bluuebunny/crossref_metadata_2025_split huggingface dataset:
MVML-MPI: Multi-View Multi-Label Learning for Metabolic Pathway Inference
Authors: Liu Xiaoyi , Yang Hongpeng , Ai Chengwei , Ding Yijie , Guo Fei , Tang Jijun 
Published: November 2023

Abstract
Development of robust and effective strategies for synthesizing new compounds, drug targeting and constructing GEnome-scale Metabolic models (GEMs) requires a deep understanding of the underlying biological processes. A critical step in achieving this goal is accurately identifying the categories of pathways in which a compound participated. However, current machine learning-based methods often overlook the multifaceted nature of compounds, resulting in inaccurate pathway predictions. Therefore, we present a novel framework on Multi-View Multi-Label Learning for Metabolic Pathway Inference, hereby named MVML-MPI. First, MVML-MPI learns the distinct compound representations in parallel with corresponding compound encoders to fully extract features. Subsequently, we propose an attention-based mechanism that offers a fusion module to complement these multi-view representations. As a result, MVML-MPI accurately represents and effectively captures the complex relationship between compounds and metabolic pathways and distinguishes itself from current machine learning-based methods. In experiments conducted on the Kyoto Encyclopedia of Genes and Genomes pathways dataset, MVML-MPI outperformed state-of-the-art methods, demonstrating the superiority of MVML-MPI and its potential to utilize the field of metabolic pathway design, which can aid in optimizing drug-like compounds and facilitating the development of GEMs. The code and data underlying this article are freely available at https://github.com/guofei-tju/MVML-MPI. Contact: jtang@cse.sc.edu, guofei@csu.edu.com or wuxi_dyj@csj.uestc.edu.cn
IMOVNN: incomplete multi-omics data integration variational neural networks for gut microbiome disease prediction and biomarker identification
Authors: Hu Mingyi , Zhu Jinlin , Peng Guohao , Lu Wenwei , Wang Hongchao , Xie Zhenping 
Published: November 2023

Abstract
The gut microbiome has been regarded as one of the fundamental determinants regulating human health, and multi-omics data profiling has been increasingly utilized to bolster the deep understanding of this complex system. However, stemming from cost or other constraints, the integration of multi-omics often suffers from incomplete views, which poses a great challenge for the comprehensive analysis. In this work, a novel deep model named Incomplete Multi-Omics Variational Neural Networks (IMOVNN) is proposed for incomplete data integration, disease prediction application and biomarker identification. Benefiting from the information bottleneck and the marginal-to-joint distribution integration mechanism, the IMOVNN can learn the marginal latent representation of each individual omics and the joint latent representation for better disease prediction. Moreover, owing to the feature-selective layer predicated upon the concrete distribution, the model is interpretable and can identify the most relevant features. Experiments on inflammatory bowel disease multi-omics datasets demonstrate that our method outperforms several state-of-the-art methods for disease prediction. In addition, IMOVNN has identified significant biomarkers from multi-omics data sources.
Graphical tools for selecting conditional instrumental sets
Authors: Henckel L , Buttenschoen M , Maathuis M H 
Published: November 2023

Summary
We consider the efficient estimation of total causal effects in the presence of unmeasured confounding using conditional instrumental sets. Specifically, we consider the two-stage least-squares estimator in the setting of a linear structural equation model with correlated errors that is compatible with a known acyclic directed mixed graph. To set the stage for our results, we characterize the class of linearly valid conditional instrumental sets that yield consistent two-stage least-squares estimators for the target total effect and derive a new asymptotic variance formula for these estimators. Equipped with these results, we provide three graphical tools for selecting more efficient linearly valid conditional instrumental sets: first, a graphical criterion that, for certain pairs of linearly valid conditional instrumental sets, identifies which of the two corresponding estimators has the smaller asymptotic variance second, an algorithm that greedily adds covariates that reduce the asymptotic variance to a given linearly valid conditional instrumental set and, third, a linearly valid conditional instrumental set for which the corresponding estimator has the smallest asymptotic variance that can be ensured with a graphical criterion.
The Impact of COVID-19 on Social Care and Social Work in the UK: A Scoping Review
Authors: Owens Janine , Young Alys , Allen Rosie , Pearson Amelia , Cartney Patricia , Robinson Catherine , McPhillips Rebecca , Davies Sue , Regan Martyn 
Published: November 2023

Abstract
Prior to the COVID pandemic, staffing levels, staff turnover and vacancies in adult social care and social work within the UK were a major concern, with staff experiencing high workloads, burnout, stress and poor morale. The paucity of published evidence in a rapidly evolving contemporary situation indicated the suitability of a scoping review. Systematic searching produced evidence published between 1 December 2019 and 9 May 2023. Out of ninety-seven articles retrieved, the final analysis included thirty nine articles. To report the review findings clearly and accessibly, the analysis used the Patterns, Advances, Gaps, Evidence for practice and Research recommendations framework. Abundant evidence emerged on psychological distress and the impact of COVID-19 on the working environment for social care and social workers, but a paucity of psychosocial resilience, supporting social care managers, Personal Assistants and moral injury. Social care needs and the statutory duties of social work are likely to become even more intense. The COVID pandemic magnified a chronic lack of funding, staffing, support and regard for adult social care, with no future planning compared to the NHS. This legacy and backlogs of social care assessment and service delivery are of concern despite the proposed actions of the Adult Social Care Reform Act in England.
Vascular cutaneous manifestations of COVID-19 and RNA viral pathogens: a systematic review
Authors: Karch Jamie L , Okorie Chiamaka L , Maymone Mayra B C , Laughter Melissa , Vashi Neelam A 
Published: November 2023

Abstract

Background
COVID-19, the widely recognized and highly contagious respiratory tract infection, has had a substantial impact on the field of dermatology since its emergence in 2019. SARS-CoV-2, the causative virus of COVID-19, is classified as an RNA virus. Various skin-related symptoms have been reported in patients with COVID-19, most notably the distinctive purple–red acral rash resembling chilblain lesions, commonly referred to as ‘COVID toe’; similarly, skin-related symptoms have been observed in connection with other RNA viruses.

Objectives
To explore the relationship between RNA viruses and their associated vascular cutaneous manifestations vs. those observed in patients infected with SARS-CoV-2.

Methods
A systematic literature review was conducted using PubMed and medical subject heading terms related to RNA viruses and related skin manifestations.

Results
In total, 3994 patients diagnosed with COVID-19 presenting with skin rashes were included. Chilblain-like lesions were most frequently observed (30.2%), followed by erythematous maculopapular/morbilliform rashes (9.1%) and urticarial rashes (4.7%). Of 8362 patients diagnosed with RNA viruses, more than half of the skin findings reported were erythematous/maculopapular/morbilliform rashes (52.3%), followed by unspecified (11.3%) and purpuric rashes (10.6%).

Conclusions
When comparing RNA viral infections with COVID-19 infection, we observed similarities in the reported skin manifestations and their presumed pathways, with many implicated in the proinflammatory response. Owing to the wide range of cutaneous symptoms associated with RNA viruses and our currently limited understanding of the underlying mechanisms, additional research is warranted to investigate the pathology behind viral-induced skin lesions.
Notes on the data quality of bibliographic records from the MEDLINE database
Authors: Bramley Robin , Howe Stephen , Marmanis Haralambos 
Published: November 2023

Abstract
The US National Library of Medicine has created and maintained the PubMed® database, a collection of over 33.8 million records that contain citations and abstracts from the biomedical and life sciences literature. This database is an important resource for researchers and information service providers alike. As part of our work related to the creation of an author graph for coronaviruses, we encountered several data quality issues with records from a curated subset of the PubMed database called MEDLINE. We provide a data quality assessment for records selected from the MEDLINE database and report on several issues ranging from parsing issues (e.g. character encodings and schema definition weaknesses) to low scores for identifiers against several data quality metrics (e.g. completeness, validity and uniqueness).
Database URL https://pubmed.ncbi.nlm.nih.gov
OncoCTMiner: streamlining precision oncology trial matching via molecular profile analysis
Authors: Xu Quan , Liu Yueyue , Sun Dawei , Huang Xiaoqian , Li Feihong , Zhai JinCheng , Li Yang , Zhou Qiming , Qian Niansong , Niu Beifang 
Published: November 2023

Abstract
By establishing omics sequencing of patient tumors as a crucial element in cancer treatment, the extensive implementation of precision oncology necessitates effective and prompt execution of clinical studies for approving molecular-targeted therapies. However, the substantial volume of patient sequencing data, combined with strict clinical trial criteria, increasingly complicates the process of matching patients to precision oncology studies. To streamline enrollment in these studies, we developed OncoCTMiner, an automated pre-screening platform for molecular cancer clinical trials. Through manual tagging of eligibility criteria for 2227 oncology trials, we identified key bio-concepts such as cancer types, genes, alterations, drugs, biomarkers and therapies. Utilizing this manually annotated corpus along with open-source biomedical natural language processing tools, we trained multiple named entity recognition models specifically designed for precision oncology trials. These models analyzed 460 952 clinical trials, revealing 8.15 million precision medicine concepts, 9.32 million entity-criteria-trial triplets and a comprehensive precision oncology eligibility criteria database. Most significantly, we developed a patient-trial matching system based on cancer patients’ clinical and genetic profiles, which can seamlessly integrate with the omics data analysis platform. This system expedites the pre-screening process for potentially suitable precision oncology trials, offering patients swifter access to promising treatment options.
Database URL https://oncoctminer.chosenmedinfo.com
Bacterial communities of the threatened Western Pond Turtle may be impacted by land use
Authors: White Alison , Giannetto Madison , Mulla Lubna , Del Rosario Amber , Lim Tammy , Culver Edward , Timmer Matthew , Bushell Jessie , Lambert Max R , Hernández-Gómez Obed 
Published: November 2023

Abstract
As semi-aquatic species that use both terrestrial and aquatic habitats, freshwater turtles and their microbial communities are especially sensitive to the impacts of habitat disturbance. In this study, we use 16S rRNA amplicon sequencing to characterize the shell and cloacal bacterial communities of turtles in the San Francisco Bay Area. We captured western pond turtles (Actinemys/Emys marmorata) across eight sites located in urban and rural environments, along with invasive red-eared sliders (Trachemys scripta elegans). We assessed differences in western pond turtle bacterial communities diversity/composition between shell and cloacal samples and evaluated how alpha/beta diversity metrics were influenced by habitat quality. We found phylum-level bacterial taxonomic turnover in the bacterial communities of western pond turtles relative to the host tissue substrate samples. Our findings indicate that location identity elicits a high degree of lower-level (i.e. species/genus) bacterial taxonomic turnover. Further, we found that samples originating from good quality habitat had poorer shell bacterial communities but more diverse cloacal ones. The shell bacterial communities of red-eared sliders overlapped with those western pond turtles suggesting the existence of microbial dispersal between these two species. Our results add to our current understanding of turtle symbiont microbial ecology by establishing patterns of bacterial symbiont variation in an urban to rural gradient.
Internet-Based Conversational Engagement Randomized Controlled Clinical Trial (I-CONECT) Among Socially Isolated Adults 75+ Years Old With Normal Cognition or Mild Cognitive Impairment: Topline Results
Authors: Dodge Hiroko H , Yu Kexin , Wu Chao-Yi , Pruitt Patrick J , Asgari Meysam , Kaye Jeffrey A , Hampstead Benjamin M , Struble Laura , Potempa Kathleen , Lichtenberg Peter , Croff Raina , Albin Roger L , Silbert Lisa C ,   the I-CONECT Team, Alfaro Elena , McDonald Mattie , Lindsey Jacob , Scavone Colton , Sheridan Nita , Nguyen Khoa , Ellis Alexis , Weisberg Louis , Moore Deborah , Peacock Brandy , Heller Brennan , Thornall Carissa , Ruhf Sandy , Ziemer-McGinn Mary , Custodio Farah , Farrell Diane , Lynch Aimee , Banker Dillon , Reyes Gracia , Rabe Kathryn , Seeton Laura , Pedroza Jessica , Forystek David , May Nicolas , Reader Jonathan , Bhaumik Arijit K 
Published: November 2023

Abstract

Background and Objectives
Social isolation is a risk factor for cognitive decline and dementia. We conducted a randomized controlled clinical trial (RCT) of enhanced social interactions, hypothesizing that conversational interactions can stimulate brain functions among socially isolated older adults without dementia. We report topline results of this multisite RCT (Internet-based conversational engagement clinical trial [I-CONECT]; NCT02871921).

Research Design and Methods
The experimental group received cognitively stimulating semistructured conversations with trained interviewers via internet/webcam 4 times per week for 6 months (induction) and twice per week for an additional 6 months (maintenance). The experimental and control groups both received weekly 10 minutes telephone check-ins. Protocol modifications were required due to the coronavirus disease 2019 pandemic.

Results
A total of 186 participants were randomized. After the induction period, the experimental group had higher global cognitive test scores (Montreal Cognitive Assessment [primary outcome]; 1.75 points [p = .03]) compared with the control group. After induction, experimental group participants with normal cognition had higher language-based executive function (semantic fluency test [secondary outcome]; 2.56 points [p = .03]). At the end of the maintenance period, the experimental group of mild cognitive impairment subjects had higher encoding function (Craft Story immediate recall test [secondary outcome]; 2.19 points [p = .04]). Measure of emotional well-being improved in both control and experimental groups. Resting-state functional magnetic resonance imaging showed that the experimental group had increased connectivity within the dorsal attention network relative to the control group (p = .02), but the sample size was limited.

Discussion and Implications
Providing frequent stimulating conversational interactions via the internet could be an effective home-based dementia risk-reduction strategy against social isolation and cognitive decline.

Clinical Trials Registration Number
NCT02871921
A periodic table of monosaccharides
Authors: Cummings Richard D 
Published: November 2023

Abstract
It is important to recognize the great diversity of monosaccharides commonly encountered in animals, plants, and microbes, as well as to organize them in a visually interesting style that also emphasizes their similarities and relatedness. This article discusses the nature of building blocks, monosaccharides, and monosaccharide derivatives—terms commonly used in discussing “glycomolecules” found in nature. To aid in awareness of monosaccharide diversity, here is presented a Periodic Table of Monosaccharides. The rationale is given for construction of the Table and the selection of 103 monosaccharides, which is largely based on those presented in the KEGG and SNFG websites of monosaccharides, and includes room to enlarge as new discoveries are made. The Table should have educational value and is intended to capture the attention and foster imagination of those not very familiar with glycosciences, and encourage researchers to delve deeper into this fascinating area.
Deciphering the Neighborhood Atlas Area Deprivation Index: the consequences of not standardizing
Authors: Petterson Stephen 
Published: November 2023

AbstractThe Area Deprivation Index (ADI) is a widely used measure recently selected for several federal payment models that adjusts payments based on where beneficiaries live. A recent debate in Health Affairs focuses on seemingly implausible ADI rankings in major cities and across New York. At the root of the issue is the importance of standardization of measures prior to calculating index scores. Neighborhood Atlas researchers are implicitly arguing that their choice to not standardize is of little consequence. Using the same data and methods as the Neighborhood Atlas, this paper focuses on this choice by calculating and comparing standardized and unstandardized ADI scores. The calculated unstandardized ADI nearly perfectly matches the Neighborhood Atlas ADI (r &gt; 0.9999), whereas the correlation with a standardized version is much lower (r = 0.7245). The main finding is that, without standardization, the ADI is reducible to a weighted average of just 2 measures—income and home values—certainly not the advertised multidimensional measure. Federal programs that have incorporated the ADI risk poorly allocating scarce resources meant to reduce health inequities.
Rescuing the liberal international order: crisis, resilience and EU security policy
Authors: Bargués Pol , Joseph Jonathan , Juncos Ana E 
Published: November 2023

Abstract
This article reflects on how European Union (EU) narratives of the crisis of the liberal international order (LIO) have reshaped its resilience approach and its foreign and security policy more broadly. Drawing on qualitative textual analysis, we trace the evolution of the EU's resilience approach over time and the way it has been shaped by crisis narratives. While the idea of resilience was introduced in EU foreign policy to foster the resilience of crisis-affected societies from the bottom up, the perception of an increasingly contested world first led to a reinterpretation of resilience in pragmatic ways, with values and interests combined selectively to protect the rules-based international order. More recently, on the grounds of a worsening crisis of the LIO, resilience has taken a defensive turn, adopting a more geopolitical stance to strengthen the EU's own resilience and that of the LIO. We argue that EU crisis narratives about the LIO thus serve to sustain and to rescue it. Furthermore, we conclude that the defensive reinterpretation of resilience is eroding the normative character of EU foreign and security policy. It also challenges the persistence of the LIO in the long term.
Authoritarian middle powers and the liberal order: Turkey's contestation of the EU
Authors: Aydın-Düzgit Senem 
Published: November 2023

Abstract
The conventional expectation that middle powers support the liberal international order (LIO) is now increasingly being questioned. This article seeks to explore why and how emerging authoritarian middle powers contest the LIO through a study of Turkey's contestation of the EU. By conceptualizing contestations of the LIO as claims to global justice, the article examines the justice claims that underlie Turkey's contestation; with regard to discourse, it does so through a qualitative content analysis of President Erdoğan's speeches, and with regard to practice, through a survey of Turkey's contestatory foreign policy practices. The article shows that middle powers can discursively attack the legitimacy of the LIO by underlining its constituents' failures in upholding their moral duties towards citizens extending beyond their borders (impartiality) and to those who suffer from structural inequalities in the international order (mutual recognition). It demonstrates that their contestatory practices, however, are made with a view to pursue the sovereign interests of the state, with minimal regard for impartiality and mutual recognition. The article unpacks this inconsistency and finds that authoritarian middle powers' contestation of the LIO is mainly driven by concerns for regime security, where the centrality of an issue area to the government's survival prospects is the key factor which determines whether contestation will occur.
Global justice and EU climate policy in a contested liberal international order
Authors: Diez Thomas , von Lucke Franziskus 
Published: November 2023

Abstract
Following the failure of the Conference of the Parties (COP15) in 2009 in Copenhagen, the European Union has significantly altered its negotiation strategy in the global climate regime. It moved from an emphasis on ‘leadership by example’ and an insistence on top-down, binding targets within a framework of strong global governance institutions (impartiality in global justice terms) towards a strategy of shared leadership, increased dialogue (mutual recognition) and acceptance of more voluntary instruments (non-domination). This article traces this shift through an examination of EU policy documents and makes sense of it by reference to learning effects of an EU with solidarist ambitions in a pluralist international society, and the changing power distribution and contestations of the post-Cold War liberal order on the global level. Furthermore, it assesses the consequences of the shift for international society (especially concerning different ‘solidarisms’) and global climate justice. We argue that while a changed EU approach has been vital to maintaining the EU's status as a relevant actor and to secure the Paris Agreement, too much emphasis on the pluralist dimension and non-domination may also hinder effective global solutions to climate change. It is therefore vital that the EU continues its solidarist ambitions by pushing for rigorous measures of accountability, but also by alleviating structural domination in the climate regime and particularly by better recognizing and including civil society actors from the global South.