bluuebunny/crossref_metadata_2025_split huggingface dataset:
Independently evolved pollution resistance in four killifish populations is largely explained by few variants of large effect
Authors: Miller Jeffrey T. , Clark Bryan W. , Reid Noah M. , Karchner Sibel I. , Roach Jennifer L. , Hahn Mark E. , Nacci Diane , Whitehead Andrew 
Published: January 2024

AbstractThe genetic architecture of phenotypic traits can affect the mode and tempo of trait evolution. Human‐altered environments can impose strong natural selection, where successful evolutionary adaptation requires swift and large phenotypic shifts. In these scenarios, theory predicts that adaptation is due to a few adaptive variants of large effect, but empirical studies that have revealed the genetic architecture of rapidly evolved phenotypes are rare, especially for populations inhabiting polluted environments. Fundulus killifish have repeatedly evolved adaptive resistance to extreme pollution in urban estuaries. Prior studies, including genome scans for signatures of natural selection, have revealed some of the genes and pathways important for evolved pollution resistance, and provide context for the genotype–phenotype association studies reported here. We created multiple quantitative trait locus (QTL) mapping families using progenitors from four different resistant populations, and using RAD‐seq genetically mapped variation in sensitivity (developmental perturbations) following embryonic exposure to a model toxicant PCB‐126. We found that one to two large‐effect QTL loci accounted for resistance to PCB‐mediated developmental toxicity. QTLs harbored candidate genes that govern the regulation of aryl hydrocarbon receptor (AHR) signaling. One QTL locus was shared across all populations and another was shared across three populations. One QTL locus showed strong signatures of recent natural selection in the corresponding wild population but another QTL locus did not. Some candidate genes for PCB resistance inferred from genome scans in wild populations were identified as QTL, but some key candidate genes were not. We conclude that rapidly evolved resistance to the developmental defects normally caused by PCB‐126 is governed by few genes of large effect. However, other aspects of resistance beyond developmental phenotypes may be governed by additional loci, such that comprehensive resistance to PCB‐126, and to the mixtures of chemicals that distinguish urban estuaries more broadly, may be more genetically complex.
STAT6 tunes maximum T cell IL‐4 production from stochastically regulated Il4 alleles
Authors: Kyle Ryan L , Prout Melanie , Le Gros Graham , Robinson Marcus J 
Published: January 2024

AbstractT helper 2 (Th2) cells stochastically express from the Il4 locus but it has not been determined whether allelic expression is linked or independent. Here, we provide evidence that alleles are independently activated and inactivated. We compared Il4 locus expression in T cells from hemizygous IL‐4 reporter mice in culture and in vivo following exposure to type 2 immunogens. In culture, Il4 alleles had independent, heritable expression probabilities. Modeling showed that in co‐expressors, dual allele transcription occurs for only short periods, limiting per‐cell mRNA variation in individual cells within a population of Th2 cells. In vivo profiles suggested that early in the immune response, IL‐4 output was derived predominantly from single alleles, but co‐expression became more frequent over time and were tuned by STAT6, supporting the probabilistic regulation of Il4 alleles in vivo among committed IL‐4 producers. We suggest an imprinted probability of expression from individual alleles with a short transcriptional shutoff time controls the magnitude of T cell IL‐4 output, but the amount produced per allele is amplified by STAT6 signaling. This form of regulation may be a relevant general mechanism governing cytokine expression.
Genetic analysis of body weight and growth curve parameters in Muzaffarnagari sheep of India
Authors: Mandal Ajoy , Gayari Indrajit , Baneh Hasan , Notter David R. 
Published: January 2024

AbstractThe objective of this study was to estimate genetic effects on parameters of the Brody and Richards growth curves using body weight records from birth to 12 months of age on 2287 Muzaffarnagari lamb for a period of 29 years (1976–2004). Estimated growth curve parameters were analysed using six univariate animal models, and genetic correlations among and between the parameters of each function and between parameters of the functions and observed birth and yearling weights were estimated using bivariate analyses. Significant environmental factors including birth year, sex, season, birth status and dam parity were included as fixed effects in all models. Likelihood ratio tests indicated that maternal genetic effects were significant only for birth weight (BW) and degree of maturity at birth (u0) for the Brody and Richards functions. For these traits, direct heritabilities were similar (0.21, 0.19 and 0.17, respectively), but the estimated maternal heritability for BW (0.18) was twice that of u0 for both functions. Heritabilites for yearling weight and asymptotic final body weights for the Brody and Richards functions were 0.28, 0.17 and 0.21, respectively. The remaining growth curve parameters were lowly heritable, ranging from zero for the predicted degree of maturity at the age of maximum growth rate for the Richards function to 0.08 for the maturing rate parameter of the Brody function. Genetic correlations between corresponding parameters for different growth functions exceeded 0.88. Our results showed that the Brody and Richards functions had similar genetic architecture, but the Richards function had no apparent advantages over the more easily interpreted Brody function. Failure to identify maternal genetic effects on maturing rate parameters suggested that both functions failed to identify potentially important maternal genetic effects. Therefore, there is no usefulness of estimated growth curve parameters in selection compared to the simple multi‐trait genetic evaluations of individual body weights.
Nuclear phylogenomics of angiosperms and insights into their relationships and evolution
Authors: Zhang Guojin , Ma Hong 
Published: January 2024

ABSTRACTAngiosperms (flowering plants) are by far the most diverse land plant group with over 300,000 species. The sudden appearance of diverse angiosperms in the fossil record was referred to by Darwin as the “abominable mystery,” hence contributing to the heightened interest in angiosperm evolution. Angiosperms display wide ranges of morphological, physiological, and ecological characters, some of which have probably influenced their species richness. The evolutionary analyses of these characteristics help to address questions of angiosperm diversification and require well resolved phylogeny. Following the great successes of phylogenetic analyses using plastid sequences, dozens to thousands of nuclear genes from next‐generation sequencing have been used in angiosperm phylogenomic analyses, providing well resolved phylogenies and new insights into the evolution of angiosperms. In this review we focus on recent nuclear phylogenomic analyses of large angiosperm clades, orders, families, and subdivisions of some families and provide a summarized Nuclear Phylogenetic Tree of Angiosperm Families. The newly established nuclear phylogenetic relationships are highlighted and compared with previous phylogenetic results. The sequenced genomes of Amborella, Nymphaea, Chloranthus, Ceratophyllum, and species of monocots, Magnoliids, and basal eudicots, have facilitated the phylogenomics of relationships among five major angiosperms clades. All but one of the 64 angiosperm orders were included in nuclear phylogenomics with well resolved relationships except the placements of several orders. Most families have been included with robust and highly supported placements, especially for relationships within several large and important orders and families. Additionally, we examine the divergence time estimation and biogeographic analyses of angiosperm on the basis of the nuclear phylogenomic frameworks and discuss the differences compared with previous analyses. Furthermore, we discuss the implications of nuclear phylogenomic analyses on ancestral reconstruction of morphological, physiological, and ecological characters of angiosperm groups, limitations of current nuclear phylogenomic studies, and the taxa that require future attention.
A reliable and cost‐effective protocol for creating bilirubin cerebral palsy model in rhesus macaque
Authors: Zhu Yong , Xiong Yanan , Xu Xiaoyan , Zhang Jin , Tong Haiyang , Yang Hongyi , Niu Xia , Shi Xiaming , Tang Jiulai , Li Jinhua 
Published: January 2024

AbstractBackgroundCerebral palsy is a severe motor disability in childhood that poses challenges for children, families, and society. Rhesus macaques are the preferred animals for cerebral palsy model, but surgical excision of motor cortex has low success rate and high cost. In this work, we created cerebral palsy rhesus macaque models by intrathecal injection of bilirubin.MethodsThe puncture point for injection was identified as the intervertebral disc space two, located below the intersection of the iliac crest line and the posterior median line.ResultsThe models showed abnormal posture and increased muscle tension. Diffuse deposits of bilirubin were found in the basal ganglia from the magnetic resonance imaging. Pathological slides also revealed the presence of brain lesions, such as vacuole formation, contraction of neuronal nuclei, and deep staining of nuclei in the histopathological sections of the hippocampus and basal ganglia.ConclusionThe model's symptoms closely resemble those observed in humans with spastic cerebral palsy.
Increasing autonomous motivation for physical activity among adolescents
Authors: Klamm Melissa M. , Stewart Mary W. , Duck Angela , Lim Crystal , Brocks Tamara , Zhang Lei , Tacy Joseph 
Published: January 2024

AbstractPurposeAdolescents need at least 60 min of physical activity (PA) every day. Yet, the number of minutes of daily PA steadily decreases from childhood through adolescence. This occurs despite evidence that high levels of PA and limited minutes of sedentary behavior (SB) decrease the incidence of heart disease, type 2 diabetes mellitus, obesity, and cancer. Motivational interviewing (MI) is a behavioral counseling technique that focuses on behavior change areas, such as diet and PA. This research aimed to evaluate a brief nurse‐led virtual MI (vMI) intervention to guide youth toward increased PA compared to an attention control group.Design and MethodsParticipants completed the Behavioral Regulation in Exercise Questionnaire (BREQ‐2) and wore an ActiGraph GT3X+ accelerometer on their dominant wrist for 8 days to operationalize SB and PA. Participants in the treatment group rec an individual vMI session, while attention‐control group participants received an individual education session. All participants received follow‐up calls from the researcher or assistant at Weeks 4 and 8. During the calls, those in the treatment group received follow‐up MI, while the control group asked follow‐up questions about information received during the education session. At 12 weeks, all participants repeated the BREQ‐2 survey and wore the accelerometer again for 7 days.ResultsThe total number of participants was 19. At post‐intervention, the treatment group had a significant decline in the frequency of prolonged SB > 60 min (p = .001) and a nonsignificant increase in the average length of moderate‐to‐vigorous PA bouts >10 min (p = .058). The treatment group had significant increases in two levels of autonomous motivation—identified (p < .001) and intrinsic (p = .003). The overall autonomous motivation score for the BREQ‐2 significantly increased in the treatment group (p < .001).Practice ImplicationsThe study revealed promise for vMI to positively impact PA among adolescents. However, for a novice in performing MI, a nurse‐led MI session elicited change talk in participants toward individualized changes to improve health behaviors.
An Occasionalist Reading of Al‐Ashʿarī's Theory of Kasb in Kitāb al‐Lumaʿ
Authors: Taskin Zeyneb Betul 
Published: January 2024

AbstractThis paper offers an occasionalist reading of al‐Ashʿarī's theory of kasb in Kitāb al‐Lumaʿ against Richard Frank's reading. Frank argues that according to al‐Ashʿarī human beings have causal power that is created by God over their acts. Binyamin Abrahamov argues against Frank's reading because while al‐Lumaʿ does not support this interpretation, the text suggests al‐Ashʿarī's denial of causal efficacy from the created power. I expand Abrahamov's claims through a deeper comparison of al‐Lumaʿ and Frank's analysis. First, I argue that the only textual evidence might be al‐Ashʿarī's use of the verb waqaaʿ bi when al‐Ashʿarī says that acquisition come through a created power. A mere employment of this word does not indicate a causal relation between the created power and acquisition. Moreover, al‐Ashʿarī uses waqaaʿ bi to describe the concurrence of the so‐called natural causes while he never attributes causal efficacy to them. Another problem in Frank's reading is that the attribution of causal efficacy to the created power not only takes al‐Ashʿarī's theory out of the boundaries of occasionalism, but also approaches it to mere conservationism. Second, I agree with Abrahamov's occasionalist reading according to which the relation between the created power and acquisition can be a conditional relation.
MicroRNA‐196a‐5p facilitates the onset and progression via targeting ITM2B in esophageal squamous cell carcinoma
Authors: Xian Dubiao , Yang Shubo , Liu Yunzhong , Liu Qingfeng , Huang Ding , Wu Yuechang 
Published: January 2024

AbstractEsophageal squamous cell carcinoma (ESCC) is a prevalent malignancy affecting the digestive tract, with an increasing incidence rate worldwide. Recently, numerous studies revealed that microRNAs were associated with gene expression regulation, particularly their involvement in the regulation of tumor cells, garnering widespread attention. Here, we discovered that miR‐196a‐5p was significantly upregulated in both ESCC tissues and cells, which was correlated with an unfavorable prognosis. Series functional in vitro investigations have confirmed that silencing miR‐196a‐5p obviously restrained the ESCC cells malignant phenotypes and promoted apoptosis. Bioinformatics analysis and rescue experiments revealed that miR‐196a‐5p directly targeted ITM2B, exerting influence on the development of ESCC cells through negative regulation of ITM2B expression. Xenograft mouse models were established for conducting in vivo experiments, providing further confirmation of the regulatory mechanism and biological significance of the miR‐196a‐5p/ITM2B axis in ESCC. Our research demonstrated miR‐196a‐5p promoted ESCC malignant progression by interacting with ITM2B, thereby providing novel clues and potential targets for the new diagnosis and thereby of ESCC.
Molecular mechanisms underlying coordinated responses of plants to shade and environmental stresses
Authors: Han Run , Ma Liang , Terzaghi William , Guo Yan , Li Jigang 
Published: January 2024

SUMMARYShade avoidance syndrome (SAS) is triggered by a low ratio of red (R) to far‐red (FR) light (R/FR ratio), which is caused by neighbor detection and/or canopy shade. In order to compete for the limited light, plants elongate hypocotyls and petioles by deactivating phytochrome B (phyB), a major R light photoreceptor, thus releasing its inhibition of the growth‐promoting transcription factors PHYTOCHROME‐INTERACTING FACTORs. Under natural conditions, plants must cope with abiotic stresses such as drought, soil salinity, and extreme temperatures, and biotic stresses such as pathogens and pests. Plants have evolved sophisticated mechanisms to simultaneously deal with multiple environmental stresses. In this review, we will summarize recent major advances in our understanding of how plants coordinately respond to shade and environmental stresses, and will also discuss the important questions for future research. A deep understanding of how plants synergistically respond to shade together with abiotic and biotic stresses will facilitate the design and breeding of new crop varieties with enhanced tolerance to high‐density planting and environmental stresses.
Parametric Influence on the Thermofluidic Characteristics of the Branched Wavy Heat Sink
Authors: Kumar Ritesh , Tiwary Badyanath , Singh Pawan Kumar 
Published: January 2024

Abstract
The branched wavy heat sink (BWHS) is found as a novel design for heat sink application. The aim of this paper is first to investigate the optimum branch angle by varying the branch angle while keeping the constant parametric value such as pitch, wavelength, and secondary width; the idea was established, and we found that a 45-deg branch angle is the best among other branch angles. After that, we varied the next important parametric value, i.e., secondary width, to know the optimum secondary width. Four secondary pass angle (branch angle) configurations (25 deg, 35 deg, 45 deg, and 55 deg) were proposed and numerically investigated by keeping the constant parametric value. The RNG k–ɛ model has been employed with the full domain model approach in the computational analysis. Further, the optimum branch angle has also been investigated with the varying secondary width. The secondary flowrates were strongly affected in all the cases. The pressure loss increases as the secondary pass angle increases. However, a secondary pass maintains pressure uniformity in the spanwise direction through flow migration. It is clear that raising the secondary pass angle reduces the hot spot region. Finally, the optimum branch angle has also been investigated with varying secondary widths of 0.5 mm, 0.25 mm, and 0.20 mm. According to the thermofluidic study, the BWHS design with 45-deg angle and 0.25-mm secondary width has better heat convection performance among all. With a 2% volumetric concentration of nanofluid, the heat transfer rate improves by about 10% compared to water. As a result, the 45-deg BWHS presents a viable avenue for further study. The heat transfer rate of the microchannel heat sink (MCHS) is greatly aided by secondary flow mixing. The branched wavy heat sinks (BWHSs) under forced convection with water/Al2O3 under the Re = 100–500 have been investigated.
Lipwall Effects on a Shore-Front Oscillating Water Column Based on DBEM and Computational Fluid Dynamic Approaches
Authors: Narendran Kumar , Vijay K. G. 
Published: January 2024

Abstract
The oscillating water column (OWC) is an economical and feasible type of wave energy converter with minimal maintenance costs which have been widely investigated. In this study, the effect of lipwalls for a shore-front OWC is investigated using dual boundary equation method (DBEM) and computational fluid dynamics (CFD) approaches. The boundary value problem is solved using the DBEM method within the framework of linear water wave theory. Whilst in the CFD approach, the volume-of-fluid (VOF) approach is used for simulating the numerical wave tank, with appropriate boundary conditions and regular wave inlet. The DBEM approach is beneficial to understand the complex phenomena inside the chamber, viz., radiation conductance and susceptance. It is inferred that case-B (vertical + shoreward-slant lipwall) is found to exhibit better performance for a wider range of non-dimensional wave frequencies due to its wave trapping configuration where the position of the lower lipwall is orthogonal. The CFD studies provide interesting insights into the optimal damping ratio concerning wave amplification factor at higher relative water depths, power output, and correlation of phase difference. Besides, the study reveals that the pressure and wave elevation inside the chamber are associated with the inhalation and exhalation process of air is attributed to the lower half of the lipwall.
Centrifuge Modeling of the Performance of Suction Anchor in Soft Clay
Authors: Fu Dongkang , Lai Ying , Xiong Gen , Zhu Bin 
Published: January 2024

Abstract
Suction anchors are large cylindrical anchors and well suited for both catenary and taut mooring systems. The determination of horizontal and vertical load components hinges upon factors such as the inclined loading angle and the padeye position, significantly influencing its failure mechanism. This study undertook a series of geotechnical centrifuge tests to scrutinize the behavior of suction anchor under lateral loading. Precise measurements were taken for variables including the pore pressure at the anchor tip, soil pressure along the anchor, anchor capacity, as well as the displacement and rotation around X-, Y-, and Z-axes. The anchor failure mechanisms and interaction coefficients within a dissipation function were determined from the experimental results. The failure angle β serves as an indicator of anchor rotation in the translational failure mechanism, and αr describes anchor rotation in backward and forward movements. Under the inclined loading angle (θm) of 35 deg, the anchor failed in the translational mechanism, with its ultimate bearing capacity surpassing that of the anchor failing through backward and forward mechanisms. Upon elevating the padeye location moved upward to 4L/7 to 2L/3, the anchor failed in a forward mechanism, accompanied by a significant decrease in soil pressure on the passive side. This separation of the soil plug from the anchor, driven by accumulated displacement and rotation, resulted in 25% decrease in ultimate bearing capacity. Conversely, when the inclined loading reduced from 35 deg to 20 deg at the padeye location, the anchor failed in a backward mechanism, with no observed separation of the soil plug from the anchor.
Simulation and Experimental Study on Crack Propagation in Slewing Bearing Steel
Authors: Jiang Shuxin , Du Jing , Wang Shuang , Li Chang 
Published: January 2024

Abstract
The study investigated the propagation characteristics of surface-initiated cracks in slewing bearing steel and analyzed the influence of initial crack length and orientation on crack propagation. A cohesive zone model incorporating continuum damage mechanics was established to simulate crack propagation under rolling contact cyclic loading. Rolling wear and contact fatigue tests were conducted using a rolling contact fatigue test machine to analyze crack propagation under different load cycle numbers. By comparing simulation results with experimental outcomes, the effectiveness of the theoretical analysis was validated.