bluuebunny/crossref_metadata_2025_split huggingface dataset:
Addressing structural mentoring barriers in postdoctoral training: a qualitative study
Authors: Lambert W. Marcus , Nana Nanda , Afonja Suwaiba , Saeed Ahsan , Amado Avelino C. , Golightly Linnie M. 
Published: November 2023

Purpose
Structural mentoring barriers are policies, practices and cultural norms that collectively disadvantage marginalized groups and perpetuate disparities in mentoring. This study aims to better understand structural mentoring barriers at the postdoctoral training stage, which has a direct impact on faculty diversity and national efforts to retain underrepresented groups in research careers.

Design/methodology/approach
A diverse sample of postdoctoral scholars (“postdocs”) from across the USA were asked to participate in focus groups to discuss their training experiences. The authors conducted five 90-min focus groups with 32 biomedical postdocs, including 20 (63%) women and 15 (47%) individuals from underrepresented racial/ethnic groups (URG).

Findings
A social-ecological framework was used to categorize both the upstream and downstream manifestations of structural mentoring barriers, as well as mentoring barriers, overall. Notable structural barriers included: academic politics and scientific hierarchy; inequalities resulting from mentor prestige; the (over) reliance on one mentor; the lack of formal training for academic and non-academic careers; and the lack of institutional diversity and institutional mentor training. To overcome these barriers, postdocs strongly encouraged developing a network or team of mentors and recommended institutional interventions that create more comprehensive professional development, mentorship and belonging.

Originality/value
For postdoctoral scientists, structural mentoring barriers can permeate down to institutional, interpersonal and individual levels, impeding a successful transition to an independent research career. This work provides strong evidence for promoting mentorship networks and cultivating a “mentoring milieu” that fosters a supportive community and a strong culture of mentorship at all levels.
International students’ experiences in graduate programs during COVID-19 and recent sociopolitical climate in the USA
Authors: Aggarwal Pankhuri , Szkody Erica , Kapoulea Eleni , Daniel Katharine , Bootes Kirsten , Boland Jennifer , Washburn Jason , Peterman Amy 
Published: November 2023

Purpose
This study aims to examine the unique lived experiences of international graduate students in light of COVID-19 and the recent sociopolitical climate in the USA (e.g. Black Lives Matter movement, protests against anti-Asian hate crimes and gun violence).

Design/methodology/approach
The authors used an exploratory qualitative design embedded within a constructivist/interpretivist paradigm. A total of 31 international health service psychology graduate students completed an online survey, 17 of whom participated in a 60-min one-on-one semi-structured interview.

Findings
Participants reported facing a range of difficulties (e.g. travel ban/inability to spend time with family, visa-related concerns, racism, decreased support) during the global pandemic and the recent sociopolitical climate in the USA. A total of 48 themes were identified and organized into six domains: COVID-19-related stress and worry, experiences of racism/discrimination, coping mechanisms, support received, recommendations for programs and higher learning institutions and advice for other international graduate students.

Originality/value
The recent sociopolitical climate in the US exacerbated some of the preexisting inequities for international graduate students due to their international student status and the global pandemic. Although few in number, students also spoke about some positive changes as a result of these major historical and political events. Implications for graduate education, clinical practice and policymaking are discussed.
Enhancing customer engagement through source appearance and self-influencer congruence in mobile advertising
Authors: Talha Muhammad , Tahir Zonaib , Mehroush Iqra 
Published: November 2023

Purpose
The aim of this study is to assess the mediating effect of source appearance (SA) and self-influencer congruence (SIC) on the relationship between visual content (VC) and customer engagement (CE) towards mobile advertisement.

Design/methodology/approach
This study uses a quantitative approach to test the proposed model based on the stimulus–organism–response (SOR) theory. The non-probability purposive sampling technique was used to collect data from Pakistani mobile users through a self-administered questionnaire.

Findings
The study results prove that VC alone cannot generate mobile users’ engagement. SA is the key in this regard, which has a relatively higher importance compared to SIC. Furthermore, the serial mediation effect of SA and SIC on CE shows that attractive sources are likely to induce higher SIC and subsequent CE.

Practical implications
The results reveal that without a pleasing SA and positive SIC, mobile users skip the ads by perceiving them to be irritating or interruptive. Mobile ads might cost relatively less, but the advertisers should understand the significance of the SA toward minimizing the mobile advertising skepticism.

Originality/value
Advertisers can enhance the user’s engagement on mobile devices by addressing both the SA and SIC in their VC. The combined effect of both the SA and SIC on CE has not been assessed before. Furthermore, this study has used the SOR mechanism to examine CE.
Building the Bioeconomy through Innovation, Monitoring and Science‐based Policies
Authors: Zilberman David , Wesseler Justus 
Published: November 2023

SummaryConcerns about climate change, food security and biodiversity loss are challenging society and the scientific community to modify our modes of operation. This involves the transition from relying on non‐renewable resources to renewable resources, reducing the emissions of greenhouse gases, sequestering and storing carbon, and at the same time, improving the well‐being of much of humanity who live in poverty. Establishing a modern bioeconomy is essential for the transition. The BioMonitor Project highlights benefits of establishing a modern bioeconomy and the constraints slowing its development. We propose policies to overcome these constraints, emphasising the importance of monitoring its progress. We present some of its findings and recommendations to improve the performance of the EU bioeconomy. This includes a science‐based regulatory process to balance risk and benefit of new innovations, combined with effective liability rules and sound assessment of the side effects of new regulations without unnecessary delay and extra regulatory costs. Government support is crucial for agricultural and industrial research and development leading to the emergence of new supply chains. Since developing bioeconomy industries that increase productivity and reduce externalities provide public goods, some government support for infant bioeconomy sectors may be justified.
Predicting nitrate exposure from groundwater wells using machine learning and meteorological conditions
Authors: Etheridge Randall , Pascual‐Gonzalez Janire , Hochard Jacob , Peralta Ariane L. , Vogel Thomas J. 
Published: November 2023

AbstractPrivate groundwater wells can be unmonitored sources of contaminated water that can harm human health. Developing models that predict exposure could allow residents to take action to reduce risk. Machine learning models have been successful in predicting nitrate contamination using geospatial information such as proximity to nitrate sources, but previous models have not considered meteorological factors that change temporally. In this study, we test random forest (regression and classification) and linear regression models to predict nitrate contamination using rainfall, temperature, and readily available soil parameters. We trained and tested models for (1) all of North Carolina, (2) each geographic region in North Carolina, (3) a three‐county region with a high density of animal agriculture, and (4) a three‐county region with a low density of animal agriculture. All regression models had poor predictive performance (R2 < 0.09). The random forest classification model for the coastal plain showed fair agreement (Cohen's κ = 0.23) when trying to predict whether contamination occurred. All other classification models had slight or poor predictive performance. Our results show that temporal changes in rainfall and temperature, or in combination with soil data, are not enough to predict nitrate contamination in most areas of North Carolina. The low level of contamination (<25%) measured during the study could have contributed to the poor performance of the models.
MuDoGeR: Multi‐Domain Genome recovery from metagenomes made easy
Authors: Rocha Ulisses , Coelho Kasmanas Jonas , Kallies René , Saraiva Joao Pedro , Toscan Rodolfo Brizola , Štefanič Polonca , Bicalho Marcos Fleming , Borim Correa Felipe , Baştürk Merve Nida , Fousekis Efthymios , Viana Barbosa Luiz Miguel , Plewka Julia , Probst Alexander J. , Baldrian Petr , Stadler Peter F. ,   CLUE‐TERRA Consortium
Published: November 2023

AbstractSeveral computational frameworks and workflows that recover genomes from prokaryotes, eukaryotes and viruses from metagenomes exist. Yet, it is difficult for scientists with little bioinformatics experience to evaluate quality, annotate genes, dereplicate, assign taxonomy and calculate relative abundance and coverage of genomes belonging to different domains. MuDoGeR is a user‐friendly tool tailored for those familiar with Unix command‐line environment that makes it easy to recover genomes of prokaryotes, eukaryotes and viruses from metagenomes, either alone or in combination. We tested MuDoGeR using 24 individual‐isolated genomes and 574 metagenomes, demonstrating the applicability for a few samples and high throughput. While MuDoGeR can recover eukaryotic viral sequences, its characterization is predominantly skewed towards bacterial and archaeal viruses, reflecting the field's current state. However, acting as a dynamic wrapper, the MuDoGeR is designed to constantly incorporate updates and integrate new tools, ensuring its ongoing relevance in the rapidly evolving field. MuDoGeR is open‐source software available at https://github.com/mdsufz/MuDoGeR. Additionally, MuDoGeR is also available as a Singularity container.
NeTaGFT: A similarity network‐based method for trait analysis
Authors: Matsumoto Hirotaka , Matsui Motomu 
Published: November 2023

Abstract

With the determination of numerous viral and bacterial genome sequences, sequence‐trait relationships, such as the evolution of virulence and associations to geographic location or host, are now being studied. In these studies, phylogenetic trees were first reconstructed, and trait data were analysed based on the trees. However, in some cases, such as fast evolution sequences and gene‐sharing network data, reconstructing the phylogenetic tree is challenging. Even in such cases, it is possible to quantify the similarity between sequences and construct an similarity network.

Here, we propose a novel approach, Network‐Trait association with Graph Fourier Transform (NeTaGFT), to analyse network‐trait associations. NeTaGFT is inspired by graph signalling process techniques. The graph in this study corresponds to a similarity network representing the similarities between virus samples, and the graph signal corresponds to trait data. By using graph Fourier transform, NeTaGFT aims to identify trait signals and associations of various traits from a similarity network.

We validated that NeTaGFT can find signals associated with network structures and associations of traits with the simulation dataset. We applied NeTaGFT for influenza type A and virome gene‐sharing datasets. As a result, we identified several network structures and their associated traits.

Our approach is expected to provide novel insights into network‐based approach not only for typical sequence‐trait relationships but also for various biological data, such as antibody evolution.
Depletion of preexisting B‐cell lymphoma 2‐expressing senescent cells before vaccination impacts antigen‐specific antitumor immune responses in old mice
Authors: Cobanoglu Ozmen , Delval Lou , Ferrari Daniele , Deruyter Lucie , Heumel Séverine , Wolowczuk Isabelle , Hussein Abir , Menevse Ayse Nur , Bernard David , Beckhove Philip , Alves Frauke , Trottein François 
Published: November 2023

AbstractThe age‐related decline in immunity reduces the effectiveness of vaccines in older adults. Immunosenescence is associated with chronic, low‐grade inflammation, and the accumulation of senescent cells. The latter express Bcl‐2 family members (providing resistance to cell death) and exhibit a pro‐inflammatory, senescence‐associated secretory phenotype (SASP). Preexisting senescent cells cause many aging‐related disorders and therapeutic means of eliminating these cells have recently gained attention. The potential consequences of senescent cell removal on vaccine efficacy in older individuals are still ignored. We used the Bcl‐2 family inhibitor ABT‐263 to investigate the effects of pre‐vaccination senolysis on immune responses in old mice. Two different ovalbumin (OVA)‐containing vaccines (containing a saponin‐based or a CpG oligodeoxynucleotide adjuvant) were tested. ABT‐263 depleted senescent cells (apoptosis) and ablated the basal and lipopolysaccharide‐induced production of SASP‐related factors in old mice. Depletion of senescent cells prior to vaccination (prime/boost) had little effect on OVA‐specific antibody and T‐cell responses (slightly reduced and augmented, respectively). We then used a preclinical melanoma model to test the antitumor potential of senolysis before vaccination (prime with the vaccine and OVA boost by tumor cells). Surprisingly, ABT‐263 treatment abrogated the vaccine's ability to protect against B16 melanoma growth in old animals, an effect associated with reduced antigen‐specific T‐cell responses. Some, but not all, of the effects were age‐specific, which suggests that preexisting senescent cells were partly involved. Hence, depletion of senescent cells modifies immune responses to vaccines in some settings and caution should be taken when incorporating senolytics into vaccine‐based cancer therapies.
Finite element study of the fatigue behaviour of nickel‐titanium endodontic files utilised with pecking motion technique
Authors: Kökan Eyüp Can , Atik Yasin , Özüpek Şebnem , Podnos Evgeny , Erişen Raif 
Published: November 2023

AbstractThe purpose of the study is to evaluate the influence of the pecking motion (reciprocal axial motion) surgical technique on the durability behaviour of the Nickel‐Titanium endodontic files using Finite Element Analysis (FEA). A commonly used endodontic file, ProTaper Universal F2, is selected for the study. Root canal treatment procedure is simulated on a test‐bench (simulated root canal) proposed by G. Gambarini for cyclic fatigue loading of endodontic files with and without the pecking motion via FEA. The hysteresis energy density is used as evaluation criteria for low cycle fatigue life estimation of Shape Memory Alloy files. In an additional study, the root canal treatment procedure is also simulated for an FEA model of a molar tooth with significant root canal curvature to understand the influence of the realistic curvature of a root canal on the fatigue behaviour of endodontic files. For the simulated root canal, analysis accurately predicts the endodontic file's failure location, and fatigue life estimation based on the hysteresis energy density is shown to increase significantly with the introduction of the pecking motion, an observation confirmed by reported experimental results. Molar tooth simulations reveal greater file fatigue resistance than in simulated root canals, confirming the pecking motion's efficacy in enhancing file durability, even in real root canal conditions. Simulations indicate that the pecking motion technique increases the fatigue life of endodontic files for simulated as well as real root canals and the hysteresis energy is confirmed as an acceptable parameter to quantify fatigue life of Nickel‐Titanium endodontic files.
Genetic diversity patterns in farmed rainbow trout (Oncorhynchus mykiss) populations using genome‐wideSNPand haplotype data
Authors: Longo Alessio , Kurta Khrystyna , Vanhala Tytti , Jeuthe Henrik , de Koning Dirk‐Jan , Palaiokostas Christos 
Published: November 2023

AbstractRainbow trout is one of the most popular aquaculture species worldwide, with a long history of domestication. However, limited information exists about the genetic diversity of farmed rainbow trout populations globally, with most available reports relying on low‐throughput genotyping technologies. Notably, no information exists about the genetic diversity status of farmed rainbow trout in Sweden. Double‐digest restriction‐site‐associated DNA sequencing was performed on more than 500 broodfish from two leading producers in Sweden and from the country's national breeding program. Following the detection of single nucleotide polymorphisms (SNPs), genetic diversity was studied by using either individual SNPs (n = 8680; one SNP retained per 300 bp sequence reads) or through SNP haplotypes (n = 20 558; all SNPs retained in 300 bp sequence reads). Similar amounts of genetic diversity were found amongst the three populations when individual SNPs were used. Furthermore, principal component analysis and discriminant analysis of principal components suggested two genetic clusters with the two industry populations grouped together. Genetic differentiation based on theFSTfixation index was ~0.01 between the industry populations and ~0.05 when those were compared with the breeding program. Preliminary estimates of effective population size (Ne) and inbreeding (based on runs of homozygosity;FROH) were similar amongst the three populations (Ne ≈ 50–80; medianFROH ≈ 0.11). Finally, the haplotype‐based analysis suggested that animals from the breeding program had higher shared coancestry levels than those from the other two populations. Overall, our study provides novel insights into the genetic diversity and structure of Sweden's three main farmed rainbow trout populations, which could guide their future management.
Brain volumetry from CT‐scan endocasts of three neotropical carnivores
Authors: Montana Marelise Moral , Kasper Carlos Benhur , Pinheiro Felipe Lima , Pereira Luis Felipe Salles , Abidu‐Figueiredo Marcelo , de Souza‐Junior Paulo 
Published: November 2023

AbstractStudies on brain anatomy can clarify specific evolutionary and behavioural aspects of wild animals. The rich diversity in a broad range of habitats makes carnivorans especially eligible for studying the relations between the brain form and behaviour, cognitive, sensorial and motor traits. This study compared the brain's contour and total and segmented brain volumetry in three species of neotropical carnivorans. CT images of 17 skulls of three species were acquired: Conepatus chinga (n = 6), Galictis cuja (n = 6) and Lontra longicaudis (n = 5). Three‐dimensional endocasts allowed for estimating the brain's total and segmented volumes (olfactory bulb, rostral cerebrum, caudal cerebrum and cerebellum/brain stem). The average volume percentage of the segments was compared interspecifically and intraspecifically between the sexes. The otter has a notably more complex gyrification, typical for semiaquatic carnivorans. Proportionally, the olfactory bulb was significantly larger in hog‐nosed skunks, possibly due to a better sense of smell for capturing insects. The proportional volumes of the rostral cerebrum, caudal cerebrum and cerebellum/brain stem segments did not differ between these species. Social behaviour traits and tactile, motor and balance skills were probably not sufficiently distinct to reflect differences in the brain segments analysed in these three species.
UP‐regulated levels of sHLA‐G in women with a history of RPL in mid‐gestation presumably to achieve ongoing pregnancy
Authors: Jahan Parveen , Bhuwalka Rashmi , Begum Mahmooda , Madduru Dhatri , Ahmad Arif , Bonu Rajeshwari 
Published: November 2023

AbstractProblemRecurrent Pregnancy Loss (RPL) is a disorder characterized by two or more pregnancy losses within 20th week of gestation. Globally 1–5% of the couples are affected, 50% of these cases are with unknown etiology. HLA‐G, an Immuno‐modulatory molecule is a non‐classical MHC‐1 protein, expressed abundantly on extravillous trophoblastic cells, responsible for spiral artery remodeling, maintaining maternal immune tolerance and fetal growth by adjusting pro and anti‐inflammatory milieu during different gestational phases.Method of studyIn the present case‐control study CD4+HLA‐G+ tTreg cells were enumerated by flow cytometry and estimation of the circulating levels of sHLA‐G in the blood samples of 300 mid‐gestation pregnant women with (iRPL) and without history of RPL (nRPL) by Enzyme‐linked Immunosorbent assay was done. The cases included 92 primary and 58 secondary RPL casesResultsA significant reduction in number of tTregs and elevated levels of circulating sHLA‐G in iRPL (.03, 200.9) versus nRPL (.09, 90.32) was observed. Further, the primary cases showed higher circulating sHLA‐G and no difference in relation to CD4+HLA‐G+ tTregs compared to the secondary cases. Receiver operating curve (ROC) characteristics of sHLA‐G (AUC = .8) was superior to CD4+HLA‐G+ (AUC = .7) for iRPL patients over nRPL group. Conclusions: Our results are suggestive of the over‐expression of sHLA‐G which may be caused due to its shedding from surface of trophoblast as a compensatory mechanism to save the on‐going pregnancy. To realize the present outcome, studies are required on on‐going pregnancy follow‐up cases with favorable and unfavorable pregnancy outcome.
How well are we collecting umbilical cord lactate and gas samples?
Authors: Bui Trang Minh , Battin Malcolm , Sadler Lynn 
Published: November 2023

AimsThe aim of this study is to measure staff compliance with the local umbilical cord lactate (UCL) sampling guideline and investigate the quality of paired UCG samples at a tertiary maternity unit.MethodsWe performed a retrospective consecutive sampling of 100 babies delivered via emergency caesarean section and 50 babies with each of all other guideline‐based indications for UCL sampling born on and before 31 December 2021. Data were extracted from physical and electronic records. Compliance with guideline‐based indications for UCL at birth was measured. The proportion of valid UCG samples was calculated. Samples were considered invalid under the following cases: (i) inadvertently collecting from the same vessel, (ii) switching arterial and venous samples, (iii) collecting from only one vessel or (iv) committing errors during sample collection and handling.ResultsOf the samples collected at birth from 321 babies, 280 (87%) had UCL. Small for gestational age and concerns about fetal well‐being in labour were indications associated with poorer compliance, 66% and 78%, respectively. About 99 (44%) babies of 226 babies with UCG performed had valid UCG samples. The most common reasons for invalid samples were collection and handling errors (22%) and inadvertent collection from the same vessel (15%).ConclusionsGenerally, compliance with the guidelines is good. However, invalid UCG samples were more frequent than expected.