bluuebunny/crossref_metadata_2025_split huggingface dataset:
Camera trapping expands the view into global biodiversity and its change
Authors: Oliver Ruth Y. , Iannarilli Fabiola , Ahumada Jorge , Fegraus Eric , Flores Nicole , Kays Roland , Birch Tanya , Ranipeta Ajay , Rogan Matthew S. , Sica Yanina V. , Jetz Walter 
Published: May 2023

Growing threats to biodiversity demand timely, detailed information on species occurrence, diversity and abundance at large scales. Camera traps (CTs), combined with computer vision models, provide an efficient method to survey species of certain taxa with high spatio-temporal resolution. We test the potential of CTs to close biodiversity knowledge gaps by comparing CT records of terrestrial mammals and birds from the recently released Wildlife Insights platform to publicly available occurrences from many observation types in the Global Biodiversity Information Facility. In locations with CTs, we found they sampled a greater number of days (mean = 133 versus 57 days) and documented additional species (mean increase of 1% of expected mammals). For species with CT data, we found CTs provided novel documentation of their ranges (93% of mammals and 48% of birds). Countries with the largest boost in data coverage were in the historically underrepresented southern hemisphere. Although embargoes increase data providers' willingness to share data, they cause a lag in data availability. Our work shows that the continued collection and mobilization of CT data, especially when combined with data sharing that supports attribution and privacy, has the potential to offer a critical lens into biodiversity.This article is part of the theme issue ‘Detecting and attributing the causes of biodiversity change: needs, gaps and solutions’.
Monitoring biodiversity loss in rapidly changing Afrotropical ecosystems: an emerging imperative for governance and research
Authors: Achieng A. O. , Arhonditsis G. B. , Mandrak N. , Febria C. , Opaa B. , Coffey T. J. , Masese F. O. , Irvine K. , Ajode Z. M. , Obiero K. , Barasa J. E. , Kaunda-Arara B. 
Published: May 2023

Africa is experiencing extensive biodiversity loss due to rapid changes in the environment, where natural resources constitute the main instrument for socioeconomic development and a mainstay source of livelihoods for an increasing population. Lack of data and information deficiency on biodiversity, but also budget constraints and insufficient financial and technical capacity, impede sound policy design and effective implementation of conservation and management measures. The problem is further exacerbated by the lack of harmonized indicators and databases to assess conservation needs and monitor biodiversity losses. We review challenges with biodiversity data (availability, quality, usability and database access) as a key limiting factor that impacts funding and governance. We also evaluate the drivers of both ecosystems change and biodiversity loss as a central piece of knowledge to develop and implement effective policies. While the continent focuses more on the latter, we argue that the two are complementary in shaping restoration and management solutions. We thus underscore the importance of establishing monitoring programmes focusing on biodiversity–ecosystem linkages in order to inform evidence-based decisions in ecosystem conservation and restoration in Africa.
This article is part of the theme issue ‘Detecting and attributing the causes of biodiversity change: needs, gaps and solutions’.
Supplementation with Berry Juice and Vitamin E Ameliorates Blood Cholesterol Level and Alters Gut Microbiota Composition
Authors: Chen Bangwei , Li Yaxin , Li Zhiming , Hu Xiaojie , Zhen Hefu , Chen Hongyun , Nie Chao , Hou Yong , Jin Xin , Xiao Liang , Li Tao 
Published: May 2023

ABSTRACTScopeAntioxidants, including vitamin E (VE) and grape seed extract, as anti-aging supplementation have been widely used to improve human health. However, the role of gut microbiota in dietary antioxidant supplementation is debatable. This study aimed to assess the longitudinal impact of dietary supplementation with antioxidant compounds on body health and the gut microbiota.Methods and resultsOne hundred and twenty healthy individuals were randomly divided into a placebo group (amylodextrin) and three experimental groups ingesting different supplement (VE, grape seed extract, or mixed berry juice). Blood and fecal samples were collected during three intervention phases. We found that VE and mixed berry juice ameliorated blood cholesterol levels by reducing the levels of low-density lipoprotein cholesterol (LDL-C) in healthy volunteers. After the intervention, there was an increase in the relative abundance of short-chain fatty acid (SCFA)-producing bacteria and bile acid metabolizers. Specifically, the abundances ofLachnospirasp. andFaecalibacteriumspp. increased in the VE and berry juice groups. Interestingly, the gut microbiota of poor responders harbored a greater proportion of disease-associated bacterial species.ConclusionJuice and VE could promote health by lowering LDL-C, partly and indirectly by affecting gut bacteria with the ability to produce SCFAs or metabolize bile acids.
Mechanical Dispersion Discriminates between Arrhythmic and Non-Arrhythmic Sudden Death: From the POST SCD Study
Authors: Tastet Lionel , Ramakrishna Satvik , Lim Lisa J. , Bibby Dwight , Olgin Jeffrey E. , Connolly Andrew J. , Moffatt Ellen , Tseng Zian H. , Delling Francesca N. 
Published: May 2023

ABSTRACTBackgroundGlobal longitudinal strain (GLS) and mechanical dispersion (MD) by speckle-tracking echocardiography can predict sudden cardiac death (SCD) beyond left ventricular ejection fraction (LVEF) alone. However, prior studies have presumed cardiac cause from EMS records or death certificates rather than gold-standard autopsies.ObjectivesWe sought to investigate whether abnormal GLS and MD, reflective of underlying myocardial fibrosis, are associated with autopsy-defined sudden arrhythmic death (SAD) in a comprehensive postmortem study.MethodsWe identified and autopsied all World Health Organization-defined (presumed) SCDs ages 18-90 via active surveillance of out of hospital deaths in the ongoing San Francisco POstmortem Systematic InvesTigation of Sudden Cardiac Death (POST SCD) Study to refine presumed SCDs to true cardiac causes. We retrieved all available pre-mortem echocardiograms and assessed LVEF, LV-GLS, and MD. The extent of LV myocardial fibrosis was assessed and quantified histologically.ResultsOf 652 autopsied subjects, 65 (10%) had echocardiograms available for primary review, obtained at a mean 1.5 years before SCD. Of these, 37 (56%) were SADs and 29 (44%) were non-SADs; fibrosis was quantified in 38 (58%). SADs were predominantly male, but had similar age, race, baseline comorbidities, and LVEF compared to non-SADs (all p>0.05). SADs had significantly reduced LV-GLS (median: –11.4% versus –18.5%, p=0.008) and increased MD (median: 14.8 ms versus 9.4 ms, p=0.006) compared to non-SADs. MD was associated with total LV fibrosis by linear regression in SADs (r=0.58, p=0.002).ConclusionIn this countywide postmortem study of all sudden deaths, autopsy-confirmed arrhythmic deaths had significantly lower LV-GLS and increased MD than non-arrhythmic sudden deaths. Increased MD correlated with higher histologic levels of LV fibrosis in SADs. These findings suggest that increased MD, which is a surrogate for the extent of myocardial fibrosis, may improve risk stratification and specification for SAD beyond LVEF.PERSPECTIVESCompetency in medical knowledgeMechanical dispersion derived from speckle tracking echocardiography provides better discrimination between autopsy-defined arrhythmic vs non-arrhythmic sudden death than LVEF or LV-GLS. Histological ventricular fibrosis correlates with increased mechanical dispersion in SAD.Translational outlookSpeckle tracking echocardiography parameters, in particular mechanical dispersion, may be considered as a non-invasive surrogate marker for myocardial fibrosis and risk stratification in SCD.
How suitable are clinical vignettes for the evaluation of symptom checker apps? A test theoretical perspective
Authors: Kopka Marvin , Feufel Markus A. , Berner Eta S. , Schmieding Malte L. 
Published: May 2023

AbstractObjectiveTo evaluate the ability of case vignettes to assess the performance of symptom checker applications and to suggest refinements of the methods of case vignette-based audit studies.MethodsWe re-analyzed the publicly available data of two prominent case vignette-based symptom checker audit studies by calculating common metrics of test theory. Furthermore, we developed a new metric, the Capability Comparison Score (CCS), which controls for different degrees of item difficulty of the set of cases each symptom checker evaluated. We then scrutinized whether applying test theory and the CCS alter the performance ranking of the investigated symptom checkers.ResultsIn both studies most symptom checkers changed their rank order of triage capability when adjusting for item difficulty with the CCS. The previously reported triage accuracies commonly overestimated the capability of symptom checkers because they do not account for the fact that symptom checkers tend to selectively appraise easier cases. Many case vignettes in both studies showed insufficient (very low and even negative) values of item-total correlation.ConclusionsA test theoretic perspective helps identify previously unreported limitations to the validity of case vignette-based symptom checker assessments and provides guidance on how to improve the quality of case vignettes and metrics for appraising their quality. A more elaborate metric, which accounts for item difficulty of vignettes an app did (not) evaluate, might prove more meaningful than accuracy alone for competitive assessment of symptom checkers. Our approach contributes to standardizing the methods to appraise symptom checker capability to yield more generalizable results.
Artificial intelligence-based histopathology image analysis identifies a novel subset of endometrial cancers with distinct genomic features and unfavourable outcome
Authors: Darbandsari Amirali , Farahani Hossein , Wiens Matthew , Cochrane Dawn , Asadi Maryam , Mirabadi Ali Khajegili , Jamieson Amy , Farnell David , Ahmadvand Pouya , Douglas Maxwell , Leung Samuel , Abolmaesumi Purang , Jones Steven JM , Talhouk Aline , Kommoss Stefan , Gilks C Blake , Huntsman David G. , Singh Naveena , McAlpine Jessica N. , Bashashati Ali 
Published: May 2023

AbstractEndometrial cancer (EC) has four molecular subtypes with strong prognostic value and therapeutic implications. The most common subtype (NSMP; No Specific Molecular Profile) is assigned after exclusion of the defining features of the other three molecular subtypes and includes patients with heterogeneous clinical outcomes. In this study, we employed artificial intelligence (AI)-powered histopathology image analysis to differentiate between p53abn and NSMP EC subtypes and consequently identified a novel sub-group of NSMP EC patients that had markedly inferior progression-free and disease-specific survival (termed ‘p53abn-like NSMP’), in a discovery cohort of 368 patients and an independent validation cohort of 290 patients from another center. Shallow whole genome sequencing revealed a higher burden of copy number abnormalities in the ‘p53abn-like NSMP’ group compared to NSMP, suggesting that this new group is biologically distinct compared to other NSMP ECs. Our work demonstrates the power of AI to detect prognostically different and otherwise unrecognizable subsets of EC where conventional and standard molecular or pathologic criteria fall short, refining image-based tumor classification.
Combined metagenomic- and culture-based approaches to investigate bacterial strain-level associations with medication-controlled mild-moderate atopic dermatitis
Authors: Lane Starr Nicole M , Al-Rayyan Numan , Smith Jennifer M , Sandstrom Shelby , Swaney Mary Hannah , Salamzade Rauf , Steidl Olivia , Kalan Lindsay R , Singh Anne Marie 
Published: May 2023

ABSTRACTBackgroundThe skin microbiome is disrupted in atopic dermatitis (AD). Existing research focuses on moderate-severe, unmedicated disease.ObjectiveInvestigate metagenomic- and culture-based bacterial strain-level differences in mild, medicated AD, and the effects these have on human keratinocytes (HK).MethodsSkin swabs from anterior forearms were collected from 20 pediatric participants; 11 participants with AD sampled at lesional and nonlesional sites and 9 age- and sex-matched controls). Participants had primarily mild-moderate AD and maintained medication use. Samples were processed for microbial metagenomic sequencing and bacterial isolation. Isolates identified asS. aureuswere tested for enterotoxin production. HK cultures were treated with cell free conditioned media from representativeStaphylococcusspecies to measure barrier effects.ResultsMetagenomic sequencing identified significant differences in microbiome composition between AD and control groups. Differences were seen at the species- and strain-levels forStaphylococci, withS. aureusonly found in AD participants and differences inS. epidermidisstrains between control and AD swabs. These strains showed differences in toxin gene presence, which was confirmedin vitroforS. aureusenterotoxins. The strain from the most severe AD participant produced enterotoxin B levels >100-fold higher than the other strains (p<0.001). Strains also displayed differential effects on HK metabolism and barrier function.ConclusionsStrain level differences in toxin genes fromStaphylococcusstrains may explain varying effects on HK, withS. aureusandnon-aureusstrains negatively impacting viability and barrier function. These differences are likely important in AD pathogenesis.KEY MESSAGESStaphylococcal strain effects, more so than species effects, impact keratinocyte barrier function and metabolism, suggesting that strain level differences, and not species-level, may be critical in AD pathogenesis.The microbiome from mild, medicated atopic dermatitis patients harborStaphylococcusstrains with detrimental effects on skin barrier, and may not only be mediated byS. aureus.CAPSULE SUMMARYPatients with mild atopic dermatitis controlled by medication may still harbor strains ofStaphylococcus spp.that carry toxins that negatively impact skin barrier function.
PYCR1 Levels Track with Premature and Chronological Skin Aging
Authors: Sotiropoulou Kortessa , Yumlu Saniye , Hirano Tomoko , Maier Michael , Loh Abigail , Ong Peh Fern , Yim Onn Siong , Liu Chunping , Vial Emmanuel , Altunoğlu Umut , Nampoothiri Sheela , de Silva Deepthi , Fischer-Zirnsak Björn , Kayserili Hülya , Lai Poh San , Dreesen Oliver , Kabashima Kenji , Kornak Uwe , Escande-Beillard Nathalie , Reversade Bruno 
Published: May 2023

ABSTRACTDe Barsy syndrome is a recessive progeroid disease classified under the group of cutis laxa syndromes. The disease is attributed to loss-of-function mutations inPYCR1orALDH18A1, leading to premature skin aging. Here we report fivePYCR1pathogenic alleles and a mouse knockout model of the disease. Through these investigations, we have confirmed the key role of PYCR1 in preventing dermal thinning and other connective tissue abnormalities. However, it remains unknown whether endogenous PYCR1 levels undergo changes during normal aging. To address this query, we examined its levels in cultured human cutaneous fibroblasts subjected to induced or replicative senescence. In both instances, PYCR1 levels dropped and correlated with the loss of proliferative capacity. Furthermore, we validated the relevance of these findingsin vivo, by comparing young and chronologically aged human skin, and found that the levels of PYCR1 in the dermis, but not the epidermis, significantly decreased with age. Our results confirm that the loss of PYCR1 is a driver of human skin aging and that its levels in healthy individuals can serve as a biomarker for connective tissues undergoing normal chronological aging.
Comparison of the urinary proteome in depressed patients before and after modified electroconvulsive therapy
Authors: Tang Shuxuan , Guo Tong , Sha Sha , Wei Jing , Liu Yuqing , Yang Jian , Wang Gang , Gao Youhe 
Published: May 2023

AbstractModified electroconvulsive therapy (MECT) is an effective treatment for mood and psychiatric disorders and provides rapid and significant improvements in severe symptoms of several mental health conditions. We attempted to compare the urinary proteome of each depressive patient before and after electroconvulsive therapy. The common biological processes enriched by differential proteins through GO analysis with most patients mainly included cell adhesion (9/9 patients), immune response (7/9), axon guidance (7/9), and oxidation stress (7/9). Moreover, the common biological pathways identified by Ingenuity Pathway Analysis software showed that acute phase response signaling (7/9 patients), NRF2-mediated oxidative stress response (7/9), synaptogenesis signaling pathway (5/9), and ephrin B signaling (5/9) were all upregulated among each patient and were involved in promoting synaptic plasticity and neuroplasticity. Common biological processes and pathways in urine were reported to be related to the mechanism of MECT in the treatment of mental illnesses. In addition, the common differential proteins CSPG4, CBG, APP, NCAM1, and ARSA were suspected to be related to memory loss, memory damage, and memory formation, which might be the effects of MECT.
Patient-specific alterations in blood plasma cfRNA profiles enable accurate classification of cancer patients and controls
Authors: Morlion Annelien , Decruyenaere Philippe , Schoofs Kathleen , Anckaert Jasper , Nuytens Justine , Vanden Eynde Eveline , Verniers Kimberly , Everaert Celine , Offner Fritz , Van Dorpe Jo , Thas Olivier , Vandesompele Jo , Mestdagh Pieter 
Published: May 2023

AbstractCirculating nucleic acids in blood plasma form an attractive resource to study human health and disease. Here, we applied mRNA capture sequencing of blood plasma cell-free RNA from 266 cancer patients and cancer-free controls (discovery n = 208, 25 cancer types; replication n = 58, 3 types). We observed cancer type-specific as well as pan-cancer alterations in cell-free transcriptomes compared to controls. Differentially abundant RNAs were heterogenous among patients and among cohorts, hampering identification of robust cancer biomarkers. Therefore, we developed a novel method that compares each individual cancer patient to a reference control population to identify so-called biomarker tail genes. The number of biomarker tail genes in a sample enables distinguishing an individual cancer patient from controls. The potential of this novel approach was confirmed in additional cohorts of 65 plasma donors (2 lymphoma types) and 24 urine donors (bladder cancer). Together, our findings demonstrate heterogeneity in cell-free RNA alterations among cancer patients and propose that case-specific alterations can be exploited for classification purposes.
Health care provider and client experiences of counselling on depot medroxyprogesterone acetate subcutaneous (DMPA-SC) for self-injection in Malawi
Authors: Erlank Chelsey Porter , Ali Gracious , Birhanu Frehiwot , Stanley Melinda , Chirwa Jessie Salamba , Kachale Fannie , Gunda Andrews 
Published: May 2023

AbstractSince the introduction of depot medroxyprogesterone acetate (DMPA-SC) in 2018, Malawi has achieved national coverage of trained providers in the public sector and steady increases in uptake of DMPA-SC. However, the rate of clients opting to self-inject DMPA-SC has remained lower than early acceptability studies suggested. Providers play an instrumental role in building client confidence to self-inject through counselling. This cross-sectional qualitative study explored the perspectives of providers and injectable clients on the integration of self-injection into contraceptive counselling, to identify best practices and gaps. The study was conducted at public sector sites in three districts (Nkhotakota, Mzimba South, Zomba) in Malawi. In-depth interviews were conducted with provider-administered injectable clients, self-injecting clients, and DMPA-SC trained providers. All providers interviewed reported successfully integrating self-injection into their approach. During health education sessions, providers tended to focus mainly on benefits of self-injection to spark interest in the method, and then follow that up with more in-depth information in individual counselling. Due to time pressures, a minority of providers reported replacing individual counselling with small-group counselling and limited their use of peer testimonials, visualizations, and demonstrations. Most providers skipped client practice on inanimate objects, feeling this was either not necessary or not appropriate given stock or resource constraints. Current self-injecting clients showed the best recall for self-injection steps and tended to report having received comprehensive, supportive counselling including aspects such as peer testimonials, visualizations, and demonstrations to build confidence. Injectable clients who had declined self-injection tended to demonstrate less detailed recall of key self-injection messages and report receiving incomplete information, and lack of peer testimonials, visualization, or demonstrations. Comprehensive counselling and training from supportive providers, including best practices identified in this study, are vital to improving client confidence to self-inject. Providers should be supported to overcome time- and resource-pressures to invest in these best practices.
Protein unfolding thermodynamics predict multicomponent phase behavior
Authors: Rana Neha , Kodirov Rukhillo , Shakya Anisha , King John T. 
Published: May 2023

AbstractAn increasing number of proteins are known to undergo liquid-liquid phase separation (LLPS), with or without nucleic acids or partner proteins, forming dense liquid-like phases termed biomolecular condensates. This physical phenomenon has been implicated in the existence of cellular membraneless organelles as well as in the formation of pathological protein aggregates in several human diseases. While common structural features of proteins with a propensity to undergo LLPS have been well documented, currently there is no thermodynamic framework capable of predicting the phase behavior of native proteins. Here, we show that two fundamental thermodynamic properties associated with the unfolding of a native protein, change in heat capacity (ΔCunfold) and change in Gibbs free energy (ΔGunfold), are sufficient to predict the formation of multicomponent biomolecular condensates. We find that proteins with smallΔCunfoldandΔGunfoldvalues, which indicate a native state that is thermodynamically similar to the fully unfolded state, promote LLPS. In contrast, proteins with largeΔCunfoldandΔGunfoldvalues promote aggregation. We also demonstrate that the stability of the liquid-like condensate can be predicted from the proximity of a protein’s thermodynamic variable values to the phase boundary. This work elucidates a deep connection between single-protein thermodynamics and multicomponent phase behavior, and provides an avenue for predicting pathological droplet-aggregate transition.Significance StatementBiomolecular phase transitions, such as LLPS of proteins and nucleic acids, is emerging as an important concept in understanding the link between dysregulation of membraneless compartmentalization in cells and several human diseases. Currently, analysis of structural features such as intrinsic disorder and charged residue content is the “rule-of-thumb” to predict a protein’s propensity to undergo LLPS. There are several instances where this qualitative approach fails, potentially due to not accounting for a protein’s native structure. We demonstrate an empirical correlation between the unfolding thermodynamics of native proteins and their phase behavior, which enables a quantitative prediction of multicomponent LLPS. This novel approach, based on single-protein thermodynamics, has the potential to quantitatively predict pathological phase transitions of proteins in degenerative human diseases.