bluuebunny/crossref_metadata_2025_split huggingface dataset:
Exploration of Modern Contraceptive Methods Using Patterns among Late Reproductive Aged Women in Bangladesh
Authors: Rana Md Shohel , Alam Md Badsha , Hassen Md Tahir , Kabir Md Iqbal , Khanam Shimlin Jahan , Khan Md Nuruzzaman 
Published: August 2023

AbstractBackgroundIn light of the increasing population of late reproductive-aged women (aged 35 and above) within the broader demographic of reproductive-aged females, the concern surrounding their contraceptive considerations has escalated to a point of critical importance. This study aims to examine the trends and determinants of modern contraceptive practices among late reproductive-aged women in Bangladesh.MethodsA total of 17,736 women aged 35 and more were included in the analysis, utilizing data from three consecutives Bangladesh Demographic and Health Surveys conducted in 2011, 2014, and 2017-18. The outcome variable was the use of modern contraceptive methods (yes or no). The explanatory variables encompassed survey years, individual characteristics of the women, as well as characteristics of their partners and the community. To examine the association of the outcome variable with the explanatory variables, a multilevel logistic regression model was used.ResultsApproximately 54% of women aged 35 and older do not utilize modern contraceptive methods, and there have been no significant shifts in their usage observed over the survey years. The probability of using modern contraceptive methods exhibited a notable decline in relation to increasing age, the educational level of women’s partners, and their categorization within the richer or richest wealth quintile. Conversely, women with higher education, increased exposure to mass media, and residing in the Dhaka or Rajshahi division displayed an elevated likelihood of embracing modern contraceptive methods.ConclusionThe study highlights the relatively stable adoption of modern contraceptive methods among women aged 35 or older in Bangladesh, despite their increasing representation within the population. This raises concerns about the elevated risk of unintended pregnancies and shorter birth intervals, emphasizing the need for targeted interventions to address the specific needs and preferences of this demographic.
A unifying model to explain high nirmatrelvir therapeutic efficacy against SARS-CoV-2, despite low post-exposure prophylaxis efficacy and frequent viral rebound
Authors: Esmaeili Shadisadat , Owens Katherine , Wagoner Jessica , Polyak Stephen J. , White Judith M. , Schiffer Joshua T. 
Published: August 2023

AbstractIn a pivotal trial (EPIC-HR), a 5-day course of oral ritonavir-boosted nirmatrelvir, given early during symptomatic SARS-CoV-2 infection (within three days of symptoms onset), decreased hospitalization and death by 89.1% and nasal viral load by 0.87 log relative to placebo in high-risk individuals. Yet, nirmatrelvir/ritonavir failed as post-exposure prophylaxis in a trial, and frequent viral rebound has been observed in subsequent cohorts. We developed a mathematical model capturing viral-immune dynamics and nirmatrelvir pharmacokinetics that recapitulated viral loads from this and another clinical trial (PLATCOV). Our results suggest that nirmatrelvir’sin vivopotency is significantly lower thanin vitroassays predict. According to our model, a maximally potent agent would reduce the viral load by approximately 3.5 logs relative to placebo at 5 days. The model identifies that earlier initiation and shorter treatment duration are key predictors of post-treatment rebound. Extension of treatment to 10 days for Omicron variant infection in vaccinated individuals, rather than increasing dose or dosing frequency, is predicted to lower the incidence of viral rebound significantly.
Genetically Guided Precision Medicine Clinical Decision Support Tools: A Systematic Review
Authors: Johnson Darren , Del Fiol Guilherme , Kawamoto Kensaku , Romagnoli Katrina , Sanders Nathan , Isaacson Grace , Jenkins Elden , Williams Marc 
Published: August 2023

AbstractObjectivePatient care using genetics presents complex challenges. Clinical decision support (CDS) tools are a potential solution because they provide patient-specific risk assessments and/or recommendations at the point of care. This systematic review evaluated literature on CDS systems which have been implemented to support genetically guided precision medicine (GPM).Materials and MethodsA comprehensive search was conducted in MEDLINE and Embase, encompassing Jan 1st, 2011 to March 14th, 2023. The review included primary English peer-reviewed research articles studying humans, focused on use of computers to guide clinical decision making and delivering genetically guided, patient-specific assessments and/or recommendations to healthcare providers and/or patients.ResultsThe search yielded 3,832 unique articles. After screening, 41 articles were identified that met the inclusion criteria. Alerts and reminders were the most common form of CDS used. 27 systems were integrated with the electronic health record; 2 of those used standards-based approaches for genomic data transfer. Three studies used a framework to analyze the implementation strategy.DiscussionFindings include limited use of standards-based approaches for genomic data transfer, system evaluations that do not employ formal frameworks, and inconsistencies in the methodologies used to assess genetic CDS systems and their impact on patient outcomes.ConclusionWe recommend that future research on CDS system implementation for genetically guided precision medicine should focus on implementing more CDS systems, utilization of standards-based approaches, user-centered design, exploration of alternative forms of CDS interventions, and use of formal frameworks to systematically evaluate genetic CDS systems and their effects on patient care.
COVID-19 Testing and Vaccination among US Older Adults with Vision Impairment: The National Health and Aging Trends Study 2021
Authors: Almidani Louay , Swenor Bonnielin K. , Ehrlich Joshua R. , Varadaraj Varshini 
Published: August 2023

AbstractPurposeTo examine the associations between vision impairment (VI) and COVID-19 testing and vaccination services in older US adults.MethodsThis cross-sectional study assessed data from adults ≥65 years who participated in the National Health and Aging Trends Study (year 2021), a nationally representative sample of Medicare beneficiaries. Exposure: Distance VI (<20/40), near VI (<20/40), contrast sensitivity impairment (CSI) (<1.55 logCS), and any VI (distance, near, or CSI). Outcomes: Self-reported COVID-19 testing and vaccination.ResultsOf 2,822 older adults, the majority were female (weighted; 55%) and White (82%), and 32% had any VI. In fully-adjusted regression analyses, older adults with any VI had similar COVID-19 vaccination rates to adults without any VI (OR:0.77, 95% CI:0.54–1.09), but had lower odds of COVID-19 testing (OR:0.82, 95% CI:0.68–0.97). Older adults with distance (OR:0.47, 95% CI:0.22–0.99) and near (OR:0.68, 95% CI:0.47–0.99) VI were less likely to be vaccinated for COVID-19, while those with CSI were less likely to test for COVID-19 (OR:0.76, 95% CI:0.61– 0.95), as compared to peers without respective impairments. The remaining associations were not significant (p>.05).Conclusions and RelevanceThese findings highlight inequities in the COVID-19 pandemic response for people with vision disability and emphasize the need for equitable prioritization of accessibility of healthcare services for all Americans.
Loci associated with maturation, migration and appetite control are linked with signals of fine-scale local selection in a large Atlantic salmon population
Authors: Miettinen Antti , Dannewitz Johan , Palm Stefan , Ahi Ehsan Pashay , Romakkaniemi Atso , Vähä Ville , Östergren Johan , Primmer Craig R. , Pritchard Victoria L. 
Published: August 2023

AbstractInsights into the genetic basis of local adaptation and drivers of population differentiation improve our understanding of evolution and the maintenance of biological diversity. Characterising adaptively important genetic variation also allows more efficient planning of conservation and management actions. We used a genome-wide SNP array to analyse the genetic population structure of a large Atlantic salmon (Salmo salar) population in the interconnected Tornio/Torne and Kalix River system of the Baltic Sea basin, and to identify genomic signatures of fine-scale selection within it. We identified signals of selection and genotype-environment associations (GEA) especially on chromosome (Chr) 9, including on a haploblock containing thesix6gene and other loci that have been earlier suggested to be adaptively important in salmonids. We also detected signals of selection in genome regions including other genes of ecological relevance, such as two known appetite-controlling genes in the melanocortin system (pomcaon Chr 9 andmc4ron Chr 14), and the maturation-associated genetaar13c-like(on Chr 21). Variation in these and other identified candidate genes may potentially reflect differential selective pressures experienced by salmon from different parts of the large river system, regarding traits related to e.g. vision, feeding and growth, age at maturity and/or migratory timing. This indicates a need for management strategies to consider ecologically important genomic regions such as these, in order to protect adaptive genetic diversity in wild salmon populations.
Admixture as a source for HLA variation in Neolithic European farming communities
Authors: da Silva Nicolas Antonio , Özer Onur , Haller Magdalena , Chen Yan-Rong , Kolbe Daniel , Schade-Lindig Sabine , Wahl Joachim , Berszin Carola , Francken Michael , Görner Irina , Schierhold Kerstin , Pechtl Joachim , Grupe Gisela , Rinne Christoph , Müller Johannes , Lenz Tobias L. , Nebel Almut , Krause-Kyora Ben 
Published: August 2023

ABSTRACTThe northern European Neolithic is characterized by two major demographic events: immigration of early farmers (EF) from Anatolia (5500 BCE) and their admixture (from ∼4200 BCE) with western hunter-gatherers (WHG) forming late farmers (LF). The influence of this admixture event on variation in the immune-relevant human leukocyte antigen (HLA) region is understudied. Here, we conducted population and immunogenetic analyses on 83 individuals from six EF and LF sites located in present-day Germany. We observed significant shifts in HLA allele frequencies from EF to LF. The HLA diversity increased from EF to LF, likely due to admixture with WHG. However, it was considerably lower than in modern populations. Both EF and LF exhibited a relatively narrow HLA allele spectrum compared to today. This coincides with sparse traces of pathogen DNA, potentially indicating a lower pathogen pressure at the time. We additionally noted that LF resulted from sex-biased admixture from male WHG.TEASERMore restricted HLA allele spectrum and lower diversity in Neolithic farmers than in modern populations
The bacterial microbiome of symbiotic and menthol-bleached polyps of long-term aquarium-rearedGalaxea fascicularis
Authors: Puntin Giulia , Wong Jane C. Y. , Röthig Till , Baker David M. , Sweet Michael , Ziegler Maren 
Published: August 2023

AbstractCoral reefs support the livelihood of half a billion people but are at high risk of collapse due to the vulnerability of corals to climate change and local anthropogenic stressors. While understanding coral functioning is essential to guide conservation efforts, research is challenged by the complex nature of corals. They exist as metaorganisms (holobionts), constituted by the association between the (coral) animal host, its obligate endosymbiotic algae (Symbiodiniaceae), and other microorganisms comprising bacteria, viruses, archaea, fungi and other protists. Researchers therefore increasingly turn to model organisms to unravel holobiont complexity, dynamics, and how these determine the health and fitness of corals. The coral Galaxea fascicularis is an emerging model organism for coral symbiosis research with demonstrated suitability to aquarium rearing and reproduction, and to manipulation of the host-Symbiodiniaceae symbiosis. However, little is known about the response of theG. fascicularismicrobiome to menthol bleaching—the experimental removal of the Symbiodiniaceae which represents the first step in coral-algal symbiosis manipulation. For this, we characterized the bacterial microbiome of symbiotic and menthol-bleachedG. fascicularisoriginating from the Red Sea and South China Sea (Hong Kong) that were long-term aquarium-reared in separate facilities. We found that the coral-associated microbiomes were composed of relatively few bacterial taxa (10-78 ASVs). Symbiotic polyps (clonal replicates) from the same colony had similar microbiomes, which were distinct from those of other colonies despite co-culturing in shared aquaria. A pattern of seemingly differential response of the bacterial microbiome to menthol bleaching between the two facilities emerged, warranting further investigation into the role of rearing conditions. Nevertheless, the changes in community composition overall appeared to be stochastic suggesting a dysbiotic state. Considering the importance of bleaching treatment of captive corals for symbiosis research, our results—although preliminary—contribute fundamental knowledge for the development of the Galaxea model for coral symbiosis research.
Evolution of resistance and disease tolerance mechanisms to oral bacterial infection inD. melanogaster
Authors: Paulo Tânia F. , Akyaw Priscilla A. , Paixão Tiago , Sucena Élio 
Published: August 2023

ABSTRACTPathogens exert strong selection on hosts, that evolve and deploy different defensive strategies, namely minimizing pathogen exposure (avoidance), directly promoting pathogen elimination (resistance), and/or managing the deleterious effects of illness (disease tolerance). However, how the response to pathogens partitions across these processes has never been directly assessed in a single system, let alone in the context of known adaptive trajectories under controlled selection regimes. Here, an experimental evolution system composed ofD. melanogasterand its natural pathogenP. entomophilais used to independently assess the role of behavioural traits, and of resistance and disease tolerance mechanisms on host evolution. We compare one replicate of a population adapted to oral infection withP. entomophila(BactOral) to a replicate of its control population to find no evidence for behavioural change but measurable differences in both resistance and disease tolerance. In BactOral, we identify a relative decrease in bacterial loads correlated with an increase in gut production of specific AMPs, but no differences in bacterial intake, in gut cell renewal rate, or in the rate of bacterial defecation, pointing to a strengthening in resistance. Additionally, we posit that disease tolerance also contributes to the adaptive response of the BactOral population through a tighter control of its immune response and of the deleterious effects of exposure. This study reveals a genetically complex and mechanistically multi-layered response, possibly reflecting the structure of adaptation to infection in natural populations.
A New Feature of the Laboratory Model PlantNicotiana benthamiana: Dead-End Trap for Sustainable Field Pest Control
Authors: Han Wen-Hao , Wang Jun-Xia , Zhang Feng-Bin , Ji Shun-Xia , Zhong Yu-Wei , Liu Yin-Quan , Liu Shu-Sheng , Wang Xiao-Wei 
Published: August 2023

SummaryHemiptera and Thysanoptera insects pose persistent threats to agricultural production. Conventional management strategies involve the release of chemical or plastic agents, causing adverse environmental and global health issues. Notably,Nicotiana benthamiana,a globally utilized model plant, exhibits remarkable lethal effects and attraction towards these pests.In this study, we explored the potential of usingN. benthamianafor Hemiptera and Thysanoptera pest control in the laboratory and field. Through net cover and three field assays over two years, we demonstrated the efficacy and benefits of usingN. benthamianaas a field-deployed pest control dead-end trap.N. benthamianademonstrated nearly 100% lethality to whiteflies, aphids, and thrips, with emitted volatiles attracting these insects. Field trials showed that potted and plantedN. benthamianablocks and traps whiteflies and thrips from several Solanaceae and Cucurbitaceae crops effectively, comparable to common commercial yellow and blue sticky boards. Moreover,N. benthamianain the field exhibits robust growth in commercial greenhouses without negatively impacting crop growth, natural enemies, and pollinators.Our study introduces an innovative, easily implementable, and sustainable approach for controlling Hemiptera and Thysanoptera pests. Moreover, it unveils the novel utility ofN. benthamianain field-based pest management.
Morphology and ultrastructure of external sense organs ofDrosophilalarvae
Authors: Richter Vincent , Rist Anna , Kislinger Georg , Laumann Michael , Schoofs Andreas , Miroschnikow Anton , Pankratz Michael , Cardona Albert , Thum Andreas S. 
Published: August 2023

ABSTRACTSensory perception is the ability through which an organism is able to process sensory stimuli from the environment. This stimulus is transmitted from the peripheral sensory organs to the central nervous system, where it is interpreted.Drosophila melanogasterlarvae possess peripheral sense organs on their head, thoracic, and abdominal segments. These are specialized to receive diverse environmental information, such as olfactory, gustatory, temperature or mechanosensory signals. In this work, we complete the description of the morphology of external larval sensilla and provide a comprehensive map of the ultrastructure of the different types of sensilla that comprise them. This was achieved by 3D electron microscopic analysis of partial and whole body volumes, which contain high-resolution and complete three-dimensional data of the anatomy of the sensilla and adjacent ganglia.Our analysis revealed three main types of sensilla on thoracic and abdominal segments: the papilla sensillum, the hair sensillum and the knob sensillum. They occur solitary or organized in compound sensilla such as the thoracic keilin’s organ or the terminal sensory cones. We present a spatial map defining these sensilla by their position on thoracic and abdominal segments. Further, we identify and name the sensilla at the larval head and the last fused abdominal segments. We show that mechanosensation dominates in the larval peripheral nervous system, as most sensilla have corresponding structural properties. The result of this work, the construction of a complete structural and neuronal map of the external larval sensilla, provides the basis for following molecular and functional studies to understand which sensory strategies theDrosophilalarva employs to orient itself in its natural environment.
Non-canonical contribution of human Dicer helicase domain in antiviral innate immune response
Authors: Baldaccini Morgane , Gaucherand Léa , Chane-Woon-Ming Béatrice , Messmer Mélanie , Gucciardi Floriane , Pfeffer Sébastien 
Published: August 2023

ABSTRACTIn mammalian somatic cells, the relative contribution of RNAi and the type I interferon response during viral infection is unclear. The apparent inefficiency of antiviral RNAi might be due to self-limiting properties and mitigating co-factors of the key enzyme Dicer. In particular, the helicase domain of human Dicer appears to be an important restriction factor of its activity. We studied the involvement of several helicase-truncated mutants of human Dicer in the antiviral response. All deletion mutants displayed a PKR-dependent antiviral phenotype against certain viruses and one of them, Dicer N1, acted in a complete RNAi-independent manner. Transcriptomic analyses showed that many genes from the interferon and inflammatory response were upregulated in Dicer N1 expressing cells. We could show that some of these genes appear to be controlled by NF-kB and that blocking this pathway abrogated the antiviral phenotype of Dicer N1. Our findings highlight the crosstalk between Dicer, PKR, and the NF-kB pathway, and suggest that human Dicer may have repurposed its helicase domain to prevent basal activation of antiviral and inflammatory pathways.
Primate-expressed EPIREGULIN promotes basal progenitor proliferation in the developing neocortex
Authors: Cubillos Paula , Ditzer Nora , Kolodziejczyk Annika , Schwenk Gustav , Hoffmann Janine , Schütze Theresa M. , Derihaci Razvan P. , Birdir Cahit , Köllner Johannes E. M. , Petzold Andreas , Sarov Mihail , Martin Ulrich , Long Katherine R. , Wimberger Pauline , Albert Mareike 
Published: August 2023

SUMMARYNeocortex expansion during evolution is linked to higher numbers of neurons thought to result from increased proliferative capacity and neurogenic potential of basal progenitor cells (BPs) during development. Here we show thatEREG, encoding the growth factor EPIREGULIN, is expressed in the human developing neocortex and in gorilla organoids, but not in the mouse neocortex. Addition of EPIREGULIN to the mouse neocortex increases proliferation of BPs via EGFR-mediated signaling, whereas ablation ofEREGin human cortical organoids reduces BP proliferation. Addition of EPIREGULIN to cortical organoids promotes a further increase in proliferation of gorilla but not human BPs. Finally, we identify putative cis-regulatory elements that may contribute to inter-species differences inEREGexpression. Overall, our results suggest that species-specific expression of EPIREGULIN may contribute to increased neocortex size in primates by providing a pro-proliferative signal to BPs in the subventricular zone progenitor niche.
Patient-Specific Analysis of Co-expression Networks for Predicting Clinical Outcomes in Breast Cancer
Authors: Wei Lanying , Xin Yucui , Pu Mengchen , Zhang Yingsheng 
Published: August 2023

AbstractTo effectively understand the underlying mechanisms of disease and inform the development of personalized therapies, it is critical to harness the power of differential co-expression network analysis. Despite the promise of differential co-expression network analysis in precision medicine, current approaches have a major limitation: they measure an average differential network across multiple samples, which means the specific etiology of individual patients is often overlooked. To address this, we present Cosinet, a differential co-expression-based single-sample network rewiring degree quantification tool. By analyzing two breast cancer datasets, we demonstrate that Cosinet can identify important differences in gene co-expression patterns between individual patients and generate scores for each individual that are significantly associated with overall survival, recurrence-free interval, and other clinical outcomes, even after adjusting for risk factors such as age, tumor size, HER2 status and PAM50 subtypes. Cosinet represents a remarkable development toward unlocking the potential of differential co-expression analysis in the context of precision medicine.