bluuebunny/crossref_metadata_2025_split huggingface dataset:
IGFBP-rP1, a potential molecule associated with colon cancer differentiation
Authors: Ruan Wenjing , Zhu Shuzhen , Wang Haibing , Xu Fangying , Deng Hong , Ma Yu , Lai Maode 
Published: December 2019

Abstract

Background
In our previous studies, we have demonstrated that insulin-like growth factor binding protein-related protein1 (IGFBP-rP1) played its potential tumor suppressor role in colon cancer cells through apoptosis and senescence induction. In this study, we will further uncover the role of IGFBP-rP1 in colon cancer differentiation and a possible mechanism by revealing responsible genes.

Results
In normal colon epithelium, immunohistochemistry staining detected a gradient IGFBP-rP1 expression along the axis of the crypt. IGFBP-rP1 strongly expressed in the differentiated cells at the surface of the colon epithelium, while weakly expressed at the crypt base. In colon cancer tissues, the expression of IGFBP-rP1 correlated positively with the differentiation status. IGFBP-rP1 strongly expressed in low grade colorectal carcinoma and weakly expressed in high grade colorectal carcinoma. In vitro, transfection of PcDNA3.1(IGFBP-rP1) into RKO, SW620 and CW2 cells induced a more pronounced anterior-posterior polarity morphology, accompanied by upregulation with alkaline phosphatase (AKP) activity. Upregulation of carcino-embryonic antigen (CEA) was also observed in SW620 and CW2 transfectants. The addition of IGFBP-rP1 protein into the medium could mimic most but not all effects of IGFBP-rP1 cDNA transfection. Seventy-eight reproducibly differentially expressed genes were detected in PcDNA3.1(IGFBP-rP1)-RKO transfectants, using Affymetrix 133 plus 2.0 expression chip platform. Directed Acyclic Graph (DAG) of the enriched GO categories demonstrated that differential expression of the enzyme regulator activity genes together with cytoskeleton and actin binding genes were significant. IGFBP-rP1 could upreguate Transgelin (TAGLN), downregulate SRY (sex determining region Y)-box 9(campomelic dysplasia, autosomal sex-reversal) (SOX9), insulin receptor substrate 1(IRS1), cyclin-dependent kinase inhibitor 2B (p15, inhibits CDK4) (CDKN2B), amphiregulin(schwannoma-derived growth factor) (AREG) and immediate early response 5-like(IER5L) in RKO, SW620 and CW2 colon cancer cells, verified by Real time Reverse Transcription Polymerase Chain Reaction (rtRT-PCR). During sodium butyrate-induced Caco2 cell differentiation, IGFBP-rP1 was upregulated and the expression showed significant correlation with the AKP activity. The downregulation of IRS1 and SOX9 were also induced by sodium butyrate.

Conclusion
IGFBP-rP1 was a potential key molecule associated with colon cancer differentiation. Downregulation of IRS1 and SOX9 may the possible key downstream genes involved in the process.
Characterization of a new simian immunodeficiency virus strain in a naturally infected Pan troglodytes troglodyteschimpanzee with AIDS related symptoms
Authors: Etienne Lucie , Nerrienet Eric , LeBreton Matthew , Bibila Godwin Tafon , Foupouapouognigni Yacouba , Rousset Dominique , Nana Ahmadou , Djoko Cyrille F , Tamoufe Ubald , Aghokeng Avelin F , Mpoudi-Ngole Eitel , Delaporte Eric , Peeters Martine , Wolfe Nathan D , Ayouba Ahidjo 
Published: December 2019

Abstract

Background
Data on the evolution of natural SIV infection in chimpanzees (SIVcpz) and on the impact of SIV on local ape populations are only available for Eastern African chimpanzee subspecies (Pan troglodytes schweinfurthii), and no data exist for Central chimpanzees (Pan troglodytes troglodytes), the natural reservoir of the ancestors of HIV-1 in humans. Here, we report a case of naturally-acquired SIVcpz infection in a P.t.troglodytes chimpanzee with clinical and biological data and analysis of viral evolution over the course of infection.

Results
A male chimpanzee (Cam155), 1.5 years, was seized in southern Cameroon in November 2003 and screened SIV positive during quarantine. Clinical follow-up and biological analyses have been performed for 7 years and showed a significant decline of CD4 counts (1,380 cells/mm3 in 2004 vs 287 in 2009), a severe thrombocytopenia (130,000 cells/mm3 in 2004 vs 5,000 cells/mm3 in 2009), a weight loss of 21.8% from August 2009 to January 2010 (16 to 12.5 kg) and frequent periods of infections with diverse pathogens.
DNA from PBMC, leftover from clinical follow-up samples collected in 2004 and 2009, was used to amplify overlapping fragments and sequence two full-length SIVcpzPtt-Cam155 genomes. SIVcpzPtt-Cam155 was phylogenetically related to other SIVcpzPtt from Cameroon (SIVcpzPtt-Cam13) and Gabon (SIVcpzPtt-Gab1). Ten molecular clones 5 years apart, spanning the V1V4 gp120 env region (1,100 bp), were obtained. Analyses of the env region showed positive selection (dN-dS >0), intra-host length variation and extensive amino acid diversity between clones, greater in 2009. Over 5 years, N-glycosylation site frequency significantly increased (p < 0.0001).

Conclusions
Here, we describe for the first time the clinical history and viral evolution of a naturally SIV infected P.t.troglodytes chimpanzee. The findings show an increasing viral diversity over time and suggest clinical progression to an AIDS-like disease, showing that SIVcpz can be pathogenic in its host, as previously described in P.t.schweinfurthii. Although studying the impact of SIV infection in wild apes is difficult, efforts should be made to better characterize the pathogenicity of the ancestors of HIV-1 in their natural host and to find out whether SIV infection also plays a role in ape population decline.
Sequence analysis of the Epstein-Barr virus (EBV) BRLF1 gene in nasopharyngeal and gastric carcinomas
Authors: Jia Yuping , Wang Yun , Chao Yan , Jing Yongzheng , Sun Zhifu , Luo Bing 
Published: December 2019

Abstract

Background
Epstein-Barr virus (EBV) has a biphasic infection cycle consisting of a latent and a lytic replicative phase. The product of immediate-early gene BRLF1, Rta, is able to disrupt the latency phase in epithelial cells and certain B-cell lines. The protein Rta is a frequent target of the EBV-induced cytotoxic T cell response. In spite of our good understanding of this protein, little is known for the gene polymorphism of BRLF1.

Results
BRLF1 gene was successfully amplified in 34 EBV-associated gastric carcinomas (EBVaGCs), 57 nasopharyngeal carcinomas (NPCs) and 28 throat washings (TWs) samples from healthy donors followed by PCR-direct sequencing. Fourteen loci were found to be affected by amino acid changes, 17 loci by silent nucleotide changes. According to the phylogenetic tree, 5 distinct subtypes of BRLF1 were identified, and 2 subtypes BR1-A and BR1-C were detected in 42.9% (51/119), 42.0% (50/119) of samples, respectively. The distribution of these 2 subtypes among 3 types of specimens was significantly different. The subtype BR1-A preferentially existed in healthy donors, while BR1-C was seen more in biopsies of NPC. A silent mutation A/G was detected in all the isolates. Among 3 functional domains, the dimerization domain of Rta showed a stably conserved sequence, while DNA binding and transactivation domains were detected to have multiple mutations. Three of 16 CTL epitopes, NAA, QKE and ERP, were affected by amino acid changes. Epitope ERP was relatively conserved; epitopes NAA and QKE harbored more mutations.

Conclusions
This first detailed investigation of sequence variations in BRLF1 gene has identified 5 distinct subtypes. Two subtypes BR1-A and BR1-C are the dominant genotypes of BRLF1. The subtype BR1-C is more frequent in NPCs, while BR1-A preferentially presents in healthy donors. BR1-C may be associated with the tumorigenesis of NPC.
CT-guided iodine-125 seed permanent implantation for recurrent head and neck cancers
Authors: Jiang Yu L , Meng Na , Wang Jun J , Jiang Ping , Yuan Hui SH , Liu Chen , Qu Ang , Yang Rui J 
Published: December 2019

Abstract

Background
To investigate the feasibility, and safety of 125I seed permanent implantation for recurrent head and neck carcinoma under CT-guidance.

Results
A retrospective study on 14 patients with recurrent head and neck cancers undergone 125I seed implantation with different seed activities. The post-plan showed that the actuarial D90 of 125I seeds ranged from 90 to 218 Gy (median, 157.5 Gy). The follow-up was 3 to 60 months (median, 13 months). The median local control was 18 months (95% CI, 6.1-29.9 months), and the 1-, 2-, 3-, and 5- year local controls were 52%, 39%, 39%, and 39%, respectively. The 1-, 2-, 3-, and 5- survival rates were 65%, 39%, 39% and 39%, respectively, with a median survival time of 20 months (95% CI, 8.7-31.3 months). Of all patients, 28.6% (4/14) died of local recurrence, 7.1% (1/14) died of metastases, one patient died of hepatocirrhosis, and 8 patients are still alive to the date of data analysis.

Conclusion
CT-guided 125I seed implantation is feasible and safe as a salvage or palliative treatment for patients with recurrent head and neck cancers.
BioBin: a bioinformatics tool for automating the binning of rare variants using publicly available biological knowledge
Authors: Moore Carrie B , Wallace John R , Frase Alex T , Pendergrass Sarah A , Ritchie Marylyn D 
Published: December 2019

Abstract

Background
With the recent decreasing cost of genome sequence data, there has been increasing interest in rare variants and methods to detect their association to disease. We developed BioBin, a flexible collapsing method inspired by biological knowledge that can be used to automate the binning of low frequency variants for association testing. We also built the Library of Knowledge Integration (LOKI), a repository of data assembled from public databases, which contains resources such as: dbSNP and gene Entrez database information from the National Center for Biotechnology (NCBI), pathway information from Gene Ontology (GO), Protein families database (Pfam), Kyoto Encyclopedia of Genes and Genomes (KEGG), Reactome, NetPath - signal transduction pathways, Open Regulatory Annotation Database (ORegAnno), Biological General Repository for Interaction Datasets (BioGrid), Pharmacogenomics Knowledge Base (PharmGKB), Molecular INTeraction database (MINT), and evolutionary conserved regions (ECRs) from UCSC Genome Browser. The novelty of BioBin is access to comprehensive knowledge-guided multi-level binning. For example, bin boundaries can be formed using genomic locations from: functional regions, evolutionary conserved regions, genes, and/or pathways.

Methods
We tested BioBin using simulated data and 1000 Genomes Project low coverage data to test our method with simulated causative variants and a pairwise comparison of rare variant (MAF < 0.03) burden differences between Yoruba individuals (YRI) and individuals of European descent (CEU). Lastly, we analyzed the NHLBI GO Exome Sequencing Project Kabuki dataset, a congenital disorder affecting multiple organs and often intellectual disability, contrasted with Complete Genomics data as controls.

Results
The results from our simulation studies indicate type I error rate is controlled, however, power falls quickly for small sample sizes using variants with modest effect sizes. Using BioBin, we were able to find simulated variants in genes with less than 20 loci, but found the sensitivity to be much less in large bins. We also highlighted the scale of population stratification between two 1000 Genomes Project data, CEU and YRI populations. Lastly, we were able to apply BioBin to natural biological data from dbGaP and identify an interesting candidate gene for further study.

Conclusions
We have established that BioBin will be a very practical and flexible tool to analyze sequence data and potentially uncover novel associations between low frequency variants and complex disease.
Edaravone reduces oxidative stress and intestinal cell apoptosis after burn through up-regulating miR-320 expression
Authors: Ke Jiaxiang , Bian Xi , Liu Hu , Li Bei , Huo Ran 
Published: December 2019

Abstract
Background
Intestinal mucosa barrier dysfunction after burn injury is an important factor for causing mortality of burn patients. The current study established a burn model in rats and used a free radical scavenger edaravone (ED) to treat the rats, so as to investigate the effect of edaravone on intestinal mucosa barrier after burn injury.

Methods
Anesthetized rats were subjected to 40% total body surface area water burn immediately, followed by treatment with ED, scrambled antagomir, or antagomiR-320. Intestinal mucosa damage was observed by hematoxylin-eosin staining and graded by colon mucosal damage index (CMDI) score. The contents of total sulfhydryl (TSH), superoxide dismutase (SOD), catalase (CAT) and malondialdehyde (MDA) were determined by spectrophotometry. Cell apoptosis, protein relative expression,and the in situ expressions of p-Akt and p-Bad were detected by flow cytometry, Western blotting and immunohistochemistry, respectively. The miR-320 expression was determined by quantitative real-time polymerase chain reaction.

Results
ED alleviated intestinal mucosal damage caused by burn injury, down-regulated the levels of MDA, cytochrome C, cleaved caspase-9 and cleaved caspase-3, but up-regulated the levels of TSH, SOD, CAT and Bcl-2. We also found that ED could reduce oxidative stress, inhibit cell apoptosis, increase the expressions of p-Akt, p-Bad and miR-320, and decrease PTEN expression. PTEN was predicted to be the target gene for miR-320, and cell apoptosis could be promoted by inhibiting miR-320 expression.

Conclusion
ED regulates Akt/Bad/Caspase signaling cascade to reduce apoptosis and oxidative stress through up-regulating miR-320 expression and down-regulating PTEN expression, thus protecting the intestinal mucosal barrier of rats from burn injury.
DeepSV: accurate calling of genomic deletions from high-throughput sequencing data using deep convolutional neural network
Authors: Cai Lei , Wu Yufeng , Gao Jingyang 
Published: December 2019

Abstract
Background
Calling genetic variations from sequence reads is an important problem in genomics. There are many existing methods for calling various types of variations. Recently, Google developed a method for calling single nucleotide polymorphisms (SNPs) based on deep learning. Their method visualizes sequence reads in the forms of images. These images are then used to train a deep neural network model, which is used to call SNPs. This raises a research question: can deep learning be used to call more complex genetic variations such as structural variations (SVs) from sequence data?

Results
In this paper, we extend this high-level approach to the problem of calling structural variations. We present DeepSV, an approach based on deep learning for calling long deletions from sequence reads. DeepSV is based on a novel method of visualizing sequence reads. The visualization is designed to capture multiple sources of information in the sequence data that are relevant to long deletions. DeepSV also implements techniques for working with noisy training data. DeepSV trains a model from the visualized sequence reads and calls deletions based on this model. We demonstrate that DeepSV outperforms existing methods in terms of accuracy and efficiency of deletion calling on the data from the 1000 Genomes Project.

Conclusions
Our work shows that deep learning can potentially lead to effective calling of different types of genetic variations that are complex than SNPs.
First evaluation of resistance to both a California OsHV-1 variant and a French OsHV-1 microvariant in Pacific oysters
Authors: Divilov Konstantin , Schoolfield Blaine , Morga Benjamin , Dégremont Lionel , Burge Colleen A. , Mancilla Cortez Daniel , Friedman Carolyn S. , Fleener Gary B. , Dumbauld Brett R. , Langdon Chris 
Published: December 2019

Abstract
Background
Variants of the Ostreid herpesvirus 1 (OsHV-1) cause high losses of Pacific oysters globally, including in Tomales Bay, California, USA. A suite of new variants, the OsHV-1 microvariants (μvars), cause very high mortalities of Pacific oysters in major oyster-growing regions outside of the United States. There are currently no known Pacific oysters in the United States that are resistant to OsHV-1 as resistance has yet to be evaluated in these oysters. As part of an effort to begin genetic selection for resistance to OsHV-1, 71 families from the Molluscan Broodstock Program, a US West Coast Pacific oyster breeding program, were screened for survival after exposure to OsHV-1 in Tomales Bay. They were also tested in a quarantine laboratory in France where they were exposed to a French OsHV-1 microvariant using a plate assay, with survival recorded from three to seven days post-infection.

Results
Significant heritability for survival were found for all time points in the plate assay and in the survival phenotype from a single mortality count in Tomales Bay. Genetic correlations between survival against the French OsHV-1 μvar in the plate assay and the Tomales Bay variant in the field trait were weak or non-significant.

Conclusions
Future breeding efforts will seek to validate the potential of genetic improvement for survival to OsHV-1 through selection using the Molluscan Broodstock Program oysters. The lack of a strong correlation in survival between OsHV-1 variants under this study’s exposure conditions may require independent selection pressure for survival to each variant in order to make simultaneous genetic gains in resistance.
Spectrum of heart diseases in children presenting to a paediatric cardiac echocardiography clinic in the Lake Zone of Tanzania: a 7 years overview
Authors: Zuechner Antke , Mhada Tumaini , Majani Naizihijwa G. , Sharau Godwin G. , Mahalu William , Freund Matthias W. 
Published: December 2019

Abstract
Background
Congenital heart diseases (CHD) are among the most common congenital malformations. It is estimated that the incidence of CHD is constant worldwide, but data are rare for most African countries including Tanzania. Even less data are available on the prevalence of acquired heart diseases (AHD) in African children. Rheumatic heart disease (RHD) is the leading cause of AHD and is remaining a public health concern in Sub-Saharan Africa affecting especially the younger population. Both, CHD and AHD contribute substantially to morbidity and mortality during infancy and childhood.

Methods
This hospital-based, retrospective review of the registry at the paediatric cardiac clinic of Bugando Medical Centre in the Lake Zone of Tanzania analysed the spectrum of heart diseases of paediatric patients during their first presentation by using simple descriptive statistics.

Results
Between September 2009 and August 2016, a total of 3982 patients received cardiac evaluation including echocardiography studies. 1830 (46.0%) pathologic findings were described, out of these 1371 (74.9%) patients had CHD, whereas 459 (25.1%) presented with AHD.
53.9% of the patients with CHD were female and the most common associated syndrome was Down syndrome in 12.8% of patients. In 807 patients (58.9%) diagnosis of CHD was established within the first year of life. The majority of patients (60.1%) were in need of surgical or interventional therapy at time of diagnosis and 6.3% of patients were judged inoperable at the time of first presentation. Nearly 50% of cases with AHD were RHDs followed by dilated cardiomyopathy and pulmonary hypertension without underlying CHD.

Conclusions
The spectrum of CHD and AHD from one centre in Tanzania is comparable to findings reported in other countries from the African continent. Echocardiography is a valuable diagnostic tool and the widespread use of it should be enhanced to diagnose heart diseases in a large number and reasonable time. Most patients present late and majority is in need of surgical or interventional treatment, which is still not readily available. Untreated heart diseases contribute substantially to morbidity and mortality during infancy and childhood. Adequate cardiac services should be established and strengthened.
Consent to data linkage in a large online epidemiological survey of 18–23 year old Australian women in 2012–13
Authors: Graves Anna , McLaughlin Deirdre , Leung Janni , Powers Jennifer 
Published: December 2019

Abstract
Background
Consent to link survey data with health-related administrative datasets is increasingly being sought but little is known about the influence of recruiting via online technologies on participants’ consents. The goal of this paper is to examine what factors (sociodemographic, recruitment, incentives, data linkage information, health) are associated with opt-in consent to link online survey data to administrative datasets (referred to as consent to data linkage).

Methods
The Australian Longitudinal Study on Women’s Health is a prospective study of factors affecting the health and well-being of women. We report on factors associated with opt-in consent to data linkage at the end of an online survey of a new cohort of 18–23 year old Australian women recruited in 2012–13. Classification and Regression Tree analysis with decision trees was used to predict consent.

Results
In this study 69% consented to data linkage. The provision of residential address by the individual, or not (as a measure of attitudes towards privacy), was the most important factor in classifying the data into similar groups of consenters (76% consenters versus 47% respectively). Thereafter, for those who did not provide their residential address, the incentives and data linkage information that was offered was the next most important factor, with incentive 2: limited-edition designer leggings and additional information about confidentiality showing increases in consent rates over Incentive 1: AUD50 gift voucher: 60% versus 37%.

Conclusions
In young Australian women, attitudes towards privacy was strongly associated with consenting to data linkage. Providing additional details about data confidentiality was successful in increasing consent and so was cohort appropriate incentives. Ensuring that prospective participants understand the consent and privacy protocols in place to protect their confidential information builds confidence in consenting to data linkage.