bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Delaware Pain Database: a set of painful expressions and corresponding norming data
Authors: Mende-Siedlecki Peter , Qu-Lee Jennie , Lin Jingrun , Drain Alexis , Goharzad Azaadeh 
Published: October 2020

Abstract

Introduction:
Facial expressions of pain serve an essential social function by communicating suffering and soliciting aid. Accurate visual perception of painful expressions is critical because the misperception of pain signals can have serious clinical and social consequences. Therefore, it is essential that researchers have access to high-quality, diverse databases of painful expressions to better understand accuracy and bias in pain perception.

Objectives:
This article describes the development of a large-scale face stimulus database focusing on expressions of pain.

Methods:
We collected and normed a database of images of models posing painful facial expressions. We also characterized these stimuli in terms of the presence of a series of pain-relevant facial action units. In addition to our primary database of posed expressions, we provide a separate database of computer-rendered expressions of pain that may be applied to any neutral face photograph.

Results:
The resulting database comprises 229 unique (and now publicly available) painful expressions. To the best of our knowledge, there are no existing databases of this size, quality, or diversity in terms of race, gender, and expression intensity. We provide evidence for the reliability of expressions and evaluations of pain within these stimuli, as well as a full characterization of this set along dimensions relevant to pain such as perceived status, strength, and dominance. Moreover, our second database complements the primary set in terms of experimental control and precision.

Conclusion:
These stimuli will facilitate reproducible research in both experimental and clinical domains into the mechanisms supporting accuracy and bias in pain perception and care.
Sexual dysfunction following traumatic pelvic fracture
Authors: Johnsen Niels V. , Cohn Eliza , Johnson Tascha , Vavilala Monica S. , Rivara Frederick P. , Moore Megan 
Published: October 2020

BACKGROUND
While sexual dysfunction (SD) in men following traumatic pelvic fracture is common, little is known of how men experience changes in their sexual health after injury. The aims of the present study were to explore the personal and interpersonal impacts of SD in men after pelvic injury and to understood how interactions with the health care system can be optimized to improve patient-centered trauma survivorship care.

METHODS
Fifteen semistructured interviews were conducted with men who had a history of traumatic pelvic fracture and self-reported SD. Interviews were audio recorded, transcribed, and uploaded to a web-based qualitative analysis platform. A codebook was developed, and intercoder reliability was verified. Inductive thematic analysis was performed to identify notable themes related to patient postinjury sexual health experiences.

RESULTS
Median age of interviewees was 46 years (interquartile range, 44–54 years), with a median time since injury of 41 months (interquartile range, 22–55 months). Five primary themes were identified from the analysis: (1) effects on self-image and romantic relationships, (2) unknown care pathways and lack of communication, (3) inconsistencies with health care provider priorities, (4) provision of sexual health information and resources, and (5) the importance of setting expectations. Interviewees suggested that improved communication, provision of information related to possible adverse effects of their injuries, and expectation setting would improve posttrauma experiences.

CONCLUSION
Men’s experiences with SD after pelvic trauma can be heavily influenced by their interactions with health care providers and the value that is placed on sexual health as a component of survivorship. Incorporating these findings into a patient-centered trauma survivorship program may improve patient experiences.

LEVEL OF EVIDENCE
Therapeutic, level V.
Deforestation reduces the genetic structure of an epiphytic weed across space and time: an IBM approach
Authors: Chaves Cleber Juliano Neves , Leal Bárbara Simões Santos , Rossatto Davi Rodrigo , Berger Uta , Palma-Silva Clarisse 
Published: October 2020

AbstractDeforestation has allowed the massive dispersal and reproduction of some plants that are commonly referred to as weeds. The rapid spread of many weeds into newly disturbed landscapes is often boosted by clonal growth and self-fertilization strategies, which conversely increases the spatial genetic structure (SGS) of populations and reduces the genetic diversity. Here, we use empirical and modeling approaches to evaluate the spatio-temporal SGS dynamics ofTillandsia recurvata(L.) L., a common epiphytic weed with selfing reproduction and clonal growth widespread in dry forests and anthropically deforested landscapes in North and South America. We constructed an individual-based model (IBM) and adjusted the parameters according to empirical genetic data, to simulate the spreading ofT. recurvataover time and across random landscapes with distinct tree densities. From empirical data, we observed a strong SGS amongT. recurvatasubpopulations hosted on neighbor trees and a contemporary spread from several population sources. Our model shows that the highest SGS appear in landscapes with more than 200 trees/ha and up to the 5thyear of colonization of open landscapes (ca. 100 trees/ha) when SGS starts to reduce drastically. These results suggest that the deforestation commonly observed in anthropically transformed landscapes may reduce the dispersal limitation and genetic structure ofT. recurvatasubpopulations, creating suitable conditions for the rapid spread ofT. recurvatafrom multiple surrounding sources. The combination of clonal growth and self-fertilization with the optimal conditions created by anthropogenic transformations may explain the spreading success ofT. recurvataand other weeds into new landscapes. Our results indicate that the drastic reductions in tree densities induced by human-modifications in natural landscapes may lead to a partial loss of resistance for dispersal by wind and increased the conditions forT. recurvatato develop massive populations in anthropogenic landscapes.
Screening and potent applicability analysis of commonly used pesticides against desert locust: an integrative entomo-informatics approach
Authors: Banik Anik , Mondal Md. Fuad , Khan Md. Mostafigur Rahman , Ahmed Sheikh Rashel , Hasan Md. Mehedi 
Published: October 2020

AbstractThe locust problem is a global threat for food security. Locusts can fly and migrate overseas within a zip and creating a large-scale devastation to the diversified agro-ecosystem. GIS based analysis showed the recent movement of locusts, among themSchistocerca gregariaandLocusta migratoriaare predominant in Indian subcontinent and are found more notorious and devastating one. This devastation needs to be stopped to save human race from food deprivation. In our study, we screened some commonly used agricultural pesticides and strongly recommended three of themviz. biphenthrin, diafenthiuron and silafluofen which might be potential to control the desert locusts based on their binding affinity towards the locust’s survival proteins. Our phylogenetic analysis reveals that these three recommended pesticides might also show potency to the other locust species as well as they are also way safer than the other commercially available pesticides. These proposed pesticide’s bioactive analogs from fungus and bacteria may also show efficacy as next generation controlling measures of locust as well as different kind of pests. These recommended pesticides are expected to be highly effective against locusts and needs to bring forward by the entomologists’ by performing experimental field trials.HighlightsGIS map unmasked the 2020 migratory pattern of locusts which now predominant towards Indian subcontinent.Biphenthrin, diafenthiuron and silafluofen showed maximum binding affinity.Biphenthrin and diafenthiuron were relatively safer than silafluofen.Bioactive analogs from fungus and bacteria could be an alternative to control locusts.Pesticides inhibition hotspots for desert locusts were unrevealed.
TRAPID 2.0: a web application for taxonomic and functional analysis ofde novotranscriptomes
Authors: Bucchini François , Del Cortona Andrea , Kreft Łukasz , Botzki Alexander , Van Bel Michiel , Vandepoele Klaas 
Published: October 2020

ABSTRACTAdvances in high-throughput sequencing have resulted in a massive increase of RNA-Seq transcriptome data. However, the promise of rapid gene expression profiling in a specific tissue, condition, unicellular organism, or microbial community comes with new computational challenges. Owing to the limited availability of well-resolved reference genomes,de novoassembled (meta)transcriptomes have emerged as popular tools for investigating the gene repertoire of previously uncharacterized organisms. Yet, despite their potential, these datasets often contain fragmented or contaminant sequences, and their analysis remains difficult. To alleviate some of these challenges, we developed TRAPID 2.0, a web application for the fast and efficient processing of assembled transcriptome data. The initial processing phase performs a global characterization of the input data, providing each transcript with several layers of annotation, comprising structural, functional, and taxonomic information. The exploratory phase enables downstream analyses from the web application. Available analyses include the assessment of gene space completeness, the functional analysis and comparison of transcript subsets, and the study of transcripts in an evolutionary context. A comparison with similar tools highlights TRAPID’s unique features. Finally, analyses performed within TRAPID 2.0 are complemented by interactive data visualizations, facilitating the extraction of new biological insights, as demonstrated with diatom community metatranscriptomes.
Does increased gait variability improve stability when faced with an expected balance perturbation during treadmill walking?
Authors: Nestico Jacqueline , Novak Alison , Perry Stephen D. , Mansfield Avril 
Published: October 2020

AbstractBackgroundCurrently, there is uncertainty as to whether movement variability is errorful or exploratory.Research questionThis study aimed to determine if gait variability represents exploration to improve stability. We hypothesized that 1) spatiotemporal gait features will be more variable prior to an expected perturbation than during unperturbed walking, and 2) increased spatiotemporal gait variability pre-perturbation will correlate with improved stability post-perturbation.MethodsSixteen healthy young adults completed 15 treadmill walking trials within a motion simulator under two conditions: unperturbed and expecting a perturbation. Participants were instructed not to expect a perturbation for unperturbed trials, and to expect a single transient medio-lateral balance perturbation for perturbed trials. Kinematic data were collected during the trials. Twenty steps were recorded post-perturbation. Unperturbed and pre-perturbation gait variabilities were defined by the short- and long-term variabilities of step length, width, and time, using 100 steps from pre-perturbation and unperturbed trials. Paired t-tests identified between-condition differences in variabilities. Stability was defined as the number of steps to centre of mass restabilization post-perturbation. Multiple regression analyses determined the effect of pre-perturbation variability on stability.ResultsLong-term step width variability was significantly higher pre-perturbation compared to unperturbed walking (mean difference=0.28cm, p=0.0073), with no significant differences between conditions for step length or time variabilities. There was no significant relationship between pre-perturbation variability and post-perturbation restabilization.SignificanceIncreased pre-perturbation step width variability was neither beneficial nor detrimental to stability. However, the increased variability in medio-lateral foot placement suggests that participants adopted an exploratory strategy in anticipation of a perturbation.
Daily running enhances molecular and physiological circadian rhythms in skeletal muscle
Authors: Casanova-Vallve Nuria , Duglan Drew , Vaughan Megan E. , Handzlik Michal K. , Fan Weiwei , Yu Ruth T. , Liddle Christopher , Downes Michael , Delezie Julien , Mello Rebecca , Chan Alanna B. , Pariollaud Marie , Westermark Pål O. , Metallo Christian M. , Evans Ronald M. , Lamia Katja A. 
Published: October 2020

Structured AbstractObjectiveExercise is a critical component of a healthy lifestyle and a key strategy for the prevention and management of metabolic disease. Identifying molecular mechanisms underlying adaptation in response to chronic physical activity is of critical interest in metabolic physiology. Circadian rhythms broadly modulate metabolism, including muscle substrate utilization and exercise capacity. Here, we define the molecular and physiological changes induced across the daily cycle by voluntary low intensity daily exercise.MethodsWildtype c57BL6/J male and female mice were housed with or without access to a running wheel for six weeks. Maximum running speed was measured at four different zeitgeber times (ZTs, hours after lights on) using either electrical or manual stimulation to motivate continued running on a motorized treadmill. RNA isolated from plantaris muscles at six ZTs was sequenced to establish the impact of daily activity on genome-wide transcription. Patterns of gene expression were analyzed using Gene Set Enrichment Analysis (GSEA) and Detection of Differential Rhythmicity (DODR). Blood glucose, lactate, and ketones, and muscle and liver glycogen were measured before and after exercise.ResultsWe demonstrate that the use of mild electrical shocks to motivate running negatively impacts maximum running speed and describe a manual method to motivate running in rodent exercise studies. Using this method, we show that time of day influences the increase in exercise capacity afforded by six weeks of voluntary wheel running: when maximum running speed is measured at the beginning of the nighttime active period in mice, there is no measurable benefit from a history of daily voluntary running, while maximum increase in performance occurs at the end of the night. We show that daily voluntary exercise dramatically remodels the muscle circadian transcriptome. Finally, we describe daily rhythms in carbohydrate metabolism associated with the timedependent response to moderate daily exercise.ConclusionsCollectively, these data indicate that chronic nighttime physical activity dramatically remodels daily rhythms of muscle gene expression, which in turn support daily fluctuations in exercise performance.
Novel Asgard archaea phylum Hermodarchaeota degrade alkanes and aromatics via alkyl/benzyl-succinate synthase and benzoyl-CoA pathway
Authors: Zhang Jia-Wei , Dong Hong-Po , Hou Li-Jun , Liu Yang , Ou Ya-Fei , Zheng Yan-Ling , Han Ping , Liang Xia , Yin Guo-Yu , Wu Dian-Ming , Liu Min , Li Meng 
Published: October 2020

AbstractAsgard superphylum is composed of a group of uncultivated archaea that are deemed the closest relatives of eukaryotes. These archaea are widely distributed in anaerobic environments and suggested to be important players in carbon cycling of sediments. Alkanes and aromatics are refractory organic compounds and abundant in sediments. However, little is known about degradation of these compounds by Asgard archaea to date. Here, we describe a previously unrecognized archaeal phylum, Hermodarchaeota, affiliated with the Asgard superphylum. The genomes of these archaea were recovered in metagenomes from mangrove sediments, and were found to encode alkyl/benzyl-succinate synthases and their activating enzymes that are similar to those found in alkanes-degrading sulfate-reducing bacteria. Hermodarchaeota also encode enzymes for alkyl-coenzyme A and benzoyl-coenzyme A oxidation, and the Wood–Ljungdahl pathway, as well as nitrate reductases. Furthermore, transcripts for these enzymes have been frequently detected in metatranscriptomes from mangrove sediments. This indicates that members of this phylum are able to anaerobically oxidize alkanes and aromatic compounds, coupling the reduction of nitrate. Genes encoding 16S rRNA and alkyl/benzyl-succinate synthases analogous to those in Hermodarchaeota were identified in a range of marine and freshwater sediments. These findings suggest that Asgard archaea capable of degrading alkanes and aromatics via formation of alkyl/benzyl-substituted succinates are ubiquitous in sediments.
Diet unmasks genetic variants that regulate lifespan in outbred Drosophila
Authors: Pallares Luisa F. , Lea Amanda J. , Han Clair , Filippova Elena V. , Andolfatto Peter , Ayroles Julien F. 
Published: October 2020

AbstractEvolutionary theory suggests that lifespan-associated alleles should be purged from the gene pool, and yet decades of GWAS and model organism studies have shown they persist. Here, we address one potential explanation, the idea that the alleles that regulate lifespan do so only in certain contexts. We exposed thousands of outbred Drosophila to a standard and a high sugar diet. We then sequenced over 10,000 individuals and track genome-wide allele frequency changes over time, as these populations aged. We mapped thousands of lifespan-altering alleles, some associated with early vs late life tradeoffs, late-onset effects, and genotype-by-environment interactions. We find that lifespan-reducing alleles are most likely to be recently derived, have stronger effects on a high-sugar diet, consistent with the hypothesis that historically neutral or beneficial alleles can become detrimental in novel conditions. We also show that the gene midway, a regulator of lipid storage and ortholog of the lifespan-associated gene DGAT1 in mice, also regulates lifespan in Drosophila. Our results provide insight into the highly polygenic and context-dependent genetic architecture of lifespan, as well as the evolutionary processes that shape this key trait.
TIGIT-Fc Promotes Antitumour Immunity
Authors: Fu Wenyan , Lei Changhai , Zhao Jian , Hu Shi 
Published: October 2020

AbstractT cell immunoreceptor with Ig and ITIM domains (TIGIT) is a checkpoint receptor that mediates both T cell and natural killer (NK) cell exhaustion in tumours. An Fc-TIGIT fusion protein was shown to induce an immune-tolerance effect in a previous report, but the relevance of the TIGIT-Fc protein to tumour immunity is unknown. Here, we unexpectedly found that TIGIT-Fc promotes rather than suppresses tumour immunity. TIGIT-Fc treatment promoted the effector function of CD8+T and NK cells in several tumour-bearing mouse models. Additionally, TIGIT-Fc treatment resulted in potent T cell and NK-cell-mediated tumour reactivity, sustained memory-induced immunity in tumour re-challenge models, enhanced therapeutic effects via an antibody against PD-L1, and induction of Th1 development in CD4+T cells. TIGIT-Fc showed a potent antibody-dependent cell-mediated cytotoxicity (ADCC) effect but no intrinsic effect on tumour cell development. Our findings elucidate the unexpected role of TIGIT-Fc in tumour immune reprogramming, suggesting that TIGIT-Fc treatment alone or in combination with other checkpoint receptor blockers is a promising anticancer therapeutic strategy.
The incubation period of COVID-19: A scoping review and meta-analysis to aid modelling and planning
Authors: Banka Prakashini , Comiskey Catherine 
Published: October 2020

AbstractBackgroundAn accurate estimate of the distribution of the incubation period for COVID-19 is the foundational building block for modelling the spread of the SARS COV2 and the effectiveness of mitigation strategies on affected communities. Initial estimates were based on early infections, the aim of this study was to provide an updated estimate and meta-analysis of the incubation period distribution for COVID-19.MethodsThe review was conducted according to the PRISMA Scoping Review guidelines. Five databases were searched; CINAHL, MEDLINE, PUBMED, EMBASE, ASSIA, and Global Index Medicus for studies published between 1 January 2020 - 27 July 2020.ResultsA total of 1,084 articles were identified through the database searches and 1 article was identified through the reference screening of retrieved articles. After screening 64 articles were included. The studies combined had a sample of 45,151 people. The mean of the incubation periods was 6.71 days with 95% CIs ranging from 1 to 12.4 days. The median was 6 days and IQR ranging from 1.8 to 16.3. The resulting parameters for a Gamma Distribution modelling the incubation period were Γ(α, λ) = Γ(2.810,0.419) with mean, μ = α/λ.ConclusionGovernments are planning their strategies on a maximum incubation period of 14 days. While our results are limited to primarily Chinese research studies, the findings highlight the variability in the mean period and the potential for further incubation beyond 14 days. There is an ongoing need for detailed surveillance on the timing of self-isolation periods and related measures protecting communities as incubation periods may be longer.
Experience replay supports non-local learning
Authors: Liu Yunzhe , Mattar Marcelo G. , Behrens Timothy E J , Daw Nathaniel D. , Dolan Raymond J 
Published: October 2020

AbstractTo make effective decisions we need to consider the relationship between actions and outcomes. They are, however, often separated by time and space. The biological mechanism capable of spanning those gaps remains unknown. One promising, albeit hypothetical, mechanism involves neural replay of non-local experience. Using a novel task, that segregates direct from indirect learning, combined with magnetoencephalography (MEG), we tested the role of neural replay in non-local learning in humans. Following reward receipt, we found significant backward replay of non-local experience, with a 160 msec state-to-state time lag, and this replay facilitated learning of action values. This backward replay, combined with behavioural evidence of non-local learning, was more pronounced in experiences that were of greater benefit for future behavior, as predicted by theories of prioritization. These findings establish rationally targeted non-local replay as a neural mechanism for solving complex credit assignment problems during learning.One Sentence SummaryReverse sequential replay is found, for the first time, to support non-local reinforcement learning in humans and is prioritized according to utility.
HAP-multitag, a PET and positive MRI contrast nanotracer for the longitudinal characterization of vascular calcifications in atherosclerosis
Authors: Pellico Juan , Fernández-Barahona Irene , Ruiz-Cabello Jesús , Gutiérrez Lucía , Sánchez-Guisado María J. , Aiestarán-Zelaia Irati , Martínez-Parra Lydia , Rodríguez Ignacio , Bentzon Jacob , Herranz Fernando 
Published: October 2020

ABSTRACTVascular microcalcifications are associated with atherosclerosis plaque instability and, therefore, to increased mortality. Because of this key role, several imaging probes have been developed for theirin vivoidentification. Among them [18F]FNa is the gold standard, showing a large uptake in the whole skeleton. Here, we push the field towards the combined anatomical and functional early characterization of atherosclerosis. For that, we have developed HAP-multitag, a bisphosphonate-functionalized68Ga magnetic nanoparticle showing high affinity towards most common calcium salts present in microcalcifications, particularly hydroxyapatite. We characterized this interactionin vitroandin vivo, showing a massive uptake in the atherosclerotic lesion identified by PET and positive contrast MRI. In addition, this accumulation was found to be dependent on the calcification progression, with a maximum uptake in the microcalcification stage. These results confirmed the ability of HAP-multitag to identify vascular calcifications by PET/(T1)MRI during the vulnerable stages of the plaque progression.