bluuebunny/crossref_metadata_2025_split huggingface dataset:
Firefly-inspired vocabulary generator for communication in multi-agent systems
Authors: Nguyen Chantal , Huang Isabella , Peleg Orit 
Published: May 2022

AbstractFireflies’ dazzling light displays are courtship rituals: flying males announce their presence as suitable mates to the females on the ground. Their light signal is composed of a species-specific on/off light sequence repeated periodically. However, thousands of fireflies flashing in a swarm can create immense visual clutter that hinders the detection of potential mates. A partial solution to this visual clutter problem is to flash according to sequences that are more distinct and detectable than those of other individuals. Here, we investigate how distinguishable flash sequences can co-evolve by developing a method for simulating sequences that minimize their mutual similarity with each other while minimizing their energetic cost and predation risk. This simple set of rules produces flash sequences that are remarkably similar to those of real fireflies. In particular, we observe an emergent periodicity in the resulting sequences, despite the lack of any periodicity requirements on the sequences. In addition, we demonstrate a method of reconstructing the evolutionary pressures acting on sets of firefly species. We do so by carrying out simulations that follow known phylogenetic relationships of extant species alongside their characteristic flash patterns.
Maximuma posteriorinatural scene reconstruction from retinal ganglion cells with deep denoiser priors
Authors: Wu Eric G. , Brackbill Nora , Sher Alexander , Litke Alan M. , Simoncelli Eero P. , Chichilnisky E.J. 
Published: May 2022

AbstractVisual information arriving at the retina is transmitted to the brain by signals in the optic nerve, and the brain must rely solely on these signals to make inferences about the visual world. Previous work has probed the content of these signals by directly reconstructing images from retinal activity using linear regression or nonlinear regression with neural networks. Maximuma posteriori(MAP) reconstruction using retinal encoding models and separately-trained natural image priors offers a more general and principled approach. We develop a novel method for approximate MAP reconstruction that combines a generalized linear model for retinal responses to light, including their dependence on spike history and spikes of neighboring cells, with the image prior implicitly embedded in a deep convolutional neural network trained for image denoising. We use this method to reconstruct natural images fromex vivosimultaneously-recorded spikes of hundreds of retinal ganglion cells uniformly sampling a region of the retina. The method produces reconstructions that match or exceed the state-of-the-art in perceptual similarity and exhibit additional fine detail, while using substantially fewer model parameters than previous approaches. The use of more rudimentary encoding models (a linear-nonlinear-Poisson cascade) or image priors (a 1/fspectral model) significantly reduces reconstruction performance, indicating the essential role of both components in achieving high-quality reconstructed images from the retinal signal.
A Gated Graph Transformer for Protein Complex Structure Quality Assessment and its Performance in CASP15
Authors: Chen Xiao , Morehead Alex , Liu Jian , Cheng Jianlin 
Published: May 2022

AbstractMotivationProteins interact to form complexes to carry out essential biological functions. Computational methods such as AlphaFold-multimer have been developed to predict the quaternary structures of protein complexes. An important yet largely unsolved challenge in protein complex structure prediction is to accurately estimate the quality of predicted protein complex structures without any knowledge of the corresponding native structures. Such estimations can then be used to select high-quality predicted complex structures to facilitate biomedical research such as protein function analysis and drug discovery.ResultsIn this work, we introduce a new gated neighborhood-modulating graph transformer to predict the quality of 3D protein complex structures. It incorporates node and edge gates within a graph transformer framework to control information flow during graph message passing. We trained, evaluated and tested the method (called DProQA) on newly-curated protein complex datasets before the 15th Critical Assessment of Techniques for Protein Structure Prediction (CASP15) and then blindly tested it in the 2022 CASP15 experiment. The method was ranked 3rd among the single-model quality assessment methods in CASP15 in terms of the ranking loss of TM-score on 36 complex targets. The rigorous internal and external experiments demonstrate that DProQA is effective in ranking protein complex structures.AvailabilityThe source code, data, and pre-trained models are available athttps://github.com/jianlin-cheng/DProQAContactchengji@missouri.eduSupplementary informationSupplementary data are available atBioinformaticsonline.
The placement of foot-mounted IMU sensors does affect the accuracy of spatial parameters during regular walking
Authors: Küderle Arne , Roth Nils , Zlatanovic Jovana , Zrenner Markus , Eskofier Bjoern , Kluge Felix 
Published: May 2022

AbstractGait analysis using foot-worn inertial measurement units has proven to be a reliable tool to diagnose and monitor many neurological and musculoskeletal indications. However, only few studies have investigated the robustness of such systems to changes in the sensor attachment and no consensus for suitable sensor positions exists in the research community. Specifically for unsupervised real-world measurements, understanding how the reliability of the monitoring system changes when the sensor is attached differently is from high importance. In these scenarios, placement variations are expected because of user error or personal preferences. In this manuscript, we present the largest study to date comparing different sensor positions and attachments. We recorded 9000 strides with motion-capture reference from 14 healthy participants with six synchronized sensors attached at each foot. Spatial gait parameters were calculated using a double-integration method and compared to the reference system. The results indicate that relevant differences in the accuracy of the stride length exists between the sensor positions. While the average error over multiple strides is comparable, single stride errors and variability parameters differ greatly. We further present a physics model and an analysis of the raw sensor data to understand the origin of the observed differences. This analysis indicates that a variety of attachment parameters can influence the systems’ performance. While this is only the starting point to understand and mitigate these types of errors, we conclude that sensor systems and algorithms must be reevaluated when the sensor position or attachment changes.
Hyperbaric Oxygen for Treatment of Long COVID Syndrome (HOT-LoCO); Protocol for a Randomised, Placebo-Controlled, Double-Blind, Phase II Clinical Trial
Authors: Kjellberg Anders , Abdel-Halim Lina , Hassler Adrian , Gharbi Sara El , Al-Ezerjawi Sarah , Boström Emil , Sundberg Carl Johan , Pernow John , Medson Koshiar , Kowalski Jan , Rodriguez-Wallberg Kenny A , Zheng Xiaowei , Catrina Sergiu-Bogdan , Runold Michael , Ståhlberg Marcus , Bruchfeld Judith , Nygren-Bonnier Malin , Lindholm Peter 
Published: May 2022

AbstractIntroductionLong COVID, where symptoms persist 12 weeks after the initial SARS-CoV-2-infection, is a substantial problem for individuals and society in the surge of the pandemic. Common symptoms are fatigue, post-exertional malaise, and cognitive dysfunction. There is currently no effective treatment, and the underlying mechanisms are unknown although several hypotheses exist, with chronic inflammation as a common denominator. In prospective studies, hyperbaric oxygen therapy (HBOT) has been suggested to be effective for the treatment of similar syndromes such as chronic fatigue syndrome and fibromyalgia. A case series has suggested positive effects of HBOT in Long COVID. This randomised placebo-controlled clinical trial will explore HBOT as a potential treatment for Long COVID. The primary objective is to evaluate if HBOT improves health related quality of life (HRQoL) for patients with Long COVID compared to placebo/sham. The main secondary objectives are to evaluate whether HBOT improves endothelial function, objective physical performance, and short term HRQoL.Methods and AnalysisA randomised, placebo-controlled, double-blind, phase II clinical trial in 80 previously healthy subjects debilitated due to Long COVID, with low HRQoL. Clinical data, HRQoL- questionnaires, blood samples, objective tests and activity meter data will be collected at baseline. Subjects will be randomised to a maximum of 10 treatments with hyperbaric oxygen or sham treatment over six weeks. Assessments for safety and efficacy will be performed at six, 13, 26 and 52 weeks, with the primary endpoint (physical domains in RAND-36) and main secondary endpoints defined at 13 weeks after baseline. Data will be reviewed by an independent Data Safety Monitoring Board.Ethics and DisseminationThe trial is approved by The Swedish National Institutional Review Board (2021-02634) and the Swedish Medical Product Agency (5.1-2020-36673). Positive, negative, and inconclusive results will be published in peer-reviewed scientific journals with open access.Trial RegistrationNCT04842448. EudraCT: 2021-000764-30Strengths and limitations of this trialStrengthsRandomised placebo-controlled, double-blind, parallel groups, clinical trial in compliance with ICH-GCPEvaluation of safety and efficacy, including objective and explanatory endpointsIndependent Data Safety Monitoring Board (DSMB)LimitationsNew syndrome with unknown mechanismsPower calculation is based on similar syndromesSelection bias as patients are enrolled from the same post-COVID clinic
Plant to animal protein ratio in the diet: nutrient adequacy, long-term health and environmental pressure
Authors: Fouillet Hélène , Dussiot Alison , Perraud Elie , Wang Juhui , Huneau Jean-François , Kesse-Guyot Emmanuelle , Mariotti François 
Published: May 2022

AbstractBackgroundAnimal and plant protein sources have contrasting relationships with nutrient adequacy and long-term health, and their adequate ratio is highly debated.ObjectiveWe aimed to explore how the percentage of plant protein in the diet (%PP) relates to nutrient adequacy and long-term health but also to environmental pressures, to determine the adequate and potentially optimal %PP values.MethodsObserved diets were extracted from the dietary intakes of French adults (INCA3, n=1 125). Using reference values for nutrients and disease burden risks for foods, we modeled diets with graded %PP values that simultaneously ensure nutrient adequacy, minimize long-term health risks and preserve at best dietary habits. This multi-criteria diet optimization was conducted in a hierarchical manner, giving priority to long-term health over diet proximity, under the constraints of ensuring nutrient adequacy and food cultural acceptability. We explored the tensions between objectives and identified the most critical nutrients and influential constraints by sensitivity analysis. Finally, environmental pressures related to the modeled diets were estimated using the AGRIBALYSE database.ResultsWe find that nutrient-adequate diets must fall within the ∼15%-80% %PP range, a slightly wider range being nevertheless identifiable by waiving the food acceptability constraints. Fully healthy diets, also achieving the minimum-risk exposure levels for both unhealthy and healthy foods, must fall within the 25%-70% %PP range. All of these healthy diets were very distant from current typical diet. Those with higher %PP had lower environmental impacts, notably on climate change and land use, while being as far from current diet.ConclusionsThere is no single optimal %PP value when considering only nutrition and health, but high %PP diets are more sustainable. For %PP>80%, nutrient fortification/supplementation and/or new foods are required.
Neurostructural associations with traumatic experiences during child- and adulthood
Authors: Siehl Sebastian , Sicorello Maurizio , Herzog Julia , Nees Frauke , Kleindienst Nikolaus , Bohus Martin , Müller-Engelmann Meike , Steil Regina , Priebe Kathlen , Schmahl Christian , Flor Herta 
Published: May 2022

AbstractBackgroundAdverse experiences can lead to severe mental health problems such as posttraumatic stress disorder (PTSD) throughout the lifespan. In individuals with PTSD, both global and local brain volume reductions have been reported—especially in the amygdala and hippocampus—while the literature on childhood maltreatment suggests strong dependency on the timing of adverse events. In the present study, we pooled data from two studies to contrast effects of reported trauma-exposure during neurodevelopmentally sensitive periods in early life with trauma-exposure during adulthood.MethodsA total of 155 women were allocated into one of six age-matched groups according to timing of traumatization (childhood vs adulthood) and psychopathology (PTSD vs trauma-exposed healthy vs trauma-naïve healthy). Volumes of amygdala and hippocampus were compared between these groups. Six additional exploratory regions of interest (ROI) were included based on a recent meta-analysis.ResultsAmygdala volume was strongly dependent on timing of traumatization: Smaller amygdala volumes were observed in the childhood sample, while larger volumes were observed in the adulthood sample. Hippocampal volume comparisons revealed no statistically significant differences, although the descriptive pattern was similar to that found for the amygdala. The remaining exploratory ROIs showed significant group effects, but no timing effects.ConclusionsTiming of traumatization was associated with amygdala volumes throughout the lifespan, with opposite effects dependent on age at trauma occurrence. The relevance of potential confounders like trauma-type and multiplicity is discussed.
Improving the efficiency of scale-up and deployment of community health workers in Mali: a geospatial analysis
Authors: Oliphant Nicholas P , Sy Zeynabou , Koné Brehima , Berthé Mohamed , Beebe Madeleine , Samake Moussa , Diabaté Mamoutou , Tounkara Salimata , Diarra Borodjan , Diarra Amadou B , Diawara Cheickna H , Yakimova Tsvetana , Florisse Sonia , Jackson Debra , Ray Nicolas , Doherty Tanya 
Published: May 2022

ABSTRACTOptimising the scale and deployment of community health workers (CHWs) is important for maximizing geographical accessibility of integrated primary health care (PHC) services. Yet little is known about approaches for doing so.We used geospatial analysis to model optimised scale-up and deployment of CHWs in Mali, to inform strategic and operational planning by the Ministry of Health and Social Development. Accessibility catchments were modelled based on travel time, accounting for barriers to movement. We compared geographic coverage of the estimated population, under-five deaths, and plasmodium falciparum (Pf) malaria cases across different hypothetical optimised CHW networks and identified surpluses and deficits of CHWs compared to the existing CHW network.A network of 15843 CHW, if optimally deployed, would ensure that 77.3% of the population beyond 5 km of the CSCom (community health centre) and CSRef (referral health facility) network would be within a 30-minute walk of a CHW. The same network would cover an estimated 59.5% of U5 deaths and 58.5% of Pf malaria cases. As an intermediary step, an optimised network of 4500 CHW, primarily filling deficits of CHW in the regions of Kayes, Koulikoro, Sikasso, and Ségou would ensure geographic coverage for 31.3% of the estimated population. There were no important differences in geographic coverage percentage when prioritizing CHW scale-up and deployment based on the estimated population, U5 deaths, or Pf malaria cases.Our geospatial analysis provides useful information to policymakers and planners in Mali for optimising the scale-up and deployment of CHW and, in turn, for maximizing the value-for-money of resources of investment in CHWs in the context of the country’s health sector reform. Countries with similar interests in optimising the scale and deployment of their CHW workforce may look to Mali as an exemplar model from which to learn.
DNA Methylation as a Potential Mediator of the Association Between Prenatal Tobacco and Alcohol Exposure and Child Neurodevelopment in a South African Birth Cohort
Authors: Abrishamcar Sarina , Chen Junyu , Feil Dakotah , Kilanowski Anna , Koen Nastassja , Vanker Aneesa , Wedderburn Catherine J. , Donald Kirsten A. , Zar Heather J. , Stein Dan J. , Hüls Anke 
Published: May 2022

AbstractPrenatal tobacco exposure (PTE) and prenatal alcohol exposure (PAE) have been associated with an increased risk of delayed neurodevelopment in children as well as differential newborn DNA methylation (DNAm). However, the biological mechanisms connecting PTE and PAE, DNAm, and neurodevelopment are largely unknown. Here we aim to determine whether differential DNAm mediates the association between PTE and PAE and neurodevelopment at 6 (N=113) and 24 months (N=187) in children from the South African Drakenstein Child Health Study. PTE and PAE were assessed antenatally using urine cotinine measurements and the ASSIST questionnaire, respectively. Cord blood DNAm was measured using the EPIC and 450K BeadChips. Neurodevelopment (cognitive, language, motor, adaptive behavior, socioemotional) was measured using the Bayley Scales of Infant and Toddler Development, Third Edition. We constructed methylation risk scores (MRS) for PTE and PAE and conducted causal mediation analysis (CMA) with these MRS as mediators. Next, we conducted a high-dimensional mediation analysis to identify individual CpG sites as potential mediators, followed by a CMA to estimate the average causal mediation effects (ACME) and total effect (TE).PTE and PAE were associated with neurodevelopment at 6 but not at 24 months. PTE MRS reached a prediction accuracy (R2) of 0.23 but did not significantly mediate the association between PTE and neurodevelopment. PAE MRS was not predictive of PAE (R2=0.006). For PTE, 31 CpG sites and 8 CpG sites were identified as significant mediators (ACME and TEP<0.05) for the cognitive and motor domains at 6 months, respectively. For PAE, 16 CpG sites and 1 CpG site were significant mediators for the motor and adaptive behavior domains at 6 months, respectively. Several genes includingMAD1L1, CAMTA1, andALDH1A2have been implicated in neurodevelopmental delay, suggesting that differential DNAm may partly explain the biological mechanisms underlying the relationship between PTE and PAE and child neurodevelopment.
The Role of HIV Partner Services in the Modern Biomedical HIV Prevention Era: A Network Modeling Study
Authors: Jenness Samuel M. , Le Guillou Adrien , Lyles Cynthia , Bernstein Kyle T. , Krupinsky Kathryn , Enns Eva A. , Sullivan Patrick S. , Delaney Kevin P. 
Published: May 2022

ABSTRACTBackgroundHIV partner services can accelerate the use of antiretroviral-based HIV prevention tools (ART and PrEP), but its population impact on long-term HIV incidence reduction is challenging to quantify with traditional PS metrics of partner identified or HIV-screened. Understanding the role of partner services within the portfolio of HIV prevention interventions, including using it to efficiently deliver antiretrovirals, is needed to achieve HIV prevention targets.MethodsWe used a stochastic network model of HIV/STI transmission for men who have sex with men (MSM), calibrated to surveillance-based estimates in the Atlanta area, a jurisdiction with high HIV burden and suboptimal partner services uptake. Model scenarios varied successful delivery of partner services cascade steps (newly diagnosed “index” patient and partner identification, partner HIV screening, and linkage or reengagement of partners in PrEP or ART care) individually and jointly.ResultsAt current levels observed in Atlanta, removal of HIV partner services had minimal impact on 10-year cumulative HIV incidence, as did improving a single partner services step while holding the others constant. These changes did not sufficiently impact overall PrEP or ART coverage to reduce HIV transmission. If all index patients and partners were identified, maximizing partner HIV screening, partner PrEP provision, partner ART linkage, and partner ART reengagement would avert 6%, 11%, 5%, and 18% of infections, respectively. Realistic improvements in partner identification and service delivery were estimated to avert 2–8% of infections, depending on the combination of improvements.ConclusionsAchieving optimal HIV prevention with partner services depends on pairing improvements in index patient and partner identification with maximal delivery of HIV screening, ART, and PrEP to partners if indicated. Improving the identification steps without improvement to antiretroviral service delivery steps, or vice versa, is projected to result in negligible population HIV prevention benefit.
The trends in the uninsured rates among non-elderly adult patients hospitalized with acute pancreatitis in the US during 2004-2019
Authors: Kumar Vivek , Barkoudah Ebrahim , Jin David X , Banks Peter , McNabb-Baltar Julia 
Published: May 2022

AbstractBackground and AimThe impact of health reforms such as affordable care act (ACA) and Medicaid expansion program on health insurance coverage among acute pancreatitis (AP) patients in the United States (US) is unknown. We report the trends and forecasts for the uninsured rates among acute pancreatitis (AP) patients in the US.MethodsWe included non-elderly adult patients (aged 18 -64 years), hospitalized with AP in the nationwide inpatient sample database years 2004-2019. We calculated the percentage of uninsured and Medicaid patients for each year and applied joinpoint (JP) regression model to study the trends.ResultsThe uninsured rates among patients hospitalized with AP were almost twice compared to the national average rates for all hospitalized patients. Uninsured rates were higher among Hispanic and African American races, rural location, lower income quartiles and in the southern US regions. A statistically significant decline was observed during 2013-2016 with an APC of - 12.23 (−20--4); p<0/01). The decline was apparent among all racial groups, locations and income groups but not in the southern region where gap in the uninsured rates worsened compared to other geographical regions. The trends reversed more recently, and the uninsured rates surged in 2018 for the first time after 2010. In 2019, 12.5% AP patients were uninsured compared to 11.6% in 2017. The forecasts after taking unemployment rates into account showed that uninsured rates would peak in 2020 followed by a gentle decline in the following years but overall uninsured rates would remain higher compared to 2017.ConclusionsThe ACA and Medicaid expansion programs resulted in overall decrease in the uninsured rates, particularly among racial minorities, rural location and in the lowest income group. However, there was a surge in uninsured rate in the most recent years (2017-2019) which will continue during the next four years