bluuebunny/crossref_metadata_2025_split huggingface dataset:
MicroHDF: predicting host phenotypes with metagenomic data using a deep forest-based framework
Authors: Shi Kai , Liu Qiaohui , Ji Qingrong , He Qisheng , Zhao Xing-Ming 
Published: October 2024

Abstract
The gut microbiota plays a vital role in human health, and significant effort has been made to predict human phenotypes, especially diseases, with the microbiota as a promising indicator or predictor with machine learning (ML) methods. However, the accuracy is impacted by a lot of factors when predicting host phenotypes with the metagenomic data, e.g. small sample size, class imbalance, high-dimensional features, etc. To address these challenges, we propose MicroHDF, an interpretable deep learning framework to predict host phenotypes, where a cascade layers of deep forest units is designed for handling sample class imbalance and high dimensional features. The experimental results show that the performance of MicroHDF is competitive with that of existing state-of-the-art methods on 13 publicly available datasets of six different diseases. In particular, it performs best with the area under the receiver operating characteristic curve of 0.9182 ± 0.0098 and 0.9469 ± 0.0076 for inflammatory bowel disease (IBD) and liver cirrhosis, respectively. Our MicroHDF also shows better performance and robustness in cross-study validation. Furthermore, MicroHDF is applied to two high-risk diseases, IBD and autism spectrum disorder, as case studies to identify potential biomarkers. In conclusion, our method provides an effective and reliable prediction of the host phenotype and discovers informative features with biological insights.
Prediction of human O-linked glycosylation sites using stacked generalization and embeddings from pre-trained protein language model
Authors: Pakhrin Subash Chandra , Chauhan Neha , Khan Salman , Upadhyaya Jamie , Beck Moriah Rene , Blanco Eduardo 
Published: October 2024

Abstract

Motivation
O-linked glycosylation, an essential post-translational modification process in Homo sapiens, involves attaching sugar moieties to the oxygen atoms of serine and/or threonine residues. It influences various biological and cellular functions. While threonine or serine residues within protein sequences are potential sites for O-linked glycosylation, not all serine and/or threonine residues undergo this modification, underscoring the importance of characterizing its occurrence. This study presents a novel approach for predicting intracellular and extracellular O-linked glycosylation events on proteins, which are crucial for comprehending cellular processes. Two base multi-layer perceptron models were trained by leveraging a stacked generalization framework. These base models respectively use ProtT5 and Ankh O-linked glycosylation site-specific embeddings whose combined predictions are used to train the meta-multi-layer perceptron model. Trained on extensive O-linked glycosylation datasets, the stacked-generalization model demonstrated high predictive performance on independent test datasets. Furthermore, the study emphasizes the distinction between nucleocytoplasmic and extracellular O-linked glycosylation, offering insights into their functional implications that were overlooked in previous studies. By integrating the protein language model’s embedding with stacked generalization techniques, this approach enhances predictive accuracy of O-linked glycosylation events and illuminates the intricate roles of O-linked glycosylation in proteomics, potentially accelerating the discovery of novel glycosylation sites.

Results
Stack-OglyPred-PLM produces Sensitivity, Specificity, Matthews Correlation Coefficient, and Accuracy of 90.50%, 89.60%, 0.464, and 89.70%, respectively on a benchmark NetOGlyc-4.0 independent test dataset. These results demonstrate that Stack-OglyPred-PLM is a robust computational tool to predict O-linked glycosylation sites in proteins.

Availability and implementation
The developed tool, programs, training, and test dataset are available at https://github.com/PakhrinLab/Stack-OglyPred-PLM.
Intra-atrial block after COVID-19 vaccination-induced fulminant myocarditis: a case report
Authors: Ozaki Masatomo , Okawa Keisuke , Oka Akihiro , Okumura Ken 
Published: October 2024

Abstract

Background
Myocarditis is associated with an increased risk of conduction disturbances during the acute phase, which recovers in most cases but rarely recurs during the chronic phase.

Case summary
A 50-year-old man who developed fulminant myocarditis after COVID-19 mRNA vaccination was discharged 24 days after admission. He was readmitted for heart failure associated with two P waves: one P wave (P1) had a normal amplitude and was dissociated from the QRS, and the other (P2) had a very low amplitude and was associated with the QRS. The patient was referred for pacemaker implantation. Before implantation, an electrophysiological study was conducted using electro-anatomical mapping (EAM). During the P1 wave activation, the sinus rhythm spread to the right atrium but was blocked in the atrioventricular (AV) node area. During P2 activation, the activation originated from the right superior pulmonary vein (RSPV), spread to the left atrium and AV node area through the interatrial septum, and was conducted to the right ventricle, exhibiting a complete intra-atrial block with two discrete rhythms. An atrial lead was successfully placed in a narrow area in the right atrial septum where the pacing captured the left atrium and AV node area under the guidance of EAM findings.

Discussion
The EAM technology has demonstrated intra-atrial block and two types of atrial rhythms, sinus and RSPV. Electro-anatomical mapping findings were also useful for identifying the ideal pacemaker implantation site. Synchrony between the left atrium and ventricle via His-Purkinje conduction, which was achieved with EAM-guided atrial septal pacing, was prioritized.
A comprehensive organ protection strategy in total arch replacement: a propensity-weighted analysis
Authors: Zhou Sangyu , Liu Yanxiang , Zhang Bowen , Wang Luchen , Zhao Ruojin , Xie Mingxin , Chen Xuyang , Dun Yaojun , Sun Xiaogang 
Published: October 2024

Abstract

OBJECTIVES
The goal was to report the outcomes and determine the effectiveness of a comprehensive organ protection strategy in total arch replacement.

METHODS
A total of 350 patients who underwent total arch replacement were enrolled. Fifty-four patients underwent the comprehensive organ protection strategy with bilateral antegrade cerebral perfusion and the aortic balloon occlusion technique (comprehensive strategy group); 296 patients underwent the standard strategy with unilateral antegrade cerebral perfusion (standard strategy group). Inverse probability of treatment weighting was used to balance the baseline characteristics.

RESULTS
After inverse probability of treatment weighting, the comprehensive strategy group had lower incidences of 30-day mortality (0.9% vs 4.9%, P = 0.002), continuous renal replacement therapy (0.6% vs 10.3%, P &lt; 0.001), renal failure (4.6% vs 13.7%, P &lt; 0.001), hepatic dysfunction (11.6% vs 21.1%, P = 0.001) and shorter duration of mechanical ventilation [16 (13, 31) vs 20 (14, 48) h, P = 0.011]. Multivariable logistic analysis showed that the comprehensive strategy was an independent protective factor of 30-day mortality [odds ratio (OR): 0.242, 95% confidence interval (CI): 0.068–0.867, P = 0.029], continuous renal replacement therapy (OR: 0.045, 95% CI: 0.008–0.264, P = 0.001), renal failure (OR: 0.351, 95% CI: 0.156–0.788, P = 0.011) and mechanical ventilation &gt;20 h (OR: 0.531, 95% CI: 0.319–0.883, P = 0.015). Kaplan–Meier analysis showed that mid-term survival was comparable.

CONCLUSIONS
The comprehensive organ protection strategy might improve early survival, reduce the use of continuous renal replacement therapy, have protective effects on the kidney and shorten mechanical ventilation time in total arch replacement. This strategy might be considered a viable alternative in total arch replacement.
Autonomic nervous system responses to hypo- and hyperglycemia in type 2 diabetes and prediabetes
Authors: Lundqvist Martin H , Pereira Maria J , Wiklund Urban , Hetty Susanne , Eriksson Jan W 
Published: October 2024

Abstract

Objective
Previous research points to a role of the brain in the regulation of glucose and pathogenesis of type 2 diabetes (T2D) via modulation of counter-regulatory hormone secretion and activity in the autonomic nervous system (ANS). The aim of this study was to investigate glucose-dependent responses of catecholamines and ANS activity in individuals with T2D, prediabetes (PD), and normoglycemia (NG).

Design
Cross-sectional.

Methods
Individuals with T2D (n = 19, 7 men, HbA1c 49 mmol/mol), PD (n = 18, 8 men), and NG (n = 17, 3 men) underwent 1 stepwise hyperinsulinemic–euglycemic–hypoglycemic and 1 hyperglycemic clamp with repeated measurements of catecholamines, symptoms, heart rate variability (HRV), and hemodynamics.

Results
The hypoglycemic response of adrenaline was augmented in T2D and PD vs NG (both P &lt; .05), and there was a strong association with insulin resistance (P &lt; .05 for M-value). In relation to achieved glucose levels in both clamps, noradrenaline exhibited a steeper rise during hypoglycemia in T2D vs NG and PD (both P &lt; .05). There were trends toward more marked autonomic hypoglycemic symptoms in T2D vs PD and NG. By contrast, insulin resistance was associated with attenuated responses of heart rate and HRV indices PLF and PHF at the target glucose plateau of 2.7 mmol/L (P &lt; .05), independent of BMI and HbA1c.

Conclusion
Alterations in glucose-dependent responses of counter-regulatory hormones and the ANS appear before, and probably contribute to, the onset of T2D. Together with other reported alterations in neuroendocrine pathways, the findings suggest that a maladaptation of the brain's responses to glucose fluctuations is important in T2D progression.
Codon optimality influences homeostatic gene expression in zebrafish
Authors: DeVore Michelle L , Bazzini Ariel A 
Published: October 2024

Abstract
The ribosome plays a crucial role in translating mRNA into protein; however, the genetic code extends beyond merely specifying amino acids. Upon translation, codons, the 3-nucleotide sequences interpreted by ribosomes, have regulatory properties affecting mRNA stability, a phenomenon known as codon optimality. Codon optimality has been previously observed in vertebrates during embryogenesis, where specific codons can influence the stability and degradation rates of mRNA transcripts. In our previous work, we demonstrated that codon optimality impacts mRNA stability in human cell lines. However, the extent to which codon content influences vertebrate gene expression in vivo remained unclear. In this study, we expand on our previous findings by demonstrating that codon optimality has a robust effect on homeostatic mRNA and protein levels in whole zebrafish during normal physiological conditions. Using reporters with nearly identical nucleotide sequences but different codon compositions, all expressed from the same genomic locus, we show that codon composition can significantly influence gene expression. This study provides new insights into the regulatory roles of codon usage in vertebrate gene expression and underscores the importance of considering codon optimality in genetic and translational research. These findings have broad implications for understanding the complexities of gene regulation and could inform the design of synthetic genes and therapeutic strategies targeting mRNA stability.
Late-Onset Caloric Restriction Improves Cognitive Performance and Restores Circadian Patterns of Neurotrophic, Clock, and Epigenetic Factors in the Hippocampus of Old Male Rats
Authors: Altamirano Fernando Gabriel , Castro-Pascual Ivanna , Ponce Ivana Tamara , Coria-Lucero Cinthia Daiana , Cargnelutti Ethelina , Ferramola Mariana Lucila , Delgado Marcela Silvia , Anzulovich Ana Cecilia , Lacoste María Gabriela 
Published: October 2024

Abstract
Aging is a complex multifactorial process that results in a general functional decline, including cognitive impairment. Caloric restriction (CR) can positively influence the aging processes and delay cognitive decline. There is a rhythmic variation in memory and learning processes throughout the day, indicating the involvement of the circadian clock in the regulation of these processes. Despite growing evidence on the efficacy of CR, it has not yet been fully determined whether starting this strategy at an advanced age is beneficial for improving quality of life and eventually, for protection against age-related diseases. Here, we investigated the effect of late-onset CR on the temporal organization of the molecular clock machinery, molecules related to cognitive processes and epigenetic regulation, in the hippocampus of old male rats maintained under constant darkness conditions. Our results evidenced the existence of a highly coordinated temporal organization of Bmal1, Clock, Bdnf, Trkb, Dnmts, Sirt1, and Pgc-1α in the hippocampus of young adult rats. We observed that aging led to cognitive deficits and loss of circadian oscillations of all the above variables. Interestingly, CR restored circadian rhythmicity in all cases and, in addition, improved the cognitive performance of the old animals. This work would highlight the importance of the circadian clock and its synchronization with feeding signals, as the basis of the beneficial effects of CR. Thus, lifestyle modifications, such as CR, might be a powerful intervention to preserve hippocampal circadian organization and cognitive health during aging.
Colonial Dis/Continuities in Cameroon and the Postcolonial Dilemma in the Archive
Authors: Ketzmerick-Calandrino Maria 
Published: October 2024

Abstract
Despite how significantly processes of decolonization have shaped contemporary political and social realities, their study remains marginal in the peace and security fields. Understanding historical legacies and how embedded they are in today’s peace and conflict structures is essential to the analysis of current conflicts. This article argues that by tracing dis/continuities in colonial relations, we can gain a better understanding of these contentious processes and of the marginalized positionalities they create. In doing so, much needed research on the ambiguities of these legacies and on who had a say in shaping historical events can be done without reiterating colonial power relations. Alongside its analysis of the Cameroonian internationalized decolonization process under a UN Trusteeship and of how it developed into the current Anglophone conflict, this article uncovers and explores the existing dilemmas in, and potential new avenues for security studies research on colonial dis/continuities using post- and decolonial theories. Its findings and discussion contribute widely to debates within post- and decolonial research, peace, security, and conflict studies.
Biodiversity loss in a gradient of urbanization: rodent community structure in a subtropical area of Northern Argentina
Authors: Burgos Eliana Florencia , Vadell Maria Victoria , Urdapilleta Mara , Salomón Oscar Daniel , Gómez Villafañe Isabel Elisa 
Published: October 2024

Abstract
Urbanization promotes habitat degradation because it involves irreversible processes that homogenize habitats and favor the exclusion of native species. This research evaluates rodent community structure at different levels of urbanization in Misiones, Argentina. We expect that rodent communities are less diverse in more highly urbanized areas and that communities differ between each level of urbanization. To assess these hypotheses, rodent capture sessions were carried out from July 2017 to March 2020, totaling 21,985 trap-nights. Alpha and beta diversity were calculated for each level of urbanization. We captured a total of 684 individuals belonging to 8 sylvan-native and 2 commensal-exotic species. Species richness was greatest and evenness was lowest in natural protected areas. The native species Akodon montensis was the most abundant, while the remaining 7 native species represented less than 23% of the total of captures. The rural area showed the second-highest richness, and the community was principally represented by 2 native and 2 exotic species. The periurban area was ranked third in richness and with the highest evenness, dominated by A. montensis followed by Mus musculus and Rattus rattus. The urban area exhibited the lowest richness represented only by the 2 commensal-exotic species. In agreement with our expectations, these results show a negative association between urbanization level and small rodent diversity, evidenced by a reduction in the number of native species in highly urbanized areas.
The Need for an Improved Mental Health Care System
Authors: Blau Gary M. , Petrila John , Keller Andy 
Published: October 2024

Abstract
What is referred to in the United States as the “mental health care system” is actually a set of fragmented services provided inequitably by a haphazard array of specialty providers, often only tenuously connected to health care systems for other health needs. COVID-19 exacerbated these challenges, significantly worsening the mental health of many people. This chapter provides a historical context for the need to transform the mental health system in America. We describe the shift from treating mental illnesses as threats to public safety to approaches that conceptualize mental illnesses as treatable health conditions. This chapter describes a path to accelerate the transformation of mental health and addiction care in the United States, offering six “seismic shifts” that will allow people with mental illness to benefit from advances in medicine and end the brain/body dichotomy that historically and culturally has marked and impeded equitable care for people with mental illness.
The Architecture of a Modern Psychiatric Facility
Authors: Murdock Pitts Francis 
Published: October 2024

Abstract
“The Architecture of a Modern Psychiatric Facility” discusses the importance of architectural design in creating therapeutic environments for people with mental illness. It emphasizes the use of environment as a clinical tool to support patient recovery. Traditional psychiatric hospitals often lacked supportive design, reflecting a gap between clinical needs and architectural innovation. Modern psychiatric hospitals emerged from interdisciplinary developments starting in the 1950s, including Humphry Osmond’s work, Team X’s human-centered design, environmental psychology, and the consumer-driven person-centered care movement. These advances have led to a new cohort of clinicians and designers who see the built environment as integral to recovery-based care. Despite these trends, there is still a tendency to prioritize functional and security mechanisms over supportive environments. This chapter highlights the need for ongoing collaboration between clinicians and architects to create spaces that truly support mental health care.
Improving Access through Collaboration and Consultation in Washington State
Authors: Unützer Jürgen , Sladek Rebecca 
Published: October 2024

Abstract
In this chapter, we discuss efforts to improve access to behavioral health care through consultation and collaboration with primary care, school-based care, and other health and social service providers. Examples of partnerships between the university, local communities, and statewide efforts are highlighted. As with the prior chapter, we incorporate considerations about the unique geography of the state that impacts relevant polices, funding and organization of behavioral health care in Washington State. This chapter describes the efforts of thousands of dedicated individuals, families, stakeholders, and experts throughout the state of Washington and the Pacific Northwest region and the work of more than a thousand faculty, staff, and trainees in the Department of Psychiatry and Behavioral Sciences at the University of Washington. The programs described are only a small sampling of local and statewide efforts, and the authors wish to express their gratitude for the seemingly endless dedication and inspiration of our colleagues and partners working together to improve behavioral health care in the state of Washington and the Pacific Northwest.
Beyond the Surface: Medical Evaluation of Anxiety Conditions
Authors: Mehra Ash , Padilla Vanessa 
Published: October 2024

Abstract
In this chapter on the medical evaluation of anxiety conditions, the case of Ms. T, a 45-year-old woman with acute-onset severe anxiety symptoms, serves as a focal point for understanding the importance of thorough medical assessment in such cases. Ms. T’s history, physical examination, and laboratory findings are explored to highlight key indicators that can point clinicians toward underlying medical illnesses causing anxiety symptoms. This chapter emphasizes that anxiety symptoms can sometimes be a result of medical conditions, medications, or substances, rather than a primary anxiety disorder. Several medical conditions commonly associated with anxiety are discussed. The importance of a comprehensive medical evaluation is emphasized. It underscores the need for clinicians to consider and investigate medical conditions that can mimic or exacerbate anxiety symptoms to ensure appropriate diagnosis and treatment. Early identification and appropriate management of underlying medical causes are essential for providing optimal care to patients presenting with anxiety.
When Fear Collides: Panic Attacks Within the Spectrum of Anxiety Disorders
Authors: Alkharboush Feras , Alhajji Lujain 
Published: October 2024

Abstract
This chapter introduces Ms. A, a 30-year-old woman with a history of generalized anxiety disorder (GAD) who presents to the emergency department in the midst of a panic attack. After a thorough medical evaluation ruling out physical causes, it becomes evident that Ms. A’s symptoms are rooted in acute panic triggered by her fear of public speaking. However, it is not just panic disorder at play here; she also exhibits signs of social anxiety disorder (SAD) and GAD. The chapter delves into the assessment of panic attacks in various anxiety disorders. The primary focus of treatment is to reduce the frequency and intensity of panic attacks while addressing underlying conditions. A combination of lifestyle changes, psychotherapy, and medications is often the approach. This chapter emphasizes the importance of accurate diagnosis and tailored treatment for panic attacks in the context of SAD and GAD.
Worry or Obsession? Distinguishing Obsessions From Everyday Worries
Authors: Kabli Moayad R. , Ezzedine Reem , Botros Mousa 
Published: October 2024

Abstract
In this chapter, Ms. S, a 34-year-old woman, visits an obstetrics clinic for a postpartum checkup 6 weeks after giving birth. While her physical condition and her newborn daughter’s health are good, she expresses increasing distress due to constant worry about her baby’s well-being. She experiences distressing thoughts about something terrible happening to her child, leading to compulsive behaviors like checking on her baby multiple times a day and frequently calling her husband for reassurance. These intrusive thoughts and behaviors disrupt her sleep and daily activities. This chapter discusses the differentiation between generalized anxiety disorder and obsessive-compulsive disorder. Treatment approaches for both disorders include psychotherapy and medication.