bluuebunny/crossref_metadata_2025_split huggingface dataset:
Long-term prognosis of adults with moderate-severe SARS-CoV-2 lower respiratory tract infection managed in primary care: prospective cohort study
Authors: Platteel T.N. , Koelmans J.C. , Cianci D. , Broers N.J.H. , de Bont E.G.P.M. , Cals J.W.L. , Venekamp R.P. , Verheij T.J.M. 
Published: June 2022

ObjectivesTo determine differences in health-related quality of life (HRQoL) and presence and duration of symptoms between adults with and without established SARS-CoV-2 moderately severe lower respiratory tract infection (LRTI) in the 12 months following their primary care visit.DesignProspective cohort studySetting35 general practices in the provinces Noord-Brabant and Utrecht, the Netherlands.ParticipantsIndividuals aged ≥18 years who presented to their general practitioner (GP) with a moderately severe LRTI during the first COVID-19 waive in The Netherlands (March-June 2021) underwent serology testing (participants, GPs and study personnel remained blinded for serology outcomes during study conduct) and completed baseline and follow-up questionnaires. Of the 315 participants who gave consent, 277 (88%) were suitable for inclusion in the analyses. Complete follow-up date was available in 97% of participants.Main outcome measures1) Scores of SF-36; physical component summary (PCS), mental component summary (MCS) and subscales. 2) Risk of any and individual persisting symptoms (of cough, dyspnea, chest pain, fatigue, brain fog, headache, and anosmia/ageusia) over time.ResultsThe change in SF-36 PSC (p=0.13), MCS (p=0.30), as well as subscale scores, over time did not differ between SARS-CoV-2 serology positive and negative participants after adjusting for sex, age, BMI, diabetes and chronic pulmonary conditions. The risk of any persisting symptom over time did not significantly differ between the groups (aHR 0.61, 95% CI 0.33-1.15), nor did the risk of individual symptoms.ConclusionsIn the 12 months following their moderately severe LRTI, primary care patients with and without confirmed SARS-CoV-2 infection had a comparable HRQoL profile. Albeit a considerable proportion of patients reported persistent symptoms, there was no evidence of a difference in the course of symptoms over time between patients with and without confirmed SARS-CoV-2 infection.Trial registrationDutch Trial Register (NTR) number NL8729
Safety of the fourth COVID-19 BNT162b2 mRNA (second booster) vaccine
Authors: Yechezkel Matan , Mofaz Merav , Patalon Tal , Gazit Sivan , Shmueli Erez , Yamin Dan 
Published: June 2022

SummaryCOVID-19 remains a global concern due to vaccine protection waning and the emergence of immuneevasive variants. While the effectiveness of a second booster vaccine dose (i.e., fourth inoculation) is well proven, its safety has yet to be fully understood, and vaccine compliance remains low. We conducted a prospective observational study to compare the short-term effects of the first and second BNT162b2 mRNA COVID-19 vaccine booster doses. 2,019 participants received smartwatches and filled in a daily questionnaire on systemic reactions to the vaccine. We found substantial changes from baseline levels in the 72 hours post-vaccination with the second booster in both self-reported and physiological reactions measured by the smartwatches. However, no significant difference in reactions was observed between the first and second boosters. We also found that participants who experienced more severe reactions to the first booster tended to likewise experience more severe reactions to the second booster. Our work supports the safety of the second booster from both subjective (self-reported questionnaires) and objective (physiological measurements) perspectives.
Survival intravascular photoacoustic imaging of lipid-rich plaque in cholesterol fed rabbits
Authors: Zhang Yi , Taylor Erik , Huang Nasi , Hamilton James , Cheng Ji-Xin 
Published: June 2022

AbstractIntravascular photoacoustic (IVPA) imaging is a promising modality for quantitative assessment of lipid-laden atherosclerotic plaques. Yet, survival IVPA imaging of the same plaque in the same animal is not demonstrated. Here, using a sheathed IVUS/PA catheter of 0.9 mm in diameter, we demonstrate MRI-guided survival IVPA imaging of same plaque in an aorta of a well-established rabbit model mimicking atherosclerosis in human patients. The IVUS/PA results were confirmed by histology. These advances open the opportunity to evaluate the effectiveness of a therapy that aims to reduce the size of atherosclerotic plaques and demonstrates the potential of translating the IVPA catheter into clinic for detection of vulnerable plaques that are at high risk for thrombosis.
prolfqua: A Comprehensive R-package for Proteomics Differential Expression Analysis
Authors: Wolski Witold E. , Nanni Paolo , Grossmann Jonas , d’Errico Maria , Schlapbach Ralph , Panse Christian 
Published: June 2022

AbstractMass spectrometry is widely used for quantitative proteomics studies, relative protein quantification, and differential expression analysis of proteins. Nevertheless, there is a need for a flexible and easy-to-use application programming interface in R that transparently supports a variety of well principled statistical procedures. The prolfqua package can model simple experimental designs with a single explanatory variable and complex experiments with multiple factors and hypothesis testing. It integrates essential steps of the mass spectrometry-based differential expression analysis workflow: quality control, data normalization, protein aggregation, statistical modeling, hypothesis testing, and sample size estimation. The application programmer interface strives to be clear, predictable, discoverable, and consistent to make proteomics data analysis easy and exciting. Furthermore, the package implements benchmark functionality that can help to compare data acquisition, data preprocessing, or data modeling methods using a gold standard dataset. Finally, we show that the implemented methods allow sensitive and specific differential expression analysis. The prolfqua R package is available on GitHub https://github.com/fgcz/prolfqua, distributed under the MIT licence, and runs on all platforms supported by the R free software environment for statistical computing and graphics.
Genomic expression responses in sensu stricto Saccharomyces yeast to DNA damage induced by methyl methanesulfonate
Authors: Ramachandran Vignesh , Hatlestad Gregory , White Travis 
Published: June 2022

AbstractBackgroundOne way single-celled eukaryotes respond to DNA damage stress is by modifying their gene expression, facilitating genomic repair. Gene expression responses to DNA damage induced by methyl methanesulfonate (MMS) have been studied in the model organism Saccharomyces cerevisiae. However, lacking are investigations of the MMS stress responses in evolutionarily-related sensu stricto Saccharomyces species, including Saccharomyces cerevisiae.MethodsNext-generation Illumina RNA-sequencing was to characterize the entire transcriptomes of four evolutionarily-related species of yeast, S. cerevisiae, S. paradoxus, S. mikatae, and S. bayanus, under control and experimental (MMS) conditions. Subsequent genomic studies included gene set enrichment analysis, promoter analysis, and concentration gradient studies.ResultsS. mikitae and S. paradoxus grew well in light of MMS while S. bayanus showed no growth. While there was fair overlap in induced and repressed genes, overall each species had unique expression responses. S. paradoxus and S. bayanus showed the most distinct changes with the former greatly inhibiting a large segment of its genome while the latter induced such segments. Gene set enrichment analysis revealed significantly modulated biologic, cellular, and molecular processes in each species. Promoter analysis revealed sets of induced/repressed transcription factors for genes highly modulated in the stress response. Concentration gradient studies of S. cerevisiae showed linear increase in gene expression of RAD54, DIN7, and IRC19 in response to increasing concentrations of MMS.ConclusionOverall, we depict the transcriptome changes of four evolutionarily-related sensu stricto yeast species and several functional genomic analyses to provide a novel understanding of their responses to MMS.
Regulation of protein translation by TRIM21
Authors: Li Huiyi , Liu Shun , Feng Qing , Deng Rilin , Wang Jingjing , Wang Xintao , Tian Renyun , Xu Yan , Chen Shengwen , Liu Qian , Wang Luoling , Li Xinran , Wan Mengyu , Peng Yousong , Tang Songqing , Xue Binbin , Zhu Haizhen 
Published: June 2022

AbstractRegulation of translation initiation is essential for maintenance of protein homeostasis and typically involves the phosphorylation of translation initiation factor eIF2α in eukaryotes. In response to stressors, cells employ eIF2α-dependent signaling to control translation initiation, which regulates multiple biological and physiological processes. However, the precise regulatory mechanism remains unclear. In this study, we focus on the role of TRIM21 in the regulation of protein translation mediated by protein kinase R (PKR), one of the classic kinases that phosphorylates eIF2α. TRIM21 deficiency enhances the activation of PKR under different types of stress. TRIM21 interacts with PKR, and the E3 ligase activity of TRIM21 is crucial for stress-triggered PKR inactivation. TRIM21 interacts with the PKR phosphatase PP1α and promotes K6-linked polyubiquitination of PP1α under stresses. Ubiquitination of PP1α augments its interaction with PKR, causing PKR inactivation and subsequent dephosphorylation of eIF2α, initiating protein synthesis. Moreover, TRIM21 constitutively restricts viral infection by reversing PKR-mediated inhibition of the protein synthesis of intrinsic antiviral genes. The TRIM21-PP1α axis acts as a newly discovered program that regulates PKR-associated protein synthesis and broadens our knowledge of antiviral genes. Moreover, TRIM21-mediated regulation of PKR activation provides evidence that TRIM21 may anticipate the interferon-dependent immunotherapy. Our study highlights the essential role of TRIM21 in regulating protein translation and may provide a novel target for the treatment of translation-associated diseases.
Speech decoding from a small set of spatially segregated minimally invasive intracranial EEG electrodes with a compact and interpretable neural network
Authors: Petrosyan Artur , Voskoboinikov Alexey , Sukhinin Dmitrii , Makarova Anna , Skalnaya Anastasia , Arkhipova Nastasia , Sinkin Mikhail , Ossadtchi Alexei 
Published: June 2022

AbstractBackgroundSpeech decoding, one of the most intriguing BCI applications, opens up plentiful opportunities from rehabilitation of patients to direct and seamless communication between human species. Typical solutions rely on invasive recordings with a large number of distributed electrodes implanted through craniotomy. Here we explored the possibility of creating speech prosthesis in a minimally invasive setting with a small number of spatially segregated intracranial electrodes.MethodsWe collected one hour of data (from two sessions) in two patients implanted with invasive electrodes. We then used only the contacts that pertained to a single sEEG shaft or an ECoG stripe to decode neural activity into 26 words and one silence class. We employed a compact convolutional network-based architecture whose spatial and temporal filter weights allow for a physiologically plausible interpretation.ResultsWe achieved on average 55% accuracy using only 6 channels of data recorded with a single minimally invasive sEEG electrode in the first patient and 70% accuracy using only 8 channels of data recorded for a single ECoG strip in the second patient in classifying 26+1 overtly pronounced words. Our compact architecture did not require the use of pre-engineered features, learned fast and resulted in a stable, interpretable and physiologically meaningful decision rule successfully operating over a contiguous dataset collected during a different time interval than that used for training. Spatial characteristics of the pivotal neuronal populations corroborate with active and passive speech mapping results and exhibit the inverse space-frequency relationship characteristic of neural activity. Compared to other architectures our compact solution performed on par or better than those recently featured in neural speech decoding literature.ConclusionsWe showcase the possibility of building a speech prosthesis with a small number of electrodes and based on a compact feature engineering free decoder derived from a small amount of training data.
Temporal distribution of cetaceans south of Pico Island (Azores, Portugal) - data obtained during whale-watching 2020
Authors: Zahn Peter , Kulike Lynn , Bloechl Armin 
Published: June 2022

AbstractLand- and boat-based surveys were conducted to collect data during whale watching excursions in July/August and October 2020. Occurrence and distribution of cetaceans south of Pico Island (Azores) were determined. Ten species were sighted, 63 schools of Delphinids and 96 individuals of large whales. The most frequently sighted species were: Sperm whale (Physeter macrocephalus), Sei whale (Balaenoptera borealis), Atlantic spotted dolphin (Stenella frontalis), Common bottlenose dolphin (Tursiops truncatus), and Risso’s dolphin (Grampus griseus). An unusual high numbers of sightings of Sei whale in August and especially in October was noticed, and is not mentioned in the literature so far.
The conditional defector strategies can violate the most crucial supporting mechanisms of cooperation
Authors: Ibrahim Ahmed M. 
Published: June 2022

AbstractCooperation is essential for all domains of life. Ironically, it is intrinsically vulnerable to exploitation by cheats. Hence, there is an explanatory necessity that triggers a lot of evolutionary biologists to search for mechanisms that could support cooperation. In general, cooperation can emerge and be maintained when cooperators are sufficiently interacting with themself to provide a kind of assortment and reciprocity. One of the most crucial and common mechanisms to achieve that task are kin selection, spatial structure, and enforcement (punishment). Here I used agent-based simulation models to investigate these pivotal mechanisms against conditional defector strategies and concluded it could easily violate all of them and take over the population. This surprising outcome may cue us to rethink the evolution of cooperation as it illustrates that maintaining cooperation may be more difficult than previously thought. Moreover, besides the theoretical findings, there are empirical applications such as invading the cooperator population of pathogens by genetically engineered conditional defectors, which could be a potential therapy for many incurable diseases.
Mesopredator-mediated trophic cascade can break persistent phytoplankton blooms in coastal waters
Authors: Berthold Maximilian , Schumann Rhena , Reiff Volker , Wulff Rita , Schubert Hendrik 
Published: June 2022

AbstractManaging eutrophied systems only bottom-up (nutrient decreases) can be economically and ecologically challenging. Top-down controls (consumption) were sometimes found to effectively control phytoplankton blooms. However, mechanistic insights, especially on possible trophic cascades, are less understood in brackish, species-poor coastal waters, where large cladocera are absent. In this study, we set-up large mesocosms for three consecutive years during growth season. One set of mesocosms was controlled by mesopredator (gobies and shrimp), whereas the other mesocosms had no such mesopredator present. The results were standardized to monitoring data of the ecosystem to denote possible differences between treatments and the system. We found that mesopredator mesocosms showed lower turbidity, phytoplankton biomass, and nutrients compared to no-mesopredator mesocosms and the ecosystem. This decrease allowed macrophytes to colonize water depths only sparsely colonized in the ecosystem. Rotifer biomass increased in mesopredator mesocosms compared to the ecosystem and no-mesopredator mesocosms. Likewise, copepod biomass that potentially grazes upon rotifers and other microzooplankton decreased in mesopredator mesocosms. No-mesopredator mesocosms were colonized by an omnivorous mesograzer (Gammarus tigrinus), potentially creating additional pressure on macrophytes and increasing grazing-mediated nutrient release. Zooplankton was not able to control the non-nutrient limited phytoplankton. We propose a new mechanism, where a higher mesopredator density will increase grazing on phytoplankton by promoting microzooplankton capable of grazing on picophytoplankton. This proposed mechanism would contrast with freshwater systems, where a decrease of zooplanktivorous fish would promote larger phytoplankton grazer like cladocera. Biomanipulation in such species-poor eutrophic coastal waters may be more successful, due to less trophic pathways that can cause complex top-down controls. Stocking eutrophic coastal waters with gobies and shrimps may be an alternative biomanipulative approach rather than selectively remove large piscivorous or omnivorous fish from eutrophic coastal waters.
The effects of data quantity on performance of temporal response function analyses of natural speech processing
Authors: Mesik Juraj , Wojtczak Magdalena 
Published: June 2022

AbstractIn recent years, temporal response function (TRF) analyses of non-invasive recordings of neural activity evoked by continuous naturalistic stimuli have become increasingly popular for characterizing response properties within the auditory hierarchy. However, despite this rise in TRF usage, relatively few educational resources for these tools exist. Here we use a dual-talker continuous speech paradigm to demonstrate how a key parameter of experimental design, the quantity of acquired data, influences TRF analyses fit to either individual data (subject-specific analyses), or group data (generic analyses). We show that although model performance monotonically increases with data quantity, the amount of data required to achieve significant prediction accuracies can vary substantially based on whether the fitted model contains densely (e.g., acoustic envelope) or sparsely (e.g., lexical surprisal) spaced features, especially when the goal of the analyses is to capture the aspect of neural responses uniquely explained by specific features. Moreover, we demonstrate that generic models can exhibit high performance on small amounts of test data (2-8 min), if they are trained on a sufficiently large data set. As such, they may be particularly useful for clinical and multi-task study designs with limited recording time. Finally, we show that the regularization procedure used in fitting TRF models can interact with the quantity of data used to fit the models, with larger training quantities resulting in systematically larger TRF amplitudes. Together, demonstrations in this work should aid the learning process of new users of TRF analyses, and in combination with other tools, such as piloting and power analyses, may serve as a detailed reference for choosing acquisition duration in future studies.
A novel cuproptosis-related long non-coding RNAs model that effectively predicts prognosis in hepatocellular carcinoma
Authors: Huang Enmin , Ma Ning , Ma Tao , Zhou Junyi , Yang Weisheng , Liu Chuangxiong , Hou Zehui , Chen Shuang , Zong Zhen , Zeng Bing , Li Yingru , Zhou Taicheng 
Published: June 2022

ABSTRACTBackgroundCuproptosis has recently been considered a novel form of programmed cell death. To date, factors crucial to the regulation of this process remain unelucidated. Here, we aimed to identify long-chain non-coding RNAs (lncRNAs) associated with cuproptosis in order to predict the prognosis of patients with hepatocellular carcinoma (HCC).MethodsUsing RNA sequence data from The Cancer Genome Atlas Live Hepatocellular Carcinoma (TCGA-LIHC), a co-expression network of cuproptosis-related mRNAs and lncRNAs was constructed. For HCC prognosis, we developed a cuproptosis-related lncRNA signature (CupRLSig) using univariate Cox, lasso, and multivariate Cox regression analyses. Kaplan-Meier analysis was used to compare overall survival among high- and low-risk groups stratified by median CupRLSig score. Furthermore, comparisons of functional annotation, immune infiltration, somatic mutation, TMB (tumor mutation burden), and pharmacologic options were made between high- and low-risk groups.ResultsOur prognostic risk model was constructed using the cuproptosis-related PICSAR, FOXD2-AS1, and AP001065.1 lncRNAs. The CupRLSig high-risk group was associated with poor overall survival (hazard ratio = 1.162, 95% CI = 1.063– 1.270; p < 0.001). Model accuracy was further supported by receiver operating characteristic and principal component analysis as well as internal validation cohorts. A prognostic nomogram developed considering CupRLSig data and a number of clinical characteristics were found to exhibit adequate performance in survival risk stratification. Mutation analysis revealed that high-risk combinations with high TMB carried worse prognoses. Finally, differences in immune checkpoint expression and responses to chemotherapy as well as in targeted therapy among CupRLSig stratified high- and low-risk groups were explored.ConclusionsThe lncRNA signature constructed in this study is valuable in prognostic estimation in the setting of HCC.
Climate-induced range shifts drive adaptive response via spatio-temporal sorting of alleles
Authors: Luqman Hirzi , Wegmann Daniel , Fior Simone , Widmer Alex 
Published: June 2022

AbstractQuaternary climate fluctuations drove many species to shift their geographic ranges, in turn shaping their genetic structures. Recently, it has been argued that adaptation may have accompanied species range shifts via the “sieving” of genotypes during colonisation and establishment. However, this has not been directly demonstrated, and knowledge remains limited on how different evolutionary forces, that are typically investigated separately, interacted to jointly mediate species responses to past climatic change. Here, through whole-genome resequencing of over 1200 individuals of the carnation Dianthus sylvestris coupled with integrated population genomic and gene-environment models, we reconstruct the past neutral and adaptive landscape of this species as it was shaped by the Quaternary glacial cycles. We show that adaptive responses emerged concomitantly with the post-glacial range shifts and expansions of this species in the last 20 thousand years. This was due to the spatial sorting of adaptive alleles through time, as populations expanded out of restrictive glacial refugia into the broader and more heterogeneous range of habitats available in the present-day inter-glacial. Our results reveal a tightly-linked interplay of migration and adaptation under past climate-induced range shifts that has acted to shape the spatial patterns of adaptive genetic variation we see in the species today.