bluuebunny/crossref_metadata_2025_split huggingface dataset:
Determination of HCV genotypes and viral loads in chronic HCV infected patients of Hazara Pakistan
Authors: Ali Amjad , Nisar Muhammad , Ahmad Habib , Saif Nausheen , Idrees Muhammad , Bajwa Mohammad A 
Published: October 2011

AbstractHepatitis C Virus (HCV) genotype and viral load are two significant predictive variables knowledge of which might persuade treatment decisions. The objective of the present study was to identify the distribution of different HCV genotypes circulating in the study area and to estimate viral load in chronically HCV infected patients. Out of total 305 HCV positive patients, 177 (58%) were males and 128 (42%) were females. Frequency breakup of the HCV positive patients was 169, 69, 38 and 29 from Abbottabad, Mansehra, Haripur and Battagram districts respectively. Out of the total 305 tested serum samples, 255 (83.06%) were successfully genotyped whereas 50 (16.4%) samples were found with unclassified genotypes. Among typable genotypes, 1a accounted for 21 (6.8%) 1b for 14 (4.6%), 2a for 4 (1.31%) 3a for 166 (54.42%) and genotype 3b for (8.19%). Twenty five (8.19%) patients were infected with mixed HCV genotypes. Viral load distribution was classified into three categories based on its viral load levels such as low (< 60, 0000 IU/mL), intermediate (60,0000-80,0000 IU/mL) and high (> 80,0000 IU/mL). The baseline HCV RNA Viral load in HCV genotype 3 infected patients was 50 (26.17%), 46 (24.08%) and 95 (49.73%) for low, intermediate and high categories respectively. For genotypes other than 3, these values for low, intermediate and high viral load categories were 50 (43.85), 35 (30.70) and 29 (25.43) respectively. Pre-treatment viral load in patients with untypable genotype was 19 (38.00%), 5 (20.00%) and 11 (44.00%) for low, intermediate and high viral load categories. Viral load distribution was also categorized sex wise; for males it was 58 (32.76%), 26 (14.68%) and 93 (52.54%) whereas for females it was 40 (31.25%), 34 (26.56%) and 54 (42.18%) for low, intermediate and high viral load respectively. In conclusion HCV genotype 3a is the most prevalent genotype circulating in Hazara Division like other parts of pakistan. Pre-treatment viral load is significantly high (p 0.014) in patients infected with HCV genotype 3 as compared to other genotypes.
Effect of herbal extract granules combined with probiotic mixture on irritable bowel syndrome with diarrhea: study protocol for a randomized controlled trial
Authors: Ko Seok-Jae , Ryu Bongha , Kim Jinsung , Hong Beom-Gi , Yeo Inkwon , Lee Beom-Joon , Lee Jin-Moo , Park Jae-Woo 
Published: October 2011

Abstract

Background
Irritable bowel syndrome (IBS) is a chronic gastrointestinal disorder characterized by abdominal pain and change of bowel habits without organic disease. Many patients seek alternative IBS treatments because of the limitations of conventional treatments. Gwakhyangjeonggisan (GJS), a herbal formula, has long been used for alleviating diarrhea-predominant IBS (D-IBS) in traditional medicine. Duolac7S, which comprises 7 bacterial species as probiotics, has been frequently used for D-IBS. Although GJS and Duolac7S have been administered simultaneously in many D-IBS patients, no study has investigated the effects of GJS and Duolac7S combination therapy on D-IBS.

Methods/Design
The current trial is a randomized, double-blinded, placebo-controlled, 4-arm study. After a 2-week run-in period, 60 patients with D-IBS will be randomly assigned to one of the 4 combination groups consisting of GJS (water extract granules, 3 g/pack, 3 times a day) with Duolac7S (powder form, 1 capsule, 2 times a day) or their placebos and followed up for 2 weeks. The assigned treatments will last for 8 weeks. The primary outcomes are adequate relief of IBS pain and discomfort and the proportion of responders (on a weekly basis). The secondary outcomes are visual analog scale for IBS symptoms (on a daily basis), quality of life (at 0, 8, and 10 weeks), intestinal permeability, and composition of intestinal microbiota (at 0 and 8 weeks).

Discussion
The present study is designed to examine the safety and efficacy of GJS and Duolac7S combination therapy on D-IBS. Our study provides the clinical evidence of a new therapeutic strategy for D-IBS.

Trial registration
ClinicalTrials.gov NCT01342718.
Maize microarray annotation database
Authors: Coetzer Nanette , Myburg Alexander A , Berger Dave K 
Published: October 2011

AbstractBackgroundMicroarray technology has matured over the past fifteen years into a cost-effective solution with established data analysis protocols for global gene expression profiling. The Agilent-016047 maize 44 K microarray was custom-designed from EST sequences, but only reporter sequences with EST accession numbers are publicly available. The following information is lacking: (a) reporter - gene model match, (b) number of reporters per gene model, (c) potential for cross hybridization, (d) sense/antisense orientation of reporters, (e) position of reporter on B73 genome sequence (for eQTL studies), and (f) functional annotations of genes represented by reporters. To address this, we developed a strategy to annotate the Agilent-016047 maize microarray, and built a publicly accessible annotation database.DescriptionGenomic annotation of the 42,034 reporters on the Agilent-016047 maize microarray was based on BLASTN results of the 60-mer reporter sequences and their corresponding ESTs against the maize B73 RefGen v2 "Working Gene Set" (WGS) predicted transcripts and the genome sequence. The agreement between the EST, WGS transcript and gDNA BLASTN results were used to assign the reporters into six genomic annotation groups. These annotation groups were: (i) "annotation by sense gene model" (23,668 reporters), (ii) "annotation by antisense gene model" (4,330); (iii) "annotation by gDNA" without a WGS transcript hit (1,549); (iv) "annotation by EST", in which case the EST from which the reporter was designed, but not the reporter itself, has a WGS transcript hit (3,390); (v) "ambiguous annotation" (2,608); and (vi) "inconclusive annotation" (6,489). Functional annotations of reporters were obtained by BLASTX and Blast2GO analysis of corresponding WGS transcripts against GenBank.The annotations are available in the Maize Microarray Annotation Databasehttp://MaizeArrayAnnot.bi.up.ac.za/, as well as through a GBrowse annotation file that can be uploaded to the MaizeGDB genome browser as a custom track.The database was used to re-annotate lists of differentially expressed genes reported in case studies of published work using the Agilent-016047 maize microarray. Up to 85% of reporters in each list could be annotated with confidence by a single gene model, however up to 10% of reporters had ambiguous annotations. Overall, more than 57% of reporters gave a measurable signal in tissues as diverse as anthers and leaves.ConclusionsThe Maize Microarray Annotation Database will assist users of the Agilent-016047 maize microarray in (i) refining gene lists for global expression analysis, and (ii) confirming the annotation of candidate genes before functional studies.
A new chapter: hematopoietic stem cells are direct players in immunity
Authors: Zheng Junke , Song Chun , Zhang Cheng Cheng 
Published: October 2011

AbstractSeveral lines of evidence support the hypothesis that hematopoietic stem cells (HSCs) directly interact with the immune system and have potential for immune privilege. Although the microenvironment or niche provides protection for HSCs from immune attack, HSCs are also capable of interacting with the immune system as signal "providers" and signal "receivers". On the one hand, HSCs display surface immune inhibitory molecules to evade the attack from the innate and adaptive immune systems; on the other hand, HSCs are capable of directly sensing the signals from the immune system through their surface receptors. Thus, HSCs are important direct players in the immune system.
Visual hallucinations in dementia with Lewy bodies: transcranial magnetic stimulation study
Authors: Taylor John-Paul , Firbank Michael , Barnett Nicola , Pearce Sarah , Livingstone Anthea , Mosimann Urs , Eyre Janet , McKeith Ian G. , O'Brien John T. 
Published: October 2011

BackgroundThe aetiology of visual hallucinations is poorly understood in dementia with Lewy bodies. Pathological alterations in visual cortical excitability may be one contributory mechanism.AimsTo determine visual cortical excitability in people with dementia with Lewy bodies compared with aged-matched controls and also the relationship between visual cortical excitability and visual hallucinations in dementia with Lewy bodies.MethodVisual cortical excitability was determined by using transcranial magnetic stimulation (TMS) applied to the occiput to elicit phosphenes (transient subjective visual responses) in 21 patients with dementia with Lewy bodies and 19 age-matched controls.ResultsPhosphene parameters were similar between both groups. However, in the patients with dementia with Lewy bodies, TMS measures of visual cortical excitability correlated strongly with the severity of visual hallucinations (P = 0.005). Six patients with dementia with Lewy bodies experienced visual hallucination-like phosphenes (for example, seeing people or figures on stimulation) compared with none of the controls (P = 0.02).ConclusionsIncreased visual cortical excitability in dementia with Lewy bodies does not appear to explain visual hallucinations but it may be a marker for their severity.
Modernity from Within: Islamic Fundamentalism and Sufism
Authors: Weismann Itzchak 
Published: October 2011

Abstract
Islamic fundamentalism is a product of modernity. Its constitution as the hegemonic discourse of modern Islam was accomplished in the course of the twentieth century over against two Others: the external Other of the West and the internal Other of tradition, especially its mystical aspect – Sufism. The article claims, however, that the fundamentalists' critique of Sufism as backward, superstitious, and apolitical involved the collective forgetting of the leading role that Ṣūfī reformist brotherhoods had filled in premodern Islam and in their own upbringing. In this light the Salafī discourse and popular socioreligious movements such as the Muslim Brothers appear as modern transformations rather than negations of Sufism. On the other hand, contemporary Sufism has constituted itself as the modern Other of the hegemonic Islamic fundamentalism. The fundamentalist estrangement from Sufism, and Islamic tradition at large, engendered a dialectics of unenlightenment culminating in the present radicalization of Islam.
Moisture and Rutting Resistances of Foamed Asphalt Mixtures Containing Recycled Coal Ash or Shingles With Moist Aggregates
Authors: Shivaprasad Punith Veeralinga , Xiao Feipeng , Amirkhanian Serji N. 
Published: October 2011

Abstract
The objective of this study was to evaluate the laboratory moisture and rutting susceptibility of foamed warm mix asphalt (WMA) mixtures containing moist aggregates and recycled materials such as manufactured roofing shingles and coal ash material. The test properties of these mixtures included the indirect tensile strength (ITS), tensile strength ratio, flow value, and rut depth of dry and wet specimens. The experimental design included two percentages of coal ash (10 % and 5 % by weight of the aggregate), two shingle contents (5 % and 3 % by weight of the aggregate), foaming WMA and control mixtures, and two aggregate sources (containing approximately 0.5 % moisture). A total of 24 mix designs were used in this study. The test results indicate that the aggregate source significantly affected the moisture and rutting resistance, regardless of the foaming technology and/or recycled material type. In addition, the dry and wet rut depth values of mixtures containing moist aggregate generally satisfied the demand of pavement performance without requiring additional treatment. Moreover, all mixtures have high dry and wet ITS values as using recycled shingle and coal ash materials along with hydrated lime or liquid anti-stripping additive. Furthermore, the utilization of recycled coal ash and roofing shingles significantly improved the moisture and rutting resistance of WMA mixtures.
Clinical Presentation and Management of Hand–Foot Skin Reaction Associated with Sorafenib in Combination with Cytotoxic Chemotherapy: Experience in Breast Cancer
Authors: Gomez Patricia , Lacouture Mario E. 
Published: October 2011

Abstract
Current combination therapies for advanced breast cancer provide a modest survival benefit but with greater toxicity than with monotherapies. New combinations are needed that improve the efficacy of current treatments and have acceptable tolerability profiles. Recent clinical trials have assessed the efficacy and safety of the multikinase inhibitor sorafenib in combination with common treatments for advanced breast cancer. Sorafenib has both antiangiogenic and antiproliferative activities and is indicated for patients with unresectable hepatocellular and advanced renal cell carcinoma. Generally, sorafenib is associated with manageable, non–life-threatening adverse events. One of the more common adverse events seen with sorafenib is hand–foot skin reaction, a dermatologic toxicity usually localized to the pressure points of the palms and soles. Although hand–foot skin reaction is reversible and not life threatening, it can have a significant impact on a patient's quality of life and may necessitate dose modification. Moreover, sorafenib is being evaluated in combination with breast cancer treatments that are associated with a similar dermatologic toxicity (e.g., capecitabine-induced hand–foot syndrome). This review looks at the use of sorafenib in combination with selected chemotherapies in patients with advanced breast cancer and considers the incidence, prevention, and management of hand–foot skin reaction.
The Environmental Protection Agency's Community-Focused Exposure and Risk Screening Tool (C-FERST) and Its Potential Use for Environmental Justice Efforts
Authors: Zartarian Valerie G. , Schultz Bradley D. , Barzyk Timothy M. , Smuts MaryBeth , Hammond Davyda M. , Medina-Vera Myriam , Geller Andrew M. 
Published: October 2011

Objectives. Our primary objective was to provide higher quality, more accessible science to address challenges of characterizing local-scale exposures and risks for enhanced community-based assessments and environmental decision-making. Methods. After identifying community needs, priority environmental issues, and current tools, we designed and populated the Community-Focused Exposure and Risk Screening Tool (C-FERST) in collaboration with stakeholders, following a set of defined principles, and considered it in the context of environmental justice. Results. C-FERST is a geographic information system and resource access Web tool under development for supporting multimedia community assessments. Community-level exposure and risk research is being conducted to address specific local issues through case studies. Conclusions. C-FERST can be applied to support environmental justice efforts. It incorporates research to develop community-level data and modeled estimates for priority environmental issues, and other relevant information identified by communities. Initial case studies are under way to refine and test the tool to expand its applicability and transferability. Opportunities exist for scientists to address the many research needs in characterizing local cumulative exposures and risks and for community partners to apply and refine C-FERST.
Mortgage Delinquency and Changes in Access to Health Resources and Depressive Symptoms in a Nationally Representative Cohort of Americans Older Than 50 Years
Authors: Alley Dawn E. , Lloyd Jennifer , Pagán José A. , Pollack Craig E. , Shardell Michelle , Cannuscio Carolyn 
Published: October 2011

Objectives. We evaluated associations between mortgage delinquency and changes in health and health-relevant resources over 2 years, with data from the Health and Retirement Study, a longitudinal survey representative of US adults older than 50 years. Methods. In 2008, participants reported whether they had fallen behind on mortgage payments since 2006 (n = 2474). We used logistic regression to compare changes in health (incidence of elevated depressive symptoms, major declines in self-rated health) and access to health-relevant resources (food, prescription medications) between participants who fell behind on their mortgage payments and those who did not. Results. Compared with nondelinquent participants, the mortgage-delinquent group had worse health status and less access to health-relevant resources at baseline. They were also significantly more likely to develop incident depressive symptoms (odds ratio [OR] = 8.60; 95% confidence interval [CI] = 3.38, 21.85), food insecurity (OR = 7.53; 95% CI = 3.01, 18.84), and cost-related medication nonadherence (OR = 8.66; 95% CI = 3.72, 20.16) during follow-up. Conclusions. Mortgage delinquency was associated with significant elevations in the incidence of mental health impairments and health-relevant material disadvantage. Widespread mortgage default may have important public health implications.
Crash and Risky Driving Involvement Among Novice Adolescent Drivers and Their Parents
Authors: Simons-Morton Bruce G. , Ouimet Marie Claude , Zhang Zhiwei , Klauer Sheila E. , Lee Suzanne E. , Wang Jing , Albert Paul S. , Dingus Thomas A. 
Published: October 2011

Objectives. We compared rates of risky driving among novice adolescent and adult drivers over the first 18 months of adolescents' licensure. Methods. Data-recording systems installed in participants’ vehicles provided information on driving performance of 42 newly licensed adolescent drivers and their parents. We analyzed crashes and near crashes and elevated g-force event rates by Poisson regression with random effects. Results. During the study period, adolescents were involved in 279 crashes or near crashes (1 involving injury); parents had 34 such accidents. The incidence rate ratio (IRR) comparing adolescent and parent crash and near-crash rates was 3.91. Among adolescent drivers, elevated rates of g-force events correlated with crashes and near crashes (r = 0.60; P < .001). The IRR comparing incident rates of risky driving among adolescents and parents was 5.08. Adolescents’ rates of crashes and near crashes declined with time (with a significant uptick in the last quarter), but elevated g-force event rates did not decline. Conclusions. Elevated g-force events among adolescents may have contributed to crash and near-crash rates that remained much higher than adult levels after 18 months of driving.
Early-Life Origins of Adult Disease: National Longitudinal Population-Based Study of the United States
Authors: Johnson Rucker C. , Schoeni Robert F. 
Published: October 2011

Objectives. We examined the relation between low birth weight and childhood family and neighborhood socioeconomic disadvantage and disease onset in adulthood. Methods. Using US nationally representative longitudinal data, we estimated hazard models of the onset of asthma, hypertension, diabetes, and stroke, heart attack, or heart disease. The sample contained 4387 children who were members of the Panel Study of Income Dynamics in 1968; they were followed up to 2007, when they were aged 39 to 56 years. Our research design included sibling comparisons of disease onset among siblings with different birth weights. Results. The odds ratios of having asthma, hypertension, diabetes, and stroke, heart attack, or heart disease by age 50 years for low–birth weight babies vs others were 1.64 (P < .01), 1.51 (P < .01), 2.09 (P < .01), and 2.16 (P < .01), respectively. Adult disease prevalence differed substantially by childhood socioeconomic status (SES). After accounting for childhood socioeconomic factors, we found a substantial hazard ratio of disease onset associated with low birth weight, which persisted for sibling comparisons. Conclusions. Childhood SES is strongly associated with the onset of chronic disease in adulthood. Low birth weight plays an important role in disease onset; this relation persists after an array of childhood socioeconomic factors is accounted for.
Parents’ Education, Mothers’ Vocabulary, and Cognitive Development in Early Childhood: Longitudinal Evidence From Ecuador
Authors: Schady Norbert 
Published: October 2011

Objectives. I estimated the association between parents’ education, mothers’ vocabulary, and early child cognitive development in a sample of poor children in rural Ecuador. Methods. I used regression analysis to estimate the association between parents’ education, mothers’ vocabulary, and the vocabulary, memory, and visual integration skills of children at early ages, controlling for possible confounders. The study is based on a longitudinal cohort of children in rural Ecuador (n = 2118). Results. The schooling and vocabulary levels of mothers were strong predictors of the cognitive development of young children. Household wealth and child's height, weight, and hemoglobin levels explained only a modest fraction of the observed associations. The vocabulary levels of mothers and children were more strongly correlated among older children in the sample, suggesting that the effects of a richer maternal vocabulary are cumulative. Conclusions. Differences in children's cognitive outcomes start very early, which has important implications for the intergenerational transmission of poverty and inequality. Programs that seek to increase early stimulation for disadvantaged children, perhaps through parenting programs or high-quality center-based care, hold promise.
Changes Over Time in the Health of Caregivers of Children With Health Problems: Growth-Curve Findings From a 10-Year Canadian Population-Based Study
Authors: Brehaut Jamie C. , Garner Rochelle E. , Miller Anton R. , Lach Lucyna M. , Klassen Anne F. , Rosenbaum Peter L. , Kohen Dafna E. 
Published: October 2011

Objectives. We used Canadian population-based data to examine changes in the health of caregivers of children with complex health problems compared with caregivers of healthy children over a 10-year time period.Methods. The National Longitudinal Survey of Children and Youth collected data biennially from 9401 children and their caregivers in 6 waves from 1994–1995 to 2004–2005. We conducted growth-curve analyses of these data to model self-reported general health and depressive symptoms for 4 groups of caregivers: caregivers of healthy children, and caregivers of children with 1, 2, or at least 3 of 4 conceptually distinct indicators of child health problems. We modeled covariates for children (age, gender, only-child status) and caregivers (age, gender, education, income, marital status).Results. After we controlled for covariates, caregiver health outcomes worsened incrementally with increasing complexity of child health problems. Change in self-reported general health and depressive symptoms over the 10-year period was consistent across all groups of caregivers.Conclusions. Poorer health among caregivers of children with health problems can persist for many years and is associated with complexity of child health problems. Attention to parental health should form a component of health care services for children with health problems.