bluuebunny/crossref_metadata_2025_split huggingface dataset:
Major threats to a migratory raptor vary geographically along the eastern Mediterranean flyway
Authors: Oppel Steffen , Arkumarev Volen , Bakari Samuel , Dobrev Vladimir , Saravia Victoria , Adefolu Solomon , Sözüer Lale Aktay , Apeverga Paul Tersoo , Arslan Şafak , Barshep Yahkat , Bino Taulant , Bounas Anastasios , Çetin Turan , Dayyoub Maher , Dobrev Dobromir , Duro Klea , El-Moghrabi Laith , ElSafoury Hana , Endris Ahmed , Asswad Nabegh Ghazal , Harry Junior Hanson , Ivande Sam T , Jbour Sharif , Kapsalis Eleftherios , Kret Elzbieta , Mahamued Bruktawit A , Manu Shiiwua A , Mengistu Solomon , Moussa Zabeirou Abdoul Razack , Muhammad Sulaiman Inuwa , Nakev Slave , Ngari Alex , Onoja Joseph , Osta Maher , Özuslu Serdar , Petrovski Nenad , Popgeorgiev Georgi , Pourchier Cloé , Ruffo Alazar , Shobrak Mohammed , Sidiropoulos Lavrentis , Skartsi Theodora , Sözüer Özgün , Stara Kalliopi , Tesfaye Million , Topi Mirjan , Vavylis Dimitrios , Velevski Metodija , Vorpsi Zydjon , Wondafrash Mengistu , Xeka Erald , Yeniyurt Can , Yordanov Emil , Nikolov Stoyan C 
Published: August 2024

AbstractMillions of large soaring birds migrate from the Palaearctic to Africa every year, and follow distinct flyways around the Mediterranean Sea. While there is conservation concern for many long-distance migratory bird populations, the magnitude and geographic range of threats affecting birds along flyways are poorly known, which complicates efficient mitigation. We used an endangered soaring migrant, the Egyptian VultureNeophron percnopterus, as an example species to assess important threats in 13 countries along the eastern Mediterranean flyway. We tracked 71 birds using satellite telemetry to quantify mortalities, surveyed 4198 km of powerlines to detect dead birds, conducted 910 interviews to quantify the prevalence of poison use, and assessed the magnitude of direct persecution by surveying markets and hunters. We lost 44 birds (50% in Europe and the Mediterranean Sea, 16% in the Middle East, and 34% in Africa), and mortality causes varied geographically. Inadvertent poisoning resulting from rural stakeholders targeting predators occurred along most of the flyway. On the breeding grounds in eastern Europe, poisoning and collision and electrocution continue to be major threats. Electrocution on small and poorly designed electricity pylons was most severe in Turkey, Ethiopia and Saudi Arabia, while direct persecution to meet market demands for belief-based use of vulture products appears to be the largest threat in Nigeria and Niger. Illegal direct persecution for leisure is a major threat in the Middle East and Egypt. Although our work cannot quantitatively estimate which of the identified threats has the greatest demographic impact on Egyptian Vultures, none of threats are species-specific and are therefore relevant for many other migratory birds. Our assessment highlights the key threats per country that range states need to address to meet their obligations under the Convention of Migratory Species to protect migratory birds.
Inhibitory control, personality, and manipulated ecological conditions influence foraging plasticity in the great tit
Authors: Coomes Jenny R. , Davidson Gabrielle L. , Reichert Michael S. , Kulahci Ipek G. , Troisi Camille A. , Quinn John L. 
Published: August 2024

AbstractOrganisms are consistently under selection to respond effectively to a diversity of, sometimes rapid, changes in their environment. Behavioural plasticity can allow individuals to do so instantaneously, but why individuals vary in this respect is poorly understood. Although personality and cognitive traits are often hypothesised to influence plasticity, the effects reported are highly inconsistent, which we hypothesise is because ecological context is usually not considered.Here we explore the roles of individual cognitive and personality variation – assayed using standard tasks for inhibitory control, a measure of self-control, and ‘reactive-proactive’ personality axis (RPPA), respectively – in driving foraging plasticity, and asked how these effects varied across two experimentally manipulated ecological contexts: food value and predation risk.After great tits (Parus major) had initially been trained to retrieve high value food hidden in sand, they were then simultaneously offered the hidden food and an alternative food choice on the surface, that was either high or low value. Their choices were further examined under high and low perceived predation risk treatments. Individuals’ choices were classified in terms of whether they continued to forage on the hidden but familiar food source, or instead switched to the new visible food source. We defined the latter option as the plastic response.Our assays captured consistent differences among individuals in foraging behaviour. Both inhibitory control and exploration influenced whether birds switched from the familiar but hidden food source to the new alternative visible food on the surface. These effects depended on the relative value of the food items available and on the perceived level of predation risk, but also on the time scale over which the response was measured.Our results demonstrate how an executive cognitive function and one specific personality axis can simultaneously influence plasticity in a key functional behaviour. That their effects on foraging were primarily observed as interactions with food value or predation risk treatments also suggest that the population level consequences of behavioural mechanisms, such as these, may only be revealed across key ecological conditions or gradients.
Prospective modelling of operational offshore windfarms on the distribution of marine megafauna in the southern North Sea
Authors: Virgili Auriane , Laran Sophie , Authier Matthieu , Doremus Ghislain , Van Canneyt Olivier , Spitz Jérôme 
Published: August 2024

AbstractIntense development of Offshore Wind Farms (OFWs) has occurred in the North Sea with several more farms planned for the near future. These OFWs pose a threat to marine megafauna stressing the need to mitigate the impact of human activities. To help mitigating impacts, the Before After Gradient (BAG) design was proposed. We thus explored the use of the BAG method on megafauna sightings recorded at different distances from wind farms in the southern North Sea. We predicted intra-annual variability in species distribution, then correlated species distribution with the presence of operational OFWs and investigated the potential impact the operation of prospective OFWs may have on species distribution. Three patterns of intra-annual variability were predicted: species present most abundantly in spring, in winter or all year-round. We recommend that future OFW constructions be planned in summer and early fall to minimise impact on cetaceans and that offshore areas off northern France and Belgium be avoided to minimise impact on seabirds. Our prospective analysis predicted an increased or a decreased density with the operation of prospective OFWs. Prospective approaches, using e.g. a BAG design, are paramount to inform species conservation as they can forecast the likely responses of megafauna to anthropogenic disturbances.
Optimizing reduction of Western blotting analytical variations: use of replicate test samples, multiple normalization methods, and sample loading positions
Authors: Rees Phyllis A. , Lowy R. Joel 
Published: August 2024

AbstractWestern blot (WB) analysis is widely used, but obtaining consistent results can be problematic, particularly if all the treatments cannot be placed on one gel. Sources of variation were investigated by analyzing a set of samples which should produce statistically identical results, an approach commonly applied to analytical instruments. Test samples were lysates from RAW 264.7 murine macrophages treated with LPS to activate MAPK and NF-kB signaling targets. The resulting WB were probed for p-ERK, ERK, IkBβ and non-target protein levels. The first test set (Set 1) was a pooled cell lysate and the second (Set 2) four independently prepared lysates.Analytical replicate data were generated by using multiple WB. Different normalization methods and sample groupings were applied to the density values and the resulting coefficients of variation (CV) and ratios of maximal to minimal values (Max/Min) were compared. Ideally, as the samples were identical (Set 1), or nearly so (Set 2), CVs would be 0 and the Max/Min 1. Results showed the raw density data variance was composed of variability between gel lanes and between gels; but only between gels after applying normalization calculations. CV and Max/Min were 30-70% and 1.5 for raw data, respectively. Common normalization methods, total lane protein, % Control, and p-ERK/ERK ratios, did not have the lowest CVs or Max/Min values. Some of these methods were counterproductive, greatly increasing CV and Max/Min. The best normalization methods resulted in CV and Max/Min value, as low as 5-10% and 1.1, respectively, but more typically 20-25% and 1.2. Application of these methods should allow reliable interpretation of complex experiments that require samples to be placed on multiple gels to provide results, even if fold changes in the target proteins are relatively modest.
Resveratrol targets G-quadruplexes to exert its pharmacological effects
Authors: Soriano-Lerma Ana , Sánchez-Martín Victoria , Murciano-Calles Javier , Ortiz-González Matilde , Tello-López María J , Pérez-Carrasco Virginia , Linde-Rodríguez Ángel , Ramírez-Macías Inmaculada , Gómez-Pìnto Irene , López-Aliaga Inmaculada , Soriano Miguel , Garcia Salcedo Jose A. 
Published: August 2024

AbstractResveratrol (RSV) is one of the most studied and used biomolecules, for which many pharmacological effects targeting multiple tissues have been described. However, a common underlying mechanism driving its full pharmacological activity has not been elucidated to date. G-quadruplexes (G4s) are non-canonical nucleic acid structures found in promoters and involved in controlling gene transcription. This study demonstrates a G4-dependent mode of action for RSV, explaining its multi-target traits. RSV was shown to stabilise cellular G4s, which accumulate around double strand breaks (DSBs) in the promoters of differentially expressed genes (DEGs). G4 targeting triggers DNA damage and controls gene expression. Unravelling the main mode of action of RSV will be helpful to improve its therapeutic potential in a wide variety of health scenarios.
Identification of Disease-relevant, Sex-based Proteomic Differences in iPSC-derived Vascular Smooth Muscle
Authors: Ariyasinghe Nethika R. , Gupta Divya , Escopete Sean , Stotland Aleksandr B. , Sundararaman Niveda , Ngu Ben , Dabke Kruttika , Rai Deepika , McCarthy Liam , Santos Roberta S. , McCain Megan L. , Sareen Dhruv , Parker Sarah J. 
Published: August 2024

AbstractThe prevalence of cardiovascular disease varies with sex, and the impact of intrinsic sex-based differences on vasculature is not well understood. Animal models can provide important insight into some aspects of human biology, however not all discoveries in animal systems translate well to humans. To explore the impact of chromosomal sex on proteomic phenotypes, we used iPSC-derived vascular smooth muscle cells from healthy donors of both sexes to identify sex-based proteomic differences and their possible effects on cardiovascular pathophysiology. Our analysis confirmed that differentiated cells have a proteomic profile more similar to healthy primary aortic smooth muscle than iPSCs. We also identified sex-based differences in iPSC- derived vascular smooth muscle in pathways related to ATP binding, glycogen metabolic process, and cadherin binding as well as multiple proteins relevant to cardiovascular pathophysiology and disease. Additionally, we explored the role of autosomal and sex chromosomes in protein regulation, identifying that proteins on autosomal chromosomes also show sex-based regulation that may affect the protein expression of proteins from autosomal chromosomes. This work supports the biological relevance of iPSC-derived vascular smooth muscle cells as a model for disease, and further exploration of the pathways identified here can lead to the discovery of sex-specific pharmacological targets for cardiovascular disease.SignificanceIn this work, we have differentiated 4 male and 4 female iPSC lines into vascular smooth muscle cells, giving us the ability to identify statistically-significant sex-specific proteomic markers that are relevant to cardiovascular disease risk (such as PCK2, MTOR, IGFBP2, PTGR2, and SULTE1).
Genetic diversity and antimicrobial resistance ofCampylobacter jejuniisolates from Gambian children under five with moderate-to-severe diarrhoea and healthy Controls
Authors: Betts Modupeh , Dione Michel , Ikumapayi Usman Nurudeen , Senghore Madikay , Lamin Modou , Foster-Nyarko Ebenezer , Jaffali James , Panchalingam Sandra , Nataro James P , Kotloff Karen L , Levine Myron M , Saha Debasish , Hossain Jahangir , Kwambana-Adams Brenda , Antonio Martin 
Published: August 2024

ABSTRACTIntroductionCampylobacteris a leading cause of bacterial gastroenteritis globally, but its molecular epidemiology remains poorly understood in sub-Saharan Africa. This study investigates the genotypic population structure ofCampylobacter jejuniisolates from children with moderate-to-severe diarrhoea (MSD) and healthy controls in The Gambia. Additionally, we determined the antimicrobial susceptibility levels of the isolates.MethodsAs part of the Global Enteric Multicenter Study (GEMS) in The Gambia, a total of 49C. jejuniisolates were collected from the stools of children under 5 years old, including 22 with MSD and 27 healthy controls. These isolates were subjected to multilocus sequence typing (MLST) and antimicrobial susceptibility testing using the disc-diffusion method.ResultsTheC. jejuniisolates belonged to 22 sequence types (STs), ten of which were novel. The most common STs were ST-353 (19.1%, 9/47), ST-7784 (12.7%, 6/47), and ST-1038 (10.6%, 5/47). All isolates were fully susceptible to erythromycin, tetracycline, gentamicin and chloramphenicol, with two isolates (4.4%, 2/45) resistant to ciprofloxacin and nalidixic acid. Antimicrobial resistance or intermediate susceptibility to trimethoprim-sulfamethoxazole, cefotaxime and ampicillin was observed in 91.1% (41/45), 90.9% (40/44), and 44.4% (20/45) of the isolates, respectively. There was no strong evidence linkingC. jejuniantimicrobial susceptibility or MLST genotype to MSD status.ConclusionThis study provides the first overview of the high genotypic diversity of humanC. jejuniisolates in The Gambia and reveals low-level resistance among the isolates to antibiotics commonly used to treat campylobacteriosis. The study contributes to understanding the epidemiology and resistance patterns ofC. jejuniin this region.
Quantitative Microscopy in Medicine
Authors: Matov Alexandre , Modiri Shayan 
Published: August 2024

ABSTRACTIntroductionMethods for personalizing medical treatment are the focal point of contemporary biomedical research. In cancer care, we can analyze the effects of therapies at the level of individual cells. Quantitative characterization of treatment efficacy and evaluation of why some individuals respond to specific regimens, whereas others do not, requires additional approaches to genetic sequencing at single time points. Methods for the analysis of changes in phenotype, such asin vivoandex vivomorphology and localization of cellular proteins and organelles can provide important insights into patient treatment options.MethodsNovel therapies are needed to extend survival in metastatic castration-resistant prostate cancer (mCRPC). Prostate-specific membrane antigen (PSMA), a cell surface glycoprotein that is commonly overexpressed by prostate cancer (PC) cells relative to normal prostate cells, provides a validated target.ResultsWe developed a software for image analysis designed to identify PSMA expression on the surface of epithelial cells in order to extract prognostic metrics. In addition, our software can deliver predictive information and inform clinicians regarding the efficacy of PC therapy. We can envisage additional applications of our software system, beyond PC, as PSMA is expressed in a variety of tissues. Our method is based on image denoising, topologic partitioning, and edge detection. These three steps allow to segment the area of each PSMA spot in an image of a coverslip with epithelial cells.ConclusionsOur objective has been to present the community with an integrated, easy to use by all, tool for resolving the complex cellular organization and it is our goal to have such software system approved for use in the clinical practice.
Uncertainty Quantification in Cost-effectiveness Analysis for Stochastic-based Infectious Disease Models: Insights from Surveillance on Lymphatic Filariasis
Authors: Antony Oliver Mary Chriselda , Graham Matthew , Manolopoulou Ioanna , Medley Graham F. , Pellis Lorenzo , Pouwels Koen B , Thorpe Matthew , Hollingsworth T. Deirdre 
Published: August 2024

AbstractCost-effectiveness analyses (CEA) typically involve comparing effectiveness and costs of one or more interventions compared to standard of care, to determine which intervention should be optimally implemented to maximise population health within the constraints of the healthcare budget. Traditionally, cost-effectiveness evaluations are expressed using incremental cost-effectiveness ratios (ICERs), which are compared with a fixed willingness-to-pay (WTP) threshold. Due to the existing uncertainty in costs for interventions and the overall burden of disease, particularly with regard to diseases in populations that are difficult to study, it becomes important to consider uncertainty quantification whilst estimating ICERs.To tackle the challenges of uncertainty quantification in CEA, we propose an alternative paradigm utilizing the Linear Wasserstein framework combined with Linear Discriminant Analysis (LDA) using a demonstrative example of lymphatic filariasis (LF). This approach uses geometric embeddings of the overall costs for treatment and surveillance, disability-adjusted lifeyears (DALYs) averted for morbidity by quantifying the burden of disease due to the years lived with disability, and probabilities of local elimination over a time-horizon of 20 years to evaluate the cost-effectiveness of lowering the stopping thresholds for post-surveillance determination of LF elimination as a public health problem. Our findings suggest that reducing the stopping threshold from <1% to <0.5% microfilaria (mf) prevalence for adults aged 20 years and above, under various treatment coverages and baseline prevalences, is cost-effective. When validated on 20% of test data, for 65% treatment coverage, a government expenditure of WTP ranging from $500 to $3,000 per 1% increase in local elimination probability justifies the switch to the lower threshold as cost-effective.Stochastic model simulations often lead to parameter and structural uncertainty in CEA. Uncertainty may impact the decisions taken, and this study underscores the necessity of better uncertainty quantification techniques within CEA for making informed decisions.
Nanopore-based analysis unravels the genetic landscape and phylogenetic placement of human-infectingTrichurisspecies in Côte d’Ivoire, Tanzania, Uganda, and Laos
Authors: Rahman Nurudeen , Bär Max A. , Dommann Julian , Hürlimann Eveline , Coulibaly Jean T. , Ali Said , Sayasone Somphou , Beinamaryo Prudence , Keiser Jennifer , Schneeberger Pierre H.H. 
Published: August 2024

AbstractSoil-transmitted helminthiases (STH), including trichuriasis, pose a significant global burden, affecting numerous mammalian hosts. Traditional diagnostic methods have struggled to differentiate species within theTrichurisgenus, prompting the use of molecular techniques to understand the diversity and zoonotic transmission ofTrichurisspp. among humans and non-human primates (NHP), dogs, and pigs. In this study, we used nanopore-based full-length ITS2 rDNA sequencing to genetically characterize and confirm the phylogenetic placement of the newly identified human-infectingTrichuris incognitaand the well-knownTrichuris trichiura. Using 670 samples from clinical studies in Côte d’Ivoire, Laos, Tanzania, and Uganda, along with publicly available ITS2 sequences, we confirmed two distinct clusters of human-infectingTrichurisspecies. We found a varying prevalence ofT. incognitaandT. trichiuraacross the four countries and that these were also present in NHP. Our findings demonstrated that ITS2 fragment length accurately differentiates both human-infectingTrichurisspecies and thus makes it a good diagnostic marker for future point-of-care applications in resource-constrained settings.
An updated and expanded characterization of the biological sciences academic job market
Authors: Flynn Brooklynn , Kozik Ariangela J. , Cheng You , Hagan Ada K. , Ng Jennifer , Smith Christopher T. , Haage Amanda , Jadavji Nafisa M. 
Published: August 2024

AbstractIn the biological sciences, many areas of uncertainty exist regarding the factors that contribute to success within the faculty job market. Earlier work from our group reported that beyond certain thresholds, academic and career metrics like the number of publications, fellowships or career transition awards, and years of experience did not separate applicants who received job offers from those who did not. Questions still exist regarding how academic and professional achievements influence job offers and if candidate demographics differentially influence outcomes. To continue addressing these gaps, we initiated surveys collecting data from faculty applicants in the biological sciences field for three hiring cycles in North America (Fall 2019 to the end of May 2022), a total of 449 respondents were included in our analysis. These responses highlight the interplay between various scholarly metrics, extensive demographic information, and hiring outcomes, and for the first time, allowed us to look at persons historically excluded due to ethnicity or race (PEER) status in the context of the faculty job market. Between 2019 and 2022, we found that the number of applications submitted, position seniority, and identifying as a women or transgender were positively correlated with a faculty job offer. Applicant age, residence, first generation status, and number of postdocs, however, were negatively correlated with receiving a faculty job offer. Our data are consistent with other surveys that also highlight the influence of achievements and other factors in hiring processes. Providing baseline comparative data for job seekers can support their informed decision-making in the market and is a first step towards demystifying the faculty job market.