bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Prospective Comparative Analysis to Study the Impact on Voice Changes Following Endoscopic Thyroidectomy
Authors: Kumar Arun , Dhar Anita , Srivastava Anurag , Kumar Rakesh 
Published: July 2024

Background:
Endoscopic approach has come up as a safe and feasible procedure for thyroidectomy with better cosmetic outcomes. However, concerns over its safety in terms of nerve injury and postoperative voice changes remain. This prospective study evaluated the role of vocal cord function assessment using laryngeal examination and voice analysis in patients who underwent endoscopic hemithyroidectomy either by the trans-oral endoscopic thyroidectomy vestibular approach (TOETVA) or the bilateral axillobreast approach (BABA).

Methods:
Thirty-nine consecutive patients were randomly allocated to either of the 2 groups of endoscopic hemithyroidectomy; 19 in TOETVA and 20 in the BABA groups. Vocal cord function was assessed subjectively using the GRBAS scale and objectively by acoustic analysis of parameters such as jitter, shimmer, mean frequency (F0), noise-to-harmonic ratio (NHR), and maximum phonatory time (MPT) at baseline, postoperative day 10, and 3 months after surgery.

Results:
There were no significant differences in mean GRBAS scores and values of mean frequency, jitter and shimmer between the 2 groups and on postoperative day 10 and at 3 months compared with baseline. The mean NHR and MPT showed no differences between the 2 procedures. However, there was a significant decrease in their values on day 10 postsurgery, compared with baseline. These values returned to their baseline at 3 months. The other operative parameters were comparable between the 2 groups, except for the shorter mean operative time in the TOETVA group.

Conclusions:
Perioperative quantitative voice parameters were comparable with no statistically significant difference between the 2 techniques of endoscopic thyroidectomy.
Wogonin Alleviates DCD Liver Ischemia/Reperfusion Injury by Regulating ALOX15/iNOS-mediated Ferroptosis
Authors: Jia Degong , Wu Kun , Luo Jiefu , Xu Xuesong , Pan Wei , Zhao Minjie , Li Shengwei , Gong Jianping , Gong Junhua 
Published: July 2024

Background.
Donation after circulatory death livers are more susceptible to ischemia/reperfusion injury (IRI) because of a longer period of warm ischemia. Growing evidence now suggests that ferroptosis plays a key regulatory role in the development of IRI, so targeting ferroptosis may be an effective strategy to alleviate IRI in liver transplantation (LT).

Methods.
Using donation after circulatory death LT models in rats and oxygen-glucose deprivation/reoxygenation (OGD/R) models in BRL-3A cells, we tested the effect of the Chinese medicine monomer wogonin on liver IRI and explored the specific mechanism.

Results.
Wogonin attenuated liver IRI and increased the survival rate of rats by inhibiting lipid peroxidation and ferroptosis. Mechanistically, arachidonic acid 15-lipoxygenase-1 (ALOX15) and inducible nitric oxide synthase (iNOS) were identified as potential targets of baicalein through bioinformatics analysis combined with in vivo and in vitro experiments. This result was further confirmed by molecular docking and cellular thermal shift assays. Finally, we silenced ALOX15 and iNOS in the OGD/R cell model and found that silencing ALOX15 and iNOS could reproduce the regulatory effect of wogonin and abrogate the regulatory effect of wogonin.

Conclusions.
In brief, this study emphasizes that wogonin exerts a protective effect in liver IRI through the regulation of ALOX15- and iNOS-mediated ferroptosis. ALOX15 and iNOS are potential targets for intervention in IRI induced by LT, and wogonin is a drug candidate for LT patients.
Comparative analysis of third-generation antipsychotics in first-episode schizophrenia: efficacy, safety, and cognitive impacts. A narrative review
Authors: Ricci Valerio , Sarni Alessandro , Martinotti Giovanni , Maina Giuseppe 
Published: June 2024

Background and objectives
Schizophrenia is a chronic, complex mental health disorder requiring effective management to mitigate its broad personal and societal impacts. This narrative review assesses the efficacy, effectiveness, and side effects of third-generation antipsychotics (TGAs) like aripiprazole, brexpiprazole, and cariprazine, focusing on their use in first-episode schizophrenia. These drugs aim to reduce side effects typical of earlier antipsychotics while more effectively addressing positive and cognitive symptoms.

Methods
Our extensive literature review, using PubMed and Scopus, includes randomized controlled trials and observational studies, showing TGAs may match older antipsychotics in efficacy with fewer side effects, notably in reducing extrapyramidal symptoms and enhancing cognitive outcomes.

Results
Aripiprazole appears effective in both acute and maintenance phases of schizophrenia, while brexpiprazole and cariprazine show potential in managing negative symptoms and improving social functioning, essential for patient recovery.

Conclusions
This review emphasizes the need for personalized treatment and further research to fully determine the long-term benefits and safety of TGAs. These findings can inform clinical decisions and underline the ongoing need for innovation in schizophrenia pharmacotherapy.
ComBatLS: A location- and scale-preserving method for multi-site image harmonization
Authors: Gardner Margaret , Shinohara Russell T. , Bethlehem Richard A.I. , Romero-Garcia Rafael , Warrier Varun , Dorfschmidt Lena ,   Lifespan Brain Chart Consortium, Shanmugan Sheila , Thompson Paul , Seidlitz Jakob , Alexander-Bloch Aaron F. , Chen Andrew A. 
Published: June 2024

AbstractRecent work has leveraged massive datasets and advanced harmonization methods to construct normative models of neuroanatomical features and benchmark individuals’ morphology. However, current harmonization tools do not preserve the effects of biological covariates including sex and age on features’ variances; this failure may induce error in normative scores, particularly when such factors are distributed unequally across sites. Here, we introduce a new extension of the popular ComBat harmonization method, ComBatLS, that preserves biological variance in features’ locations and scales. We use UK Biobank data to show that ComBatLS robustly replicates individuals’ normative scores better than other ComBat methods when subjects are assigned to sex-imbalanced synthetic “sites”. Additionally, we demonstrate that ComBatLS significantly reduces sex biases in normative scores compared to traditional methods. Finally, we show that ComBatLS successfully harmonizes consortium data collected across over 50 studies. R implementation of ComBatLS is available athttps://github.com/andy1764/ComBatFamily.
Evaluate the efficiency of Mr BMT in macrophage replacement of peripheral organs
Authors: Du Jinjin , Yang Baozhi , He Yang , Rao Yanxia 
Published: June 2024

AbstractThe successful replacement of endogenous tissue-resident macrophages with healthy bone marrow-derived cells through transplantation presents a promising therapeutic approach for treating disease associated with macrophage dysfunction. Our previous development of the novel microglia replacement by bone marrow transplantation (Mr BMT) method achieved high engraftment efficiency in the central nervous system (CNS), overcoming the limitation of traditional bone marrow transplantation (tBMT). In this study, we aimed to investigate the potential impacts of Mr BMT approach on peripheral organs. The Mr BMT approach involves depleting resident microglia through colony stimulating factor-1 receptor (CSF-1R) inhibition, so we first evaluated the survival of peripheral macrophages after CSF-1R inhibition. We observed that the CSF-1R antagonist, PLX5622, exerted significant elimination of peripheral tissue macrophages, albeit with lower efficiency than in the CNS. Furthermore, we discovered that Mr BMT achieved replacement efficiencies comparable to tBMT in peripheral tissues such as the liver, kidney, lung, and spleen. Our findings suggested Mr BMT is a highly efficient strategy for allogeneic macrophage replacement in both the CNS and peripheral organs, and it could have potential clinical applications.
Regulator of G Protein Signaling 14 protein expression profile in the adult mouse brain
Authors: Bramlett Sara N. , Fitzmaurice Shana M. , Harbin Nicholas H. , Yan Wuji , Bandlamudi Charan , Van Doorn G. Emme , Smith Yoland , Hepler John R. 
Published: June 2024

ABSTRACTRegulator of G protein signaling 14 (RGS14) is a multifunctional signaling protein that serves as a natural suppressor of synaptic plasticity in the mouse brain. Our previous studies showed that RGS14 is highly expressed in postsynaptic dendrites and spines of pyramidal neurons in hippocampal area CA2 of the developing mouse brain. However, our more recent work with adult rhesus macaque brain shows that RGS14 is found in multiple neuron populations throughout hippocampal area CA1 and CA2, caudate nucleus, putamen, globus pallidus, substantia nigra, and amygdala in the adult rhesus monkey brain. In the mouse brain, we also have observed RGS14 protein in discrete limbic regions linked to reward behavior and addiction, including the central amygdala and the nucleus accumbens, but a comprehensive mapping of RGS14 protein expression in the adult mouse brain is lacking. Here, we report that RGS14 is more broadly expressed in mouse brain than previously known. Intense RGS14 staining is observed in specific neuron populations of the hippocampal formation, amygdala, septum, bed nucleus of stria terminalis and ventral striatum/nucleus accumbens. RGS14 is also observed in axon fiber tracts including the dorsal fornix, fimbria, stria terminalis, and the ventrohippocampal commissure. Moderate RGS14 staining is observed in various other adjacent regions not previously reported. These findings show that RGS14 is expressed in brain regions that govern aspects of core cognitive functions such as sensory perception, emotion, memory, motivation, and execution of actions, and suggests that RGS14 may serve to suppress plasticity and filter inputs in these brain regions to set the overall tone on experience-to-action processes.
An improved tetracycline-inducible expression system for fission yeast
Authors: Lyu Xiao-Hui , Yang Yu-Sheng , Pan Zhao-Qian , Ning Shao-Kai , Suo Fang , Du Li-Lin 
Published: June 2024

AbstractThe ability to manipulate gene expression is valuable for elucidating gene function. In the fission yeastSchizosaccharomyces pombe, the most widely used regulatable expression system is thenmt1promoter and its two attenuated variants. However, these promoters have limitations, including a long lag, incompatibility with rich media, and unsuitability for non-dividing cells. Here, we present a tetracycline-inducible system free of these shortcomings. Our system features theenotetSpromoter, which achieves a similar induced level and a higher induction ratio compared to thenmt1promoter, without exhibiting a lag. Additionally, our system includes four weakenedenotetSvariants, offering an expression range similar to thenmt1series promoters but with more intermediate levels. To enhance usability, each promoter is combined with a Tet-repressor-expressing cassette in an integration plasmid. Importantly, our system can be used in non-dividing cells, enabling the development of a synchronous meiosis induction method with high spore viability. Moreover, our system allows for the shutdown of gene expression and the generation of conditional loss-of-function mutants. This system provides a versatile and powerful tool for manipulating gene expression in fission yeast.Summary statementA new inducible expression system for fission yeast enhances control, offers compatibility with non-dividing cells, and enables synchronous meiosis induction and conditional loss-of-function analysis.
100 years domestication of penaeid shrimp and meta-analysis of breeding traits
Authors: Ren Shengjie , Yáñez José M. , Perez-Enriquez Ricardo , Rye Morten , Houston Ross D. , Hurwood David A. , Gonzalez-Galaviz Jose R. , Salazar Marcela , Jerry Dean R. 
Published: June 2024

AbstractPenaeid shrimp farming plays a pivotal role in ensuring future food security and promoting economic sustainability. Compared to the extensive long history of domestication observed in terrestrial agriculture species, the domestication and selective breeding of penaeids are relatively recent endeavors. Selective breeding aimed at improving production traits holds significant promise for enhancing efficiency and reducing the environmental impact of shrimp farming, thereby contributing to its long-term sustainability. Assessing genotype-by-environment (G-by-E) interactions is essential in breeding programs to ensure that improved penaeid shrimp strains perform consistently across different production environments, with genomic selection proving more effective than sib-testing alone in mitigating environmental sensitivity. Genome editing tools like CRISPR/Cas9 offer significant potential to accelerate genetic gains in penaeid shrimp by enabling rapid introduction of desired genetic changes, with recent advancements showing promising results in achieving high transfection efficiency in shrimp embryos. Additionally, artificial intelligence and machine learning are being leveraged to streamline phenotyping and enhance decision-making in shrimp breeding and farming, improving efficiency and accuracy in managing traits and predicting disease outbreaks. Herein, we provide an overview and update on the domestication of penaeid shrimp, including the current status of domestication for principal farmed species, key milestones in domestication history, targeted breeding traits in selective breeding programs, the advantages of integrating genomeic selection for enhancing production traits, and future directions for selective breeding of penaeid shrimp.
A Computational Approach to Interpreting the Embedding Space of Dimension Reduction
Authors: Zhang Bingyuan , Uno Kohei , Kodama Hayata , Himori Koichi , Matsui Yusuke 
Published: June 2024

SummaryNonlinear dimension reduction methods are widely applied in studies analyzing gene and protein expression, by revealing patterns of discrete groups and continuous orders in high-dimensional data. However, the tools are limited to understanding the obtained embedding structures of biological mechanisms, hindering the full exploitation of data. Here, we propose a novel framework to interpret embedding systematically by identifying and mapping associated biological functions. The method performs statistical tests and visualizes significantly enriched functions essential for the organization of the embedding structure, by applying it to the embedding results of two datasets: the Genotype Tissue Expression dataset and aCaenorhabditis elegansembryogenesis dataset, one capturing distinct cluster structures and the other capturing continuous developmental trajectories. We identified the associated functions for interpreting the two embeddings and confirmed it as a useful explainable AI tool in exploratory data analysis by providing annotations to the embedding space.
The development of ecological systems along paths of least resistance
Authors: Deng Jie , Cordero Otto X. , Fukami Tadashi , Levin Simon A. , Pringle Robert M. , Solé Ricard , Saavedra Serguei 
Published: June 2024

AbstractA long-standing question in biology is whether there are common principles that characterize the development of ecological systems (the appearance of a group of taxa), regardless of organismal diversity and environmental context. Classic ecological theory holds that these systems develop following a sequenced orderly process that generally proceeds from fast-growing to slow-growing taxa and depends on life-history trade-offs. However, it is also possible that this developmental order is simply the path with the least environmental resistance for survival of the component species and hence favored by probability alone. Here, we use theory and data to show that the order from fast-to slow-growing taxa is the most likely developmental path for diverse systems when local taxon interactions self-organize to minimize environmental resistance. First, we demonstrate theoretically that a sequenced development is more likely than a simultaneous one, at least until the number of iterations becomes so large as to be ecologically implausible. We then show that greater diversity of taxa and life histories improves the likelihood of a sequenced order from fast-to slow-growing taxa. Using data from bacterial and metazoan systems, we present empirical evidence that the developmental order of ecological systems moves along the paths of least environmental resistance. The capacity of simple principles to explain the trend in the developmental order of diverse ecological systems paves the way to an enhanced understanding of the collective features characterizing the diversity of life.
β-defensin gene copy number variation in cattle
Authors: Sidekli Ozge , Oketch John , Fair Sean , Meade Kieran G. , Hollox Edward J. 
Published: June 2024

Abstractβ-defensins are peptides with antimicrobial roles, characterized by a conserved tertiary structure. Beyond antimicrobial functions, they exhibit diverse roles in both the immune response and fertility, including involvement in sperm maturation and function. Copy number variation (CNV) of β-defensin genes is extensive across mammals, including cattle, with possible implications for reproductive traits and disease resistance. In this study, we comprehensively catalogue 55 β-defensin genes in cattle. By constructing a phylogenetic tree to identify human orthologues and lineage-specific expansions, we identify 1:1 human orthologues for 35 bovine β-defensins. We also discover extensive β-defensin gene CNV across breeds, withDEFB103in particular showing extensive multiallelic CNV. By comparing β-defensin expression levels in testis from calves and adult bulls, we find that 14 β-defensins, includingDEFB103, increase in expression during sexual maturation. Analysis of β-defensin gene expression levels in the caput of adult bull epididymis, and β-defensin gene copy number, in 94 matched samples shows expression level of four β-defensins are correlated with genomic copy number, includingDEFB103. We therefore demonstrate extensive copy number variation in bovine β-defensin genes, in particularDEFB103, with potential functional consequences for fertility.
High-resolution chromosome-level genome provides molecular insights into adaptive evolution in crabs
Authors: Zhang Yin , Yuan Ye , Zhang Mengqian , Yu Xiaoyan , Qiu Bixun , Wu Fangchun , Tocher Douglas R. , Zhang Jiajia , Ye Shaopan , Cui Wenxiao , Leung Jonathan Y. S. , Ikhwanuddin Mhd , Waqas Waqas , Dildar Tariq , Ma Hongyu 
Published: June 2024

AbstractCrabs thrive in diverse ecosystems, from coral reefs to hydrothermal vents and terrestrial habitats. Here, we report a comprehensive genomic analysis of the mud crab using ultralong sequencing technologies, achieving a high-quality chromosome-level assembly. The refined 1.21 Gb genome, with an impressive contig N50 of 11.45 Mb, offers a valuable genomic resource. Gene family analysis shows expansion in development-related pathways and contraction in metabolic pathways, indicating niche adaptations. Notably, Investigation into Hox gene regulation sheds light on their role in pleopod development, with theAbd-Agene identified as a linchpin. Posttranscriptional regulation involving novel-miR1317 negatively regulatesAbd-Alevels. Furthermore, thefrugene’s potential role in ovarian development and the identification of novel-miRNA-35 as a regulator ofSpfru2add complexity to gene regulatory networks. Comparative functional analysis across Decapoda species reveals neofunctionalization of theelovl6gene in the synthesis of long-chain polyunsaturated fatty acids (LC-PUFA), suggesting its importance in environmental adaptation. These findings contribute significantly to our understanding of crab adaptability and evolutionary dynamics, offering a robust foundation for future investigations.
Zebrafish use conserved CLR and TLR signaling pathways to respond to fungal PAMPs in zymosan
Authors: Glass Erin , Robinson Stephan L. , Rosowski Emily E. 
Published: June 2024

AbstractPattern recognition receptors (PRRs) such as C-type lectin receptors (CLRs) and Toll-like receptors (TLRs) are used by hosts to recognize pathogen-associated molecular patterns (PAMPs) in microorganisms and to initiate innate immune responses. While PRRs exist across invertebrate and vertebrate species, the functional homology of many of these receptors is still unclear. In this study, we investigate the innate immune response of zebrafish larvae to zymosan, a β-glucan-containing particle derived from fungal cell walls. Macrophages and neutrophils robustly respond to zymosan and are required for zymosan-induced activation of the NF-κB transcription factor. Full activation of NF-κB in response to zymosan depends on Card9/Syk and Myd88, conserved CLR and TLR adaptor proteins, respectively. Two putative CLRs, Clec4c and Sclra, are both required for maximal sensing of zymosan and NF-κB activation. Altogether, we identify conserved PRRs and PRR signaling pathways in larval zebrafish that promote recognition of fungal PAMPs. These results inform modeling of human fungal infections in zebrafish and increase our knowledge of the evolution and conservation of PRR pathways in vertebrates.
Estimates of molecular convergence reveal pleiotropic genes underlying adaptive variation across teleost fish
Authors: Barua Agneesh , Beinsteiner Brice , Laudet Vincent , Robinson-Rechavi Marc 
Published: June 2024

AbstractTeleosts are the most diverse group of vertebrates on earth. Their diversity is a testament to the combined effects of genetic, developmental, and evolutionary forces. However, disentangling the interactions between these forces is challenging due to the complexity of the genotype-phenotype relationship and the masking of adaptive genetic signals by genetic noise. Estimates of molecular convergence where changes in the sequence of protein-coding genes lead to identical amino acid substitution across multiple lineages provide strong evidence of adaptive evolution. In this study, we estimated signals for molecular convergence in protein-coding genes across 143 teleost genomes to identify genes and processes that experienced adaptive changes. We find that genes with signals of molecular convergence are implicated in diverse processes ranging from embryonic development, tissue morphogenesis, metabolism, to hormone and heat response. Some convergent substitutions are located on functionally important sites on proteins potentially providing the molecular basis for adaptations to hypoxia, salinity fluctuations, and varying skeletal morphologies. Additionally, single-cell RNA sequencing data from zebrafish showed that the convergent genes have dynamic expression across various cell types during embryonic development. These results highlight the functional importance of the convergent genes as well as their pleiotropic nature. Although traditionally considered a source of genetic constraint, we argue that adaptation via changes in pleiotropic genes are particularly advantageous during periods of ecological shifts. We present the pleiotropic release model which describes how adaptive variation on pleiotropic genes can have large fitness effects, allowing organisms to overcome selective pressures during periods of ecological shifts.