bluuebunny/crossref_metadata_2025_split huggingface dataset:
Asymmetric and parallel subgenome selection co-shape common carp domestication
Authors: Wang Min , Li Xinxin , Wang Chongnv , Zou Ming , Yang Jing , Li Xiang-dong , Guo Baocheng 
Published: January 2024

AbstractBackgroundThe common carp (Cyprinus carpio) might best represent the domesticated allopolyploid animals. Although subgenome divergence which is well-known to be a key to allopolyploid domestication has been comprehensively characterized in common carps, the link between genetic architecture underlying agronomic traits and subgenome divergence is unknown in the selective breeding of common carps globally.ResultsWe utilized a comprehensive SNP dataset in 13 representative common carp strains worldwide to detect genome-wide genetic variations associated with scale reduction, vibrant skin color, and high growth rate in common carp domestication. We identified numerous novel candidate genes underlie the three agronomically most desirable traits in domesticated common carps, providing potential molecular targets for future genetic improvement in the selective breeding of common carps. We found that independently selective breeding of the same agronomic trait (e.g., fast growing) in common carp domestication could result from completely different genetic variations, indicating the potential advantage of allopolyploid in domestication. We observed that candidate genes associated with scale reduction, vibrant skin color, and/or high growth rate are repeatedly enriched in the immune system, suggesting that domestication of common carps was often accompanied by the disease resistance improvement.ConclusionsIn common carp domestication, asymmetric subgenome selection is prevalent, while parallel subgenome selection occurs in selective breeding of common carps. This observation is not due to asymmetric gene retention/loss between subgenomes but might be better explained by reduced pleiotropy through transposable element-mediated expression divergence between ohnologs. Our results demonstrate that domestication benefits from polyploidy not only in plants but also in animals.
Carrier frequency estimation of pathogenic variants of autosomal recessive and X-linked recessive mendelian disorders using exome sequencing data in 1,642 Thais
Authors: Chetruengchai Wanna , Phowthongkum Prasit , Shotelersuk Vorasuk 
Published: January 2024

Abstract
Background
People with autosomal recessive disorders often were born without awareness of the carrier status of their parents. The American College of Medical Genetics and Genomics (ACMG) recommends screening 113 genes known to cause autosomal recessive and X-linked conditions in couples seeking to learn about their risk of having children with these disorders to have an appropriate reproductive plan.

Methods
We analyzed the exome sequencing data of 1,642 unrelated Thai individuals to identify the pathogenic variant (PV) frequencies in genes recommended by ACMG.

Results
In the 113 ACMG-recommended genes, 165 PV and likely PVs in 60 genes of 559 exomes (34%, 559/1642) were identified. The carrier rate was increased to 39% when glucose-6-phosphate dehydrogenase (G6PD) was added. The carrier rate was still as high as 14.7% when thalassemia and hemoglobinopathies were excluded. In addition to thalassemia, hemoglobinopathies, and G6PD deficiency, carrier frequencies of > 1% were found for Gaucher disease, primary hyperoxaluria, Pendred syndrome, and Wilson disease. Nearly 2% of the couples were at risk of having offsprings with the tested autosomal recessive conditions.

Conclusions
Based on the study samples, the expanded carrier screening, which specifically targeted common autosomal recessive conditions in Thai individuals, will benefit clinical outcomes, regarding preconception/prenatal genetic carrier screening.
TEP SNORD12B, SNORA63, and SNORD14E as novel biomarkers for hepatitis B virus-related hepatocellular carcinoma (HBV-related HCC)
Authors: Zhao Xuan , Chen Guanxuan , Wu Yawen , Li Xiao , Zhang Zhe , Xie Li , Song Xianrang , Song Xingguo 
Published: January 2024

Abstract
Purpose
The alterations of RNA profile in tumor-educated platelets (TEPs) have been described as a novel biosource for cancer diagnostics. This study aimed to explore the potential snoRNAs in TEP as biomarkers for diagnostics of hepatitis B virus-related hepatocellular carcinoma (HBV-related HCC).

Methods
Platelets were isolated using low-speed centrifugation and subjected to a quantitative polymerase chain reaction (qPCR) for snoRNAs detection.

Results
Down-regulated SNORD12B and SNORD14E as well as up-regulated SNORA63 were identified in TEP from HBV-related HCC, which could act as diagnostic biomarkers for HBV-related HCC as well as the early disease. Besides, TEP SNORD12B, SNORD14E, and SNORA63 facilitate the diagnostic performance of AFP and achieve favorable diagnostics efficiency for HBV-related HCC when combined with platelet parameters.

Conclusions
Aberrant expression of SNORD12B, SNORA63, and SNORD14E in TEPs could serve as the novel and non-invasive biomarkers for HBV-related HCC diagnosis.
Urban–rural differences in seasonal malaria chemoprevention coverage and characteristics of target populations in nine states of Nigeria: a comparative cross-sectional study
Authors: Ibinaiye Taiwo , Rotimi Kunle , Balogun Ayodeji , Aidenagbon Adaeze , Oguoma Chibuzo , Baker Kevin , Ogunmola Olabisi , Oresanya Olusola , Rassi Christian , Nnaji Chuks 
Published: January 2024

Abstract
Background
Differences between urban and rural contexts in terms of sociodemographic characteristics, geographical features and risk perceptions may lead to disparities in coverage and related outcomes of community-based preventive interventions, such as seasonal malaria chemoprevention (SMC). This study investigated urban–rural differences in SMC coverage and other programme outcomes, as well as child and caregiver characteristics of target populations in nine implementing states in Nigeria during the 2022 SMC round.

Methods
This is a comparative cross-sectional study based on comprehensive end-of-round household surveys conducted in nine states where SMC was delivered in Nigeria in 2022. Data of 11,880 caregiver-child pairs were included in the analysis. Rural-urban differences in SMC outcomes and child and caregiver characteristics were assessed, first by using Pearsons’ chi-square test for independence for categorical variables. Univariate multilevel mixed-effect logistic regression models, with random intercepts for cluster units, were used to quantify the strength of association between location and each SMC coverage and related outcomes.

Results
Significant urban-rural differences were observed in caregivers’ sociodemographic characteristics, such as age, gender, level of education, occupation status and health-seeking behaviour for febrile childhood illnesses. Disparities were also seen in terms of SMC coverage and related outcomes, with lower odds of the receipt of Day 1 dose direct observation of the administration of Day 1 dose by community distributors, receipt of the full three-day course of SMC medicines and receipt of SMC in all cycles of the annual round among children residing in urban areas, compared with those residing in rural areas. Similarly, urban-dwelling caregivers had lower odds of being knowledgeable of SMC and believing in the protective effect of SMC than rural-dwelling caregivers.

Conclusion
Findings highlight observable urban-rural disparities in SMC programme delivery and related outcomes, as well as target population characteristics, underscoring the need for context-specific strategies to ensure optimal delivery of SMC and improve programme implementation outcomes in urban settings.
Elevated first-trimester neutrophil elastase and proteinase 3 increase the risk of gestational diabetes mellitus and adverse fetal outcomes
Authors: Wang Lihong , Zhou Zhoujunhao , Xu Xinming , Li Yue , Zhang Rui , Yu Zhiyan , Huang Xinmei , Zang Shufei , Sun Tiange 
Published: January 2024

Abstract
Background
Chronic inflammation plays a vital role in the development of gestational diabetes mellitus (GDM). Studies in mouse models show that neutrophil serine proteases (NSPs), neutrophil elastase (NE) and proteinase-3 (PR3) are important drivers of chronic inflammation with consequent metabolic disturbances. This study evaluated the association of NE and PR3 with GDM development and adverse fetal outcomes.

Method(s)
This was a prospective cohort study. Serum PR3 and NE concentration was measured in all enrolled pregnant women in the first and the second trimester to determine the connection between NSPs and GDM and adverse fetal outcomes. Logistic regression, spline regression and linear regression analyses were applied to investigate the association of NE or PR3 with GDM development and adverse fetal outcomes. The concentration of NE and PR3 in placental biopsies was evaluated by semi-quantitative analysis of immunohistochemistry staining.

Result(s)
NE or PR3 concentration in the first trimester, rather than the second, increased more significantly in women with GDM than in those without, regardless of pre-pregnancy body mass index and age. There was a stepwise increase in GDM occurrence as well as comprehensive adverse fetal outcomes across tertiles of NE and PR3. NE and PR3 were positively associated with neutrophil count, pre-pregnancy BMI, plasma glucose level and newborn weight. Logistic regression revealed NE or PR3 to be independent risk factors for the development of GDM and comprehensive adverse fetal outcomes. Spline regression showed a significant increased risk of GDM occurrence and comprehensive adverse fetal outcomes when serum NE concentration exceeded 417.60 ng/mL and a similar result for PR3 and GDM occurrence when the latter exceeded 88.52 ng/mL. Immunohistochemistry data confirmed that enriched NE and PR3 content in placental tissue may have contributed to the development of GDM.

Conclusion(s)
This work demonstrates that excessive first-trimester NE and PR3 increase the risk of GDM development and comprehensive adverse fetal outcomes.
The impact of COVID-19 on the mental and sexual health of patients with infertility: a prospective before-and-after study
Authors: Qi Jing , Sun Meng , Yue Xingchen , Hong Xintong , Dong Meng , Tan Jichun 
Published: January 2024

Abstract
Background
The coronavirus disease (COVID-19) pandemic has seriously impacted the mental and sexual health of the general population. Patients dealing with infertility constitute a unique subset within society, susceptible to heightened sensitivity amid pressures and crises. However, to the best of our knowledge, the impact of the different stages of the COVID-19 pandemic on the mental and sexual health of patients with infertility has not been investigated. Therefore, this study aimed to investigate the mental and sexual health of patients with infertility during different stages of the COVID-19 pandemic (during the lockdown, when controls were fully liberalized, and during the post-pandemic era).

Methods
This prospective before-and-after study was conducted between April and May 2022 (during the lockdown), December and January 2023 (when controls were fully liberalized), and May and August 2023 (during the post-pandemic era). This study explored the sexual and mental health of women with infertility during the three stages of the COVID-19 pandemic using standardized mental health and sexual function questionnaires. The Chi-square test was used to compare categorical data, and the ANOVA test was used to compare numerical data.

Results
Patients had the highest 7-item Generalized Anxiety Disorder Scale (GAD-7) and 9-item Patient Health Questionnaire (PHQ-9) scores and the highest rates of anxiety and depression during the immediate full-release phase. During the complete liberalization phase, patients had the lowest Female Sexual Function Index (FSFI) scores and the highest incidence of sexual dysfunction.

Conclusion
This study is the first one to report the repercussions of COVID-19 on the mental and sexual well-being of individuals experiencing infertility across various phases of the pandemic. Upon the complete lifting of control measures, close to 99% of participants exhibited varying degrees of anxiety and depression. Our research underscores that individuals with infertility faced elevated levels of anxiety, depression, and sexual dysfunction during the phase of full liberalization of COVID-19 control measures, in stark contrast to the periods of lockdown and the post-pandemic era.
Ferroptosis: a promising candidate for exosome-mediated regulation in different diseases
Authors: Liu Limin , Ye Yulin , Lin Rui , Liu Tianyu , Wang Sinan , Feng Zelin , Wang Xiaoli , Cao Hailong , Chen Xin , Miao Junming , Liu Yifei , Jiang Kui , Han Zhibo , Li Zongjin , Cao Xiaocang 
Published: January 2024

AbstractFerroptosis is a newly discovered form of cell death that is featured in a wide range of diseases. Exosome therapy is a promising therapeutic option that has attracted much attention due to its low immunogenicity, low toxicity, and ability to penetrate biological barriers. In addition, emerging evidence indicates that exosomes possess the ability to modulate the progression of diverse diseases by regulating ferroptosis in damaged cells. Hence, the mechanism by which cell-derived and noncellular-derived exosomes target ferroptosis in different diseases through the system Xc−/GSH/GPX4 axis, NAD(P)H/FSP1/CoQ10 axis, iron metabolism pathway and lipid metabolism pathway associated with ferroptosis, as well as its applications in liver disease, neurological diseases, lung injury, heart injury, cancer and other diseases, are summarized here. Additionally, the role of exosome-regulated ferroptosis as an emerging repair mechanism for damaged tissues and cells is also discussed, and this is expected to be a promising treatment direction for various diseases in the future.
Small-molecule agonist AdipoRon alleviates diabetic retinopathy through the AdipoR1/AMPK/EGR4 pathway
Authors: Wang Yihan , Liu Yujuan , Fang Junwei , Xing Xindan , Wang Hanying , Shi Xin , Liu Xinyi , Niu Tian , Liu Kun 
Published: January 2024

Abstract
Background
Diabetes mellitus (DM) is a progressive disease that involves multiple organs due to increased blood glucose, and diabetic retinopathy (DR) is the main complication of DM in the eyes and causes irreversible vision loss. In the pathogenesis of diabetic vascular disease, oxidative stress caused by hyperglycemia plays an important role in Müller cell impairment. In recent years, AdipoRon, an adiponectin analog that demonstrated important physiological functions in obesity, diabetes, inflammation, and cardiovascular diseases, demonstrated cellular protection from apoptosis and reduced inflammatory damage through a receptor-dependent mechanism. Here, we investigated how AdipoRon reduced oxidative stress and apoptosis in Müller glia in a high glucose environment.

Results
By binding to adiponectin receptor 1 on Müller glia, AdipoRon activated 5ʹ adenosine monophosphate-activated protein kinase (AMPK)/acetyl-CoA carboxylase phosphorylation downstream, thereby alleviating oxidative stress and eventual apoptosis of cells and tissues. Transcriptome sequencing revealed that AdipoRon promoted the synthesis and expression of early growth response factor 4 (EGR4) and inhibited the cellular protective effects of AdipoRon in a high-glucose environment by reducing the expression of EGR4. This indicated that AdipoRon played a protective role through the EGR4 and classical AMPK pathways.

Conclusions
This provides a new target for the early treatment of DR.

Graphical Abstract
Recent advances of engineered oncolytic viruses-based combination therapy for liver cancer
Authors: Zhang Junhe , Xiao Yunxi , Zhang Jie , Yang Yun , Zhang Liao , Liang Fan 
Published: January 2024

AbstractLiver cancer is a major malignant tumor, which seriously threatens human health and increases the economic burden on patients. At present, gene therapy has been comprehensively studied as an excellent therapeutic measure in liver cancer treatment. Oncolytic virus (OV) is a kind of virus that can specifically infect and kill tumor cells. After being modified by genetic engineering, the specificity of OV infection to tumor cells is increased, and its influence on normal cells is reduced. To date, OV has shown its effectiveness and safety in experimental and clinical studies on a variety of tumors. Thus, this review primarily introduces the current status of different genetically engineered OVs used in gene therapy for liver cancer, focuses on the application of OVs and different target genes for current liver cancer therapy, and identifies the problems encountered in OVs-based combination therapy and the corresponding solutions, which will provide new insights into the treatment of liver cancer.
Partial loss of Sorting Nexin 27 resembles age- and Down syndrome-associated T cell dysfunctions
Authors: Rodriguez-Rodriguez Cristina , González-Mancha Natalia , Ochoa-Echeverría Ane , Liébana Rosa , Merida Isabel 
Published: January 2024

Abstract
Background
Sorting Nexin 27 (SNX27)-retromer complex facilitates cargo recycling from endosomes to the plasma membrane. SNX27 downregulation in neurons, as the result of Trisomy 21 (T21), has been linked with cognitive deficits due to impairment of AMPA and NMDA receptor recycling. Studies in human T cell lines likewise demonstrated that SNX27 regulates the correct delivery of cargoes to the immune synapse limiting the activation of pro-inflammatory pathways. Nevertheless, the physiological consequences of partial SNX27 loss in T cell homeostasis are still unclear.

Results
In this study, we have explored the consequences of T cell specific partial SNX27 downregulation in mice. T cells with partial SNX27 deficiency show a marked deficit in the CD4+ T cell pool, a hallmark of aging in mice and humans, and a well-characterized comorbidity of individuals with Down syndrome (DS). When analyzed ex vivo, CD4+ T cells with partial SNX27 deletion demonstrate enhanced proliferation but diminished IL-2 production. In contrast, the CD8+ population show enhanced expression of pro-inflammatory cytokines and lytic enzymes.

Conclusions
This mouse model supports the relevance of SNX27 in the organization of the immune synapse, previously described in cell lines, as well as in the control of T cell homeostasis. Individuals with DS experiment an acceleration of the aging process, which particularly affects the immune and central nervous systems. Thus, we hypothesize that reduced SNX27 expression in DS could contribute to the dysregulation of these systems and further research in SNX27 will shed light on the molecular factors underlying the phenotypes observed in people with DS and its contribution to aging.
Statistical evaluation of tongue capability with visual feedback
Authors: Bratland Veronica , Coda Kyle , Merei Mohamad , Ahmadian Leila , Babbitt Edna M. , Patton James. L. , Esmailbeigi Hananeh 
Published: January 2024

Abstract
Background
Analysis of tongue movement would benefit from a reference showcasing healthy tongue capability. We aimed to develop a reference of tongue capability and evaluated the role of visual feedback on the expression of movement.

Methods
Using a wireless tracking intraoral wearable device, we composed probability distributions of the tongue tip as subjects were asked to explore the entire sensing surface area. Half of the 32 subjects received live visual feedback of the location of the center of the tongue tip contact.

Results
We observed that the visual feedback group was 51.0% more consistent with each other in the position domain, explored 21.5% more sensing surface area, and was 50.7% more uniformly distributed. We found less consistent results when we evaluated velocity and acceleration.

Conclusion
Visual feedback best established a healthy capability reference which can be used for designing new interfaces, quantifying tongue ability, developing new diagnostic and rehabilitation techniques, and studying underlying mechanisms of tongue motor control.
Photoinactivation of the bacteriophage PhiX174 by UVA radiation and visible light in SM buffer and DMEM-F12
Authors: Sommerfeld Florian , Weyersberg Laura , Vatter Petra , Hessling Martin 
Published: January 2024

Abstract
Objective
It has been observed that viruses can be inactivated by UVA radiation and visible light. The aim of this study is to investigate whether a medium that contains a photosensitizer might have an influence on viral reduction under irradiation by UVA, violet or blue light. Test virus is the bacteriophage PhiX174 in the photosensitizer-free SM buffer and DMEM-F12, which contains the known photosensitizer riboflavin.

Results
The determined PhiX174 D90 doses in SM buffer and DMEM were 36.8 J/cm² and 13.6 J/cm² at 366 nm, 153.6 J/cm² and 129.1 J/cm² at 408 nm and 4988 J/cm² and 2477.1 J/cm² at 455 nm, respectively. It can be concluded that the medium has a large influence on the results. This might be caused by the photosensitizer riboflavin in DMEM-F12. As riboflavin is a key component in many cell culture media, irradiation experiments with viruses in cell culture media should be avoided if the investigation of intrinsical photoinactivation properties of viruses is aimed for.
Gene function annotations for the maize NAM founder lines
Authors: Fattel Leila , Yanarella Colleen F. , Ngara Blessing , Johnson Olivia T. , Campbell Darwin A. , Wimalanathan Kokulapalan , Lawrence-Dill Carolyn J. 
Published: January 2024

Abstract
Objectives
We annotated the latest published sequences of the 26 Zea mays Nested Association Mapping (NAM) founder lines using GOMAP, the Gene Ontology Meta Annotator for Plants. The maize NAM panel enables researchers to understand and identify the genetic basis of complex traits. Annotations of predicted functions for genes can help researchers investigate gene-phenotype associations, prioritize candidate genes for phenotypes of interest, and formulate testable hypotheses about gene function/phenotype associations. The creation and release of high-confidence, high-coverage gene function annotation sets for the NAM founder lines is critical to accelerate the generation of knowledge in maize genetics research. GOMAP is a high-throughput computational pipeline that annotates gene functions genome-wide in plant genomes using Gene Ontology functional class terms. Here we report and share GOMAP-generated functional annotations for the NAM founder lines.

Data description
Datasets include the protein sequences used as input, GOMAP-generated annotation files, scripts used to update obsolete terms, and GAF-formatted tab-delimited text files of gene function annotations along with README files that describe formatting, content, and how files relate to each other.
First report of Cryptosporiopsis tarraconensis causing leaf lesion of Corylus avellana in Central Europe (Poland)
Authors: Patejuk Katarzyna , Baturo-Cieśniewska Anna , Kaczmarek-Pieńczewska Agata , Piegdoń Amelia , Fałtynowicz Wiesław , Wasilewska Pola , Ogonowska Magdalena 
Published: January 2024

Abstract
Key message
As a result of our research, we determined that Cryptosporiopsis tarraconensis—as a new species for Central Europe—is the causative agent of leaf lesions in natural populations of hazel (Corylus avellana). Until now, this species had not been described in a natural population of C. avellana or out of the temperate climate. This is the fifth notification of this rare fungus in the world and the first from Central Europe and the natural population of the host.