bluuebunny/crossref_metadata_2025_split huggingface dataset:
Low back pain in compensated Australian workers: a retrospective cohort study
Authors: Di Donato Michael , Buchbinder Rachelle , Iles Ross , Gray Shannon , Collie Alex 
Published: February 2020

ABSTRACTObjectivesTo describe incidence, duration, and patterns of working time loss claims in compensated Australian workers with low back pain (LBP), and compare this with other musculoskeletal conditions.MethodsThe National Dataset for Compensation-based Statistics (NDS) was used for this study. Any accepted workers’ compensation time loss claims for LBP, limb fracture or limb soft tissue disease occurring between July 2010 and June 2015 were included. Demographic information, occupation, and total cumulative time loss data were extracted. Counts, rates per 10,000 covered workers, the relative risk and median duration of time loss were calculated. Multivariate Cox and quantile regression models were used to determine factors affecting time loss duration and patterns.ResultsThere were 56,102 LBP claims, 42,957 limb fracture claims, and 18,249 limb soft tissue disease claims. The relative risk of a claim for LBP was significantly greater than limb fractures after adjustment for all covariates (RR 1.30, 95%CI 1.29 – 1.32, p < 0.001). LBP claims had longer median time loss (9.39 weeks) than limb fracture claims (9.21 weeks). Quantile regression demonstrated that LBP claims were more likely than limb fracture claims to resolve within seven weeks, and to persist for periods beyond seven weeks.ConclusionsThere were differential patterns of time loss in LBP claims and limb fracture claims. The interaction between conditions, and policies and practices may contribute to these patterns. The findings should reiterate to workers’ compensation stakeholders the importance of returning a worker to work as soon as practicable, to avoid future delays or challenges.KEY MESSAGESWhat is already known about this subject?LBP is a prevalent musculoskeletal symptom the leading contributor to the burden of disability for people of working age.Musculoskeletal conditions like LBP comprise the largest proportion of compensated conditions in Australia.What are the new findings?The incidence of claims for work-related LBP is higher than other work-related musculoskeletal conditions.Median time loss associated with a claim for LBP is similar to time loss for a claim for a limb fracture but less than for limb soft tissue disease claims.The likelihood of time loss duration is greater for workers with claims LBP than claims for limb fracture in the short term (seven weeks), but lower than limb fracture claims after this time.How might this impact on policy or clinical practice in the foreseeable future?Workers’ compensation stakeholders including clinicians, insurers, and workers’ compensation authorities should carefully consider the importance of returning a worker to work as soon as practicable to avoid future challenges, particularly for a condition as burdensome as LBP.
Prevalence and clinical features of 2019 novel coronavirus disease (COVID-19) in the Fever Clinic of a teaching hospital in Beijing: a single-center, retrospective study
Authors: Liang Ying , Liang Jingjin , Zhou Qingtao , Li Xiaoguang , Lin Fei , Deng Zhonghua , Zhang Biying , Li Lu , Wang Xiaohua , Zhu Hong , Ma Qingbian , Tong Xiaomei , Xu Jie , Sun Yongchang 
Published: February 2020

AbstractBackgroundWith the spread of COVID-19 from Wuhan, Hubei Province to other areas of the country, medical staff in Fever Clinics faced the challenge of identifying suspected cases among febrile patients with acute respiratory infections. We aimed to describe the prevalence and clinical features of COVID-19 as compared to pneumonias of other etiologies in a Fever Clinic in Beijing.MethodsIn this single-center, retrospective study, 342 cases of pneumonia were diagnosed in Fever Clinic in Peking University Third Hospital between January 21 to February 15, 2020. From these patients, 88 were reviewed by panel discussion as possible or probable cases of COVID-19, and received 2019-nCoV detection by RT-PCR. COVID-19 was confirmed by positive 2019-nCoV in 19 cases, and by epidemiological, clinical and CT features in 2 cases (the COVID-19 Group, n=21), while the remaining 67 cases served as the non-COVID-19 group. Demographic and epidemiological data, symptoms, laboratory and lung CT findings were collected, and compared between the two groups.FindingsThe prevalence of COVID-19 in all pneumonia patients during the study period was 6.14% (21/342). Compared with the non-COVID-19 group, more patients with COVID-19 had an identified epidemiological history (90.5% versus 32.8%, P<0.001). The COVID-19 group had lower WBC [5.19×109/L (±1.47) versus 7.21×109/L (±2.94), P<0.001] and neutrophil counts [3.39×109/L (±1.48) versus 5.38×109/L (±2.85), P<0.001] in peripheral blood. However, the count of lymphocytes was not different. On lung CT scans, involvement of 4 or more lobes was more common in the COVID-19 group (45% versus 16.4%, P=0.008).InterpretationIn the period of COVID-19 epidemic outside Hubei Province, the prevalence of COVID-19 in patients with pneumonia visiting our Fever Clinic in Beijing was 6.14%. Epidemiological evidence was important for prompt case finding, and lower blood WBC and neutrophil counts may be useful for differentiation from pneumonia of other etiologies.FundingNone.
It’s risky to wander in September: modelling the epidemic potential of Rift Valley fever in a Sahelian setting
Authors: Cecilia Hélène , Métras Raphaëlle , Fall Assane Gueye , Lo Modou Moustapha , Lancelot Renaud , Ezanno Pauline 
Published: February 2020

AbstractEstimating the epidemic potential of vector-borne diseases, along with the relative contribution of underlying mechanisms, is crucial for animal and human health worldwide. In West African Sahel, several outbreaks of Rift Valley fever (RVF) have occurred over the last decades, but uncertainty remains about the conditions necessary to trigger these outbreaks. We use the basic reproduction number (R0) as a measure of RVF epidemic potential in Northern Senegal, and map its value in two distinct ecosystems, namely the Ferlo and the Senegal river delta and valley. We consider three consecutive rainy seasons (July-November 2014, 2015 and 2016) and account for several vector and animal species. Namely, we parametrize our model with estimates of Aedes vexans arabiensis, Culex poicilipes, Culex tritaeniorhynchus, cattle, sheep and goats abundances. The impact of RVF virus introduction is assessed every week, in 4367 pixels of 3,5km2. The results of our analysis indicate that September was the month with highest epidemic potential in each study area, while at-risk locations varied between seasons. We show that decreased vector densities do not highly reduce R0 and that cattle immunity has a greater impact on reducing transmission than small ruminants immunity. The host preferences of vectors and the temperature-dependent time interval between their blood meals are crucial parameters needing further biological investigations.HighlightsSeptember is a period of high Rift Valley fever epidemic potential in northern Senegal regardless of the year, but exact locations where epidemics might start change between rainy seasons.Decreased vector densities during the rainy season did not highly reduce the epidemic potential of at-risk locations.High levels of immunity in cattle populations reduce more Rift Valley fever virus transmission than a high immunity in small ruminants in our study area. This aspect should be investigated further for targeted vaccination campaigns.Precise estimates of vector feeding preferences and the temperature-dependent lenght of their gonotrophic cycle are key to ensure a good detection of at-risk pixels.
High laboratory mouse pre-weaning mortality associated with litter overlap, advanced mother age, small and large litters
Authors: Morello Gabriela Munhoz , Hultgren Jan , Capas-Peneda Sara , Whiltshire Marc , Thomas Aurelie , Wardle-Jones Hannah , Brajon Sophie , Gilbert Colin , Olsson I. Anna S. 
Published: February 2020

AbstractHigh and variable pre-weaning mortality is a persistent problem among the main mouse strains used in biomedical research. If a modest 15% mortality rate is assumed across all mouse strains used in the EU, approximately 1 million more pups must be produced yearly to compensate for those which die. A few environmental and social factors have been identified as affecting pup mortality, but optimizing these factors does not cease the problem. This study is the first large study to mine data records from 219,975 pups from two breeding facilities to determine the major risk factors associated with mouse pre-weaning mortality. It was hypothesized that litter overlap (i.e. the presence of older siblings in the cage when new pups are born), a recurrent social configuration in trio-housed mice, is associated with increased newborn mortality, along with high mother age, large litter size, as well as a high number and age of older siblings in the cage. The estimated probability of pup death was two to seven percentage points higher in cages with compared to those without litter overlap. Litter overlap was associated with an increase in percentage of litter losses of 19% and 103%, respectively, in the two breeding facilities. Increased number and age of older siblings, high mother age, small litter size (less than four pups born) and large litter size (over 11 pups born) were associated with increased probability of pup death. Results suggest that common social cage configurations at breeding facilities are dangerous for the survivability of young mouse pups. The underlying mechanisms and strategies to avoid these situations should be further investigated.
Global Screening of Sentrin-Specific Protease Family Substrates in SUMOylation
Authors: Wang Yunzhi , Wu Xiaohui , Ge Rui , Song Lei , Li Kai , Tian Sha , Cai Lili , Liu Mingwei , Shi Wenhao , Yu Guoying , Zhen Bei , Wang Yi , He Fuchu , Qin Jun , Ding Chen 
Published: February 2020

AbstractPost-translational modification of proteins by the addition of small ubiquitin-related modifier (SUMO) is a dynamic process, in which deSUMOylation is carried out by members of the Sentrin/SUMO-specific protease (SENP) family. While identification of SUMOylation sites at global scale has made great progress, much less effort has been made on the SENP family-dependent deSUMOylation. Here we report a dataset of 3,763 high confident SUMO1 modification sites and their dependence on the 6 members of SENP proteins. Interrogation of the dataset led to the discovery that SENP3 regulates the innate immune response via deSUMOylation of DHX15 and PCBP2 and recruitment of inflammatory molecules. Collectively, this dataset presents a site-resolved network of the SUMO-SENP system, providing information for potential substrates of the SENP proteins.
Anxiety and the neurobiology of temporally uncertain threat anticipation
Authors: Hur Juyoen , Smith Jason F. , DeYoung Kathryn A. , Anderson Allegra S. , Kuang Jinyi , Kim Hyung Cho , Tillman Rachael M. , Kuhn Manuel , Fox Andrew S. , Shackman Alexander J. 
Published: February 2020

ABSTRACTWhen extreme, anxiety—a state of distress and arousal prototypically evoked by uncertain danger—can be debilitating. Uncertain anticipation is a shared feature of situations that elicit signs and symptoms of anxiety across psychiatric disorders, species, and assays. Despite the profound significance of anxiety for human health and wellbeing, the neurobiology of uncertain-threat anticipation remains unsettled. Leveraging a paradigm adapted from animal research and optimized for functional MRI signal decomposition, we examined the neural circuits engaged during the anticipation of temporally uncertain and certain threat in 99 men and women. Results revealed that the neural systems recruited by uncertain and certain threat anticipation are anatomically co-localized in fronto-cortical regions, extended amygdala, and periaqueductal gray. Comparison of the threat conditions demonstrated that this circuitry can be fractionated, with fronto-cortical regions showing relatively stronger engagement during the anticipation of uncertain threat, and the extended amygdala showing the reverse pattern. Although there is widespread agreement that the bed nucleus of the stria terminalis and dorsal amygdala—the two major subdivisions of the extended amygdala—play a critical role in orchestrating adaptive responses to potential danger, their precise contributions to human anxiety have remained contentious. Follow-up analyses demonstrated that these regions show statistically indistinguishable responses to temporally uncertain and certain threat anticipation. These observations provide a framework for conceptualizing anxiety and fear, for understanding the functional neuroanatomy of threat anticipation in humans, and for accelerating the development of more effective intervention strategies for pathological anxiety.SIGNIFICANCE STATEMENTAnxiety—an emotion prototypically associated with the anticipation of uncertain harm—has profound significance for public health, yet the underlying neurobiology remains unclear. Leveraging a novel neuroimaging paradigm in a relatively large sample, we identify a core circuit responsive to both uncertain and certain threat anticipation, and show that this circuitry can be fractionated into subdivisions with a bias for one kind of threat or the other. The extended-amygdala occupies center-stage in neuropsychiatric models of anxiety, but its functional architecture has remained contentious. Here we demonstrate that its major subdivisions show statistically indistinguishable responses to temporally uncertain and certain threat. Collectively, these observations indicate the need to revise how we think about the neurobiology of anxiety and fear.RESOURCE SHARINGRaw data are available at the National Institute of Mental Health’s Data Archive. Key statistical maps are or will be publicly available at NeuroVault.org.
Effective Biophysical Modeling of Cell Free Transcription and Translation Processes
Authors: Adhikari Abhinav , Vilkhovoy Michael , Vadhin Sandra , Lim Ha Eun , Varner Jeffrey D. 
Published: February 2020

AbstractTranscription and translation are at the heart of metabolism and signal transduction. In this study, we developed an effective biophysical modeling approach to simulate transcription and translation processes. We tested this approach by simulating the dynamics of two cell free synthetic circuits. First, we considered a simple circuit in which sigma factor 70 induced the expression of green fluorescent protein. This relatively simple case was then followed by a more complex negative feedback circuit in which two control genes were coupled to the expression of a third reporter gene, green fluorescent protein. While many of the model parameters were estimated from previous biophysical literature, the remaining unknown model parameters for each circuit were estimated from messenger RNA (mRNA) and protein measurements using multi-objective optimization. In particular, either the literature parameter estimates were used directly in the model simulations, or characteristic literature values were used to establish feasible ranges for the multiobjective parameter search. Next, global sensitivity analysis was used to determine the influence of individual model parameters on the expression dynamics. Taken together, the effective biophysical modeling approach captured the expression dynamics, including the transcription dynamics, for the two synthetic cell free circuits. While we considered only two circuits here, this approach could potentially be extended to simulate other genetic circuits in both cell free and whole cell biomolecular applications. The model code, parameters, and analysis scripts are available for download under an MIT software license from the Varnerlab GitHub repository.
Methods for High Fidelity Spectral Data Collection for Generating Ground Truth Data for Simulated Tissues
Authors: Gong Alex T. , Dulal Arjun , Crane Matthew M. , Reihsen Troy E. , Sweet Robert M. , Mendenhall Alexander R. 
Published: February 2020

ABSTRACTOur research is focused on creating and simulating hyper-realistic artificial human tissue analogues. Generation and simulation of macroscopic biological material depends upon accurate ground-truth data on spectral properties of materials. Here, we developed methods for high fidelity spectral data collection using two differently colored simulated skin tissue samples and a portable spectral imaging camera. Using the standard procedure, we developed, we quantified the reproducibility of the spectral image signatures of the two synthetic skin samples under natural and artificial lighting conditions commonly found in clinical settings. We found high coefficients of determination for all measures taken under the same lighting. As expected, we found the spectral image signature of each sample was dependent on the illumination source. Our results confirm that illumination spectra data should be included with spectral image data. The high-fidelity methods for spectral image data collection we developed here should facilitate accurate collection of spectral image signature data for gross biological samples and synthetic materials collected under the same illumination source.
Top-down Control of Inhibition Reshapes Neural Dynamics Giving Rise to a Diversity of Computations
Authors: Chen Zhen , Padmanabhan Krishnan 
Published: February 2020

AbstractGrowing evidence shows that top-down projections from excitatory neurons in higher brain areas selectively synapse onto local inhibitory interneurons in sensory systems. While this connectivity is conserved across sensory modalities, the role of this feedback in shaping the dynamics of local circuits, and the resultant computational benefits it provides remains poorly understood. Using rate models of neuronal firing in a network consisting of excitatory, inhibitory and top-down populations, we found that changes in the weight of feedback to inhibitory neurons generated diverse network dynamics and complex transitions between these dynamics. Additionally, modulation of the weight of top-down feedback supported a number of computations, including both pattern separation and oscillatory synchrony. A bifurcation analysis of the network identified a new mechanism by which gamma oscillations could be generated in a model of neural circuits, which we termedTop-down control ofInhibitoryNeuronGamma (TING). We identified the unique roles that top-down feedback of inhibition plays in shaping network dynamics and computation, and the ways in which these dynamics can be deployed to process sensory inputs.Significance StatementThe functional role of feedback projections, connecting excitatory neurons in higher brain areas to inhibitory neurons in primary sensory regions, remains a fundamental open question in neuroscience. Growing evidence suggests that this architecture is recapitulated across a diverse array of sensory systems, ranging from vision to olfaction. Using a rate model of top-down feedback onto inhibition, we found that changes in the weight of feedback support both pattern separation and oscillatory synchrony, including a mechanism by which top-down inputs could entrain gamma oscillations within local networks. These dual functions were accomplished via a codimension-2 bifurcation in the dynamical system. Our results highlight a key role for this top-down feedback, gating inhibition to facilitate often diametrically different local computations.
Predicting missing links in global host-parasite networks
Authors: Farrell Maxwell J. , Elmasri Mohamad , Stephens David , Davies T. Jonathan 
Published: February 2020

AbstractParasites that infect multiple species cause major health burdens globally, but for many, the full suite of susceptible hosts is unknown. Predicting undocumented host-parasite associations will help expand knowledge of parasite host specificities, promote the development of theory in disease ecology and evolution, and support surveillance of multi-host infectious diseases. Analysis of global species interaction networks allows for leveraging of information across taxa, but link prediction at this scale is often limited by extreme network sparsity, and lack of comparable trait data across species.Here we use recently developed methods to predict missing links in global mammal-parasite networks using readily available data: network properties and evolutionary relationships among hosts. We demonstrate how these link predictions can efficiently guide the collection of species interaction data and increase the completeness of global species interaction networks.We amalgamate a global mammal host-parasite interaction network (>29,000 interactions) and apply a hierarchical Bayesian approach for link prediction that leverages information on network structure and scaled phylogenetic distances among hosts. We use these predictions to guide targeted literature searches of the most likely yet undocumented interactions, and identify empirical evidence supporting many of the top “missing” links.We find that link prediction in global host-parasite networks can accurately predict parasites of humans, domesticated animals, and endangered wildlife, representing a combination of published interactions missing from existing global databases, and potential but currently undocumented associations.Our study provides further insight into the use of phylogenies for predicting host-parasite interactions, and highlights the utility of iterated prediction and targeted search to efficiently guide the collection of host-parasite interaction. These data are critical for understanding the evolution of host specificity, and may be used to support disease surveillance through a process of predicting missing links, and targeting research towards the most likely undocumented interactions.
Expressions for Bayesian confidence of drift diffusion observers in dynamic stimuli tasks
Authors: Calder-Travis Joshua , Bogacz Rafal , Yeung Nick 
Published: February 2020

AbstractWe introduce a new approach to modelling decision confidence, with the aim of enabling computationally cheap predictions while taking into account, and thereby exploiting, trial-by-trial variability in dynamic stimuli. Using the framework of the drift diffusion model of decision making, along with time-dependent thresholds and the idea of a Bayesian confidence readout, we derive expressions for the probability distribution over confidence reports. In line with current models of confidence, the derivations allow for the accumulation of “pipeline” evidence that has been received but not processed by the time of response, the effect of drift rate variability, and metacognitive noise. The expressions are valid for stimuli that change over the course of a trial with normally-distributed fluctuations in the evidence they provide. A number of approximations are made to arrive at the final expressions, and we test all approximations via simulation. The derived expressions contain only a small number of standard functions, and require evaluating only once per trial, making trial-by-trial modelling of confidence data in dynamic stimuli tasks more feasible. We conclude by using the expressions to gain insight into the confidence of optimal observers, and empirically observed patterns.