bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of outcome-correlated cytokine clusters in chronic lymphocytic leukemia
Authors: Yan Xiao-Jie , Dozmorov Igor , Li Wentian , Yancopoulos Sophia , Sison Cristina , Centola Michael , Jain Preetesh , Allen Steven L. , Kolitz Jonathan E. , Rai Kanti R. , Chiorazzi Nicholas , Sherry Barbara 
Published: September 2011

Abstract
Individual cytokines and groups of cytokines that might represent networks in chronic lymphocytic leukemia (CLL) were analyzed and their prognostic values determined. Serum levels of 23 cytokines were measured in 84 patients and 49 age-matched controls; 17 levels were significantly elevated in patients. Unsupervised hierarchical bicluster analysis identified 3 clusters (CLs) of highly correlated but differentially expressed cytokines: CL1 (CXCL9, CXCL10, CXCL11, CCL3, CCL4, CCL19, IL-5, IL-12, and IFNγ), CL2 (TNFα, IL-6, IL-8, and GM-CSF), and CL3 (IL-1β, IL-2, IL-4, IL-15, IL-17, and IFNα). Combination scores integrating expression of CL1/CL2 or CL1/CL3 strongly correlated (P < .005) with time-tofirst-treatment and overall survival (OS), respectively. Patients with the worst course had high CL1 and low CL2 or CL3 levels. Multivariate analysis revealed that CL1/CL2 combination score and immunoglobulin heavy chain variable region mutation status were independent prognostic indicators for time-to-first-treatment, whereas CL1/CL3 combination score and immunoglobulin heavy chain variable region mutation status were independent markers for OS. Thus, we identified groups of cytokines differentially expressed in CLL that are independent prognostic indicators of aggressive disease and OS. These findings indicate the value of multicytokine analyses for prognosis and suggest therapeutic strategies in CLL aimed at reducing CL1 and increasing CL2/CL3 cytokines.
Characterizing genetic interactions in human disease association studies using statistical epistasis networks
Authors: Hu Ting , Sinnott-Armstrong Nicholas A , Kiralis Jeff W , Andrew Angeline S , Karagas Margaret R , Moore Jason H 
Published: September 2011

Abstract

Background
Epistasis is recognized ubiquitous in the genetic architecture of complex traits such as disease susceptibility. Experimental studies in model organisms have revealed extensive evidence of biological interactions among genes. Meanwhile, statistical and computational studies in human populations have suggested non-additive effects of genetic variation on complex traits. Although these studies form a baseline for understanding the genetic architecture of complex traits, to date they have only considered interactions among a small number of genetic variants. Our goal here is to use network science to determine the extent to which non-additive interactions exist beyond small subsets of genetic variants. We infer statistical epistasis networks to characterize the global space of pairwise interactions among approximately 1500 Single Nucleotide Polymorphisms (SNPs) spanning nearly 500 cancer susceptibility genes in a large population-based study of bladder cancer.

Results
The statistical epistasis network was built by linking pairs of SNPs if their pairwise interactions were stronger than a systematically derived threshold. Its topology clearly differentiated this real-data network from networks obtained from permutations of the same data under the null hypothesis that no association exists between genotype and phenotype. The network had a significantly higher number of hub SNPs and, interestingly, these hub SNPs were not necessarily with high main effects. The network had a largest connected component of 39 SNPs that was absent in any other permuted-data networks. In addition, the vertex degrees of this network were distinctively found following an approximate power-law distribution and its topology appeared scale-free.

Conclusions
In contrast to many existing techniques focusing on high main-effect SNPs or models of several interacting SNPs, our network approach characterized a global picture of gene-gene interactions in a population-based genetic data. The network was built using pairwise interactions, and its distinctive network topology and large connected components indicated joint effects in a large set of SNPs. Our observations suggested that this particular statistical epistasis network captured important features of the genetic architecture of bladder cancer that have not been described previously.
The hOGG1 Ser326Cys polymorphism and prostate cancer risk: a meta-analysis of 2584 cases and 3234 controls
Authors: Zhang Hongtuan , Xu Yong , Zhang Zhihong , Li Liang 
Published: September 2011

AbstractBackgroundGenetic polymorphism of human 8-oxoguanine glycosylase 1 (hOGG1) Ser326Cys (rs1052133) has been implicated to alter the risk of prostate cancer, but the results are controversial.MethodsTwo investigators independently searched the Medline, and Cochrane Library up to June 7, 2011. Summary odds ratios (OR) and 95% confidence interval (CI) for Ser326Cys polymorphism and prostate cancer were calculated. Statistical analysis was performed with the software program Review Manage, version 5.0 and Stata 10.0.ResultsA total of 8 independent studies, including 2584 cases and 3234 controls, were identified. Our analysis suggested that Ser326Cys was not associated with prostate cancer risk in overall population. In the subgroup analysis, we detected the significant association between Ser326Cys polymorphism and decreased prostate risk in mixed population under additive model (OR = 0.67, 95% CI = 0.50-0.90, P = 0.007), recessive model (OR = 0.68, 95% CI = 0.51-0.91, P = 0.008), and Cys allele versus Ser allele (OR = 0.88, 95% CI = 0.78-0.98, P = 0.02). Subanalysis on Caucasian subjects demonstrated that Ser326Cys was not associated with prostate cancer risk.ConclusionThis meta-analysis showed the evidence that hOGG1 Ser326Cys polymorphism was associated with a decreased risk of prostate cancer development in mixed populations.
A prospective study of mental health care for comorbid depressed mood in older adults with painful osteoarthritis
Authors: Gleicher Yehoshua , Croxford Ruth , Hochman Jacqueline , Hawker Gillian 
Published: September 2011

Abstract

Background
Comorbid depression is common among adults with painful osteoarthritis (OA). We evaluated the relationship between depressed mood and receipt of mental health (MH) care services.

Methods
In a cohort with OA, annual interviews assessed comorbidity, arthritis severity, and MH (SF-36 mental health score). Surveys were linked to administrative health databases to identify mental health-related visits to physicians in the two years following the baseline interview (1996-98). Prescriptions for anti-depressants were ascertained for participants aged 65+ years (eligible for drug benefits). The relationship between MH scores and MH-related physician visits was assessed using zero-inflated negative binomial regression, adjusting for confounders. For those aged 65+ years, logistic regression examined the probability of receiving any MH-related care (physician visit or anti-depressant prescription).

Results
Analyses were based on 2,005 (90.1%) individuals (mean age 70.8 years). Of 576 (28.7%) with probable depression (MH score < 60/100), 42.5% experienced one or more MH-related physician visits during follow-up. The likelihood of a physician visit was associated with sex (adjusted OR women vs. men = 5.87, p = 0.005) and MH score (adjusted OR per 10-point decrease in MH score = 1.63, p = 0.003). Among those aged 65+, 56.7% with probable depression received any MH care. The likelihood of receiving any MH care exhibited a significant interaction between MH score and self-reported health status (p = 0.0009); with good general health, worsening MH was associated with increased likelihood of MH care; as general health declined, this effect was attenuated.

Conclusions
Among older adults with painful OA, more than one-quarter had depressed mood, but almost half received no mental health care, suggesting a care gap.
Enhancing the stress responses of probiotics for a lifestyle from gut to product and back again
Authors: Mills Susan , Stanton Catherine , Fitzgerald Gerald F , Ross RPaul 
Published: August 2011

AbstractBefore a probiotic bacterium can even begin to fulfill its biological role, it must survive a battery of environmental stresses imposed during food processing and passage through the gastrointestinal tract (GIT). Food processing stresses include extremes in temperature, as well as osmotic, oxidative and food matrix stresses. Passage through the GIT is a hazardous journey for any bacteria with deleterious lows in pH encountered in the stomach to the detergent-like properties of bile in the duodenum. However, bacteria are equipped with an array of defense mechanisms to counteract intracellular damage or to enhance the robustness of the cell to withstand lethal external environments. Understanding these mechanisms in probiotic bacteria and indeed other bacterial groups has resulted in the development of a molecular toolbox to augment the technological and gastrointestinal performance of probiotics. This has been greatly aided by studies which examine the global cellular responses to stress highlighting distinct regulatory networks and which also identify novel mechanisms used by cells to cope with hazardous environments. This review highlights the latest studies which have exploited the bacterial stress response with a view to producing next-generation probiotic cultures and highlights the significance of studies which view the global bacterial stress response from an integrative systems biology perspective.
Influence of environmental factors on the abundance of Anopheles farauti larvae in large brackish water streams in Northern Guadalcanal, Solomon Islands
Authors: Bugoro Hugo , Hii Jeffery , Russell Tanya L , Cooper Robert D , Chan Benny KK , Iro'ofa Charles , Butafa Charles , Apairamo Allen , Bobogare Albino , Chen Cheng-Chen 
Published: September 2011

AbstractBackgroundThe main vector of malaria in Solomon Islands isAnopheles farauti, which has a mainly coastal distribution. In Northern Guadalcanal, Solomon Islands, high densities ofAn. farautiare supported by large brackish streams, which in the dry season are dammed by localized sand migration. The factors controlling the high larval productivity of these breeding sites have not been identified. Accordingly the influence of environmental factors on the presence and density ofAn. farautilarvae was assessed in three large naturally dammed streams.MethodsLarval sites were mapped and anopheline larvae were collected monthly for 12 months (July 2007 to June 2008) from three streams using standard dippers. Larval collections were made from 10 locations spaced at 50 m intervals along the edge of each stream starting from the coast. At each collection point, floating filamentous algae, aquatic emergent plants, sun exposure, and salinity were measured. These environmental parameters along with rainfall were correlated with larval presence and density.ResultsThe presence and abundance ofAn. farautilarvae varied between streams and was influenced by the month of collection, and distance from the ocean (p <0.001). Larvae were more frequently present and more abundant within 50 m of the ocean during the dry season when the streams were dammed. The presence and density of larvae were positively associated with aquatic emergent plants (presence: p = 0.049; density: p = 0.001). Although filamentous algae did not influence the presence of larvae, this factor did significantly influence the density of larvae (p < 0.001). Rainfall for the month prior to sampling was negatively associated with both larval presence and abundance (p < 0.001), as high rainfall flushed larvae from the streams. Salinity significantly influenced both the presence (p = 0.002) and density (p = 0.014) of larvae, with larvae being most present and abundant in brackish water at < 10‰ seawater.ConclusionThis study has demonstrated that the presence and abundanceAn. farautilarvae are influenced by environmental factors within the large streams. Understanding these parameters will allow for targeted cost effective implementation of source reduction and larviciding to support the frontline malaria control measures i.e. indoor residual spraying (IRS) and distribution of long-lasting insecticidal nets (LLINs).
Randomized, placebo-controlled, double-blind trial of Swedish snus for smoking reduction and cessation
Authors: Joksić Gordana , Spasojević-Tišma Vera , Antić Ruza , Nilsson Robert , Rutqvist Lars E 
Published: September 2011

Abstract

Background
Epidemiological studies suggest that smokeless tobacco in the form of Swedish snus has been used by many smokers in Scandinavia to quit smoking, but the efficacy of snus has so far not been evaluated in controlled clinical trials.

Methods
We conducted a randomized, double-blind, placebo-controlled, clinical trial aimed at assessing the efficacy of snus to help adult cigarette smokers in Serbia to substantially reduce, and, eventually, completely stop smoking. The study enrolled 319 healthy smokers aged 20-65 years at two occupational health centers in Belgrade, Serbia. Most of them (81%) expressed an interest to quit rather than just reduce their smoking. Study products were used ad libitum throughout the 48-week study period. The main study objective during the first 24 weeks was smoking reduction. The primary end-point was defined as a biologically verified reduction of ≥ 50% in the average number of smoked cigarettes per day during week 21-24 compared to baseline. During week 25-48 participants were actively instructed to stop smoking completely. Outcome measures of biologically verified, complete smoking cessation included 1-week point prevalence rates at clinical visits after 12, 24, 36, and 48 weeks, as well as 4-, 12- and 24-week continued cessation rates at the week 36 and 48 visits.

Results
At the week 24 visit, the proportion of participants who achieved the protocol definition of a ≥ 50% smoking reduction was similar in the two treatment groups. However, the proportion that reported more extreme reductions (≥ 75%) was statistically significantly higher in the snus group than in the placebo group (p < 0.01). The results for biologically verified complete cessation suggested that participants in the snus group were more likely to quit smoking completely than the controls; the odds ratio (snus versus placebo) for the protocol estimates of cessation varied between 1.9 to 3.4, but these ratios were of borderline significance with p-values ranging from 0.04-0.10. Snus was well tolerated and only 2/158 (1.3%) participants in the snus group discontinued treatment due to an adverse event (in both cases unrelated to snus).

Conclusions
Swedish snus could promote smoking cessation among smokers in Serbia, that is, in a cultural setting without traditional use of oral, smokeless tobacco.

Trial registration
www.clinicaltrials.gov, identifier: NCT00601042
An augmented Lagrangian multi-scale dictionary learning algorithm
Authors: Liu Qiegen , Luo Jianhua , Wang Shanshan , Xiao Moyan , Ye Meng 
Published: September 2011

AbstractLearning overcomplete dictionaries for sparse signal representation has become a hot topic fascinated by many researchers in the recent years, while most of the existing approaches have a serious problem that they always lead to local minima. In this article, we present a novel augmented Lagrangian multi-scale dictionary learning algorithm (ALM-DL), which is achieved by first recasting the constrained dictionary learning problem into an AL scheme, and then updating the dictionary after each inner iteration of the scheme during which majorization-minimization technique is employed for solving the inner subproblem. Refining the dictionary from low scale to high makes the proposed method less dependent on the initial dictionary hence avoiding local optima. Numerical tests for synthetic data and denoising applications on real images demonstrate the superior performance of the proposed approach.
Malignant peritoneal mesothelioma presenting as recurrent adhesion obstruction in general surgery: a case report
Authors: Naraynsingh Vijay , Ramdass Michael J , Lum Crystal Lee 
Published: August 2011

Abstract

Introduction
Malignant peritoneal mesothelioma is a well-described entity in many reports in the literature in which it has been associated with asbestosis. However, there is no information describing the gross appearance and cardinal features seen during laparotomy, hence it is easy for the unwary surgeon to miss the diagnosis of this rare condition.

Case presentation
A 49-year-old man of African descent presented to our hospital with a three-month history of weight loss, anorexia, abdominal distension, and general signs of cachexia and ascites on second presentation. At first presentation one year prior to this, he had undergone a laparotomy at our institution by a different team for intestinal obstruction secondary to adhesions with no biopsy taken. The patient's condition subsequently progressively deteriorated, and investigations including upper and lower gastrointestinal endoscopies and computed tomography of the abdomen were inconclusive, except for some free fluid in the peritoneal cavity and diffuse, mild thickening of the gut wall and mesentery. A second-look exploratory laparotomy revealed widespread nodular thickening of the visceral peritoneum with a striking, uniformly diffuse, erythematous, and velvety appearance. The peritoneal biopsy histology showed that the patient had malignant peritoneal mesothelioma. His condition deteriorated rapidly, and he died eight weeks after surgery.

Conclusion
Our report aims to increase the diagnosing clinician's awareness of the cardinal features of malignant peritoneal mesothelioma and thus reduce diagnostic errors and delays in treatment.
Clinical and Prognostic Implications of Plasma Insulin-Like Growth Factor-1 and Vascular Endothelial Growth Factor in Patients With Hepatocellular Carcinoma
Authors: Kaseb Ahmed O. , Morris Jeffrey S. , Hassan Manal M. , Siddiqui Adnan M. , Lin E , Xiao Lianchun , Abdalla Eddie K. , Vauthey Jean-Nicolas , Aloia Thomas A. , Krishnan Sunil , Abbruzzese James L. 
Published: September 2011

Purpose Cirrhosis and hepatocellular carcinoma (HCC) together form a two-disease state that affects survival of patients with HCC and dictates treatment decisions and prognostic stratification of patients in clinical trials. The study objective was to improve prognostic stratification of patients with HCC. Patients and Methods We prospectively collected plasma samples and baseline clinicopathologic features from 288 new patients with HCC, and plasma insulin-like growth factor-1 (IGF-1) and vascular endothelial growth factor (VEGF) levels were tested. We applied Cox regression and log-rank tests to assess association of IGF-1 and VEGF with overall survival (OS), Kaplan-Meier curves to estimate OS, and recursive partitioning to determine optimal cutoff points for IGF-1 and VEGF. Prognostic ability of conventional and molecular Barcelona Clinic Liver Cancer classifications was compared using the c-index. Results Lower plasma IGF-1 and higher plasma VEGF levels significantly correlated with advanced clinicopathologic parameters and poor OS, with optimal cut points of 26 ng/mL and 450 pg/mL, respectively. The combination of low IGF-1 and high VEGF predicted median OS of 2.7 months compared with 19 months for patients with high IGF-1 and low VEGF (P < .001), further refining the prognostic ability of conventional HCC staging (P < .001). Conclusion Baseline levels of plasma IGF-1 and VEGF correlated significantly with survival in patients with HCC. Integrating IGF-1 and VEGF into HCC staging significantly enhanced prognostic stratification of patients. If validated, these results may prove to be useful in designing strategies to personalize management approaches among these patients.
Design, development and validation of the RedBrick Health Assessment: a questionnaire-based study
Authors: Mills Peter R , Masloski Wendy S , Bashaw Carole M , Butler Jolene Rw , Hillstrom Molly E , Zimmerman Eric M 
Published: September 2011

Objectives Health risk assessment (HRA) questionnaires have become a popular tool to help quantify health issues within populations. Over the last decade HRAs have increasingly been delivered in the online environment. The objective of this study was to create and validate an HRA that is optimized for delivery via the Internet. Design After an iterative process of user testing and interface design the RedBrick Health Assessment (RBHA) was validated against known domain specific questionnaires with 464 working Americans, and with medical claims data from over 25,000 employees. Setting All consumer testing, data capture and analysis occurred at the offices of RedBrick Health Corporation, Minneapolis, USA and via a secure online portal. Participants Individuals in full-time employment in the USA, who were between 18 and 65 years of age at the time inquiry. Main outcome measures Correlation of the included RBHA domains with the output from known gold standard health question sets for each assessed health domain. Results The iterative development process employed in creating the RBHA produced a tool that had a high degree of user acceptability. The domains demonstrated good correlations with relevant gold standard questionnaire measures, good internal consistency, and acceptable sensitivity and specificity when compared to gold standard risk stratification and high-risk classification (specificity of domains ranged from 76–94%). A test–retest correlation co-efficient of 0.7, or greater, was achieved 8 weeks after initial completion. Conclusions The RBHA is a new breed of HRA that has been specifically developed for capturing health status information in an online environment. At its heart is user centricity and this focus has enabled the creation of a tool that is not only highly engaging but also captures accurate and robust health status information.
Oxidative status in the lungs associated with tobacco smoke exposure
Authors: Doruk Sibel , Ozyurt Huseyin , Inonu Handan , Erkorkmaz Unal , Saylan Oguzhan , Seyfikli Zehra 
Published: September 2011

AbstractOxidative stress has a critical role in inflammatory responce against tobacco smoke (TS). Testing exhaled breath condensate (EBC) samples is one of the methods used for assessment of airway inflammation caused by TS. We aimed to investigate oxidative stress in the lungs associated with TS and to evaluate the effect of this stress with pulmonary function tests (PFTs).We included 69 subjects as three groups into the study (Group I; 26 smokers, Group II; 21 passive smokers, Group III; 22 non-smokers without TS exposure). Levels of malondialdehyde (MDA), 8-hydroxydeoxyguanosine (8-OHdG), nitrite/nitrate ;ibindex of nitric oxide (NO) production;ic, vitamin C, superoxide dismutase (SOD), and glutathione peroxidase (GSH-Px) were measured in EBC samples collected using a condenser and PFTs were performed.The levels of MDA, 8-OHdG, SOD and GSH-Px were higher in smokers. NO levels gradually increased from Group I to Group III. MDA levels were lower in Group III than Group II. The levels of vitamin C were similar in all groups. We determined negative correlation between 8-OHdG levels and forced expiratory volume in one second (FEVTS exposure affected the balance between oxidative stress and antioxidant capacity of lungs. Preventing environmental TS exposure might decrease oxidative damage. Increased levels of 8-OHdG and SOD levels could be assessed as an early sign of airway damage.