bluuebunny/crossref_metadata_2025_split huggingface dataset:
ECM-related gene expression profile in vascular smooth muscle cells from human saphenous vein and internal thoracic artery
Authors: Zhu Tian-xiang , Lan Bin , Meng Ling-ying , Yang Yan-long , Li Rui-xiong , Li En-min , Zheng Shao-yi , Xu Li-yan 
Published: June 2013

Abstract

Background
Currently, Saphenous vein (SV) and internal thoracic artery (ITA) are still the most common graft materials in Coronary Artery Bypass Grafting (CABG) whereas SV graft have a lower long-term patency than ITA. Vascular smooth muscle cells (VSMCs) phenotype conversion, proliferation and migration may play a key role in mechanism of vein graft restenosis. To explore differential gene expression profile in VSMCs from SV and ITA will help to further elucidate the mechanism of VSMCs in vein graft restenosis after CABG and to provide new thread of gene therapy.

Methods
VSMCs from paired SV and ITA were cultured for experiments of Affymetrix microarrays and verification using FQ RT-PCR, while the database for annotation, visualization and integrated discovery bioinformatics resources (DAVID 2.0) was utilized for bioinformatics analysis of differential gene expression profile between SV VSMCs and ITA VSMCs. RNA of tunica media from SV and ITA segments were extracted for FQ RT-PCR to display differential expression of PLAT

Results
54,613 probe sets were examined by gene microarray experiments. In SV VSMCs, 1,075 genes were up-regulated and 406 of them were higher than two-fold; 1,399 genes were down-regulated and 424 of them were lower than two-fold as compare with ITA VSMCs.14 ECM-related genes differentially expressed were verificated and listed as following: COL4A4, COL11A1, FN1, TNC, THBS, FBLN, MMP3, MMP9, TIMP3, WNT5A, SGCD were higher whereas COL14A1, ELN, PLAT lower in SV VSMCs than ITA VSMCs. In addition, PLAT was lower in tunica media from SV segments than ITA.

Conclusion
VSMCs from SV and ITA have distinct phenotypes characteristics. Both promoting and inhibiting migration ECM-related genes were higher in VSMCs from SV as compared with ITA, suggesting that VSMCs from SV have more potential migrating capability whereas less PLAT both in SV VSMCs and vascular tissue,implying that SV may prone to be restenosis after CABG.
Intestinal ischemia after cardiac surgery: analysis of a large registry
Authors: Nilsson Johan , Hansson Erika , Andersson Bodil 
Published: June 2013

AbstractBackgroundIntestinal ischemia after cardiac surgery is a rare but severe complication with a high mortality. Early surgery can be lifesaving. The aim was to analyze the incidence, outcome, and risk factors for these patients.MethodsA prospectively collected database with patients who underwent 18,879 cardiac surgical procedures between 1996 and 2011 was investigated. All patients with registered gastrointestinal complications were retrospectively reviewed. Univariate and multivariate analyses were performed to compare patients with and without intestinal ischemia.ResultsSeventeen patients suffered from intestinal ischemia (0.09%), 10 of whom (59%) died. By investigating preoperative parameters independent risk factors were steroids, peripheral vascular disease, cardiogenic shock, and New York Heart Association class 4. When including pre-, per-, and postoperative parameters, only postoperative ones were significant, including elevated creatinine (> 200 μmol/L), prolonged ventilator time, need for intra-aortic balloon pump, and cerebrovascular insult (CVI). The gastrointestinal complications score (GICS) showed a ROC area of 0.87. This was superior compared with EuroSCORE (0.74), to predict intestinal ischemia.ConclusionsIntestinal ischemia after cardiac surgery is more common in patients with a poor cardiac state, but the use of steroids, peripheral vascular disease, postoperative kidney failure, and CVI were also predictive. GICS score, developed for all GI complications after cardiac surgery, is also of value in predicting this particular complication. The risk factors presented can be used as an aid in the diagnosis of these patients.
Novel agents and biomarkers for acute lymphoid leukemia
Authors: Zhao Yanmin , Huang He , Wei Guoqing 
Published: June 2013

Abstract
New genetic markers for adult acute lymphoblastic leukemia (ALL) have been found to have prognostic impact, such as the lymphoid transcription factor gene IKZF1 alterations, which are associated with a high rate of leukemic relapse in B-ALL. Although complete remission rates by induction chemotherapy in ALL are now high, the long-term survival is still disappointing. Improvements in the survival outcome of ALL have been observed in young adults as a result of the use of pediatric inspired regimens and the broadening of the number of patients who are eligible for allogeneic SCT. Development of new and less toxic agents also provide promise to improve the outcome in adult ALL, such as tyrosine kinase inhibitors in Ph-positive ALL, rituximab in CD20-positive disease, blinatumomab in precursor B-ALL and nelarabine in T-lineage ALL. Challenges for the future are to implement genomic profiling into the clinical setting to guide risk stratification and providing novel targets for tailored therapies.
Characterisation of enterovirus 71 replication kinetics in human colorectal cell line, HT29
Authors: Lui Yan Long Edmund , Timms Peter , Hafner Louise Marie , Tan Tuan Lin , Tan Kian Hwa , Tan Eng Lee 
Published: June 2013

Abstract
Hand, Foot and Mouth Disease (HFMD), a contagious viral disease that commonly affects infants and children with blisters and flu like symptoms, is caused by a group of enteroviruses such as Enterovirus 71 (EV71) and coxsackievirus A16 (CA16). However some HFMD caused by EV71 may further develop into severe neurological complications such as encephalitis and meningitis. The route of transmission was postulated that the virus transmit from one person to another through direct contact of vesicular fluid or droplet from the infected or via faecal-oral route. To this end, this study utilised a human colorectal adenocarcinoma cell line (HT29) with epithelioid morphology as an in vitro model for the investigation of EV71 replication kinetics. Using qPCR, viral RNA was first detected in HT29 cells as early as 12 h post infection (hpi) while viral protein was first detected at 48 hpi. A significant change in HT29 cells’ morphology was also observed after 48 hpi. Furthermore HT29 cell viability also significantly decreased at 72 hpi. Together, data from this study demonstrated that co-culture of HT29 with EV71 is a useful in vitro model to study the pathogenesis of EV71.
Improving outcomes of acute kidney injury using mouse renal progenitor cells alone or in combination with erythropoietin or suramin
Authors: Han Xiao , Zhao Li , Lu Guodong , Ge Junke , Zhao Yalin , Zu Shulu , Yuan Mingzhen , Liu Yuqiang , Kong Feng , Xiao Zhiying , Zhao Shengtian 
Published: June 2013

Abstract
Introduction
So far, no effective therapy is available for acute kidney injury (AKI), a common and serious complication with high morbidity and mortality. Interest has recently been focused on the potential therapeutic effect of mouse adult renal progenitor cells (MRPC), erythropoietin (EPO) and suramin in the recovery of ischemia-induced AKI. The aim of the present study is to compare MRPC with MRPC/EPO or MRPC/suramin concomitantly in the treatment of a mouse model of ischemia/reperfusion (I/R) AKI.

Methods
MRPC were isolated from adult C57BL/6-gfp mice. Male C57BL/6 mice (eight-weeks old, n = 72) were used for the I/R AKI model. Serum creatinine (Cr), blood urea nitrogen (BUN) and renal histology were detected in MRPC-, MRPC/EPO-, MRPC/suramin- and PBS-treated I/R AKI mice. E-cadherin, CD34 and GFP protein expression was assessed by immunohistochemical assay.

Results
MRPC exhibited characteristics consistent with renal stem cells. The features of MRPC were manifested by Pax-2, Oct-4, vimentin, α-smooth muscle actin positive, and E-cadherin negative, distinguished from mesenchymal stem cells (MSC) by expression of CD34 and Sca-1. The plasticity of MRPC was shown by the ability to differentiate into osteoblasts and lipocytes in vitro. Injection of MRPC, especially MRPC/EPO and MRPC/suramin in I/R AKI mice attenuated renal damage with a decrease of the necrotic injury, peak plasma Cr and BUN. Furthermore, seven days after the injury, MRPC/EPO or MRPC/suramin formed more CD34+ and E-cadherin+ cells than MRPC alone.

Conclusions
These results suggest that MRPC, in particular MRPC/EPO or MRPC/suramin, promote renal repair after injury and may be a promising therapeutic strategy.
Follicular Lymphoma Cells Induce Changes in T-Cell Gene Expression and Function: Potential Impact on Survival and Risk of Transformation
Authors: Kiaii Shahryar , Clear Andrew J. , Ramsay Alan G. , Davies Derek , Sangaralingam Ajanthah , Lee Abigail , Calaminici Maria , Neuberg Donna S. , Gribben John G. 
Published: June 2013

PurposePrevious studies have demonstrated the prognostic importance of the immune microenvironment in follicular lymphoma (FL). To investigate the molecular mechanisms during which tumor-infiltrating T cells (TILs) are altered in the FL microenvironment, we studied highly purified CD4 and CD8 TILs from lymph node biopsies at diagnosis in treatment-naive patients with FL compared with reactive tonsils and the peripheral blood of healthy donors.Patients and MethodsGene expression profiling of highly purified CD4 and CD8 TILs was performed on the Affymetrix platform. Diagnostic tissue microarrays from an independent patient set (n = 172) were used to verify protein expression and analyze any impact of TIL-expressed genes on outcome. Time-lapse imaging was used to assess T-cell motility.ResultsThe most upregulated genes in both CD4 and CD8 TILs were PMCH, ETV1, and TNFRSF9. PMCH is not expressed in peripheral blood T cells, but expression is highly induced on culture with FL. Both CD4 and CD8 TILs from patients with FL have significantly impaired motility compared with those of healthy TILs from reactive tonsils and this can be induced on healthy T cells by FL cells. During multivariate analysis, a model incorporating the number and location of T cells expressing PMCH, NAMPT, and ETV1 showed prognostic significance for overall survival and for time to transformation.ConclusionWe showed altered gene expression in TILs in FL and demonstrated that altering the immune microenvironment in FL affects overall survival and time to transformation in this disease.
Randomized Phase III Trial of Single-Agent Pemetrexed Versus Carboplatin and Pemetrexed in Patients With Advanced Non–Small-Cell Lung Cancer and Eastern Cooperative Oncology Group Performance Status of 2
Authors: Zukin Mauro , Barrios Carlos H. , Rodrigues Pereira Jose , De Albuquerque Ribeiro Ronaldo , de Mendonça Beato Carlos Augusto , do Nascimento Yeni Neron , Murad Andre , Franke Fabio A. , Precivale Maristela , de Lima Araujo Luiz Henrique , Da Rocha Baldotto Clarissa Serodio , Vieira Fernando Meton , Small Isabele A. , Ferreira Carlos G. , Lilenbaum Rogerio C. 
Published: June 2013

Purpose To compare single-agent pemetrexed (P) versus the combination of carboplatin and pemetrexed (CP) in first-line therapy for patients with advanced non–small-cell lung cancer (NSCLC) with an Eastern Cooperative Oncology Group (ECOG) performance status (PS) of 2. Patients and Methods In a multicenter phase III randomized trial, patients with advanced NSCLC, ECOG PS of 2, any histology at first and later amended to nonsquamous only, no prior chemotherapy, and adequate organ function were randomly assigned to P alone (500 mg/m2) or CP (area under the curve of 5 and 500 mg/m2, respectively) administered every 3 weeks for a total of four cycles. The primary end point was overall survival (OS). Results A total of 205 eligible patients were enrolled from eight centers in Brazil and one in the United States from April 2008 to July 2011. The response rates were 10.3% for P and 23.8% for CP (P = .032). In the intent-to-treat population, the median PFS was 2.8 months for P and 5.8 months for CP (hazard ratio [HR], 0.46; 95% CI, 0.35 to 0.63; P < .001), and the median OS was 5.3 months for P and 9.3 months for CP (HR, 0.62; 95% CI, 0.46 to 0.83; P = .001). One-year survival rates were 21.9% and 40.1%, respectively. Similar results were seen when patients with squamous disease were excluded from the analysis. Anemia (grade 3, 3.9%; grade 4, 11.7%) and neutropenia (grade 3, 1%; grade 4, 6.8%) were more frequent with CP. There were four treatment-related deaths in the CP arm. Conclusion Combination chemotherapy with CP significantly improves survival in patients with advanced NSCLC and ECOG PS of 2.
Expectations About the Effectiveness of Radiation Therapy Among Patients With Incurable Lung Cancer
Authors: Chen Aileen B. , Cronin Angel , Weeks Jane C. , Chrischilles Elizabeth A. , Malin Jennifer , Hayman James A. , Schrag Deborah 
Published: June 2013

Purpose Although radiation therapy (RT) can palliate symptoms and may prolong life, it is not curative for patients with metastatic lung cancer. We investigated patient expectations about the goals of RT for incurable lung cancers. Patients and Methods The Cancer Care Outcomes Research and Surveillance Consortium enrolled a population- and health system–based cohort of patients diagnosed with lung cancer from 2003 to 2005. We identified patients with stage wet IIIB or IV lung cancer who received RT and answered questions on their expectations about RT. We assessed patient expectations about the goals of RT and identified factors associated with inaccurate beliefs about cure. Results In all, 384 patients completed surveys on their expectations about RT. Seventy-eight percent of patients believed that RT was very or somewhat likely to help them live longer, and 67% believed that RT was very or somewhat likely to help them with problems related to their cancer. However, 64% did not understand that RT was not at all likely to cure them. Older patients and nonwhites were more likely to have inaccurate beliefs, and patients whose surveys were completed by surrogates were less likely to have inaccurate beliefs. Ninety-two percent of patients with inaccurate beliefs about cure from RT also had inaccurate beliefs about chemotherapy. Conclusion Although patients receiving RT for incurable lung cancer believe it will help them, most do not understand that it is not at all likely to cure their disease. This indicates a need to improve communication regarding the goals and limitations of palliative RT.
A Comprehensive Assay for CFTR Mutational Analysis Using Next-Generation Sequencing
Authors: Abou Tayoun Ahmad N , Tunkey Christopher D , Pugh Trevor J , Ross Tristen , Shah Minita , Lee Clarence C , Harkins Timothy T , Wells Wendy A , Tafe Laura J , Amos Christopher I , Tsongalis Gregory J 
Published: June 2013

BACKGROUND
Cystic fibrosis is a life-threatening genetic disorder that has been associated with mutations in the CFTR [cystic fibrosis transmembrane conductance regulator (ATP-binding cassette sub-family C, member 7)] gene. Hundreds of CFTR mutations have been detected to date. Current CFTR genotyping assays target a subset of these mutations, particularly a mutation panel recommended by the American College of Medical Genetics for carrier screening of the general population. Fast sequencing of the entire coding sequence in a scalable manner could expand the detection of CFTR mutations and facilitate management of costs and turnaround times in the clinical laboratory.

METHODS
We describe a proof-of-concept CFTR assay that uses PCR target enrichment and next-generation sequencing on the Ion Torrent Personal Genome Machine™ (PGM™) platform.

RESULTS
The scalability of the assay was demonstrated, with an average mean depth of coverage ranging from 500× to 3500×, depending on the number of multiplexed patient samples and the Ion Torrent chip used. In a blinded study of 79 previously genotyped patient DNA samples and cell lines, our assay detected most of the mutations, including single-nucleotide variants, small insertions and deletions, and large copy-number variants. The reproducibility was 100% for detecting mutations in independent runs. Our assay demonstrated high specificity, with only 2 false-positive calls (at 2184delA) found in 2 samples caused by a sequencing error in a homopolymer stretch of sequence. The detection rate for variants of unknown significance was very low in the targeted region.

CONCLUSIONS
With continued optimization and system refinements, PGM sequencing promises to be a powerful, rapid, and scalable means of clinical diagnostic sequencing.
Poverty, Inequality, Political Instability and Property Crimes in Pakistan: A Time Series Analysis
Authors: Syed Shabib Haider , Ahmed Eatzaz 
Published: June 2013

Abstract
In a formal econometric analysis of crime statistics in Pakistan, this paper estimates five systems of equations determining crime rates against property, conviction rates and police and justice input using time series annual data. The study finds substantial empirical support for the model of crime, punishment and deterrence based on economic theory. The main conclusion of the study is that in the fight against crime Pakistan needs to divert resources from the provision of legal justice through various deterrence measures, like a large police force, conviction and punishment, towards the provision of social justice in the form of the fight against poverty, inequality and unemployment and maintenance of political stability. Resources also need to be diverted from punishments to apprehension of criminals.
Analyzing the Motivations of a Joint Venture to Provide High-Quality Music Download Service to Mobile Phones
Authors: Arai Koki 
Published: June 2013

Abstract
This article explores the motivations of a joint venture to provide a high-quality music download service for mobile phones that resulted from a case of a concerted refusal to trade; this refusal was a violation of Antimonopoly Law. We analyze 5 years of monthly compact disk (CD) singles sales in order to identify the incentive for the concerted refusal to trade. The results show that when a CD single is ranked within the top three according to national sales charts, the effect of this factor is significantly greater than can be attributed to any simple ranking proportional effect, which is a prediction of the rank based on the number of sales in the week. Furthermore, we find that the complementary relationship among major companies as expressed by a joint venture could offer benefits. Commitment to a joint venture for the purpose of conveying one’s recognition of the venture and potentially beneficial intentions are a key determinant for joint venture formation.
Asymptotics of random Betti tables
Authors: Ein Lawrence , Erman Daniel , Lazarsfeld Robert 
Published: June 2013

Abstract

This paper is motivated by the question of understanding the asymptotic behavior of the Betti numbers of the resolution of the ideal of a projective variety as the positivity of the embedding line bundle grows. We present a conjecture asserting that these invariants approach a Gaussian distribution, and we verify this in the case of curves. Then we work out the asymptotics of “random” Betti tables with a fixed number of rows, sampled according to a uniform choice of Boij–Söderberg coefficients. This analysis suggests that the normal distribution of Betti numbers is in any event the typical behavior from a probabilistic viewpoint.
Simple groups are characterized by their non-commuting graphs
Authors: Solomon Ronald M. , Woldar Andrew J. 
Published: June 2013

Abstract.
The non-commuting graph of a finite group G is a highly symmetrical object (indeed, embeds in ), yet its complexity pales in comparison to that of G. Still, it is natural to seek conditions under which G can be reconstructed from . Surely some conditions are necessary, as is evidenced by the minuscule example . A conjecture made in [J. Algebra 298 (2006), 468–492], commonly referred to as the AAM Conjecture, proposes that the property of being a nonabelian simple group is sufficient. In [Sib. Math. J. 49 (2008), no. 6, 1138–1146], this conjecture is verified for all sporadic simple groups, while in [J. Algebra 357 (2012), 203–207], it is verified for the alternating groups. In this paper we verify it for the simple groups of Lie type, thereby completing the proof of the conjecture.
Voice Activity Detection Algorithm Using Zero Frequency Filter Assisted Peaking Resonator and Empirical Mode Decomposition
Authors: Rudramurthy M.S. , Prasad V. Kamakshi , Kumaraswamy R. 
Published: June 2013

AbstractIn this article, a new adaptive data-driven strategy for voice activity detection (VAD) using empirical mode decomposition (EMD) is proposed. Speech data are decomposed using an a posteriori, adaptive, data-driven EMD in the time domain to yield a set of physically meaningful intrinsic mode functions (IMFs). Each IMF preserves the nonlinear and nonstationary property of the speech utterance. Among a set of IMFs, the IMF that contains source information dominantly called characteristic IMF (CIMF) can be identified and extracted by designing a zero-frequency filter-assisted peaking resonator. The detected CIMF is used to compute energy using short-term processing. Choosing proper threshold, voiced regions in speech utterances are detected using frame energy. The proposed framework has been studied on both clean speech utterance and noisy speech utterance (0-dB white noise). The proposed method is used for voice activity detection (VAD) in the presence of white noise and shows encouraging result in the presence of white noise up to 0 dB.
Low-power tunnel field effect transistors using mixed As and Sb based heterostructures
Authors: Zhu Yan , Hudait Mantu K. 
Published: June 2013

AbstractReducing supply voltage is a promising way to address the power dissipation in nano-electronic circuits. However, the fundamental lower limit of subthreshold slope (SS) within metal oxide semiconductor field effect transistors (MOSFETs) is a major obstacle to further scaling the operation voltage without degrading ON/OFF ratio in current integrated circuits. Tunnel field-effect transistors (TFETs) benefit from steep switching characteristics due to the quantum-mechanical tunneling injection of carriers from source to channel, rather than by conventional thermionic emission in MOSFETs. TFETs based on group III-V compound semiconductor materials further improve the ON-state current and reduce SS due to the low band gap energies and smaller carrier tunneling mass. The mixed arsenide/antimonide (As/Sb) InxGa1-xAs/GaAsySb1-y heterostructures allow a wide range of band gap energies and various staggered band alignments depending on the alloy compositions in the source and channel materials. Band alignments at source/channel heterointerface can be well modulated by carefully controlling the compositions of the mixed As/Sb material system. In particular, this review introduces and summarizes the progress in the development and optimization of low-power TFETs using mixed As/Sb based heterostructures including basic working principles, design considerations, material growth, interface engineering, material characterization, device fabrication, device performance investigation, band alignment determination, and high temperature reliability. A review of TFETs using mixed As/Sb based heterostructures shows superior structural properties and distinguished device performance, both of which indicate the mixed As/Sb staggered gap TFET as a promising option for high-performance, low-standby power, and energy-efficient logic circuit application.