bluuebunny/crossref_metadata_2025_split huggingface dataset:
A natural language fMRI dataset for voxelwise encoding models
Authors: LeBel Amanda , Wagner Lauren , Jain Shailee , Adhikari-Desai Aneesh , Gupta Bhavin , Morgenthal Allyson , Tang Jerry , Xu Lixiang , Huth Alexander G. 
Published: September 2022

AbstractSpeech comprehension is a complex process that draws on humans’ abilities to extract lexical information, parse syntax, and form semantic understanding. These sub-processes have traditionally been studied using separate neuroimaging experiments that attempt to isolate specific effects of interest. More recently it has become possible to study all stages of language comprehension in a single neuroimaging experiment using narrative natural language stimuli. The resulting data are richly varied at every level, enabling analyses that can probe everything from spectral representations to high-level representations of semantic meaning. We provide a dataset containing BOLD fMRI responses recorded while 8 subjects each listened to 27 complete, natural, narrative stories (~6 hours). This dataset includes pre-processed and raw MRIs, as well as hand-constructed 3D cortical surfaces for each participant. To address the challenges of analyzing naturalistic data, this dataset is accompanied by a python library containing basic code for creating voxelwise encoding models. Altogether, this dataset provides a large and novel resource for understanding speech and language processing in the human brain.
Polylactide Degradation Activates Immune Cells by Metabolic Reprogramming
Authors: Maduka Chima V. , Alhaj Mohammed , Ural Evran , Habeeb Michael O. , Kuhnert Maxwell M. , Smith Kylie , Makela Ashley V. , Pope Hunter , Chen Shoue , Hix Jeremy M. , Mallett Christiane L. , Chung Seock-Jin , Hakun Maxwell , Tundo Anthony , Zinn Kurt R. , Hankenson Kurt D. , Goodman Stuart B. , Narayan Ramani , Contag Christopher H. 
Published: September 2022

ABSTRACTPolylactide (PLA) is the most widely utilized biopolymer in medicine. However, chronic inflammation and excessive fibrosis resulting from its degradation remain significant obstacles to extended clinical use. Immune cell activation has been correlated to the acidity of breakdown products, yet methods to neutralize the pH have not significantly reduced adverse responses. Using a bioenergetic model, we observed delayed cellular changes that were not apparent in the short-term. Amorphous and semi-crystalline PLA degradation products, including monomeric L-lactic acid, mechanistically remodel metabolism in cells leading to a reactive immune microenvironment characterized by elevated proinflammatory cytokines. Selective inhibition of metabolic reprogramming and altered bioenergetics both reduce these undesirable high cytokine levels and stimulate anti-inflammatory signals. Our results present a new biocompatibility paradigm by identifying metabolism as a target for immunomodulation to increase tolerance to biomaterials, ensuring safe clinical application of PLA-based implants for soft- and hard-tissue regeneration, and advancing nanomedicine and drug delivery.
Genome-wide ribosome profiling uncovers the role of iron in the control of protein translation
Authors: Barlit Hanna , Romero Antonia M. , Gülhan Ali , Patnaik Praveen K. , Tyshkovskiy Alexander , Martínez-Pastor María T. , Gladyshev Vadim N. , Puig Sergi , Labunskyy Vyacheslav M. 
Published: September 2022

AbstractIron is an essential trace element that serves as a cofactor for enzymes involved in multiple metabolic pathways, including ribosome biogenesis, protein translation, DNA synthesis and repair, lipid metabolism, and mitochondrial oxidative phosphorylation. In eukaryotes, iron deficiency leads to global inhibition of protein synthesis and coordinated changes in gene expression to limit iron utilization. Although several steps of protein translation depend on iron-containing enzymes, the contribution of iron to the translation process is not understood at the molecular level. Here, we report a genome-wide analysis of protein translation in response to iron deficiency in yeast using ribosome profiling. We show that iron depletion affects global protein synthesis as well as leads to translational repression of several groups of genes involved in iron-related processes. We further demonstrate that the RNA-binding proteins Cth1 and Cth2 play a central role in controlling the changes in protein translation by repressing the activity of the iron-dependent Rli1 ribosome recycling factor, inhibiting mitochondrial translation, and affecting the translation of genes involved in heme biosynthesis. We also discovered a mechanism, whereby iron deficiency represses translation ofMRS3mRNA, encoding mitochondrial iron transporter, through increased expression of antisense long non-coding RNA. Together, our results reveal complex gene expression and protein synthesis remodeling in response to low iron showing how this important metal affects protein translation at multiple levels.
DPAM: A Domain Parser for AlphaFold Models
Authors: Zhang Jing , Schaeffer R. Dustin , Durham Jesse , Cong Qian , Grishin Nick V. 
Published: September 2022

AbstractThe recent breakthroughs in structure prediction, where methods such as AlphaFold demonstrated near atomic accuracy, herald a paradigm shift in structure biology. The 200 million high-accuracy models released in the AlphaFold Database are expected to guide protein science in the coming decades. Partitioning these AlphaFold models into domains and subsequently assigning them to our evolutionary hierarchy provides an efficient way to gain functional insights of proteins. However, classifying such a large number of predicted structures challenges the infrastructure of current structure classifications, including our Evolutionary Classification of protein Domains (ECOD). Better computational tools are urgently needed to automatically parse and classify domains from AlphaFold models. Here we present a Domain Parser for AlphaFold Models (DPAM) that can automatically recognize globular domains from these models based on predicted aligned errors, inter-residue distances in 3D structures, and ECOD domains found by sequence (HHsuite) and structural (DALI) similarity searches. Based on a benchmark of 18,759 AlphaFold models, we demonstrated that DPAM could recognize 99.5% domains and assign correct boundaries for 85.2% of them, significantly outperforming structure-based domain parsers and homology-based domain assignment using ECOD domains found by HHsuite or DALI. Application of DPAM to the massive set of AlphaFold models will allow for more efficient classification of domains, providing evolutionary contexts and facilitating functional studies.
Neotropical birds and mammals show divergent behaviour responses to human pressure
Authors: Negret Pablo Jose , Luskin Mathew Scott , Gomez-Valencia Bibiana , Diaz-Pulido Angelica , Romero Luis Hernando , Restrepo Adriana , Zaehringer Julie G. , Ochoa-Quintero Jose Manuel , Mendes Calebe Pereira 
Published: September 2022

AbstractHuman presence and habitat disturbance (together ‘human pressure’ hereafter) can generate a deep fear in animals and this can influence their behaviour. Altered animal behaviour, such as shifts in diel activity patterns, affect many species and species interactions, which can induce changes in individual fitness, species-level population persistence, evolutionary dynamics, and ecosystem-level biodiversity. However, whether dial activity behavioural responses to human pressure are consistent among key functional groups has been poorly studied. For example, while medium to large mammal species tend to become more nocturnal in areas with high human pressure, it’s unclear if sympatric/co-occurring birds display similar or opposite patterns. This is an important knowledge gap because synchronous or opposing guild-level shifts can shape consequences for food-web dynamics (predation and competition), stability of interaction networks and ecosystem functioning. Here we used information from camera trapping along a gradient of human pressure in the Colombian Llanos region to assess diel activity changes in birds and mammals. We found that the diel activity of over 45% of the bird and 50% of the mammals assessed significantly changed where there was higher human pressures, with mammals becoming more nocturnal and birds more diurnal. The opposing behavioural responses to humans among vertebrate functional groups has significant repercussions for the fields of community ecology, including intraguild predation and competition, and may be a significant ecosystem-level conservation consideration.
Study on the mechanism of HE4 in hyperoxia-induced alveolar damage in rats
Authors: Yan Xiaofang , Feng Xing , Gao Yan , Liu Dawei , Bai Lin , Xu Lu 
Published: September 2022

AbstractObjectiveThis study investigated the mechanism of human epididymis protein 4 (HE4) in hyperoxia-induced alveolar damage in rats.MethodsThe pathological changes of SD rat lung tissue were detected by hematoxylin-eosin staining. Plasma protein levels were measured by enzyme-linked immunosorbent assay (ELISA). The expression of mRNA was detected by real-time RT-PCR.ResultsHyperoxia intervention within 7 days could induce acute lung injury in neonatal SD rats. Hyperoxia induction can increase HE4, MMP9 and TIMP1 in plasma and tissue of neonatal SD rats. By overexpressing and silencing HE4 gene in neonatal rat primary alveolar type II epithelial cells, we found that HE4 protein activates the phosphorylation of ERK and p65, activates the downstream MMP9 signaling pathway, inhibits MMP9 mRNA expression, inhibits protein activity, and reduces COLI degradation, increases collagen secretion, promoting matrix remodeling and fibrosis.ConclusionHE4 mediates the pathophysiological process of hyperoxia-induced lung injury in rats through ERK, MMP9 and TIMP1 signaling pathways. HE4 overexpression mediates lung basal remodeling and lung injury.
National trends in rates of undiagnosed HIV in key populations in Australia: a retrospective observational analysis from 2008 to 2019
Authors: Gray Richard T. , Camara Hawa , Khawar Laila , Grulich Andrew , Guy Rebecca , McGregor Skye , Medland Nicholas 
Published: September 2022

AbstractIntroductionDetermining the proportion of people living with HIV who are undiagnosed is critical for Australia to accurately assess the country’s progress toward UNAIDS’ 95-95-95 interim targets by 2025 and progress with elimination goals. We aimed to investigate the utility of two additional measures, the Yearly Diagnosed Fraction, and the Case Detection Rate, in elucidating trends over time in the rate of undiagnosed HIV.MethodsUsing routinely collected national HIV surveillance data, we produced estimates for the number living with undiagnosed HIV and the number of new HIV infections using the European Centre for Disease Protection and Control (ECDC) HIV modelling tool to calculate the Total Diagnosed Fraction (TDF), the Yearly Diagnosed Fraction (YDF), and the Case Detection Rate (CDR) from 2008 to 2019 for Australian-born and overseas-born individuals who have reported having male-to-male sexual contact, and heterosexual women and men. We calculated rate ratios using Poisson Regression models to compare trends for each sub-population.ResultsOver 2008-2019, each metric for the Australian-born male-to-male sexual contact group improved consistently over the period with the case detection rate rising above one in 2013. The total diagnosed fraction for the overseas born group fell slightly from 85.0% to 81.9%, the yearly diagnosed fraction fell from 23.1% to 17.8% and the case detection rate stayed below one, falling from 0.74 to 0.63. In the heterosexual group, women and men had consistent increasing trends for the total diagnosed fraction and yearly diagnosed fraction but with women having consistently higher estimates than men, 92.6% vs 80.8% and 26.3% vs 17.4%, respectively in 2019. However, heterosexual men had a declining case detection rate, falling below one in 2019 (0.83), compared to an increase for women.ConclusionThe additional metrics presented provide important information on Australia’s progress toward HIV elimination. The more dynamic changes in the undiagnosed population seen highlight diverging trends for key populations with growing undiagnosed populations not seen in the total diagnosed fraction. Periodic trend analyses will help strengthen the use of the metrics and ease of interpretation for national surveillance reporting.
Natural ventilation, low CO2 and air filtration are associated with reduced indoor air respiratory pathogens
Authors: Raymenants Joren , Geenen Caspar , Budts Lore , Thibaut Jonathan , Thijssen Marijn , De Mulder Hannelore , Gorissen Sarah , Craessaerts Bastiaan , Laenen Lies , Beuselinck Kurt , Ombelet Sien , Keyaerts Els , André Emmanuel 
Published: September 2022

SummaryCurrently, the real-life impact of indoor climate, human behavior, ventilation and air filtration on respiratory pathogen detection and concentration are poorly understood. This hinders the interpretability of bioaerosol quantification in indoor air to surveil respiratory pathogens and transmission risk. We tested 341 indoor air samples from 21 community settings for 29 respiratory pathogens using qPCR. On average, 3.9 pathogens were positive per sample and 85.3% of samples tested positive for at least one. The number of detected pathogens and their respective concentrations varied significantly by pathogen, month, and age group in generalized linear (mixed) models and generalized estimating equations. High CO2 and low natural ventilation were independent risk factors for detection. CO2 concentration and air filtration were independently associated with their concentration. Occupancy, sampling time, mask wearing, vocalization, temperature, humidity and mechanical ventilation were not significant. Our results support the importance of ventilation and air filtration to reduce transmission.
Effects of exercise on sleep in children with overweight/obesity: A randomized clinical trial
Authors: Torres-Lopez Lucia V. , Migueles Jairo H. , Cadenas-Sanchez Cristina , Bendtsen Marcus , Henriksson Pontus , Mora-Gonzalez Jose , Löf Marie , Chaput Jean-Philippe , Ortega Francisco B. 
Published: September 2022

AbstractObjectivesTo examine 1) the chronic effects of a 20-week physical exercise program on device-assessed sleep and on sleep-disordered breathing (SDB); and 2) whether attending to a session of the exercise program had effects on device-assessed sleep the subsequent night in children with overweight/obesity.MethodsA total of 99 children with overweight/obesity (n=47 in the exercise group) participated in this secondary analysis of the ActiveBrains randomized clinical trial. The exercise program included a combination of aerobic and resistance exercise training, 3-5 days/week (90 min/session). The control group was asked to maintain usual lifestyle. Sleep outcomes were measured using wrist actigraphy and included: total sleep time, total time in bed, sleep efficiency, and wake after sleep onset (WASO) time. SDB was assessed via the Paediatric Sleep Questionnaire.ResultsThe ActiveBrains exercise program had a statistically significant effect on WASO time (−10.8 min/day, -0.5 standard deviations (SD), P=0.040). Furthermore, we observed a small non-statistically significant effect on sleep efficiency (+2%, 0.4 SD, P=0.1). No other chronic effects were observed on the other sleep outcomes. The nights (at maximum of 4) after attending the ActiveBrains exercise sessions, children showed higher total sleep time (+8 min, P=0.17), sleep efficiency (+1%, P=0.15), and lower WASO time (−6 min, P=0.18) although did not reach statistical significance.ConclusionA 20-week physical exercise program reduced WASO time in children with overweight/obesity in comparison with control group peers, yet we did not observe effects on SDB. Future randomized trials that include a clinical sample of children with poor sleep health at baseline are needed to better appreciate the role of exercise in sleep health.Clinal Trial RegistrationThe ActiveBrains project is registered at ClinicalTrials.gov, no. NCT02295072. Data Sharing Statement: We did not obtain children’s parents consent to widely share the data nor was it included in the IRB protocol.What’s known on this subjectSleep is an essential component in children’s health. Previous researchers have found positive effects of exercise on sleep in adolescents with obesity, but the literature in childhood obesity is lacking.What this study addsA physical exercise program showed positive effects on device-assessed sleep habits in children with overweight/obesity, yet not on sleep-disordered breathing. Exercise programs should be promoted in children to improve their sleep health, especially in those with overweight/obesity.
Psychological safety, hierarchy, and other issues in operating room debriefing: reflexive thematic analysis of interviews from the frontline
Authors: McElroy Canice , Skegg Emma , Mudgway Mercedes , Murray Ngaire , Holmes Linda , Weller Jennifer , Hamill James 
Published: September 2022

AbstractBackgroundDebriefing is a team discussion in a constructive, supportive environment. Barriers exist to consistent, effective, operative team debriefing.AimTo identify barriers to debriefing and their potential solutions as articulated by operating room personnel.DesignQualitative study.MethodsBetween December 2021 and February 2022 we interviewed operating room workers in a tertiary children’s hospital. We used purposive sampling to interview a variety of professions and specialties who work in the operating room environment. Interviews were audio-recorded, transcribed, and coded. The qualitative approach was reflexive thematic analysis with the theoretical framework was critical realism.ResultsInterviews were analysed from 40 operating room staff: 14 nurses,7 anaesthetic technicians, 7 anaesthetists, and 12 surgeons; 25 (62%) were female. The five key themes were: 1) “commitment to learning” – healthcare workers are committed to teamwork, quality improvement, and teamwork; 2) “it’s a safe space” – psychological safety is a pre-requisite for, and is enhanced by, debriefing; “natural born leader” – the value of leadership and also the limitations caused by psychological constructs about what and who is a leader; 4) “space-time” – finding time to debrief after routine operations and after critical events; and 5) “doing the basics well” – debriefing needs structure without being over-complicated.ConclusionPsychological safety is both a prerequisite for and a product of debriefing. Leadership, if viewed as a collective responsibility, could help break down power structures. Given the results of this study and evidence in the literature, it is likely that routine debriefing, if well done, will improve psychological safety, facilitate team learning, reduce errors, and improve patient safety.Relevance to Clinical PracticeDebriefing is challenging to perform, requires leadership and training, but is worth the effort. Nurses can take a leading role in promoting routine debriefing in healthcare.What does this paper contribute to the wider global clinical community?Debriefing, if done well, promotes teamwork, psychological safety in the workplace, quality and safety, and organisational learning.Setting up an effective debriefing programme is challenging but worth the effort.Debriefing requires collaboration and nurses are well placed to be leaders in debriefing policy design and to lead multidisciplinary debriefs.
Fully Quantitative Measurements of Differential Antibody Binding to Spike Proteins from Wuhan, Alpha, Beta, Gamma, Delta and Omicron BA.1 variants of SARS-CoV-2: Antibody Immunity Endotypes
Authors: James-Pemberton Philip H. , Kohli Shivali , Twynham Jordan , Westlake Aaron C. , Antill Alex , Hunt Jade , Olkhov Rouslan V. , Shaw Andrew M. 
Published: September 2022

AbstractA fully quantitative comparative analysis of the differential binding to spike variant proteins to SARS-CoV-2 has been performed for the variants: Wuhan (ancestral strain), Alpha, Beta, Gamma, Delta and Omicron BA.1. Evolution of immunity through five patient cohorts was studied including pre-pandemic, first infection, first vaccine, second vaccine and triple-vaccinated cohorts. A series of immunity endotypes has been observed: U(+) showing protection to all variants; single, double, triple, quadruple and quintuple dropout endotypes U(±); some with no variant protection other than Wuhan vaccine spike U(-); and some unclassified, U(∼). These endotypes may be imprinted. In the triple-vaccinated cohort (n = 54) there is a U(+) incidence of 65% (95% CI 51% - 76%) suggesting between half and three-quarters of the population have universal variant vaccine antibody protection; U(-) 6% (95% CI 2% - 15%) of the population have no variant antibody protection provided by the vaccine; and U(±)) with at least one dropout has a incidence of 20% (95% CI 12% - 33%). Extending the cohort incidence to the population, up to 76% of the population may have an imprinted immunity endotype to an epitope that is effective against all variants; critical for both protection and binding to the ACE2 receptor: a universal immunity endotype. However, up to 33% of the population may have an immunity endotype that will never produce an effective antibody response to SARS-CoV-2 unless the immunity imprint is broken.FundingExeter University Alumni, Attomarker Ltd funded PhD studentship at the University of Exeter and Attomarker Ltd funding directly.
A rapid protocol for ribosome profiling of low input samples
Authors: Meindl Andreas , Romberger Markus , Lehmann Gerhard , Eichner Norbert , Kleemann Leon , Wu Jie , Danner Johannes , Boesl Maria , Mesitov Mikhail , Meister Gunter , König Julian , Leidel Sebastian , Medenbach Jan 
Published: September 2022

AbstractRibosome profiling provides quantitative, comprehensive, and high-resolution snapshots of cellular translation by the high-throughput sequencing of short mRNA fragments that are protected from nucleolytic digestion by ribosomes. While the overall principle is simple, the workflow of ribosome profiling experiments is complex and challenging, and typically requires large amounts of sample, limiting its broad applicability. Here, we present a new protocol for ultra-rapid ribosome profiling from low-input samples. It features a robust strategy for sequencing library preparation within one day that employs solid phase purification of reaction intermediates, allowing to reduce the input to as little as 0.1 pmol of RNA. Hence, it is particularly suited for the analyses of small samples or targeted ribosome profiling. Its high sensitivity and its ease of implementation will foster the generation of higher quality data from small samples, which opens new opportunities in applying ribosome profiling.