bluuebunny/crossref_metadata_2025_split huggingface dataset:
A comprehensive survey of copy number variation in 18 diverse pig populations and identification of candidate copy number variable genes associated with complex traits
Authors: Chen Congying , Qiao Ruimin , Wei Rongxing , Guo Yuanmei , Ai Huashui , Ma Junwu , Ren Jun , Huang Lusheng 
Published: December 2012

Abstract

Background
Copy number variation (CNV) is a major source of structural variants and has been commonly identified in mammalian genome. It is associated with gene expression and may present a major genetic component of phenotypic diversity. Unlike many other mammalian genomes where CNVs have been well annotated, studies of porcine CNV in diverse breeds are still limited.

Result
Here we used Porcine SNP60 BeadChip and PennCNV algorithm to identify 1,315 putative CNVs belonging to 565 CNV regions (CNVRs) in 1,693 pigs from 18 diverse populations. Total 538 out of 683 CNVs identified in a White Duroc × Erhualian F2 population fit Mendelian transmission and 6 out of 7 randomly selected CNVRs were confirmed by quantitative real time PCR. CNVRs were non-randomly distributed in the pig genome. Several CNV hotspots were found on pig chromosomes 6, 11, 13, 14 and 17. CNV numbers differ greatly among different pig populations. The Duroc pigs were identified to have the most number of CNVs per individual. Among 1,765 transcripts located within the CNVRs, 634 genes have been reported to be copy number variable genes in the human genome. By integrating analysis of QTL mapping, CNVRs and the description of phenotypes in knockout mice, we identified 7 copy number variable genes as candidate genes for phenotypes related to carcass length, backfat thickness, abdominal fat weight, length of scapular, intermuscle fat content of logissimus muscle, body weight at 240 day, glycolytic potential of logissimus muscle, mean corpuscular hemoglobin, mean corpuscular volume and humerus diameter.

Conclusion
We revealed the distribution of the unprecedented number of 565 CNVRs in pig genome and investigated copy number variable genes as the possible candidate genes for phenotypic traits. These findings give novel insights into porcine CNVs and provide resources to facilitate the identification of trait-related CNVs.
Correlation of the presence and extent of loss of heterozygosity mutations with histological classifications of Barrett’s esophagus
Authors: Ellsworth Eric , Jackson Sara A , Thakkar Shyam J , Smith Dennis M , Finkelstein Sydney 
Published: December 2012

Abstract

Background
Recent advances in the management of Barrett’s Esophagus (BE) have placed greater emphasis on accurate diagnosis of BE as well as better prediction of risk for progression to esophageal adenocarcinoma (EAC). Histological evaluation of BE is particularly challenging with significant inter-observer variability. We explored the presence and extent of genomic instability in BE biopsy specimens as a means to add supplementary information to the histological classification and clinical decision-making related to early disease.

Methods
We reviewed histology slides from 271 patients known to have BE. Using histological features as a guide, we microdissected target cell populations with various histological classifications of BE (intestinal metaplasia, “indefinite for dysplasia”, low grade dysplasia, or high grade dysplasia). DNA was extracted from microdissected targets and analyzed for loss of heterozygosity (LOH) using a panel of 16 LOH mutational markers associated with tumor suppressor genes at chromosomal loci 1p, 3p, 5q, 9p, 10q, 17p, 17q, 18q, 21q, 22q. The presence or absence of mutations and the clonality of each mutation were determined for each marker.

Results
The presence and clonal expansion of LOH mutations was formulated into mutational load (ML) for each microdissected target analyzed. ML correlated with the histological classification of microdissected targets, with increasingly severe histology having higher ML. Three levels of mutation load (no ML, low ML, and high ML) were defined based on the population of microdissected targets histologically classified as intestinal metaplasia. All microdissected targets with dysplasia had mutations, with a high ML consistently present in high grade dysplasia targets. Microdissected targets histologically classified as intestinal metaplasia or “indefinite for dysplasia” spanned a range of no, low, and high ML.

Conclusions
The results of this study reinforce the association of genomic instability with disease progression in BE. The presence and extent (clonality) of genomic instability, as assessed by mutational load, may assist histology in defining early stages of BE that are potentially at greater risk for disease progression. Assessment of mutational load using our panel of LOH mutational markers may be a useful adjunct to microscopic inspection of biopsy specimens, and thereby, improve patient management.
The risk allele of SNP rs3803662 and the mRNA level of its closest genes TOX3 and LOC643714predict adverse outcome for breast cancer patients
Authors: Gudmundsdottir Eydis Th , Barkardottir Rosa B , Arason Adalgeir , Gunnarsson Haukur , Amundadottir Laufey Th , Agnarsson Bjarni A , Johannsson Oskar Th , Reynisdottir Inga 
Published: December 2012

AbstractBackgroundThe minor allele of SNP rs3803662 has been shown to correlate with increased breast cancer risk and with lower expression ofTOX3. The SNP is closely located toTOX3residing within an uncharacterised geneLOC643714. The aim of the study was to examine the association of the risk allele with expression ofTOX3andLOC643714,and of mRNA levels and genotype with clinical and pathological characteristics.MethodsThe SNP was genotyped in DNA isolated from blood and normal tissue from 160 breast cancer patients and mRNA levels were measured by microarrays and quantitative real-time (qRT)-PCR in breast tumours. Association with clinical and pathological characteristics was analysed by parametric tests.ResultsAn association of the risk allele of rs3803662 with lowerTOX3expression was confirmed in oestrogen receptor (ER) positive tumours. It was more often observed in lobular tumours (p = 0.04), and carriers of the risk allele who had been diagnosed with luminal A tumours had shorter overall survival (OS) than carriers of the non-risk allele (p = 0.01). Positive correlation between the mRNA levels ofTOX3andLOC643714was observed (r = 0.44 and p < 0.001). Association analysis with tumour pathology showed that lowTOX3andLOC643714expression correlated with high Ki67 levels (p = 0.026 and p = 0.002) and the basal subtype (p < 0.001 and p < 0.001), whereas high expression correlated with ER (p = 0.004 and p < 0.001) and progesterone receptor (PgR) (p = 0.005 and p < 0.001) expression. Furthermore, high TOX3 and LOC643714 correlated with positive lymph nodes (p < 0.001 and p = 0.01). Patients with ER positive tumours and high levels ofTOX3mRNA had shorter overall- and distant metastasis free-survival (p = 0.017 and p = 0.021), an effect mostly attributable to patients with luminal B tumours.ConclusionsThe results suggest that the effect of the risk allele of rs3803662 is strongest in luminal A tumours and that the expression levels ofTOX3and/orLOC643714affect the progression of breast cancer. The effect may vary depending on the subtype and developmental stage of the tumour.
Autophagy-independent enhancing effects of Beclin 1 on cytotoxicity of ovarian cancer cells mediated by proteasome inhibitors
Authors: Liu Chuan , Yan Xu , Wang Hua-Qin , Gao Yan-Yan , Liu Juanjuan , Hu Zhenhua , Liu Dawo , Gao Jian , Lin Bei 
Published: December 2012

Abstract

Background
The ubiquitin-proteasome system and macroautophagy (hereafter referred to autophagy) are two complementary pathways for protein degradation. Emerging evidence suggests that proteasome inhibition might be a promising approach for tumor therapy. Accumulating data suggest that autophagy is activated as a compensatory mechanism upon proteasome activity is impaired.

Method
Autophagy activation was measured using acridine orange staining and LC3 transition. Cell viability and apoptosis were measured using MTT assay and flow cytometry, respectively. Beclin 1 expression vectors or shRNA against Beclin 1 (shBeclin 1) were transfected to investigate the role of Beclin 1 in autophagy activation and cytotoxicity of ovarian cancer cells induced by proteasome inhibitors.

Results
Proteasome inhibitors suppressed proliferation and induced autophagy in ovarian cancer cells. Neither phosphoinositide 3-kinase (PI3K) inhibitors nor shRNA against Beclin 1 could abolish the formation of acidic vacuoles and the processing of LC3 induced by proteasome inhibitors. Moreover, Beclin 1 overexpression enhanced anti-proliferative effects of proteasome inhibitors in ovarian cancer cells.

Conclusions
For the first time, the current study demonstrated that proteasome inhibitors induced PI3K and Beclin 1-independent autophagy in ovarian cancer cells. In addition, this study revealed autophagy-independent tumor suppressive effects of Beclin 1 in ovarian cancer cells.
Predictors of malaria-association with rubber plantations in Thailand
Authors: Satitvipawee Pratana , Wongkhang Warunnee , Pattanasin Sarika , Hoithong Penprapai , Bhumiratana Adisak 
Published: December 2012

Abstract

Background
The national Global Fund-supported malaria (GFM) program in Thailand, which focuses on the household-level implementation of vector control via insecticide-treated nets (ITNs)/long-lasting insecticidal nets (LLINs) combined with indoor residual spraying (IRS), has been combating malaria risk situations in different provinces with complex epidemiological settings. By using the perception of malaria villagers (MVs), defined as villagers who recognized malaria burden and had local understanding of mosquitoes, malaria, and ITNs/LLINs and practiced preventive measures, this study investigated the predictors for malaria that are associated with rubber plantations in an area of high household-level implementation coverage of IRS (2007–2010) and ITNs/LLINs (2008–2010) in Prachuap Khiri Khan Province.

Methods
A structured questionnaire addressing socio-demographics, household characteristics and health behavioral factors (knowledge, perceptions and practices) regarding the performed interventions was administered to the 313 households (70 malaria-affected and 243 malaria-unaffected) that had respondents aged ≥18 years of both genders. In the univariate and multivariate analyses, only 246 (78.6%) MV respondents (62 malaria-affected and 184 malaria-unaffected) were analyzed to determine the predictors for risk (morbidity).

Results
The majority (70%) of households were covered by IRS. For a combination of ITNs/LLINs, there were 74% of malaria-affected households covered and 46% of malaria-unaffected households. In a logistic regression analysis using odds ratios (aORs) adjusted on the variables and a 95% confidence interval (CI), malaria affecting MVs was associated with daily worker (i.e., earning daily income by normally practicing laborious activities mostly in agriculture such as rubber tapping and rubber sheet processing at the smallholdings of rubber plantations) (aOR = 2.9, 95% CI: 1.1-7.4), low-moderate level of malaria knowledge (aOR = 2.4, 95% CI: 1.1-5.0) and sleeping under mosquito-nets (nets/ITNs/LLINs intermittently and ITNs/LLINs only) (aOR = 2.0, 95% CI: 1.0-3.7).

Conclusions
The MV predictors for malaria-association with rubber plantations included occupation (daily worker), misconceptions about malaria (mosquito and prevention) and the use of mosquito-nets. Human practices such as revisiting rubber plantations while exposed to multiple bites at multiple locations are more likely to apply to daily workers than to rubber farmers/tappers and others. The promotion and use of ITNs/LLINs depends substantially on cultural factors and defensive behaviors relevant to their occupational risk despite the perceived threats of malaria and the perceived benefits of ITNs/LLINs. This information supports the conclusion that GFM program implementation in Thailand or elsewhere for malaria-associated with rubber plantations would benefit from the potential use of ITNs/LLINs and changes in personal protection behaviors.
Clinical significance of troponin elevations in acute decompensated diabetes without clinical acute coronary syndrome
Authors: Eubanks Anthony , Raza Farhan , Alkhouli Mohamad , Glenn April N , Homko Carol , Kashem Abul , Bove Alfred 
Published: December 2012

Abstract

Background
Elevation of cardiac troponin has been documented in multiple settings without acute coronary syndrome. However, its impact on long-term cardiac outcomes in the context of acute decompensated diabetes remains to be explored.

Methods
We performed a retrospective analysis of 872 patients admitted to Temple University Hospital from 2004–2009 with DKA or HHS. Patients were included if they had cardiac troponin I (cTnI) measured within 24 hours of hospital admission, had no evidence of acute coronary syndrome and had a follow up period of at least 18 months. Of the 264 patients who met the criteria, we reviewed the baseline patient characteristics, admission labs, EKGs and major adverse cardiovascular events during the follow up period. Patients were categorized into two groups with normal and elevated levels of cardiac enzymes. The composite end point of the study was the occurrence of a major cardiovascular event (MACE) during the follow up period and was compared between the two groups.

Results
Of 264 patients, 24 patients were found to have elevated cTnI. Compared to patients with normal cardiac enzymes, there was a significant increase in incidence of MACE in patients with elevated cTnI. In a regression analysis, which included prior history of CAD, HTN and ESRD, the only variable that independently predicted MACE was an elevation in cTnI (p = 0.044). Patients with elevated CK-MB had increased lengths of hospitalization compared to the other group (p < 0.001).

Conclusions
Elevated cardiac troponin I in patients admitted with decompensated diabetes and without evidence of acute coronary syndrome, strongly correlate with a later major cardiovascular event. Thus, elevated troponin I during metabolic abnormalities identify a group of patients at an increased risk for poor long-term outcomes. Whether these patients may benefit from early detection, risk stratification and preventive interventions remains to be investigated.
Synthesis, characterization and toxicological evaluation of maltodextrin capped cadmium sulfide nanoparticles in human cell lines and chicken embryos
Authors: Rodríguez-Fragoso Patricia , Reyes-Esparza Jorge , León-Buitimea Angel , Rodríguez-Fragoso Lourdes 
Published: December 2012

Abstract

Background
Semiconductor Quantum dots (QDs) have become quite popular thanks to their properties and wide use in biological and biomedical studies. However, these same properties entail new challenges in understanding, predicting, and managing potential adverse health effects following exposure. Cadmium and selenium, which are the major components of the majority of quantum dots, are known to be acutely and chronically toxic to cells and organisms. Protecting the core of nanoparticles can, to some degree, control the toxicity related to cadmium and selenium leakage.

Results
This study successfully synthesized and characterized maltodextrin coated cadmium sulfide semiconductor nanoparticles. The results show that CdS-MD nanoparticles are cytotoxic and embryotoxic. CdS-MD nanoparticles in low concentrations (4.92 and 6.56 nM) lightly increased the number of HepG2 cell. A reduction in MDA-MB-231 cells was observed with concentrations higher than 4.92 nM in a dose response manner, while Caco-2 cells showed an important increase starting at 1.64 nM. CdS-MD nanoparticles induced cell death by apoptosis and necrosis in MDA-MD-231 cells starting at 8.20 nM concentrations in a dose response manner. The exposure of these cells to 11.48-14.76 nM of CdS-MD nanoparticles induced ROS production. The analysis of cell proliferation in MDA-MB-231 showed different effects. Low concentrations (1.64 nM) increased cell proliferation (6%) at 7 days (p < 0.05). However, higher concentrations (>4.92 nM) increased cell proliferation in a dose response manner (15-30%) at 7 days. Exposures of chicken embryos to CdS-MD nanoparticles resulted in a dose-dependent increase in anomalies that, starting at 9.84 nM, centered on the heart, central nervous system, placodes, neural tube and somites. No toxic alterations were observed with concentrations of < 3.28 nM, neither in cells nor chicken embryos.

Conclusions
Our results indicate that CdS-MD nanoparticles induce cell death and alter cell proliferation in human cell lines at concentrations higher than 4.92 nM. We also demonstrated that they are embryotoxic. However, no toxic effects were observed with doses lower than 3.28 nM in neither cells nor chicken embryos. The CdS-MD nanoparticles used in this study can be potentially used in bio-imaging applications. However, further studies using mammalian species are required in order to discard more toxic effects.
A best proximity point theorem for Geraghty-contractions
Authors: Caballero J , Harjani J , Sadarangani K 
Published: December 2012

Abstract
The purpose of this paper is to provide sufficient conditions for the existence of a unique best proximity point for Geraghty-contractions.
Our paper provides an extension of a result due to Geraghty (Proc. Am. Math. Soc. 40:604-608, 1973).
Approximate perfect differential equations of second order
Authors: Abdollahpour Mohammad Reza , Najati Abbas , Park Choonkil , Rassias Themistocles M , Shin Dong Yun 
Published: December 2012

Abstract
In this paper we prove the Hyers-Ulam stability of the perfect linear differential equation

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Application of iron nanaoparticles in landfill leachate treatment - case study: Hamadan landfill leachate
Authors: Kashitarash Zahra Esfahani , Taghi Samadi Mohammad , Kazem Naddafi , Abbass Afkhami , Alireza Rahmani 
Published: December 2012

Abstract
This study was performed with the objective of determining the efficiency of iron nanoparticles for reducing chemical oxygen demand (COD), 5-day biological oxygen demand (BOD5), total solids (TS) and color of Hamadan city landfill leachate. Experiments were performed in a batch reactor and the main effective factors of pH, reaction time and concentration of iron nanoparticles were investigated. The obtained data were analyzed with One-Way ANOVA statistical test and SPSS-13 software. Maximum removal efficiencies were 47.94%, 35%, 55.62% and 76.66% for COD, BOD5, TS and color, respectively (for 2.5 g/L iron nanoparticles dosage, pH = 6.5 and 10 min reaction time). The results showed that the removal of COD, BOD5 and color had reverse relationship with contact time and TS removal followed a direct relationship (P < 0.05). Iron nanoparticles could remove averagely 53% of leachate COD, BOD5, TS and color in a short contact time (10 min) increasing pH up to 6.5, increased the removal efficiency for COD, BOD5, TS and color and then removal efficiency decreased with increasing pH to 8.5. Increasing the dosage of nanoparticles to 2.5 g/L increased the efficiency of process. High compatibility and efficiency of this process was proven by landfill leachate pre-treatment or post-treatment, so this removal method may be recommended for municipal solid waste landfill leachate treatment plants.
Immunotherapy using slow-cycling tumor cells prolonged overall survival of tumor-bearing mice
Authors: Sun Qing , Zhong Yong , Wu Fan , Zhou Chunxia , Wang Dongmei , Ma Wenbo , Zhang Youhui , Zhang Shuren 
Published: December 2012

Abstract

Background
Despite considerable progress in the development of anticancer therapies, there is still a high mortality rate caused by cancer relapse and metastasis. Dormant or slow-cycling residual tumor cells are thought to be a source of tumor relapse and metastasis, and are therefore an obstacle to therapy. In this study, we assessed the drug resistance of tumor cells in mice, and investigated whether vaccination could promote survival.

Methods
The mouse colon carcinoma cell line CT-26 was treated with 5-fluorouracil to assess its sensitivity to drug treatment. Mice with colon tumors were immunized with inactivated slow-cycling CT-26 cells to estimate the efficacy of this vaccine.

Results
We identified a small population of slow-cycling tumor cells in the mouse colon carcinoma CT-26 cell line, which was resistant to conventional chemotherapy. To inhibit tumor recurrence and metastasis more effectively, treatments that selectively target the slow-cycling tumor cells should be developed to complement conventional therapies. We found that drug-treated, slow-cycling tumor cells induced a more intense immune response in vitro. Moreover, vaccination with inactivated slow-cycling tumor cells caused a reduction in tumor volume and prolonged the overall survival of tumor-bearing mice.

Conclusions
These findings suggest that targeting of slow-cycling tumor cells application using immunotherapy is a possible treatment to complement traditional antitumor therapy.
Development of a loop-mediated isothermal amplification method to rapidly detect porcine circovirus genotypes 2a and 2b
Authors: Qiu Xiaohuo , Li Tian , Zhang Guorui , Cao Jingjing , Jin Yulan , Xing Gang , Liao Min , Zhou Jiyong 
Published: December 2012

Abstract

Background
Porcine circovirus type 2 (PCV2), is nowadays associated with a number of diseases known as porcine circovirus-associated diseases (PCVAD), especially postweaning multisystemic wasting syndrome (PMWS). The epidemiological investigation of PCV2 infection was usually conducted by PCR, nested PCR, PCR-RFLP, TaqMan-based assay and nucleotide sequencing. However, there is still no rapid, sensitive and practical method for detecting PCV2 genotypes. As a novel nucleic acid amplification method, the loop-mediated isothermal amplification method (LAMP) has been used to detect a variety of pathogenic microorganisms.

Results
Herein, a LAMP method is developed to detect the genotypes of PCV2. The diagnostic sensitivity of LAMP is 1 copy/reaction for differentiating genotypes PCV2a and PCV2b. The reaction process was completed at 65°C for 1 hour in a water bath. Cross-reactivity assay shows that this method is specific for PCV2a and PCV2b and no reactive for PCV2c and other swine-origin viruses (i.e. CSFV, PRRSV, BVDV, TGEV and PEDV, etc). Identity between LAMP and nested PCR was 92.3% on 52 field clinical samples.

Conclusions
LAMP method provides a rapid, sensitive, reliable way to detect PCV2a and PCV2b, and a better means for the large scale investigation of PCV2a and PCV2b infection.