bluuebunny/crossref_metadata_2025_split huggingface dataset:
Generative adversarial networks in cell microscopy for image augmentation. A systematic review
Authors: Lesmes-Leon Duway Nicolas , Dengel Andreas , Ahmed Sheraz 
Published: August 2023

AbstractCell microscopy is the main tool that allows researchers to study microorganisms and plays a key role in observing and understanding the morphology, interactions, and development of microorganisms. However, there exist limitations in both the techniques and the samples that impair the amount of available data to study. Generative adversarial networks (GANs) are a deep learning alternative to alleviate the data availability limitation by generating nonexistent samples that resemble the probability distribution of the real data. The aim of this systematic review is to find trends, common practices, popular datasets, and analyze the impact of GANs in image augmentation of cell microscopy images. We used ScienceDirect, IEEE Xplore, PubMed, bioRxiv, and arXiv to select English research articles that employed GANs to generate any kind of cell microscopy images independently of the main objective of the study. We conducted the data collection using 15 selected features from each study, which allowed us to analyze the results from different perspectives using tables and histograms. 32 studies met the legibility criteria, where 18 had image augmentation as the main task. Moreover, we retrieved 21 publicly available datasets. The results showed a lack of consensus with performance metrics, baselines, and datasets. Additionally, we evidenced the relevance of popular architectures such as StyleGAN and losses including Vanilla and Wasserstein adversarial loss. This systematic review presents the most popular configurations to perform image augmentation. It also highlights the importance of design good practices and gold standards to guarantee comparability and reproducibility. This review implemented the ROBIS tool to assess the risk of bias, and it was not registered in PROSPERO.
Utilizing mentorship education to promote a culturally responsive research training environment in the biomedical sciences
Authors: Suiter Sarah , Byars-Winston Angela , Sancheznieto Fátima , Pfund Christine , Sealy Linda 
Published: August 2023

AbstractThere is an urgent and compelling need for systemic change to achieve diversity and inclusion goals in the biomedical sciences. Since faculty hold great influence in shaping research training environments, faculty development is a key aspect in building institutional capacity to create climates in which persons excluded because of their ethnicity or race (PEERs) can succeed. In this paper, we present a mixed methods case study of one institution’s efforts to improve mentorship of PEER doctoral students as a strategy to improve graduate trainees’ experiences, and as a strategy to positively affect institutional climate with respect to racial and ethnic diversity. We found evidence that our culturally responsive mentorship education increased faculty mentors’ self-reported mentorship competencies, though their valuing of culturally responsive mentoring behaviors were comparatively higher than their confidence to enact those behaviors. PEER doctoral students reported that they noticed mentors’ efforts to address cultural diversity matters and identified some guidance for how to approach such topics. We discuss future directions and implications for using mentorship education to activate systemic change toward inclusive research training environments and promoting the value of mentorship within institutions.
GraphMHC: neoantigen prediction model applying the graph neural network to molecular structure
Authors: Jeong Hoyeon , Cho Young-Rae , Gim Jungsoo , Cha Seung-Kuy , Kim Maengsup , Kang Dae Ryong 
Published: August 2023

AbstractNeoantigens are biomarkers that can predict the prognosis associated with immune checkpoint inhibition by estimating the binding potential of candidate peptides to somatic mutation and major histocompatibility complex (MHC) proteins. Although deep neural networks have been primarily used for these prediction models, it is difficult to consider the models reported thus far as accurately representing the interactions between biomolecules. In this study, we propose the GraphMHC model, which utilizes a graph neural network model through molecular structure to simulate the binding between MHC proteins and peptide sequences. Amino acid sequences sourced from the immune epitope database (IEDB) undergo conversion into molecular structures. Subsequently, atomic intrinsic informations and inter-atomic connections are extracted and structured as a graph representation. Bindings are classified by feeding them into the GraphMHC network, comprising stacked graph attention and convolution layers. The prediction results from the test set using the GraphMHC model showed a high performance with an area under the receiver operating characteristic curve of 92.2% (91.9-92.5%), surpassing the baseline model. Moreover, by applying the GraphMHC model to melanoma patient data from the Cancer Genome Atlas project, we found a borderline difference in overall survival and a significant difference in stromal score between the high and low neoantigen load groups. This distinction was not present in the baseline model. This study presents the first feature-intrinsic method based on biochemical molecular structure for modeling the binding between MHC protein sequences and neoantigen candidate peptide sequences. The model can provide highly accurate suitability information for cancer patients who want to apply immune checkpoint inhibitors.Author summary
How frequently are insects wounded in the wild? A case study usingDrosophila melanogaster
Authors: Subasi Bengisu S. , Grabe Veit , Kaltenpoth Martin , Rolff Jens , Armitage Sophie A.O. 
Published: August 2023

AbstractWounding occurs across multicellular organisms. There is a deep understanding of infections and immune responses from lab studies, yet wounds remain relatively comparatively understudied in nature. Ecological interactions like predator attacks, intra- and inter-specific competition can lead to wounding. Furthermore, rates of wounding may vary depending on factors such as sex and geographic location, with consequences for host mobility, reproduction, and susceptibility to pathogens.Wounds initiate an immune response, resulting in the deposition of the brown-black pigment melanin in insects, and they are potential entry points for pathogens. Despite the potential ecological and evolutionary implications of wounding, and the relative abundance of lab immunity studies utilisingDrosophila melanogaster, wounding in the wild in this model is unstudied. Our aim, therefore, was to investigate the prevalence and examine potential causes of wounds in wild-collectedD. melanogaster.From systematic collections of female and male flies, over three seasons and locations, we found that 31% ofD. melanogasterwere wounded. The abdomen was more frequently wounded than other body parts, and females were more likely to be injured particularly on the ventral abdomen, compared to males. Encapsulated parasitoid egg frequency was just under ten percent. Moreover, just under one percent of Drosophilidae species had mites attached to their body, the majority of which also caused wounds, i.e., were potentially parasitic.Wounding is prevalent inD. melanogaster, and as such it is likely to exert selection pressure on host immunity for two reasons: on a rapid and efficient wound repair, and on responding to opportunistic infections. Wounds are thus expected to be important drivers of immune system evolution and to affect individual fitness and population dynamics.
African elephants address one another with individually specific calls
Authors: Pardo Michael A. , Fristrup Kurt , Lolchuragi David S. , Poole Joyce , Granli Petter , Moss Cynthia , Douglas-Hamilton Iain , Wittemyer George 
Published: August 2023

SUMMARYPersonal names are a universal feature of human language, yet few analogs exist in other species. While dolphins and parrots address conspecifics by imitating the calls of the addressee1,2, human names are not imitations of the sounds typically made by the name’s owner3. Labeling objects or individuals without relying on imitation of the sounds made by that object or individual is key to the expressive power of language. Thus, if non-imitative name analogs were found in other species, this could have important implications for our understanding of language evolution. Here, we show that wild African elephants address one another with individually specific calls without any evidence of imitating the receiver’s vocalizations. A random forest model correctly predicted receiver identity from call structure better than expected by chance, regardless of whether the calls were more or less similar to the receiver’s calls than typical for that caller. Moreover, elephants differentially responded to playbacks of calls originally addressed to them relative to calls addressed to a different individual, indicating that they can determine from a call’s structure if it was addressed to them. Our findings offer the first evidence for a non-human species individually addressing conspecifics without imitating the receiver.
Competition and the century-long decline of a once common lizard,Sceloporus consobrinus
Authors: Murray Alexander H. , Folfas Edita , Page Morgan A. , Lange Zachary K. , Mruzek Joseph L. , Frishkoff Luke O. 
Published: August 2023

AbstractHabitat modification and climate change are primary mechanisms responsible for historical and ongoing population declines. Species interactions however, though difficult to study, may be of similar importance. Here we use a combination of historical species records, standardized transect surveys, and staged competition trials to assess the role of competition in recent population trends and distributions of two closely related lizard species: the prairie lizard (Sceloporus consobrinus) and the Texas Spiny lizard (S. olivaceus). Occurrence data reveals divergent population trends.S. consobrinushas decreased whileS. olivaceushas increased in relative frequency over the last 100 years. We analyzed spatially-aggregated records of all lizards within the range ofS. consobrinusto determine the role of climate suitability, climate change, landcover, and species interactions in shaping the occurrence patterns ofS. consobrinus. In contrast to other lizard species, presence ofS. olivaceuswas associated with substantial reductions ofS. consobrinusoccurrence, and explains occurrence patterns better than either climate suitability or landcover. To test whether patterns of broad scale co-occurrence are indicative of local competitive exclusion we conducted 200m transects surveys to assess lizard communities and paired this with staged behavioral trials in the lab. Despite occurring in similar habitats, and across similar regions, transect surveys revealed lower-than-expected abundance ofS. consobrinuson transects containingS. olivaceus, with both species co-occurring on only 2 of 176 transects. Shifts in habitat use implicate competitive displacement, withS. consobrinusoccupying areas with three times less canopy cover at sites withS. olivaceuscompared to those without. Finally, behavioral trials revealed competitive dominance ofS. olivaceus, which controlled the prime basking position, and initiated more interactions that led to retreat or hiding byS. consobrinus. Our study implicates competitive interactions as in important force in structuring species’ distributions and population trends.
Identifying dysregulated regions in amyotrophic lateral sclerosis through chromatin accessibility outliers
Authors: Celik Muhammed Hasan , Gagneur Julien , Lim Ryan G , Wu Jie , Thompson Leslie M. , Xie Xiaohui 
Published: August 2023

AbstractThe high heritability of ALS and similar rare diseases contrasts with their low molecular diagnosis rate post-genetic testing, pointing to potential undiscovered genetic factors. Chromatin accessibility assays quantify the activity of functional elements genome-wide, offering invaluable insights into dysregulated regions. In this research, we introduced EpiOut, a computational toolbox to identify outliers in chromatin accessibility. These outliers represent dysregulated regions where chromatin accessibility uniquely diverges from the population baseline in a single or few samples. Annotation of accessible regions with histone ChIP-seq and Hi-C indicates that outliers are concentrated in functional loci, especially among promoters interacting with active enhancers. Across different omics levels, outliers are robustly replicated, and chromatin accessibility outliers are reliable predictors of gene expression outliers and aberrant protein levels. For example, 59% of gene expression outliers can be linked to aberration in chromatin accessibility. When promoter accessibility does not align with gene expression, our results indicate that molecular aberrations are more likely to be linked to post-transcriptional regulation rather than transcriptional regulation. Our findings demonstrate that the outlier detection paradigm can uncover dysregulated regions in rare diseases. EpiOut is open-sourced and freely available atgithub.com/uci-cbcl/EpiOut.
CoFrEE: An Application to Estimate DNA Copy Number from Genome-wide RNA Expression Data
Authors: Gaenko Anita , Ray Dipankar , Nancarrow Derek J. 
Published: August 2023

ABSTRACTWe introduce CoFrEE, a simple python-based approach to extracting copy number data from expression values that works with either RNAseq or array-based expression data. CoFrEE works best in tumor cohorts that include a subset of non-tumor tissues and is applied to processed (RSEM, RPKM or TPM) expression, rather than raw data. Experiments with real public data suggest CoFrEE can provide copy number estimations comparable to existing RNAseq-based approaches, with the advantage of also being applicable to the multitude of older expression-array cohorts.
Cytomegalovirus seropositivity relates inversely to cancer incidences across races and ethnicities: implications for oncoprevention
Authors: Janković Marko , Milićević Ognjen , Todorović-Balint Milena , Đunić Irena , Mihaljević Biljana , Jovanović Tanja , Knežević Aleksandra 
Published: August 2023

AbstractBackgroundRace and ethnic disparities in cancer incidence rates and the prevalence ofcytomegalovirus(CMV) are known to exist in the United States (U.S.) but also across broad geographic expanses. CMV prevalence seems to inversely contrast tumor incidence rates both in ethnic groups and globally. Is there a biological link between cancer and CMV infection? Most recent clinical results seem to certify it.MethodsGlobal cancer data were retrieved from the World Health Organization (WHO) database. Incidence of cancer and CMV seroprevalence (73 countries) were subjected to Spearman’s correlation test. The Bayesian framework was adopted for CMV seropositivity variables. Relevant data for the U.S. were extracted from publications based on the Surveillance, Epidemiology, and End Results (SEER) registries and the National Health and Nutrition Examination Surveys (NHANES), 1988-2004.ResultsAn inversely directed coupling between cancer and CMV seropositivity across diverse ecologies and cultural domains suggest a global oncoprotective effect of the CMV (Spearman’sρ= -0.732;p<0.001). Rates of all cancers combined and CMV seropositivity show an opposite association (p<0.001) among the races and foremost U.S. ethnic groups.ConclusionThe racial/ethnic incidence of cancers and CMV seropositivity are inversely proportional both in the U.S. and globally. This would support a view that CMV is a potential driver against tumorigenesis. An absence of CMV infection abrogates protection against malignant clones afforded to an infected host. Abating CMV seroprevalence may relate causally to the buildup of malignancies in U.S. and the West world countries with thriving hygiene and healthcare systems.ImportanceIncreasing evidence substantiates the potential of cytomegalovirus (CMV) to counteract tumors, particularly in the field of anti-cancer vaccinology, leading to extended periods of survival. This research unveils a robust and inverse correlation between the prevalence of CMV and the occurrence of cancer both within the United States and on a global scale (73 countries), hinting at the ability of CMV to inhibit tumor development. Furthermore, this phenomenon remains consistent across various racial and ethnic groups within the United States and applies to a diverse range of cancer types. A notable pattern emerges: the higher the prevalence of the viral infection, the lower the incidence of tumors within a given country. These findings support existing insights from clinical and experimental investigations, underscoring the notion that this effect becomes apparent at the level of entire nations and populations worldwide.
Polygenic scores of subcortical brain volumes as possible modulators of treatment response in depression
Authors: Oliva Vincenzo , Martone Alfonso , Fanelli Giuseppe , Domschke Katharina , Minelli Alessandra , Gennarelli Massimo , Martini Paolo , Bortolomasi Marco , Maron Eduard , Squassina Alessio , Pisanu Claudia , Kasper Siegfried , Zohar Joseph , Souery Daniel , Montgomery Stuart , Albani Diego , Forloni Gianluigi , Ferentinos Panagiotis , Rujescu Dan , Mendlewicz Julien , De Ronchi Diana , Baune Bernhard T ,   European College of Neuropsychopharmacology (ECNP) Pharmacogenomics & Transcriptomics Network, Serretti Alessandro , Fabbri Chiara 
Published: August 2023

AbstractA significant proportion of patients with major depressive disorder (MDD) do not experience remission after one or more pharmacological treatments. Research has explored brain structural measures, particularly the hippocampus, as potential predictors of treatment response in MDD, as well as genetic factors.This study investigated the association of polygenic scores (PGSs) for seven subcortical brain volumes (including the hippocampus, nucleus accumbens, amygdala, and caudate nucleus) with treatment non-response and non-remission in MDD.Patients with MDD were recruited in the context of five clinical studies, including a total of 3,637 individuals. PGSs were estimated using a Bayesian framework and continuous shrinkage priors (PRS-CS-auto) after standard genotype quality control and imputation. Logistic regressions were performed between PGSs and non-response or non-remission in each sample, adjusting for age, sex, baseline symptom severity, recruitment sites, and population stratification. Results were meta-analysed across samples, using a random-effect model.Caudate volume PGS was nominally associated with non-remission (OR=1.09, 95% CI=1.01–1.19, p=0.036). Leave-one-out sensitivity analyses suggested a possible association with the amygdala and thalamus PGSs. However, no association was significant after multiple testing correction.These results, although preliminary, suggest a possible link between caudate volume PGS and lack of symptom remission. Methodological improvements in PGSs estimation and statistical power may enhance their predictive performance and provide a contribution to precision psychiatry.
Pattern of Cutaneous Neoplasms and Associated Factors at a Tertiary Teaching Hospital Pathology Center in Ethiopia: An Eight-Year Histopathological Review
Authors: Temam Fuad , Yahya Samia Metena , Berhane Bereket , Daba Frehiwot , Teka Amanuel Yeneneh , Yesuf Indris Ahmed , Leulseged Tigist Workneh 
Published: August 2023

ABSTRACTBackgroundCancer is the leading cause of death globally and is on the rise in Africa. Cutaneous neoplasms are becoming increasingly common worldwide. Understanding the patterns of this disease is essential for developing data-driven preventive, screening, and treatment services. However, there are limited studies in Ethiopia so far. Therefore, the study aimed to assess the pattern and associated factors of cutaneous neoplasm among patients with histopathologically confirmed biopsy results at a tertiary teaching hospital in Ethiopia from March, 2014 to October, 2022.MethodsA retrospective record review study was conducted among 1006 patients with histopathologically confirmed cutaneous neoplasms from the biopsies that were assessed at St. Paul’s Hospital Millennium Medical College. Data was summarized using frequencies (percentages), median (interquartile range), and graphs. To identify significant factors associated with malignant cutaneous neoplasm, a multivariable binary logistic regression model was fitted, where Adjusted Odds ratio (AOR), 95% CIs for AOR, and p-values were used for interpretation of results.ResultFrom the 1006 cases, 265 (26.3%, 95%CI=23.5%-29.3%) were malignant, of which sarcoma (26.0%) and squamous cell carcinoma (25.7%) were the most frequent and found to be prevalent in younger (19-29 years) and older (≥60 years) patients, respectively. The trunk was the commonest site (54.2%) for all the malignancies, especially sarcoma (80.4%). Age was found to be a significant exposure that is associated with the development of malignant cutaneous neoplasm for those ≥30 years as compared with those ≤18 years, with the odds increasing with age (AOR=2.66, 95% CI=1.10,6.45 for 30-39 years, AOR=4.98, 95% CI= 2.01,12.36 for 40-49 years, AOR=5.33, 95% CI=2.15,13.22 for 50-59 years and AOR= 6.62, 95% CI=2.79,15.66 for ≥60).ConclusionThe prevalence of malignant cutaneous neoplasm is higher than previously reported in the country and the malignancy pattern and distribution are different from what is known so far. This could signal a shift in disease epidemiology, and the findings should be factored into clinical decision making and program design for disease prevention, screening, and treatment. It also calls for further prospective research to learn more about the condition in the context of additional relevant personal and clinical characteristics.
Rapidin-situdiversification rates in Rhamnaceae explain the parallel evolution of high diversity in temperate biomes from global to local scales
Authors: Tian Qin , Stull Gregory W. , Kellermann Jürgen , Medan Diego , Nge Francis J. , Liu Shuiyin , Kates Heather R. , Soltis Douglas E. , Soltis Pamela S. , Guralnick Robert P. , Folk Ryan A. , Onstein Renske E. , Yi Ting-Shuang 
Published: August 2023

SummaryThe macroevolutionary processes that have shaped biodiversity across the temperate realm remain poorly understood and may have resulted from evolutionary dynamics related to diversification rates, dispersal rates, and colonization times, closely coupled with Cenozoic climate change.We integrated phylogenomic, environmental ordination, and macroevolutionary analyses for the cosmopolitan angiosperm family Rhamnaceae to disentangle the evolutionary processes that have contributed to high species diversity within and across temperate biomes.Our results show independent colonization of environmentally similar but geographically separated temperate regions mainly during the Oligocene, consistent with the global expansion of temperate biomes. High global, regional, and local temperate diversity was the result of highin-situdiversification rates, rather than high immigration rates or accumulation time, except for Southern China, which was colonized much earlier than other regions. The relatively common lineage dispersals out of temperate hotspots highlights strong source-sink dynamics across the cosmopolitan distribution of Rhamnaceae.The proliferation of temperate environments since the Oligocene may have provided the ecological opportunity for rapidin-situdiversification of Rhamnaceae across the temperate realm. Our study illustrates the importance of highin-situdiversification rates for the establishment of modern temperate biomes and biodiversity hotspots across spatial scales.