bluuebunny/crossref_metadata_2025_split huggingface dataset:
High-throughput metabolome comparison of cutaneous squamous cell carcinoma, basal cell carcinoma, and healthy skin with e-biopsy sampling
Authors: Louie Leetal , Wise Julia , Berl Ariel , Shir-az Ofir , Kravtsov Vladimir , Yakhini Zohar , Shalom Avshalom , Golberg Alexander , Vitkin Edward 
Published: March 2024

AbstractA standard histopathology-slides based diagnostics becomes a serious process bottleneck due to rising incidence rates of cutaneous squamous cell carcinoma (cSCC) and basal cell carcinoma (BCC). Leveraging tissue molecular information for diagnostics can be a beneficial alternative in certain cases. Sampling and processing of a constantly growing number of tumors can be enhanced with faster specimen collection methods together with high-throughput molecular identification approaches. Tumor specimens can be collected with electroporation-based biopsy (e-biopsy), a minimally invasive sampling collection tool with a proven ability, while mass spectrometry can be used for molecular identification.The aim of this study was (i) to confirm the ability of e-biopsy technique to harvest metabolites, (ii) to obtain high-resolution metabolomic profiles of cSCC, BCC, and healthy skin tissues, and (iii) to perform a comparative analysis of the collected profiles.Data, collected with e-biopsy coupled with ultra performance liquid chromatography and tandem mass spectrometry (UPLC-MS-MS), expands the current metabolomic profiles reported for cSCC, BCC, and healthy skin. Here we report measurements of 2325 small metabolites identified (301 with high confidence) in 13 tissue samples from 12 patients. Comparative analysis identified 34 significantly (p<0.05) differentially expressed high-confidence metabolites. Generally, we observed a greater number of metabolites with higher expression, in cSCC and in BCC compared to healthy tissues, belonging to the subclass amino acids, peptides, and analogues.
How to mitigate selection bias in COVID-19 surveys: evidence from five national cohorts
Authors: Narayanan Martina K. , Dodgeon Brian , Katsoulis Michail , Ploubidis George B. , Silverwood Richard J. 
Published: March 2024

ABSTRACTBackgroundNon-response is a common problem, and even more so during the COVID-19 pandemic where social distancing measures challenged data collections. As non-response is often systematic, meaning that respondents are usually healthier and from a better socioeconomic background, this potentially introduces serious bias in research findings based on COVID-19 survey data. The goal of the current study was to see if we can reduce bias and restore sample representativeness despite systematic non-response in the COVID-19 surveys embedded within five UK cohort studies using the rich data available from previous time points.MethodsA series of three surveys was conducted during the pandemic across five UK cohorts: National Survey of Health and Development (NSHD, born 1946), 1958 National Child Development Study (NCDS), 1970 British Cohort Study (BCS70), Next Steps (born 1989-90) and Millennium Cohort Study (MCS, born 2000-02). We applied non-response weights and utilised multiple imputation, making use of covariates from previous waves which have been commonly identified as predictors of non-response, to attempt to reduce bias and restore sample representativeness.ResultsResponse rates in the COVID-19 surveys were lower compared to previous cohort waves, especially in the younger cohorts. We identified bias due to systematic non-response in the distributions of variables including parental social class and childhood cognitive ability. In each cohort, respondents of the COVID-19 survey had a higher percentage of parents in the most advantaged social class, and a higher mean of childhood cognitive ability, compared to the original (full) cohort sample. The application of non-response weights and multiple imputation was successful in reducing bias in parental social class and childhood cognitive ability, nearly eliminating it for the former.ConclusionsThe current paper demonstrates that it is possible to reduce bias from non-response and to a large degree restore sample representativeness in multiple waves of a COVID-19 survey embedded within long running longitudinal cohort studies through application of non-response weights or multiple imputation. Such embedded COVID-19 surveys therefore have an advantage over cross-sectional COVID-19 surveys, where non-response bias cannot be handled by leveraging previously observed information on non-respondents. Our findings suggest that, if non-response is appropriately handled, analyses based on the COVID-19 surveys within these five cohorts can contribute significantly to COVID-19 research, including studying the medium and long-term effects of the pandemic.
Nephroprotective effects of cilastatin in people at risk of acute kidney injury: A systematic review and meta-analysis
Authors: Acharya Dilaram , Ghanim Fanar , Harrison Tyrone G. , Scory Tayler Dawn , Shommu Nusrat , Ronksley Paul E. , Elliott Meghan J. , Collister David , Pannu Neesh , James Matthew T. 
Published: March 2024

ABSTRACTRationale & ObjectiveCilastatin is an inhibitor of drug metabolism in the proximal tubule that demonstrates nephroprotective effects in animals. It has been used in humans in combination with the antibiotic imipenem to prevent imipenem’s degradation. This systematic review and meta-analysis evaluated the nephroprotective effects of cilastatin in humans.Study DesignSystematic review and meta-analysis of observational (comparative effectiveness) studies or randomized clinical trials (RCTs)Setting & Study PopulationsPeople of any age at risk of acute kidney injury (AKI).Selection Criteria for StudiesWe systematically searched MEDLINE, Embase, Web of Science, and the Cochrane Controlled Trials registry from database inception to November 2023 for observational studies or RCTs that compared kidney outcomes among groups treated with cilastatin, either alone or as combination imipenem-cilastatin, versus an inactive or active control group not treated with cilastatin.Data ExtractionTwo reviewers independently evaluated studies for inclusionand risk of bias.Analytical ApproachTreatment effects were estimated using random effects models and heterogeneity was quantified using the I2statistic.ResultsWe identified 10 studies (five RCTs, n=531 patients; 5 observational studies, n=6,321 participants) that met the inclusion criteria, including 6 studies with comparisons of imipenem-cilastatin to an inactive control and 4 studies with comparisons to alternate antibiotics. Based on pooled results from 5 studies, the risk of AKI was lower with imipenem-cilastatin (risk ratio [RR] 0.53 [95% CI, 0.38 to 0.74]; I2=42.2%), with consistent results observed from randomized trials (two trials, RR 0.30 [95% CI, 0.09 to 1.00]; I2=62.8%) and observational studies (three studies, RR 0.55 [95% CI, 0.38 to 0.81]; I2=62.8%). Based on results from six studies, kidney function was also better with imipenem-cilastatin than comparators (weighted mean difference [WMD] in serum creatinine -0.14 mg/dL [95% CI, -0.21 to -0.07]; I2=0%). The overall certainty of the evidence was low due to heterogeneity of the results, high risk of bias, and indirectness among the identified studies.LimitationsClinical and statistical heterogeneity could not be fully explained due to a limited number of studies.ConclusionPatients treated with imipenem-cilastatin developed AKI less frequently and had better short-term kidney function than control groups or those receiving comparator antibiotics. Larger clinical trials with less risk of detection bias due to lack of allocation concealment and blinding are needed to establish the efficacy of cilastatin for AKI prevention.RegistrationInternational Prospective Register of Systematic Reviews (PROSPERO) database (ID: CRD42023488809)
Comparison of Deep Learning Approaches for Conversion of International Classification of Diseases Codes to the Abbreviated Injury Scale
Authors: Doshi Ayush , Marche Charbel , Chernyavskiy Pavel , Glass George , Hartka Thomas 
Published: March 2024

ABSTRACTThe injury severity classifications generated from the Abbreviated Injury Scale (AIS) provide information that allows for standardized comparisons in the field of trauma injury research. However, the majority of injuries are coded in International Classification of Diseases (ICD) and lack this severity information. A system to predict injury severity classifications from ICD codes would be beneficial as manually coding in AIS can be time-intensive or even impossible for some retrospective cases. It has been previously shown that the encoder-decoder-based neural machine translation (NMT) model is more accurate than a one-to-one mapping of ICD codes to AIS. The objective of this study is to compare the accuracy of two architectures, feedforward neural networks (FFNN) and NMT, in predicting Injury Severity Score (ISS) and ISS ≥16 classification. Both architectures were tested in direct conversion from ICD codes to ISS score and indirect conversion through AIS for a total of four models. Trauma cases from the U.S. National Trauma Data Bank were used to develop and test the four models as the injuries were coded in both ICD and AIS. 2,031,793 trauma cases from 2017-2018 were used to train and validate the models while 1,091,792 cases from 2019 were used to test and compare them. The results showed that indirect conversion through AIS using an NMT was the most accurate in predicting the exact ISS score, followed by direct conversion with FFNN, direct conversion with NMT, and lastly indirect conversion with FFNN, with statistically significant differences in performance on all pairwise comparisons. The rankings were similar when comparing the accuracy of predicting ISS ≥16 classification, however the differences were smaller. The NMT architecture continues to demonstrate notable accuracy in predicting exact ISS scores, but a simpler FFNN approach may be preferred in specific situations, such as if only ISS ≥16 classification is needed or large-scale computational resources are unavailable.
Neuroanatomical variability associated with early substance use initiation: Results from the ABCD Study
Authors: Miller Alex P. , Baranger David A. A. , Paul Sarah E. , Garavan Hugh , Mackey Scott , Tapert Susan F. , LeBlanc Kimberly H. , Agrawal Arpana , Bogdan Ryan 
Published: March 2024

AbstractThe extent to which neuroanatomical variability associated with substance involvement reflects pre-existing risk and/or consequences of substance exposure remains poorly understood. In the Adolescent Brain Cognitive DevelopmentSM(ABCD®) Study, we identify associations between global and regional differences in brain structure and early substance use initiation (i.e., occurring <15 years of age; nsanalytic=6,556-9,804), with evidence that associations precede initiation. Neurodevelopmental variability in brain structure may confer risk for substance involvement.
Immune history influences SARS-CoV-2 booster impacts: the role of efficacy and redundancy
Authors: Larsen Sophie L. , Noor Iffat , West Haylee , Chandra Eliana , Martinez Pamela P. , Kraay Alicia N. M. 
Published: March 2024

AbstractGiven the continued emergence of SARS-CoV-2 variants of concern as well as unprecedented vaccine development, it is crucial to understand the effect of the updated vaccine formulations at the population level. While bivalent formulations have higher efficacy in vaccine trials, translating these findings to real-world effectiveness is challenging due to the diversity in immune history, especially in settings with a high degree of natural immunity. Known socioeconomic disparities in key metrics such as vaccine coverage, social distancing, and access to healthcare have likely shaped the development and distribution of this immune landscape. Yet little has been done to investigate the impact of booster formulation in the context of host heterogeneity. Using two complementary mathematical models that capture host demographics and immune histories over time, we investigated the potential impacts of bivalent and monovalent boosters in low– and middle-income countries (LMICs). These models allowed us to test the role of natural immunity and cross-protection in determining the optimal booster strategy. Our results show that to avert deaths from a new variant in populations with high immune history, it is more important that a booster is implemented than which booster is implemented (bivalent vs. monovalent). However, in populations with low preexisting immunity, bivalent boosters can become optimal. These findings suggest that for many LMICs – where acquiring a new vaccine stock may be economically prohibitive – monovalent boosters can still be implemented as long as pre-existing immunity is high.
Recommendations for implementing the INTERACT3 care bundle for intracerebral hemorrhage in Latin America: a Delphi Study
Authors: Allende Ma.Ignacia , Muñoz-Venturelli Paula , Gonzalez Francisca , Bascur Francisca , Anderson Craig S. , Ouyang Menglu , Cabieses Báltica , Obach Alexandra , Cano-Nigenda Vanessa , Arauz Antonio 
Published: March 2024

AbstractBackground and aimsThe third Intensive Care Bundle with Blood Pressure Reduction in Acute Cerebral Hemorrhage Trial (INTERACT3) showed that the implementation of a care bundle improves outcomes after acute intracerebral hemorrhage (ICH). We aimed to establish consensus-based recommendations for the broader integration of the care bundle across Latin American countries (LAC).MethodsA 3-phase Delphi study allowed a panel of 32 healthcare workers from 14 LAC to sequentially rank various statements that commenced with 43 statements relevant to 7 domains (training, resources and infrastructure, education of patients, blood pressure, temperature, glycemic control, and reversal of anticoagulation). The pre-defined consensus threshold was 75%.ResultsA total of 55 statements reached consensus by the third round, which included 12 new statements that emerged through rounds. The highest-ranked statements in each domain emphasized critical aspects with successful implementation requiring a minimum level of resources to be made available. Key priorities included the continuous training of all healthcare workers involved in the management of ICH, establishing protocols aligned with available resources, and a collaborative inter-disciplinary approach to care being supported by institutional networks. Statements related to anticoagulation reversal were given the highest priority, which highlighted interest in the topic but limited availability of treatment in the region.ConclusionsConsensus statements are provided to facilitate integration of the INTERACT3 care bundle to reduce disparities in ICH outcomes in LAC.
Anab initioinformation-theoretic approach to proteins and protein-ligand interactions
Authors: Nath Deep , Grewal Rajdeep Kaur , Mitra Devrani , Roy Soumen 
Published: March 2024

AbstractDiffering conformational structure of a protein, associated with two distinct signaling states or between ligand-free and ligand-bound states, leads to differing inter-residue interactions and consequently different biological function. We propose a fresh first-principles information-theoretic approach for studying such proteins and their interactions. Ade novomeasure called protein residue information (PRI), which incorporates details of interactions between all pairs of atoms within and across all residues of the protein, is introduced herein. We formulate a method to calculate the intrastate and inter-state entropy of every residue, needed to determine PRI across any two states of a protein. The intra-state entropy can be determined for every state of a protein possessing one or more states. The inter-state entropy can be calculated pairwise for proteins possessing more than one state. We analyze twenty eight distinct pairs of protein structures from ten different classes. PRI successfully identifies important residues displaying significant conformational changes bearing influence with respect to itself and all other residues. Furthermore, it also successfully identifies important residues displaying rather subtle conformational changes. The identified residues exhibit influential roles in diverse performative features of proteins like stability, allostery, signaling, etc. PRI successfully recovers known experimental results from literature and predicts important roles for many hitherto unstudied residues.
Population genetics and phylogeographic history of the insular lizardPodarcis lilfordi(Gunther, 1874) from the Balearic Islands based on genome-wide polymorphic data
Authors: Otalora Katherin , Riera Joan Lluís , Tavecchia Giacomo , Rotger Andreu , Igual José Manuel , Trotta Jean-Remi Paul , Baldo Laura 
Published: March 2024

AbstractIslands provide a great system to explore the processes that maintain genetic diversity and promote local adaptation. We explored the genomic diversity of the Balearic lizardPodarcis lilfordi, an endemic species characterized by numerous small insular populations with large phenotypic diversity. Using the newly available genome for this species, we characterized more than 300,000 SNPs, merging Genotype by Sequencing (GBS) data with previously published Restriction-site associated DNA sequencing (RADSeq) data, providing a dataset of 16 island populations (191 individuals) across the range of species distribution (Menorca, Mallorca, and Cabrera). Results indicate that each islet hosts a well-differentiated population (Fst=0.247±0.09), with no recent immigration/translocation events. Contrary to expectations, most populations harbor a considerable genetic diversity (mean nucleotide diversity, Pi=0.144±0.021), characterized by overall low inbreeding values (Fis<0.1). While the genetic diversity significantly decreased with decreasing islet surface, maintenance of substantial genetic diversity even in tiny islets suggests variable selection or other mechanisms that buffer genetic drift. Maximum-likelihood tree based on concatenated SNP data confirmed the existence of the two major independent lineages of Menorca and Mallorca/Cabrera. Multiple lines of evidence, including admixture and root testing, robustly placed the origin of the species in the Mallorca Island, rather than in Menorca. Outlier analysis mainly retrieved a strong signature of genome differentiation between the two major archipelagos, especially in the sexual chromosome Z. A set of proteins were target of multiple outliers and primarily associated with binding and catalytic activity, providing interesting candidates for future selection studies. This study provides the framework to explore crucial aspects of the genetic basis of phenotypic divergence and insular adaptation.
Motivational modulation of flight speed in foraging bumblebees
Authors: Willemet Romain 
Published: March 2024

AbstractThe set of cognitive mechanisms employed by foraging bees is the subject of intense research due to the importance of pollination as an ecological process and as a study system in comparative psychology. Yet, our understanding of how reward valuation influences flight behaviour, and, more generally, the motivational control of behavioural vigour, remains limited. Here, the flight behaviour of individual bumblebeesBombus impatienswas recorded during a series of foraging trials in which the reward intrinsic value and predictability was manipulated. The bees could access a feeder whose sugar concentration varied from trial to trial following an increase, constant peak, and decrease pattern. Neither the feeder itself nor its position changed during the experiment. Hence, potential differences between trials could be interpreted in the context of decision-making and behavioural vigour, rather than search behaviour. The average flight speed towards the feeder increased when the sugar concentration was both high and constant, and returned to baseline as it became lower. This suggests that, as in other species including humans, the behavioural vigour of foraging bees towards a potential reward reflects its expected value. This motivational modulation of flight speed offer new ways of interpreting and studying decision-making in foraging bees.
Learn!Bio- A time-limited cross-sectional study on biosciences students’ pathway to resilience during and post the Covid-19 pandemic at an UK university from 2020-2023 and insights into future teaching approaches
Authors: Andrews Katy , Stoneley Rosalie , Eckl Katja 
Published: March 2024

AbstractHigher education in biosciences is significantly informed by hands-on field trips and practical laboratory skills-training. With the first Covid-19 national lock-down in England in March 2020, on-campus education at higher education institutions was swiftly moved to alternative provisions, including online only options, a mix of synchronous or asynchronous blended, or hybrid adaptions. Students enrolled on an undergraduate bioscience programme have been faced with unprecedented changes and interruptions to their education. This study aimed to evaluate bioscience students’ ability to adjust to a fast-evolving learning environment and to capture students’ journey building up resilience and graduate attributes.Bioscience undergraduate students in years 1-3 at the biology department at a Northwest English university participated in this anonymous, cross-sectional, mixed-method study with open and closed questions evaluating their perception and feedback to remote and blended learning provisions during the Covid-19 pandemic and post pandemic learning capturing academic years 2019/20 to 2022/23.The Covid-19 pandemic and the consequent restriction of personal social interaction resulted in an significant decrease in the mental wellbeing of undergraduate bioscience students in this study, cumulating in poor or very poor self-rating of wellbeing in spring 2021; while at the same time students showed evidence of advanced adaption to the new learning and social environment by acquisition of additional technical, social and professional graduate-level skills, indicative of an, albeit unconscious, transition to resilience. Post pandemic, bioscience students worry about the increased living costs and are strongly in favour of a mixture of face-to-face and blended learning approaches.Our results show that bioscience students can experience poor mental health while developing resilience, indicating tailored support can aid students’ resilience performance. Students have adjusted with ease to digital teaching provisions and expect higher education institutions continue to offer both, face-to-face, and blended teaching, reducing the burden on students’ significantly risen living costs.