bluuebunny/crossref_metadata_2025_split huggingface dataset:
Robust and Accurate Bayesian Inference of Genome-Wide Genealogies for Large Samples
Authors: Deng Yun , Nielsen Rasmus , Song Yun S. 
Published: March 2024

AbstractThe Ancestral Recombination Graph (ARG), which describes the full genealogical history of a sample of genomes, is a vital tool in population genomics and biomedical research. Recent advancements have increased ARG reconstruction scalability to tens or hundreds of thousands of genomes, but these methods rely on heuristics, which can reduce accuracy, particularly in the presence of model misspecification. Moreover, they reconstruct only a single ARG topology and cannot quantify the considerable uncertainty associated with ARG inferences. To address these challenges, we here introduce SINGER, a novel method that accelerates ARG sampling from the posterior distribution by two orders of magnitude, enabling accurate inference and uncertainty quantification for large samples. Through extensive simulations, we demonstrate SINGER’s enhanced accuracy and robustness to model misspecification compared to existing methods. We illustrate the utility of SINGER by applying it to African populations within the 1000 Genomes Project, identifying signals of local adaptation and archaic introgression, as well as strong support of trans-species polymorphism and balancing selection in HLA regions.
The distribution of particulate organic matter in the heterogeneous soil matrix - balancing between aerobic respiration and denitrification
Authors: Lucas Maik , Rohe Lena , Apelt Bernd , Stange Claus Florian , Vogel Hans-Jörg , Well Reinhard , Schlüter Steffen 
Published: March 2024

ABSTRACTDenitrification, a key process in soil nitrogen cycling, occurs predominantly within microbial hotspots, such as those around particulate organic matter (POM), where denitrifiers use nitrate as an alternative electron acceptor. For accurate prediction of dinitrogen (N2) and nitrous oxide (N2O) emissions from denitrification, a precise quantification of these microscale hotspots is required. The distribution of POM is of crucial importance in this context, as the local oxygen (O2) balance is governed not only by its high O2demand but also by the local O2availability.Employing a unique combination of X-ray CT imaging, microscale O2measurements, and15N labeling, we were able to quantify hotspots of aerobic respiration and denitrification. We analyzed greenhouse gas (GHG) fluxes, soil oxygen supply, and the distribution of POM in intact soil samples from grassland and cropland under different moisture conditions. Our findings reveal that both proximal and distal POM, identified through X-ray CT imaging, contribute to GHG emissions. The distal POM, i.e. POM at distant locations to air-filled pores, emerged as a primary driver of denitrification within structured soils of both land uses. Thus, the higher denitrification rates in the grassland could be attributed to the higher content of distal POM. Conversely, despite possessing compacted areas that could favor denitrification, the cropland had only small amounts of distal POM to stimulate denitrification in it. This underlines the complex interaction between soil structural heterogeneity, organic carbon supply, and microbial hotspot formation and thus contributes to a better understanding of soil-related GHG emissions.In summary, our study provides a holistic understanding of soil-borne greenhouse gas emissions and emphasizes the need to refine predictive models for soil denitrification and N2O emissions by incorporating the microscale distribution of POM.HighlightsN2O originates from hotspots at the microscale and thus is largely unpredictableWe combined X-ray CT imaging, microscale O2sensors, and15N labeling to map hotspotsThe position of the POM separates enhanced aerobic respiration and denitrificationDistal POM (to air-filled pores) as driver of denitrification (N2O+N2) in soilsIncluding POM distribution in models will enhance accuracy for soil GHG predictionsAbstract Figure
Evaluation of methods for RNA-Seq analysis for uncovering key components of estrogen receptor-alpha signaling pathway in breast cancer
Authors: Guo Wanru 
Published: March 2024

ABSTRACTBreast cancer is the most common female cancer worldwide. Higher estrogen receptor (ER) expression is often associated with poor prognosis in ER positive breast cancer, however the exact mechanism is unknown. RNA-Seq data of three different experiments of ER knockdown (siE1, siE2, siE3) was used by researchers previously to identify TNFAIP1/BACURD2 as the mediator of ER induced increase in cell migration typical of breast cancer. We herein present a more comprehensive analysis of the data using DESEq2, along with comparison of results using a non-parametric approach, SAM-Seq, in order to cover the low sample size used in the study, and compared the results. We have found that, SAM-Seq uncovers more significant genes and is as robust as DESeq2 in discovering genes deemed significant by DESeq2. Excitingly, our approach was able to uncover three most significantly DE genes among the three independent experiments, namely, UHMK1, ACLY and CLIC4. The fact that they are involved in cancer regulation, metabolism and cell signaling, but so far has barely been studied, serves as additional exciting avenues of targeting ER pathway in breast cancer. Lastly, neither of our DESeq2 nor SAM-Seq analysis results showed consistent downregulation of TNPAIP1 upon ERR-alpha knockout across three independent experiments. Since our analysis approaches are both more conservative and robust in situations of model assumption violations, we came to the conclusion that further experiments are needed to ascertain the involvement of TNFAIP1 in the ER signaling pathway in breast cancer.
The Impact of Model Assumptions in Interpreting Cell Kinetic Studies
Authors: Yan Ada , Sadreev Ildar , Mackerodt Jonas , Zhang Yan , Macallan Derek , Busch Robert , Asquith Becca 
Published: March 2024

Author summaryStable isotope labelling is one of the best available methods for quantifying cell dynamics in vivo, particularly in humans where the absence of toxicity makes it preferable over other techniques such as CFSE or BrdU. Interpretation of stable isotope labelling data necessitates simplifying assumptions. Here we investigate the impact of three of the most commonly used simplifying assumptions (that the cell population of interest is closed, that the population of interest is kinetically homogeneous, and that the population is spatially homogeneous) and suggest pragmatic ways in which the resulting errors can be reduced.
Endopiriform neurons projecting to ventral CA1 are a critical node for recognition memory
Authors: Yamawaki Naoki , Login Hande , Feld-Jakobsen Solbjørg Østergaard , Molnar Bernadett Mercedesz , Kirkegaard Mads Zippor , Moltesen Maria , Okrasa Aleksandra , Radulovic Jelena , Tanimura Asami 
Published: March 2024

AbstractThe claustrum complex is viewed as fundamental for higher order cognition; however, the circuit organization and function of its neuroanatomical subregions are not well understood. We demonstrated that some of the key roles of the CLA complex can be attributed to the connectivity and function of a small group of neurons in its ventral subregion, the endopiriform (EN). We identified a subpopulation of EN neurons by their projection to the ventral CA1 (ENvCA1-proj.neurons), embedded in recurrent circuits with other EN neurons and the piriform cortex. Although the ENvCA1-proj.neuron activity was biased toward novelty across stimulus categories, their chemogenetic inhibition selectively disrupted the memory-guided but not innate responses of mice to novelty. Based on our functional connectivity analysis, we suggest that ENvCA1-proj.neurons serve as an essential node for recognition memory through recurrent circuits mediating sustained attention to novelty, and through feed forward inhibition of distal vCA1 neurons shifting memory-guided behavior from familiarity to novelty.
Map of epigenetic age acceleration: a worldwide meta-analysis
Authors: Yusipov Igor , Kalyakulina Alena , Franceschi Claudio , Ivanchenko Mikhail 
Published: March 2024

AbstractThis study is the first systematic meta-analysis of epigenetic age acceleration of the largest publicly available DNA methylation data for healthy samples (93 datasets, 23K samples), focusing on geographic and ethnic aspects of different countries (25 countries) and populations (31 ethnicities) around the world. The most popular epigenetic tools for assessing age acceleration were examined in detail, their quality metrics were analyzed, and their ability to extrapolate to epigenetic data from different tissue types and age ranges different from the training data of these models was explored. In most cases, the models are not consistent with each other and show different signs of age acceleration, with the PhenoAge model tending to systematically underestimate and different versions of the GrimAge model tending to systematically overestimate the age prediction of healthy subjects. Although GEO is the largest open-access epigenetic database, most countries and populations are not represented, and different datasets use different criteria for determining healthy controls. Because of this, it is difficult to fully isolate the contribution of “geography/environment”, “ethnicity” and “healthiness” to epigenetic age acceleration. However, the DunedinPACE metric, which measures aging rate, adequately reflects the standard of living and socioeconomic indicators in countries, although it can be applied only to blood methylation data. When comparing epigenetic age acceleration, males age faster than females in most of the countries and populations considered.
Effects of arbuscular mycorrhizal fungi on nitrogen uptake in cotton (Gossypium hirsutumL.) under low-nitrogen conditions
Authors: Wang Hushan , Wang Yijian , Cheng Xiaojiao , He Yunzhu , Shen Zihui , Zhang Wangfeng , Pu Xiaozhen 
Published: March 2024

SummaryCotton is an important global cash crop whose yield and quality are highly influenced by soil nitrogen. Therefore, examining the interactions between roots and arbuscular mycorrhizal fungi (AMF) under reduced nitrogen conditions is of great significance.We investigated the effects of nitrogen application (0, 250, and 375 kg· hm-2) on the AMF infection rate of cotton, the nitrogen content of each organ, root morphological characteristics and biomass, soil extracellular enzyme activity, and soil carbon and nitrogen content using a compartmentalized culture system.The contribution of AMF to plant nitrogen was 10.40, 22.72, and 16.67% under high, low, and no nitrogen treatments, respectively. Under low-nitrogen conditions, the symbiosis between AMF and roots increased root surface area, tip number, branch number, mean diameter, and biomass; and increased soil extracellular enzyme activity (protease, NAG, PER, and PPO), the microbial biomass carbon-to-nitrogen ratio, active carbon content, and the soil nitrogen mineralization rate. Soil NO3--N, NH4+-N, and organic nitrogen content decreased, whereas the absorption of NO3--N by AMF hyphae was higher than that of NH4+-N.Under low-nitrogen conditions, AMF promoted the decomposition of soil organic matter and the transformation of soil nitrogen through the action of hyphal microorganisms.
Knowledge and perceptions of uterine fibroids: A descriptive cross-sectional survey among women of childbearing age in KwaZulu-Natal, South Africa
Authors: Dlamini Amanda , Nxumalo Celenkosini Thembelenkosini , Mpofana Nomakhosi , Paulse Michael , Makgobole Mokgadi , Pillay Pavitra 
Published: March 2024

AbstractBackgroundUterine fibroids are the leading cause of hysterectomies among women of childbearing age. This study aims to elicit the knowledge, attitude and perceptions of childbearing women towards uterine fibroids in order to provide empirical evidence informing relevant interventions oriented toward health promotion in this regard.MethodsA quantitative, cross-sectional descriptive design was used and data were collected from a sample of 362 women of reproductive age residing in a selected township in KwaZulu-Natal, South Africa. Ethical approval to conduct the study was obtained from the Durban University of Technology’s Institutional Research Ethics’ Committee (IREC – Ref No. BIREC 014/21). A pre-tested survey was conducted to gather data on knowledge, attitudes, and perceptions concerning uterine fibroids. The collected data were analyzed using SPSS version 27, employing descriptive statistics. Inferential statistics were also conducted to examine associations between key variables and respondents who self-reported being diagnosed with uterine fibroids.ResultsMost participants, 73.8% (n=267), had no awareness of uterine fibroids. Participants also demonstrated poor knowledge regarding the aetiology and symptoms of the condition. However, most participants, 49.2% (n=178), perceived uterine fibroids to be of spiritual origin, citing evil spirits and witchcraft as the cause. Participants subsequently reported that treatment would require herbal approaches and consultation with spiritualists such as traditional healers and seers. In summary, the study highlights various factors influencing self-reporting behaviours, including age, education level, employment status, marital status, number of children, awareness of the condition, perception of requiring treatment, family history, and symptom severity.Discussion and conclusionThe study findings seem to suggest that women in the selected township lack accurate knowledge about uterine fibroids. These insights are valuable for shaping targeted health interventions and policies. Recognizing the complexities of self-reporting is crucial for improving health outcomes through early detection and tailored interventions.
Prevalence and factors associated with short birth interval in Kaya Municipality, North Central Burkina Faso: a multilevel Poisson regression modeling with a robust variance of a community survey
Authors: Coulibaly Abou , Baguiya Adama , Meda Bertrand Ivlabèhiré , Millogo Tiéba , Koumbem Aristide Marie Arsène , Garanet Franck , Kouanda Seni 
Published: March 2024

AbstractA short birth interval adversely affects the health of mothers and children. This study aimed to measure the prevalence of short birth intervals and identify their associated factors in a semi-urban setting in Burkina Faso. We conducted a cross-sectional study in which data were collected in households between May and October 2022. The dependent variable was the short birth interval (SBI), defined by the World Health Organization as the time between two live births. We performed a multilevel mixed-effects Poisson regression with robust variance to determine the factors associated with the SBI by reporting adjusted prevalence ratios (aPR) with a 95% confidence interval (CI). A total of 5544 birth intervals were recorded from 4067 women. A short birth interval was found in 1503 cases out of 5544, i.e., a frequency of 27.1%. The prevalence of short birth interval (time between two live births less than 33 months) was higher in never users of modern contraceptive users (aPR=1.24; 95% CI [1.14-1.34] vs. previous users), in younger ages with aPR of 4.21 (95% CI [3.30-5.37]), 2.47 (95% CI [1.96-3.11]), and 1.45 (95% CI [1.16-1.81]), respectively for under 18, 18-24 years old, and 25-34 years old, compared to 35 and over. Childbirths occurring before the implementation of the maternal and infant free health care policy (aPR=2.13; 95% CI [1.98-2.30]) and also before the free FP policy (aPR=1.53; 95% CI [1.28-1.81]) were found also protective against SBI. Women with low socio-economic positions were more likely to have SBI. This study found a high SBI in Burkina Faso (more than one woman out of four). Our results have programmatic implications, as some factors, such as contraceptive practice and socioeconomic status, are modifiable. These factors need particular attention to lengthen birth intervals and, in turn, improve mother-child couple health by reducing short birth interval consequences.
Examination of a novel limb symmetry index to discriminate movement strategies during bilateral jump landing in individuals with ACLR and with and without a history of ankle sprains
Authors: Sugimoto Yuki A. , Garrison Craig J. , Acosta Ana Maria , Dewald Julius P.A. 
Published: March 2024

ABSTRACTINTRODUCTIONThe Limb Symmetry Index (LSI), computed from kinetic parameters, tracks knee functionality post Anterior Cruciate Ligament Reconstruction (ACLR). However, LSI may lack accuracy in individuals with ACLR and ankle sprains, as it overlooks kinetic chain coordination across lower limb joints. Previous ankle sprains (AS) contribute to altered neuromuscular control in ACLR, emphasizing the need to evaluate within-limb coordination during bilateral tasks to prevent secondary ACL injuries. The effect of Energy Absorption Contribution (EAC) on joint work provides insight into the coordination between joints during observed movements. Thus, the purpose of this study was to validate a novel LSI based on EAC for discriminating movement strategies in bilateral drop vertical jump landing (DVJL) among individuals with ACLR and ACLR-ASMETHODS39 healthy athletes, including 13 healthy controls, 13 ACLR, and 13 ACLR-AS were matched by age, height, weight, sex, sports involvement, and limb dominance. Participants performed five DVJLs with kinematics and ground reaction forces recorded. Individual joint work (M) and EAC were calculated and averaged across the middle three trials to compute the LSI on individual joint work (LSIM) and EAC (LSIEAC). Negative LSI indicates asymmetry toward the nonsurgical limb, while positive LSI indicates asymmetry toward the surgical limb. A 3x2x3 repeated measures analysis of variance was utilized to analyze interactions between groups, the LSI method, and joint. Tukey’s LSD post-hoc analyses were used to examine within and between groups (alpha=0.05).RESULTSThere was a significant interaction between the group, LSI method, and joint (F4,72=3.216,P=.017). LSIEACidentified significant loading asymmetry at the hip (P=.046) and knee (P=.015) when compared to healthy controls.CONCLUSIONSLSIEACproved to be the method capable of distinguishing group differences in loading asymmetry at the hip and knee for the ACLR-AS group compared to healthy controls during bilateral DVJL. Overall, LSIEACprovided a more comprehensive insight into the movement strategies employed during DVJL, particularly for individuals with ACLR and ACLR-AS. This emphasizes its suitability for effectively monitoring the rehabilitation progression post ACLR towards RTS. Our findings suggest that clinicians should prioritize computing the LSI based on EAC and assessing the history of ankle sprains for precise RTS decision-making. This approach not only aids in identifying loading asymmetry at the knee and hip but also underscores the critical importance of restoring modified movement strategies in adolescents with ACLR-AS, ultimately reducing the risk of secondary ACL injury following RTS.
Comparative venom analysis between melanistic and normally-colored phenotypes of the common adder (Vipera berus)
Authors: Schulte Lennart , Uhrig Lilien , Eichberg Johanna , Schwartze Michael , Auth Ingve , Schulz Miriam , Lindner Thomas , Hien Paul , Hardes Kornelia , Vilcinskas Andreas , Lüddecke Tim 
Published: March 2024

1AbstractSnake venom is an ecologically-relevant functional trait directly linked with a snake’s fitness and survival, facilitating predation and defense. Snake venom variation occurs at all taxonomic levels, but the study of variation at intraspecific level is still in its early stages. The common adder (Vipera berus) exhibits considerable variation in color phenotypes across its distribution range. Melanistic (fully black) individuals are the subject of myths and fairytales, and in German folklore such “hell adders” are considered more toxic than their normally-colored conspecifics. However, these claims have never been formally tested. Here, we provide the first comparative analysis of venoms from melanistic and normally-colored common adders. Specifically, we compared the venom profiles by SDS-PAGE and RP-HPLC, and tested the protease, phospholipase A2and cytotoxic activities of the venoms of both phenotypes. Phospholipase A2activity was similar in both phenotypes, whereas general protease activity was higher in the melanistic venom, which was also more cytotoxic at two concentrations (6.25 and 12.5 µg/ml). These minor differences between the venoms of melanistic and normally-colored adders are unlikely to be of clinical relevance in the context of human envenomation. In light of our results, the claim that melanistic adders produce more toxic venom than their normally-colored conspecifics appears rooted entirely in folklore.
GLP-1 receptor agonist exenatide uncouples food intake from hedonic and anticipatory regulation in non-human primates: Insights from an operant meal schedule paradigm
Authors: Knakker Balázs , Inkeller Judit , Kovács Péter , Lendvai Balázs , Hernádi István 
Published: March 2024

AbstractGlucagon-like peptide 1 (GLP-1), a neuroendocrine signal of energy balance and satiety, has a major role in regulating food intake behaviour. Here we investigated the effects of the GLP-1 agonist exenatide on palatability-driven feeding regulation in adult male rhesus macaques (n=5) using a novel operant food intake paradigm with four meal schedule conditions where two types of pellets with different palatability values were offered as meal in all combinations in two consecutive daily feeding sessions (S1 and S2). In control conditions, a strong, palatability-driven anticipatory effect was found in S1, followed by a complementary positive contrast effect in S2. After acute subcutaneous treatment with 1 µg/kg dose of exenatide 1 h before S1, food intake decreased to the same very low level in all meal schedule conditions in S1, completely erasing the previously observed anticipatory effect. Conversely, exenatide induced hypoglycaemia in an anticipatory meal schedule dependent pattern. Interestingly, the previously observed positive contrast effect was spared in S2, with a weaker residual effect specifically on the consumption of the more palatable pellet type. To conclude, the food intake reducing effects of exenatide may temporally evolve from strong anorectic to weak anhedonic modulations, where hedonic experience and anticipation during the early anorectic phase is conserved but uncoupled from food intake behaviour.