bluuebunny/crossref_metadata_2025_split huggingface dataset:
Coda
Authors: Laurence Stephen , Margolis Eric 
Published: July 2024

Abstract
This chapter provides a brief conclusion to the book, highlighting some of its major themes. The Building Blocks of Thought comprehensively rethinks the rationalism-empiricism debate about the origins of concepts by revisiting and updating the theoretical foundations of the debate and defending a form of concept nativism according to which many concepts across many conceptual domains are either innate or acquired via rationalist learning mechanisms. Our concept nativism stands in stark contrast with empiricist approaches in philosophy and cognitive science, with Fodor’s scepticism about concepts being learned, and with views that refer to core knowledge systems in only a handful of content domains. We conclude that the best account of the origins of concepts is one that posits a rich innate entry point into many different conceptual domains—one in which characteristically rationalist learning mechanisms are critical to explaining how the human mind acquires its vast stock of concepts.
The Black Church
Authors: Delgado Melvin 
Published: July 2024

Abstract
Few, if any, racial or ethnic groups in the United States are more identified with religion and churches than Blacks. The Black church occupies a unique perch in the religious landscape and history of the United States. Blacks historically had to set up their own cultural institutions because of society’s racist policies and practices. The historical and current-day significance of Black churches in urban America is undisputable. The future of Black churches, however, is open to debate and represents a cause of alarm for these institutions and the communities where they are situated due to a series of significant cross-currents.
The Latino Church
Authors: Delgado Melvin 
Published: July 2024

Abstract
Like the Black church, the Latino church is not monolithic. Although the two churches share broad similarities, each presents unique challenges and rewards in terms of church closures and repurposing. They both have a significant urban presence, but differ in terms of demographics, history, culture, language, and immigration status. Due to its growth, the Latino community will undoubtedly be a significant presence in the future of the United States, with their presence felt throughout the country, and that applies to their churches as well. Despite this population increase, the Latino community still faces a religious crisis, with church closures as indicators of this situation.
Experiences of healthcare staff caring for hospitalised people with delirium: a qualitative systematic review
Authors: Siostrom Kristy , Snowdon David , Sriamareswaran Rumes Kanna , Law Yu Mei , Jolliffe Laura , Moran Chris 
Published: July 2024

Abstract

Background
Inpatient delirium is common and associated with poor outcomes. Although most organisations have evidence-based guidelines to improve delirium prevention and management, delirium rates and outcomes have remained relatively unchanged over time. A lack of understanding of healthcare providers’ experience of caring for people with delirium and its integration into existing guidance may explain some of the slow progress in improving delirium care.

Objective
To review and synthesise existing qualitative evidence on healthcare providers’ experience of caring for inpatients with delirium within and across disciplines.

Methods
We systematically searched OVID Medline, CINAHL, Embase, Emcare, PsychINFO, AMED and Web of Science databases for articles published between January 1990 and November 2022. Article inclusion and study quality were assessed by two independent reviewers. Both thematic synthesis and content analysis were then conducted to synthesise findings from included studies.

Results
Within the 25 included studies, the experience of nurses was the most commonly studied perspective, followed by medical and allied health. Nursing, medical and allied health staff all reported that their experience of caring for people with delirium was challenging, highlighting difficulties in delirium recognition and that they felt unsupported at organisational and local levels. Attitudes towards older people and the importance of delirium influenced identification and prioritisation.

Conclusions
Healthcare providers often find caring for hospitalised patients with delirium challenging and complex. Although good communication within multidisciplinary teams was deemed helpful, more work is required to understand how to achieve this, recognising the unique perspectives of individual disciplines.
A survey analysis of the adoption of large language models among pathologists
Authors: Laohawetwanit Thiyaphat , Pinto Daniel Gomes , Bychkov Andrey 
Published: July 2024

Abstract

Objectives
We sought to investigate the adoption and perception of large language model (LLM) applications among pathologists.

Methods
A cross-sectional survey was conducted, gathering data from pathologists on their usage and views concerning LLM tools. The survey, distributed globally through various digital platforms, included quantitative and qualitative questions. Patterns in the respondents’ adoption and perspectives on these artificial intelligence tools were analyzed.

Results
Of 215 respondents, 100 (46.5%) reported using LLMs, particularly ChatGPT (OpenAI), for professional purposes, predominantly for information retrieval, proofreading, academic writing, and drafting pathology reports, highlighting a significant time-saving benefit. Academic pathologists demonstrated a better level of understanding of LLMs than their peers. Although chatbots sometimes provided incorrect general domain information, they were considered moderately proficient concerning pathology-specific knowledge. The technology was mainly used for drafting educational materials and programming tasks. The most sought-after feature in LLMs was their image analysis capabilities. Participants expressed concerns about information accuracy, privacy, and the need for regulatory approval.

Conclusions
Large language model applications are gaining notable acceptance among pathologists, with nearly half of respondents indicating adoption less than a year after the tools’ introduction to the market. They see the benefits but are also worried about these tools’ reliability, ethical implications, and security.
Current laboratory testing practices for mismatch repair deficiency and microsatellite instability testing: A survey-based review of current laboratory practices
Authors: Austin Amy L , Broaddus Russell R , Souers Rhona J , Kane Megan E , Kolhe Ravindra , Miller Dylan V , Moncur Joel T , Ramkissoon Shakti , Tafe Laura J , Trembath Dimitri G , Graham Rondell P 
Published: July 2024

Abstract

Objectives
To describe mismatch repair (MMR) and microsatellite instability (MSI) testing practices in laboratories using the College of American Pathologists (CAP) MSI/MMR proficiency testing programs prior to the 2022 publication of the MSI/MMR practice guidelines copublished by CAP and the Association of Molecular Pathology (AMP).

Methods
Data from supplemental questionnaires provided with the 2020-B MSI/MMR programs to 542 laboratories across different practice settings were reviewed. Questionnaires contained 21 questions regarding the type of testing performed, specimen/tumor types used for testing, and clinical practices for checkpoint blockade therapy.

Results
Domestic laboratories test for MSI/MMR more often than international laboratories (P = .04) and academic hospitals/medical centers test more frequently than nonhospital sites/clinics (P = .03). The most commonly used testing modality is immunohistochemistry, followed by polymerase chain reaction, then next-generation sequencing. Most laboratories (72.6%; 347/478) reported awareness of the use of immune checkpoint inhibitor therapy for patients with high MSI or MMR-deficient results.

Conclusions
The results demonstrate the state of MMR and MSI testing in laboratories prior to the publication of the CAP/AMP best practice guidelines, highlighting differences between various laboratory types. The findings indicate the importance of consensus guidelines and provide a baseline for comparison after their implementation.
Alcohol hangover recognized as a separate medical condition in ICD-11: could effective treatments be counterproductive?
Authors: Išerić Emina , Scholey Andrew , Verster Joris C , Karadayian Analia G 
Published: July 2024

Abstract
Recently, the alcohol hangover has been accepted by the International Classification of Diseases – 11th revision as a separate ‘child entity’ to alcohol intoxication, a disease. Currently there are no marketed hangover treatments with support for clinical efficacy. Furthermore, diverse perspectives exist among healthcare professionals, policymakers, and alcohol consumers regarding the necessity and desirability of developing such treatments.
Enabling Population Protein Dynamics Through Bayesian Modeling
Authors: Lehmann Sylvain , Vialaret Jérôme , Gabelle Audrey , Bauchet Luc , Villemin Jean-Philippe , Hirtz Christophe , Colinge Jacques 
Published: July 2024

Abstract

Motivation
The knowledge of protein dynamics, or turnover, in patients provides invaluable information related to certain diseases, drug efficacy, or biological processes. A great corpus of experimental and computational methods has been developed, including by us, in the case of human patients followed in vivo. Moving one step further, we propose a novel modeling approach to capture population protein dynamics using Bayesian methods.

Results
Using two datasets, we demonstrate that models inspired by population pharmacokinetics can accurately capture protein turnover within a cohort and account for inter-individual variability. Such models pave the way for comparative studies searching for altered dynamics or biomarkers in diseases.

Availability
R code and preprocessed data are available from zenodo.org. Raw data are available from panoramaweb.org.

Supplementary information
Supplementary data are available at Bioinformatics online.
Genome-wide detection of somatic mosaicism at short tandem repeats
Authors: Sehgal Aarushi , Ziaei Jam Helyaneh , Shen Andrew , Gymrek Melissa 
Published: July 2024

Abstract

Motivation
Somatic mosaicism has been implicated in several developmental disorders, cancers, and other diseases. Short tandem repeats (STRs) consist of repeated sequences of 1–6 bp and comprise &gt;1 million loci in the human genome. Somatic mosaicism at STRs is known to play a key role in the pathogenicity of loci implicated in repeat expansion disorders and is highly prevalent in cancers exhibiting microsatellite instability. While a variety of tools have been developed to genotype germline variation at STRs, a method for systematically identifying mosaic STRs is lacking.

Results
We introduce prancSTR, a novel method for detecting mosaic STRs from individual high-throughput sequencing datasets. prancSTR is designed to detect loci characterized by a single high-frequency mosaic allele, but can also detect loci with multiple mosaic alleles. Unlike many existing mosaicism detection methods for other variant types, prancSTR does not require a matched control sample as input. We show that prancSTR accurately identifies mosaic STRs in simulated data, demonstrate its feasibility by identifying candidate mosaic STRs in Illumina whole genome sequencing data derived from lymphoblastoid cell lines for individuals sequenced by the 1000 Genomes Project, and evaluate the use of prancSTR on Element and PacBio data. In addition to prancSTR, we present simTR, a novel simulation framework which simulates raw sequencing reads with realistic error profiles at STRs.

Availability and implementation
prancSTR and simTR are freely available at https://github.com/gymrek-lab/trtools. Detailed documentation is available at https://trtools.readthedocs.io/.
Harmonizing immune cell sequences for computational analysis with large language models
Authors: Alsaafin Areej , Tizhoosh Hamid R 
Published: July 2024

Abstract
We present SEQuence Weighted Alignment for Sorting and Harmonization (Seqwash), an algorithm designed to process sequencing profiles utilizing large language models. Seqwash harmonizes immune cell sequences into a unified representation, empowering LLMs to embed meaningful patterns while eliminating irrelevant information. Evaluations using immune cell sequencing data showcase Seqwash’s efficacy in standardizing profiles, leading to improved feature quality and enhanced performance in both supervised and unsupervised downstream tasks for sequencing data.
Contesting Neoliberal Reform of Statutory Social Work in Switzerland and England: Discretionary Spaces, Collective Resistance and Ethico-Political Professionalism
Authors: Moth Rich , Schilling Sigrid , Neuhaus Lukas , Lavalette Michael , Mürner Beat 
Published: July 2024

Abstract
This article reports findings from a qualitative study of the impacts of, and practitioner responses to, neoliberal social work reforms in Switzerland and England. The article highlights commonalities, and contrasts, in how neoliberalism has restructured social work across the two jurisdictions. Social workers responded to neoliberalisation in a variety of ways, often through adaptation but sometimes by challenging reforms. This resistance primarily involved individualised forms of agency promoting social justice in practice, such as carving out discretionary spaces within casework. However, in Switzerland, collective agency also emerged in the form of anti-cuts campaigning alongside service users. The literature tends to counterpose these micro and macro levels of agency, theorising discretion and resistance to the contradictions and value tensions generated by neoliberal reform as largely a product of practitioners’ individual ethical dispositions. However, we argue that enduring legacies of social justice values and relationship-based practices within social work institutions are also relevant in shaping how social workers navigate reforms. These enduring features offer institutional and normative resources of solidarity which can strengthen the possibilities for practitioner agency, at both individual and collective levels, to resist neoliberal reconfigurations and promote more liberatory and transformative forms of practice. We call this orientation ‘ethico-political professionalism’.
Multiple cognition associated multimodal brain networks in major depressive disorder
Authors: Yang Xiao , Wang Min , Liao Qimeng , Zhao Liansheng , Wei Jinxue , Wang Qiang , Sui Jing , Qi Shile , Ma Xiaohong 
Published: July 2024

Abstract
Major depressive disorder frequently leads to cognitive impairments, significantly affecting patients’ quality of life. However, the neurobiological mechanisms underlying cognitive deficits remain unclear. This study aimed to explore multimodal imaging biomarkers associated with cognitive function in major depressive disorder. Five cognitive scores (sustained attention, visual recognition memory, pattern recognition memory, executive function, and working memory) were used as references to guide the fusion of gray matter volume and amplitude of the low frequency fluctuation. Social function was assessed after 2 yr. Linear regression analysis was performed to identify brain features that were associated with social function of patients with major depressive disorder. Finally, we included 131 major depressive disorder and 145 healthy controls. A multimodal frontal-insula-occipital network associated with sustained attention was found to be associated with social functioning in major depressive disorders. Analysis across different cognitive domains revealed that gray matter volume exhibited greater sensitivity to differences, while amplitude of the low frequency fluctuation consistently decreased in the right temporal-occipital-hippocampus circuit. The consistent functional changes across the 5 cognitive domains were related to symptom severity. Overall, these findings provide insights into biomarkers associated with multiple cognitive domains in major depressive disorder. These results may contribute to the development of effective treatment targeting cognitive deficits and social function.
Elucidating trauma-related and disease-related regional cortical activity in post-traumatic stress disorder
Authors: Zhong Ruihan , Zhang Lianqing , Li Hailong , Wang Yingying , Cao Lingxiao , Bao Weijie , Gao Yingxue , Gong Qiyong , Huang Xiaoqi 
Published: July 2024

Abstract
Trauma exposure may precipitate a cascade of plastic modifications within the intrinsic activity of brain regions, but it remains unclear which regions could be responsible for the development of post-traumatic stress disorder based on intrinsic activity. To elucidate trauma-related and post-traumatic stress disorder–related alterations in cortical intrinsic activity at the whole-brain level, we recruited 47 survivors diagnosed with post-traumatic stress disorder, 64 trauma-exposed controls from a major earthquake, and 46 age- and sex-matched healthy controls. All subjects were scanned with an echo-planar imaging sequence, and 5 parameters including the amplitude of low-frequency fluctuations, fractional amplitude of low-frequency fluctuations, regional homogeneity, degree centrality, and voxel-mirrored homotopic connectivity were calculated. We found both post-traumatic stress disorder patients and trauma-exposed controls exhibited decreased amplitude of low-frequency fluctuations in the bilateral posterior cerebellum and inferior temporal gyrus, decreased fractional amplitude of low-frequency fluctuation and regional homogeneity in the bilateral anterior cerebellum, and decreased fractional amplitude of low-frequency fluctuation in the middle occipital gyrus and cuneus compared to healthy controls, and these impairments were more severe in post-traumatic stress disorder patients than in trauma-exposed controls. Additionally, fractional amplitude of low-frequency fluctuation in left cerebellum was positively correlated with Clinician-Administered PTSD Scale scores in post-traumatic stress disorder patients. We identified brain regions that might be responsible for the emergence of post-traumatic stress disorder, providing important information for the treatment of this disorder.
Fluctuation in cortical excitation/inhibition modulates capability of attention across time scales ranging from hours to seconds
Authors: Yang Binghao , Liu Hao , Jiang Tianzi , Yu Shan 
Published: July 2024

Abstract
Sustained attention, as the basis of general cognitive ability, naturally varies across different time scales, spanning from hours, e.g. from wakefulness to drowsiness state, to seconds, e.g. trial-by-trail fluctuation in a task session. Whether there is a unified mechanism underneath such trans-scale variability remains unclear. Here we show that fluctuation of cortical excitation/inhibition (E/I) is a strong modulator to sustained attention in humans across time scales. First, we observed the ability to attend varied across different brain states (wakefulness, postprandial somnolence, sleep deprived), as well as within any single state with larger swings. Second, regardless of the time scale involved, we found highly attentive state was always linked to more balanced cortical E/I characterized by electroencephalography (EEG) features, while deviations from the balanced state led to temporal decline in attention, suggesting the fluctuation of cortical E/I as a common mechanism underneath trans-scale attentional variability. Furthermore, we found the variations of both sustained attention and cortical E/I indices exhibited fractal structure in the temporal domain, exhibiting features of self-similarity. Taken together, these results demonstrate that sustained attention naturally varies across different time scales in a more complex way than previously appreciated, with the cortical E/I as a shared neurophysiological modulator.
Distinguishable neural circuit mechanisms associated with the clinical efficacy of rTMS in aMCI patients
Authors: Chen Ya , Hou Xinle , Zhou Huijuan , Han RuiChen , Lv Tingyu , Yang Zhiyuan , Zheng Wenao , Bai Feng 
Published: July 2024

Abstract
Repetitive transcranial magnetic stimulation is used in early-stage Alzheimer’s disease to slow progression, but heterogeneity in response results in different treatment outcomes. The mechanisms underlying this heterogeneity are unclear. This study used resting-state neuroimaging to investigate the variability in episodic memory improvement from angular gyrus repetitive transcranial magnetic stimulation and tracked the neural circuits involved. Thirty-four amnestic mild cognitive impairment patients underwent angular gyrus repetitive transcranial magnetic stimulation (4 weeks, 20 Hz, 100% resting motor threshold) and were divided into high-response and low-response groups based on minimal clinically important differences in auditory verbal learning test scores. Baseline and pre/post-treatment neural circuit activities were compared. Results indicated that the orbital middle frontal gyrus in the orbitofrontal cortex network and the precuneus in the default mode network had higher local activity in the low-response group. After treatment, changes in local and remote connectivity within brain regions of the orbitofrontal cortex, default mode network, visual network, and sensorimotor network showed opposite trends and were related to treatment effects. This suggests that the activity states of brain regions within the orbitofrontal cortex and default mode network could serve as imaging markers for early cognitive compensation in amnestic mild cognitive impairment patients and predict the aftereffects of repetitive transcranial magnetic stimulation response.
Antibiotic Prescribing for Respiratory Tract Infections in Urgent Care: A Comparison of In-Person and Virtual Settings
Authors: Martinez Kathryn A , Deshpande Abhishek , Stanley Elizabeth , Rothberg Michael B 
Published: July 2024

Abstract

Background
Little is known about antibiotic prescribing for respiratory tract infections (RTIs) in virtual versus in-person urgent care.

Methods
In this retrospective study, we used electronic health record data from Cleveland Clinic Health System. We identified RTI patients via International Classification of Diseases, Tenth Revision, Clinical Modification, codes and assessed whether the visit resulted in an antibiotic. We described differences in diagnoses and prescribing by setting (virtual versus in-person). We used mixed effects logistic regression to model the odds of antibiotic receipt by urgent care setting. We applied the model first to all physicians and second only to those who saw patients in both settings.

Results
There were 69 189 in-person and 19 003 virtual visits. Fifty-eight percent of virtual visits resulted in an antibiotic compared with 43% of in-person visits. Sinusitis diagnoses were more than twice as common in virtual versus in-person care (36% vs 14%) and were associated with high rates of prescribing in both settings (95% in-person, 91% virtual). Compared with in-person care, virtual urgent care was positively associated with a prescription (odds ratio, 1.64; 95% confidence interval [CI]: 1.53–1.75). Among visits conducted by 39 physicians who saw patients in both settings, odds of antibiotic prescription in virtual care were 1.71 times higher than in in-person care (95% CI: 1.53–1.90).

Conclusions
Antibiotic prescriptions were more common in virtual versus in-person urgent care, including among physicians who provided care in both platforms. This appears to be related to the high rate of sinusitis diagnosis in virtual urgent care.