bluuebunny/crossref_metadata_2025_split huggingface dataset:
Beethoven and the Catholic Enlightenment in Bonn
Authors: Chong Nicholas 
Published: November 2024

AbstractThis chapter focuses on the religious aspects of Beethoven’s upbringing in Bonn. Many accounts of the composer’s youth have emphasized Bonn’s progressive and enlightened environment but have overlooked the central role of the Catholic Enlightenment in this situation. Beethoven was exposed to Catholic Enlightenment ideas through his training as a church musician and his interactions with various intellectual and artistic figures, including those sympathetic to Freemasonry, which was often considered compatible with Catholic belief. His Bonn works Der freie Mann and the Joseph Cantata also reflect Catholic Enlightenment concerns. In addition, the only copy of the Bible he is known to have owned can be tied indirectly to the Catholic Enlightenment. The chapter concludes by considering the possibility that during the first decade after he moved from Bonn to Vienna, Beethoven’s outlook may have become open to more conservative ideas in reaction to the upheavals caused by war and revolution.
The Quiet Death of Broughtonism
Authors: Macfarlane Kirsten 
Published: November 2024

Abstract
With the return of Pynchon and others to England, the community they had established in New England lost its momentum. Although Pynchon and Holyoke’s books circulated for several generations, the ideals that motivated them ceased to have significance for North American religious life. And yet there was one surprising legacy of Broughtonism in the figure of the renowned Hebraist John Lightfoot. Lightfoot was inspired to learn Hebrew due to his contact with old members of the London Broughtonians, and his 1662 edition of Broughton’s works marked simultaneously the ossification of their community and their most enduring scholarly contribution. As well as surveying the quiet death of Broughtonism, this chapter highlights the importance of this book’s findings for our understanding of the intellectual dimensions of puritanism, and particularly the dynamic, mutually renewing interactions between the elite world of neo-Latin scholarship and the vernacular religious culture of lay men and women.
Francis Johnson’s Letter to William Pynchon, 16 September 1615
Authors: Macfarlane Kirsten 
Published: November 2024

Abstract
Appendix 2 offers an annotated semi-diplomatic edition of a letter sent in 1615 from Francis Johnson, pastor of the Ancient Separatist Church at Amsterdam, to a young William Pynchon. The letter, preserved in Harvard University Archives, sets out Johnson’s interpretation of Matthew 18:17 in light of the fierce controversies over excommunication that were then rocking the English exile churches in the Netherlands.
Machine learning–assisted literature screening for a medication-use process–related systematic review
Authors: Cawley Michelle , Carlson Rebecca , Vest Tyler A , Eckel Stephen F 
Published: November 2024

Abstract

Purpose
This article summarizes a novel methodology of applying machine learning (ML) algorithms trained with external training data to assist with article screening for 2 annual review series related to the medication-use process (MUP) generally and the MUP in ambulatory care settings (ACMUP) specifically. As the literature review for these 2 series grew over time, it became essential for the authors to develop methods to be efficient while still capturing most of the relevant literature. The ML model can be used to predict whether search results are likely to be relevant or not relevant. Results least likely to be relevant can then be excluded without manual screening, allowing research teams to save time that would otherwise be spent reviewing a portion of the search results for inclusion. ML models require a large training dataset typically derived from the unclassified corpus. In this study, the authors demonstrate the efficacy of training the ML model using external training data, which is possible in scenarios such as a systematic review update or ongoing review series such as those for the MUP and ACMUP.

Summary
The authors ran 3 simulations using screening decisions from previous publications and in-process manuscripts for the MUP and ACMUP review series to test the efficacy of the approach. The simulations were compared to actual manual screening decisions made by the research teams to include or exclude articles using title and abstract text. For each simulation, the authors developed a training dataset using a sample of screening decisions from previous years to predict article relevance in an “unclassified” corpus. In this case, the screening decisions for the unclassified corpus were actually known, allowing us to calculate recall (percent of relevant articles captured) and time saved using the number of articles that would be excluded without manual review. Combined, the ML approach correctly labeled 187 of 192 relevant studies. The 3 simulations included 17,227 unique studies, and using ML the authors demonstrated that 13,201 studies could have been excluded without manual screening while still maintaining recall of relevant articles of 95% or greater.

Conclusion
This novel approach is applicable to systematic reviews and ongoing review series, including those for the MUP and ACMUP. Pharmacists have a duty to review and incorporate best practices into their organizations to improve the efficiency and cost of care, optimally utilize technology, and reduce the potential for medication errors. This methodology will allow evidence syntheses for the MUP and other disciplines in pharmacy practice to be published more expeditiously by saving significant time during the article screening step.
Bridging the continuity: Practice-enhancing publications about the ambulatory care medication-use process in 2021
Authors: Gazda Nicholas P , Vest Tyler A , Peek Grayson K , Eckel Stephen F 
Published: November 2024

Abstract

Purpose
This article identifies, prioritizes, and summarizes published literature on the ambulatory care medication-use process (ACMUP) from calendar year 2021 that can impact ambulatory pharmacy practice. The MUP is the foundational system that provides the framework for safe medication utilization within the healthcare environment and was reimagined to focus on new innovations and advancements in ambulatory pharmacy practice. The ACMUP is defined in this article as having the following components: transitions of care, prescribing and collaborative practice, accessing care, adherence, and monitoring and quality. Articles evaluating at least one step of the ACMUP were assessed for their usefulness toward practice improvement.

Summary
A PubMed search was conducted in January 2022 for the year 2021 using targeted Medical Subject Headings keywords and the tables of contents of selected pharmacy journals were also searched, providing a total of 6,026 articles. A thorough review identified 86 potentially practice-enhancing articles: 10 for transitions of care, 9 for prescribing and collaborative practice, 20 for adherence, 17 for accessing care, 18 for monitoring and quality, and 12 for monitoring and medication therapy management. Ranking of the articles for importance by peers led to the selection of key articles from each category. The highest ranked articles are briefly summarized, with a mention of why each article is important. The other articles are listed for further review and evaluation.

Conclusion
It is important to routinely review the published literature and to incorporate significant findings into daily practice. This article continues a series of articles defining and evaluating the currently published literature around the ACMUP. As healthcare continues to advance and care shifts to ambulatory settings, the ACMUP will continue to be a crucial process to evaluate.
Challenge of validation in whole-cell spike-in amplicon sequencing to comprehensively quantify food lactic acid bacteriota
Authors: Oshiro Mugihito , Nakamura Keisuke , Tashiro Yukihiro 
Published: November 2024

Abstract
Lactic acid bacteria (LAB) shape diverse communities in fermented foods. Developing comprehensive quantification methods for community structure will revolutionize our understanding of food LAB microbiome. For this purpose, 16S rRNA gene amplicon-based quantification, using spiked exogenous bacterial cells as an internal standard, shows potential for comprehensiveness and accuracy. We validated cell spike-in amplicon sequencing for quantifying LAB communities in food. Low efficiency of LAB DNA extraction underscores the importance of compensating for DNA loss by spiking internal standard cells. Quantitative equations generated using 15 selected LAB mock species showed positive relationships between the ratio of MiSeq read counts and the expected 16S rRNA gene copy numbers, with coefficients of determination (R2) ≥ 0.6823. The fold differences between observed and expected 16S copy numbers were within the range of 1/3 to 3-fold. Our validation highlights that accurate preparation of the LAB mock community is crucial for cell spike-in amplicon sequencing accuracy.
Androgens suppress the sialyltransferases ST3GAL1 and ST3GAL4 and modulate mucin 10 glycosylation in the submandibular gland, related to sex differences in commensal microbiota composition in mice
Authors: Deminami Mana , Hashimoto Miku , Takahashi Hiroki , Harada Naoki , Minami Yukari , Kitakaze Tomoya , Masuda Wataru , Takenaka Shigeo , Inui Hiroshi , Yamaji Ryoichi 
Published: November 2024

Abstract
Sex differences exist in the commensal microbiota that impact on multiple physiological processes in the host. Here, we examined the mechanism by which the sex differences are formed. In addition to the epithelial ductal cell, the acinar cell mass in the submandibular gland was associated with androgen–androgen receptor (AR) signaling. Sex differences in the formation of submandibular mucin 10 (MUC10) were identified using SDS-PAGE. Neuraminidase treatment, which hydrolyzes terminal sialic acid, influenced the mobility shift of MUC10. Androgen–AR signaling negatively regulated ST3 β-galactoside α-2,3-sialyltransferase 1 (St3gal1) and St3gal4 in the submandibular gland. There was a trend and significant sex differences in α-diversity (Shannon, P = .09) and β-diversity (unweighted UniFrac) in oral microbiota composition, respectively. Some female-preferring bacteria including Akkermansia muciniphila can assimilate mucin by degrading terminal sialic acids. Our results indicate that androgen–AR signaling suppresses ST3GAL1 and ST3GAL4, which can influence sex differences in commensal microbiota composition.
LncLSTA: a versatile predictor unveiling subcellular localization of lncRNAs through long-short term attention
Authors: Wang Kai , Hu Yueming , Li Sida , Chen Ming , Li Zhong 
Published: November 2024

Abstract

Motivation
Much evidence suggests that the subcellular localization of long-stranded noncoding RNAs (LncRNAs) provides key insights for the study of their biological function.

Results
This study proposes a novel deep learning framework, LncLSTA, designed for predicting the subcellular localization of LncRNAs. It firstly exploits LncRNA sequence, electron-ion interaction pseudopotentials, and nucleotide chemical property as feature inputs. Departing from conventional k-mer approaches, this model uses a set of 1D convolutional and maxpooling operations for dynamical feature aggregation. Furthermore, LncLSTA integrates a long-short term attention module with a bidirectional long and short term memory network to comprehensively extract sequence information. In addition, it incorporates a TextCNN module to enhance accuracy and robustness in subcellular localization tasks. Experimental results demonstrate the efficacy of LncLSTA, showcasing its superior performance compared to other state-of-the-art methods. Notably, LncLSTA exhibits the transfer learning capability, extending its utility to predict the subcellular localization prediction of mRNAs, while maintaining consistently satisfactory prediction results. This research contributes valuable insights into understanding the biological functions of LncRNAs through subcellular localization, emphasizing the potential of deep learning approaches in advancing RNA-related studies.

Availability and implementation
The source code is publicly available at https://bis.zju.edu.cn/LncLSTA.
ICoN: integration using co-attention across biological networks
Authors: Tasnina Nure , Murali T M 
Published: November 2024

Abstract

Motivation
Molecular interaction networks are powerful tools for studying cellular functions. Integrating diverse types of networks enhances performance in downstream tasks such as gene module detection and protein function prediction. The challenge lies in extracting meaningful protein feature representations due to varying levels of sparsity and noise across these heterogeneous networks.

Results
We propose ICoN, a novel unsupervised graph neural network model that takes multiple protein–protein association networks as inputs and generates a feature representation for each protein that integrates the topological information from all the networks. A key contribution of ICoN is exploiting a mechanism called “co-attention” that enables cross-network communication during training. The model also incorporates a denoising training technique, introducing perturbations to each input network and training the model to reconstruct the original network from its corrupted version. Our experimental results demonstrate that ICoN surpasses individual networks across three downstream tasks: gene module detection, gene coannotation prediction, and protein function prediction. Compared to existing unsupervised network integration models, ICoN exhibits superior performance across the majority of downstream tasks and shows enhanced robustness against noise. This work introduces a promising approach for effectively integrating diverse protein–protein association networks, aiming to achieve a biologically meaningful representation of proteins.

Availability and implementation
The ICoN software is available under the GNU Public License v3 at https://github.com/Murali-group/ICoN.
Sensitivity analysis for studies transporting prediction models
Authors: Steingrimsson Jon A , Robertson Sarah E , Voter Sarah , Dahabreh Issa J 
Published: November 2024

ABSTRACT
We consider estimation of measures of model performance in a target population when covariate and outcome data are available from a source population and covariate data, but not outcome data, are available from the target population. In this setting, identification of measures of model performance is possible under an untestable assumption that the outcome and population (source or target) are independent conditional on covariates. In practice, this assumption is uncertain and, in some cases, controversial. Therefore, sensitivity analysis may be useful for examining the impact of assumption violations on inferences about model performance. Here, we propose an exponential tilt sensitivity analysis model and develop statistical methods to determine how measures of model performance are affected by violations of the assumption of conditional independence between outcome and population. We provide identification results and estimators for the risk in the target population under the sensitivity analysis model, examine the large-sample properties of the estimators, and apply them to data on lung cancer screening.
Taxonomic adjustments in Mimoseae (Fabaceae): new genera described to accommodate Zygia/Inga inundata and Zygia sabatieri, and a recombination of Marmaroxylon ocumarense
Authors: Ferm Julia , Rydin Catarina 
Published: November 2024

Abstract
In recent phylogenetic studies of legumes the species Zygia/Ingainundata and Zygiasabatieri have been shown to not belong in neither Inga nor Zygia. Inga inundata was originally placed in the genus Inga based on morphological characters such as having pinnate leaves, but was transferred to the genus Zygia when the pod was discovered. The species was placed in its own section in Zygia, Zygia sect. Ingopsis, due to the similarity in leaf morphology to the species in Inga. Zygia sabatieri is another species placed in its own section in Zygia, Zygia sect. Pseudocojoba, due to similarity in flower morphology to the legume genus Cojoba. The genus Marmaroxylon has been synonymized under Zygia but the species Marmaroxylonocumarense has been shown to be closer related to species of the genus Macrosamanea and is not resolved within Zygia. In this study these results are compared and discussed. Zygia/Ingainundata and Zygiasabatieri are morphologically distinct from Inga and Zygia, and from each other, and taxonomic adjustments are made. Two new genera are described, Ingopsis gen. nov. to accommodate Zygia/Inga inundata and Pseudocojoba gen. nov. to accommodate Zygia sabatieri. In addition, Marmaroxylon ocumarense is transferred to the genus Macrosamanea where it fits phylogenetically and morphologically.
Cerebral amyloid angiopathy impacts neurofibrillary tangle burden and cognition
Authors: Godrich Dana , Pasteris Jeremy , Martin Eden R , Rundek Tatjana , Schellenberg Gerard , Foroud Tatiana , Vance Jeffery M , Pericak-Vance Margaret A , Cuccaro Michael L , Scott William K , Kukull Walter , Montine Thomas J , Beecham Gary W 
Published: November 2024

Abstract
Cerebral amyloid angiopathy commonly co-occurs with amyloid β plaques and neurofibrillary degeneration and is proposed to contribute to cognitive impairment. However, the interplay among these pathologic changes of Alzheimer disease is not well understood. Here we replicate and extend findings of a recent study that suggested the association of cerebral amyloid angiopathy and cognitive impairment is mediated by neurofibrillary degeneration. We employed similar approaches but in a larger, clinical-based (as opposed to community-based) set of 4915 autopsied National Alzheimer’s Coordinating Center participants (60% with dementia). Neuropathologic lesions were measured ordinally; longitudinal change in cognition was used to measure cognitive impairment. Statistical analyses included ordinal logistic regression, mediation analyses and extension of models to include presence of APOE e4. We show a statistical interaction between cerebral amyloid angiopathy and neuritic plaques that impacts the burden of neurofibrillary tangles. Mediation analyses show that cerebral amyloid angiopathy is associated with cognitive impairment, but only by modifying the impact of neurofibrillary tangles on cognition. We expanded the mediation analysis to include APOE e4 and show similar results. Findings indicate that cerebral amyloid angiopathy plays an important role in the burden and impact of neurofibrillary degeneration contributing to cognitive impairment.
GLP-1 receptor agonists in patients with chronic kidney disease and either overweight or obesity
Authors: Abasheva Daria , Ortiz Alberto , Fernandez-Fernandez Beatriz 
Published: November 2024

ABSTRACT
Glucagon-like peptide-1 receptor agonists (GLP-1 RAs) have emerged as game-changers across the cardiovascular–kidney–metabolic (CKM) spectrum: overweight/obesity, type 2 diabetes mellitus (T2DM) and associated chronic kidney disease (CKD) and cardiovascular disease (CVD). Liraglutide, semaglutide and tirzepatide are European Medicines Agency approved to improve metabolic control in T2DM and to decrease weight in persons with obesity [body mass index (BMI) ≥30 kg/m2] or with overweight (BMI ≥27 kg/m2) associated with weight-related comorbidities such as hypertension, dyslipidaemia, CVD and others. Additionally, liraglutide and semaglutide are approved to reduce CVD risk in patients with CVD and T2DM. Semaglutide is also approved to reduce CVD risk in patients with CVD and either obesity or overweight and in phase 3 clinical trials showed kidney and cardiovascular protection in patients with T2DM and albuminuric CKD (FLOW trial) as well as in persons without diabetes that had CVD and overweight/obesity (SELECT trial). Thus, nephrologists should consider prescribing GLP-1 RAs to improve metabolic control, reduce CVD risk or improve kidney outcomes in three scenarios: patients with overweight and a related comorbid condition such as hypertension, dyslipidaemia or CVD, patients with obesity and patients with T2DM. This review addresses the promising landscape of GLP-1 RAs to treat persons with overweight or obesity, with or without T2DM, within the context of CKD, assessing their safety and impact on weight, metabolic control, blood pressure and kidney and cardiovascular outcomes, as part of a holistic patient-centred approach to preserve CKM health.
A pair of two atrial myxomas mimic thrombus in left atrial appendage and cause ischemic stroke in a young adult: a case report
Authors: Shahverdi Ehsan , Bolte Hendrik , Schneider Carsten , Lange Mathias 
Published: November 2024

Abstract

Background
Stroke is one of the leading causes of mortality and disability and can be rarely caused by cardiac myxoma.

Case Summary
Here, we report about a 56-year-old man who suffered from a stroke presented with acute dysarthria and left hemiparesis. Magnetic resonance imaging (MRI) of the brain revealed an acute stroke. Atrial fibrillation (AF) was assumed the cause of stroke. Because of contraindication to anticoagulation due to previous cerebral haemorrhage with rivaroxaban the patient was admitted to interventional occlusion of left atrial appendage. Echocardiography revealed two left atrial masses suggestive of atrial myxomas. The patient was transferred to remove the two myxomas operatively with simultaneous resection of left atrial appendage.

Discussion
Atrial myxomas should be considered as a possible differential diagnosis of cardioembolic stroke. They should be managed early to prevent recurrent strokes.
Transcatheter aortic valve implantation in patient with combined aortic and subaortic membrane stenosis: a case report
Authors: Tayel Hesham , Elhakim Abdelrahman , Elsoudi Mohamed , Nour Amira , Saad Mohammed 
Published: November 2024

Abstract

Background
The combination of symptomatic aortic stenosis (AS) and subaortic membrane (SAM) is rare, and the haemodynamic consequences of this combination are challenging to diagnose and manage.

Case summary
We present the case of a 78-year-old male who presented with symptomatic AS and chronic heart failure. On echocardiography, the combination of AS and SAM was diagnosed. Transoesophageal echocardiography (TOE) was performed to confirm the presence and severity of AS and SAM. Based on the patient’s clinical profile and the high risk of surgical repair, a self-expandable transcatheter aortic valve implantation (TAVI) was performed. Three-month follow-up was uneventful. In addition, we discuss the assessment and management strategy challenges for SAM in patients with aortic regurgitation or AS.

Discussion
As transcatheter valve implantation expands its indications for more complex anatomy and patient’s comorbidity. Self-expandable TAVI-prosthesis under TOE guidance is feasible for the treatment of symptomatic AS and SAM, especially in patients with high surgical risk.