bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of breed-specific genomic variants in Colombian Creole pig breeds by whole-genome sequencing
Authors: Mesa Rafael Suárez , Ros-Freixedes Roger , Laghouaouta Houda , Pena Ramona N. , Hernández-Ortiz Byron , Rondón-Barragán Iang , Estany Joan 
Published: December 2022

Abstract
Dissecting genetic variation of local breeds is important for the success of conservation. In this research, we investigated the genomic variation of Colombian Creole (CR) pigs, with a focus on the breed-specific variants in the exonic region of 34 genes with reported effects on adaptive and economical traits. Seven individuals of each of the three CR breeds (CM: Casco de Mula; SP: San Pedreño; and ZU: Zungo) were whole-genome sequenced along with seven Iberian (IB) pigs and seven pigs of each of the four most used cosmopolitan (CP) breeds (Duroc, Large White × Landrace, and Pietrain). Molecular variability in CR (6,451,218 variants; from 3,919,242, in SP, to 4,648,069, in CM) was comparable to that in CP, but higher than in IB. For the investigated genes, SP pigs displayed less exonic variants (178) than ZU (254), CM (263), IB (200), and the individual CP genetic types (201 to 335). Sequence variation at these genes confirmed the resemblance of CR to IB, but also that CR, particularly ZU and CM, are not exempt from selective introgression of other breeds. A total of 50 exonic variants were identified as being potentially specific to CR, including a high-impact deletion in the intron between exons 15 and 16 of the leptin receptor gene that is only present in CM and ZU. The identification of breed-specific variants in genes related to adaptive and economical traits can bolster the understanding of the role of gene-environment interactions on local adaptation and points the way for effective breeding and conservation of CR pigs.
MMP14 expression levels accurately predict the presence of extranodal extensions in oral squamous cell carcinoma: a retrospective cohort study
Authors: Noda Yuri , Ishida Mitsuaki , Yamaka Ryosuke , Ueno Yasuhiro , Sakagami Tomofumi , Fujisawa Takuo , Iwai Hiroshi , Tsuta Koji 
Published: December 2022

Abstract
Background: Extranodal extension (ENE) is an adverse prognostic factor for oral squamous cell carcinoma (OSCC), and OSCC patients with ENE require neck dissection. In this study, we developed a novel ENE histology-based pathological predictor using MMP14 expression patterns in small biopsy specimens.
Methods: A total of 71 surgically resected tissue, 64 dissected lymph node (LN), and 46 biopsy specimens were collected from 71 OSCC patients. Immunohistochemical analyses of total MMP14 expression in the tumour nest and cancer-associated fibroblasts (CAFs) were performed using the MMP14 co-scoring system (high- or low-risk). The association analysis of MMP14 expression in metastatic LNs was performed with respect to the presence and absence of ENE. Clinicopathological analyses and multivariate examinations were performed to assess the risks of metastasis and ENE presence. The predictive value of ENE was examined.
Results: High-risk MMP14 expression was detected in metastatic LN specimens with ENE. MMP14 expression in tumour nests and CAFs and its overexpression at the tumour–stromal interface significantly correlated with the presence of ENE. The MMP14 co-scoring system was an independent risk predictor for ENE, with sensitivity, specificity, and accuracy of over 80% in biopsy samples.
Conclusions: The MMP14 co-scoring system accurately predicted ENE presence via immunohistochemical evaluation of small biopsies. This system is a simple, accurate, and inexpensive immunohistochemical approach that can be used in routine pathological diagnosis for effective treatment planning.
Dissection and validation of a novel QTL controlling spikelet number on 5B in bread wheat
Authors: Si Yaoqi , Tian Shuiquan , Niu Jianqing , Yu Zhongqing , Ma Shengwei , Lu Qiao , Wu Huilan , Ling Hong-Qing , Zheng Shusong 
Published: December 2022

Abstract
Spikelet number per spike (SNS)is an important target trait for improving wheat yield. Thus, the identification and verification of novel quantitative trait loci (QTL)/genes controlling SNS isessential for dissecting the underlying molecular basisand hence for grain yield improvement. In thisstudy, we constructed a high-density genetic map for the recombinant inbred line (RIL)population derived from Zhengnong 17 (ZN17) and Yangbaimai (YBM) using 99,031 single-nucleotide polymorphism (SNP) markers from the Wheat660K SNP array. Based on this genetic map, a total of 19 QTL associated with SNS were detected in nine environments. Among them, four QTL were identifiedin more than six environments, explaining the phenotypic variance ranging from 2.91% to 37.71%. Particularly, QSns.ucas-5B isprobably a novellocus, which islocated on chromosome arm 5BL flanking by the markers AX-110648717 and AX-109557107, withexplained the phenotypic variation range from 5.09% to 7.26% in sixenvironments. A residual heterozygous line was developed for QSns.ucas-5B, and the SNSshowed 6.74~13.17% higher in lines of elite haplotype from ZN17 than that from YBM at four diverse environments, which implied the promising potential to improve SNS using this QTL. Simultaneously, the ZN17haplotype in QSns.ucas-5B has a consistent positive effect on grain number per spike and grain weight per spike. These results lay the foundation for the precise mappingand cloning of gene(s) underlying QSns.ucas-5B in the future. The developed and validated InDel marker of QSns.ucas-5Bcould be appliedin molecular breeding aiming to improve wheat grain yield.
Prospective, longitudinal analysis of the gut microbiome in patients with locally advanced rectal cancer predicts response to neoadjuvant concurrent chemoradiotherapy
Authors: Sun Yi , Zhang Xiang , Jin Chuandi , Yue Kaile , Sheng Dashuang , Zhang Tao , Dou Xue , Liu Jing , Jing Hongbiao , Zhang Lei , Yue Jinbo 
Published: December 2022

Abstract
Background
Neoadjuvant concurrent chemoradiotherapy (nCCRT) is a standard treatment for locally advanced rectal cancer (LARC). The gut microbiome may be reshaped by radiotherapy through its effects on microbial composition, mucosal immunity, and the systemic immune system. We sought to clarify dynamic, longitudinal changes in the gut microbiome and blood immunomodulators throughout nCCRT and to explore the relationship of such changes with outcomes after nCCRT
Methods
A total of 39 LARC patients were recruited in this study. Fecal samples and peripheral blood samples were collected from 39 LARC patients before, during nCCRT (at week 3), and after nCCRT (at week 5). The gut microbiota and the community structure were analyzed based on the 16S rRNA sequencing of the V3-V4 region. Levels of blood immunomodulatory proteins were measured with a Millipore HCKPMAG-11K kit and Luminex 200 platform (Luminex, USA).
Results
Cross-sectional and longitudinal analysis revealed that the gut microbiome profile and enterotype exhibited characteristic variations in patients with good response (TRG 0–1) vs poor response (TRG 2–3) to nCCRT. Sparse partial least squares regression and canonical correspondence analyses showed multivariate associations between specific microbial taxa, host immunomodulatory proteins, immune cells, and outcomes after nCCRT. An integrated model consisting of baseline Clostridium sensu stricto 1 levels, fold changes in Intestinimonas, blood levels of the herpes virus entry mediator (HVEM/CD270), and lymphocyte counts could predict good vs poor outcome after nCCRT (area under the receiver-operating characteristics curve [1] = 0.821; area under the precision-recall curve [AUPR] = 0.911).
Conclusions
Our results showed that longitudinal variations in specific gut taxa, associated host immune cells and immunomodulatory proteins before and during nCCRT could be useful for early predictions of the efficacy of nCCRT, which could guide the choice of individualized treatment for patients with LARC.
Cool Kids Group-CBT in a Spanish Sample of Children and Adolescents with Anxiety Disorders
Authors: Galí¹ Dafne , Forcadell² Eduard , Primé-Tous² Mireia , Puig² Olga , Lera-Miguel² Sara 
Published: December 2022

Abstract
Aim: Anxiety disorders (AD) are estimated in a 6’5% worldwide childhood and adolescence and produce a negative impact over functioning and life quality. Individual and group Cognitive Behavioural Therapies (CBT) have demonstrated their short and long-term efficacy. Cool Kids (CK) is a 10-session CBT-based group program to be administered to 7-17 aged participants with AD and their parents. CK has demonstrated its efficacy compared to control groups. Our aim was to analyze the effectiveness of CK in a clinical cohort of Spanish children and teens with AD.
Methods: CK was offered to 57 patients with AD and caregivers attended in the Hospital Clínic, Barcelona. The Spence Children Anxiety Scale (SCAS) and the Child Anxiety Life Interference Scale (CALIS), children and parent versions, were administered at pre-treatment and post-treatment.
Results: The results in all global registered measures showed a reduction of the symptoms and their interference in daily functioning, as well as a greater improvement in those participants with more completed sessions.
Conclusions: These results have showed that CK has benefits in reducing the anxiety severity and its interference over individual and family functioning in a Spanish clinical cohort.
Spatial distribution of PD-1+CD39+CD8+ T cell in TME refined its tumorigenic and immunotherapeutic biomarker in lung cancer
Authors: Zhai Jiawei , Zhang Yaoxin , Wang Hongbin , lv Leilei , Shen Yu , Qu Qiuxia , Chen Cheng 
Published: December 2022

Abstract
Purpose
CD8 + T cells in tumors are heterogenous and comprise multiple differentiation states. It has been reported that human tumor-infiltrating CD8 + T cells can express CD39 and more evidences proposed CD39 as a marker of exhausted and tumor reactive CD8 + T cells. However, no studies have delved into the spatial distribution of the CD39 + CD8 + T cell subsets in lung cancer, which could help to evaluate the immune microenvironment for developing the future immunotherapy approaches.
Methods
A total of 53 lung cancer patients prior to any therapy were included. A subset of tumor-infiltrating CD8 + T cells marked by expression of the immunosuppressive ATP ecto-nucleotidase CD39 and PD-1 was analyzed. Neoplasm-superficial biopsy and intratumoral EBUS-TBNA were used to assess the peripheral and central tumor microenvironment respectively.
Results
The CD39 + CD8 + T cells were ubiquitously infiltrated in lung cancer tissue, as well as dominantly accumulated in peritumoral compartment of larger tumor. In comparison to their CD39- counterparts, CD39 + CD8 + T cells from both sites showed significantly higher expression of PD-1 in line with co-distribution of PD-1 + CD8 + T cell in TME of lung cancer. Particularly, most of CD39 + CD8 + T cells located at peripheral TME exhibited an exhausted phenotype compatible with PD-1 expression in contrast to the reported center of tumor. Furthermore, compared with CD39 + CD8 + T cells, PD-1 + CD39 + CD8 + T cells act as a better biomarker to predict response to anti-PD-1 therapy.
Conclusion
Spatial heterogeneity may be critical to elicit CD39 expression on lung cancer associated CD8 + T cells. More increased of PD-1 + CD39 + CD8 + T cells within peripheral TME constitute tumorigenic role and act as a candidate biomarker for immunotherapy to lung cancer.
How photo editing in social media shapes self-perceived attractiveness and self-esteem via self-objectification and physical appearance comparisons
Authors: Ozimek Phillip , Lainas Semina , Bierhoff Hans-Werner , Rohmann Elke 
Published: December 2022

Abstract
As photo editing behavior (PEB) to enhance one’s appearance in photos becomes more and more prevalent on social network sites (SNSs), potential risks are increasingly discussed as well. The purpose of this study is to examine the relationship between PEB, self-objectification, physical appearance comparisons, self-perceived attractiveness, and self-esteem. 403 participants completed self-report questionnaires measuring these constructs. A parallel-sequential multiple mediation model was conducted to investigate the impact of PEB on self-esteem via multiple mediators. The results indicate that PEB has a negative effect on self-perceived attractiveness and self-esteem mediated via self-objectification and physical appearance comparisons. Therefore, SNS users should be aware of potential negative consequences when using photo editing applications or filters.
Different molecular pathways are disrupted in Pyoderma gangrenosum patients and are associated with the severity of the disease.
Authors: Moura Ronald Rodrigues , Brandão Lucas , Moltrasio Chiara , Agrelli Almerinda , Tricarico Paola M. , Maronese Carlo A. , Crovella Sergio , Marzano Angelo Valerio 
Published: December 2022

Abstract
Pyoderma gangrenosum (PG) is a rare inflammatory skin disease classified within the spectrum of neutrophilic dermatoses. The pathophysiology of PG is yet incompletely understood but a prominent role of genetics facilitating immune dysregulation has been proposed. This study investigated the potential contribution of disrupted molecular pathways in determining the susceptibility and clinical severity of PG. Variant Enrichment Analysis (VEA), a bioinformatic pipeline applicable for Whole Exome Sequencing (WES) data was performed in unrelated PG patients. Eleven patients were enrolled, including 5 with localized and 6 with multilesional PG. Fourteen pathways were exclusively enriched in the “multilesional” group, mainly related to immune system (i.e., type I interferon signaling pathway), cell metabolism and structural functions. In the “localized” group, nine pathways were found to be exclusively enriched, mostly related to cell signaling and cell metabolism. Genetically altered pathways involved in immune system biology and wound repair appear to be nodal pathogenic drivers in PG pathogenesis.
CT-based radiomics for predicting radio-chemotherapy response and overall survival in nonsurgical esophageal carcinoma
Authors: Li Chao , Pan Yuteng , Yang Xianghui , Luo Chenhua , Qiu Jianfeng , Hu Yongmei , Zhang Zijian , Shi Liting , Shen Liangfang , Zhou Rongrong , Lu Fushan , Xiao Xiang , Chen Tingyin , Jing Di 
Published: December 2022

Abstract
Background
To predict treatment response and 2 years overall survival (OS) of radio-chemotherapy in patients with esophageal cancer (EC) by radiomics based on the computed tomography (CT) images.
Methods
This study retrospectively collected 171 nonsurgical EC patients treated with radiochemotherapy from Jan 2010 to Jan 2019. 80 patients were randomly divided into training (n = 64) and validation (n = 16) cohorts to predict the radiochemotherapy response. The models predicting treatment response were established by Lasso and logistic regression. A total of 156 patients were allocated into the training cohort (n = 110), validation cohort (n = 23) and test set (n = 23) to predict 2-year OS. The models predicting 2-year OS were established by the Lasso Cox model and Cox proportional hazards model.
Results
To predict the radiochemotherapy response, WFK as a radiomics feature, and clinical stages and clinical M stages (cM) as clinical features were selected to construct the clinical-radiomics model, achieving 0.78 and 0.75 AUC (area under the curve) in the training and validation sets, respectively. Furthermore, radiomics features called WFI and WGI combined with clinical features (smoking index, pathological types, cM) were the optimal predictors to predict 2-year OS. The AUC values of the clinical-radiomics model were 0.71 and 0.70 in the training set and validation set, respectively.
Conclusions
This study demonstrated that planning CT-based radiomics showed the predictability of the radiochemotherapy response and 2-year OS in nonsurgical esophageal carcinoma. The predictive results prior to treatment have the potential to assist physicians in choosing the optimal therapeutic strategy to prolong overall survival.
Improved GNSS integer ambiguity resolution method based on the column oriented Cholesky decomposition
Authors: Jiao Yingxiang , Li Kezhao , Tian Chendong , Zhu Guoku , Yue Zhe , Xu Keke 
Published: December 2022

Abstract
Because the traditional Cholesky decomposition algorithm still has some problems such as computational complexity and scattered structure among matrices when solving the GNSS ambiguity, in order to further improve the computational efficiency of the least squares ambiguity reduction correlation process in the carrier phase integer ambiguity solution. In this paper, the decomposition process of traditional matrix elements is divided into two steps: multiplication update and column reduction of square root calculation and column division calculation. The existing Cholesky decomposition algorithm is improved, and a column oriented Cholesky (C-Cholesky) algorithm is proposed to further improve the efficiency of matrix decomposition, so as to shorten the calculation time of integer ambiguity reduction correlation. The results show that this method is effective and superior, and can improve the data processing efficiency by about 12% without changing the integer ambiguity accuracy of the traditional Cholesky algorithm.
The psc-CVM assessment system: A three-stage type system for CVM assessment based on deep learning
Authors: Li Hairui , Li Haizhen , Yuan Lingjun , Liu Chao , Xiao Shengzhao , Liu Zhen , Zhou Guoli , Dong Ting , Ouyang Ningjuan , Liu Lu , Ma Chenglong , Feng Yang , Zheng Youyi , Xia Lunguo , Fang Bing 
Published: December 2022

Abstract
Background
Many scholars have proven cervical vertebral maturation (CVM) method can predict the growth and development and assist in choosing the best time for treatment. However, assessing CVM is a complex process. The experience and seniority of the clinicians have an enormous impact on judgment. This study aims to establish a fully automated, high-accuracy CVM assessment system called the psc-CVM assessment system, based on deep learning, to provide valuable reference information for the growth period determination.
Methods
This study used 10200 lateral cephalograms as the data set (7111 in train set, 1544 in validation set and 1545 in test set) to train the system. The psc-CVM assessment system is designed as three parts with different roles, each operating in a specific order. 1) Position Network for locating the position of cervical vertebrae; 2) Shape Recognition Network for recognizing and extracting the shapes of cervical vertebrae; and 3) CVM Assessment Network for assessing CVM according to the shapes of cervical vertebrae. Statistical analysis was conducted to detect the performance of the system and the agreement of CVM assessment between the system and the expert panel. Heat maps were analyzed to understand better what the system had learned.
Results
The system has achieved good performance for CVM assessment with an average AUC (the area under the curve) of 0.94 and total accuracy of 70.42%, as evaluated on the test set. The overall ICC between the psc-CVM assessment system and the expert panel was 0.946. The F1 score rank for the psc-CVM assessment system was: CVS (cervical vertebral maturation stage) 6 > CVS1 > CVS4 > CVS5 > CVS3 > CVS2. The area of the third (C3), fourth (C4) cervical vertebrae and the lower edge of second (C2) cervical vertebrae were activated when the system were assessing the images.
Conclusions
The results showed that the psc-CVM assessment system achieved high accuracy in CVM assessment. The system in this study was significantly consistent with expert panels in CVM assessment, indicating that the system can be used as an efficient, accurate, and stable diagnostic aid to provide a clinical aid for determining growth and developmental stages by CVM.
Prevalence and Predictors of Smartphone Addiction among Medical Students in China during the COVID-19 pandemic: A cross-sectional study
Authors: Liu Huan , Tao Xiubin , Chi Chenru , He Yumei , Zhang Ming 
Published: December 2022

Abstract

ObjectiveSmartphone addiction is a common condition among medical students. Recent studies have reported the prevalence of Smartphone addiction among students, but there are fewer studies on the situation and influencing factors of smartphone addiction among medical students during the COVID-19 pandemic. In our study, we aimed to assess the prevalence of Chinese medical students’ smartphone addiction and its Predictors.MethodA cross-sectional survey was conducted from March 13 to 30, 2022, by administering an online questionnaire to the students of Wannan Medical College. Data analysis was conducted using IBM SPSS ver. 20.0.ResultsOf 3227 students who completed the survey, 1,968 (61.0%) had smartphone addiction. Gender (p=0.000), adaptation to the online learning (p=0.001), perceived study pressure (p=0.000), high psychological stress (p=0.000), academic burnout (p=0.000) and eHealth Literacy (p=0.000) strong associations of smartphone addiction. PSS-4 and academic burnout were highly correlated with smartphone addiction （P<0.001）. EHealth Literacy was a protective factor of smartphone addiction.ConclusionThis survey shows that the Chinese medical students had a very high rate of smartphone addiction during the COVID-19 pandemic. The COVID-19 pandemic has brought about changes in the way medical students learn and increased associated, which has exacerbated the already existing smartphone addiction among medical college students. Therefore, medical colleges educators develop educational strategies to reduce smartphone addiction is essential.
Interspecific interactions between an invasive and an imperiled reptile
Authors: McKnight Sean Lewis , Kluever Bryan , MacKenzie Darryl , Acevedo Miguel , Johnson Steve 
Published: December 2022

Abstract
Invasive species are a major driver in the global decline of biodiversity. Invasive herpetofauna cause ecological harm through different mechanisms that vary in scope and severity, and Florida boasts more established nonnative herpetofauna species than any other region in the world. There, black spiny-tailed iguanas (Ctenosaura similis) are one of several large invasive reptiles known to occupy the burrows of the imperiled, native gopher tortoise (Gopherus polyphemus) and may even exclude tortoises from their burrows. To test the hypothesis that iguanas exclude tortoises from their burrows, we conducted a field study on Gasparilla Island, Florida, USA. We used a burrow scope to estimate occupancy of each species within tortoise burrows at sites with and without sustained iguana removal efforts and modelled co-occurrence patterns between the two species. We used two-species occupancy analyses to test three predictions relating to gopher tortoise burrow use. Our results support the hypothesis that gopher tortoises are excluded from their burrows by black spiny-tailed iguanas. The energetic cost to a tortoise of excavating a new burrow is unknown but may be substantial. In addition, tortoises are more vulnerable to extreme temperatures and predation while searching for a new burrow location and digging a burrow. Our results also show that sustained iguana removal is likely effective at reducing iguana occupancy of tortoise burrows. Other large invasive reptiles and perhaps even some native species typically thought of as “burrow commensals” may have similar deleterious effects on tortoise behavior.