bluuebunny/crossref_metadata_2025 huggingface dataset:
Effects of Selective Serotonin Reuptake Inhibitors on Auditory Processing: Case Study
Authors: Gopal Kamakshi V. , Daly D. Michael , Daniloff Raymond G. , Pennartz Lori
Published: April 2022

Auditory sensitivity and processing ability were evaluated in a patient who suffered from hyperacusis, difficulty understanding speech, withdrawn depression, lethargy, and hypersensitivity to touch, pressure, and light. Treatment with fluvoxamine and fluoxetine (selective serotonin reuptake inhibitors) reversibly alleviated complaints. Testing while medicated and unmedicated (after voluntary withdrawal from medication for several weeks) revealed no difference in pure-tone thresholds, speech thresholds, word recognition scores, tympanograms, or acoustic reflex thresholds. Medicated SCAN ● A (a screening test for central auditory processing disorders) results were normal, and unmedicated results were abnormal. Unmedicated transient otoacoustic emissions and auditory brainstem response waves I, III, and V were significantly larger bilaterally. Uncomfortable loudness levels indicated greater tolerance during the medicated condition. Central processing and vigilance were evaluated with analog-synthesized three-formant consonant-vowel syllables. While medicated, responses to stimuli at each ear revealed well-defined, labeling crossovers of about 90 msec. Vowel identification matched normal subject responses; labeling of /gE/jE/ and /bE/wE/ continua was well defined but all crossover points differed from normals (p < .0001). During unmedicated testing, responses to /gE/jE/ began at medicated levels but approached chance levels for the entire continuum within 10 min; labeling of /bE/wE/ was consistent with medicated responses throughout with earlier than normal crossover points.

Abbreviations: ABRs = auditory brainstem responses, ALRs = auditory late potentials, CNS = central nervous system, GABA = gamma-aminobutyric acid, 5–HT = 5–hydroxytryptamine, OCB = olivocochlear bundle, SAS = sparse acoustic stimuli, SSRIs = selective serotonin reuptake inhibitors, TEOAEs = transient evoked otoacoustic emissions, UCL = uncomfortable loudness level
Investigation of Binaural Interference in Normal-Hearing and Hearing-Impaired Adults
Authors: Allen Rose L. , Schwab Brady M. , Cranford Jerry L. , Carpenter Michael D.
Published: April 2022

When speech recognition testing is performed under diotic conditions, some elderly persons with asymmetric hearing loss exhibit a phenomenon in which the performance of the poorer ear interferes with that of the better ear. This binaural interference phenomenon has been estimated to occur in 8 to 10 percent of elderly hearing aid users. The purpose of the present study was to investigate the prevalence of this phenomenon in groups (n = 12) of young and elderly listeners with normal hearing, plus groups of elderly listeners with hearing loss who were aided or unaided. Of 48 subjects tested, only 2 exhibited significant evidence of binaural interference, a result that is close to that expected by chance. Although both of these subjects were elderly, one had normal hearing and the other was aided binaurally. A third elderly unaided subject exhibited a significant binaural advantage. Further studies are needed to determine the prevalence of binaural interference in normal-hearing or hearing-impaired listeners in any decade of life.

Abbreviations: ANOVA = analysis of variance, HFPTA = high-frequency pure-tone average of hearing levels at 1000, 2000, and 4000 Hz, OA = older aided hearing-impaired adults, OHI = older unaided hearing-impaired adults, ON = older normal-hearing adults, SRT = speech reception threshold, WRS = word recognition score, YN = young, normal-hearing adults
Optimising self-organised volunteer efforts in response to the COVID-19 pandemic
Authors: Zhang Anping , Zhang Ke , Li Wanda , Wang Yue , Li Yang , Zhang Lin
Published: April 2022

Crowdsource volunteering efforts have contributed significantly to pandemic response and recovery during the COVID-19 outbreak. In such efforts, individual volunteers can collaborate to achieve rapid mobilisation toward emergent community demands. In this study, we quantitively study this phenomenon using the concept of self-organisation, by proposing a data-driven framework to investigate when and how self-organisation emerged during the pandemic response and how it relates to effectiveness of volunteer organisations in general. Using activity data collected from a mobile volunteer platform in Shenzhen, China, we found that volunteers’ task participation and social and task preferences show multiple phases of self-organisation in response to changing epidemic situations and centralised interventions. Simulation experiments further show that the self-organised volunteer system can become more responsive and more robust in the face of uncertain community demands with minimal centralised guidance.
Picking fights with politicians
Authors: Joyce Jack B. , Walz Linda
Published: April 2022

In 2016 the UK held a divisive referendum on its membership of the European Union. In the aftermath, difference and division were rife in politics and in everyday life. This article explores how such difference and division play out in and through interaction through examining a citizen ‘picking a fight’ with a politician over how Brexit has been handled. Drawing on membership categorisation analysis we show how antagonism is interactionally accomplished. The analysis focuses on three categorial strategies which interlocutors use to achieve antagonism: establishing omnirelevant devices, categories and their predicates; explicitly challenging category membership; and partitioning a population. Beyond offering insights into moments of social life that are not easily captured, the findings contribute to an empirical conceptualisation of antagonism and illustrate how membership categorisation analysis can shed light on its interactional achievement.
Physiological effects of exercising at different intensities wearing surgical or double‐layer cotton facemasks compared to not wearing a mask
Authors: Braga Fabrício , Espinosa Gabriel , Monteiro Amanda , Marinho Beatriz , Drummond Eduardo
Published: April 2022

Since the beginning of the SARS‐CoV‐2 pandemic, the community use of facemasks has been widely recommended. However, their use during exercise has raised safety concerns. Thus, we compared the physiological differences between exercising wearing a surgical (SM) or a double‐layer‐cotton (DLC) facemask and not wearing a mask (NM). Sixteen volunteers underwent 4 bouts of cycling‐based exercise, which consisted of two different intensities: light‐to‐moderate and moderate‐to‐high. Facemasks were used as follows: bout‐1 and 4: NM; bout‐2: SM or DLC and bout‐3: DLC or SM. Ventilatory, metabolic, pulmonary gas exchange (PGE) and perceptual variables were collected. At both exercise intensities compared to NM, both facemasks induced similar ventilatory adaptations, increasing inspiratory time and tidal volume and decreasing breathing frequency. Effect sizes (ES) were larger for DLC than for SM. At moderate‐to‐high, both facemasks reduced the minute ventilation, whereas at light‐to‐moderate, it was only seen with DLC. End tidal and mixed CO2 pressures, as well as the difference between them, increased with both facemasks. Again, ES was larger for DLC than SM. No relevant oxygen saturation drop was observed with both facemaks and exercise intensities. A small ES increament in VO2 and VCO2 were seen with both facemasks. Effort perception increased at moderate‐to‐high for both exercise intensities, buth larger EF were with DLC than SM. DLC increased facial temperature during both exercise intensities. In conclusion, ventilatory adjustments imposed during facemask exercise influenced PGE and metabolic and perceptual changes. Larger ES were mostly seen for DLC than SM.

Abbreviations: Bf : Breathing frequency.; CPET: Cardiopulmonary exercise test.; CI: Confidence interval.; DLC: Double‐layer cotton.; ETCO2: End tidal CO2 pressure.; ES: Effect size.; ΔET‐PECO2: Difference between ETCO2 and PECO2.; FMMT: Facemask microclimate temperature.; HR : Heart rate.; IQR: Interquartile range.; NM: No mask.; PECO2: Mixed‐expired CO2 pressure.; RER: Respiratory exchange ratio.; RPE: Rate of perceived effort.; SD: Standard deviation.; SM: Surgical Mask.; SpO2: Oxygen saturation.; STP: Subjective thermal perception.; Ti/TTOT: Duty cycle.; VE: Minute ventilation.; VCO2: Carbon dioxide output.; VO2: Oxygen uptake.; VT : Tidal volume.; VT: Ventilatory threshold.

Highlights

Facemasks affect the breathing pattern by changing the frequency and amplitude of pulmonary ventilation.

The augmented ventilatory work increases VO2, VCO2, and RPE and promotes nonconcerning drops in SpO2 and CO2 retention.

Increased inspiratory and expiratory pressure can account for the reduction in pulmonary physiological dead space.
Monte Carlo evaluation of high-gradient magnetically focused planar proton minibeams in a passive nozzle
Authors: McAuley Grant A , Lim Crystal J , Teran Anthony V , Slater Jerry D , Wroe Andrew J
Published: April 2022

Objective. To investigate the potential of using a single quadrupole magnet with a high magnetic field gradient to create planar minibeams suitable for clinical applications of proton minibeam radiation therapy. Approach. We performed Monte Carlo simulations involving single quadrupole Halbach cylinders in a passively scattered nozzle in clinical use for proton therapy. Pencil beams produced by the nozzle of 10–15 mm initial diameters and particle range of ∼10–20 cm in water were focused by magnets with field gradients of 225–350 T m−1 and cylinder lengths of 80–110 mm to produce very narrow elongated (planar) beamlets. The corresponding dose distributions were scored in a water phantom. Composite minibeam dose distributions composed from three beamlets were created by laterally shifting copies of the single beamlet distribution to either side of a central beamlet. Modulated beamlets (with 18–30 mm nominal central SOBP) and corresponding composite dose distributions were created in a similar manner. Collimated minibeams were also compared with beams focused using one magnet/particle range combination. Main results. The focusing magnets produced planar beamlets with minimum lateral FWHM of ∼1.1–1.6 mm. Dose distributions composed from three unmodulated beamlets showed a high degree of proximal spatial fractionation and a homogeneous target dose. Maximal peak-to-valley dose ratios (PVDR) for the unmodulated beams ranged from 32 to 324, and composite modulated beam showed maximal PVDR ranging from 32 to 102 and SOBPs with good target dose coverage. Significance. Advantages of the high-gradient magnets include the ability to focus beams with phase space parameters that reflect beams in operation today, and post-waist particle divergence allowing larger beamlet separations and thus larger PVDR. Our results suggest that high gradient quadrupole magnets could be useful to focus beams of moderate emittance in clinical proton therapy.
Fast generation of cat states in Kerr nonlinear resonators via optimal adiabatic control
Authors: Xue Jiao-Jiao , Yu Ke-Hui , Liu Wen-Xiao , Wang Xin , Li Hong-Rong
Published: April 2022

Macroscopic cat states have been widely studied to illustrate fundamental principles of quantum physics as well as their applications in quantum information processing. In this paper, we propose a quantum speed-up method for the creation of cat states in a Kerr nonlinear resonator (KNR) via optimal adiabatic control. By simultaneously adiabatic tuning the cavity-field detuning and driving field strength, the width of the minimum energy gap between the target trajectory and non-adiabatic trajectory can be widened, which allows us to accelerate the evolution along the adiabatic path. Compared with the previous proposal, preparing cat states only by controlling two-photon pumping strength, our method can prepare the target state with a shorter time, a high-fidelity and a large non-classical volume. It is worth noting that the cat state prepared here is also robust against single-photon loss. Moreover, when we consider the KNR with a large initial detuning, our proposal will create a large-size cat state successfully. This proposal for preparing cat states can be implemented in superconducting quantum circuits, which provides a quantum state resource for quantum information encoding and fault-tolerant quantum computing.
The solution to the problem of time in quantum gravity also solves the time of arrival problem in quantum mechanics
Authors: Gambini Rodolfo , Pullin Jorge
Published: April 2022

We introduced with coauthors some years ago a solution to the problem of time in quantum gravity which consists in formulating the quantum theory in terms of real clocks. It combines Page and Wootters’ relational proposal with Rovelli’s evolving constants of the motion. Time is associated with an operator and not a classical parameter. We show here that this construction provides a natural solution to the time of arrival problem in quantum mechanics and leads to a well defined time-energy uncertainty relation for the clocks.
Extragalactic H i Survey with FAST: First Look at the Pilot Survey Results
Authors: Kang Jiangang , Zhu Ming , Ai Mei , Yu Haiyang , Sun Chun
Published: April 2022

We present the first data release of H i sources extracted from a pilot extragalactic survey using the Five-hundred-meter Aperture Spherical radio Telescope (FAST). We extracted sources from three-dimensional (3D) spectral data cubes datacubes to perform interactive searching and computing, yielding global parameters for each source, extending redshift ranges of H i emission up to z = 0.04. A total of 544 extragalactic H i sources has been detected by the pilot FAST H i drift scan survey covering part of the sky region in R.A. (R.A. or α) and decl. (decl. or δ) range 00h47m < R. A. (J2000) < 23h22m and +24° < decl. (J2000) < +43°. Of which, 528 sources are matched with optical counterparts via examination of digital optical survey databases collected from NED and Vizier data center, and 449 of them have optical velocities. Furthermore, we detect 36 galaxies with H i mass <108
M
⊙, which is significant for the study of low-mass systems in the local universe. We present catalogs for all H i detections with signal-to-noise ratio (S/N) greater than 5.1. The data are classified into four categories based on their S/N and baseline qualities, which are flagged with code 1 to 4: (1) 422 sources with S/N > 6.5; (2) 61 sources with 5.1 ≲ S/N ≲ 6.5; (3) 28 sources with relatively poor baselines; (4) 33 sources that are partly masked by strong radio frequency interferences (RFIs). In addition, we find 16 H i sources that have not been matched with any counterparts in the existing galaxy catalogs. This data release can provide guidance for the future extragalactic H i survey with FAST.
Orbital angular momentum underwater wireless optical communication system based on convolutional neural network
Authors: Ma Wenqi , Lu Huimin , Chen Danyang , Jin Jianli , Wang Jianping
Published: April 2022

In this work, a novel 16-ary orbital angular momentum shift keying (OAM-SK) underwater wireless optical communication (UWOC) system based on convolutional neural network (CNN) demodulator and Gerchberg-Saxton CNN (GS-CNN) beam generator is proposed. The bit error rate (BER) performance of the proposed UWOC system with different turbulence intensity, transmission distance, and relative intensity of temperature and salinity is further investigated. By comparing with the results from the UWOC system based on GS beam generator, it is revealed that the BER performance can be improved obviously for the proposed OAM-SK UWOC system combining the CNN demodulator and GS-CNN beam generator.
Physical simulation on Joining of 700 MC steel: A HAZ and CCT curve study
Authors: Roshan Rakesh , Naik Ajit Kumar , Saxena Kuldeep Kumar , Msomi Velaphi
Published: April 2022

In the present work, coarse grain heat-affected zone (CGHAZ) was simulated by Gleeble 3800 thermo-mechanical simulator. A continuous cooling transformation (CCT) diagram was generated from the results of the dilatometer, hardness, and microstructure analysis. The heating rate of 100 °C s−1, the peak temperature of 1300 °C, the holding time of one second, and thirteen different cooling conditions representing the actual welding condition were chosen here for simulation where the cooling rate was controlled by t8/3. At slow cooling rate ferrite, cementite, pearlite, and bainite were obtained. At a medium cooling rate, ferrite, bainite, and a small amount of martensite were observed. At a fast-cooling rate i.e., 100 °C s−1 fully martensite was obtained. The obtained hardness values were 225 HV, 263 HV, and 342 HV for slower, medium, and fast cooling rates respectively. The increase in hardness value shows that the amount of non-diffusional phases increases with an increase in cooling rate. The CCT curve shows the range of cooling rate and phase transformation temperature of ferrite, bainite, and martensite.
Branches of ZnO nanostructure grown on sub-microrod template with seed layer coated by ultrasonic-assisted immersion technique: effect of surface energy on the growth of branches
Authors: Siriphongsapak Nontakoch , Denchitcharoen Somyod
Published: April 2022

Branches of ZnO nanostructure were hydrothermally grown on seed layer coated on sub-microrod template by ultrasonic-assisted immersion technique. Zinc acetate, monoethanolamine, and isopropanol were used as a precursor, stabilizer, and solvent for coating seed layer, respectively. The crystallization of seed layer, which was confirmed by x-ray diffractometer (XRD) and x-ray photoelectron spectrometer (XPS), was facilitated by ultrasonic irradiation. The sol concentration was adjusted to be 20 and 50 mM with the coating cycles of 8 and 16 for controlling the uniformity and surface energy of seed layer. The increase of sol concentration and coating cycles led to the increase of crystal orientation in (002) plane causing the improvement of seed layer’s surface energy which was estimated from water contact angle of the template. Atomic force microscope (AFM) was revealed that the seed layer did not cover the template only at the lowest condition of both sol concentration and coating cycles. However, the roughness and maximum peak-to-valley value tended to be increased for other conditions and dropped for the last condition which was suitable to vertically grow branches. After the growth of branches, the morphology of hierarchical ZnO nanostructure was investigated by field-emission scanning electron microscope (FESEM). It was found that the branches were vertically grown on the surface of rod template in every condition except the lowest sol concentration and coating cycles. Moreover, when the sol concentration and coating cycle of seed layer were increased, the branch density was also increased.
Beyond quantum cluster theories: multiscale approaches for strongly correlated systems
Authors: Fotso Herbert F , Tam Ka-Ming , Moreno Juana
Published: April 2022

The degrees of freedom that confer to strongly correlated systems their many intriguing properties also render them fairly intractable through typical perturbative treatments. For this reason, the mechanisms responsible for their technologically promising properties remain mostly elusive. Computational approaches have played a major role in efforts to fill this void. In particular, dynamical mean field theory and its cluster extension, the dynamical cluster approximation have allowed significant progress. However, despite all the insightful results of these embedding schemes, computational constraints, such as the minus sign problem in quantum Monte Carlo (QMC), and the exponential growth of the Hilbert space in exact diagonalization (ED) methods, still limit the length scale within which correlations can be treated exactly in the formalism. A recent advance aiming to overcome these difficulties is the development of multiscale many body approaches whereby this challenge is addressed by introducing an intermediate length scale between the short length scale where correlations are treated exactly using a cluster solver such QMC or ED, and the long length scale where correlations are treated in a mean field manner. At this intermediate length scale correlations can be treated perturbatively. This is the essence of multiscale many-body methods. We will review various implementations of these multiscale many-body approaches, the results they have produced, and the outstanding challenges that should be addressed for further advances.
Three-body CsD2 calculation in Pd12 cage and E2 transition in ultra-low energy nuclear reaction
Authors: Watanabe T , Hiratsuka Y , Takeda M , Oryu S , Watari N , Kakigami H , Toyoda I
Published: April 2022

The three-body energy levels of the

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135

CsD2 quasi-molecule in a CsD2Pd12 cluster are calculated using the Cs-D, D-D, Cs-Pd and D-Pd repulsive Coulomb interactions with electronic effects, the central Woods-Saxon potential for the two-body nuclear interactions, and a nuclear three-body potential term. The calculation was performed for distances ranging from fermis to nanometers, in one pass, using 100-figure numerical precision, and for energies between the

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139

La ground state (-25.92 MeV) to the top of the Pd-barrier. The ion bases calculated results are adjusted to the electron bases chemical ones at the ground state and at the first excited state of CsD2Pd12. The possibility of

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Cs(2D, γ)

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139

La reaction is investigated for the E2 transition between J

π
= 7/2+ of

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CsD2 and 7/2+ of the

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La ground state.
Direct methods applied to phase retrieval in high resolution transmission electron microscopy
Authors: Bhat Usha , Datta Ranjan
Published: April 2022

An alternative reconstruction method is proposed for retrieving the object exit wave function (OEW) directly from the recorded image intensity pattern in high resolution transmission electron microscopy (HRTEM). The method is based on applying a modified intensity equation representing the HRTEM image. A comparative discussion is provided between the existing methodologies involved in the reconstruction of OEW, off-axis electron holography and the present proposal. Phase shift extracted from the experimental images of MoS2, BN and ZnO are found to be in excellent agreement for most of the atom types investigated with the theoretical reference values. Additionally, it is shown that the Fourier series expansion of diffraction pattern is effective in retrieving the isolated and periodic image functions of certain forms directly. However, for aperiodic object information e.g., defects, dopants, edges etc, the first method works in entirety.
In-materio computing in random networks of carbon nanotubes complexed with chemically dynamic molecules: a review
Authors: Tanaka H , Azhari S , Usami Y , Banerjee D , Kotooka T , Srikimkaew O , Dang T-T , Murazoe S , Oyabu R , Kimizuka K , Hakoshima M
Published: April 2022

The need for highly energy-efficient information processing has sparked a new age of material-based computational devices. Among these, random networks (RNWs) of carbon nanotubes (CNTs) complexed with other materials have been extensively investigated owing to their extraordinary characteristics. However, the heterogeneity of CNT research has made it quite challenging to comprehend the necessary features of in-materio computing in a RNW of CNTs. Herein, we systematically tackle the topic by reviewing the progress of CNT applications, from the discovery of individual CNT conduction to their recent uses in neuromorphic and unconventional (reservoir) computing. This review catalogues the extraordinary abilities of random CNT networks and their complexes used to conduct nonlinear in-materio computing tasks as well as classification tasks that may replace current energy-inefficient systems.
Life-Course Neighborhood Socioeconomic Status and Cardiovascular Events in Black and White Adults in the Atherosclerosis Risk in Communities Study
Authors: Xiao Qian , Heiss Gerardo , Kucharska-Newton Anna , Bey Ganga , Love Shelly-Ann M , Whitsel Eric A
Published: April 2022

It has been reported that residents of low–socioeconomic-status (SES) neighborhoods have a higher risk of developing cardiovascular disease (CVD). However, most of the previous studies focused on 1-time measurement of neighborhood SES in middle-to-older adulthood and lacked demographic diversity to allow for comparisons across different race/ethnicity and sex groups. We examined neighborhood SES in childhood and young, middle, and older adulthood in association with CVD risk among Black and White men and women in the Atherosclerosis Risk in Communities Study (1996–2019). We found that lower neighborhood SES in young, middle, and older adulthood, but not in childhood, was associated with a higher risk of CVD later in life. When compared with the highest quartile, the lowest quartile of neighborhood SES in young, middle, and older adulthood was associated with 18% (hazard ratio (HR) = 1.18, 95% confidence interval (CI): 1.02, 1.36), 21% (HR = 1.21, 95% CI: 1.04, 1.39), and 12% (HR = 1.12, 95% CI: 0.99, 1.26) increases in the hazard of total CVD, respectively. The association between lower neighborhood SES in older adulthood and higher CVD hazard was particularly strong among Black women. Our study findings support the role of neighborhood SES in cardiovascular health in both Black and White adults.
Active Cigarette Smoking Is Associated With Increased Age-Related Decline on Measures of Visuospatial Learning and Memory and Executive Function in Alcohol Use Disorder
Authors: Padula Claudia B , Durazzo Timothy C
Published: April 2022

Aims

The goal of this study was to determine if active cigarette smoking in Veterans with alcohol use disorder (AUD) was associated with greater age-related neurocognitive decline.

Methods

Veterans with AUD, in residential treatment (n = 125; 47 ± 14 years of age, min = 24, max = 76, 29 ± 26 days of abstinence), completed measures of executive functions, learning and memory, processing speed and working memory. Actively smoking AUD (AsAUD, n = 47) were active daily cigarette smokers; former smoking AUD (FsAUD, n = 45) were predominately daily smokers prior to study but did not smoke at the time of study; non-smoking AUD (NsAUD, n = 33) never used cigarettes or smoked ‘only a few times’ during lifetime.

Results

AsAUD demonstrated greater age-related decline on measures of visuospatial learning and memory, and response inhibition/cognitive flexibility, primarily relative to NsAUD; there were no age-related differences between FsAUD and NsAUD on any measure. There were few significant mean differences between groups across the 15 neurocognitive measures. In AsAUD, higher scores on indices of smoking severity were associated with poorer performance on measures of auditory-verbal learning and memory, response inhibition, set-shifting and working memory. In FsAUD, longer smoking cessation duration was related to lower PTSD, anxiety and depressive symptomatology.

Conclusions

Active smoking was associated with accelerated age-related decline on cognitive functions implicated in response to common evidence-based AUD interventions. Results suggest that smoking history contributes to the considerable heterogeneity observed in neurocognitive function in early AUD recovery, and reinforce the clinical movement to offer smoking cessation resources concurrent with treatment for AUD.
A Novel Use of Latent Class Analysis to Identify Patterns of Workplace Hazards among Informally Employed Domestic Workers in 14 Cities, United States, 2011–2012
Authors: Wright Emily , Chen Jarvis T , Beckfield Jason , Theodore Nik , González Paulina López , Krieger Nancy
Published: April 2022

Introduction

Few studies, mostly descriptive, have quantitatively analyzed the working conditions of domestic workers (DWers) informally employed by private households in the USA. These workers are explicitly or effectively excluded from numerous workplace protections, and scant data exist on their exposures or how best to categorize them.

Methods

We analyzed data from the sole nationwide survey of informally employed US DWers with work-related hazards data, conducted by the National Domestic Workers Alliance, the University of Illinois Chicago Center for Urban Economic Development, and the DataCenter in 14 US cities (2011–2012; N = 2086). We used exploratory latent class analysis to identify groups of DWers with distinct patterns of exposure to 21 self-reported economic, social, and occupational workplace hazards (e.g. pay violations, verbal abuse, heavy lifting). We then used multinomial logistic latent class regression to examine associations between workers’ individual, household, and occupational characteristics and latent class membership.

Results

Among the 2086 DWers, mean age was 42.6 years, 97.3% were women, 56.0% Latina/o, 26.5% White, 33.2% undocumented immigrants, and 11.7% live-in. 53.5%, 32.0%, and 14.5% primarily worked doing housecleaning, child care, and adult care, respectively. 49.9% of workers reported ≥3 hazards. Latent class analysis identified four groups of DWers doing: ‘Low hazard domestic work’ (lowest exposure to all hazards), ‘Demanding care work’ (moderate exposure to pay violations [item response probability (IRP) = 0.42] and contagious illness care [IRP = 0.39]), ‘Strenuous cleaning work’ (high exposure to cleaning-related occupational hazards, such as climbing to clean [IRP = 0.87]), and ‘Hazardous domestic work’ (highest exposure to all but one hazard). Covariates were strongly associated, in many cases, with latent class membership. For example, compared to other DWers, DWers doing ‘hazardous domestic work’ had the largest predicted probability of being economically insecure (0.53) and living-in with their employers (0.17).

Conclusions

Results indicate that informally employed US DWers experience distinct patterns of workplace hazards, and that it is informative to characterize DWers’ exposures to different sets of multiple hazards using latent class analysis.
Shoaling in the Trinidadian guppy: costs, benefits, and plasticity in response to an ambush predator
Authors: Li Anna , Richardson Jean M L , Helen Rodd F
Published: April 2022

Shoaling, the formation of social groupings in fish, can provide benefits including reduced predation risk. However, it can also inflict costs including increased competition for resources, transmission of parasites, and salience to predators. Trinidadian guppies exhibit inter-population variation in shoaling behavior where individuals coexisting with large piscivorous predators (high predation localities) spend most of their time in shoals and those coexisting with an ambush predator, Rivulus hartii (recently, Anablepsoides hartii), that preys primarily on smaller guppies (low predation localities) do not. It has been suggested that this predator selects for reduced shoaling because doing so reduces salience to the predator. Here, as far as we know, we perform the first test of this idea. First, we investigated the effectiveness of shoaling in encounters with this predator. In survival trials, where one rivulus interacted with a group of guppies, we found that the predator was more likely to attack individuals in shoals than singletons. However, we also found that attacks directed at shoals were less likely to succeed. This suggests that the optimal strategy for guppies co-existing with this predator is to reduce shoaling to reduce the probability of being attacked, and to form shoals when an attack is initiated. We then asked if guppies modified their shoaling behavior in response to visual and olfactory cues from this predator during development. We found changes in guppy behavior in response to the treatment: guppies increased shoaling behavior when there was heightened risk of predation.
Once an optimist, always an optimist? Studying cognitive judgment bias in mice
Authors: Bračić Marko , Bohn Lena , Siewert Viktoria , von Kortzfleisch Vanessa T , Schielzeth Holger , Kaiser Sylvia , Sachser Norbert , Richter S Helene
Published: April 2022

Individuals differ in the way they judge ambiguous information: some individuals interpret ambiguous information in a more optimistic, and others in a more pessimistic way. Over the past two decades, such “optimistic” and “pessimistic” cognitive judgment biases (CJBs) have been utilized in animal welfare science as indicators of animals’ emotional states. However, empirical studies on their ecological and evolutionary relevance are still lacking. We, therefore, aimed at transferring the concept of “optimism” and “pessimism” to behavioral ecology and investigated the role of genetic and environmental factors in modulating CJB in mice. In addition, we assessed the temporal stability of individual differences in CJB. We show that the chosen genotypes (C57BL/6J and B6D2F1N) and environments (“scarce” and “complex”) did not have a statistically significant influence on the responses in the CJB test. By contrast, they influenced anxiety-like behavior with C57BL/6J mice and mice from the “complex” environment displaying less anxiety-like behavior than B6D2F1N mice and mice from the “scarce” environment. As the selected genotypes and environments did not explain the existing differences in CJB, future studies might investigate the impact of other genotypes and environmental conditions on CJB, and additionally, elucidate the role of other potential causes like endocrine profiles and epigenetic modifications. Furthermore, we show that individual differences in CJB were repeatable over a period of seven weeks, suggesting that CJB represents a temporally stable trait in laboratory mice. Therefore, we encourage the further study of CJB within an animal personality framework.
Syotti: scalable bait design for DNA enrichment
Authors: Alanko Jarno N , Slizovskiy Ilya B , Lokshtanov Daniel , Gagie Travis , Noyes Noelle R , Boucher Christina
Published: April 2022

Motivation

Bait enrichment is a protocol that is becoming increasingly ubiquitous as it has been shown to successfully amplify regions of interest in metagenomic samples. In this method, a set of synthetic probes (‘baits’) are designed, manufactured and applied to fragmented metagenomic DNA. The probes bind to the fragmented DNA and any unbound DNA is rinsed away, leaving the bound fragments to be amplified for sequencing. Metsky et al. demonstrated that bait-enrichment is capable of detecting a large number of human viral pathogens within metagenomic samples.

Results

We formalize the problem of designing baits by defining the Minimum Bait Cover problem, show that the problem is NP-hard even under very restrictive assumptions, and design an efficient heuristic that takes advantage of succinct data structures. We refer to our method as Syotti. The running time of Syotti shows linear scaling in practice, running at least an order of magnitude faster than state-of-the-art methods, including the method of Metsky et al. At the same time, our method produces bait sets that are smaller than the ones produced by the competing methods, while also leaving fewer positions uncovered. Lastly, we show that Syotti requires only 25 min to design baits for a dataset comprised of 3 billion nucleotides from 1000 related bacterial substrains, whereas the method of Metsky et al. shows clearly super-linear running time and fails to process even a subset of 17% of the data in 72 h.

Availability and implementation

https://github.com/jnalanko/syotti.

Supplementary information

Supplementary data are available at Bioinformatics online.
PolarMorphism enables discovery of shared genetic variants across multiple traits from GWAS summary statistics
Authors: von Berg Joanna , ten Dam Michelle , van der Laan Sander W , de Ridder Jeroen
Published: April 2022

Motivation

Pleiotropic SNPs are associated with multiple traits. Such SNPs can help pinpoint biological processes with an effect on multiple traits or point to a shared etiology between traits. We present PolarMorphism, a new method for the identification of pleiotropic SNPs from genome-wide association studies (GWAS) summary statistics. PolarMorphism can be readily applied to more than two traits or whole trait domains. PolarMorphism makes use of the fact that trait-specific SNP effect sizes can be seen as Cartesian coordinates and can thus be converted to polar coordinates r (distance from the origin) and theta (angle with the Cartesian x-axis, in the case of two traits). r describes the overall effect of a SNP, while theta describes the extent to which a SNP is shared. r and theta are used to determine the significance of SNP sharedness, resulting in a P-value per SNP that can be used for further analysis.

Results

We apply PolarMorphism to a large collection of publicly available GWAS summary statistics enabling the construction of a pleiotropy network that shows the extent to which traits share SNPs. We show how PolarMorphism can be used to gain insight into relationships between traits and trait domains and contrast it with genetic correlation. Furthermore, pathway analysis of the newly discovered pleiotropic SNPs demonstrates that analysis of more than two traits simultaneously yields more biologically relevant results than the combined results of pairwise analysis of the same traits. Finally, we show that PolarMorphism is more efficient and more powerful than previously published methods.

Availability and implementation

code: https://github.com/UMCUGenetics/PolarMorphism, results: 10.5281/zenodo.5844193.

Supplementary information

Supplementary data are available at Bioinformatics online.
Exploring automatic inconsistency detection for literature-based gene ontology annotation
Authors: Chen Jiyu , Goudey Benjamin , Zobel Justin , Geard Nicholas , Verspoor Karin
Published: April 2022

Motivation

Literature-based gene ontology annotations (GOA) are biological database records that use controlled vocabulary to uniformly represent gene function information that is described in the primary literature. Assurance of the quality of GOA is crucial for supporting biological research. However, a range of different kinds of inconsistencies in between literature as evidence and annotated GO terms can be identified; these have not been systematically studied at record level. The existing manual-curation approach to GOA consistency assurance is inefficient and is unable to keep pace with the rate of updates to gene function knowledge. Automatic tools are therefore needed to assist with GOA consistency assurance. This article presents an exploration of different GOA inconsistencies and an early feasibility study of automatic inconsistency detection.

Results

We have created a reliable synthetic dataset to simulate four realistic types of GOA inconsistency in biological databases. Three automatic approaches are proposed. They provide reasonable performance on the task of distinguishing the four types of inconsistency and are directly applicable to detect inconsistencies in real-world GOA database records. Major challenges resulting from such inconsistencies in the context of several specific application settings are reported. This is the first study to introduce automatic approaches that are designed to address the challenges in current GOA quality assurance workflows. The data underlying this article are available in Github at https://github.com/jiyuc/AutoGOAConsistency.
Phage–bacterial contig association prediction with a convolutional neural network
Authors: Tang Tianqi , Hou Shengwei , Fuhrman Jed A , Sun Fengzhu
Published: April 2022

Motivation

Phage–host associations play important roles in microbial communities. But in natural communities, as opposed to culture-based lab studies where phages are discovered and characterized metagenomically, their hosts are generally not known. Several programs have been developed for predicting which phage infects which host based on various sequence similarity measures or machine learning approaches. These are often based on whole viral and host genomes, but in metagenomics-based studies, we rarely have whole genomes but rather must rely on contigs that are sometimes as short as hundreds of bp long. Therefore, we need programs that predict hosts of phage contigs on the basis of these short contigs. Although most existing programs can be applied to metagenomic datasets for these predictions, their accuracies are generally low. Here, we develop ContigNet, a convolutional neural network-based model capable of predicting phage–host matches based on relatively short contigs, and compare it to previously published VirHostMatcher (VHM) and WIsH.

Results

On the validation set, ContigNet achieves 72–85% area under the receiver operating characteristic curve (AUROC) scores, compared to the maximum of 68% by VHM or WIsH for contigs of lengths between 200 bps to 50 kbps. We also apply the model to the Metagenomic Gut Virus (MGV) catalogue, a dataset containing a wide range of draft genomes from metagenomic samples and achieve 60–70% AUROC scores compared to that of VHM and WIsH of 52%. Surprisingly, ContigNet can also be used to predict plasmid-host contig associations with high accuracy, indicating a similar genetic exchange between mobile genetic elements and their hosts.

Availability and implementation

The source code of ContigNet and related datasets can be downloaded from https://github.com/tianqitang1/ContigNet.
DRUMMER—rapid detection of RNA modifications through comparative nanopore sequencing
Authors: Abebe Jonathan S , Price Alexander M , Hayer Katharina E , Mohr Ian , Weitzman Matthew D , Wilson Angus C , Depledge Daniel P
Published: April 2022

Motivation

The chemical modification of ribonucleotides regulates the structure, stability and interactions of RNAs. Profiling of these modifications using short-read (Illumina) sequencing techniques provides high sensitivity but low-to-medium resolution i.e. modifications cannot be assigned to specific transcript isoforms in regions of sequence overlap. An alternative strategy uses current fluctuations in nanopore-based long read direct RNA sequencing (DRS) to infer the location and identity of nucleotides that differ between two experimental conditions. While highly sensitive, these signal-level analyses require high-quality transcriptome annotations and thus are best suited to the study of model organisms. By contrast, the detection of RNA modifications in microbial organisms which typically have no or low-quality annotations requires an alternative strategy. Here, we demonstrate that signal fluctuations directly influence error rates during base-calling and thus provides an alternative approach for identifying modified nucleotides.

Results

DRUMMER (Detection of Ribonucleic acid Modifications Manifested in Error Rates) (i) utilizes a range of statistical tests and background noise correction to identify modified nucleotides with high confidence, (ii) operates with similar sensitivity to signal-level analysis approaches and (iii) correlates very well with orthogonal approaches. Using well-characterized DRS datasets supported by independent meRIP-Seq and miCLIP-Seq datasets we demonstrate that DRUMMER operates with high sensitivity and specificity.

Availability and implementation

DRUMMER is written in Python 3 and is available as open source in the GitHub repository: https://github.com/DepledgeLab/DRUMMER.

Supplementary information

Supplementary data are available at Bioinformatics online.
An atlas of human viruses provides new insights into diversity and tissue tropism of human viruses
Authors: Ye Sifan , Lu Congyu , Qiu Ye , Zheng Heping , Ge Xingyi , Wu Aiping , Xia Zanxian , Jiang Taijiao , Zhu Haizhen , Peng Yousong
Published: April 2022

Motivation

Viruses continue to threaten human health. Yet, the complete viral species carried by humans and their infection characteristics have not been fully revealed.

Results

This study curated an atlas of human viruses from public databases and literature, and built the Human Virus Database (HVD). The HVD contains 1131 virus species of 54 viral families which were more than twice the number of the human-infecting virus species reported in previous studies. These viruses were identified in human samples including 68 human tissues, the excreta and body fluid. The viral diversity in humans was age-dependent with a peak in the infant and a valley in the teenager. The tissue tropism of viruses was found to be associated with several factors including the viral group (DNA, RNA or reverse-transcribing viruses), enveloped or not, viral genome length and GC content, viral receptors and the virus-interacting proteins. Finally, the tissue tropism of DNA viruses was predicted using a random-forest algorithm with a middle performance. Overall, the study not only provides a valuable resource for further studies of human viruses but also deepens our understanding toward the diversity and tissue tropism of human viruses.

Availability and implementation

The HVD is available at http://computationalbiology.cn/humanVirusBase/#/.

Supplementary information

Supplementary data are available at Bioinformatics online.
Deephos: predicted spectral database search for TMT-labeled phosphopeptides and its false discovery rate estimation
Authors: Na Seungjin , Choi Hyunjin , Paek Eunok
Published: April 2022

Motivation

Tandem mass tag (TMT)-based tandem mass spectrometry (MS/MS) has become the method of choice for the quantification of post-translational modifications in complex mixtures. Many cancer proteogenomic studies have highlighted the importance of large-scale phosphopeptide quantification coupled with TMT labeling. Herein, we propose a predicted Spectral DataBase (pSDB) search strategy called Deephos that can improve both sensitivity and specificity in identifying MS/MS spectra of TMT-labeled phosphopeptides.

Results

With deep learning-based fragment ion prediction, we compiled a pSDB of TMT-labeled phosphopeptides generated from ∼8000 human phosphoproteins annotated in UniProt. Deep learning could successfully recognize the fragmentation patterns altered by both TMT labeling and phosphorylation. In addition, we discuss the decoy spectra for false discovery rate (FDR) estimation in the pSDB search. We show that FDR could be inaccurately estimated by the existing decoy spectra generation methods and propose an innovative method to generate decoy spectra for more accurate FDR estimation. The utilities of Deephos were demonstrated in multi-stage analyses (coupled with database searches) of glioblastoma, acute myeloid leukemia and breast cancer phosphoproteomes.

Availability and implementation

Deephos pSDB and the search software are available at https://github.com/seungjinna/deephos.