental Ethics Committee of Jilin Agricultural University. All operations were performed under pentobarbital sodium anesthesia, and every effort was made to reduce pain.120 male Jilin white geese of similar weight at 7 d of age were used. There was a pre-feeding period of 7 d, and the trial period was 21 d. After the pre-feeding period, the 120 Jilin white geese were randomly divided into six groups with five replicates (four birds in each group). Groups F1 (60 mg/kg feed FA), F2 (120 mg/kg feed FA), F3 (180 mg/kg feed FA), F4 (240 mg/kg feed FA), and L were given intraperitoneal injections of LPS (500 μg/kg BW) on days 14, 17, and 20. The doses and routes of LPS administration referred to the previous studies. Group C was given intraperitoneal injections of normal saline (0.5 mg/kg BW). The test was carried out by establishing an oxidative stress model. shows the composition of rations. During the test period, all geese had access to feed and water ad libitum throughout the trial. Water was provided in a half-open plastic cylindrical water tank, and the feed was provided in feeders on one side of each pen. The geese were reared indoors conditions (temperature: 26.0°C ± 3.0°C; relative humidity (RH): 60.5 ± 5.0%; lighting period: 16 h; space allocation: 0.49 m2/gander), and the feed intake and body weight were recorded daily. On day 21, 10 animals in each group were randomly selected for slaughter, and tissue samples of the heart, liver, spleen, kidney, bursa of fabricius, and thymus organs, duodenum, jejunum, and ileum were collected. 1\) The premix provided the following per kg of diets: VA 2500 IU, VD<sub>3</sub> 1000 IU, VE 3100 mg, VK<sub>3</sub> 200 mg, VB<sub>1</sub> 100 mg, VB<sub>2</sub> 1 200 mg, VB<sub>6</sub> 200 mg, VB<sub>12</sub> 2 mg, Nicotinic acid 600 mg. Pantothenic acid 1 700 mg, Folic acid 200 mg, Biotin 20 mg, Fe (as ferrous sulfate) 6 000 mg, Cu (as copper sulfate) 300 mg, Mn (as manganese sulfate) 15 000 mg. Zn (as zinc sulfate) 8 500 mg, I (as potassium iodide) 10 mg, Se (as sodium selenite) 30 mg. ## Test materials ### Test animals and reagents The test animals were purchased from Jilin Yuhong Ecological Agriculture Technology Co. We also used *E*. *coli* lipopolysaccharide (Sigma Chemical Co., St. Louis, MO, USA), FA (97%) (Shanghai Maclean Biochemical Technology Co., Ltd), and Malondialdehyde assay (MDA)kit, Total Antioxidant Dismutase Assay (SOD) Kit, Glutathione peroxidase assay (GSH-PX) kit, Hydrogen peroxidase assay (CAT) kit, Total Antioxidant Capacity Assay(T-AOC) Kit (Nanjing Jiancheng Bioengineering Institute, Nanjing, China). ## Sample collection and indicator determination Growth performance. The initial weight, day 14 weight, and final weight of the geese were recorded. The average daily gain (ADG), average daily feed intake (ADFI), and feed conversion ratio (F/G) in the stages of days 1–14, 15–21, and 1–21 in the trial were calculated. ### Visceral index All surgeries are performed under pentobarbital sodium anesthesia, and every effort was made to reduce pain. Slaughter was carried out on day 21 of the trial. The organs of the geese (heart, liver, spleen, bursa, and thymus) were removed after slaughter and were weighed after removing excess fat. Measurement of intestinal oxidative stress indicators. Determination of MDA, SOD, GSH-PX, CAT and T-AOC in the intestinal tract of geese. ## Data analysis The raw data were processed using Microsoft Excel. A one-way ANOVA and Duncan’s multiple comparison test were performed using SPSS 26.0 software. Results are presented as mean ± standard error (SE), with *P \<* 0.05 indicating a significant difference. # Results ## Growth performance The LPS damage model was developed to observe the change in growth performance of each group before and after oxidative stress. Between days 1 and 14, final body weight (FB) and ADG were significantly higher in group F3 than in group L (*P \<* 0.05), and ADFI was significantly higher in groups F2 and F3 than in groups C and L (*P* \< 0.05). The FCR was significantly lower in group F3 than in group L (*P* \< 0.05). On days 15–21, FB was significantly higher in the groups with FA added than in group L (*P* \< 0.05). ADG was significantly higher in the groups with FA added than in group L and significantly lower than in group C (*P* \< 0.05). ADFI was significantly higher in the groups with F1 and F4 than in group L and significantly lower in the groups with FA added and L than in group C (*P* \< 0.05). FCR was significantly lower in the groups with FA added than in group L and significantly higher in groups F1, F2, F3, and L than in group C (*P \<* 0.05). From days 1 to 21, ADG was significantly higher in the groups with FA added than in group L and significantly lower in groups F1 and L than in group C (*P \<* 0.05). ADFI was significantly higher in groups C, F2, and F3 than in group L (*P \<* 0.05). FCR was significantly higher in group L than in the other groups (*P \<* 0.05). ## Organs indices To reflect the changes in organ weight in geese after oxidative stress, samples were taken at 21 days and the organs indices was measured. The thymic indices was significantly higher in group F4 than in groups C (*P \<* 0.05). ## Antioxidant activity in the duodenum We measured the changes in antioxidant activity in the duodenum of geese after oxidative stress to reflect the antioxidant activity of the duodenum. Groups F1, F3, F4, and C showed a significant decrease in MDA compared to group L (*P \<* 0.05). Group F1 showed a significant decrease in SOD compared to group C and Group F4 showed a significant reduce in GSH-Px compared to group C (*P \<* 0.05). Group C showed a significant increase in SOD and GSH-Px compared to group L (*P \<* 0.05). Groups L, F1, F2, and F4 showed a significant decrease in CAT compared to group C (*P \<* 0.05). ## Antioxidant activity in the jejunum We measured the changes in antioxidant activity in the jejunum of geese after oxidative stress to reflect the antioxidant activity in the duodenum. MDA was significantly lower in groups F3 and F4 than in group L and in group F4 than in group F1 (*P \<* 0.05). SOD was significantly higher in group C than in groups L and F1 (*P \<* 0.05). GSH-Px was significantly higher in group F3 than in groups L, C, and F1 (*P \<* 0.05). The CAT content of group L was significantly lower than that of all other groups (*P \<* 0.05). ## Antioxidant activity in the ileum We measured the changes in antioxidant activity in the jejunum of geese after oxidative stress to reflect the antioxidant activity in the duodenum. MDA was significantly lower in groups F2, and C than in group L, (*P \<* 0.05). GSH-Px was significantly higher in group C than in groups L and F1, F2, F4 and significantly higher in group F2, F3, F4 than in group L and significantly higher in group F3 than in group F1 (*P* \< 0.05). # Discussion During the process of goose breeding, oxidative stress can lead to a decrease in gse growth performance and a loss of economic benefits. LPS, a major component of the cell wall of gram-nega-tive bacteria, is a pathogenic compound. In this study, we obtained equivalent experimental results: LPS injection at 0.5 mg/kg body weight significantly reduced both the body weight gain of geese at d 15 to 21 and the feed intake during, and, but increased the FCR of geese on d 15 to 21. These initial results indicated that the oxidative stress model was established successfully and was suitable for subsequent investigation of the effects of FA on geese health. The addition of 6 mg/kg of FA to the feed increased beef the tenderness, juiciness, flavor intensity, and amount of some fatty acids. Supplementation with 180 mg/kg of FA in the present study enhanced growth performance and reversed the decline in growth performance brought about by oxidative stress, indicating that ferulic acid can alleviate the damage caused by oxidative stress. The liver, as the main metabolic and detoxification organ in the body, is closely related to various physiological functions and circulation, and the effects of immune organs such as the liver on oxidative stress occur through the recruitment of immune cells. In the present study, the addition of 240 mg/kg FA increased the thymic index, probably because FA mitigates the effects of oxidative stress from LPS by affecting the weight of the thymus and increasing body immunity. Reported that FA has cytoprotective capacity and may promote gastrointestinal health and microbial protein synthesis. In mice with high oxidative stress levels, insulin synthesis was improved in pancreatic β-cells. In the present study, the addition of 180 mg/kg of FA significantly alleviated the intestinal damage caused by oxidative stress, may be related to the enhancement of intestinal epithelial cell activity by ferulic acid, enhances cell activity to resist LPS induced damage. FA also inhibited the activation of the ROCK/NF-κB signaling pathway, thereby improving the dysregulation of oxidative stress and inflammation and exerting an effective hepatoprotective effect. The above growth performance and intestinal oxidative indexes were due to excessive reactive oxygen species production from LPS-induced oxidative stress, which indirectly affected the changes in physiological indexes and enzyme activities. This may be related to antioxidant signaling pathways, such as Nrf2/HO-1 and ROCK/NF-κB. Administering FA after LPS-induced oxidative stress can alleviate the effects of oxidative stress on growth performance and reduce intestinal antioxidant activity. # Conclusion 1\. Adding 180 mg/kg of FA can increase the body weight of geese and promote their growth. Adding 60 mg/kg FA can improve the thymus index, alleviate the damage to immune function caused by stress, and reduce the negative effects of stress. 2\. Adding 180 mg/kg FA can alleviate oxidative stress damage in the duodenum, ileum, and jejunum, reduce cell membrane damage, maintain the homeostasis of the membrane lipid bilayer, and protect cells from oxygen ions. In conclusion, adding 180 mg/kg of FA promoted the growth of geese and alleviated the effects of oxidative stress and the damage caused by oxidative stress in the duodenum, jejunum, and ileum. [^1]: The authors have declared that no competing interests exist.
# Introduction Computational fluid dynamic (CFD) simulations of biological valves have steadily improved over the years; however, procedures accounting for the formation of actual solid aggregates, such as calcifications or clots, have not been implemented yet. At the same time, researchers have also devised mathematical models for clot formation and growth; however, these models have been developed independently and are not usually associated to the dynamics of the valve. We propose a particle-based method that, by taking advantage of its mesh-free nature, can compute the fluid dynamics, together with valve deformation and formation of solid aggregates. In general, the simulation of biological valves, where a solid structure interacts with the surrounding flow, constitutes a fluid-structure interaction (FSI) problem. The algorithms to solve FSI problems may be broadly classified into two categories: conforming mesh methods and non-conforming mesh methods. Conforming mesh methods divide the computational domain in two parts: (i) a part occupied by the liquid where the Navier-Stokes equations are solved, and (ii) a part occupied by the structure where the stress-deformation equations are solved. Since the structure moves and/or deforms with time, re-meshing is needed as the solution advances. Non-conforming mesh methods, most notably the Immersed boundary methods (IBM), treat the interface between the fluid and the structure as a constraint and the force exerted by the structure to the fluid becomes a source term in the momentum equation. As a result, the fluid and solid equations are solved independently and re-meshing is not necessary. Both methods, however, have difficulties handling phenomena such as calcification and clotting that involve some sort of transition where part of the liquid transforms into a solid. In general, attempts to account for the formation of solid aggregates in CFD/FSI studies are based on ‘numerical artifices’ such as fluids with higher viscosities to mimic clotting, or membranes with higher stiffness to mimic calcification. For a different approach see. On the other hand, modelling of clot formation and growth had followed an independent path that, in some cases, has brought to particle-based techniques such as Lattice-Boltzmann or Coarse grained Molecular Dynamics. In general, however, these models assume simple hydrodynamic conditions and/or refer to straight blood vessels with not moving/deforming parts. Additionally, coupling fluid dynamics and solid deformation can be implemented with the Smoothed Particle Hydrodynamics method. But, it can’t easily account for other phenomena such as contact mechanics and agglomeration. In order to account for the fluid dynamics, the valve deformation, and the formation of solid aggregates at the same time, we propose *discrete multi- physics*: a mesh-free approach, where computational particles are employed for both the flow and the structure. With this method, the distinction between liquid and solid depends exclusively on the types of forces that act on each particle: pressure and viscous forces characterize liquid particles, while elastic forces characterize solid particles. By changing the type of forces on specific groups of particles, we can change their status form liquid to solid and vice versa. In, we used this idea to model melting and solidifying flows; in this paper, we extend it to the formation of agglomerates in biological valves. This article is organized as follows. Initially, we discuss the basic ideas behind our discrete multi-physics technique and describe the geometry used in the simulations. Next, we validate the model against both traditional modelling techniques and experimental data. Finally, we introduce the formation of solid aggregates at the membrane surface and in the flow. The objective of this paper is to apply discrete multi-physics to biological valves in general. For this reason, we do not focus on a specific type of valve at this stage. However, in order to test our model in the most challenging scenario, we chose dimensions and velocities similar to those occurring in aortic valves. We consider these conditions to be the most challenging scenario because (i) they involve higher velocities, which generate complex recirculation patterns, and (ii) they involve higher stresses, which generate larger membrane deformations. From this point of view, the fact that we simulate bicuspid valves, while the aortic valve has three leaflets, is not a limitation. Given the same mechanical stress, in fact, deformations are higher in bicuspid valves than in tricuspid valves. Therefore, by forcing velocities that are typical of aortic valves in bicuspid valves, we test our model under conditions that are even more critical (i.e. produce higher deformations) than those occurring in aortic valves. # Modelling ## Discrete multiphysics Our discrete multi-physics approach is based on the so-called discrete multi- hybrid system (DMHS). This technique combines various mathematical models to achieve a representation of fluid-structure interactions and solid-liquid systems that is not attainable with each model separately. Elsewhere, we showed that the linkage of different models is mathematically complex and computationally time consuming. In order to facilitate this, the DMHS combines models that share a common discrete (particle-based) paradigm, such as SPH (Smoothed Particle Hydrodynamics), CGMD (Coarse-grained Molecular Dynamics), DEM (Discrete Element Method) or BD (Brownian Dynamics). In this study, models for solid contact/collision (i.e. DEM), or for fluctuating hydrodynamics (i.e. BD) are not necessary; consequently, the coupling is limited to SPH (liquid phase) and CGMD (solid phase). For the numerical solution, the model was implemented in LAMMPS. A mathematical introduction to SPH and CGMD and the approach used to couple the models is given in. Specific details of the DMHS and other mesh-free hybrid techniques can be found in. In previous DMHS publications, there is an interchangeable use of the terms CGMD and Mass-Spring Model (MSM). This depends on the fact that these articles cover different scales. Articles dealing with microscopic scales use CGMD, whereas articles dealing with macroscopic scales use MSM. Mathematically, however, the two techniques are equivalent. In the main text, we prefer MSM, which is more consistent with the scale under investigation. In, we use CGMD, which is more consistent with the original DMHS formulation. ## Geometry We use a 2D simplified geometry for modelling a generic bicuspid valve as illustrated in. The channel half-thickness is *Z* = 0.0125 m, the length of the membrane is *L* = 0.016m and the radius of the circular area is *R* = 0.0215 m. As mentioned above, the DMHS combines various particle-based modelling techniques. In this study, the simulations are based on two models and three types of particles: SPH particles for the fluid, fixed SPH particles for the walls and MSM particles for the flexible leaflets (membrane). Periodic boundary conditions are used at the inlet/outlet. To model the Young modulus *E* and the flexural rigidity *F* of the membrane, the MSM particles are joined together by numerical ‘springs’ and ‘hinges’, as described in. The relation between the spring (*k*<sub>*b*</sub>) and hinge (*k*<sub>*a*</sub>) constants and the actual Young modulus and the flexural rigidity is given in. ## Pulsatile flow In order to test the model in the most critical conditions, we target high velocities typical of cardiac valves such as the aortic valve. The flow is pulsatile and corresponds to a normal cardiac output of 5.5 L min<sup>-1</sup>, a beat rate of 72 bpm and an aortic pressure of 100 mmHg. This frequency gives a peak velocity of around 0.9 m s<sup>-1</sup>. In the simulation, we force the flow by means of a sinusoidal pressure *P* gradient $$\frac{dP}{dx} = A\text{sin}(\frac{2\pi}{T}t),$$ where *A* is the force amplitude and *T* the period. To obtain this pressure gradient in the simulations, we impose to each liquid particle the acceleration $$g = g_{0}\text{sin}(2\pi ft),$$ with *g*<sub>*0*</sub> = 500 m s<sup>-2</sup> and oscillation frequency *f* = 1/*T* (*T* = 1 s). Under these conditions, we reach high velocities but the flow remains laminar. We focus on the laminar regime for two reasons: (i) blood flow under normal conditions is laminar, and (ii) we want to test, at this stage, the accuracy of our model without dealing with the additional complexity of turbulence. ## Dimensionless analysis In Section *Membrane deformation*, we compare our simulations with experimental data. The comparison is based on specific dimensional groups that are defined in this section. Dimensional analysis bring to three fundamental groups Re (Reynolds Number), N<sub>f</sub> (dimensionless frequency) and Λ (geometric ratio), defined as $$\text{Re} = \frac{\rho UZ}{\mu},$$ $$N_{\text{f}} = \frac{\rho f^{2}d^{5}}{F/L},$$ and $$\Lambda = \frac{Z}{L},$$ where *ρ* is the density of the fluid, *U* is a reference velocity (here we use the max velocity in the channel), *Z* the half-thickness of the channel, *μ* the fluid viscosity, *f* the oscillation frequency, *d* the membrane thickness, *F* the flexural rigidity, and *L* the length of the membrane. The computational particles used in our simulations are point particles; strictly speaking, they do not have an actual thickness. Their thickness is the result of the repulsive forces acting on the particles to impose no-penetration boundary conditions. The value of *d* in, therefore, is calculated from *k*<sub>*a*</sub> and *k*<sub>*b*</sub> as discussed in. The value of the Young modulus *E* does not compare explicitly in any of the dimensionless numbers above; this is due to the fact that *F* and *E* are interchangeable as discussed in. In theory, we should also account for another dimensionless group based on *R* (radius of the convex area). In practice, however, this group is not necessary as discussed in Section *Membrane deformation*. Each dimensionless number provides specific information about the geometric constants and the physical forces acting in the system. Re indicates the extent of the inertial forces with respect to the viscous forces. N<sub>f</sub> indicates the membrane resistance with respect to the stress generated by the oscillating flow. Λ indicates the geometric ratio between the channel thickness and the membrane length. In comparing the simulations with the experimental data (see Section *Membrane deformation*), we found that the group $$\text{N}_{\text{R}} = \text{Re}.\text{N}_{\text{f}} = \frac{\rho^{2}f^{2}d^{5}UZ}{\mu F/L}$$ is particular relevant. This dimensionless number compares the effect of the forces that tend to deform the membrane (numerator) with those that tend to oppose the deformation (denominator). In Section *Membrane deformation*, we show that different geometries and flow conditions generate the same type of membrane deformation if N<sub>R</sub> is the same. # Results There are two types of parameters required for the simulations: model parameters and simulation parameters. The first group consists of internal parameters used by the SPH and MSM solvers; the second refers to the operative conditions. This Section focuses on the second group (i.e. *Z*, *L*, *R*, μ, *ρ* and *F*); the internal parameters (e.g. *k*<sub>*a*</sub>, *k*<sub>*b*</sub>, number of particles, time step, smoothing length, etc.) can be found in. The geometric parameters *L*, *Z*, *R* are given in Section *Geometry* (see also ). All the simulations assume blood as liquid medium. Blood is a viscoelastic fluid, but in flow simulations is often considered Newtonian. In our calculations, we also use the Newtonian approximation with *ρ* = 1056 kg m<sup>-3</sup> and *μ* = 0.0035 Pa s. We consider membranes with different flexural rigidities, the specific value of *F*, for each case, is given in Section *Membrane deformation*. This section is divided in three parts. The first part is dedicated to the flow, and we validate our results against traditional CFD simulations. The second part is dedicated to the membrane, and we validate our results against experimental data. The third part focus on the formation of solid aggregates, and highlights the main advantages of the DMHS in modelling biological valves. ## Hydrodynamics We compare results obtained with our model with traditional CFD simulations performed with Abaqus 6.14<sup>®</sup> with the same geometry and under similar flow conditions. In these simulations, the membrane is fixed in order to focus solely on the hydrodynamics. This is done on purpose: if at this stage we had considered both the fluid and the membrane together, we could not have distinguished whether potential errors originated from the fluid dynamics or the membrane mechanics. Calculations are run at two constant inlet velocities, 0.2 m s<sup>-1</sup> and 0.9 m s<sup>-1</sup>. Because of the different nature of the two modelling techniques, the inlet/outlet boundary conditions (b.c.) are not the same. The DMHS uses periodic inlet/outlet b.c., while in the CFD simulation the inlet has constant velocity and the outlet fixed pressure. shows the CFD results; shows the DMHS results. Comparison between Figs and shows a good agreement between the CFD and the DMHS calculations. Both models, in particular, capture the recirculation zones in the circular chamber in the centre. For the velocity, minor differences (2–5%) can be found at the tip of the valve. These differences depend on the different inlet conditions between the DMHS and the CFD model and the nature of the discretization method (particles vs. mesh). Another important variable often reported in literature is shear stress (Figs). But also in this case CFD and DMHS results are similar. Both models, in particular, identify a region of high stress near, but not exactly at, the end of the leaflets. ## Membrane deformation In this section, we account for the flexibility of the leaflets and calculate both the flow and the membrane dynamics. For validation purposes, we compare the membrane deformation observed during the simulations with those obtained experimentally by. In both simulations and experiments the valve has two leaflets and the flow is pulsatile. The geometric conditions, however, are not exactly the same: in, in fact, *L* = 0.0263 m, *Z* = 0.015m, and the channel is straight without the circular chamber in the centre (this is why, in Section *Dimensionless analysis*, we did not introduce a forth dimensionless number). Additionally, our simulations are 2D and based on blood, while employ water in a rectangular channel with depth *w* = 0.05 m. gathers all the parameters used in the simulations and in the experiments. The values of *k*<sub>*a*</sub> and *k*<sub>*b*</sub> corresponding to a specific *F* in the simulations are given in. The values of *d* for the simulations are calculated according to the procedure described in. After running a large number of simulations and observing how the membrane deforms under various flow conditions, we realized that the fundamental group that affects the membrane dynamics is N<sub>R</sub>. Therefore, we chose specific values of *f*, *g*<sub>0</sub> (which gives *U*), *k*<sub>*a*</sub> and *k*<sub>*b*</sub> (which give *F* and *d*) to obtain in our simulations the same N<sub>R</sub> of the experiments. We consider three cases that we call, soft membrane, intermediate membrane, and hard membrane. We start with the case of the intermediate membrane: the ‘normal’ case, which subsequently is compared to the soft and the hard membrane. shows the comparison between simulations and experiments in the case of the intermediate membrane. The overall dynamics is very similar, but there are same noticeable differences. In the simulation, the maximum opening of the membrane is wider. This is due to the absence of the central chamber in the experimental set-up. Another minor difference occurs at the end of the cycle when the backpressure closes the valve completely. When closed, the experimental valve has a more elongated shape since the leaflets are longer. This is a consequence of the fact that, besides the main group N<sub>R</sub>, also Λ has a (minor) effect on the membrane. Experiments and simulation have the same N<sub>R</sub>, but not exactly the same Λ; some (minor) differences, therefore, are expected. shows the comparison between simulations and experiments in the case of the soft membrane. The soft membrane can be considered defective since its position is completely reversed by the backflow. As in the previous case, there are some minor differences, but overall the membrane behaviour is well captured by the model. Similar deformation profiles have also been by other studies. shows the comparison between simulations and experiments in the case of the hard membrane. Also the hard membrane can be considered defective since it does not completely opens. In this case, the comparison focuses on the membrane’s tip. At this location, the two leaflets slide one over the other and symmetry is lost. This phenomenon is captured in both the simulations and the experiments. The loss of symmetry suggests that the simulations should account for the whole geometry and not only half of it (considering only one leaflet). Besides validating our model, this section also highlights the importance of N<sub>R</sub>. The values of Re, Λ and N<sub>f</sub> between the simulations and in the experiments are different, but, since N<sub>R</sub> is the same, the membrane behaviour in both cases is similar (with the little caveat about Λ as discussed above). ## Formation of solid aggregates This section introduces solid aggregation in the DMHS. We consider two cases: solid deposits at the membrane surface, and formation of aggregates in the main flow. We generally indicate the first case as ‘calcification’ and the second as ‘clotting’. Our focus, however, is not to the formation and the evolution of actual calcifications and clots. These are very complicated biochemical phenomena and their full dynamics is beyond the scope of this article. The goal is here to illustrate how, given a criterion for aggregation, this can be implemented in our model. Once this has been achieved, more complicated agglomeration models can be implemented. Both calcification and clotting imply the formation of solid aggregates developing from the liquid. In the DMHS framework, this can be achieved by changing the forces acting on certain particles from SPH to MSM. describes the algorithm used in the simulations. The procedure starts from an agglomeration seed. In our simulations, the seed is chosen arbitrarily, but it can depend on a specific criterion; for example, when local shear stress exceeds a threshold value, the particle at that location becomes a seed. Once the position of the seed is known, the algorithm propagates the agglomerate. Every *N* time-steps, it identifies all the particles within a distance *R*<sub>MAX</sub> from the seed, and, with a certain probability, transforms some of the liquid-particles in solid agglomerate-particles by (i) changing the forces acting on the particles from SPH to MSM, (ii) and creating a bond between the seed and the newly created agglomerate-particle. The strength of the new bond determines the material properties of the agglomerate. In our simulations, the probability of transforming a liquid-particle in an agglomerate-particle has been related to a fixed value, but, as mention before, it can be associated to a specific criterion (e.g. shear stress threshold). The algorithm repeats the above procedure iteratively to propagate the agglomerate further and new agglomerate particles create bonds only to other fluid particles and not to existing agglomerate particles. At the next time step, the previously generated agglomerate-particles become seeds; these seeds create new agglomerate-particles and so on as illustrated in. We can affect the final shape of the agglomerate by changing, as time progresses, the behaviour of the seeds. If the seeds are active all the time, they continue to create new agglomerate-particles around them until they are fully surrounded by the agglomerate. In this case, the overall shape of the agglomerate tends to be circular. If the seeds remain active only for one time step, the agglomerate propagates in one preferential direction and tends to assume a filiform (thread-like) shape. shows three types of simulations where the algorithm is applied to three different configurations. The simulation parameters (*N*, *R*<sub>MAX</sub>, agglomeration probability, etc.) for all three cases are gathered in. With the goal of obtaining a sizable aggregate in a few cycles, we accelerated the agglomerate formation by using higher aggregation probabilities. This is a typical technique used to study phenomena with very different timescales as those occurring in pipelines erosion. In the first case (called ‘calcification’), the initial seed is located in the region between the membrane and the wall and the deposit propagates following the circular agglomeration algorithm illustrated in. An interesting feature of the simulation is that, as time progresses, the agglomerate makes increasingly difficult the movement of the lower leaflet until it stops almost completely. In the second case (called ‘free clot’), the initial seed is located in the flow and the agglomerate propagates following the circular algorithm. The presence of a solid aggregate alters the hydrodynamics as indicated in. Once a liquid particle transform into a solid particle, the fluid streamlines must change direction to account for the new solid-liquid boundaries. This feature would not be possible with mesh-based algorithms and highlights one of the advantages of discrete multi-physics. The third case (called ‘filiform clot’) is similar to the previous case. This time, however, the initial seed is located at the tip of the leaflet and the agglomerate propagates according to the filiform algorithm. As the filiform aggregate grows, it moves alternately on the right and on the left of the membrane due to the oscillating flow. We can emphasize another advantage of using a particle-based technique by introducing fragmentation. The drag between the fluid and the agglomerate creates internal stresses in the solid. These stresses tend to pull apart the agglomerate-particles that respond with a stronger binding force (according to equation J). At this point, we can slightly modify the algorithm and introduce a criterion for break-up: if the force between two agglomerate-particles exceeds a certain value, the bond breaks. In, we used a threshold force of 1.3·10<sup>−7</sup> N. At a certain point of the simulation, the threshold force is exceeded and the agglomerate breaks in two parts. One part remains attached to the leaflet; the other becomes free and moves unrestricted with the flow. # Conclusions Mesh-free methods are usually considered viable alternatives to traditional modelling, but have never enjoyed the same popularity of mesh-based techniques. Many mesh-free methods have been developed only in relatively recent years and offer, to the potential user, less available information, experience and software. On the other hand, a specific sub-set of mesh-free algorithm (e.g. SPH, DEM, CGMD, BD etc.) share a common particle-based framework that makes particularly easy their linkage in multi-physics problems. We call this approach *discrete multi-physics* and, in this paper, we show that, in certain circumstances, it is more than a mere alternative to traditional modelling. Discrete multi-physics can tackle, with relatively little effort, problems that are considered very challenging with mesh-based multi-physics. Elsewhere, we focused on solid-liquid flows where the dispersed phase is made of deformable, breakable, dissolving, melting or solidifying particles. Here, we apply the same approach to biological valves including the formation of solid aggregates in the flow and at the membrane surface. To the best of our knowledge, this is the first study to directly account for the hydrodynamics, the membrane deformation and the formation of solid aggregates at the same time and, as such, it has the potential to open a new prospective to the modelling of biological valves. # Supporting information [^1]: The authors from LivaNova didn't provide any financial support to these works. Commercial affiliation of authors from LivaNova does not alter our adherence to PLOS ONE policies on sharing data and materials. [^2]: **Conceptualization:** MA M. Bussone FG AA. **Data curation:** MA AA. **Formal analysis:** MA MHA M. Bussone FG FB M. Barigou AA. **Funding acquisition:** M. Barigou AA. **Investigation:** MA MHA AA. **Methodology:** MA AA. **Project administration:** M. Barigou AA. **Resources:** M. Bussone FG FB M. Barigou AA. **Software:** MA MHA. **Supervision:** AA. **Validation:** AA. **Visualization:** MA AA. **Writing – original draft:** MA AA. **Writing – review & editing:** MA AA. [^3]: ‡ These authors also contributed equally to this work.
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Dataset Card for Only Clean Data (OCD)

If you are training base language models and want the cleanest sources available, OCD was built just for you.

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It is without question that the quality of a language model rests on the quality of its training data. OCD is a meticulously curated and cleaned corpus of text documents, ensuring the highest quality text from a variety of sources. Part of this process includes manually inspecting (and sometimes manually fixing) thousands of documents. Whenever problem documents are found (from e.g. conversion errors, or spam that got through), they are fixed for the next release.

Dataset Sources

OCD currently consists of 3 subsets:

  • Web data originating from C4. This subset was heavily filtered to remove a lot of spam, templates, and other low quality data. It consists of approximately 18M documents, which is roughly 5% of the original 365M documents.
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This dataset is actively in development, and will continue to be extended to include books, research, and other documents from various domains, code, documentation, and more.

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OCD is released under the cc-by-4.0 license. Note that this is directly compatible with PLOS and CCOpenBooks (cc-by-4.0).

Documents originating from C4 were released under the ODC-BY license as noted here. As this subset was derived from an enormous Common Crawl corpus, there is a possibility that it contains documents not compatible with this license. However, the heavy filtering applied as part of the OCD project greatly reduces this possibility. Additionally, any opt-out requests from content authors will be respected.

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The primary intended use of this dataset is for training base language models.

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