bluuebunny/crossref_metadata_2025_split huggingface dataset:
Over-expression of SOX8 predicts poor prognosis in colorectal cancer
Authors: Wang Yang , Yang Wangshuo , Liu Tianyi , Bai Guang , Liu Mingxing , Wang Wei 
Published: July 2019

Abstract
Aberrant expression of SRY-box 8 (SOX8) is closely correlated with the development and progression of many types of cancers in human. Limited studies report the relationship between SOX8 expression and overall survival in colorectal cancer (CRC). This study aimed to collect the pathological tissues and clinical data in order to analyze the relationship between SOX8 expression and clinicopathological parameters and prognosis of CRC patients. Tissue microarrays were constructed from 424 primary CRC patients with clinicopathological information and follow-up data. Immunohistochemistry (IHC) was performed on tissue microarrays to explore the relationship between SOX8 expression and clinicopathological information and patient's prognosis. The expression of SOX8 was higher in CRC tissues than that in non-tumor adjacent tissues (NATs, P <.001). High expression of SOX8 was associated with tumor stage (P = .04) and shorter overall survival (OS) after operation of patients (P = .004). Subsequently, univariate COX analysis identified that high expression of SOX8 (P = .004), differentiation (P = .006), distant metastasis (P <.001), tumor stage (P = .003), and higher rate of lymph node metastasis (P <.001), all significantly predicted decrease in OS. Multivariate analysis demonstrated that distant metastasis (P <.001), high SOX8 expression, (P = .013) and lymph node metastasis (P <.001) were independent poor prognostic factors in CRC patients. This study showed that SOX8 is over-expressed in patients with high T stage, which affects the outcome of prognosis in CRC patients. High expression of SOX8 usually has a poor independent prognostic factor for CRC.
Identification of crucial miRNAs and genes in esophageal squamous cell carcinoma by miRNA-mRNA integrated analysis
Authors: Zhong Xiaowu , Huang Guangcheng , Ma Qiang , Liao Hebin , Liu Chang , Pu Wenjie , Xu Lei , Cai Yan , Guo Xiaolan 
Published: July 2019

Abstract
Esophageal squamous cell carcinoma (ESCC) is a malignancy that severely threatens human health and carries a high incidence rate and a low 5-year survival rate. MicroRNAs (miRNAs) are commonly accepted as a key regulatory function in human cancer, but the potential regulatory mechanisms of miRNA-mRNA related to ESCC remain poorly understood.
The GSE55857, GSE43732, and GSE6188 miRNA microarray datasets and the gene expression microarray datasets GSE70409, GSE29001, and GSE20347 were downloaded from Gene Expression Omnibus databases. The differentially expressed miRNAs (DEMs) and differentially expressed genes (DEGs) were obtained using GEO2R. Gene ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis for DEGs were performed by Database for Annotation, Visualization and Integrated Discovery (DAVID). A protein–protein interaction (PPI) network and functional modules were established using the STRING database and were visualized by Cytoscape. Kaplan-Meier analysis was constructed based on The Cancer Genome Atlas (TCGA) database.
In total, 26 DEMs and 280 DEGs that consisted of 96 upregulated and 184 downregulated genes were screened out. A functional enrichment analysis showed that the DEGs were mainly enriched in the ECM-receptor interaction and cytochrome P450 metabolic pathways. In addition, MMP9, PCNA, TOP2A, MMP1, AURKA, MCM2, IVL, CYP2E1, SPRR3, FOS, FLG, TGM1, and CYP2C9 were considered to be hub genes owing to high degrees in the PPI network. MiR-183-5p was with the highest connectivity target genes in hub genes. FOS was predicted to be a common target gene of the significant DEMs. Hsa-miR-9-3p, hsa-miR-34c-3p and FOS were related to patient prognosis and higher expression of the transcripts were associated with a poor OS in patients with ESCC.
Our study revealed the miRNA-mediated hub genes regulatory network as a model for predicting the molecular mechanism of ESCC. This may provide novel insights for unraveling the pathogenesis of ESCC.
Successful treatment of tumor-induced osteomalacia causing by phosphaturic mesenchymal tumor of the foot
Authors: Liu Shuzhong , Zhou Xi , Song An , Huo Zhen , Wang Yipeng , Xia Weibo , Liu Yong 
Published: July 2019

Abstract
Tumor-induced osteomalacia causing by phosphaturic mesenchymal tumor of the foot is exceedingly rare, thus may bring great challenges to the timely and proper diagnosis and treatment of clinicians. The only definitive management is removal of the phosphaturic mesenchymal tumor completely. The objective of this article is to report 2 unusual cases with tumor-induced osteomalacia causing by phosphaturic mesenchymal tumor of the foot.
We describe 2 patients with phosphaturic mesenchymal tumor involving the foot who were successfully treated with tumor resection. On presentation to our institution, the patients both had signs of severe osteomalacia, and the patients’ most outstanding complaints were diffuse bone pain, general weakness, and disabled walking. A 53-year-old female underwent surgical excision of pathogenic tumor on the sole of left foot. A 62-year-old female underwent complete excision of pathogenic tumor of right plantar. The patients showed appropriate destruction of the tumor, adequate pain relief, and the elevated blood phosphorus levels compared with the previous status.
Surgical resection is the most effective treatment option for patients with tumor-induced osteomalacia who can undergo appropriate surgical treatment. This represents a safe and reasonable approach to sustainably relieve pain and other symptoms with tumor-induced osteomalacia in the foot.
The outcome of Bishop-Koop procedure compared to divided stoma in neonates with meconium ileus, congenital intestinal atresia and necrotizing enterocolitis
Authors: Martynov Illya , Raedecke Jochen , Klima-Frysch Jessica , Kluwe Wolfram , Schoenberger Joachim 
Published: July 2019

Abstract
To determine the potential value and suitability of Bishop-Koop procedure (BK) compared to divided stoma (DS) in neonates with meconium ileus (MI), congenital intestinal atresia (CIA), and necrotizing enterocolitis (NEC).
A retrospective data collection from 2000 to 2019 on neonates undergoing BK and DS formation and closure for MI, CIA, and NEC was conducted. Ostomy related complications following both procedures were analyzed.
One hundred two consecutive patients managed with a BK (n = 57, 55.8%) and DS (n = 45, 44.2%) for MI (n = 38, 37.2%), CIA (n = 31, 30.5%), and NEC (n = 33, 32.3%) were analyzed. Mean operating time for ostomy creation did not differ significantly between BK and DS groups (156 ± 54 vs 135 ± 66.8 min, P = .08). The prevalence of stoma-related complications following BK and DS formation was 8.7% and 31.1%, respectively (P = .005). The complication rate after BK and DS closure was 3.5% and 6.7%, respectively (P = .65). The operating time for ostomy reversal and length of hospital stay after stoma closure were significantly shorter in BK group (82.2 ± 51.4 vs 183 ± 84.5 min and 5.5 ± 2.7 vs 11.3 ± 3.9 days, P < .001).
BK procedure is safe, reliable, and suitable technique in neonatal surgery with low complications rate following ostomy creation as well as shorter operating time and length of hospital stay after ostomy closure compared to DS ostomies. Surgeons should keep this technique as an alternative approach in their repertoire.
The effect of sex hormones on normal breast tissue metabolism
Authors: Jung Yongsik , Kim Tae Hee , Kim Ji Young , Han Sehwan , An Young-Sil 
Published: July 2019

Abstract
This study investigated the effect of sex hormones on 18F-fluorodeoxyglucose (FDG) uptake in normal breast tissue.
The retrospective study included 249 premenopausal women (median age, 45 years) who were diagnosed with unilateral breast cancer and underwent FDG positron emission tomography/computed tomography and hormone tests. The volume of interest was within the contralateral normal breast and the standardized uptake values (SUVs) were measured. The correlations of sex hormones (including estrogen, progesterone, testosterone, follicle-stimulating hormone [FSH] and luteinizing hormone [LH]) with the SUVs of the normal breast were analyzed.
There was a weak negative correlation between age and breast FDG uptake (P = .012, Spearman coefficient = −.16 for the maximum standardized uptake values [SUVmax]), especially in the luteal phase group (P = .005, Spearman coefficient = −.27 for SUVmax). The SUVs of normal breast tissue were increased when progesterone levels were higher (P = .043, Spearman coefficient = .13 for SUVmax). In the irregular menstrual cycle group, FDG uptake in the breast decreased as FSH (P = .027, Spearman coefficient = −.42 for SUVmax) and LH (P = .048, Spearman coefficient = −.44 for SUVmax) increased.
Glucose metabolism of normal breast tissue decreases with age, and progesterone weakly affects breast FDG uptake. Gonadotropins may affect breast FDG uptake in premenopausal women with irregular menstrual cycles.
Driving scene-based driving errors in brain injury patients and their relevance to cognitive-perceptual function and functional activity level
Authors: Park Myoung-Ok 
Published: July 2019

Abstract
Driving is an essential activity for community engagement in patients with brain injury. However, brain injury patients have cognitive-perceptual deficits and low independence in daily activities. The aims of this study were to identify the driving errors of brain injury patients and determine their relevance to cognitive-perception function and daily activity level. This study was conducted at a single rehabilitation hospital. Thirty-one brain injury patients were included in the study. The patients underwent a driving-scene-based simulator evaluation in the rehabilitation clinic. Driving errors were checked using automatic software. Perceptual ability was measured using Motor-free Visual Perceptual Test (MVPT) and Cognitive-perceptual Assessment for Driving (CPAD). A linear relationship was found between the driving aptitude score, steering wheel and judgment, simultaneous operation items, total score of road course test, and cognitive-perceptual functions and daily activity levels of the participants (P <.05). The general factors that affected driving errors included driving experience, age, part of the hemispheric affected, and presence of vascular injury (P <.05). In addition, the Korean version of Mini-Mental State Examination (K-MMSE) score and the CPAD score correlated with driving errors (P <.05). The total error score of the participants correlated with the Korean version of the Modified Barthel Index (K-MBI) score (P <.05).These findings suggest that driving experience and age have more influence on driving error than perceptual level due to brain damage. In addition, it was found that the basic level of daily living influences overall operating errors.
Maternal depression treatment in HIV (M-DEPTH)
Authors: Wagner Glenn J. , McBain Ryan K. , Akena Dickens , Ngo Victoria , Nakigudde Janet , Nakku Juliet , Chemusto Harriet , Beyeza-Kashesya Jolly , Gwokyalya Violet , Faherty Laura J. , Kyohangirwe Leticia , Nabitaka Linda Kisaakye , Lukwata Hafsa , Linnemayr Sebastian , Ghosh-Dastidar Bonnie , Businge Juliet , Mukasa Barbara , Wanyenze Rhoda K. 
Published: July 2019

Abstract

Introduction:
Over one-third of human immunodeficiency virus (HIV)-infected pregnant women are clinically depressed, increasing the risk of mother-to-child transmission (MTCT) of HIV, as well as negative birth and child development outcomes. This study will evaluate the efficacy and cost-effectiveness of an evidence-based stepped care treatment model for perinatal depression (maternal depression treatment in HIV [M-DEPTH]) to improve adherence to prevention of MTCT care among HIV+ women in Uganda.

Methods:
Eight antenatal care (ANC) clinics in Uganda will be randomized to implement either M-DEPTH (n=4) or usual care (n=4) for perinatal depression among 400 pregnant women (n=50 per clinic) between June 2019 and August 2022. At each site, women who screen positive for potential depression will be enrolled and followed for 18 months post-delivery, assessed in 6-month intervals: baseline, within 1 month of child delivery or pregnancy termination, and months 6, 12, and 18 following delivery. Primary outcomes include adherence to the prevention of mother-to-child transmission (PMTCT) care continuum—including maternal antiretroviral therapy and infant antiretrovial prophylaxis, and maternal virologic suppression; while secondary outcomes will include infant HIV status, post-natal maternal and child health outcomes, and depression treatment uptake and response. Repeated-measures multivariable regression analyses will be conducted to compare outcomes between M-DEPTH and usual care, using 2-tailed tests and an alpha cut-off of P <.05. Using a micro-costing approach, the research team will relate costs to outcomes, examining the incremental cost-effectiveness ration (ICER) of M-DEPTH relative to care as usual.

Discussion:
This cluster randomized controlled trial will be one of the first to compare the effects of an evidence-based depression care model versus usual care on adherence to each step of the PMTCT care continuum. If determined to be efficacious and cost-effective, this study will provide a model for integrating depression care into ANC clinics and promoting adherence to PMTCT.

Trial Registration:
NIH Clinical Trial Registry NCT03892915 (clinicaltrials.gov).
Perforation rates in double latex gloves and protective effects of outer work gloves in a postmortem examination room
Authors: Idota Nozomi , Nakamura Mami , Akasaka Yoshihisa , Tsuboi Hajime , Bando Risa , Ikegaya Hiroshi 
Published: July 2019

Abstract
Medical staff face the risk of exposure to blood-borne infectious agents during postmortem examinations. This study investigated the effectiveness of non-slip work gloves worn over 2 layers of surgical latex gloves (outer and inner gloves) as a means of reducing hand and finger injuries. Complete sets of outer and inner gloves worn during postmortem examinations were collected from participating forensic staff. Latex gloves were categorized into 2 groups based on the users’ actions during the examination: the wearing group if the wearer wore their work gloves continuously without interruption, and the taking-off group if the wearer removed them at least once. Perforation rates, locations, and shapes were compared between these groups. Outer-glove perforation occurred significantly more often in the taking-off group (n = 102 pairs) than in the wearing group (n = 91 pairs) (30.4% vs 3.8%, P < .001). Inner-glove perforation occurred at rates of 2.0% and 0.5% (P = .38), respectively. The wearers did not incur hand or finger injuries. Perforation rates were similar between the dominant and non-dominant hands (P = .18). Regarding location, gloves were punctured most frequently at the thumb, followed by the index finger. Most examiners (85.6%) did not notice the perforation when the damage occurred. Therefore, we could not confirm that a specific operation within a set of plural operations affected the rate of perforation. Additionally, we could not prove a relationship between glove perforation and each operation performed with/without work gloves. The perforation appearances varied greatly in shape and size, suggesting multiple causes of perforation. The continuous (i.e., uninterrupted) wear of work gloves during postmortem examinations reduced the incidence of perforations in both latex glove layers and thus reduced the risk of hand and finger injury.
Single cell chromatin accessibility reveals pancreatic islet cell type- and state-specific regulatory programs of diabetes risk
Authors: Chiou Joshua , Zeng Chun , Cheng Zhang , Han Jee Yun , Schlichting Michael , Huang Serina , Wang Jinzhao , Sui Yinghui , Deogaygay Allison , Okino Mei-Lin , Qiu Yunjiang , Sun Ying , Kudtarkar Parul , Fang Rongxin , Preissl Sebastian , Sander Maike , Gorkin David , Gaulton Kyle J 
Published: July 2019

AbstractGenetic risk variants for complex, multifactorial diseases are enriched incis-regulatory elements. Single cell epigenomic technologies create new opportunities to dissect cell type-specific mechanisms of risk variants, yet this approach has not been widely applied to disease-relevant tissues. Given the central role of pancreatic islets in type 2 diabetes (T2D) pathophysiology, we generated accessible chromatin profiles from 14.2k islet cells and identified 13 cell clusters including multiple alpha, beta and delta cell clusters which represented hormone-producing and signal-responsive cell states. We cataloged 244,236 islet cell type accessible chromatin sites and identified transcription factors (TFs) underlying both lineage- and state-specific regulation. We measured the enrichment of T2D and glycemic trait GWAS for the accessible chromatin profiles of single cells, which revealed heterogeneity in the effects of beta cell states and TFs on fasting glucose and T2D risk. We further used machine learning to predict the cell type-specific regulatory function of genetic variants, and single cell co-accessibility to link distal sites to putative cell type-specific target genes. We localized 239 fine-mapped T2D risk signals to islet accessible chromatin, and further prioritized variants at these signals with predicted regulatory function and co-accessibility with target genes. At theKCNQ1locus, the causal T2D variant rs231361 had predicted effects on an enhancer with beta cell-specific, long-range co-accessibility to the insulin promoter, and deletion of this enhancer reduced insulin gene and protein expression in human embryonic stem cell-derived beta cells. Our findings provide a cell type- and state-resolved map of gene regulation in human islets, illuminate likely mechanisms of T2D risk at hundreds of loci, and demonstrate the power of single cell epigenomics for interpreting complex disease genetics.
Development of a genetic toolset for the highly engineerable and metabolically versatile Acinetobacter baylyi ADP1
Authors: Biggs Bradley W. , Bedore Stacy R. , Arvay Erika , Huang Shu , Subramanian Harshith , McIntyre Emily A. , Duscent-Maitland Chantel V. , Neidle Ellen L. , Tyo Keith E.J. 
Published: July 2019

AbstractOne primary objective of synthetic biology is to improve the sustainability of chemical manufacturing. Biological systems can utilize a variety of carbon sources, including waste streams that pose challenges to traditional chemical processing such as lignin biomass, providing opportunity for remediation and valorization of these materials. Success, however, depends on identifying microorganisms that are both metabolically versatile and engineerable. This has been a historic hindrance. Here, we leverage the facile genetics of the metabolically versatile bacterium Acinetobacter baylyi ADP1 to create easy and rapid molecular cloning workflows, a promoter library, ribosomal binding site (RBS) variants, and an unprecedented number of bacterial chromosomal protein expression sites and variants. Moreover, we demonstrate the utility of these tools by examining ADP1’s catabolic repression regulation, creating a strain with improved potential for lignin bioprocessing. Taken together, this work establishes ADP1 as an ideal host for a variety of sustainability and synthetic biology applications.
A single cell framework for multi-omic analysis of disease identifies malignant regulatory signatures in mixed phenotype acute leukemia
Authors: Granja Jeffrey M. , Klemm Sandy , McGinnis Lisa M. , Kathiria Arwa S. , Mezger Anja , Parks Benjamin , Gars Eric , Liedtke Michaela , Zheng Grace X.Y. , Chang Howard Y. , Majeti Ravindra , Greenleaf William J. 
Published: July 2019

AbstractIn order to identify the molecular determinants of human diseases, such as cancer, that arise from a diverse range of tissue, it is necessary to accurately distinguish normal and pathogenic cellular programs.1–3Here we present a novel approach for single-cell multi-omic deconvolution of healthy and pathological molecular signatures within phenotypically heterogeneous malignant cells. By first creating immunophenotypic, transcriptomic and epigenetic single-cell maps of hematopoietic development from healthy peripheral blood and bone marrow mononuclear cells, we identify cancer-specific transcriptional and chromatin signatures from single cells in a cohort of mixed phenotype acute leukemia (MPAL) clinical samples. MPALs are a high-risk subtype of acute leukemia characterized by a heterogeneous malignant cell population expressing both myeloid and lymphoid lineage-specific markers.4, 5Our results reveal widespread heterogeneity in the pathogenetic gene regulatory and expression programs across patients, yet relatively consistent changes within patients even across malignant cells occupying diverse portions of the hematopoietic lineage. An integrative analysis of transcriptomic and epigenetic maps identifies 91,601 putative gene-regulatory interactions and classifies a number of transcription factors that regulate leukemia specific genes, includingRUNX1-linked regulatory elements proximal toCD69. This work provides a template for integrative, multi-omic analysis for the interpretation of pathogenic molecular signatures in the context of developmental origin.
The Genome of the Zebra Mussel,Dreissena polymorpha: A Resource for Invasive Species Research
Authors: McCartney Michael A. , Auch Benjamin , Kono Thomas , Mallez Sophie , Zhang Ying , Obille Angelico , Becker Aaron , Abrahante Juan E. , Garbe John , Badalamenti Jonathan P. , Herman Adam , Mangelson Hayley , Liachko Ivan , Sullivan Shawn , Sone Eli D. , Koren Sergey , Silverstein Kevin A. T. , Beckman Kenneth B. , Gohl Daryl M. 
Published: July 2019

AbstractThe zebra mussel,Dreissena polymorpha, continues to spread from its native range in Eurasia to Europe and North America, causing billions of dollars in damage and dramatically altering invaded aquatic ecosystems. Despite these impacts, there are few genomic resources forDreissenaor related bivalves, with nearly 450 million years of divergence between zebra mussels and its closest sequenced relative. Although theD. polymorphagenome is highly repetitive, we have used a combination of long-read sequencing and Hi-C-based scaffolding to generate the highest quality molluscan assembly to date. Through comparative analysis and transcriptomics experiments we have gained insights into processes that likely control the invasive success of zebra mussels, including shell formation, synthesis of byssal threads, and thermal tolerance. We identified multiple intact Steamer-Like Elements, a retrotransposon that has been linked to transmissible cancer in marine clams. We also found thatD. polymorphahave an unusual 67 kb mitochondrial genome containing numerous tandem repeats, making it the largest observed in Eumetazoa. Together these findings create a rich resource for invasive species research and control efforts.