bluuebunny/crossref_metadata_2025_split huggingface dataset:
“Spin” in Observational Studies in Deep Inferior Epigastric Perforator Flap Breast Reconstruction: A Systematic Review
Authors: Kim Patrick J. , Yuan Morgan , Wu Jeremy , Gallo Lucas , Uhlman Kathryn , Voineskos Sophocles H. , O’Neill Anne , Hofer Stefan O.P. 
Published: June 2023

Background:
The deep inferior epigastric artery perforator (DIEP) flap is widely used in autologous breast reconstruction. However, the technique relies heavily on nonrandomized observational research, which has been found to have high risk of bias. “Spin” can be used to inappropriately present study findings to exaggerate benefits or minimize harms. The primary objective was to assess the prevalence of spin in nonrandomized observational studies on DIEP reconstruction. The secondary objectives were to determine the prevalence of each spin category and strategy.

Methods:
MEDLINE and Embase databases were searched from January 1, 2015, to November 15, 2022. Spin was assessed in abstracts and full-texts of included studies according to criteria proposed by Lazarus et al.

Results:
There were 77 studies included for review. The overall prevalence of spin was 87.0%. Studies used a median of two spin strategies (interquartile range: 1–3). The most common strategies identified were causal language or claims (n = 41/77, 53.2%), inadequate extrapolation to larger population, intervention, or outcome (n = 27/77, 35.1%), inadequate implication for clinical practice (n = 25/77, 32.5%), use of linguistic spin (n = 22/77, 28.6%), and no consideration of the limitations (n = 21/77, 27.3%). There were no significant associations between selected study characteristics and the presence of spin.

Conclusions:
The prevalence of spin is high in nonrandomized observational studies on DIEP reconstruction. Causal language or claims are the most common strategy. Investigators, reviewers, and readers should familiarize themselves with spin strategies to avoid misinterpretation of research in DIEP reconstruction.
Toward a universal theory of stable evolution
Authors: Ván Peter 
Published: June 2023

The backbone of non-equilibrium thermodynamics is the stability structure, where entropy is related to a Lyapunov function of thermodynamic equilibrium. Stability is the background of natural selection: unstable systems are temporary, and stable ones survive. The physical concepts from the stability structure and the related formalism of constrained entropy inequality are universal by construction. Therefore, the mathematical tools and the physical concepts of thermodynamics help formulate dynamical theories of any systems in social and natural sciences.
This article is part of the theme issue ‘Thermodynamics 2.0: Bridging the natural and social sciences (Part 1)’.
Social sciences and energy research interactions
Authors: Gunes Umit 
Published: June 2023

Energy has had a definitive impact on human life throughout history. Beginning with the harnessing of fire, which offered warmth, improved shelter and more food, humanity's standard of living has been defined by the power derived from fuels and food. Access to energy is the briefest way in which to summarize the history of the world. Direct and indirect causes of war have involved access to energy, and the results of conflicts have been determined by who controlled the energy resources. Therefore, the scientific literature reveals very close interactions between energy studies and social science studies. The Scopus database contains about 118 000 publications in the fields of social sciences and energy. The current study aims to exploit this resource to identify the interactions that exist between the fields so that future research can investigate these more deeply and thus develop solutions to the problems of the modern world. The present article will analyse these publications systematically according to author, country, institution and year, in addition to examining the changes in keywords that have occurred in these studies over the years.
This article is part of the theme issue 'Thermodynamics 2.0: Bridging the natural and social sciences (Part 1)'.
The fall -- and rise -- in hospital-based care for people with HIV in South Africa: 2004-2017
Authors: Lauren Evelyn , Shumba Khumbo , Fox Matthew P. , MacLeod William , Stevens Wendy , Mlisana Koleka , Bor Jacob , Onoya Dorina 
Published: June 2023

ABSTRACTBackgroundART scale-up has reduced HIV mortality in South Africa. However, less is known about trends in hospital-based HIV care, which is costly and may indicate HIV-related morbidity.MethodsWe assessed trends in hospital-based HIV care using a novel database: the National Health Laboratory Service (NHLS) National HIV Cohort. Our study included all adults ≥18 years receiving care in South Africa’s public sector HIV program from 2004 to 2017 with at least one CD4 count/viral load test in the NHLS database. We compared trends in the number of patients presenting for and receiving HIV care by facility type: hospitals vs. primary care clinics. We then assessed trends and predictors of incident hospitalization, defined as 2 or more hospital-based lab tests taken within 7 days. Finally, we assessed whether trends in incident hospitalizations could be explained by changes in patient demographics, CD4 counts, or facility type at presentation.ResultsData were analyzed on 9,624,951 patients. The percentage of patients presenting and receiving HIV care at hospitals (vs. clinics) declined over time, from approximately 60% in 2004 to 15% in 2017. Risk of hospitalization declined for patients entering care between 2004-2012 and modestly increased for patients entering care after 2012. The risk of hospitalization declined the most in age groups most affected by HIV. Over time, patients presented with higher CD4 counts and were more likely to present at clinics, and these changes explained almost half the decline in hospitalizations.ConclusionsThe percentage of HIV care provided in hospitals declined as patients presented in better health and as treatment was increasingly managed at clinics. However, there may still be opportunities to reduce incident hospitalizations in people with HIV.FundingThis work was supported by grant R01AI152149 from the National Institute of Allergy and Infectious Diseases. NIH had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Global Longitudinal Active Strain Energy Density (GLASED): A Powerful Prognostic Marker in a Community-Based Cohort
Authors: Aung Nay , MacIver David H. , Zhang Henggui , Chadalavada Sucharitha , Petersen Steffen E. 
Published: June 2023

ABSTRACTBACKGROUNDIdentifying the imaging methods that best predict heart failure risk, cardiovascular adverse events and death is crucial for tailoring optimal management. Potential prognostic markers include myocardial mass, left ventricular ejection fraction, myocardial strain, stroke work, contraction fraction, pressure-strain product and a new measurement called global active longitudinal strain density (GLASED).OBJECTIVESThis study sought to assess the utility of a range of potential prognostic markers of left ventricular structure and contractile function in a community-based cohort.METHODSThe impact of cardiovascular magnetic resonance image-derived markers, extracted by machine learning algorithms were compared to the future risk of adverse events in a group of 44,957 UK Biobank participants.RESULTSMost markers, including the left ventricular ejection fraction, had limited prognostic value. GLASED was significantly associated with heart failure, all-cause mortality and major adverse cardiovascular events with hazard ratios of approximately 1.4.CONCLUSIONSGLASED predicted major cardiovascular adverse events and mortality with the highest hazard ratios compared with conventional markers. The routine use of GLASED is recommended for assessing prognosis.Graphical abstract
Proteo-genomics of soluble TREM2 in cerebrospinal fluid provides novel insights and identifies novel modulators for Alzheimer’s disease
Authors: Wang Lihua , Nykänen Niko-Petteri , Western Daniel , Gorijala Priyanka , Timsina Jigyasha , Li Fuhai , Wang Zhaohua , Ali Muhammad , Yang Chengran , Marquié Marta , Boada Mercè , Alvarez Ignacio , Aguilar Miquel , Pastor Pau , Ruiz Agustín , Puerta Raquel , Orellana Adelina , Rutledge Jarod , Oh Hamilton , Greicius Michael D , Guen Yann Le , Perrin Richard J. , Wyss-Coray Tony , Jefferson Angela , Hohman Timothy J. , Graff-Radford Neill , Mori Hiroshi , Goate Alison , Levin Johannes , Sung Yun Ju , Cruchaga Carlos 
Published: June 2023

AbstractTriggering receptor expressed on myeloid cells 2 (TREM2) plays a critical role in microglial activation, survival, and apoptosis, as well as in Alzheimer’s disease (AD) pathogenesis. We previously reported theMS4Alocus as a key modulator for soluble TREM2 (sTREM2) in cerebrospinal fluid (CSF). To identify additional novel genetic modifiers of sTREM2, we performed the largest genome-wide association study (GWAS) and identified four loci for CSF sTREM2 in 3350 individuals of European ancestry. Through multi-ethnic fine mapping, we identified two independent missense variants (p.M178V inMS4A4Aand p.A112T inMS4A6A) that drive the association inMS4Alocus and showed an epistatic effect for sTREM2 levels and AD risk. The novelTREM2locus on chr 6 contains two rare missense variants (rs75932628 p.R47H, P=7.16×10-19; rs142232675 p.D87N, P=2.71×10-10) associated with sTREM2 and AD risk. The third novel locus in theTGFBR2andRBMS3gene region (rs73823326, P=3.86×10-9) included a regulatory variant with a microglia-specific chromatin loop for the promoter ofTGFBR2. Using cell-based assays we functionally validated that overexpression ofTGFBR2increased sTREM2 and silencing reduced sTREM2, whereas modulatingRBMS3did not. The last novel locusNECTIN2on chr 19 (rs11666329, P=2.52×10-8) was independent ofAPOEgenotype and colocalized with cis-eQTL ofNECTIN2in the brain cortex and cis-pQTL of NECTIN2 in CSF. To our knowledge, this is the largest study to date aimed at identifying genetic modifiers of CSF sTREM2. This study provided novel insights into theMS4AandTREM2loci, two well-known AD risk genes, and identifiedTGFBR2andNECTIN2as additional modulators involved in TREM2 biology.
Autoencoder-based phenotyping of ophthalmic images highlights genetic loci influencing retinal morphology and provides informative biomarkers
Authors: Sergouniotis Panagiotis I. , Diakite Adam , Gaurav Kumar , Birney Ewan , Fitzgerald Tomas 
Published: June 2023

ABSTRACTGenome-wide association studies (GWAS) have been remarkably successful in identifying associations between genetic variation and imaging-derived phenotypes. To date, the main focus of these analyses has been established, clinically-used imaging features. Here, we sought to investigate if deep learning approaches can help detect more nuanced patterns of image variability. To this end, we used an autoencoder to represent retinal optical coherence tomography (OCT) images from 31,135 UK Biobank participants. For each study subject, we obtained a 64-dimensional vector representing features of retinal structure. GWAS of these autoencoder-derived imaging parameters identified 118 statistically significant loci; 17 of these associations also reached genome-wide significance in a replication analysis that included 10,409 UK Biobank volunteers. These loci encompassed variants previously linked with retinal thickness measurements, ophthalmic disorders and/or neurodegenerative conditions (including dementia). Notably, the generated retinal phenotypes were found to contribute to predictive models for glaucoma and cardiovascular disorders. Overall, we demonstrate that self-supervised phenotyping of OCT images enhances the discoverability of genetic factors influencing retinal morphology and provides epidemiologically informative biomarkers.
Covid-19 Excess Mortality in China: A Regional Comparison
Authors: Liu Lee 
Published: June 2023

AbstractEstimates of Covid-19 excess mortality are often considered to reflect the true death toll of the pandemic. As such, information on excess mortality is urgently needed to better understand the impact of the pandemic and prepare for future crises. This study estimated Covid-19 excess mortality at the provincial, regional, and national levels in China and investigated its associated regional disparities. The analyses were based on population and death rates data published by the national and provincial bureaus of statistics in China. The results suggest that excess deaths in China were over 1 million during each year of the pandemic, totaling to over 4 million by the end of 2022, at an excess death rate of 15.4%. This rate was likely comparable to that of the Organization for Economic Cooperation and Development (OECD), but higher than the US rate. Striking disparities were discovered among the 31 provinces with excess death rates ranging from negative rates in two eastern provinces to over 30% in three inland provinces. Rates in western China were over twice as high as those in eastern China. Variations with each individual regions were the largest in the central region and the smallest in the Northeast, which was the hardest hit with excess death rate of over 23%. The regional disparities in excess mortality rates seem to reflect pre-existing regional inequalities in socio-economic development in China. Such findings suggest that China has far to go to mitigate regional inequalities, achieve sustainability, and prepare for the next major crises.
Changes in self-reported health and wellbeing outcomes in 36,951 primary school children from 2014 to 2022 in Wales: A descriptive analysis using annual survey data
Authors: Einhorn Johanna , James Michaela , Kennedy Natasha , Marchant Emily , Brophy Sinead 
Published: June 2023

AbstractThis study examines the changes in childhood self-reported health and wellbeing between 2014 and 2022. An annual survey delivered by HAPPEN-Wales, in collaboration with 500 primary schools, captured self-reported data on physical health, dietary habits, mental health, and overall wellbeing for children aged 8-11 years. The findings reveal a decline in physical health between 2014 and 2022, as evidenced by reduced abilities in swimming and cycling. For example, 68% of children (95%CI: 67%-69%) reported being able to swim 25m in 2022, compared to 85% (95% CI: 83%-87%) in 2018. Additionally, unhealthy eating habits, such as decreased fruit and vegetable consumption and increased consumption of sugary snacks, have become more prevalent. Mental health issues, including emotional and behavioural difficulties, have also increased, with emotional difficulties affecting 13%-15% of children in 2017-2018 and now impacting 29% of children in 2021-2022. Moreover, indicators of wellbeing, autonomy, and competence have declined. Importantly, this trend of declining health and wellbeing predates the onset of the Covid-19 pandemic, suggesting that it is not solely attributed to the pandemic’s effects. The health of primary school children has been on a declining trajectory since 2018/2019 and has continued to decline through the COVID recovery period. The study suggests that these trends are unlikely to improve without targeted intervention and policy focus.
Identification of two new genetic loci associated with atrial fibrillation in the Taiwanese population-implication of metabolism and fibrosis in atrial fibrillation mechanism
Authors: Lee Guan-Wei , Chen Jien-Jiun , Chang Sheng-Nan , Chiu Fu-Chun , Huang Pang-Shuo , Chuang Eric Y. , Tsai Chia-Ti 
Published: June 2023

ABSTRACTBackgroundGenome-wide association studies (GWASs) have identified common single nucleotide polymorphisms (SNPs) in more than 100 genomic regions associated with atrial fibrillation (AF). Genes for AF identified by GWAS in the Caucasian populations may show ethnic differences in the Asian populations. We sought to identify other novel AF genes in the Taiwanese population by multi-stage GWAS.MethodsIn exploratory stage, GWAS with whole genome genotypes (4,512,191 SNPs) were done in 516 young AF Patients (58.1±8.7 years-old, 438 men [84.9%]) from the National Taiwan University AF registry (NTUAFR) and 5160 normal sinus rhythm controls (57.8 ±8.7 years-old, 2460 men [47.7%]) from Taiwan Biobank. Significant loci were replicated in 1002 independent AF patients and 2003 NSR controls, and also in UK biobank (5630 AF cases and 24000 NSR controls). Quantitative trait locus mapping was performed to implicate functional significance.ResultsStage I GWAS revealed 3 loci associated with AF with the genome-wide significance level, which included locus close to previously reportedPITX2gene (chromosome 4q25, rs2723329,P=1.53×10−10) and two novel loci close toRAP1AandHNF4Ggenes (chromosome 1p13.2, rs7525578,P= 1.24×10−26; chromosome 8q21.13, rs2980218,P=2.19×10−9, respectively). They were further validated in a stage II replication population (P=4.60×10−9, 4.45×10−10and 6.97×10−5forRAP1A, PITX2andHNF4G, respectively). These 3 genes were also validated in the UK population. These 3 significant SNPs also show significant association with tissue expressions (RAP1Aexpression in thyroid,PITX2in testicular, andHNF4Gin lymphocyte tissues, respectively).ConclusionsGWAS in Taiwan revealed previously reportedPITX2and two novel AF genes (RAP1AandHNF4G) with the most significant locus inRAP1A.RAP1AandHNF4Ggenes may implicate fibrosis and metabolic pathways, respectively, in the mechanism of AF.
Target-decoy false discovery rate estimation using Crema
Authors: Lin Andy , See Donavan , Fondrie William E. , Keich Uri , Noble William Stafford 
Published: June 2023

AbstractAssigning statistical confidence estimates to discoveries produced by a tandem mass spectrometry proteomics experiment is critical to enabling principled interpretation of the results and to assess the cost/benefit ratio of experimental follow-up. The most common technique for computing such estimates is to usetarget-decoy competition(TDC), in which observed spectra are searched against a database of real (target) peptides and a database of shuffled or reversed (decoy) peptides. TDC procedures for estimating the false discovery rate (FDR) at a given score threshold have been developed for application at the level of spectra, peptides, or proteins. Although these techniques are relatively straightforward to implement, it is common in the literature to skip over the implementation details or even to make mistakes in how the TDC procedures are applied in practice. Here we present Crema, an open source Python tool that implements several TDC methods of spectrum-, peptide- and protein-level FDR estimation. Crema is compatible with a variety of existing database search tools and provides a straightforward way to obtain robust FDR estimates.
Integrating Image and Molecular Profiles for Spatial Transcriptomics Analysis
Authors: Jiang Xi , Wang Shidan , Guo Lei , Wen Zhuoyu , Jia Liwei , Xu Lin , Xiao Guanghua , Li Qiwei 
Published: June 2023

AbstractThe spatially resolved transcriptomics (SRT) field has revolutionized our ability to comprehensively leverage image and molecular profiles to elucidate spatial organization of cellular microenvironments. Current clustering analysis of SRT data primarily relies on molecular information and fails to fully exploit the morphological features present in histology images, leading to compromised accuracy and interpretability. To overcome these limitations, we have developed a multi-stage statistical method called iIMPACT. It includes a finite mixture model to identify and define histology-based spatial domains based on AI-reconstructed histology images and spatial context of gene expression measurements, and a negative binomial regression model to detect domain-specific spatially variable genes. Through multiple case studies, we demonstrate iIMPACT outperformed existing methods, confirmed by ground truth biological knowledge. These findings underscore the accuracy and interpretability of iIMPACT as a new clustering approach, providing valuable insights into the cellular spatial organization and landscape of functional genes within spatial transcriptomics data.
Inpatient Antibacterial Drug Prescribing for Patients with COVID-19 in Hong Kong
Authors: Blais Joseph Edgar , Zhang Weixin , Lin Yun , Chui Celine SL , Cheng Vincent Chi-Chung , Cowling Benjamin John , Wu Peng 
Published: June 2023

ABSTRACTBackgroundHong Kong experienced four epidemic waves caused by the ancestral strain of SARS-CoV-2 in 2020-2021 and a large Omicron wave in 2022. Few studies have assessed antibacterial drug prescribing for COVID-19 inpatients throughout the pandemic.ObjectivesTo describe inpatient antibacterial drug prescribing for COVID-19 patients throughout the pandemic and to determine factors associated with their prescription.MethodsThis cohort study used electronic health records of COVID-19 cases admitted to public hospitals in Hong Kong from 21 January 2020 to 30 September 2022. We assessed the prevalence and rates of inpatient antibacterial drug use, using days of therapy/1000 patient days (DOT/1000PD), and examined the association of baseline factors and disease severity with receipt of an inpatient antibacterial drug prescription.ResultsAmong 65,810 inpatients, 54.0% were prescribed antibacterial drugs at a rate of 550.5 DOT/1000PD. Antibacterial use was lowest during wave 4 (28.0%; 246.9 DOT/1000PD), peaked in early wave 5 (64.6%; 661.2 DOT/1000PD), and then modestly declined in late wave 5 (43.2%; 464.1 DOT/1000PD) starting on 23 May 2022.Older age, increased disease severity, and residing in an elderly care home were strongly associated with increased odds of prescription, while receiving ≥ 2 doses of COVID-19 vaccines and pre-admission use of coronavirus antivirals were associated with lower odds.ConclusionsThe rate of inpatient antibacterial prescribing initially declined during the pandemic, but increased during the Omicron wave when hospital capacity was overwhelmed. Despite the availability of COVID-19 vaccines and antiviral drugs, antibacterial drug use among COVID-19 inpatients remained high into late 2022.HIGHLIGHTSThe prevalence of antibacterial drug use in hospitalized COVID-19 cases in Hong Kong declined gradually during the first four COVID-19 epidemic waves to 28.0%, but increased to 64.6% with the spread of the Omicron variant in early 2022.The majority of antibacterial drug prescriptions were for Access and Watch drugs, with limited use of combination therapy or macrolides.Older age and more severe disease were strongly associated with an inpatient antibacterial drug prescription, while vaccination and initiation of COVID-19-specific antivirals reduced the odds of antibacterial prescription.Despite moderate-to-high levels of vaccine coverage and the availability of antiviral drugs, 43% of COVID-19 inpatients still received antibacterial drugs in late 2022.