bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evolution of Skipper (SK), a family of DD34E/Tc1 transposons, in animals
Authors: Wang Saisai , Guan Zhongxia , Diaby Mohamed , Asare Emmanuel , Ullah Numan , Jia Wenzhu , Gao Bo , Yu Duonan , Song Chengyi 
Published: October 2023

Abstract
High diversity and differential evolution profiles have been observed for DD34E/Tc1 transposons; several families originating from these groups, such as DD34E/ZB, DD34E/SB, DD35E/TR, DD36E/IC, and DD38E/IT, have been well defined. Even though Frisky, Tiang, Tsessebe, and Topi transposons have been identified in Anopheles gambiae, their taxonomic distribution and phylogenetic relationship in nature remain largely unknown. The evolutionary profiles of Frisky, Tiang, Tsessebe, and Topi homology transposons were investigated in the current study. In total, 254 homology transposons of Frisky, Tiang, Hob, Tsessebe, and Topi were obtained in 200 species by data mining. The phylogenetic tree revealed that these transposons were classified into five main clades (Frisky, Tiang, Hob, Tsessebe, and Topi) forming a monophyletic clade with 98% bootstrap support, belonging to the DD34E/Tc1 group, and named as Skipper (SK). SK transposons show a wide distribution in animals; however, differential taxonomic distribution patterns were observed for the subfamilies of Frisky, Tiang, Hob, Tsessebe, and Topi; extensive invasion of Frisky in animals was found, whereas Tiang, Hob, Tsessebe, and Topi were mainly detected in Diptera. SK elements share a similar structural organization and display high sequence identities across subfamilies. Evolutionary dynamics and structural analysis revealed that SKs in some species, such as Bombyx mori, Lordiphosa magnipectinata, Carassius gibelio, Triplophysa dalaica, and Silurus glanis, have recently evolved and present as intact copies, indicating that SKs in these genomes may be active. Together, these observations improve our understanding of the diversity of DD34E/Tc1 transposons and their impacts on genome evolution in animals.
Value Compatibility: Work–Family Conflict, Psychological Ownership, Person–Organisation Value Congruence and Turnover Intention amongst Chinese Social Workers
Authors: Chen Yutian , Liang Zurong 
Published: October 2023

Abstract
Chinese social work has experienced a sharp rise in staff turnover. Work–family conflict is a key risk factor for employees’ turnover intention. Whilst the relationship between work–family conflict and turnover intention has been widely documented, little is known about its mediating and moderating mechanisms, especially amongst social workers in China. This study explored the mediating role of job-based and collective psychological ownership and the moderating role of person–organisation value congruence. The study drew on data from the China Social Work Longitudinal Study 2019, a nationally representative sample of 1,421 Chinese social workers (79.73 per cent female; mean age = 28.9 years old). We performed a moderated mediation analysis combining a simple slope test and the Johnson–Neyman technique. Both job-based psychological ownership and collective psychological ownership were found to mediate the association between work–family conflict and turnover intention. Person–organisation value congruence moderated the indirect relationship between work–family conflict and turnover intention via collective psychological ownership. This study enhances understanding of the impact of the psychological mechanisms of work–family conflict on Chinese social workers’ turnover intention. Specific strategies should be adopted to establish a work environment that supports psychological ownership, enhance social workers’ identification with and attachment to their organisations, and thus reduce their turnover intention.
Increased presynaptic excitability in a migraine with aura mutation
Authors: Suryavanshi Pratyush , Sawant-Pokam Punam , Clair Sarah , Brennan K C 
Published: October 2023

Abstract
Migraine is a common and disabling neurological disorder. The headache and sensory amplifications of migraine are attributed to hyperexcitable sensory circuits, but a detailed understanding remains elusive. A mutation in casein kinase 1 delta (CK1δ) was identified in non-hemiplegic familial migraine with aura and advanced sleep phase syndrome. Mice carrying the CK1δT44A mutation were more susceptible to spreading depolarization (the phenomenon that underlies migraine aura), but mechanisms underlying this migraine-relevant phenotype were not known. We used a combination of whole-cell electrophysiology and multiphoton imaging, in vivo and in brain slices, to compare CK1δT44A mice (adult males) to their wild-type littermates.
We found that despite comparable synaptic activity at rest, CK1δT44A neurons were more excitable upon repetitive stimulation than wild-type, with a reduction in presynaptic adaptation at excitatory but not inhibitory synapses. The mechanism of this adaptation deficit was a calcium-dependent enhancement of the size of the readily releasable pool of synaptic vesicles, and a resultant increase in glutamate release, in CK1δT44A compared to wild-type synapses. Consistent with this mechanism, CK1δT44A neurons showed an increase in the cumulative amplitude of excitatory post-synaptic currents, and a higher excitation-to-inhibition ratio during sustained activity compared to wild-type.
At a local circuit level, action potential bursts elicited in CK1δT44A neurons triggered an increase in recurrent excitation compared to wild-type, and at a network level, CK1δT44A mice showed a longer duration of ‘up state’ activity, which is dependent on recurrent excitation. Finally, we demonstrated that the spreading depolarization susceptibility of CK1δT44A mice could be returned to wild-type levels with the same intervention (reduced extracellular calcium) that normalized presynaptic adaptation.
Taken together, these findings show a stimulus-dependent presynaptic gain of function at glutamatergic synapses in a genetic model of migraine, that accounts for the increased spreading depolarization susceptibility and may also explain the sensory amplifications that are associated with the disease.
The Orbits of Folded Crossed Cubes
Authors: Liu Jia-Jie 
Published: October 2023

Abstract
Two vertices $u$ and $v$ in a graph $G=(V,E)$ are in the same orbit if there exists an automorphism $\phi $ of $G$ such that $\phi (u)=v$. The orbit number of a graph $G$, denoted by $Orb(G)$, is the smallest number of orbits, which form a partition of $V(G)$, in $G$. All vertex-transitive graphs $G$ are with $Orb(G)=1$. Since the $n$-dimensional hypercube, denoted by $Q_{n}$, is vertex-transitive, it follows that $Orb(Q_{n})=1$ for $n\geq 1$. Pai, Chang, and Yang proved that the $n$-dimensional folded crossed cube, denoted by $FCQ_{n}$, is vertex-transitive if and only if $n\in \{1,2,4\}$, namely $Orb(FCQ_{1})=Orb(FCQ_{2})=Orb(FCQ_{4})=1$. In this paper, we prove that $Orb(FCQ_{n})=2^{\lceil \frac{n}{2}\rceil -2}$ if $n\geq 6$ is even and $Orb(FCQ_{n}) = 2^{\lceil \frac{n}{2}\rceil -1}$ if $n\geq 3$ is odd.
Successful treatment of frequent premature ventricular contractions and non-sustained ventricular tachycardia with verapamil and flecainide in RYR1-related myopathy: a case report
Authors: Maruo Yuji , Saito Yoshihiko , Nishino Ichizo , Takeda Atsuhito 
Published: October 2023

Abstract

Background
Ryanodine receptor 1 (RYR1)-related myopathies are a group of congenital muscle diseases caused by RYR1 mutations. These mutations may cause centronuclear myopathy, a congenital neuromuscular disorder characterized by clinical muscle weakness and pathological presence of centrally placed nuclei on muscle biopsy. Mutations in RYR2 cause ventricular arrhythmias that can be treated with flecainide; however, reports of ventricular arrhythmias in RYR1-related myopathies are rare. Herein we report a case of centronuclear myopathy with RYR1 mutations who exhibited frequent premature ventricular contractions (PVCs) and non-sustained ventricular tachycardia (NSVT), which was successfully treated with verapamil and flecainide.

Case summary
At 7 months, the patient presented neurological manifestations of hypotonia and delayed motor development. A skeletal muscle biopsy performed at age 4 years led to the diagnosis of centronuclear myopathy. At age 15 years, frequent PVCs and NSVT were identified on the electrocardiogram and 24 h Holter monitoring. Treatment with verapamil was initiated; however, it was not beneficial. Therefore, flecainide was added to the treatment, decreasing the frequency of PVCs and NSVT. Non-sustained ventricular tachycardia disappeared at the age of 21, and PVCs almost disappeared at the age of 22. Genetic testing revealed c.13216delG (p.E4406Rfs*35), c.14874G&gt;C (p.K4958N), and c.9892G&gt;A (p.A3298T) in RYR1, and the compound heterozygosity of variants was confirmed by analysis of the parents.

Discussion
This is the first report of ventricular arrhythmia associated with RYR1-related myopathy that was successfully treated with verapamil and flecainide. The combination of verapamil and flecainide may be a useful treatment option for ventricular arrhythmias in patients with RYR1-related myopathies.
Adult height improved over decades in patients with X-linked hypophosphatemia: a cohort study
Authors: Boros Emese , Ertl Diana-Alexandra , Berkenou Jugurtha , Audrain Christelle , Lecoq Anne Lise , Kamenicky Peter , Briot Karine , Amouroux Cyril , Zhukouskaya Volha , Gueorguieva Iva , Mignot Brigitte , Girerd Barbara , Porquet Bordes Valerie , Salles Jean Pierre , Edouard Thomas , Coutant Régis , Bacchetta Justine , Linglart Agnès , Rothenbuhler Anya 
Published: October 2023

Abstract

Objectives
The aim of this study is to analyze height after cessation of growth (final height [FH]) and its evolution over the last decades in X-linked hypophosphatemia (XLH) patients in France, as the data on natural history of FH in XLH are lacking.

Design
We performed a retrospective observational study in a large cohort of French XLH patients with available data on FH measurements.

Materials and methods
We divided patients into 3 groups according to their birth year: group 1 born between 1950 and 1974, group 2 born between 1975 and 2000, and group 3 born between 2001 and 2006, respectively, and compared their FHs.

Results
A total of 398 patients were included. Mean FHs were the following: for group 1, −2.31 ± 1.11 standard deviation score (SDS) (n = 127), 156.3 ± 9.7 cm in men and 148.6 ± 6.5 cm in women; for group 2, −1.63 ± 1.13 SDS (n = 193), 161.6 ± 8.5 cm in men and 153.1 ± 7.2 cm in women; and for group 3, −1.34 ± 0.87 SDS (n = 78), 165.1 ± 5.5 cm in men and 154.7 ± 6 cm in women. We report a significant increase in mean FH SDS over 3 generations of patients, for both men and women (P &lt; .001). Final height SDS in male (−2.08 ± 1.18) was lower than in female (−1.70 ± 1.12) (P = .002).

Conclusion
The FH of XLH patients in France increased significantly over the last decades. Even though men's FHs improved more than women's, men with XLH remain shorter reflecting a more severe disease phenotype. While the results are promising, most patients with XLH remain short leaving room for improvement.
AlexandrusPS: A User-Friendly Pipeline for the Automated Detection of Orthologous Gene Clusters and Subsequent Positive Selection Analysis
Authors: Ceron-Noriega Alejandro , Schoonenberg Vivien A C , Butter Falk , Levin Michal 
Published: October 2023

Abstract
The detection of adaptive selection in a system approach considering all protein-coding genes allows for the identification of mechanisms and pathways that enabled adaptation to different environments. Currently, available programs for the estimation of positive selection signals can be divided into two groups. They are either easy to apply but can analyze only one gene family at a time, restricting system analysis; or they can handle larger cohorts of gene families, but require considerable prerequisite data such as orthology associations, codon alignments, phylogenetic trees, and proper configuration files. All these steps require extensive computational expertise, restricting this endeavor to specialists. Here, we introduce AlexandrusPS, a high-throughput pipeline that overcomes technical challenges when conducting transcriptome-wide positive selection analyses on large sets of nucleotide and protein sequences. The pipeline streamlines 1) the execution of an accurate orthology prediction as a precondition for positive selection analysis, 2) preparing and organizing configuration files for CodeML, 3) performing positive selection analysis using CodeML, and 4) generating an output that is easy to interpret, including all maximum likelihood and log-likelihood test results. The only input needed from the user is the CDS and peptide FASTA files of proteins of interest. The pipeline is provided in a Docker image, requiring no program or module installation, enabling the application of the pipeline in any computing environment. AlexandrusPS and its documentation are available via GitHub (https://github.com/alejocn5/AlexandrusPS).
Assessment of Physical Resilience Using Residual Methods and Its Association With Adverse Outcomes in Older Adults
Authors: Zhang Hui , Hao Meng , Li Yi , Hu Zixin , Liu Zuyun , Jiang Shuai , Jin Li , Wang Xiaofeng 
Published: October 2023

Abstract

Background and Objectives
Physical resilience (PR) is recognized as the ability to recover from the adverse effects of a stressor. However, there is a lack of consensus on how to optimally measure PR in older adults in general. We aimed to measure PR using residuals from regression analyses and investigated its association with adverse outcomes in older adults.

Research Design and Methods
A total of 6 508 older adults were included from the National Health and Aging Trends Study, which was a population-based prospective cohort study. PR was assessed using residual methods from a linear model regressing the short physical performance battery on clinical diseases, age, sex, race/ethnicity, and health condition. Adverse outcomes included all-cause mortality, falls, and overnight hospitalization.

Results
The mean age was 77.48 (7.84) years. Increased PR was associated with a lower risk of all-cause mortality (hazard ratio [HR] = 0.85, 95% confidence interval [CI]: 0.83–0.87). Compared to participants with reduced PR, those with normal PR had a lower risk for mortality (HR = 0.51, 95% CI: 0.46–0.56). Specifically, restricted cubic spline regression revealed a dose–response relationship between PR and all-cause mortality (p-overall &lt; .0001, p-nonlinear = .011). Additionally, we also found significant associations of increased PR with lower risks of falls (HR = 0.98, 95% CI: 0.96–0.99) and overnight hospitalization (HR = 0.98, 95% CI: 0.97–1.00).

Discussion and Implications
PR, measured by residual methods, was robustly and independently associated with all-cause mortality, falls, and overnight hospitalization. Our findings provide evidence that this approach may be a simple and feasible strategy to assess PR.
The haplotype-resolved T2T genome of teinturier cultivar Yan73 reveals the genetic basis of anthocyanin biosynthesis in grapes
Authors: Zhang Kekun , Du Mengrui , Zhang Hongyan , Zhang Xiaoqian , Cao Shuo , Wang Xu , Wang Wenrui , Guan Xueqiang , Zhou Penghui , Li Jin , Jiang Wenguang , Tang Meiling , Zheng Qiuling , Cao Muming , Zhou Yongfeng , Chen Keqin , Liu Zhongjie , Fang Yulin 
Published: October 2023

Abstract
Teinturier grapes are characterized by the typical accumulation of anthocyanins in grape skin, flesh, and vegetative tissues, endowing them with high utility value in red wine blending and nutrient-enriched foods developing. However, due to the lack of genome information, the mechanism involved in regulating teinturier grape coloring has not yet been elucidated and their genetic utilization research is still insufficient. Here, the cultivar ‘Yan73’ was used for assembling the telomere-to-telomere (T2T) genome of teinturier grapes by combining the High Fidelity (HiFi)， Hi-C and ultralong Oxford Nanopore Technologies (ONT) reads. Two haplotype genomes were assembled, at the sizes of 501.68 Mb and 493.38 Mb, respectively. In the haplotype 1 genome, the transposable elements (TEs) contained 32.77% of long terminal repeats (LTRs), while in the haplotype 2 genome, 31.53% of LTRs were detected in TEs. Furthermore, obvious inversions were identified in chromosome 18 between the two haplotypes. Transcriptome profiling suggested that the gene expression patterns in ‘Cabernet Sauvignon’ and ‘Yan73’ were diverse depending on tissues, developmental stages, and varieties. The transcription program of genes in the anthocyanins biosynthesis pathway between the two cultivars exhibited high similarity in different tissues and developmental stages, whereas the expression levels of numerous genes showed significant differences. Compared with other genes, the expression levels of VvMYBA1 and VvUFGT4 in all samples, VvCHS2 except in young shoots and VvPAL9 except in the E-L23 stage of ‘Yan73’ were higher than those of ‘Cabernet Sauvignon’. Further sequence alignments revealed potential variant gene loci and structure variations of anthocyanins biosynthesis related genes and a 816 bp sequence insertion was found in the promoter of VvMYBA1 of ‘Yan73’ haplotype 2 genome. The ‘Yan73’ T2T genome assembly and comparative analysis provided valuable foundations for further revealing the coloring mechanism of teinturier grapes and the genetic improvement of grape coloring traits.
Partitioning genetic effects on birthweight at classical human leukocyte antigen loci into maternal and fetal components, using structural equation modelling
Authors: Wang Geng , Warrington Nicole M , Evans David M 
Published: October 2023

Abstract

Background
Single nucleotide polymorphisms in the human leukocyte antigen (HLA) region in both maternal and fetal genomes have been robustly associated with birthweight (BW) in previous genetic association studies. However, no study to date has partitioned the association between BW and classical HLA alleles into maternal and fetal components.

Methods
We used structural equation modelling (SEM) to estimate the maternal and fetal effects of classical HLA alleles on BW. Our SEM leverages the data structure of the UK Biobank (UKB), which includes ∼270 000 participants’ own BW and/or the BW of their firstborn child.

Results
We show via simulation that our model yields asymptotically unbiased estimates of the maternal and fetal allelic effects on BW and appropriate type I error rates, in contrast to simple regression models. Asymptotic power calculations show that we have sufficient power to detect moderate-sized maternal or fetal allelic effects of common HLA alleles on BW in the UKB. Applying our SEM to imputed classical HLA alleles and own and offspring BW from the UKB replicated the previously reported association at the HLA-C locus and revealed strong evidence for maternal (HLA-A*03:01, B*35:01, B*39:06, P &lt;0.001) and fetal allelic effects (HLA-B*39:06, P &lt;0.001) of non-HLA-C alleles on BW.

Conclusions
Our model yields asymptotically unbiased estimates, appropriate type I error rates and appreciable power to estimate maternal and fetal effects on BW. These novel allelic associations between BW and classical HLA alleles provide insight into the immunogenetics of fetal growth in utero.
Deformations of Pairs of Kleinian Singularities
Authors: Klyuev Daniil 
Published: October 2023

Abstract
Kleinian singularities, that is, the varieties corresponding to the algebras of invariants of Kleinian groups are of fundamental importance for Algebraic geometry, Representation theory, and Singularity theory. The filtered deformations of these algebras of invariants were classified by Brieskorn (the commutative case) and Losev (the general case). To an inclusion of Kleinian groups, there is the corresponding inclusion of algebras of invariants. We classify deformations of these inclusions when the smaller subgroup is normal in the larger.
Comparative anatomy of venom glands suggests a role of maternal secretions in gall induction by cynipid wasps (Hymenoptera: Cynipidae)
Authors: Guiguet Antoine , Tooker John F , Deans Andrew R , Mikó István , Ning Gang , Schwéger Szabina , Hines Heather M 
Published: October 2023

Abstract
Many herbivorous insect species are capable of hijacking plant development to induce novel plant organs called galls. In most groups of galling insects, the insect organs and molecular signals involved in gall induction are poorly understood. We focused on gall wasps (Hymenoptera:Cynipidae), the second largest clade of gall inducers (~1,400 spp.), for which the developmental stages and organs responsible for gall development are unclear. We investigated the female metasomal anatomy of 69 gall-inducing and 29 non-gall-inducing species across each of the major lineages of Cynipoidea, to test relationships between this lifestyle and the relative size of secretory organs. We confirmed that the venom apparatus in gall-inducing species is greatly expanded, although gall-inducing lineages vary in the relative size of these glands. Among these gallers, we measured the largest venom gland apparatus relative to body size ever recorded in insects. Non-galling inquiline species are accompanied by a reduction of this apparatus. Comparative microscopic analysis of venom glands suggests varying venom gland content across the lineages. Some oak gallers also had enlarged accessory glands, a lipid-rich organ whose function remains unclear, and which has not been previously studied in relation to gall formation. Together, the massive expansion of secretory organs specifically in gall-inducing species suggests a role of these secretions in the process of gall formation, and the variance in size of venom glands, accessory glands, and the contents of these glands among gallers, suggests that gall formation across this clade is likely to employ a diversity of molecular strategies.
Evaluation of phenotypical and genotypical methods for the identification and typing of Stenotrophomonas maltophilia isolated from a pharmaceutical facility
Authors: de Miranda Rebeca Vitória da Silva Lage , Monteiro Giovanna Merrelho , da Costa Luciana Veloso , dos Santos Milena Cristina Silva , dos Reis Cristhiane Moura Falavina , Braga Lygia Maria Paulo da Silva , Forsythe Stephen James , Villas Bôas Maria Helena Simões , Brandão Marcelo Luiz Lima 
Published: October 2023

Abstract

Aims
Evaluate methods for identification and typing of Stenotrophomonas maltophilia isolated from a pharmaceutical facility.

Methods and results
From 270 S. maltophilia strains identified by VITEK®2, 40 were selected and submitted to MALDI TOF-MS, 16S and 23S rRNA gene analysis, enterobacterial repetitive intergenic consensus-polymerase chain reaction (ERIC-PCR), and an antimicrobial susceptibility profile. 16S rRNA sequencing was able to identify 39 (97.5%) strains as Stenotrophomonas spp. and one (2.5%) as Luteimonas huabeiensis. MALDI TOF-MS identified 37 (92.5%) strains as S. maltophilia, and three (7.5%) were not identified. PCR targeting 23S rRNA yielded a positive result for 39 (97.5%) strains. However, after sequencing, two strains were identified as Stenotrophomonas rhizophila, showing false-positive results. The confirmed S. maltophilia strains (n = 37) showed 35 distinct ERIC-PCR profiles and exhibited sensitivity to minocycline and levofloxacin, and six (16.3%) showed intermediate resistance to sulfamethoxazole-trimethoprim.

Conclusion
Matrix-assisted laser desorption lonization-time of flight mass spectrometry (MALDI-TOF MS) was a satisfactory methodology for the identification of S. maltophilia, but expansion of the database is necessary for the identification of other species. 16S rDNA sequencing showed low resolution for Stenotrophomonas species differentiation. PCR targeting 23S rRNA could not differentiate S. maltophilia from S. rhizophila. ERIC-PCR was shown to be a useful tool for the microbial source tracking of S. maltophilia.