bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nurse Resiliency and Health in Practicing Nurses Before and During COVID-19
Authors: Stallings Welden Lois M. , Chen Chen , Willegal-Russ Kate , Kalb Elizabeth 
Published: July 2023

OBJECTIVES
The aim of this study was to compare the degree of resilience and self-perceived physical and mental health in nurses before and during the COVID-19 pandemic.

BACKGROUND
Work-related stress among nurses is recognized as an antecedent of burnout, which in turn impacts resiliency and well-being. The work of nursing has long been noted as stressful. Although nurse resilience and perceived well-being have been shown to decrease during a period of usual stress (constant and chronic), the impact and significance of prolonged stress on nurse resilience and well-being illuminates throughout the literature.

METHODS
Replicating a cross-sectional prepandemic study, nurses were resurveyed in 2020 during the COVID-19 pandemic. In both studies, the Connor-Davidson Resilience Scale and PROMIS Global Health was used to measure respondent's: 1) resilience level; 2) physical health status; and 3) mental health status, respectively. Independent 2-sample t tests were performed to compare the pre-and-post score differences in the 3 outcomes. To identify characteristics that were associated with the pre-and-post differences, comparison analyses were also performed within each level of the respondents' characteristic variables.

RESULTS
A higher proportion of postsurvey respondents reported working more than 8 hours of overtime per week, had thoughts of quitting their current job, and thought their workload was too much compared with the presurvey respondents. Generally, the postgroup resilience scores and self-perceived physical and mental scores were statistically significantly lower compared with the pregroup scores, but those differences were only observed in certain subgroups defined by respondents' characteristics.

CONCLUSIONS AND IMPLICATIONS
Self-perceived physical and mental health are significantly associated with the degree of resilience and worsened during the COVID-19 pandemic, especially in younger and older nurse cohorts. Engaged nurse leaders are key to implement interventions that build resilience and perceived well-being during periods of usual and prolonged stress.
Combined Plate and Long Screw Fixation of Transverse Condylar Head Fractures
Authors: Diarra Drissa , Ni Xiao-Qi , Li Zhi 
Published: July 2023

We describe a method of fixing transverse condylar head fractures using a combination of a plate and long screw fixation. In the technical procedure, a 4-hole mini-plate was placed on the lateral side of the condylar head and the condylar stump after the fracture reduction. The first hole was drilled in the lateral side of the condylar head, and one 9 mm mini-screw was inserted, a second hole drilled from the lateral side of the condyle stump through the medial pole of the condylar head and a 16 mm screw was inserted in an oblique direction from inferior to superior, then 2 more 9 mm mini-screws were inserted just below the long one to complete the procedure. This technique showed excellent results in both short and long-term stability of and healing of the fracture. Furthermore, it is more standardized, reproducible, and less technically demanding.
The scientific chaos phase of the Great Pandemic: A longitudinal analysis and systematic review of the first surge of clinical research concerning COVID-19
Authors: Adami Till , Ries Markus 
Published: July 2023

AbstractBackgroundEarly stages of catastrophes like COVID-19 are often led by chaos and panic. To characterize the initial chaos phase of clinical research in such situations, we analyzed the first surge of more than 1000 clinical trials about the new disease at baseline and after two years follow-up. Our 3 main objectives were: (1) Assessment of spatial and temporal evolution of clinical research of COVID-19 across the globe, (2) Assessment of transparency and quality - trial registration, (3) Assessment of research waste and redundancies.MethodsBy entering the keyword “COVID-19” we screened the International Clinical Trials Registry Platform of the WHO and downloaded the search output when our goal of 1000 trials was reached on the 1stof April. Additionally, we verified the integrity of the downloaded data from the meta registry by comparing the data with each individual registration record on their source register. Also, we conducted a follow-up after two years to track their progress.Results(1) The spatial evolution followed the geographical spread of the disease as expected, however, the temporal development suggested that panic was the main driver for clinical research activities. (2) Trial registrations and registers showed a huge lack of transparency by allowing retrospective registrations and not keeping their registration records up to date. Quality of trial registration seems to have improved over the last decade, yet crucial information still was missing. (3) Research waste and redundancies were present as suggested by discontinuation of trials, preventable flaws in study design, and similar but uncoordinated research topics operationally fragmented in isolated silo-structures.ConclusionThe scientific response mechanism across the globe was intact during the chaos phase. However, supervision, leadership, and accountability are urgently needed to prevent research waste, to ensure effective structure, quality, and validity to ultimately break the “panic-then-forget” cycle in future catastrophes.
Multivariate prediction of temper outbursts in youth enriched for irritability using Ecological Momentary Assessment data
Authors: Saha Dipta , Naim Reut , Pereira Francisco , Brotman Melissa A. , Zheng Charles Y. 
Published: July 2023

AbstractIrritability and temper outbursts are among the most common reasons youth are referred for psychiatric assessment and care. Identifying clinical variables (e.g. momentary anxiety) that precede the onset of temper outbursts would provide valuable clinical utility. Here, we provide the rationale for a study to test the performance of classifiers trained to predict temper outbursts in a group of clinically-referred youth, in a home setting, enriched for symptoms of irritability and temper outbursts. Using observational data--digital based event sampling from previous Ecological Momentary Assessment data, we demonstrate promising results in our ability to predict the presence of a temper outburst based on clinical responses (e.g., whether the participant is grouchy, hungry, happy, sad, anxious, tired, etc.) prior to the emotional event, as well as external features (e.g., time of day, day of week). In exploratory analyses of existing data, consisting of n=57 subjects with a total of 1296 time points, we evaluate the feasibility of using a logistic regression-based classifier and a random-forest based classifier for predicting the temper outburst prospectively. In order to more rigorously assess these classifiers, we propose the collection of a large confirmatory set, consisting of at least an additional 20 subjects with an expected total of 400 time points, and will perform confirmatory analyses of the precision and recall of several classifiers for predicting temper outbursts. This work provides the foundation for the identification of features predictive of risk and future development of novel mobile-device-based interventions in youth affected with severe and impairing psychopathology.
Mycobacterium tuberculosisinfection associated immune perturbations correlate with antiretroviral immunity
Authors: Tepekule Burcu , Jörimann Lisa , Schenkel Corinne D. , Opitz Lennart , Tschumi Jasmin , Wolfensberger Rebekka , Neumann Kathrin , Kusejko Katharina , Zeeb Marius , Boeck Lucas , Kälin Marisa , Notter Julia , Furrer Hansjakob , Hoffmann Matthias , Hirsch Hans H. , Calmy Alexandra , Cavassini Matthias , Labhardt Niklaus D. , Bernasconi Enos , Metzner Karin J , Braun Dominique L. , Günthard Huldrych F. , Kouyos Roger D. , Duffy Fergal , Nemeth Johannes ,   the Swiss HIV Cohort Study
Published: July 2023

AbstractInfection with Mycobacterium tuberculosis (MTB) remains one of the most important opportunistic infections in people with HIV-1 (PWH). While active Tuberculosis (TB) leads to rapid progression of immunodeficiency in PWH, the interaction between MTB and HIV-1 during the asymptomatic phase of both infections remains poorly understood.In a cohort of individuals with HIV (PWH) with and without suppressed HIV-1 viral load, the transcriptomic profiles of peripheral blood mononuclear cells (PBMC) clustered in individuals infected with Mycobacterium tuberculosis (MTB) compared to carefully matched controls. Subsequent functional annotation analysis disclosed alterations in the IL-6, TNF, and KRAS pathways. Notably, MTB-associated genes demonstrated an inverse correlation with HIV-1 viremia, evident at both on individual gene level and when employed as a gene score.In sum, our data show that MTB infection in PWH is associated with a shift in the activation state of the immune system, displaying an inverse relationship with HIV-1 viral load. These results could provide an explanation for the observed increased antiretroviral control associated with MTB infection in PWH.
Towards the automated detection of interictal epileptiform discharges with magnetoencephalography
Authors: Fernández-Martín Raquel , Feys Odile , Juvené Elodie , Aeby Alec , Urbain Charline , De Tiège Xavier , Wens Vincent 
Published: July 2023

AbstractThe analysis of clinical magnetoencephalography (MEG) in patients with epilepsy traditionally relies on the visual identification of interictal epileptiform discharges (IEDs), which is time consuming and dependent on (subjective) human criteria. Data-driven approaches enabling both spatial and temporal localization of epileptic spikes would represent a major leap forward in clinical MEG practice. Here, we explore the ability of Independent Components Analysis (ICA) and Hidden Markov Modeling (HMM) to automatically detect and localize IEDs. Combined with kurtosis mapping, we developed a fully automated identification of epileptiform independent components (ICs) or HMM states. We tested our pipeline on MEG recordings at rest from 10 school-age children with either focal or multifocal epilepsy and compared results with the traditional MEG analysis performed by an experienced clinical magnetoencephalographer. In patients with focal epilepsy, both ICA- and HMM-based pipelines successfully detected visually identified IEDs with high sensitivity, but also revealed low-amplitude IEDs unidentified by the visual detection. Success was more mitigated in patients with multifocal epilepsy, as our automated pipeline missed IED activity associated with some foci—an issue that could be alleviated bypost-hocmanual selection of epileptiform ICs or HMM states. Therefore, IED detection based on ICA or HMM represents an efficient way to identify spike localization and timing, with heightened sensitivity to IEDs compared to visual MEG signal inspection and requiring minimal input from clinical practitioners.
Systematic analysis of microorganisms’ metabolism for selective targeting
Authors: Manshadi Mehdi Dehghan , Setoodeh Payam , Zare Habil 
Published: July 2023

AbstractSelective drug targets (i.e., narrow-spectrum antibiotics) can minimize side effects of antibiotic treatments compared to broad-spectrum antibiotics due to their specific targeting of the organisms responsible for the infection. Furthermore, combating an infectious pathogen, especially a drug-resistant organism, is more efficient by attacking multiple targets. Here, we combined synthetic lethality with selective drug targeting to obtain multi-target and organism-specific potential drug candidates by systematically analyzing the genome-scale metabolic models of six different microorganisms. By considering microorganisms as targeted or conserved in one- to six-member groups, we designed 665 individual case studies. For each case, we identified single essential reactions as well as double, triple, and quadruple synthetic lethal reaction sets that are lethal for targeted microorganisms and neutral for conserved ones. As expected, the number of obtained solutions for each case depends on the genomic similarity between the studied microorganisms. Mapping the identified potential drug targets to their corresponding pathways showed the importance of key subsystems such as cell envelope biosynthesis, glycerophospholipid metabolism, membrane lipid metabolism, and the nucleotide salvage pathway. To assist validation and further investigation of our proposed potential drug targets, we introduced two sets of targets that can potentially address a substantial portion of the 665 cases. We expect that the obtained solutions provide helpful insights into designing narrow-spectrum drugs that selectively cause system-wide damage only to the target microorganisms.
Intercellular communication atlas reveals Oprm1 as a neuroprotective factor for retinal ganglion cells
Authors: Qian Cheng , Xin Ying , Qi Cheng , Wang Hui , Dong Bryan C. , Zack Donald , Blackshaw Seth , Hattar Samer , Zhou Feng-Quan , Qian Jiang 
Published: July 2023

ABSTRACTThe progressive death of mature neurons often results in neurodegenerative diseases. While the previous studies have mostly focused on identifying intrinsic mechanisms controlling neuronal survival, the extracellular environment also plays a critical role in regulating cell viability. Here we explore how intercellular communication contributes to the survival of retinal ganglion cells (RGCs) following the optic nerve crush (ONC). Although the direct effect of the ONC is restricted to the RGCs, we observed transcriptomic responses in other retinal cells to the injury based on the single-cell RNA-seq, with astrocytes and Müller glia having the most interactions with RGCs. By comparing the RGC subclasses with distinct resilience to ONC-induced cell death, we found that the high-survival RGCs tend to have more ligand-receptor interactions with other retinal cells, suggesting that these RGCs are intrinsically programmed to foster more communication with their surroundings. Furthermore, we identified the top 47 interactions that are stronger in the high-survival RGCs, likely representing neuroprotective interactions. We performed functional assays on one of the receptors, μ-opioid receptor (Oprm1), a receptor known to play roles in regulating pain, reward, and addictive behavior. Although Oprm1 is preferentially expressed in intrinsically photosensitive retinal ganglion cells (ipRGC), its neuroprotective effect could be transferred to multiple RGC subclasses by selectively overexpressing Oprm1 in pan-RGCs in ONC, excitotoxicity, and glaucoma models. Lastly, manipulating Oprm1 activity improved visual functions or altered pupillary light response in mice. Our study provides an atlas of cell-cell interactions in intact and post-ONC retina, and a strategy to predict molecular mechanisms controlling neuroprotection, underlying the principal role played by extracellular environment in supporting neuron survival.
Prior probability cues bias sensory encoding with increasing task exposure
Authors: Walsh Kevin , McGovern David P. , Dully Jessica , Kelly Simon , O’Connell Redmond 
Published: July 2023

AbstractWhen observers have prior knowledge about the likely outcome of their perceptual decisions, they exhibit robust behavioural biases in reaction time and choice accuracy. Computational modelling typically attributes these effects to strategic adjustments in the criterion amount of evidence required to commit to a choice alternative - usually implemented by a starting point shift - but recent work suggests that expectations may also fundamentally bias the encoding of the sensory evidence itself. Here, we recorded neural activity with EEG while participants performed a contrast discrimination task with valid, invalid, or neutral probabilistic cues across multiple testing sessions. We measured sensory evidence encoding via contrast-dependent steady-state visual-evoked potentials (SSVEP), while a read-out of criterion adjustments was provided by effector-selective mu-beta band activity over motor cortex. In keeping with prior modelling and neural recording studies, cues evoked substantial biases in motor preparation consistent with criterion adjustments, but we additionally found that the cues produced a significant modulation of the SSVEP during evidence presentation. While motor preparation adjustments were observed in the earliest trials, the sensory-level effects only emerged with extended task exposure. Our results suggest that, in addition to strategic adjustments to the decision process, probabilistic information can also induce subtle biases in the encoding of the evidence itself.
EpiGePT: a Pretrained Transformer model for epigenomics
Authors: Gao Zijing , Liu Qiao , Zeng Wanwen , Jiang Rui , Wong Wing Hung 
Published: July 2023

AbstractThe inherent similarities between natural language and biological sequences have given rise to great interest in adapting the transformer-based large language models (LLMs) underlying recent breakthroughs in natural language processing (references), for applications in genomics. However, current LLMs for genomics suffer from several limitations such as the inability to include chromatin interactions in the training data, and the inability to make prediction in new cellular contexts not represented in the training data. To mitigate these problems, we propose EpiGePT, a transformer-based pretrained language model for predicting context-specific epigenomic signals and chromatin contacts. By taking the context-specific activities of transcription factors (TFs) and 3D genome interactions into consideration, EpiGePT offers wider applicability and deeper biological insights than models trained on DNA sequence only. In a series of experiments, EpiGePT demonstrates superior performance in a diverse set of epigenomic signals prediction tasks when compared to existing methods. In particular, our model enables cross-cell-type prediction of long-range interactions and offers insight on the functional impact of genetic variants under different cellular contexts. These new capabilities will enhance the usefulness of LLM in the study of gene regulatory mechanisms. We provide free online prediction service of EpiGePT throughhttp://health.tsinghua.edu.cn/epigept/.
Brain aromatase and its relationship with parental experience and behavior in male mice
Authors: Duarte-Guterman Paula , Skandalis Dimitri A. , Merkl Ariane , Geissler Diana B. , Ehret Günter 
Published: July 2023

AbstractIn most mammals, paternal care is not mandatory for raising offspring. In house mice, experience with pups governs the extent and quality of paternal care. First-time fathers undergo a dramatic transition from ignoring or killing pups to caring for pups. The behavioral shift occurs together with changes in brain estrogen signaling as indicated by changes in estrogen receptor presence and distribution in multiple areas regulating olfaction, emotion, and motivation. Here, we report changes in the expression of aromatase, the enzyme converting testosterone into estrogen, as an indirect measure of estrogen synthesis. The amount of paternal experience (5 or 27 days) was associated with increased numbers of immunocytochemically-identified aromatase expressing cells in the medial and cortical amygdala, posterior piriform cortex, and ventromedial hypothalamus. Functionally, these changes can be related to the disappearance of aggression or neglect towards pups when first-time fathers or, even more, well-experienced fathers are handling their own pups. In the lateral septum, the anterior piriform cortex and to some extent in the medial preoptic area, parental experience increased the number of aromatase-positive cells only in fathers with 27 days of experience, and only in the right hemisphere. This is a new case of brain-functional lateralization due to experience that has activated certain instinctive behavior. Nuclei/areas associated with maternal care (medial preoptic area, bed nucleus of stria terminalis, nucleus accumbens) exhibited a left-hemisphere advantage in aromatase expressing cells, both in pup-naïve and pup-experienced males. This newly found lateralization may contribute to the left-hemisphere dominant processing and perception of pup calls to release parental behavior. In general, the experience-dependent changes in aromatase expression we observed in most brain areas did not mirror the previously reported changes in estrogen receptors (ERα) when pup-naïve males became pup-caring fathers. Hence, paternal behavior may depend in a brain area-specific way on the differential action of estrogen through its receptors and/or direct local modulation of neural processing.
Contextual protein and antibody encodings from equivariant graph transformers
Authors: Mahajan Sai Pooja , Ruffolo Jeffrey A. , Gray Jeffrey J. 
Published: July 2023

AbstractThe optimal residue identity at each position in a protein is determined by its structural, evolutionary, and functional context. We seek to learn the representation space of the optimal amino-acid residue in different structural contexts in proteins. Inspired by masked language modeling (MLM), our training aims to transduce learning of amino-acid labels from non-masked residues to masked residues in their structural environments and from general (e.g., a residue in a protein) to specific contexts (e.g., a residue at the interface of a protein or antibody complex). Our results on native sequence recovery and forward folding with AlphaFold2 suggest that the amino acid label for a protein residue may be determined from its structural context alone (i.e., without knowledge of the sequence labels of surrounding residues). We further find that the sequence space sampled from our masked models recapitulate the evolutionary sequence neighborhood of the wildtype sequence. Remarkably, the sequences conditioned on highly plastic structures recapitulate the conformational flexibility encoded in the structures. Furthermore, maximum-likelihood interfaces designed with masked models recapitulate wildtype binding energies for a wide range of protein interfaces and binding strengths. We also propose and compare fine-tuning strategies to train models for designing CDR loops of antibodies in the structural context of the antibody-antigen interface by leveraging structural databases for proteins, antibodies (synthetic and experimental) and protein-protein complexes. We show that pretraining on more general contexts improves native sequence recovery for antibody CDR loops, especially for the hypervariable CDR H3, while fine-tuning helps to preserve patterns observed in special contexts.