bluuebunny/crossref_metadata_2025_split huggingface dataset:
Decoding face recognition abilities in the human brain
Authors: Faghel-Soubeyrand Simon , Ramon Meike , Bamps Eva , Zoia Matteo , Woodhams Jessica , Richoz Anne-Raphaelle , Caldara Roberto , Gosselin Frédéric , Charest Ian 
Published: March 2022

AbstractWhy are some individuals better at recognising faces? Uncovering the neural mechanisms supporting face recognition ability has proven elusive. To tackle this challenge, we used a multi-modal data-driven approach combining neuroimaging, computational modelling, and behavioural tests. We recorded the high-density electroencephalographic brain activity of individuals with extraordinary face recognition abilities—super-recognisers—and typical recognisers in response to diverse visual stimuli. Using multivariate pattern analyses, we decoded face recognition abilities from 1 second of brain activity with up to 80% accuracy. To better understand the mechanisms subtending this decoding, we compared computations in the brains of our participants with those in artificial neural network models of vision and semantics, as well as with those involved in human judgments of shape and meaning similarity. Compared to typical recognisers, we found stronger associations between early brain computations of super-recognisers and mid-level computations of vision models as well as shape similarity judgments. Moreover, we found stronger associations between late brain representations of super-recognisers and computations of the artificial semantic model as well as meaning similarity judgments. Overall, these results indicate that important individual variations in brain processing, including neural computations extending beyond purely visual processes, support differences in face recognition abilities. They provide the first empirical evidence for an association between semantic computations and face recognition abilities. We believe that such multi-modal data-driven approaches will likely play a critical role in further revealing the complex nature of idiosyncratic face recognition in the human brain.SignificanceThe ability to robustly recognise faces is crucial to our success as social beings. Yet, we still know little about the brain mechanisms allowing some individuals to excel at face recognition. This study builds on a sizeable neural dataset measuring the brain activity of individuals with extraordinary face recognition abilities—super-recognisers—to tackle this challenge. Using state-of-the-art computational methods, we show robust prediction of face recognition abilities in single individuals from a mere second of brain activity, and revealed specific brain computations supporting individual differences in face recognition ability. Doing so, we provide direct empirical evidence for an association between semantic computations and face recognition abilities in the human brain—a key component of prominent face recognition models.
Unsupervised approach to decomposing neural tuning variability
Authors: Zhu Rong , Wei Xue-Xin 
Published: March 2022

AbstractNeural representation is often described by the tuning curves of individual neurons with respect to certain stimulus variables. Despite this tradition, it has become increasingly clear that neural tuning can vary substantially in accordance with a collection of internal and external factors. A challenge we are facing is the lack of appropriate methods to accurately capture trial-to-trial tuning variability directly from the noisy neural responses. Here we introduce an unsupervised statistical approach, Poisson functional principal component analysis (Pf-PCA), which identifies different sources of systematic tuning fluctuations, moreover encompassing several current models (e.g.,multiplicative gain models) as special cases. Applying this method to neural data recorded from macaque primary visual cortex– a paradigmatic case for which the tuning curve approach has been scientific essential– we discovered a novel simple relationship governing the variability of orientation tuning, which unifies different types of gain changes proposed previously. By decomposing the neural tuning variability into interpretable components, our method enables discovery of new structure of the neural code, capturing the influence of the stimulus drive and internal states simultaneously.
Exploiting deep transfer learning for the prediction of functional noncoding variants using genomic sequence
Authors: Chen Li , Wang Ye 
Published: March 2022

ABSTRACTMotivationThough genome-wide association studies have identified tens of thousands of variants associated with complex traits and most of them fall within the noncoding regions, they may not the causal ones. The development of high-throughput functional assays leads to the discovery of experimental validated noncoding functional variants. However, these validated variants are rare due to technical difficulty and financial cost. The small sample size of validated variants makes it less reliable to develop a supervised machine learning model for achieving a whole genome-wide prediction of noncoding causal variants.ResultsWe will exploit a deep transfer learning model, which is based on convolutional neural network, to improve the prediction for functional noncoding variants. To address the challenge of small sample size, the transfer learning model leverages both large-scale generic functional noncoding variants to improve the learning of low-level features and context-specific functional noncoding variants to learn high-level features toward the contextspecific prediction task. By evaluating the deep transfer learning model on three MPRA datasets and 16 GWAS datasets, we demonstrate that the proposed model outperforms deep learning models without pretraining or retraining. In addition, the deep transfer learning model outperforms 18 existing computational methods in both MPRA and GWAS datasets.Availabilityhttps://github.com/lichen-lab/TLVarSupplementary InformationSupplementary data are available at Bioinformatics online.Contactchen61@iu.edu
Environmental and genetic disease modifiers of haploinsufficiency of A20
Authors: Zammit Nathan W. , Gray Paul E. , Siggs Owen M. , Yap Jin Yan , Russell Amanda , Cultrone Daniele , Warren Joanna , Walters Stacey N. , Brink Robert , Zahra David , Burnett Deborah L. , Gayevskiy Velimir , Minoche Andre E. , Ziegler John B. , Craig Maria E. , Wong Melanie , Benitez-Aguirre Paul , Teo Juliana , Cowley Mark J. , Dinger Marcel E. , Tangye Stuart G. , Burke Catherine , Phan Tri G. , Goodnow Christopher C. , Grey Shane T. 
Published: March 2022

ABSTRACTMonogenic diseases can often manifest diverse clinical phenotypes and cause diagnostic dilemmas. While monoallelic loss-of-function variants in TNFAIP3 (Haploinsufficiency of A20; HA20) cause a highly penetrant autoinflammatory disease, the variable expressivity suggest a role for additional genetic and environmental disease modifiers. Here, we identify critically ill children who inherited a family-specific TNFAIP3 deletion from one of their otherwise healthy parents. Each of the probands also inherited in trans a subtle loss-of-function I207L TNFAIP3 variant that is common in Oceania, originally introgressed from Denisovans. Modelling this compound heterozgous state in mice under specific pathogen free conditions demonstrated a reduced threshold to break immune tolerance. Exaggerated immune responses were precipitated by inheriting the two genetic hits on the TNFAIP3 checkpoint coupled with increasing the microbial challenge to immune tolerance, either by co-housing with pet store mice carrying a wild microbial burden or by transient dietary exposure to a chemical that diminishes the intestinal mucin barrier separating gut microbes from immune sensing systems. These data illuminate second-hit genetic and environmental modifiers contributing to complex inflammatory and autoimmune disease. Increased mechanistic understanding of the presence and contribution of disease modifiers will aid diagnostic and prognostic patient stratification and potentially reveal novel therapeutic opportunities.
A Cambrian soft-bodied conical animal illustrates the origins of lophophorate phyla
Authors: Zeng Han , Chen Xiangyuan , Liu Yao , Zhu Maoyan , Zhao Fangchen , Yang Aihua 
Published: March 2022

AbstractThe origin and early evolution of lophotrochozoans remain a difficult but crucial issue in reconstructing metazoan phylogeny. Exceptionally preserved fossils have provided hopeful information for resolving this lophotrochozoan problem. Here we identify that Conicula striata, a soft-bodied conical animal from the early Cambrian Chengjiang Lagerstätte, has mosaic characteristics of different lophophorate phyla. C. striata possesses a phoronid-like vermiform trunk housing a U-shaped gut and a coiled lophophore comprising ≥12 arms with numerous tentacles, but it also bears brachiopod-like features including an undivided mantle enclosing lophophore and a pedicle-like protrusion on annulated trunk. Phylogenetic analysis retrieves C. striata as a total-group lophophorate and as an intermediate taxon between Phoronida and Brachiopoda. This suggests that the bivalved architecture of brachiopods originated from an undivided mantle in a phoronid-like ancestor, and that the ancestral vermiform trunk became reduced during the origin of Brachiopoda, illuminating the origins of body plans in the lophophorate phyla.
SER: an R package to compute environmental regime over a certain time period
Authors: Wu Naicheng , Guo Kun , Zou Yi , He Fengzhi , Riis Tenna 
Published: March 2022

SummaryEnvironmental regime (or environmental legacy or historical legacy) is the environmental dynamic characteristics over a given (either long or short) time period, such as frequency of mean or extreme events and rate of change, which might be masked by using only contemporary variables.We present SER, an R package for estimating environmental regimes for different environmental variables. Using the data included in the package, several examples are shown.SER is suitable for any types of environmental variables e.g., nutrient concentration, light, dissolved oxygen. In addition, by changing the argument “days_bf”, it is possible to compute environmental regimes in any interested time period, such as days, months or years.Our case study showed that inclusion of environmental regimes dramatically increased the explained variation of temporal β-diversity and its components. Environmental regimes, particularly in a given time period, are expected to advance the “environment - community” relationships in ecological studies. In addition, they can be implemented in other subjects, e.g., social science, socioeconomics, epidemiology, with important applied implications.
Epidemiology and medical costs of orthopedic conditions in a tertiary hospital in Kenya; A five-year analysis of admission data
Authors: Kihuba Elesban 
Published: March 2022

AbstractBackgroundOrthopedic services are a key component of the surgical healthcare system. Scaling up these services would not only reduce the musculoskeletal diseases burden but also the overall disease burden significantly. As such quality intelligence on epidemiology and costs of orthopedic services should be accurately represented for guiding effective policy formulation and implementation.AimThe aim of the study was to provide a snapshot of the pattern of orthopedic admissions, care and associated medical costs in Kenya.MethodsA retrospective study was conducted reviewing case files of patients admitted to the orthopedic department from 1st January 2015 to 30st November 2019.ResultsThere were 4320 distinct musculoskeletal admission diagnoses among the 3527 admissions. The study shows that trauma accounts for 53.04% of all admissions while joint replacement, shoulder and knee, limb deformities, infection, removal of hardware, ankle and foot and tumour procedures accounts for 15.01%, 8.87%, 7.29%, 6.44%, 3.94% and 3.23% respectively. Joint replacement is the leading diagnosis among patients in the 61 to 75 years age group and fragility fractures and posttraumatic arthritis featured prominently as the key reasons for joint reconstruction. The proportion of admissions with health insurance (60.82%) was exceptionally high compared to the national average (19.59%). However, current financing mechanism provide inadequate social protection against cost of orthopedic surgery.ConclusionThe case volume and mix highlight the growing importance of trauma, fragility fractures and degenerative joint diseases in orthopedic care in developing country set up. Overall, the observed model of care and associated outcome and costs provide a blueprint for orthopedic system development.
A Systematic Review of Human Challenge Trials, Designs, and Safety
Authors: Adams-Phipps Jupiter , Toomey Danny , Więcek Witold , Schmit Virginia , Wilkinson James , Scholl Keller , Jamrozik Euzebiusz , Osowicki Joshua , Roestenberg Meta , Manheim David 
Published: March 2022

AbstractBackgroundThere exists no prior systematic review of human challenge trials (HCTs) that focuses on participant safety. Key questions regarding HCTs include how risky such trials have been, how often adverse events (AEs) and serious adverse events (SAEs) occur, and whether risk mitigation measures have been effective.MethodsA systematic search of PubMed and PubMed Central for articles reporting on results of HCTs published between 1980 and 2021 was performed and completed by 10/7/2021.ResultsOf 2,838 articles screened, 276 were reviewed in full. 15,046 challenged participants were described in 308 studies that met inclusion criteria. 286 (92.9%) of these studies reported mitigation measures used to minimize risk to the challenge population. Among 187 studies which reported on SAEs, 0.2% of participants experienced at least one challenge-related SAE. Among 94 studies that graded AEs by severity, challenge-related AEs graded “severe” were reported by between 5.6% and 15.8% of participants. AE data were provided as a range to account for unclear reporting. 80% of studies published after 2010 were registered in a trials database.ConclusionsHCTs are increasingly common and used for an expanding list of diseases. Although AEs occur, severe AEs and SAEs are rare. Reporting has improved over time, though not all papers provide a comprehensive report of relevant health impacts. From the available data, most HCTs do not lead to a high number of severe symptoms or SAEs. This study was preregistered on PROSPERO as CRD42021247218.
CMLD-2 Attenuates Myofibroblast Activation and Bleomycin-Induced Pulmonary Fibrosis in Mice through Antagonizing ELAVL1-Mediated Osteopontin mRNA Stabilization
Authors: Qiongya Guo , Hongyan Ren , Meng Li , Lifan Liu , Wenting Li , Jingjing Zhang , Xiaoli Wang , Yiping Hu , Kaixuan Zang , Yunxia An , Lin Li , Li Wei , Zhiwei Xu , Zhiping Guo , Costabel Ulrich , Xiaoju Zhang , Zheng Wang 
Published: March 2022

AbstractBackgroundFibroblast-myofibroblasts transition (FMT) is one of the hallmark cellular processes in pulmonary fibrosis. This study is to investigate the effects of CMLD-2 in FMT and pulmonary fibrosis, which antagonizes HuR, a supposedly key regulatory RNA binding protein (RBP).MethodsHuR or other deferentially expressed RBPs during TGF-β1-induced FMT were analyzed by transcriptomic methods, and further validatedin vitroor in fibrotic lung specimens. The effects of HuR overexpression, down-regulation or inhibition by an antagonist CMLD-2 were analyzed in FMT or bleomycin-induced experimental lung fibrosis. HuR-targeting RNA and their interactions were analyzed by CLIP-seq.ResultsHuR, hnRNPA1, hnRNPE1, TIA1 and TFRC were significantly up-regulated, while ESRP1, ESRP2 and TTP were significantly down-regulated. Cytoplasmic expression of HuR was activated in IPF lung tissue and rat lungs of bleomycin-induced fibrosis. HuR overexpression induced α-SMA and collagen I expression, increased the proliferation and migration capacities of fibroblasts with or without the stimulation of TGF-β1. HuR knockdown by shRNA inhibited the proliferation, transition, collagen production and migration properties in fibroblasts or in TGF-β1-stimulated myofibroblasts. Combinative analysis of RNA-seq and CLIP-seq data revealed major HuR binding motifs and several HuR-bound, differentially expressed mRNAs in FMT, specifically SPP1 mRNA encoding osteopontin. HuR-mediated SPP1 mRNA stabilization was further validated by RIP-PCR and half-life analysis using SPP1 mutant transcripts. Inhibiting HuR using CMLD-2 attenuated SPP1/osteopontin expression, TGF-β1-induced FMTin vitroand bleomycin-induced pulmonary fibrosis in mice. Nuclear-cytoplasmic shuttle of HuR was activated in TGF-β1-induced FMT, which was inhibited by p38MAPK (SB203580) or PKC (Go-6976) inhibition, but not associated with phosphorylation of HuR.ConclusionsFibroblast-myofibroblast transition is activated by HuR-SPP1 mRNA interactions, and CMLD-2 is potentiated to be a therapeutic agent targeting HuR for fibroblast-myofibroblast transition and pulmonary fibrosis.
Short-term and bystander effects of radiation on murine submandibular glands
Authors: Uchida Hitoshi , Ingalls Matthew H. , Maruyama Eri O. , Johnston Carl J. , Hernady Eric , Faustoferri Roberta C. , Ovitt Catherine E. 
Published: March 2022

AbstractMany patients treated for head and neck cancers experience salivary gland hypofunction due to radiation damage. Understanding the mechanisms of cellular damage induced by radiation treatment is important in order to design methods of radioprotection. In addition, it is crucial to recognize the indirect effects of IR and the systemic responses that may alter saliva secretion. In this study, radiation was delivered to murine submandibular glands (SMG) bilaterally, using a 137Cs gamma ray irradiator, or unilaterally, using a small animal radiation research platform (SARRP). Analysis at 3, 24 and 48 hours showed dynamic changes in mRNA levels and protein abundance in SMG irradiated bilaterally. Unilateral irradiation using the SARRP caused similar changes in the irradiated SMG, as well as significant off-target, bystander effects in the non-irradiated contralateral SMG.Summary statementRapid changes in gene expression occur in irradiated salivary glands within hours of irradiation, and in non-irradiated contralateral glands, due to bystander effects.
Combination of the Systemin peptide with the beneficial fungus Trichoderma afroharzianum T22 improves plant defense responses against pests and diseases
Authors: Maria Aprile Anna , Mariangela Coppola , David Turrà , Stefania Vitale , Pasquale Cascone , Gianfranco Diretto , Alessia Fiore , Valeria Castaldi , Alessadra Romanelli , Concetta Avitabile , Emilio Guerrieri , Lois Woo Sheridan , Rosa Rao 
Published: March 2022

AbstractTrichoderma spp. are among the most widely used plant beneficial fungi in agriculture. A novel approach to enhance their effectiveness in plant defense is to use the fungi in combination with bioactive molecules including plant-derived compounds. Here, we show that plant treatment with Trichoderma afroharzianum (strain T22) and Systemin (Sys), a tomato plant peptide active in triggering plant defense, confers protection against the fungal pathogens Fusarium oxysporum, Botrytis cinerea and the insect pest Tuta absoluta. The observed defensive response was associated with increased accumulation of metabolites and transcripts involved in the Jasmonic acid (JA) pathway. Our findings suggest that the innovative combination of T. afroharzianum T22 and Sys can result in a more effective and robust control of different biotic stress agents.
Sexual selection moderates heat stress response in males and females
Authors: Moiron Maria , Winkler Lennart , Martin Oliver Yves , Janicke Tim 
Published: March 2022

AbstractA widespread effect of climate change is the displacement of organisms from their thermal optima. The associated thermal stress imposed by climate change has been argued to have a particularly strong impact on male reproduction but evidence for this postulated sex-specific stress response is equivocal. One important factor that may explain intra- and interspecific variation in stress responses is sexual selection, which is predicted to magnify negative effects of stress. Nevertheless, empirical studies exploring the interplay of sexual selection and heat stress are still scarce. We tested experimentally for an interaction between sexual selection and thermal stress in the red flour beetle Tribolium castaneum by contrasting heat responses in male and female reproductive success between setups of enforced monogamy versus polygamy. We found that polygamy magnifies detrimental effects of heat stress in males but relaxes the observed negative effects in females. Our results suggest that sexual selection can reverse sex differences in thermal sensitivity, and may therefore alter sex-specific selection on alleles associated with heat tolerance. We argue that these findings have important implications for predicting the role of sexual selection for the adaptation to current global warming and increased frequency of extreme climatic events.
RAD52 underlies the synthetic-lethal relationship between BRCA1/2 and 53BP1 deficiencies and DNA polymerase theta loss
Authors: Starowicz Katarzyna , Ronson George , Anthony Elizabeth , Clarke Lucy , Garvin Alexander J. , Beggs Andrew D , Whalley Celina M , Edmonds Matthew , Beesley James , Morris Joanna R 
Published: March 2022

Introductory paragraphCells lacking several DNA repair proteins, including those promoting homologous recombination (HR), are sensitive to polymerase theta (Polθ) repression1–4. Polθ drives theta-mediated end joining (TMEJ) and suppresses HR but what mediates its synthetic lethal relationships is unclear. Here we examine murine Brca1C61G/C61G 53bp1-/-cells and find they are largely HR proficient by using RNF168 and RAD52. They exhibit no more TMEJ than 53bp1-/- cells yet are more sensitive to targeting of Polθ. We find that RAD52 recruitment to damaged chromatin is increased following Polθ depletion. RAD52 accumulation and cellular sensitivity to Polθ repression can be curbed by the RAD51-binding regions of BARD1 and BRCA2, and sensitivity of BRCA1/2 depleted cells to Polθ repression is suppressed by RAD52 inhibition. 53bp1-/- cells exhibit a smaller increase in RAD52 recruitment following Polθ repression and also become resistant to Polθ repression following RAD52 inhibition. Thus, RAD52 mediates sensitivity to targeting Polθ in these contexts.