bluuebunny/crossref_metadata_2025 huggingface dataset:
Simultaneous directional full-field OCT using path-length and carrier multiplexing
Authors: Valente Denise , Vienola Kari V. , Zawadzki Robert J. , Jonnal Ravi S.
Published: September 2021

Full-field swept-source optical coherence tomography (FF-SS-OCT) is an emerging technology with potential applications in ophthalmic imaging, microscopy, metrology, and other domains. Here we demonstrate a novel method of multiplexing FF-SS-OCT signals using carrier modulation (CM). The principle of CM could be used to inspect various properties of the scattered light, e.g. its spectrum, polarization, Doppler shift, or distribution in the pupil. The last of these will be explored in this work, where CM was used to acquire images passing through two different optical pupils. The two pupils contained semicircular optical windows with perpendicular orientations, with each window permitting measurement of scattering anisotropy in one dimension by inducing an optical delay between the images formed by the two halves of the pupil. Together, the two forms of multiplexing permit measurement of differential scattering anisotropy in the x and y dimensions simultaneously. To demonstrate the feasibility of this technique our carrier multiplexed directional FF-OCT (CM-D-FF-OCT) system was used to acquire images of a microlens array, human hair, onion skin and in vivo human retina. The results of these studies are presented and briefly discussed in the context of future development and application of this technique.
Roles of fiber birefringence and Raman scattering in the spontaneous four-wave mixing process through birefringent fibers
Authors: Xie Mengyu , Seok Lee Youn , Tannous Ramy , Long Gui-Lu , Jennewein Thomas
Published: September 2021

We investigate the impact of fiber birefringence and spontaneous Raman scattering on the properties of photon pairs that are generated by the spontaneous four-wave mixing process in birefringent fibers. Starting from the formulation of the theory of four-wave mixing, we show a theoretical model for a generated optical field with the consideration of the Raman scattering and a Gaussian-distributed pump. The theoretical model is then applied for deriving the closed expressions of the photon-pair spectral properties as a function of the fiber birefringence. Also, with the modeled Raman gain, we evaluate the reduction of the pair production rate due to the presence of the Raman effect as well as the contributions of the Raman-scattered photons over a broad wavelength range. The predictions are experimentally verified with a commercial polarization-maintaining fiber.
Design of multilayer optical thin-films based on light scattering properties and using deep neural networks
Authors: Fouchier Marin , Zerrad Myriam , Lequime Michel , Amra Claude
Published: September 2021

Despite limiting the performance of multilayer optical thin-films, light scattering properties are not as yet controllable by current design methods. These methods usually consider only specular properties: transmittance and reflectance. Among other techniques, design of thin-film components assisted by deep neural networks have seen growing interest over the last few years. This paper presents an implementation of a deep neural network model for light scattering design and proposes an optimization process for complex multilayer thin-film components to comply with expectations on both specular and scattering spectral responses.
Hybrid design of diffractive optical elements for optical beam shaping
Authors: Doskolovich Leonid L. , Mingazov Albert A. , Byzov Egor V. , Skidanov Roman V. , Ganchevskaya Sofiya V. , Bykov Dmitry A. , Bezus Evgeni A. , Podlipnov Vladimir V. , Porfirev Alexey P. , Kazanskiy Nikolay L.
Published: September 2021

Hybrid methods combining the geometrical-optics and diffraction-theory methods enable designing diffractive optical elements (DOEs) with high performance due to the suppression of stray light and speckles and, at the same time, with a regular and fabrication-friendly microrelief. Here, we propose a geometrical-optics method for calculating the eikonal function of the light field providing the generation of a required irradiance distribution. In the method, the problem of calculating the eikonal function is formulated in a semi-discrete form as a problem of maximizing a concave function. For solving the maximization problem, a gradient method is used, with analytical expressions obtained for the gradient. In contrast to geometrical-optics approaches based on solving the Monge–Ampére equation using finite difference methods, the proposed method enables generating irradiance distributions defined on disconnected regions with non-smooth boundaries. As an example, we calculate an eikonal function, which provides the generation of a "discontinuous" irradiance distribution in the form of a hexagram. It is shown that the utilization of the hybrid approach, in which the obtained geometrical-optics solution is used as a starting point in iterative Fourier transform algorithms, enables designing DOEs with a quasi-regular or piecewise-smooth microrelief structure. The calculation results are confirmed by the results of experimental investigations of a DOE generating a hexagram-shaped irradiance distribution.
Alignment procedure for off-axis-parabolic telescopes in the context of high-intensity laser beam transport
Authors: Ohland J. B. , Zobus Y. , Eisenbarth U. , Zielbauer B. , Reemts D. , Bagnoud V.
Published: September 2021

Off-axis parabolic telescopes are rarely used in high-intensity, high-energy lasers, despite their favorable properties for beam transport such as achromatism, low aberrations and the ability to handle high peak intensities. One of the major reasons for this is the alignment procedure which is commonly viewed as complicated and time consuming. In this article, we revisit off-axis parabolic telescopes in the context of beam transport in high-intensity laser systems and present a corresponding analytical model. Based on that, we propose a suitable setup that enables fast and repeatable alignment for everyday operation.
Full-color photon-counting single-pixel imaging
Authors: Zhao Ya-Nan , Hou Hong-Yun , Han Jia-Cheng , Liu Hong-Chao , Zhang Su-Heng , Cao De-Zhong , Liang Bao-Lai
Published: September 2021

We propose and experimentally demonstrate a high-efficiency single-pixel imaging (SPI) scheme by integrating time-correlated single-photon counting (TCSPC) with time-division multiplexing to acquire full-color images at an extremely low light level. This SPI scheme uses a digital micromirror device to modulate a sequence of laser pulses with preset delays to achieve three-color structured illumination, then employs a photomultiplier tube into the TCSPC module to achieve photon-counting detection. By exploiting the time-resolved capabilities of TCSPC, we demodulate the spectrum-image-encoded signals, and then reconstruct high-quality full-color images in a single round of measurement. Based on this scheme, strategies such as single-step measurement, high-speed projection, and undersampling can further improve imaging efficiency.
Ultrawide-band silicon microring avalanche photodiode with linear photocurrent-wavelength response
Authors: Ren Yang , Van Vien
Published: September 2021

We report a CMOS-compatible silicon microring-enhanced avalanche photodiode based on
linear defect-state absorption in a

p

+

p

n

+

junction, with high responsivities
exceeding 1 A/W at telecommunication wavelengths. The large
photogenerated currents give rise to giant thermo-optic nonlinearity
in the microring resonator, resulting in a linear
photocurrent-wavelength response spanning the full free spectral range
of the microring. This unique photocurrent spectrum could enable novel
applications in wavelength-resolved photodetection, such as compact
on-chip spectrometers, linear chirp frequency laser source
characterization, and low-cost refractometric sensors without
requiring precise wavelength-tunable lasers.
Assessment of single-vessel cerebral blood velocity by phase contrast fMRI
Authors: Chen Xuming , Jiang Yuanyuan , Choi Sangcheon , Pohmann Rolf , Scheffler Klaus , Kleinfeld David , Yu Xin
Published: September 2021

Current approaches to high-field functional MRI (fMRI) provide 2 means to map hemodynamics at the level of single vessels in the brain. One is through changes in deoxyhemoglobin in venules, i.e., blood oxygenation level–dependent (BOLD) fMRI, while the second is through changes in arteriole diameter, i.e., cerebral blood volume (CBV) fMRI. Here, we introduce cerebral blood flow–related velocity-based fMRI, denoted CBFv-fMRI, which uses high-resolution phase contrast (PC) MRI to form velocity measurements of flow. We use CBFv-fMRI in measure changes in blood velocity in single penetrating microvessels across rat parietal cortex. In contrast to the venule-dominated BOLD and arteriole-dominated CBV fMRI signals, CBFv-fMRI is comparable from both arterioles and venules. A single fMRI platform is used to map changes in blood pO2 (BOLD), volume (CBV), and velocity (CBFv). This combined high-resolution single-vessel fMRI mapping scheme enables vessel-specific hemodynamic mapping in animal models of normal and diseased states and further has translational potential to map vascular dementia in diseased or injured human brains with ultra–high-field fMRI.
Genome-wide methylation data improves dissection of the effect of smoking on body mass index
Authors: Amador Carmen , Zeng Yanni , Barber Michael , Walker Rosie M. , Campbell Archie , McIntosh Andrew M. , Evans Kathryn L. , Porteous David J. , Hayward Caroline , Wilson James F. , Navarro Pau , Haley Chris S.
Published: September 2021

Variation in obesity-related traits has a genetic basis with heritabilities between 40 and 70%. While the global obesity pandemic is usually associated with environmental changes related to lifestyle and socioeconomic changes, most genetic studies do not include all relevant environmental covariates, so the genetic contribution to variation in obesity-related traits cannot be accurately assessed. Some studies have described interactions between a few individual genes linked to obesity and environmental variables but there is no agreement on their total contribution to differences between individuals. Here we compared self-reported smoking data and a methylation-based proxy to explore the effect of smoking and genome-by-smoking interactions on obesity related traits from a genome-wide perspective to estimate the amount of variance they explain. Our results indicate that exploiting omic measures can improve models for complex traits such as obesity and can be used as a substitute for, or jointly with, environmental records to better understand causes of disease.
How beliefs in traditional healers impact on the use of allopathic medicine: In the case of indigenous snakebite in Eswatini
Authors: Nann Sarah
Published: September 2021

Snakebite is a major public health problem in Eswatini and serious envenomations can be responsible for considerable morbidity and mortality if not treated correctly. Antivenom should be administered in hospital in case of adverse reactions and any delays due to distance, transport, costs, antivenom availability and cultural beliefs can be critical. Myths and superstition surround snakes, with illness from snakebite considered a supernatural phenomenon best treated by traditional medicine since healers can explore causes through communication with the ancestors. Traditional consultations can cause significant delays and the remedies may cause further complications. Four rural focus group discussions were held in varying geographical regions to establish why people may choose traditional medicine following snakebite. The study revealed four themes, with no apparent gender bias. These were ‘beliefs and traditions’, ‘logistical issues’, ‘lack of knowledge’ and ‘parallel systems’. All snakes are feared, regardless of geographical variations in species distribution. Deep-seated cultural beliefs were the most important reason for choosing traditional medicine, the success of which is largely attributed to the ‘placebo effect’ and positive expectations. Collaboration and integration of the allopathic and traditional systems assisted by the regulation of healers and their methods could improve future treatment success. The plight of victims could be further improved with more education, lower costs and improved allopathic facilities.
Immunogenic amino acid motifs and linear epitopes of COVID-19 mRNA vaccines
Authors: Wisnewski Adam V. , Redlich Carrie A. , Liu Jian , Kamath Kathy , Abad Queenie-Ann , Smith Richard F. , Fazen Louis , Santiago Romero , Campillo Luna Julian , Martinez Brian , Baum-Jones Elizabeth , Waitz Rebecca , Haynes Winston A. , Shon John C.
Published: September 2021

Reverse vaccinology is an evolving approach for improving vaccine effectiveness and minimizing adverse responses by limiting immunizations to critical epitopes. Towards this goal, we sought to identify immunogenic amino acid motifs and linear epitopes of the SARS-CoV-2 spike protein that elicit IgG in COVID-19 mRNA vaccine recipients. Paired pre/post vaccination samples from N = 20 healthy adults, and post-vaccine samples from an additional N = 13 individuals were used to immunoprecipitate IgG targets expressed by a bacterial display random peptide library, and preferentially recognized peptides were mapped to the spike primary sequence. The data identify several distinct amino acid motifs recognized by vaccine-induced IgG, a subset of those targeted by IgG from natural infection, which may mimic 3-dimensional conformation (mimotopes). Dominant linear epitopes were identified in the C-terminal domains of the S1 and S2 subunits (aa 558–569, 627–638, and 1148–1159) which have been previously associated with SARS-CoV-2 neutralization in vitro and demonstrate identity to bat coronavirus and SARS-CoV, but limited homology to non-pathogenic human coronavirus. The identified COVID-19 mRNA vaccine epitopes should be considered in the context of variants, immune escape and vaccine and therapy design moving forward.
Improved bacterial leaf blight disease resistance in the major elite Vietnamese rice cultivar TBR225 via editing of the OsSWEET14 promoter
Authors: Duy Phuong Nguyen , Lan Dai Tran , Pham Thu Hang , Thi Thu Huong Phung , Nguyen Thanh Ha , Pham Ngoc Phuong , Auguy Florence , Bui Thi Thu Huong , Manh Tran Bao , Cunnac Sebastien , Pham Xuan Hoi
Published: September 2021

TBR225 is one of the most popular commercial rice varieties in Northern Vietnam. However, this variety is highly susceptible to bacterial leaf blight (BLB), a disease caused by Xanthomonas oryzae pv. oryzae (Xoo) which can lead to important yield losses. OsSWEET14 belongs to the SWEET gene family that encodes sugar transporters. Together with other Clade III members, it behaves as a susceptibility (S) gene whose induction by Asian Xoo Transcription-Activator-Like Effectors (TALEs) is absolutely necessary for disease. In this study, we sought to introduce BLB resistance in the TBR225 elite variety. First, two Vietnamese Xoo strains were shown to up-regulate OsSWEET14 upon TBR225 infection. To investigate if this induction is connected with disease susceptibility, nine TBR225 mutant lines with mutations in the AvrXa7, PthXo3 or TalF TALEs DNA target sequences of the OsSWEET14 promoter were obtained using the CRISPR/Cas9 editing system. Genotyping analysis of T0 and T1 individuals showed that mutations were stably inherited. None of the examined agronomic traits of three transgene-free T2 edited lines were significantly different from those of wild-type TBR225. Importantly, one of these T2 lines, harboring the largest homozygous 6-bp deletion, displayed decreased OsSWEET14 expression as well as a significantly reduced susceptibility to a Vietnamese Xoo strains and complete resistance to another one. Our findings indicate that CRISPR/Cas9 editing conferred an improved BLB resistance to a Vietnamese commercial elite rice variety.
Costs and cost-effectiveness of a comprehensive tuberculosis case finding strategy in Zambia
Authors: Jo Youngji , Kagujje Mary , Johnson Karl , Dowdy David , Hangoma Peter , Chiliukutu Lophina , Muyoyeta Monde , Sohn Hojoon
Published: September 2021

Introduction

Active-case finding (ACF) programs have an important role in addressing case detection gaps and halting tuberculosis (TB) transmission. Evidence is limited on the cost-effectiveness of ACF interventions, particularly on how their value is impacted by different operational, epidemiological and patient care-seeking patterns.

Methods

We evaluated the costs and cost-effectiveness of a combined facility and community-based ACF intervention in Zambia that utilized mobile chest X-ray with computer-aided reading/interpretation software and laboratory-based Xpert MTB/RIF testing. Programmatic costs (in 2018 US dollars) were assessed from the health system perspective using prospectively collected cost and operational data. Cost-effectiveness of the ACF intervention was assessed as the incremental cost per TB death averted over a five-year time horizon using a multi-stage Markov state-transition model reflecting patient symptom-associated care-seeking and TB care under ACF compared to passive care.

Results

Over 18 months of field operations, the ACF intervention costed $435 to diagnose and initiate treatment for one person with TB. After accounting for patient symptom-associated care-seeking patterns in Zambia, we estimate that this one-time ACF intervention would incrementally diagnose 407 (7,207 versus 6,800) TB patients and avert 502 (611 versus 1,113) TB-associated deaths compared to the status quo (passive case finding), at an incremental cost of $2,284 per death averted over the next five-year period. HIV/TB mortality rate, patient symptom-associated care-seeking probabilities in the absence of ACF, and the costs of ACF patient screening were key drivers of cost-effectiveness.

Conclusions

A one-time comprehensive ACF intervention simultaneously operating in public health clinics and corresponding catchment communities can have important medium-term impact on case-finding and be cost-effective in Zambia. The value of such interventions increases if targeted to populations with high HIV/TB mortality, substantial barriers (both behavioral and physical) to care-seeking exist, and when ACF interventions can optimize screening by achieving operational efficiency.
Systemic adverse events after screening of retinopathy of prematurity with mydriatic
Authors: Obata Shumpei , Imamura Taku , Kakinoki Masashi , Yanagi Takahide , Maruo Yoshihiro , Ohji Masahito
Published: September 2021

Purpose

To evaluate systemic adverse events after screening for retinopathy of prematurity (ROP) performed with mydriatic.

Methods

This was a retrospective case series study. Medical records of consecutive patients who underwent screening for ROP with 0.5% phenylephrine and 0.5% tropicamide eyedrops were retrospectively reviewed. The score of abdominal distention (0–5), volume of milk sucked and volume of stool, along with systemic details (pulse and respiration rates, blood pressure and number of periods of apnea) were collected at 1 week and 1 day before ROP examination, and at 1 day after examination. Results were compared between the days before and after examination. Correlation between body weight at the time of examination and the score of abdominal distention was examined. The numbers of infants with abdominal and/or systemic adverse events were compared between pre- and post-examination periods.

Results

Eighty-six infants met the inclusion criteria. The score of abdominal distention increased from 2.0 at 1 day before examination to 2.3 at 1 day after examination (p = 0.005), and the number of infants who had worsened abdominal distension increased after examination (p = 0.01). Infants with lower body weight had a higher score of abdominal distention (p < 0.0001, r = −0.57). The number of infants with reduced milk consumption increased after examination (p = 0.0001), as did the number of infants with decreased pulse rate (p = 0.0008).

Conclusions

Screening for ROP with mydriatic may have adverse effects on systemic conditions. Infants should be carefully monitored after ROP screening with mydriatic.
Climate suitability predictions for the cultivation of macadamia (Macadamia integrifolia) in Malawi using climate change scenarios
Authors: Zuza Emmanuel Junior , Maseyk Kadmiel , Bhagwat Shonil A. , de Sousa Kauê , Emmott Andrew , Rawes William , Araya Yoseph Negusse
Published: September 2021

Climate change is altering suitable areas of crop species worldwide, with cascading effects on people reliant upon those crop species as food sources and for income generation. Macadamia is one of Malawi’s most important and profitable crop species; however, climate change threatens its production. Thus, this study’s objective is to quantitatively examine the potential impacts of climate change on the climate suitability for macadamia in Malawi. We utilized an ensemble model approach to predict the current and future (2050s) suitability of macadamia under two Representative Concentration Pathways (RCPs). We achieved a good model fit in determining suitability classes for macadamia (AUC = 0.9). The climatic variables that strongly influence macadamia’s climatic suitability in Malawi are suggested to be the precipitation of the driest month (29.1%) and isothermality (17.3%). Under current climatic conditions, 57% (53,925 km2) of Malawi is climatically suitable for macadamia. Future projections suggest that climate change will decrease the suitable areas for macadamia by 18% (17,015 km2) and 21.6% (20,414 km2) based on RCP 4.5 and RCP 8.5, respectively, with the distribution of suitability shifting northwards in the 2050s. The southern and central regions of the country will suffer the greatest losses (≥ 8%), while the northern region will be the least impacted (4%). We conclude that our study provides critical evidence that climate change will reduce the suitable areas for macadamia production in Malawi, depending on climate drivers. Therefore area-specific adaptation strategies are required to build resilience among producers.
Vertical sonar beam width and scanning behavior of wild belugas (Delphinapterus leucas) in West Greenland
Authors: Zahn Marie J. , Laidre Kristin L. , Stilz Peter , Rasmussen Marianne H. , Koblitz Jens C.
Published: September 2021

Echolocation signals of wild beluga whales (Delphinapterus leucas) were recorded in 2013 using a vertical, linear 16-hydrophone array at two locations in the pack ice of Baffin Bay, West Greenland. Individual whales were localized for 4:42 minutes of 1:04 hours of recordings. Clicks centered on the recording equipment (i.e. on-axis clicks) were isolated to calculate sonar parameters. We report the first sonar beam estimate ofin siturecordings of wild belugas with an average -3 dB asymmetrical vertical beam width of 5.4°, showing a wider ventral beam. This narrow beam width is consistent with estimates from captive belugas; however, our results indicate that beluga sonar beams may not be symmetrical and may differ in wild and captive contexts. The mean apparent source level for on-axis clicks was 212 dB pp re 1 μPa and whales were shown to vertically scan the array from 120 meters distance. Our findings support the hypothesis that highly directional sonar beams and high source levels are an evolutionary adaptation for Arctic odontocetes to reduce unwanted surface echoes from sea ice (i.e., acoustic clutter) and effectively navigate through leads in the pack ice (e.g., find breathing holes). These results provide the first baseline beluga sonar metrics from free-ranging animals using a hydrophone array and are important for acoustic programs throughout the Arctic, particularly for acoustic classification between belugas and narwhals (Monodon monoceros).
Maternal PCOS status and metformin in pregnancy: Steroid hormones in 5–10 years old children from the PregMet randomized controlled study
Authors: Hanem Liv Guro Engen , Salvesen Øyvind , Madsen André , Sagen Jørn V. , Mellgren Gunnar , Juliusson Petur Benedikt , Carlsen Sven Magnus , Vanky Eszter , Ødegård Rønnaug
Published: September 2021

Objective

Polycystic ovary syndrome (PCOS) is a common endocrine disorder, with potential effects on offspring both genetically and through altered intrauterine environment. Metformin, which ameliorate hormonal disturbances in non-pregnant women with PCOS is increasingly used in pregnancy. It passes the placenta, and the evidence on potential consequences for offspring endocrine development is scarce. We explore the potential effects of maternal PCOS status and intrauterine metformin exposure on offspring steroid hormone levels.

Design

This is a follow-up study of 5–10 years old children from the PregMet-study–a randomized controlled trial comparing metformin (2000 mg/day) to placebo during PCOS pregnancies. Of the 255 children invited, 117 (46%) were included.

Methods

There was no intervention in this follow-up study. Outcomes were serum levels of androstenedione, testosterone, SHBG, cortisol, 17-hydroxyprogesterone, 11-deoxycortisol and calculated free testosterone converted to gender-and age adjusted z-scores from a Norwegian reference population. These were compared in i) placebo-exposed children versus children from the reference population (z-score zero) by the deviation in z-score by one-sample t-tests and ii) metformin versus placebo-exposed children by two-sample t-tests. Holm-Bonferroni adjustments were performed to account for multiple endpoints.

Results

Girls of mothers with PCOS (n = 30) had higher mean z-scores of androstenedione (0.73 (95% confidence interval (CI) 0.41 to 1.06), p<0.0001), testosterone (0.76 (0.51 to 1.00), p<0.0001), and free testosterone (0.99 (0.67 to 1.32), p<0.0001) than the reference population. Metformin-exposed boys (n = 31) tended to have higher 11-deoxycortisol z-score than placebo-exposed boys (n = 24) (mean difference 0.65 (95% CI 0.14–1.17), p = 0.014).

Conclusion

Maternal PCOS status was associated with elevated androgens in 5- to 10-year-old daughters, which might indicate earlier maturation and increased risk of developing PCOS. An impact of metformin in pregnancy on steroidogenesis in children born to mothers with PCOS cannot be excluded. Our findings need confirmation in studies that include participants that have entered puberty.
Discovery of re-purposed drugs that slow SARS-CoV-2 replication in human cells
Authors: Pickard Adam , Calverley Ben C. , Chang Joan , Garva Richa , Gago Sara , Lu Yinhui , Kadler Karl E.
Published: September 2021

COVID-19 vaccines based on the Spike protein of SARS-CoV-2 have been developed that appear to be largely successful in stopping infection. However, therapeutics that can help manage the disease are still required until immunity has been achieved globally. The identification of repurposed drugs that stop SARS-CoV-2 replication could have enormous utility in stemming the disease. Here, using a nano-luciferase tagged version of the virus (SARS-CoV-2-ΔOrf7a-NLuc) to quantitate viral load, we evaluated a range of human cell types for their ability to be infected and support replication of the virus, and performed a screen of 1971 FDA-approved drugs. Hepatocytes, kidney glomerulus, and proximal tubule cells were particularly effective in supporting SARS-CoV-2 replication, which is in-line with reported proteinuria and liver damage in patients with COVID-19. Using the nano-luciferase as a measure of virus replication we identified 35 drugs that reduced replication in Vero cells and human hepatocytes when treated prior to SARS-CoV-2 infection and found amodiaquine, atovaquone, bedaquiline, ebastine, LY2835219, manidipine, panobinostat, and vitamin D3 to be effective in slowing SARS-CoV-2 replication in human cells when used to treat infected cells. In conclusion, our study has identified strong candidates for drug repurposing, which could prove powerful additions to the treatment of COVID.
Bacterial evolution during human infection: Adapt and live or adapt and die
Authors: Culyba Matthew J. , Van Tyne Daria
Published: September 2021

Microbes are constantly evolving. Laboratory studies of bacterial evolution increase our understanding of evolutionary dynamics, identify adaptive changes, and answer important questions that impact human health. During bacterial infections in humans, however, the evolutionary parameters acting on infecting populations are likely to be much more complex than those that can be tested in the laboratory. Nonetheless, human infections can be thought of as naturally occurring in vivo bacterial evolution experiments, which can teach us about antibiotic resistance, pathogenesis, and transmission. Here, we review recent advances in the study of within-host bacterial evolution during human infection and discuss practical considerations for conducting such studies. We focus on 2 possible outcomes for de novo adaptive mutations, which we have termed “adapt-and-live” and “adapt-and-die.” In the adapt-and-live scenario, a mutation is long lived, enabling its transmission on to other individuals, or the establishment of chronic infection. In the adapt-and-die scenario, a mutation is rapidly extinguished, either because it carries a substantial fitness cost, it arises within tissues that block transmission to new hosts, it is outcompeted by more fit clones, or the infection resolves. Adapt-and-die mutations can provide rich information about selection pressures in vivo, yet they can easily elude detection because they are short lived, may be more difficult to sample, or could be maladaptive in the long term. Understanding how bacteria adapt under each of these scenarios can reveal new insights about the basic biology of pathogenic microbes and could aid in the design of new translational approaches to combat bacterial infections.
The type 3 secretion system requires actin polymerization to open translocon pores
Authors: Russo Brian C. , Duncan-Lowey Jeffrey K. , Chen Poyin , Goldberg Marcia B.
Published: September 2021

Many bacterial pathogens require a type 3 secretion system (T3SS) to establish a niche. Host contact activates bacterial T3SS assembly of a translocon pore in the host plasma membrane. Following pore formation, the T3SS docks onto the translocon pore. Docking establishes a continuous passage that enables the translocation of virulence proteins, effectors, into the host cytosol. Here we investigate the contribution of actin polymerization to T3SS-mediated translocation. Using the T3SS model organism Shigella flexneri, we show that actin polymerization is required for assembling the translocon pore in an open conformation, thereby enabling effector translocation. Opening of the pore channel is associated with a conformational change to the pore, which is dependent upon actin polymerization and a coiled-coil domain in the pore protein IpaC. Analysis of an IpaC mutant that is defective in ruffle formation shows that actin polymerization-dependent pore opening is distinct from the previously described actin polymerization-dependent ruffles that are required for bacterial internalization. Moreover, actin polymerization is not required for other pore functions, including docking or pore protein insertion into the plasma membrane. Thus, activation of the T3SS is a multilayered process in which host signals are sensed by the translocon pore leading to the activation of effector translocation.
Coastal Landscapes and Invisible Archaeology
Authors: Miano Pasquale , Coppolino Francesca
Published: September 2021

The contribution aims to investigate the relationship between coastal landscapes, invisible archaeology and architectural design through the case of St. Peter’s Abbey archaeological site, in the fjord of Crapolla in Massa Lubrense, that has been the subject of an interdisciplinary research.
In these particular situations, architectural design works on an interpretative condition where the intersection between reciprocal learnings takes on great importance in order to define design strategies for the valorization of the weaker archaeological traces in the contemporary territory.
The Crapolla’s Abbey is an emblematic case, where the results achieved by different studies, from archaeological excavations to surveys, from studies on ancient materials and construction techniques to those on the spolia architecture, from landscape studies to geological ones, inevitably become the basis of architectural design, which has to be constantly updated, taking the connotations of an “open work” and becoming a sort of “building site of knowledge” in progress.
WILL FISH DISAPPEAR BY 2048?
Authors: Kurniawan Wanwan
Published: September 2021

In 2006, a tumult arose in the world of fisheries. A controversial paper titled “Impacts of biodiversity loss on ocean ecosystem services” by Worm et al. (2006) was published in Science. The paper was sensational since it alluded to a prediction that global populations of marine fish (finfish and invertebrates) will be 100% collapsed by 2048. The paper was written by a group of marine ecologists and economists in which Boris Worm from Dalhousie University Canada led the authorship. After the paper was published, the issue of fish disappearance in 2048 became hot topics in the world’s mass media. In fact, the Worm et al. paper triggered the debates among researchers. Over time the debates heated up. Surprisingly, a reconciliation took place in 2009, marked by a collaboration between Worm’s team and his critics, writing another paper in Science. The present essay reaffirms the invalidity of the global collapse prediction in 2048 as revealed by many researchers. It is also shown that the Worm et al. paper did not state that all fish will disappear and through the joint paper in 2009, Worm and colleagues have indirectly rectified the prediction already.
ASPEK BIOLOGI UBUR-UBUR API, Physalia physalis (LINNAEUS, 1758)
Authors: Firdaus Mochamad Ramdhan
Published: September 2021

Physalia physalis is one of the jellyfish believed to be responsible for a significant proportion of jellyfish attack cases in the world. As one of the most dangerous members of the Cnidarian in the sea, P. physalis has a sting that can paralyze their prey. To humans, the sting can cause cardiotoxic, neurotoxic, musculartoxic, and hemolytic effects. P. physalis has different biological characteristics than most organisms. For example, an individual of P. physalis actually is a colony consisting of four groups of individuals who have different structures and functions. The arrangement of the colony has a complex structure and shows a polymorphism. P. physalis is a pleustonic organism because they live on the surface of the water. P. physalis still leaves many mysteries to scientists. For example, the life cycle of a P. physalis is not yet fully known. Besides, the diversity of P. physalis also still leaves questions among scientists. Some believe that P. physalis is monotypic, while others suspect there is cryptic diversity. Therefore, the study of P. physalis is very interesting, especially under the issue of climate change. Many scientists believe that jellyfish get benefit from increasing sea temperatures, so the population is predicted to increase. The high population of P. physalis threatens the sustainability of fish stocks in the ocean, mainly due to P. physalis are productive predators of fish larvae. This paper aims to provide information on the biological aspects of P. physalis, which are still limited in Indonesia.
PROFIL VERTIKAL DAN HORIZONTAL PARAMETER SALINITAS, DHL, DAN TDS BERDASARKAN VARIASI MUSIMAN DI ESTUARI SUNGAI CITARUM
Authors: Fahimah Nurul , Damayanti Annisa Dwi , Bunga Venny Ulya , Mubiarto Haryo
Published: September 2021

Salinity, electrical conductivity (EC), and Total Dissolved Solid (TDS) are parameters that pose an important role in the distributions of environmental pollution substances in the estuary. The difference in salinity, EC, and TDS concentration vertically (based on the depth in the water column) and horizontally (based on the distance from the estuary mouth) will affect the process of pollutant’s transportation and transformation in the estuary. On the other hand, seasonal variations will also affect parameters. Therefore, the information related to the vertical and horizontal profiles of salinity and other parameters based on seasonal variations is necessary to study. The purpose of this study is to analyze the vertical profile and horizontal-vertical of salinity, EC, and TDS concentrations during the rainy season and dry season in the estuary of Citarum River. This research was conducted in April 2018 (rainy season) and August 2018 (dry season) when the low tide. The measurement of salinity, EC, and TDS was directly conducted in the field using a conductivity meter. The results show that the concentration level of salinity, EC, and TDS showed a vertical and horizontal difference in the estuary of the Citarum River. In addition, there are differences in the concentration of salinity, electrical conductivity, TDS in the rainy season and dry season in the estuary of the Citarum River. The level of TDS has a linear relationship between salinity and electrical conductivity, with a value of R2 >95%.
To the 225th Anniversary of the Birth of Robert James Graves
Authors: Kurchakov A. L. , Likhova I. A.
Published: September 2021

Robert James Graves is an eminent medical practitioner who has made significant contributions to this field. The main path of the scientist began by no means with medical practice, but with extensive travels that prompted him to start and fruitfully carry out scientific activity in the future. The scientific activity carried out by Robert James Graves throughout his life formed special preconditions for the development of medical education and entire fields of medicine. The practice of students, according to his teaching model, was not typical, but many experts in this field spoke about it quite positively, for example, such as T.J. McKenn and Armand Trousseau. He made history 180 years ago by discovering an autoimmune disease, which causes hyperthyroidism, he was known as a physician whose contribution covered the entire field of endocrinology, cardiology, infectious diseases and neurology.
In a Memory of Vilen I. Kandror
Authors: Editorial Article
Published: September 2021

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Computational and Experimental Study for Reducing Forebody Wake Effect by Proper Designing of a Slit cut Square Parachute used for Sonobuoy Drop
Authors: Pratap Mahendra , Agrawal A. K. , Sati S. C. , Saxena A. K.
Published: September 2021

This paper discusses the design of a square parachute based on classical approach, computational analysis and experimentation. This parachute will be used to drop directional sonobuoy on the sea to locate and classify the submarines. Design improvements are brought out by providing slits into a solid square canopy of parachute to bring in more stability and minimum drift during descend. Specifically, the effect of upstream sonobuoy, RANS model, suspension line length, canopy size and slit size in flow structure were considered. The predicted drag coefficients obtained from CFD for square canopy with slit-cuts compared with the results of wind tunnel experiment and found that the increase in the suspension-line length and/or of the surface area of the parachute canopy helps in better stability and results in the minimum drag loss.
Los Aportes de la MAPP–OEA a la Justicia Transicional en Colombia
Authors: España Isabel Cristina
Published: September 2021

Este artículo analiza los principales aportes de la MAPP–OEA a la justicia transicional en Colombia, cuyo resultado es parte de las acciones de apoyo de este organismo internacional al proceso de justicia y paz entre los años 2005 y 2016. Se utilizó una metodología cualitativa de investigación, que incluyó la utilización de herramientas metodológicas como: entrevistas y revisión documental. Entre los principales hallazgos se encontró que las acciones de apoyo de la MAPP–OEA al proceso de justicia y paz en Colombia aportaron en: a) el fortalecimien­to del ordenamiento jurídico de justicia y paz; b) el fortalecimiento de las instituciones esta­tales responsables del proceso y, c) el fortalecimiento de los juicios penales de justicia y paz. Este estudio proporciona insumos interesantes sobre los aportes de un organismo regional (como lo es la OEA), en la implementación de procesos de justicia transicional, al tiempo que sirve como referencia inicial para el análisis de la justicia transicional en Colombia, de cara a la implementación de la Justicia Especial para la Paz.
Novel H2S donor proglumide-ADT-OH protects HUVECs from ox-LDL-induced injury through NF-κB and JAK/SATA pathway
Authors: Ou Xuelan , Xia Tianqin , Yang Chunyan , Yu Chunlei , Zhang Shipeng , Huang Rong , Chen Chuan , Zhou Chunyang
Published: September 2021

As a gaseous mediator, hydrogen sulfide (H2S) has many physiological effects and pathological effects in atherosclerosis. In recent years, many exogenous H2S donors have been synthesized to study atherosclerosis diseases. In this study, proglumide-(5-(4-hydroxyphenyl)-3H-1,2-dithiole-3-thione) (P-A) was synthesized as a H2S donor. The protective effect and mechanism of P-A on HUVEC that was injured by ox-LDL were detected. The HUEVCs were affected by 100 μmol/L P-A for 24 h; the release of H2S was the largest. After 100 μmol/L P-A acted on HUVEC damage model for 12 h, the cell proliferation activity was the best. The results showed that P-A can downregulate the expression of p-NF-кBp65 protein and reduce the amount of TNF-α and IL-6 and promote the formation of IL-10 by inhibiting the NF-кB pathway, and also induce the expression of superoxide dismutase (SOD) to protect HUVEC from ox-LDL injury. P-A can also regulate JAK/STAT pathway to reduce the expression of p-JAK2 protein and reduce the production of IL-6 and TNF-α. P-A has protective effect on HUVEC injured by ox-LDL, and the protective mechanism is related to the regulation of JAK/STAT pathway and NF-кB pathway.
Morphophysiological changes and reactive oxygen species metabolism inCorchorus olitoriusL. under different abiotic stresses
Authors: Rahman Khussboo , Rahman Mira , Ahmed Naznin , Alam Md. Mahabub , Rahman Anisur , Islam Md. Mahbubul , Hasanuzzaman Mirza
Published: September 2021

Abiotic stress has become an alarming issue for plant survival due to the constant changes in the environment. Abiotic stresses such as drought, salt, waterlogging, and heavy metals largely influence plant growth and development that finally reduce crop productivity. The present study was carried out to investigate the responses of jute (Corchorus olitoriuscv. O-9897) plant under different abiotic stresses. At 15th days after sowing plants were exposed to different abiotic stresses for various duration. Two doses of NaCl (200 and 400 mM) were applied to impose salt stress, while two doses of CdCl2(2 and 4 mM) were applied for cadmium (Cd) stress. Waterlogging stress was applied for 5 and 15 days. Whereas drought stress was imposed on plants for 10 and 15 days. Leaf relative water content, SPAD value, plant height, above ground fresh and dry weight, leaf area, and stem diameter decreased upon exposure to salt, water deficit, Cd, and waterlogging stresses. These abiotic stresses resulted in oxidative damage which was evident by the increased levels of lipid peroxidation, H2O2, and electrolyte leakage (EL) together with altered antioxidant enzymes activities and glyoxalase system which are crucial for plants to fight against oxidative damage. Both duration of waterlogging and drought stress drastically affected plant morphophysiology, whereasC. olitoriuscould tolerate moderate level of salt (200 mM NaCl) and Cd (2 mM CdCl2). So the present study reveals that abiotic stresses cause substantial damages to the morphophysiology and oxidative stress tolerance ofC. olitoriuswhere the higher doses of NaCl and CdCl2as well as the increased duration of waterlogging and drought resulted in more deleterious effect.
Synthesis and extraction routes of allelochemicals from plants and microbes: A review
Authors: Singh Apurva Anand , Rajeswari Gunasekaran , Nirmal Louis Anto , Jacob Samuel
Published: September 2021

Allelopathy, a complex phenomenon has unveiled both stimulatory and inhibitory effects in plant processes that are mediated by the release of certain chemical compounds commonly known as allelochemicals. Allelochemicals, a form of bioactive secondary metabolites are produced by a diverse group of plants and microbes in response to biotic and abiotic stress. It ranges from a simple hydrocarbon to complex polycyclic aromatic compounds like phenol, flavonoids, tannins, steroids, amino acids, alkaloids and quinones. These plant bioactive compounds are released into the environment via decomposition, exudation, leaching and volatilization that play a significant role in regulating the intra-specific or inter-specific relations with counterparts. A wide variety of methods has been proposed for analyzing the basic mechanism and overall effect of allelochemicals. However, the lack of a reliable and effective method to identify their molecular mode of action and their modulation in the metabolic pathway still remains as a great challenge. From a commercial perspective, these allelochemicals are deemed to be better candidates for green natural herbicides and weedicides that are proven to be environment friendly, unlike synthetic chemicals. In order to pave a way for the economic viability of these chemicals, a basic understanding of their chemistry is inevitable. This review article is focused to give an in-depth understanding of metabolic pathways genes responsible for the elicitation/secretion and the adoption of a suitable downstream process and analytical techniques that can intensify the process.
Promoting and Optimizing the Use of 3D-Printed Objects in Spontaneous Recognition Memory Tasks in Rodents: A Method for Improving Rigor and Reproducibility
Authors: Inayat Mehreen , Cruz-Sanchez Arely , Thorpe Hayley H. A. , Frie Jude A. , Richards Blake A , Khokhar Jibran Y. , Arruda-Carvalho Maithe
Published: September 2021

Spontaneous recognition memory tasks are widely used to assess cognitive function in rodents and have become commonplace in the characterization of rodent models of neurodegenerative, neuropsychiatric and neurodevelopmental disorders. Leveraging an animal’s innate preference for novelty, these tasks use object exploration to capture the what, where and when components of recognition memory. Choosing and optimizing objects is a key feature when designing recognition memory tasks. Although the range of objects used in these tasks varies extensively across studies, object features can bias exploration, influence task difficulty and alter brain circuit recruitment. Here, we discuss the advantages of using 3D-printed objects in rodent spontaneous recognition memory tasks. We provide strategies for optimizing their design and usage, and offer a repository of tested, open-source designs for use with commonly used rodent species. The easy accessibility, low-cost, renewability and flexibility of 3D-printed open-source designs make this approach an important step toward improving rigor and reproducibility in rodent spontaneous recognition memory tasks.