bluuebunny/crossref_metadata_2025_split huggingface dataset:
High prevalence of gastroesophageal reflux symptoms in type 2 diabetics with hypoadiponectinemia and metabolic syndrome
Authors: Hirata Ayumu , Kishida Ken , Nakatsuji Hideaki , Inoue Kana , Hiuge-Shimizu Aki , Funahashi Tohru , Shimomura Iichiro 
Published: January 2012

Abstract

Background
The prevalence of gastroesophageal reflux disease (GERD) has been increasing worldwide. Abdominal obesity or visceral fat accumulation rather than simple obesity is associated with GERD. Previous reports demonstrated the association between GERD and type 2 diabetes mellitus (T2DM). Signification of visceral fat accumulation and adiponectin in T2DM patients with GERD remains unclear. The present study investigated the relationships between GERD symptoms, visceral fat accumulation and adiponectin in subjects with T2DM.

Findings
The study (ADMIT study) subjects were 66 Japanese T2DM outpatients, who answered the questionnaire regarding GERD symptoms in Frequency Scale for the Symptoms of GERD (FSSG), and were measured visceral fat area by bioelectrical impedance analysis. Patients with FSSG scores of more than 8 were considered as positive. The prevalence of FSSG score ≥ 8 and average FSSG score in T2DM subjects with the metabolic syndrome (Mets) were significantly higher compared to those without Mets. The prevalence of FSSG score ≥ 8 and average FSSG score in T2DM subjects with low levels of serum adiponectin were significantly higher compared to those with high levels of serum adiponectin. Moreover, the combination of Mets and hypoadiponectinemia had a multiplicative effect on GERD symptom score (p = 0.047).

Conclusions
Our study showed that the coexistence of MetS and low levels of serum adiponectin was associated with the higher prevalence of FSSG score ≥ 8 and the higher scores of GERD symptom in subjects with T2DM.

Trial Registration
UMIN 000002271.
Linear normalised hash function for clustering gene sequences and identifying reference sequences from multiple sequence alignments
Authors: Helal Manal , Kong Fanrong , Chen Sharon CA , Zhou Fei , Dwyer Dominic E , Potter John , Sintchenko Vitali 
Published: January 2012

Abstract

Background
Comparative genomics has put additional demands on the assessment of similarity between sequences and their clustering as means for classification. However, defining the optimal number of clusters, cluster density and boundaries for sets of potentially related sequences of genes with variable degrees of polymorphism remains a significant challenge. The aim of this study was to develop a method that would identify the cluster centroids and the optimal number of clusters for a given sensitivity level and could work equally well for the different sequence datasets.

Results
A novel method that combines the linear mapping hash function and multiple sequence alignment (MSA) was developed. This method takes advantage of the already sorted by similarity sequences from the MSA output, and identifies the optimal number of clusters, clusters cut-offs, and clusters centroids that can represent reference gene vouchers for the different species. The linear mapping hash function can map an already ordered by similarity distance matrix to indices to reveal gaps in the values around which the optimal cut-offs of the different clusters can be identified. The method was evaluated using sets of closely related (16S rRNA gene sequences of Nocardia species) and highly variable (VP1 genomic region of Enterovirus 71) sequences and outperformed existing unsupervised machine learning clustering methods and dimensionality reduction methods. This method does not require prior knowledge of the number of clusters or the distance between clusters, handles clusters of different sizes and shapes, and scales linearly with the dataset.

Conclusions
The combination of MSA with the linear mapping hash function is a computationally efficient way of gene sequence clustering and can be a valuable tool for the assessment of similarity, clustering of different microbial genomes, identifying reference sequences, and for the study of evolution of bacteria and viruses.
Reprogramming of TAM toward proimmunogenic type through regulation of MAP kinases using a redox-active copper chelate
Authors: Chakraborty Paramita , Chatterjee Shilpak , Ganguly Avishek , Saha Piu , Adhikary Arghya , Das Tanya , Chatterjee Mitali , Choudhuri Soumitra Kumar 
Published: January 2012

ABSTRACTTAMs, present in the tumor microenvironment, play an immunosuppressive role, leading to tumor progression and metastasis. Recently, numerous attempts have been made to switch immunosuppressive TAMs into an immunostimulatory type. Previously, we showed that a copper chelate, viz., copper N-(2-hydroxy acetophenone) glycinate [CuNG], can reprogram TAMs toward the proimmunogenic type to mount an antitumor immune response, but the underlying molecular mechanisms of skewing TAMs toward the proimmunogenic type remain elusive. Herein, we tried to explore the signaling mechanisms responsible for the reprogramming of TAMs. We observed that CuNG-induced ROS generation triggers activation of two MAPKs, i.e., p38MAPK and ERK1/2, and also causes up-regulation of intracellular glutathione. Furthermore, activation of p38 MAPK up-regulated the initial IL-12 production and the activation of ERK1/2 in tandem with GSH, found responsible for IFN-γ production by TAMs. This IFN-γ, in turn, prolonged IL-12 production and down-regulated TGF-β production and thus, plays the decisive role in CuNG-mediated reprogramming of regulatory cytokine production by TAMs. Our work highlights that ROS-mediated activation of MAPKs can convert suppressive macrophages toward the proimmunogenic type. Thus, the present study opens the possibility of targeting TAMs by the use of redox-active compounds for designing a novel, therapeutic strategy against cancer.
CLM94, a Novel Cyclic Amide with Anti-VEGFR-2 and Antiangiogenic Properties, Is Active against Primary Anaplastic Thyroid Cancer in Vitro and in Vivo
Authors: Antonelli Alessandro , Bocci Guido , La Motta Concettina , Ferrari Silvia Martina , Fallahi Poupak , Ruffilli Ilaria , Di Domenicantonio Andrea , Fioravanti Anna , Sartini Stefania , Minuto Michele , Piaggi Simona , Corti Alessandro , Alì Greta , Di Desidero Teresa , Berti Piero , Fontanini Gabriella , Danesi Romano , Da Settimo Federico , Miccoli Paolo 
Published: January 2012

Context and Objective:
We have studied the antitumor activity of a novel cyclic amide, CLM94, with anti-vascular endothelial growth factor (VEGF) receptor-2 and antiangiogenic activity in primary anaplastic thyroid cancer (ATC) cells in vitro and in vivo.

Design and Main Outcome Measures:
CLM94 was tested: 1) in two human cell lines (HMVEC-d, dermal microvascular endothelial cells; and 8305C, undifferentiated thyroid cancer) at 0.001–100 μm; 2) in ATC cells at the concentrations of 10, 30, and 50 μm; and 3) in an ATC cell line (AF) in CD nu/nu mice.

Results:
CLM94 significantly inhibited VEGF receptor-2 and epidermal growth factor receptor phosphorylation in HMVEC-d and proliferation in HMVEC-d and 8305C cells. A significant reduction of proliferation with CLM94 in ATC cells (P &lt; 0.01, ANOVA) and a slight but significant reduction of proliferation with CLM94 30 and 50 μm in normal thyroid follicular cells (P &lt; 0.01, ANOVA) were shown. CLM94 increased the percentage of apoptotic ATC cells dose-dependently (P &lt; 0.001, ANOVA) and inhibited migration (P &lt; 0.01) and invasion (P &lt; 0.001). AF cell line was injected sc in CD nu/nu mice, and tumor masses became detectable 25 d afterward. CLM94 (40 mg/kg · d) significantly inhibited tumor growth (starting 10 d after the beginning of treatment). CLM94 significantly decreased the VEGF-A gene expression in the AF cell line and the VEGF-A protein and microvessel density in AF tumor tissues.

Conclusions:
The antitumor and antiangiogenic activity of a new “cyclic amide” compound, CLM94, is very promising in ATC, opening the way to a future clinical evaluation.
An enhancer from the 8q24 prostate cancer risk region is sufficient to direct reporter gene expression to a subset of prostate stem-like epithelial cells in transgenic mice
Authors: Ting Man-Chun , Liao Chun-Peng , Yan Chunli , Jia Li , Groshen Susan , Frankel Baruch , Roy-Burman Pradip , Coetzee Gerhard A. , Maxson Robert 
Published: January 2012

SummaryRegions in the 8q24 gene desert contribute significantly to the risk of prostate cancer and other adult cancers. This region contains several DNA regions with enhancer activity in cultured cells. One such segment, histone acetylation peak 10 (AcP10), contains a risk single nucleotide polymorphism (SNP) that is significantly associated with the pathogenesis of colorectal, prostate and other cancers. The mechanism by which AcP10 influences cancer risk remains unknown. Here we show that AcP10 contains a sequence that is highly conserved across terrestrial vertebrates and is capable in transgenic mice of directing reporter gene expression to a subset of prostate lumenal epithelial cells. These cells include a small population of Nkx3.1-positive cells that persist even after androgen ablation. Castration-resistant Nkx3.1-positive (CARN) cells were shown by others to function both as stem cells and cells of origin of prostate cancer. Our results thus provide a mechanism by which AcP10 could influence prostate cancer risk.
Single Molecule Sequencing of Free DNA from Maternal Plasma for Noninvasive Trisomy 21 Detection
Authors: van den Oever Jessica M E , Balkassmi Sahila , Verweij E Joanne , van Iterson Maarten , van Scheltema Phebe N Adama , Oepkes Dick , van Lith Jan M M , Hoffer Mariëtte J V , den Dunnen Johan T , Bakker Egbert , Boon Elles M J 
Published: January 2012

Abstract

BACKGROUND
Noninvasive fetal aneuploidy detection by use of free DNA from maternal plasma has recently been shown to be achievable by whole genome shotgun sequencing. The high-throughput next-generation sequencing platforms previously tested use a PCR step during sample preparation, which results in amplification bias in GC-rich areas of the human genome. To eliminate this bias, and thereby experimental noise, we have used single molecule sequencing as an alternative method.

METHODS
For noninvasive trisomy 21 detection, we performed single molecule sequencing on the Helicos platform using free DNA isolated from maternal plasma from 9 weeks of gestation onwards. Relative sequence tag density ratios were calculated and results were directly compared to the previously described Illumina GAII platform.

RESULTS
Sequence data generated without an amplification step show no GC bias. Therefore, with the use of single molecule sequencing all trisomy 21 fetuses could be distinguished more clearly from euploid fetuses.

CONCLUSIONS
This study shows for the first time that single molecule sequencing is an attractive and easy to use alternative for reliable noninvasive fetal aneuploidy detection in diagnostics. With this approach, previously described experimental noise associated with PCR amplification, such as GC bias, can be overcome.
Hope, Meaning and Responsibility across Stages of Recovery for Individuals Living With an Enduring Mental Illness
Authors: Copic Vedrana , Deane Frank P. , Crowe Trevor P. , Oades Lindsay G. 
Published: January 2012

AbstractThis study reports on the relationship between stage of recovery and hope, meaning and responsibility for individuals diagnosed with severe mental illness.Methods:Seventy-seven people with a diagnosis of a psychotic disorder of at least 6 months' duration participated in the study. Participants completed the Self-Identified Stage of Recovery (SISR) scale, measures of component processes of recovery (Hope Scale; Positive Interpretation of Disease, SpREUK; Active Involvement, Personal Health Management Questionnaire (PHMQ) and the Recovery Assessment Scale-short (RAS).Results:Hope, meaning,Personal Confidence and HopeandNot Being Dominated by Symptomsvaried significantly across stages of recovery; however, neither in a parallel nor linear fashion. Hopefulness and sense of meaning in relation to the experience of mental illness increase before personal confidence and resilience in the face of setbacks.Conclusions and implications:Symptoms appear to take less prominence in individuals' lives in later stages of recovery. Greater insight into the relationship between stage of recovery and component processes may allow for more targeted recovery-oriented support for individuals at different stages of recovery.
Differences Between Veteran Suicides With and Without Psychiatric Symptoms
Authors: Britton Peter C. , Ilgen Mark A. , Valenstein Marcia , Knox Kerry , Claassen Cynthia A. , Conner Kenneth R. 
Published: January 2012

Objectives. Our objective was to examine all suicides (n = 423) in 2 geographic areas of the Veterans Health Administration (VHA) over a 7-year period and to perform detailed chart reviews on the subsample that had a VHA visit in the last year of life (n = 381).Methods. Within this sample, we compared a group with 1 or more documented psychiatric symptoms (68.5%) to a group with no such symptoms (31.5%). The groups were compared on suicidal thoughts and behaviors, somatic symptoms, and stressors using the χ2test and on time to death after the last visit using survival analyses.Results. Veterans with documented psychiatric symptoms were more likely to receive a suicide risk assessment, and have suicidal ideation and a suicide plan, sleep problems, pain, and several stressors. These veterans were also more likely to die in the 60 days after their last visit.Conclusions. Findings indicated presence of 2 large and distinct groups of veterans at risk for suicide in the VHA, underscoring the value of tailored prevention strategies, including approaches suitable for those without identified psychiatric symptoms.
Effects of Iraq/Afghanistan Deployments on Major Depression and Substance Use Disorder: Analysis of Active Duty Personnel in the US Military
Authors: Shen Yu-Chu , Arkes Jeremy , Williams Thomas V. 
Published: January 2012

Objectives. Our objective was to analyze the association between deployment characteristics and diagnostic rates for major depression and substance use disorder among active duty personnel. Methods. Using active duty personnel serving between 2001 and 2006 (n = 678 382) and deployment information from the Contingent Tracking System, we identified individuals diagnosed with substance use disorders and major depression from TRICARE health records. We performed logistic regression analysis to assess the effect of deployment location and length on these diagnostic rates. Results. Increased odds of diagnosis with both conditions were associated with deployment to Iraq or Afghanistan compared with nondeployed personnel and with Army and Marine Corps personnel compared with Navy and Air Force personnel. Increases in the likelihood of either diagnosis with deployment length were only observed among Army personnel. Conclusions. There were increased substance use disorders and major depression across services associated with combat conditions. It would be important to assess whether the public health system has adequate resources to handle the increasing need of mental health services in this population.
Suicidal Behavior in a National Sample of Older Homeless Veterans
Authors: Schinka John A. , Schinka Katherine C. , Casey Roger J. , Kasprow Wes , Bossarte Robert M. 
Published: January 2012

Objectives. We examined self-reported suicidal behavior of older homeless veterans to establish frequencies and predictors of recent suicidal behaviors, and their impact on transitional housing interventions.Methods. We analyzed the records of a national sample of 10 111 veterans who participated in a transition housing program over a 6-year period, ending in 2008.Results. Approximately 12% of homeless veterans reported suicidal ideation before program admission; 3% reported a suicide attempt in the 30 days before program admission. Older homeless veterans exhibiting suicidal behavior had histories of high rates of psychiatric disorders and substance abuse. Regression analyses showed that self-report of depression was the primary correlate of suicidal behavior. Suicidal behavior before program entry did not predict intervention outcomes, such as program completion, housing outcome, and employment.Conclusions. Suicidal behavior was prevalent in older homeless veterans and was associated with a history of psychiatric disorder and substance abuse. Self-reported depression was associated with these behaviors at the time of housing intervention. Despite the association with poor mental health history, suicidal behavior in older homeless veterans did not impact outcomes of transitional housing interventions.
The Role of Pain, Functioning, and Mental Health in Suicidality Among Veterans Affairs Primary Care Patients
Authors: Magruder Kathyrn M. , Yeager Derik , Brawman-Mintzer Olga 
Published: January 2012

Objectives. We examined suicidality, pain, functioning, and psychiatric disorders among veterans in primary care by using both self-report and clinical measures of pain and mental health to determine correlates that might be clinically useful in primary care settings. Methods. Data were from 884 Veterans Affairs patients enrolled in a regional 4-site cross-sectional study. Patients were administered measures that assessed functioning (including pain) and psychiatric disorders. Data were merged with medical records for clinical pain indicators. Results. Overall, 9.1% (74 of 816) of patients indicated suicidal ideation, with those who were middle-aged, unemployed because of disability, had less than college education, and served in a warzone most likely to consider suicidality. Suicidal patients had worse functioning (measured by the Short Form-36) than did nonsuicidal patients in every domain, including bodily pain, and were more likely to meet criteria for a psychiatric diagnosis. However, when pain and mental health were jointly considered, only mental health (both psychiatric diagnosis and mental health functioning) was related to suicidality. Conclusions. Although providers should be alert to the possibility of suicidality in patients with pain, they should be vigilant when patients have a psychiatric disorder or poor mental health.
Suicide Among Patients in the Veterans Affairs Health System: Rural–Urban Differences in Rates, Risks, and Methods
Authors: McCarthy John F. , Blow Frederic C. , Ignacio Rosalinda V. , Ilgen Mark A. , Austin Karen L. , Valenstein Marcia 
Published: January 2012

Objectives. Using national patient cohorts, we assessed rural–urban differences in suicide rates, risks, and methods in veterans. Methods. We identified all Department of Veterans Affairs (VA) patients in fiscal years 2003 to 2004 (FY03–04) alive at the start of FY04 (n = 5 447 257) and all patients in FY06–07 alive at the start of FY07 (n = 5 709 077). Mortality (FY04–05 and FY07–08) was assessed from National Death Index searches. Census criteria defined rurality. We used proportional hazards regressions to calculate rural–urban differences in risks, controlling for age, gender, psychiatric diagnoses, VA mental health services accessibility, and regional administrative network. Suicide method was categorized as firearms, poisoning, strangulation, or other. Results. Rural patients had higher suicide rates (38.8 vs 31.4/100 000 person-years in FY04–05; 39.6 vs 32.4/100 000 in FY07–08). Rural residence was associated with greater suicide risks (20% greater, FY04–05; 22% greater, FY07–08). Firearm deaths were more common in rural suicides (76.8% vs 61.5% in FY07–08). Conclusions. Rural residence is a suicide risk factor, even after controlling for mental health accessibility. Public health and health system suicide prevention should address risks in rural areas.
Haphazard Sampling: Selection Biases Induced by Control Listing Properties and the Estimation Consequences of these Biases
Authors: Hall Thomas W. , Higson Andrew W. , Pierce Bethane Jo , Price Kenneth H. , Skousen Christopher J. 
Published: January 2012

ABSTRACT
Haphazard sampling is a nonstatistical technique used by auditors to simulate a variety of random sampling techniques when testing the error status of accounting populations. In this study, we compare the properties of haphazard samples selected from control listings with the properties of simple random samples. We hypothesize that control listing entries exhibit salience values that result from the effort required to locate entries and the visual properties of entries. We further hypothesize these salience values influence sample selections and result in sample properties that are different from those of simple random samples. To test these hypotheses, we examine the properties of haphazard samples selected by three participant groups. In each group, sample properties differ from those of simple random sampling and include a lack of independence across sample selections and biased sample inclusion probabilities. We also develop models showing how biased sample inclusion probabilities influence error projections and discuss the estimation consequences of these biases.
Data Availability: For information about data availability, please contact the first author.
Use of contrast echocardiography for quantitative and qualitative evaluation of myocardial perfusion and pulmonary transit time in healthy dogs
Authors: Crosara Serena , Ljungvall Ingrid , Margiocco Marco L. , Häggström Jens , Tarducci Alberto , Borgarelli Michele 
Published: January 2012

Abstract
Objective—To evaluate reproducibility of ejection fraction (EF), myocardial perfusion (MP), and pulmonary transit time (PTT) measured in a group of dogs by use of contrast echocardiography and to examine safety of this method by evaluating cardiac troponin I concentrations.
Animals—6 healthy dogs.
Procedures—2 bolus injections and a constant rate infusion of contrast agent were administered IV. Echocardiographic EF was determined by use of the area-length method and was calculated without and with contrast agent. The PTT and normalized PTT (PTT/mean R-R interval) were measured for each bolus. Constant rate infusion was used for global MP evaluation, and regional MP was calculated by use of a real-time method in 4 regions of interest of the left ventricle. Cardiac troponin I concentration was analyzed before and after contrast agent administration. Intraoberserver and interobserver variability was calculated.
Results—EF was easier to determine with the ultrasonographic contrast agent. For the first and second bolus, mean ± SD PTT was 1.8 ± 0.2 seconds and 2.1 ± 0.3 seconds and normalized PTT was 3.4 ± 0.3 seconds and 3.5 ± 0.3 seconds, respectively. A coefficient of variation < 15% was obtained for global MP but not for the regional MPs. No differences were detected between precontrast and postcontrast cardiac troponin I concentrations.
Conclusions and Clinical Relevance—Contrast echocardiography appeared to be a repeat-able and safe technique for use in the evaluation of global MP and PTT in healthy dogs, and it improved delineation of the endocardial border in dogs.