julilili42/papers huggingface dataset:
Testing, explaining, and exploring models of facial expressions of emotions
2023-02-10

Models are the hallmark of mature scientific inquiry. In psychology, this maturity has been reached in a pervasive question—what models best represent facial expressions of emotion? Several hypotheses propose different combinations of facial movements [action units (AUs)] as best representing the six basic emotions and four conversational signals across cultures. We developed a new framework to formalize such hypotheses as predictive models, compare their ability to predict human emotion categorizations in Western and East Asian cultures, explain the causal role of individual AUs, and explore updated, culture-accented models that improve performance by reducing a prevalent Western bias. Our predictive models also provide a noise ceiling to inform the explanatory power and limitations of different factors (e.g., AUs and individual differences). Thus, our framework provides a new approach to test models of social signals, explain their predictive power, and explore their optimization, with direct implications for theory development.
New horizons in the sociology of sport
2023-02-10

The relevance of a sociological view on the problems of society has never been as important as it is today. To quote the editors of the journal Nature in their editorial, Time for the Social Sciences, from 2015: if you want science to deliver for society, you need to support a capacity to understand that society. In other words, the technological and scientific disciplines cannot simply transfer their findings into everyday life without knowing how society works. But this realisation does not seem to have caught on everywhere. The sociology of sport is entering a critical period that will shape its development and potential transformation over the next decade. In this paper, we review key features and trends within the sociology of sport in recent times, and set out potential future challenges and ways forward for the subdiscipline. Accordingly, our discussion spans a wide range of issues concerning the sociology of sport, including theories and approaches, methods, and substantive research topics. We also discuss the potential contributions of the sociology of sport to addressing key societal challenges. To examine these issues, the paper is organized into three main parts. First, we identify three main concentric challenges, or types of peripheral status, that sociologists of sport must confront: as social scientists, as sociologists, and as sociologists of sport, respectively. Second, we consider various strengths within the positions of sociology and the sociology of sport. Third, in some detail, we set out several ways forward for the sociology of sport with respect to positioning within academe, scaling up research, embracing the glocal and cosmopolitan aspects of sociology, enhancing plurality in theory, improving transnational coordination, promoting horizontal collaborations, and building greater public engagement. The paper is underpinned by over 60 years (combined) of work within the sociology of sport, including extensive international research and teaching.
Neural text generation in regulatory medical writing
2023-02-10

Background: A steep increase in new drug applications has increased the overhead of writing technical documents such as medication guides. Natural language processing can contribute to reducing this burden. Objective: To generate medication guides from texts that relate to prescription drug labeling information. Materials and Methods: We collected official drug label information from the DailyMed website. We focused on drug labels containing medication guide sections to train and test our model. To construct our training dataset, we aligned “source” text from the document with similar “target” text from the medication guide using three families of alignment techniques: global, manual, and heuristic alignment. The resulting source-target pairs were provided as input to a Pointer Generator Network, an abstractive text summarization model. Results: Global alignment produced the lowest ROUGE scores and relatively poor qualitative results, as running the model frequently resulted in mode collapse. Manual alignment also resulted in mode collapse, albeit higher ROUGE scores than global alignment. Within the family of heuristic alignment approaches, we compared different methods and found BM25-based alignments to produce significantly better summaries (at least 6.8 ROUGE points above the other techniques). This alignment surpassed both the global and manual alignments in terms of ROUGE and qualitative scoring. Conclusion: The results of this study indicate that a heuristic approach to generating inputs for an abstractive summarization model increased ROUGE scores, compared to a global or manual approach when automatically generating biomedical text. Such methods hold the potential to significantly reduce the manual labor burden in medical writing and related disciplines.
Does negation influence the choice of sentence continuations? Evidence from a four-choice cloze task
2023-02-10

Event plausibility facilitates the processing of affirmative sentences, but little is known about how it affects negative sentences. In six behavioural experiments, we investigated negation’s impact on the choice of sentence continuations that differ with respect to event plausibility. In a four-choice cloze task, participants saw affirmative and negative sentence fragments ( The child will [not] eat the . . .) in combination with four potential continuations: yoghurt (a plausible word), shellfish (a weak world knowledge violating word), branch (a severe world knowledge violating word), and minivan (a word resulting in a semantic violation). Across all experiments the plausible word was highly preferred in both affirmative and negative sentences. Experiment 2 replicated Experiment 1 while ruling out the possibility that the lack of effect of negation in Experiment 1 stemmed from participants not fully processing the negation. Experiment 3 showed that the observed plausibility effects can be generalised to other aspectual forms ( The child has [not] eaten the yoghurt). Experiment 4 ruled out the possibility that the choices were mainly driven by lexical associations and additionally suggested a role for informativity. Experiment 5 replicated Experiment 4 and reinforced the general pattern according to which negative sentences express the denial of plausible positive events. Experiment 6 provided evidence that informativity might be driving patterns of choices in the negative sentences. All in all, these findings suggest that upcoming continuations are chosen to maximise the plausibility of the event in the affirmative sentences and to deny that event in the negative sentences. The observed plausibility effects do not seem to be modulated by the internal representation of events, but they can be modulated by changes to the expected informativity of the sentence.
Age-associated changes in endothelial transcriptome and chromatin landscape correlate with elevated risk of hemorrhage
2023-02-10

Abstract Intracerebral hemorrhage (ICH), a devastating form of stroke, is a leading global cause of human death and disability. The major risk factors for ICH include increasing age, hypertension and cerebral amyloid angiopathy. Despite high mortality and morbidity associated with ICH, the mechanisms leading to blood-brain barrier (BBB) dysfunction with age and development of hemorrhagic stroke is poorly understood. In the vasculature of the central nervous system, endothelial cells (ECs) constitute the core component of the BBB and provide a physical barrier due to tight junctions, adherens junctions, and basement membrane layers. In this study, we show in brains of mice that incidents of intracerebral bleeding increase with advancing age. After isolation of an enriched population of cerebral ECs, we studied gene expression in ECs isolated from murine brains of increasing ages of 2, 6, 12, 18, and 24 months. The study reveals agedependent dysregulation of 1388 genes in the ECs, including many involved in the maintenance of BBB and vascular integrity. Since epigenetic mechanisms regulate gene expression, we also investigated age-dependent changes at the levels of CpG methylation and accessible chromatin in cerebral ECs. Our study reveals correlations between age-dependent changes in chromatin structure and gene expression. We find significant age-dependent downregulation of the apelin receptor ( Aplnr ) gene along with an age-dependent reduction in chromatin accessibility of the promoter of this gene. Aplnr is known to play a crucial role in positive regulation of vasodilation and is implicated in vascular health. Interestingly, we also observe an age-dependent reduction in the protein expression levels of the apelin receptor in the brain, potentially implicating the apelin receptor to be critical for the increased risk of intracerebral hemorrhage with ageing.
Acute and long-term exercise adaptation of adipose tissue and skeletal muscle in humans: a matched transcriptomics approach after 8-week training-intervention
2023-02-11

Abstract Background Exercise exerts many health benefits by directly inducing molecular alterations in physically utilized skeletal muscle. Molecular adaptations of subcutaneous adipose tissue (SCAT) might also contribute to the prevention of metabolic diseases. Aim To characterize the response of human SCAT based on changes in transcripts and mitochondrial respiration to acute and repeated bouts of exercise in comparison to skeletal muscle. Methods Sedentary participants (27 ± 4 yrs) with overweight or obesity underwent 8-week supervised endurance exercise 3×1h/week at 80% VO2peak. Before, 60 min after the first and last exercise bout and 5 days post intervention, biopsies were taken for transcriptomic analyses and high-resolution respirometry ( n = 14, 8 female/6 male). Results In SCAT, we found 37 acutely regulated transcripts (FC &gt; 1.2, FDR &lt; 10%) after the first exercise bout compared to 394, respectively, in skeletal muscle. Regulation of only 5 transcripts overlapped between tissues highlighting their differential response. Upstream and enrichment analyses revealed reduced transcripts of lipid uptake, storage and lipogenesis directly after exercise in SCAT and point to β-adrenergic regulation as potential major driver. The data also suggest an exercise-induced modulation of the circadian clock in SCAT. Neither term was associated with transcriptomic changes in skeletal muscle. No evidence for beigeing/browning was found in SCAT along with unchanged respiration. Conclusions Adipose tissue responds completely distinct from adaptations of skeletal muscle to exercise. The acute and repeated reduction in transcripts of lipid storage and lipogenesis, interconnected with a modulated circadian rhythm, can counteract metabolic syndrome progression toward diabetes.
A pile of pipelines: an overview of the bioinformatics software for metabarcoding data analyses
2023-02-11

Environmental DNA (eDNA) metabarcoding has gained growing attention as a strategy for monitoring biodiversity in ecology. However, taxa identifications produced through metabarcoding require sophisticated processing of high-throughput sequencing data from taxonomically informative DNA barcodes. Various sets of universal and taxon-specific primers have been developed, extending the usability of metabarcoding across archaea, bacteria, and eukaryotes. Accordingly, a multitude of metabarcoding data analysis tools and pipelines have also been developed. Often, several developed workflows are designed to process the same amplicon sequencing data, making it somewhat puzzling to choose one amongst the plethora of existing pipelines. However, each pipeline has its own specific philosophy, strengths, and limitations, which should be considered depending on the aims of any specific study, as well as the bioinformatics expertise of the user. In this review, we outline the input data requirements, supported operating systems, and particular attributes of thirty-one amplicon processing pipelines with the goal of helping users to select a pipeline for their metabarcoding projects.
Phylogenetic distance and structural diversity directing a reclassification of glycopeptide antibiotics
2023-02-11

Abstract Antibiotics have been an essential part of modern medicine since their initial discovery. The continuous search for new antibiotic candidates remains a necessity given the increasing emergence of resistance to antimicrobial compounds among pathogens. The glycopeptide antibiotics (GPAs) represent an important group of last resort antibiotics which inhibit bacterial growth through non-covalent binding to the cell wall precursor lipid II. The so far reported GPAs exhibit an enormous diversity in the biosynthetic gene clusters that encode their production, which is in turn reflected in the variety of their structures. GPAs are typically composed of seven amino acids, which are highly crosslinked and decorated with a variable collection of sugar moieties as well as other modifications. Based on their structural characteristics, they have been classified into four main types. More recently, atypical GPAs have been identified that differ from type I-IV GPAs in both their structure and function and have consequently been classified as type V GPAs. Given these differences, we studied the phylogeny of all gene sequences related to the biosynthesis of the GPAs and observed a clear evolutionary diversification between the lipid II binding GPA classes and the so-called type V GPAs. Here we suggest the adoption of a phylogeny-driven reclassification and a separation of classical lipid II binding GPAs from type V GPAs, which we propose to identify instead as glycopeptide- related peptides (GRPs).
Empirical evidence on the global minimum tax: what is a critical mass and how large is the substance‐based income exclusion?
2023-02-11

Abstract This paper presents empirical evidence on the proposed global minimum tax (GMT) of the OECD's Pillar 2. First, it addresses how many, and which, countries or country groups can be seen as constituting a ‘critical mass’ for its successful implementation; given such a critical mass, remaining jurisdictions worldwide will have an incentive to implement the GMT as well. Second, it assesses the generosity of the substance‐based income exclusion (SBIE), which is informative for the revenue collected under the GMT.
Icex: Advances in the automatic extraction and volume calculation of cranial cavities
2023-02-11

Abstract The use of non‐destructive approaches for digital acquisition (e.g. computerised tomography—CT) allows detailed qualitative and quantitative study of internal structures of skeletal material. Here, we present a new R‐based software tool, Icex , applicable to the study of the sizes and shapes of skeletal cavities and fossae in 3D digital images. Traditional methods of volume extraction involve the manual labelling (i.e. segmentation) of the areas of interest on each section of the image stack. This is time‐consuming, error‐prone and challenging to apply to complex cavities. Icex facilitates rapid quantification of such structures. We describe and detail its application to the isolation and calculation of volumes of various cranial cavities. The R tool is used here to automatically extract the orbital volumes, the paranasal sinuses, the nasal cavity and the upper oral volumes, based on the coordinates of 18 cranial anatomical points used to define their limits, from 3D cranial surface meshes obtained by segmenting CT scans. Icex includes an algorithm ( Icv ) for the calculation of volumes by defining a 3D convex hull of the extracted cavity. We demonstrate the use of Icex on an ontogenetic sample (0–19 years) of modern humans and on the fossil hominin crania Kabwe (Broken Hill) 1, Gibraltar (Forbes' Quarry) and Guattari 1. We also test the tool on three species of non‐human primates. In the modern human subsample, Icex allowed us to perform a preliminary analysis on the absolute and relative expansion of cranial sinuses and pneumatisations during growth. The performance of Icex , applied to diverse crania, shows the potential for an extensive evaluation of the developmental and/or evolutionary significance of hollow cranial structures. Furthermore, being open source, Icex is a fully customisable tool, easily applicable to other taxa and skeletal regions.
Decompressive surgery in cerebral venous sinus thrombosis due to vaccine‐induced immune thrombotic thrombocytopenia
2023-02-11

Abstract Background and purpose Cerebral venous sinus thrombosis due to vaccine‐induced immune thrombotic thrombocytopenia (CVST‐VITT) is an adverse drug reaction occurring after severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) vaccination. CVST‐VITT patients often present with large intracerebral haemorrhages and a high proportion undergoes decompressive surgery. Clinical characteristics, therapeutic management and outcomes of CVST‐VITT patients who underwent decompressive surgery are described and predictors of in‐hospital mortality in these patients are explored. Methods Data from an ongoing international registry of patients who developed CVST within 28 days of SARS‐CoV‐2 vaccination, reported between 29 March 2021 and 10 May 2022, were used. Definite, probable and possible VITT cases, as defined by Pavord et al. (N Engl J Med 2021; 385: 1680–1689), were included. Results Decompressive surgery was performed in 34/128 (27%) patients with CVST‐VITT. In‐hospital mortality was 22/34 (65%) in the surgical and 27/94 (29%) in the non‐surgical group ( p &lt; 0.001). In all surgical cases, the cause of death was brain herniation. The highest mortality rates were found amongst patients with preoperative coma (17/18, 94% vs. 4/14, 29% in the non‐comatose; p &lt; 0.001) and bilaterally absent pupillary reflexes (7/7, 100% vs. 6/9, 67% with unilaterally reactive pupil, and 4/11, 36% with bilaterally reactive pupils; p = 0.023). Postoperative imaging revealed worsening of index haemorrhagic lesion in 19 (70%) patients and new haemorrhagic lesions in 16 (59%) patients. At a median follow‐up of 6 months, 8/10 of surgical CVST‐VITT who survived admission were functionally independent. Conclusions Almost two‐thirds of surgical CVST‐VITT patients died during hospital admission. Preoperative coma and bilateral absence of pupillary responses were associated with higher mortality rates. Survivors often achieved functional independence.
Localization Techniques for Non-Palpable Breast Lesions: Current Status, Knowledge Gaps, and Rationale for the MELODY Study (EUBREAST-4/iBRA-NET, NCT 05559411)
2023-02-12

Background: Surgical excision of a non-palpable breast lesion requires a localization step. Among available techniques, wire-guided localization (WGL) is most commonly used. Other techniques (radioactive, magnetic, radar or radiofrequency-based, and intraoperative ultrasound) have been developed in the last two decades with the aim of improving outcomes and logistics. Methods: We performed a systematic review on localization techniques for non-palpable breast cancer. Results: For most techniques, oncological outcomes such as lesion identification and clear margin rate seem either comparable with or better than for WGL, but evidence is limited to small cohort studies for some of the devices. Intraoperative ultrasound is associated with significantly higher negative margin rates in meta-analyses of randomized clinical trials (RCTs). Radioactive techniques were studied in several RCTs and are non-inferior to WGL. Smaller studies show higher patient preference towards wire-free localization, but little is known about surgeons’ and radiologists’ attitudes towards these techniques. Conclusions: Large studies with an additional focus on patient, surgeon, and radiologist preference are necessary. This review aims to present the rationale for the MELODY (NCT05559411) study and to enable standardization of outcome measures for future studies.
Odor cueing of declarative memories during sleep enhances coordinated spindles and slow oscillations
2023-02-12

Abstract Long-term memories are formed by repeated reactivation of newly encoded information during sleep. This process can be enhanced by using memory-associated reminder cues like sounds and odors. While auditory cueing has been researched extensively, few electrophysiological studies have exploited the various benefits of olfactory cueing. We used high-density electroencephalography in an odor-cueing paradigm that was designed to isolate the neural responses specific to the cueing of declarative memories. We show widespread cueing-induced increases in the duration and rate of sleep spindles. Higher spindle rates were most prominent over centro-parietal areas and largely overlapping with a concurrent increase in the amplitude of slow oscillations (SOs). Interestingly, greater SO amplitudes were linked to a higher likelihood of coupling a spindle and coupled spindles expressed during cueing were more numerous in particular around SO up states. We thus identify temporally and spatially coordinated enhancements to sleep spindles and slow oscillations as a candidate mechanism behind the benefits of odor cueing. Our results further demonstrate the feasibility of studying neural activity patterns related to memory processing using olfactory cueing during sleep. Statement of Significance Memory cueing during sleep allows insights into memory consolidation. This study is the first to investigate olfactory cueing-induced declarative memory processing using high-density EEG, while robustly controlling for critical confounding factors. The use of odors as cues, instead of more common auditory stimuli, further minimizes possible distortions due to sensory-evoked potentials. We demonstrate intricate changes in brain activity in response to cueing, such as the patterns of sleep spindles, slow oscillations, and their spatiotemporal coupling. We provide evidence that the enhancement of slow oscillation amplitudes, together with associated increases in sleep spindle rates, could be the key mechanism behind cueing-related memory benefits. We moreover show that prior findings obtained using auditory cueing are not the mere result of tone-evoked responses but might be genuine signatures of memory processing.
The Use of Collagen-Based Materials in Bone Tissue Engineering
2023-02-13

Synthetic bone substitute materials (BSMs) are becoming the general trend, replacing autologous grafting for bone tissue engineering (BTE) in orthopedic research and clinical practice. As the main component of bone matrix, collagen type I has played a critical role in the construction of ideal synthetic BSMs for decades. Significant strides have been made in the field of collagen research, including the exploration of various collagen types, structures, and sources, the optimization of preparation techniques, modification technologies, and the manufacture of various collagen-based materials. However, the poor mechanical properties, fast degradation, and lack of osteoconductive activity of collagen-based materials caused inefficient bone replacement and limited their translation into clinical reality. In the area of BTE, so far, attempts have focused on the preparation of collagen-based biomimetic BSMs, along with other inorganic materials and bioactive substances. By reviewing the approved products on the market, this manuscript updates the latest applications of collagen-based materials in bone regeneration and highlights the potential for further development in the field of BTE over the next ten years.