bluuebunny/crossref_metadata_2025_split huggingface dataset:
Deep neural network learning biological condition information refines gene-expression-based cell subtypes
Authors: Fan Zhenjiang , Sun Jie , Thorpe Henry , Lee Stephen , Kim Soyeon , Park Hyun Jung 
Published: January 2024

Abstract
With the recent advent of single-cell level biological understanding, a growing interest is in identifying cell states or subtypes that are homogeneous in terms of gene expression and are also enriched in certain biological conditions, including disease samples versus normal samples (condition-specific cell subtype). Despite the importance of identifying condition-specific cell subtypes, existing methods have the following limitations: since they train models separately between gene expression and the biological condition information, (1) they do not consider potential interactions between them, and (2) the weights from both types of information are not properly controlled. Also, (3) they do not consider non-linear relationships in the gene expression and the biological condition. To address the limitations and accurately identify such condition-specific cell subtypes, we develop scDeepJointClust, the first method that jointly trains both types of information via a deep neural network. scDeepJointClust incorporates results from the power of state-of-the-art gene-expression-based clustering methods as an input, incorporating their sophistication and accuracy. We evaluated scDeepJointClust on both simulation data in diverse scenarios and biological data of different diseases (melanoma and non-small-cell lung cancer) and showed that scDeepJointClust outperforms existing methods in terms of sensitivity and specificity. scDeepJointClust exhibits significant promise in advancing our understanding of cellular states and their implications in complex biological systems.
Detection of acute coronary occlusion with a novel mobile electrocardiogram device: a pilot study
Authors: Zepeda-Echavarria Alejandra , van de Leur Rutger R , Vessies Melle , de Vries Nynke M , van Sleuwen Meike , Hassink Rutger J , Wildbergh Thierry X , van Doorn J L , van der Zee Rien , Doevendans Pieter A , Jaspers Joris E N , van Es René 
Published: January 2024

Abstract

Aims
Many portable electrocardiogram (ECG) devices have been developed to monitor patients at home, but the majority of these devices are single lead and only intended for rhythm disorders. We developed the miniECG, a smartphone-sized portable device with four dry electrodes capable of recording a high-quality multi-lead ECG by placing the device on the chest. The aim of our study was to investigate the ability of the miniECG to detect occlusive myocardial infarction (OMI) in patients with chest pain.

Methods and results
Patients presenting with acute chest pain at the emergency department of the University Medical Center Utrecht or Meander Medical Center, between May 2021 and February 2022, were included in the study. The clinical 12-lead ECG and the miniECG before coronary intervention were recorded. The recordings were evaluated by cardiologists and compared the outcome of the coronary angiography, if performed. A total of 369 patients were measured with the miniECG, 46 of whom had OMI. The miniECG detected OMI with a sensitivity and specificity of 65 and 92%, compared with 83 and 90% for the 12-lead ECG. Sensitivity of the miniECG was similar for different culprit vessels.

Conclusion
The miniECG can record a multi-lead ECG and rule-in ST-segment deviation in patients with occluded or near-occluded coronary arteries from different culprit vessels without many false alarms. Further research is required to add automated analysis to the recordings and to show feasibility to use the miniECG by patients at home.
Evolution of journal clubs: fostering collaborative learning in modern research
Authors: Balamurali Deepak , Preda Mihai Bogdan , Ben-Aicha Soumaya , Martino Fabiana , Palioura Dimitra , Kocken Jordy M M , Emanueli Costanza , Devaux Yvan 
Published: January 2024

Abstract
Journal clubs have been a staple in scientific communities, facilitating discussions on recent publications. However, the overwhelming volume of biomedical information poses a challenge in literature selection. This article provides an overview of journal club types and their efficacy in training potential peer reviewers, enhancing communication skills, and critical thinking. Originating in the 19th century, journal clubs have evolved from traditional in-person meetings to virtual or hybrid formats, accelerated by the COVID-19 pandemic. Face-to-face interactions offer personal connections, while virtual events ensure wider participation and accessibility. Organizing journal clubs demands effort, but it has several benefits, including promoting new publications and providing a platform for meaningful discussions. The virtual CardioRNA J-club experience exemplifies successful multidisciplinary collaboration, fostering international connections and inspiring new research. Journal clubs remain a vital component of academic research, equipping senior researchers with the latest developments and nurturing the next generation of scientists. As millennial and Gen Z researchers join the scientific field, journal clubs continue to evolve as a fertile ground for education and collaborative learning in an ever-changing scientific landscape.
Effects of mango and partridge tea extracts on microbial, physical, and chemical properties of tilapia fillets treated with in-package cold plasma during refrigerator storage
Authors: Liu Chencheng , Wang Jiamei , Su Weiming , Chen Gu , Zhang Jianhao 
Published: January 2024

Abstract

Objectives
The effect of natural extracts on the oxidative quality of cold plasma (CP)-treated tilapia fillets during 9 d refrigerator storage was explored by adding mango and partridge tea extracts as natural antioxidants.

Materials and Methods
The effects of mango and partridge tea extracts on the fish during storage were evaluated using the total viable count (TVC), total volatile basic nitrogen (TVB-N), thiobarbituric acid reactive substance (TBARS), carbonyl values, and color.

Results
The results showed that on the ninth day, the TVC of the mango extract (ME)-CP group was 3.52±0.08 log colony-forming units/g, which was significantly (P&lt;0.05) lower than that of the other groups, while the TBARS of ME-CP and partridge tea extract (MOE)-CP was similar. The TVB-N values in the ME-CP and MOE-CP groups were 10.21±0.7 mg/100 g and 14.27±0.31 mg/100 g, respectively, which were within the acceptable values. The sulfhydryl and carbonyl contents in ME-CP were lower than those in MOE-CP; however, no significant variation was detected in texture. No significant changes were observed in the L* values among the treatment groups, while the b* values in the MOE-CP group were significantly increased (P&lt;0.05).

Conclusions
Therefore, the addition of ME combined with CP treatment can inhibit microbial growth, lipid oxidation, and protein oxidation in tilapia fillets without significantly impacting their color.
Antibody-Mediated Serum Resistance Protects Pseudomonas aeruginosa During Bloodstream Infections
Authors: Hickson Sarah M , Hoehensteiger Johannes K , Mayer-Coverdale Johanna , Torres Von Vergel L , Feng Wenkang , Monteith Joshua N , Henderson Ian R , McCarthy Kate L , Wells Timothy J 
Published: January 2024

Abstract

Background
Pseudomonas aeruginosa is a frequent pathogen isolated from bacterial bloodstream infection (BSI) and is associated with high mortality. To survive in the blood, P aeruginosa must resist the bactericidal action of complement (ie, serum killing). Antibodies usually promote serum killing through the classical complement pathway; however, “cloaking antibodies” (cAbs) have been described, which paradoxically protect bacteria from serum killing. The relevance of cAbs in P aeruginosa BSI is unknown.

Methods
Serum and P aeruginosa were collected from a cohort of 100 patients with BSI. Isolates were tested for sensitivity to healthy control serum (HCS). cAb prevalence was determined in sera. Patient sera were mixed with HCS to determine if killing of the matched isolate was inhibited.

Results
Overall, 36 patients had elevated titers of cAbs, and 34 isolates were sensitive to HCS killing. Fifteen patients had cAbs and HCS-sensitive isolates; of these patients, 14 had serum that protected their matched bacteria from HCS killing. Patients with cAbs were less likely to be neutropenic or have comorbidities.

Conclusions
cAbs are prevalent in patients with P aeruginosa BSI and allow survival of otherwise serum-sensitive bacteria in the bloodstream. Generation of cAbs may be a risk factor for the development of BSI.
Baldwin and Wittgenstein on White Supremacism and Religion
Authors: Carroll Thomas D 
Published: January 2024

Abstract
This article contends that James Baldwin’s exploration of racism and resistance to it in The Fire Next Time may be put into conversation with Ludwig Wittgenstein’s consideration of fundamental epistemic commitments in On Certainty. Out of this constructive engagement, I argue that white supremacism in the United States may be interpreted as being like a Wittgensteinian grounding or “hinge” commitment and that this viewpoint illuminates some of the ways in which white supremacism may interact with various kinds of religious commitments. This combined analysis depicts, first, the extent to which fundamental commitments about race deeply affect people, including the formation of their ethical and civic values, existential and religious commitments, and range of empathetic capacity and, second, similarities between Baldwin and Wittgenstein when it comes to their contentions that there is ethical value in the clarification of language and work on oneself.
Influence of season on the microbial population dynamics of activated sludge
Authors: Stratton Helen M , Nittami Tadashi , Esteban Nicolas Herraiz , Petrovski Steve , Seviour Robert J 
Published: January 2024

Abstract
This review discusses critically how seasonal changes might affect the community composition and dynamics of activated sludge wastewater treatment plants, and examines the factors thought more generally to control microbial community assembly, including the role of taxa–time relationships and stochastic and deterministic influences. The review also questions the differences in protocols used in these studies, which make any subsequent attempts at data comparisons problematic. These include bacterial DNA extraction and PCR methodologies, 16S rRNA sequencing and especially its depth, and subsequent statistical analyses of the data, which together often fail to reveal seasonal dynamic community shifts. Suggestions are given as to how experimental protocols need to be improved and standardized, and especially the requirement to examine bacterial populations at the species level. This review looks critically at what is known currently about seasonal influences on key members of this community, including viruses, the bacteria responsible for nitrogen and phosphorus removal and those causing bulking and foaming. The data show many of these species exhibit replicative seasonal abundances over several years, but not under all conditions, illustrating how complex these community dynamics are. Fungal and protozoal/metazoal seasonal community dynamics, less studied, are also discussed. The current data suggest that seasonal temperature fluctuations are responsible for most of the seasonal community dynamics by selectively favouring or otherwise individual populations. However, more longer term studies carried out under much stricter controlled conditions are required.
Urban sprawl and racial inequality in intergenerational mobility
Authors: Xiong Ning , Wei Yehua Dennis , Rey Sergio J 
Published: January 2024

Abstract
Persistent racial inequality in socioeconomic status within urban areas has been a significant concern in both the US and European countries. Differences across racial groups in intergenerational mobility (IM) have been identified as a key source of this persistence. However, efforts to understand racial inequality in IM have rarely considered the role of urban sprawl. This article argues that urban sprawl affects differences in IM between racial groups directly and indirectly through racial segregation, racial bias, and social capital. We analyze data from 874 metropolitan counties in the US using structural equation models to test these direct and indirect effects of sprawl on racial inequality in IM. We found that urban sprawl was negatively associated with racial inequality in IM. The direct effect, which we partially attribute to higher racial disparities in social capital in more compact counties, was statistically significant. For the indirect effects, racial segregation had the largest mediating effects between urban sprawl and racial inequality in IM, followed by economic connectedness (EC) and racial bias. The net indirect effect of sprawl on racial inequality in IM was negative because negative indirect effects through racial segregation and EC outweigh positive indirect effects through racial bias. Our findings demonstrate the significant role of urban form in racial inequality in IM.
Alteration of functionality and differentiation directed by changing gene expression patterns in myeloid-derived suppressor cells (MDSCs) in tumor microenvironment and bone marrow through early to terminal phase of tumor progression
Authors: Mahanti Krishna , Saha Jayasree , Sarkar Debanjan , Pramanik Anik , Roy Chattopadhyay Nabanita , Bhattacharyya Sankar 
Published: January 2024

Abstract
Myeloid-derived suppressor cells are heterogenous immature myeloid lineage cells that can differentiate into neutrophils, monocytes, and dendritic cells as well. These cells have been characterized to have potent immunosuppressive capacity in neoplasia and a neoplastic chronic inflammatory microenvironment. Increased accumulation of myeloid-derived suppressor cells was reported with poor clinical outcomes in patients. They support neoplastic progression by abrogating antitumor immunity through inhibition of lymphocyte functions and directly by facilitating tumor development. Yet the shifting genetic signatures of this myeloid lineage cell toward immunosuppressive functionality in progressive tumor development remain elusive. We have attempted to identify the gene expression profile using lineage-specific markers of these unique myeloid lineage cells in a tumor microenvironment and bone marrow using a liquid transplantable mice tumor model to trace the changing influence of the tumor microenvironment on myeloid-derived suppressor cells. We analyzed the phenotype, functional shift, suppressive activity, differentiation status, and microarray-based gene expression profile of CD11b+Gr1+ lineage-specific cells isolated from the tumor microenvironment and bone marrow of 4 stages of tumor-bearing mice and compared them with control counterparts. Our analysis of differentially expressed genes of myeloid-derived suppressor cells isolated from bone marrow and the tumor microenvironment reveals unique gene expression patterns in the bone marrow and tumor microenvironment–derived myeloid-derived suppressor cells. It also suggests T-cell suppressive activity of myeloid-derived suppressor cells progressively increases toward the mid-to-late phase of the tumor and a significant differentiation bias of tumor site myeloid-derived suppressor cells toward macrophages, even in the presence of differentiating agents, indicating potential molecular characteristics of myeloid-derived suppressor cells in different stages of the tumor that can emerge as an intervention target.
‘Trying to patch a broken system’: Exploring institutional work among care professions for interprofessional collaboration
Authors: Hald Andreas Nielsen , Bech Mickael , Enemark Ulrika , Shaw Jay , Burau Viola 
Published: January 2024

Abstract
There is a growing interest in understanding when and why interprofessional collaborations are well functioning, especially within healthcare systems. However, more knowledge is needed about how professionals affect and contribute to these collaborations when they engage in them. To address this shortcoming, this study aims to contribute to professional and organizational studies of interprofessional collaboration by providing novel insights into how professionals engage in and contribute to interprofessional collaborations. It builds on a theoretical perspective of examining professionals’ everyday collaboration practices through the interplay between temporal-oriented agency and institutional work. It applies this perspective to a case study of interprofessional collaboration between personal workers (PWs), nurses, and therapists in the home care sector in Denmark. Overall, the findings show that the professionals engaged in and contributed to the interprofessional collaboration by ‘trying to patch a broken system’. All three professional groups did this primarily by ‘adopting new practices to deal with inept institutionalized practices’ to maintain collaboration. Additionally, some PWs ‘failed to enact institutionalized practices’ to disrupt the collaboration, and some nurses and therapists ‘invented and established mechanisms’ to create new arrangements for the collaboration. Based on the findings, the study demonstrates that certain dimensions of agency are associated with certain types of institutional work. Furthermore, the study suggests that the interplay between agency and institutional work varies between professional groups, influenced by their relative autonomy.
Stevens–Johnson syndrome/toxic epidermal necrolysis in an orthotopic liver transplant recipient: a case report
Authors: Huang Chun-Sing , Strouphauer Emily , O’Mahony Christine , Galván Nhu T N , Cotton Ronald , Goss John , Rana Abbas 
Published: January 2024

Abstract
Stevens–Johnson syndrome/toxic epidermal necrolysis (SJS/TEN) is a rare spectrum of acute, mucocutaneous drug reactions characterized by epidermal necrosis of the skin and mucous membranes with progressive multiorgan failure. Cutaneous presentation of SJS/TEN is similar to that of acute graft-versus-host disease, creating a diagnostic dilemma in solid-organ transplant recipients presenting with diffuse, erythematous eruptions, skin sloughing, and systemic sequelae, reflective of both diseases. This case report details a 48-year-old woman post-orthotopic liver transplantation (OLT) who developed a diffuse, painful, morbilliform rash with progressive desquamation, along with corresponding pathological analysis indicative of SJS/TEN. There are few documented reports of SJS/TEN in solid-organ transplant recipients, and this case illustrates successful intervention and resolution of SJS/TEN in an OLT recipient while managing intraabdominal sepsis and an episode of acute rejection. Despite its rarity, prompt diagnosis of SJS/TEN and the implementation of tailored therapeutic strategies are crucial in the care of solid-organ transplant recipients.
Microsurgery for brain aneurysms in an accessory A2 and basilar arteries: a rare case presentation and surgical video
Authors: Bocanegra-Becerra Jhon E , Acha Sánchez José Luis , Contreras Montenegro Luis 
Published: January 2024

AbstractWe present the case of a 58-year-old male with a 3-day history of sudden onset headache, loss of consciousness, and uncontrolled vomiting. The patient had 3/5 quadriparesis and a Glasgow coma scale (GCS) score of 8, which merited neurocritical intensive care. Brain imaging suggested the presence of two lesions: (i) a fusiform aneurysm of 12 × 7 mm in an accessory A2 artery of the anterior cerebral artery and (ii) an unruptured saccular aneurysm of 3.3 × 2.8 mm in the distal segment of the basilar artery. He was deemed a candidate for microsurgical management. Postoperatively, he had 4/5 quadriparesis, paresis of the right oculomotor nerve, and a GCS score of 13. A 3-month follow-up showed a significant improvement in neurological function with a score of 2 on the modified Rankin scale. The presented case illustrates the relevance of a nuanced acquaintance to operate in diseased anatomical variants and complex pathologies of narrow corridors.
Search for interacting galaxy clusters from SDSS DR-17 employing optimized friends-of-friends algorithm and multimessenger tracers
Authors: Oak Tejas , Paul Surajit 
Published: January 2024

ABSTRACT
In the theoretical framework of hierarchical structure formation, galaxy clusters evolve through continuous accretion and mergers of substructures. Cosmological simulations have revealed the best picture of the universe as a 3D filamentary network of dark-matter distribution called the cosmic web. Galaxy clusters are found to form at the nodes of this network and are the regions of high merging activity. Such mergers being highly energetic, contain a wealth of information about the dynamical evolution of structures in the Universe. Observational validation of this scenario needs a colossal effort to identify numerous events from all-sky surveys. Therefore, such efforts are sparse in literature and tend to focus on individual systems. In this work, we present an improved search algorithm for identifying interacting galaxy clusters and have successfully produced a comprehensive list of systems from SDSS DR-17. By proposing a set of physically motivated criteria, we classified these interacting clusters into two broad classes, ‘merging’ and ‘pre-merging/postmerging’ systems. Interestingly, as predicted by simulations, we found that most cases show cluster interaction along the prominent cosmic filaments of galaxy distribution (i.e. the proxy for dark matter filaments), with the most violent ones at their nodes. Moreover, we traced the imprint of interactions through multiband signatures, such as diffuse cluster emissions in radio or X-rays. Although we could not find direct evidence of diffuse emission from connecting filaments and ridges; our catalogue of interacting clusters will ease locating such faintest emissions as data from sensitive telescopes such as eROSITA or SKA, becomes accessible.
Characteristics of patients presenting with concomitant carpal tunnel syndrome at the initial diagnosis with rheumatoid arthritis
Authors: Nakamura Taiki , Nagira Keita , Nakagawa Naoki , Takasu Yuta , Ishida Koji , Hayashibara Masako , Hagino Hiroshi , Nagashima Hideki 
Published: January 2024

ABSTRACT

Objective
To investigate the clinical characteristics of patients who presented with concomitant carpal tunnel syndrome (CTS) at the initial diagnosis with rheumatoid arthritis (RA).

Methods
We analyzed patients with newly diagnosed RA at a single institution between 2012 and 2021. Patient demographic and laboratory data, the 2010 ACR/EULAR classification criteria, and the duration from the initial visit to RA diagnosis were compared between RA patients with concomitant CTS (RA with CTS group) and those without CTS (RA without CTS group).

Results
The study included 235 patients (157 females), of which 11 patients (4.7%) presented with CTS at the initial diagnosis with RA. In the RA with CTS group, the age was significantly higher (P = .033), all patients were female, and anti-cyclic citrullinated peptide antibody (ACPA) was negative, and the duration to RA diagnosis was longer than in the RA without CTS group. Among all RA with CTS patients, ultrasonography showed power Doppler signal-positive tenosynovitis in the carpal tunnel, which is not usually detected in idiopathic CTS.

Conclusions
Patients with concomitant CTS at the initial diagnosis with RA were characterized by old age, female sex, and negative ACPA. Patients with symptoms of CTS should undergo ultrasonography for early diagnosis of RA.