bluuebunny/crossref_metadata_2025_split huggingface dataset:
Modulation of adipose inflammation by cellular retinoic acid-binding protein 1
Authors: Wei Chin-Wen , Nhieu Jennifer , Lin Yu-Lung , Wei Li-Na 
Published: July 2022

Abstract
Objectives
Obesity, a metabolic syndrome, is known to be related to inflammation, especially adipose tissue inflammation. Cellular interactions within the expanded white adipose tissue (WAT) in obesity contribute to inflammation and studies have suggested that inflammation is triggered by inflamed adipocytes that recruit M1 macrophages into WAT. What causes accumulation of unhealthy adipocytes is an important topic of investigation. This study aims to understand the action of Cellular Retinoic Acid Binding Protein 1 (CRABP1) in WAT inflammation.

Methods
Eight weeks-old wild type (WT) and Crabp1 knockout (CKO) mice were fed with a normal diet (ND) or high-fat diet (HFD) for 8 weeks. Body weight and food intake were monitored. WATs and serum were collected for cellular and molecular analyses to determine affected signaling pathways. In cell culture studies, primary adipocyte differentiation and bone marrow-derived macrophages (BMDM) were used to examine adipocytes’ effects, mediated by CRABP1, in macrophage polarization. The 3T3L1-adipocyte was used to validate relevant signaling pathways.

Results
CKO mice developed an obese phenotype, more severely under high-fat diet (HFD) feeding. Further, CKO’s WAT exhibited a more severe inflammatory state as compared to wild type (WT) WAT, with a significantly expanded M1-like macrophage population. However, this was not caused by intrinsic defects of CKO macrophages. Rather, CKO adipocytes produced a significantly reduced level of adiponectin and had significantly lowered mitochondrial DNA content. CKO adipocyte-conditioned medium, compared to WT control, inhibited M2-like (CD206+) macrophage polarization. Mechanistically, defects in CKO adipocytes involved the ERK1/2 signaling pathway that could be modulated by CRABP1.

Conclusions
This study shows that CRABP1 plays a protective role against HFD-induced WAT inflammation through, in part, its regulation of adiponectin production and mitochondrial homeostasis in adipocytes, thereby modulating macrophage polarization in WAT to control its inflammatory potential.
Application of ATAC-seq in tumor-specific T cell exhaustion
Authors: Chen Chufeng , Liu Jiaying , Chen Yidong , Lin Anqi , Mou Weiming , Zhu Lingxuan , Yang Tao , Cheng Quan , Zhang Jian , Luo Peng 
Published: July 2022

AbstractResearches show that chronic viral infection and persistent antigen and/or inflammatory signal exposure in cancer causes the functional status of T cells to be altered, mainly by major changes in the epigenetic and metabolic environment, which then leads to T cell exhaustion. The discovery of the immune checkpoint pathway is an important milestone in understanding and reversing T cell exhaustion. Antibodies targeting these pathways have shown superior ability to reverse T cell exhaustion. However, there are still some limitations in immune checkpoint blocking therapy, such as the short-term nature of therapeutic effects and high individual heterogeneity. Assay for transposase-accessible chromatin with sequencing(ATAC-seq) is a method used to analyze the accessibility of whole-genome chromatin. It uses hyperactive Tn5 transposase to assess chromatin accessibility. Recently, a growing number of studies have reported that ATAC-seq can be used to characterize the dynamic changes of epigenetics in the process of T cell exhaustion. It has been determined that immune checkpoint blocking can only temporarily restore the function of exhausted T cells because of an irreversible change in the epigenetics of exhausted T cells. In this study, we review the latest developments, which provide a clearer molecular understanding of T cell exhaustion, reveal potential new therapeutic targets for persistent viral infection and cancer, and provide new insights for designing effective immunotherapy for treating cancer and chronic infection.
Nuclear speed and cycle length co-vary with local density during syncytial blastoderm formation in a cricket
Authors: Donoughe Seth , Hoffmann Jordan , Nakamura Taro , Rycroft Chris H. , Extavour Cassandra G. 
Published: July 2022

AbstractThe blastoderm is a broadly conserved stage of early animal development, wherein cells form a layer at the embryo’s periphery. The cellular behaviors underlying blastoderm formation are varied and poorly understood. In most insects, the pre-blastoderm embryo is a syncytium: nuclei divide and move throughout the shared cytoplasm, ultimately reaching the cortex. In Drosophila melanogaster, some early nuclear movements result from pulsed cytoplasmic flows that are coupled to synchronous divisions. Here, we show that the cricket Gryllus bimaculatus has a different solution to the problem of creating a blastoderm. We quantified nuclear dynamics during blastoderm formation in G. bimaculatus embryos, finding that: (1) cytoplasmic flows are unimportant for nuclear movement, and (2) division cycles, nuclear speeds, and the directions of nuclear movement are not synchronized, instead being heterogeneous in space and time. Moreover, nuclear divisions and movements co-vary with local nuclear density. We show that several previously proposed models for nuclear movements in D. melanogaster cannot explain the dynamics of G. bimaculatus nuclei. We introduce a geometric model based on asymmetric pulling forces on nuclei, which recapitulates the patterns of nuclear speeds and orientations of both unperturbed G. bimaculatus embryos, and of embryos physically manipulated to have atypical nuclear densities.
Deep learning from phylogenies to uncover the epidemiological dynamics of outbreaks
Authors: Voznica J. , Zhukova A. , Boskova V. , Saulnier E. , Lemoine F. , Moslonka-Lefebvre M. , Gascuel O. 
Published: July 2022

AbstractWidely applicable, accurate and fast inference methods in phylodynamics are needed to fully profit from the richness of genetic data in uncovering the dynamics of epidemics. Standard methods, including maximum-likelihood and Bayesian approaches, generally rely on complex mathematical formulae and approximations, and do not scale with dataset size. We develop a likelihood-free, simulation-based approach, which combines deep learning with (1) a large set of summary statistics measured on phylogenies or (2) a complete and compact representation of trees, which avoids potential limitations of summary statistics and applies to any phylodynamics model. Our method enables both model selection and estimation of epidemiological parameters from very large phylogenies. We demonstrate its speed and accuracy on simulated data, where it performs better than the state-of-the-art methods. To illustrate its applicability, we assess the dynamics induced by superspreading individuals in an HIV dataset of men-having-sex-with-men in Zurich. Our tool PhyloDeep is available on github.com/evolbioinfo/phylodeep.
Dispersed emergence and protracted domestication of polyploid wheat uncovered by mosaic ancestral haploblock inference
Authors: Wang Zihao , Wang Wenxi , Xie Xiaoming , Wang Yongfa , Yang Zhengzhao , Peng Huiru , Xin Mingming , Yao Yingyin , Hu Zhaorong , Liu Jie , Su Zhenqi , Xie Chaojie , Li Baoyun , Ni Zhongfu , Sun Qixin , Guo Weilong 
Published: July 2022

AbstractMajor crops are all survivors of domestication bottlenecks. Studies have focused on the genetic loci related to the domestication syndrome, while the contribution of ancient haplotypes remains largely unknown. Here, an ancestral genomic haploblock dissection method is developed and applied to a resequencing dataset of 386 tetraploid/hexaploid wheat accessions, generating a pan-ancestry haploblock map. Together with cytoplastic evidences, we reveal that domesticated polyploid wheat emerged from the admixture of six founder wild emmer lineages, which contributed the foundation of ancestral mosaics. The key domestication-related loci, originated over a wide geographical range, were gradually pyramided through a protracted process. Diverse stable-inheritance ancestral haplotype groups of the chromosome central zone are identified, revealing the expanding routes of wheat and the trends of modern wheat breeding. Finally, an evolution model of polyploid wheat is proposed, highlighting the key role of wild-to-crop and interploidy introgression, that increased genomic diversity following bottlenecks introduced by domestication and polyploidization.
Loss-of-function, gain-of-function and dominant-negative mutations have profoundly different effects on protein structure
Authors: Gerasimavicius Lukas , Livesey Benjamin J. , Marsh Joseph A. 
Published: July 2022

AbstractMost known pathogenic mutations occur in protein-coding regions of DNA and change the way proteins are made. Taking protein structure into account has therefore provided great insight into the molecular mechanisms underlying human genetic disease. While there has been much focus on how mutations can disrupt protein structure and thus cause a loss of function (LOF), alternative mechanisms, specifically dominant-negative (DN) and gain-of-function (GOF) effects, are less understood. Here, we investigate the protein-level effects of pathogenic missense mutations associated with different molecular mechanisms. We observe striking differences between recessive vs dominant, and LOF vs non-LOF mutations, with dominant, non-LOF disease mutations having much milder effects on protein structure, and DN mutations being highly enriched at protein interfaces. We also find that nearly all computational variant effect predictors, even those based solely on sequence conservation, underperform on non-LOF mutations. However, we do show that non-LOF mutations could potentially be identified by their tendency to cluster in three-dimensional space. Overall, our work suggests that many pathogenic mutations that act via DN and GOF mechanisms are likely being missed by current variant prioritisation strategies, but that there is considerable scope to improve computational predictions through consideration of molecular disease mechanisms.
Hippocampal place cells have goal-oriented vector fields during navigation
Authors: Ormond Jake , O’Keefe John 
Published: July 2022

AbstractThe hippocampal cognitive map supports navigation towards, or away from, salient locations in familiar environments1. Although much is known about how the hippocampus encodes location in world-centred coordinates, how it supports flexible navigation is less well understood. We recorded CA1 place cells while rats navigated to a goal on the honeycomb maze2. The maze tests navigation via direct and indirect paths to the goal and allows the directionality of place cells to be assessed at each choice point. Place fields showed strong directional polarization characterized by vector fields that converged to sinks distributed throughout the environment. The distribution of these ‘convergence sinks’ (ConSinks) was centred near the goal location and the population vector field converged on the goal, providing a strong navigational signal. Changing the goal location led to movement of ConSinks and vector fields towards the new goal. The honeycomb maze allows independent assessment of spatial representation and spatial action in place cell activity and shows how the latter relates to the former. The results suggest that the hippocampus creates a vector-based model to support flexible navigation, allowing animals to select optimal paths to destinations from any location in the environment.
Single-cell roadmap of human gonadal development
Authors: Garcia-Alonso Luz , Lorenzi Valentina , Mazzeo Cecilia Icoresi , Alves-Lopes João Pedro , Roberts Kenny , Sancho-Serra Carmen , Engelbert Justin , Marečková Magda , Gruhn Wolfram H. , Botting Rachel A. , Li Tong , Crespo Berta , van Dongen Stijn , Kiselev Vladimir Yu , Prigmore Elena , Herbert Mary , Moffett Ashley , Chédotal Alain , Bayraktar Omer Ali , Surani Azim , Haniffa Muzlifah , Vento-Tormo Roser 
Published: July 2022

AbstractGonadal development is a complex process that involves sex determination followed by divergent maturation into either testes or ovaries1. Historically, limited tissue accessibility, a lack of reliable in vitro models and critical differences between humans and mice have hampered our knowledge of human gonadogenesis, despite its importance in gonadal conditions and infertility. Here, we generated a comprehensive map of first- and second-trimester human gonads using a combination of single-cell and spatial transcriptomics, chromatin accessibility assays and fluorescent microscopy. We extracted human-specific regulatory programmes that control the development of germline and somatic cell lineages by profiling equivalent developmental stages in mice. In both species, we define the somatic cell states present at the time of sex specification, including the bipotent early supporting population that, in males, upregulates the testis-determining factor SRY and sPAX8s, a gonadal lineage located at the gonadal–mesonephric interface. In females, we resolve the cellular and molecular events that give rise to the first and second waves of granulosa cells that compartmentalize the developing ovary to modulate germ cell differentiation. In males, we identify human SIGLEC15+ and TREM2+ fetal testicular macrophages, which signal to somatic cells outside and inside the developing testis cords, respectively. This study provides a comprehensive spatiotemporal map of human and mouse gonadal differentiation, which can guide in vitro gonadogenesis.
Enhancing wind direction prediction of South Africa wind energy hotspots with Bayesian mixture modeling
Authors: Rad Najmeh Nakhaei , Bekker Andriette , Arashi Mohammad 
Published: July 2022

AbstractWind energy production depends not only on wind speed but also on wind direction. Thus, predicting and estimating the wind direction for sites accurately will enhance measuring the wind energy potential. The uncertain nature of wind direction can be presented through probability distributions and Bayesian analysis can improve the modeling of the wind direction using the contribution of the prior knowledge to update the empirical shreds of evidence. This must align with the nature of the empirical evidence as to whether the data are skew or multimodal or not. So far mixtures of von Mises within the directional statistics domain, are used for modeling wind direction to capture the multimodality nature present in the data. In this paper, due to the skewed and multimodal patterns of wind direction on different sites of the locations understudy, a mixture of multimodal skewed von Mises is proposed for wind direction. Furthermore, a Bayesian analysis is presented to take into account the uncertainty inherent in the proposed wind direction model. A simulation study is conducted to evaluate the performance of the proposed Bayesian model. This proposed model is fitted to datasets of wind direction of Marion island and two wind farms in South Africa and show the superiority of the approach. The posterior predictive distribution is applied to forecast the wind direction on a wind farm. It is concluded that the proposed model offers an accurate prediction by means of credible intervals. The mean wind direction of Marion island in 2017 obtained from 1079 observations was 5.0242 (in radian) while using our proposed method the predicted mean wind direction and its corresponding $$95\%$$

95
%

credible interval based on 100 generated samples from the posterior predictive distribution are obtained 5.0171 and (4.7442, 5.2900). Therefore, our results open a new approach for accurate prediction of wind direction implementing a Bayesian approach via mixture of skew circular distributions.
Infrared optical properties modulation of VO2 thin film fabricated by ultrafast pulsed laser deposition for thermochromic smart window applications
Authors: Barimah Eric Kumi , Boontan Artitsupa , Steenson David P. , Jose Gin 
Published: July 2022

AbstractOver the years, vanadium dioxide, (VO2(M1)), has been extensively utilised to fabricate thermochromic thin films with the focus on using external stimuli, such as heat, to modulate the visible through near-infrared transmittance for energy efficiency of buildings and indoor comfort. It is thus valuable to extend the study of thermochromic materials into the mid-infrared (MIR) wavelengths for applications such as smart radiative devices. On top of this, there are numerous challenges with synthesising pure VO2 (M1) thin films, as most fabrication techniques require the post-annealing of a deposited thin film to convert amorphous VO2 into a crystalline phase. Here, we present a direct method to fabricate thicker VO2(M1) thin films onto hot silica substrates (at substrate temperatures of 400 °C and 700 °C) from vanadium pentoxide (V2O5) precursor material. A high repetition rate (10 kHz) femtosecond laser is used to deposit the V2O5 leading to the formation of VO2 (M1) without any post-annealing steps. Surface morphology, structural properties, and UV–visible optical properties, including optical band gap and complex refractive index, as a function of the substrate temperature, were studied and reported below. The transmission electron microscopic (TEM) and X-ray diffraction studies confirm that VO2 (M1) thin films deposited at 700 °C are dominated by a highly texturized polycrystalline monoclinic crystalline structure. The thermochromic characteristics in the mid-infrared (MIR) at a wavelength range of 2.5–5.0 μm are presented using temperature-dependent transmittance measurements. The first-order phase transition from metal-to-semiconductor and the hysteresis bandwidth of the transition were confirmed to be 64.4 °C and 12.6 °C respectively, for a sample fabricated at 700 °C. Thermo-optical emissivity properties indicate that these VO2 (M1) thin films fabricated with femtosecond laser deposition have strong potential for both radiative thermal management or control via active energy-saving windows for buildings, and satellites and spacecraft.
Life table construction for crapemyrtle bark scale (Acanthococcus lagerstroemiae): the effect of different plant nutrient conditions on insect performance
Authors: Xie Runshi , Wu Bin , Gu Mengmeng , Qin Hongmin 
Published: July 2022

AbstractCrapemyrtle Bark Scale (Acanthococcus lagerstroemiae; CMBS) is an invasive pest species that primarily infest crapemyrtles (Lagerstroemia spp.) in the United States. Recent reports have revealed the dire threat of CMBS to attack not only crapemrytles but also the U.S. native species with expanded host plants such as American beautyberry (Callicarpa spp.) and Hypericum kalmianum L. (St. Johnswort). A better understanding of plant–insect interaction will provide better and environmental-friendly pest management strategies. In this study, we constructed the first comprehensive life table for CMBS to characterize its biological parameters, including developmental stages, reproductive behavior, and fecundity. The indirect effects of three plant nutrient conditions (water, 0.01MS, and 0.1MS) on CMBS populations were examined using the age-stage, two-sex life table. The demographic analyses revealed that the plant nutrient conditions had significantly altered CMBS development in terms of the intrinsic rate of increase (r), the finite rate of increase (λ), the net reproductive rate (R0), and mean generation time (T). Higher r, λ, and R0 were recorded under nutrient-deficient conditions (water), while CMBS reared on plants with healthier growing conditions (0.1MS) had the most prolonged T. Overall, CMBS shows better insect performance when reared on plants under nutrient-deficient conditions.
Interplay between different forms of power and meritocratic considerations shapes fairness perceptions
Authors: Lois Giannis , Riedl Arno 
Published: July 2022

AbstractPower imbalance often leads to unequal allocations. However, it remains largely unknown how different forms of power and meritocratic considerations interact to shape fairness perceptions. Using modified Ultimatum Games, we examined how two power forms—decision power and availability of attractive outside option—affect bargaining behavior and fairness perceptions, and how meritocratic considerations are incorporated into the fairness perceptions of powerful and powerless individuals. We identified an asymmetric power effect: having increased decision power or attractive outside options independently increased self-advantageous allocations and self-serving fairness perceptions, whereas the combined lack of both power forms led to self-disadvantageous allocations but had no influence on fairness perceptions. The power effect on fairness perceptions became symmetric when power was obtained through a meritocratic process (procedural justice). In contrast, relative contributions to resource production (distributive justice) did not moderate power effects. We provide causal evidence that the powerful, but not the powerless, strive to minimize cognitive dissonance between behavior and fairness perceptions by interpreting fairness in self-serving ways. This study contributes novel insights into the interplay between different power forms, the asymmetry of power effects, the moderating role of procedural justice, and the mediating role of behavior in the power-driven adjustment of fairness perceptions.
Investigation of cypermethrin toxicity in Swiss albino mice with physiological, genetic and biochemical approaches
Authors: Seven Baran , Kültiğin  , Çavuşoğlu  , Yalçin Emine , Acar Ali 
Published: July 2022

AbstractIn this study, cypermethrin toxicity was investigated using physiological, biochemical and cytogenetic parameters, and more than one organ and cell type was preferred to determine these effects. In this multifaceted study, the genotoxicity mechanism of cypermethrin was elucidated by molecular docking. In addition, comet assay technique was applied to detect and quantify DNA damage at the cell level. For this aim, body and organ weights, aspartate aminotransferase (AST), alanine aminotransferase (ALT), malondialdehyde (MDA), glutathione (GSH), blood urea nitrogen (BUN) and creatinine levels, mitotic index (MI), DNA fragmentation, frequency of micronucleus (MN) and chromosomal aberrations (CAs) were used as indicators of toxicity. Mice were divided into 4 groups. The control group was fed with tap water and the administration groups were orally exposed to 62.5, 125 and 250 mg/kg b.w cypermethrin for 28 days. Then, the mice were sacrificed and tissue samples were collected. Cypermethrin caused a decrease in body and organ weights, GSH levels and MI and an increase in AST, ALT, MDA, BUN, creatinine levels and the frequency of MN and CAs (break, ring, gap, acentric, etc.). Cypermethrin promoted MN formation in leukocyte, erythrocyte, buccal mucosa epithelial cells. CAs and MN formation promoted by cypermethrin have been associated with DNA-cypermethrin interactions. This interaction has been demonstrated by simulation with molecular docking method and experimentally by spectral measurements of DNA. As a result, all three doses of cypermethrin caused toxicity in different cell types. In other words, the effect of cypermethrin taken into the body was not limited to only one cell type or region. Therefore, cypermethrin is a pyrethroid insecticide that promotes multifaceted toxicity in non-target organisms.