bluuebunny/crossref_metadata_2025_split huggingface dataset:
A comparative analysis reveals the genomic diversity among 8 Muscovy duck populations
Authors: Li Te , Wang Yiming , Zhang Zhou , Ji Congliang , Zheng Nengzhu , Huang Yinhua 
Published: May 2024

Abstract
The Muscovy duck (Cairina moschata) is a waterfowl indigenous to the neotropical regions of Central and South America. It has low demand for concentrated feed and strong adaptability to different rearing conditions. After introduced to China through Eurasian commercial trade, Muscovy ducks have a domestication history of around 300 years in the Fujian Province of China. In the 1990s, the commodity Muscovy duck breed “Crimo,” cultivated in Europe, entered the Chinese market for consumption and breeding purposes. Due to the different selective breeding processes, Muscovy ducks have various populational traits and lack transparency of their genetic background. To remove this burden in the Muscovy duck breeding process, we analyzed genomic data from 8 populations totaling 83 individuals. We identify 11.24 million single nucleotide polymorphisms (SNPs) and categorized these individuals into the Fujian-bred and the Crimo populations according to phylogenetic analyses. We then delved deeper into their evolutionary relationships through assessing population structure, calculating fixation index (FST) values, and measuring genetic distances. Our exploration of runs of homozygosity (ROHs) and homozygous-by-descent (HBD) uncovered genomic regions enriched for genes implicated in fatty acid metabolism, development, and immunity pathways. Selective sweep analyses further indicated strong selective pressures exerted on genes including TECR, STAT2, and TRAF5. These findings provide insights into genetic variations of Muscovy ducks, thus offering valuable information regarding genetic diversity, population conservation, and genome associated with the breeding of Muscovy ducks.
Limited impact of cancer-derived gangliosides on anti-tumor immunity in colorectal cancer
Authors: van der Haar Àvila Irene , Zhang Tao , Lorrain Victor , de Bruin Florance , Spreij Tianne , Nakayama Hitoshi , Iwabuchi Kazuhisa , García-Vallejo Juan J , Wuhrer Manfred , van Kooyk Yvette , van Vliet Sandra J 
Published: May 2024

Abstract
Aberrant glycosylation is a key mechanism employed by cancer cells to evade immune surveillance, induce angiogenesis and metastasis, among other hallmarks of cancer. Sialic acids, distinctive terminal glycan structures located on glycoproteins or glycolipids, are prominently upregulated across various tumor types, including colorectal cancer (CRC). Sialylated glycans modulate anti-tumor immune responses through their interactions with Siglecs, a family of glycan-binding receptors with specificity for sialic acid-containing glycoconjugates, often resulting in immunosuppression. In this paper, we investigated the immunomodulatory function of ST3Gal5, a sialyltransferase that catalyzes the addition of α2-3 sialic acids to glycosphingolipids, since lower expression of ST3Gal5 is associated with better survival of CRC patients. We employed CRISPR/Cas9 to knock out the ST3Gal5 gene in two murine CRC cell lines MC38 and CT26. Glycomics analysis confirmed the removal of sialic acids on glycolipids, with no discernible impact on glycoprotein sialylation. Although knocking out ST3Gal5 in both cell lines did not affect in vivo tumor growth, we observed enhanced levels of regulatory T cells in CT26 tumors lacking ST3Gal5. Moreover, we demonstrate that the absence of ST3Gal5 affected size and blood vessel density only in MC38 tumors. In summary, we ascertain that sialylation of glycosphingolipids has a limited influence on the anti-tumor immune response in CRC, despite detecting alterations in the tumor microenvironment, possibly due to a shift in ganglioside abundance.
Evolution of Maternal Provisioning and Development in the Ophiuroidea: Egg Size, Larval Form, and Parental Care
Authors: Byrne Maria , Cisternas Paula , O'Hara Timothy D , Sewell Mary A , Selvakumaraswamy Paulina 
Published: May 2024

Synopsis
The Ophiuroidea is the most speciose class of echinoderms and has the greatest diversity of larval forms, but we know less about the evolution of development (evo-devo) in this group than for the other echinoderm classes. As is typical of echinoderms, evo-devo in the Ophiuroidea resulted in the switch from production of small eggs and feeding (planktotrophic) larvae to large eggs and non-feeding (lecithotrophic) larvae. Parental care (ovoviviparity or viviparity/matrotrophy) is the most derived life history. Analysis of egg data for 140 species (excluding viviparity and facultative planktotrophy) indicated a bimodal distribution in egg volume corresponding to planktotrophy and lecithotrophy + ovoviviparity, with three significant egg size groups due to the very large eggs of the ovoviviparous species. The marked reduction in fecundity in species with extremely large eggs is exemplified by the ovoviviparous species. Egg size in the two species with facultative planktotrophy was intermediate with respect to the two modes. Identifying the ancestral larval life history pattern and the pathways in the switch from feeding to non-feeding larvae is complicated by the two patterns of metamorphosis seen in species with planktotrophic development: Type I (ophiopluteus only) and Type II (ophiopluteus + vitellaria larva). The variability in arm resorption at metamorphosis across ophiuroid families indicates that the Type I and II patterns may be two ends of a morphological continuum. This variability indicates ancestral morphological plasticity at metamorphosis, followed by canalization in some taxa to the vitellaria as the metamorphic larva. Vestigial ophiopluteal traits in lecithotrophic ophioplutei and vitellaria indicate evolution from the ancestral (feeding larva) state. Parental care has evolved many times from an ancestor that had a planktonic ophiopluteus or vitellaria and is often associated with hermaphroditism and paedomorphosis. A secondary reduction in egg size occurred in the viviparous species.
Palestine as a Litmus Test for Transitional Justice
Authors: Sirleaf Matiangai V. S 
Published: May 2024

ABSTRACT∞
We are currently witnessing another sustained and significant mobilization of people across the globe, coming on the heels of the racial justice uprising of 2020. This postscript of the International Journal for Transitional Justice’s (IJTJ) Special Issue on Race, Racism and Transitional Justice reflects on whether transitional justice as a field can offer meaningful avenues for rectifying past and ongoing racial injustices, by examining the concrete and pressing example of Palestine. It argues that transitional justice has never fully grappled with the ‘question’ of Palestine, which was a live one at its birth and remains a live one today. It concludes that it is an open question whether the appeal of transitional justice to the rule of law and universal principles in the current international context can be divorced from how the rule of law operates in practice and how it selectively applies to racialized others.
Viral Genomic Variation and the Severity of Genital Herpes Simplex Virus-2 Infection as Quantified by Shedding Rate: A Viral Genome-Wide Association Study
Authors: Casto Amanda M , Song Hoseung , Xie Hong , Selke Stacy , Roychoudhury Pavitra , Wu Michael C , Wald Anna , Greninger Alexander L , Johnston Christine 
Published: May 2024

Abstract

Background
The clinical severity of genital herpes simplex virus-2 (HSV-2) infection varies widely among infected persons with some experiencing frequent genital lesions while others are asymptomatic. The viral genital shedding rate is closely associated with, and has been established as, a surrogate marker of clinical severity.

Methods
To assess the relationship between viral genetics and shedding, we assembled a set of 145 persons who had the severity of their genital herpes quantified through determination of their HSV genital shedding rate. An HSV-2 sample from each person was sequenced and biallelic variants among these genomes were identified.

Results
We found no association between metrics of genome-wide variation in HSV-2 and shedding rate. A viral genome-wide association study identified the minor alleles of 3 individual unlinked variants as significantly associated with higher shedding rate (P &lt; 8.4 × 10−5): C44973T (A512T), a nonsynonymous variant in UL22 (glycoprotein H); A74534G, a synonymous variant in UL36 (large tegument protein); and T119283C, an intergenic variant. We also found an association between the total number of minor alleles for the significant variants and shedding rate (P = 6.6 × 10−7).

Conclusions
These results add to a growing body of literature for HSV suggesting a connection between viral genetic variation and clinically important phenotypes of infection.
Effects of a manganese complex with lysine and glutamic acid on growth performance, manganese deposition, and emission, antioxidant capacity and metacarpal strength in weaned piglets
Authors: Qi Keke , Deng Bo , Ma Qian , Ji Fei , Wu Jie , Zhang Cheng , Xu Ziwei 
Published: May 2024

Abstract
The present study sought to assess the effects of manganese complexes with lysine and glutamic acid (Mn-LG) as manganese (Mn) sources on growth performance, trace element deposition, antioxidant capacity, and metacarpal strength in weaned piglets. The study involved 288 healthy Duroc × Landrace × Yorkshire piglets that were weaned at 25 to 28 d of age and weighed 8.66 ± 0.96 kg. These piglets were randomly divided into six groups: a control group (Mn-LG-0, receiving a basal diet without Mn supplementation), a Mn sulfate group (basal diet supplemented with 40 mg·kg−1 diet of Mn, Mn-S-40 group), and four Mn-LG groups (Mn-LG-20, Mn-LG-40, Mn-LG-60, Mn-LG-80, supplemented with 20, 40, 60, and 80 mg·kg−1 Mn from Mn-LG in the basal diet). Grouping began at weaning on the 0th day of the experiment. The corn–soybean-based basal diet during the early (days 0 to 14) and late (days 15 to 42) phases of the experiment contained 20.88 and 30.12 mg·kg−1 Mn, respectively. Blood samples were collected on days 14 and 42, and pigs were sacrificed for sample collection on day 42. The results indicated no significant differences in average daily gain, average daily feed intake, or feed-to-gain ratio among the groups (P &gt; 0.05). The diarrhea rates of all Mn-LG groups and the Mn-S-40 group were significantly lower in the 0 to 14 d and during the entire experimental period than in the Mn-LG-0 group (P &lt; 0.001). The Mn-LG-40 group exhibited a significant increase in liver Mn concentration and serum Mn superoxide dismutase (Mn-SOD) activity on day 42 (P &lt; 0.01), as well as a significant decrease in fecal Mn concentration (P &lt; 0.05), compared to those of the Mn-S-40 group. Significant differences (P &lt; 0.05) were detected in the serum, liver, and fecal Mn concentrations, as well as in the serum and liver Mn-SOD activity, across the different Mn-LG groups. The serum and fecal Mn concentrations and serum Mn-SOD activity increased linearly or quadratically (P &lt; 0.01) with increasing Mn-LG supplementation. No significant differences (P &gt; 0.05) were found in kidney, heart, or metacarpal bone Mn concentrations or in bone strength indices. In summary, compared with the Mn-LG-0 diet, dietary supplementation with Mn-LG enhanced serum Mn deposition and Mn-SOD activity and decreased the incidence of diarrhea. Additionally, the fecal Mn concentration was lower in the Mn-LG group than in the inorganic group at equivalent dosages.
Functional characterization of the InR/PI3K/AKT signaling pathway in female reproduction of the predatory bug Cyrtorhinus lividipennis (Hemiptera: Miridae)
Authors: Hu Kui , Jin Rong , Liu Jianqi , Zhu Jun , Dai Wei , Wang Ying , Li Yao , Liu Fang 
Published: May 2024

Abstract
The insulin signaling (IIS) pathway plays a key role in the regulation of various physiological functions in animals. However, the involvement of IIS pathway in the reproduction of natural enemy insects remains enigmatic. Here, 3 key genes (named ClInR, ClPI3K, and ClAKT) related to IIS pathway were cloned from Cyrtorhinus lividipennis (Reuter) (Hemiptera: Miridae), an important natural enemy in the rice ecosystem. These 3 proteins had the typical features of corresponding protein families and shared high similarity with their respective homologs from the Hemipteran species. The ClInR, ClPI3K, and ClAKT were highly expressed in the adult stage. Tissue distribution analysis revealed that ClInR, ClPI3K, and ClAKT were highly expressed in the midgut and ovary of adults. Silencing of ClInR, ClPI3K, and ClAKT caused 92.1%, 72.1%, and 57.8% reduction in the expression of ClVg, respectively. Depletion of these 3 genes impaired vitellogenin synthesis and ovary development. Moreover, the fecundity in the dsInR, dsPI3K, and dsAKT injected females were 53.9%, 50.8%, and 48.5% lower than the control treatment, respectively. These results indicated that ClInR, ClPI3K, and ClAKT are of great importance for the reproduction of C. lividipennis. Our results advance the knowledge about the molecular mechanism of reproduction regulation in natural enemy insects.
Waveform inversion with structural regularizing constraint based on gradient decomposition
Authors: Wang Ziying , Wang Jianhua , Sun Wenbo , Huang Jianping , Li Zhenchun , Wang Yandong 
Published: May 2024

Abstract
Full waveform inversion (FWI) can simultaneously update low-to-medium wavenumber velocity components and high-wavenumber velocity components. However, if seismic data lack large-offset data and effective low-frequency components, FWI updates will be dominated by high-wavenumber velocity perturbation. Meanwhile, providing that the initial model is inaccurate, inversion will have the problem of local minima. In this study, FWI is developed with structural regularizing constraint based on gradient decomposition (RGDFWI). By correlating the separated forward wavefield and backward wavefield with specific propagating direction, the FWI gradient is decomposed into a tomography-mode gradient and migration-mode gradient. We propose an optimized strategy taking full advantage of the two modes of FWI gradient. On the one hand, we use the tomography-mode gradient to enhance low-to-medium wavenumber updates. On the other hand, we use the migration-mode gradient to apply structural regularizing constraint by estimating structure dip and adding sparsity constraint in the seislet domain. During the inversion process, high-wavenumber structural information constrains and guides low-wavenumber model updates. The results of two numerical tests, the Marmousi model test and Overthrust model test, validate the optimized strategy, which can produce a better initial velocity model for FWI. The inversion finally generates a high-precision and high-resolution velocity model.
Investigation on the vibration characteristics of rock based on circular plate and cylinder models: dimension, geometric shape and boundary condition
Authors: Zhang Zhao , Liu Bing , Liu Jianlin 
Published: May 2024

Abstract
The declaration on the “natural frequency of rock” exists in many engineering areas, and it has caused many misunderstandings. Different from the mass-spring model usually used, the circular plate and cylinder models are respectively established to clarify the relationship between the vibration characteristics (including the natural frequency and vibration mode) and their influencing factors of rock by modal analysis. The effect of the dimension, geometric shape and boundary condition on the vibration characteristics of rock with plate structure is investigated, in which the semi-analytical solutions agree well with the simulation results. By using the cylinder model based upon the Lamé–Navier equation, the effect of such influencing factors on the vibration characteristics of the block rock sample is further studied and verified by numerical simulation and experimental results. The results suggest that the natural frequency of “rock” (including the experimental rock sample) is strongly dependent on the dimension, geometric shape and boundary condition. The resonance frequency observed in the excitation experiment is not only closely associated with the natural frequency of a specific order but also dependent on the dominance of the particular vibration mode. These findings contribute to a better understanding of the rock-breaking mechanism under dynamic loads with a certain excitation frequency.
Impairment in a member of AP2/ERF and F-box family protein enhances complete panicle exsertion in rice
Authors: Ballichatla Suneel , C. G. Gokulan , Barbadikar Kalyani M , Hake Anil A , Potupureddi Gopi , Guha Pritam Kanti , Phule Amol S , Magar Nakul D , Balija Vishalakshi , Awalellu Komal , Kokku Premalatha , Golla Suresh , Raman Meenakshi Sundaram , Ayyangari Phani Padmakumari , Gouri Shankar Laha , Ponnuvel Senguttuvel , Lella Venkata SubbaRao , Patel Hitendra K , Sonti Ramesh Venkata , Maganti Sheshu Madhav 
Published: May 2024

Abstract
Complete panicle exsertion (CPE) is an economically important quantitative trait that contributes to grain yield in rice. We deployed an integrated approach for understanding the molecular mechanism of CPE using a stable ethyl methanesulfonate mutant line, CPE-109 of the Samba Mahsuri (SM) variety of rice (Oryza sativa), which exhibits CPE. Two consistent genomic regions were identified for CPE through quantitative trait locus (QTL) mapping [qCPE-4 (28.24–31.22 Mb) and qCPE-12 (2.30–3.18 Mb)] and QTL-sequencing [chr 4 (31.21–33.69 Mb) and chr 12 (0.12–3.15 Mb)]. Two non-synonymous single nucleotide polymorphisms, namely KASP 12–12 (T→C; chr12:1269983) in Os12g0126300, encoding an AP2/ERF transcription factor, and KASP 12–16 (G→A; chr12:1515198) in Os12g0131400, encoding an F-box domain-containing protein, explained 81.05% and 59.61% of the phenotypic variance, respectively, and exhibited strong co-segregation with CPE in F2 mapping populations, advanced generation lines, and CPE-exhibiting SM mutants through KASP assays. Down-regulation of these genes in CPE-109 compared with SM (wild type) was observed in transcriptome sequencing of flag leaves, which was validated through qRT-PCR. We propose that the abrogation of Os12g0126300 and Os12g0131400 in CPE-109 combinatorially influences down-regulation of ethylene biosynthetic genes, Os01g0192900 (ACC synthase) and Os05g0497300 (ethylene-responsive factor-2), and up-regulation of a gibberellic acid synthetic gene, Os06g0569900 (ent-kaurene synthase) and the two cytokinin biosynthetic genes Os07g0486700 (cytokinin-O-glucosyltransferase 2) and Os10g0479500 (similar to carboxy-lyase), which results in complete panicle exsertion.
Mapping the Milky Way with LAMOST – IV. The large Galactic disc extending to 35 kpc
Authors: Tian Hao , Liu Chao , Li Jiadong , Zhang Bo 
Published: May 2024

ABSTRACT
We investigate extent of the disc in both vertical and radial directions by separately analysing the density and azimuthal velocity distributions using 31116 M giant stars selected from LAMOST DR5. We first measure the metallicities, radial velocities, and the distances with precision of 0.26 dex, 5.01 km s−1, and 20.8 per cent, respectively. Then, a Bayesian method is applied to model the distributions of the outer Galaxy including components of the thin, thick discs and the halo, to obtain the scale height and azimuthal velocity distributions for the thin and thick discs as a function of galactocentric distance R. The density profile of the thin disc shows that it extends out to R ∼ 35 kpc, beyond which there are no M giant stars in the halo except for Sagittarius Stream members. By using azimuthal velocity to trace the thin disc out to 26 kpc from the Galactic Centre, we show that both the density profile and azimuthal velocity decrease with Galactocentric distance R. In both the density and azimuthal velocity distributions, there is a significant breakpoint at a galactocentric distance of R ∼ 14 kpc. The scale height distribution shows that the thin disc is significantly flared, consistent with previous works. We also find that there is no significant thick disc (as traced by M giant stars) in the outer region beyond R ∼ 15.5 kpc.
Faraday rotation as a probe of radio galaxy environment in RMHD AGN jet simulations
Authors: Jerrim L A , Shabala S S , Yates-Jones P M , Krause M G H , Turner R J , Anderson C S , Stewart G S C , Power C , Rodman P E 
Published: May 2024

ABSTRACT
Active galactic nuclei (AGNs) play an integral role in galaxy formation and evolution by influencing galaxies and their environments through radio jet feedback. Historically, interpreting observations of radio galaxies and quantifying radio jet feedback has been challenging due to degeneracies between their physical parameters. In particular, it is well established that different combinations of jet kinetic power and environment density can yield indistinguishable radio continuum properties, including apparent size and Stokes I luminosity. We present an approach to breaking this degeneracy by probing the line-of-sight environment with Faraday rotation. We study this effect in simulations of three-dimensional relativistic magnetohydrodynamic AGN jets in idealized environments with turbulent magnetic fields. We generate synthetic Stokes I emission and Faraday rotation measure (RM) maps, which enable us to distinguish between our simulated sources. We find enhanced RMs near the jet head and lobe edges. We show that increasing the environment density and the average cluster magnetic field strength broadens the distribution of Faraday rotation measure values. We study the depolarization properties of our sources, finding that the hotspot regions depolarize at lower frequencies than the lobes. We quantify the effect of depolarization on the RM distribution, finding that the frequency at which the source is too depolarized to measure the RM distribution accurately is a probe of environmental properties. This technique offers a range of new opportunities for upcoming surveys, including probing radio galaxy environments and determining more accurate estimates of the AGN feedback budget.
Effectiveness of halo and galaxy properties in reducing the scatter in the stellar-to-halo mass relation
Authors: Pei Wenxiang , Guo Qi , Shao Shi , He Yi , Gu Qing 
Published: May 2024

ABSTRACT
The stellar-to-halo mass relation (SHMR) is a fundamental relationship between galaxies and their host dark matter haloes. In this study, we examine the scatter in this relation for primary galaxies in the semi-analytic l-galaxies model and two cosmological hydrodynamical simulations, EAGLE (Evolution and Assembly of Galaxies and their Environments) and TNG100-1. We find that in low-mass haloes, more massive galaxies tend to reside in haloes with higher concentration, earlier formation time, greater environmental density, earlier major mergers, and, to have older stellar populations, which is consistent with findings in various studies. Quantitative analysis reveals the varying significance of halo and galaxy properties in determining SHMR scatter across simulations and models. In EAGLE and TNG100-1, halo concentration and formation time primarily influence SHMR scatter for haloes with $M_{\rm h}\lt 10^{12}{\, \rm M_\odot }$, but the influence diminishes at high mass. Baryonic processes play a more significant role in LGal. For haloes with $M_{\rm h} \lt 10^{11}{\, \rm M_\odot }$ and $10^{12}{\, \rm M_\odot }\lt M_{\rm h}\lt 10^{13}{\, \rm M_\odot }$, the main drivers of scatter are galaxy star formation rate and age. In the $10^{11.5}{\, \rm M_\odot }\lt M_{\rm h} \lt 10^{12}{\, \rm M_\odot }$ range, halo concentration and formation time are the primary factors. And for haloes with $M_{\rm h} \gt 10^{13}{\, \rm M_\odot }$, supermassive black hole mass becomes more important. Interestingly, it is found that active galactic nucleus feedback may increase the amplitude of the scatter and decrease the dependence on halo properties at high masses.