bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome-wide nucleosome mapping of Plasmodium falciparum reveals histone-rich coding and histone-poor intergenic regions and chromatin remodeling of core and subtelomeric genes
Authors: Westenberger Scott J , Cui Long , Dharia Neekesh , Winzeler Elizabeth , Cui Liwang 
Published: December 2009

Abstract

Background
Epigenetic modifications of histones and regulation of chromatin structure have been implicated in regulation of virulence gene families in P. falciparum. To better understand chromatin-mediated gene regulation, we used a high-density oligonucleotide microarray to map the position and enrichment of nucleosomes across the entire genome of P. falciparum at three time points of the intra-erythrocytic developmental cycle (IDC) in vitro. We used an unmodified histone H4 antibody for chromatin immunoprecipitation of nucleosome-bound DNA.

Results
We observed generally low nucleosomal occupancy of intergenic regions and higher occupancy of protein coding regions. In contract to the overall small fluctuation of nucleosomal occupancy in most coding regions throughout the IDC, subtelomeric genes encoding surface proteins such as var and rif, as well as some core chromosomal genes such as transcription factors, showed large changes in chromatin structure. Telomeres harbored a region with the highest nucleosomal occupancy of the genome and also exhibited large changes with higher nucleosomal occupancy at schizont stages. While many of these subtelomeric genes were previously shown to be modified by H3K9 trimethylation, we also identified some housekeeping genes in core chromosome regions that showed extensive changes in chromatin structure but do not contain this modification. tRNA and basal transcription factor genes showed low nucleosomal occupancy at all times, suggesting of an open chromatin structure that might be permissive for constitutively high levels of expression. Generally, nucleosomal occupancy was not correlated with the steady-state mRNA levels. Several var genes were exceptions: the var gene with the highest expression level showed the lowest nucleosomal occupancy, and selection of parasites for var2CSA expression resulted in lower nucleosomal occupancy at the var2CSA locus. We identified nucleosome-free regions in intergenic regions that may serve as transcription start sites or transcription factor binding sites. Using the nucleosomal occupancy data as the baseline, we further mapped the genome-wide enrichment of H3K9 acetylation and detected general enrichment of this mark in intergenic regions.

Conclusions
These data on nucleosome enrichment changes add to our understanding of the influence of chromatin structure on the regulation of gene expression. Histones are generally enriched in coding regions, and relatively poor in intergenic regions. Histone enrichment patterns allow for identification of new putative gene-coding regions. Most genes do not show correlation between chromatin structure and steady-state mRNA levels, indicating the dominant roles of other regulatory mechanisms. We present a genome-wide nucleosomal occupancy map, which can be used as a reference for future experiments of histone modification mapping.
Association between CYP19 gene SNP rs2414096 Polymorphism and polycystic ovary syndrome in Chinese women
Authors: Jin Jia-Li , Sun Jing , Ge Hui-Juan , Cao Yun-Xia , Wu Xiao-Ke , Liang Feng-Jing , Sun Hai-Xiang , Ke Lu , Yi Long , Wu Zhi-Wei , Wang Yong 
Published: December 2009

Abstract

Background
Several studies have reported the association of the SNP rs2414096 in the CYP19 gene with hyperandrogenism, which is one of the clinical manifestations of polycystic ovary syndrome (PCOS). These studies suggest that SNP rs2414096 may be involved in the etiopathogenisis of PCOS. To investigate whetherthe CYP19 gene SNP rs2414096 polymorphism is associated with the susceptibility to PCOS, we designed a case-controlled association study including 684 individuals.

Methods
A case-controlled association study including 684 individuals (386 PCOS patients and 298 controls) was performed to assess the association of SNP rs2414096 with PCOS. Genotyping of SNP rs2414096 was conducted by the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method that was performed on genomic DNA isolated from blood leucocytes. Results were analyzed in respect to clinical test results.

Results
The genotypic distributions of rs2414096 (GG, AG, AA) in the CYP19 gene (GG, AG, AA) in women with PCOS (0.363, 0.474, 0.163, respectively) were significantly different from that in controls (0.242, 0.500, 0.258, respectively) (P = 0.001). E2/T was different between the AA and GG genotypes. Age at menarche (AAM) and FSH were also significantly different among the GG, AG, and AA genotypes in women with PCOS (P = 0.0391 and 0.0118, respectively). No differences were observed in body mass index (BMI) and other serum hormone concentrations among the three genotypes, either in the PCOS patients or controls.

Conclusions
Our data suggest that SNP rs2414096 in the CYP19 gene is associated with susceptibility to PCOS.
Transcutaneous electrical nerve stimulation for the management of tennis elbow: a pragmatic randomized controlled trial: the TATE trial (ISRCTN 87141084)
Authors: Chesterton Linda S , van der Windt Daniëlle A , Sim Julius , Lewis Martyn , Mallen Christian D , Mason Elizabeth E , Warlow Catherine , Vohora Kanchan , Hay Elaine M 
Published: December 2009

AbstractBackgroundTennis elbow is a common and often extremely painful musculoskeletal condition, which has considerable impact on individuals as well as economic implications for healthcare utilization and absence from work. Many management strategies have been studied in clinical trials. Whilst corticosteroid injections offer short term pain relief, this treatment is unpleasant and is used with caution due to an associated high risk of pain recurrence in the long term. Systematic reviews conclude that there is no clear and effective treatment for symptoms of pain in the first 6 weeks of the condition. There is a clear need for an intervention that is acceptable to patients and provides them with effective short-term pain relief without increasing the risk of recurrence. Transcutaneous electrical nerve stimulation (TENS) is an inexpensive, non-invasive, non-pharmacological form of analgesia that is commonly used in the treatment of pain. TENS has very few contraindications and is simple to apply. It also benefits from being patient controlled, thereby promoting self-management. This study aims to assess the effectiveness, in terms of pain relief, and cost-effectiveness of a self-management package of treatment that includes TENS.Methods/DesignThe design of the study will be a two-group pragmatic randomized clinical trial. 240 participants aged 18 years and over with tennis elbow will be recruited from 20-30 GP practices in Staffordshire, UK. Participants are to be randomized on a 1:1 basis to receive either primary care management (standard GP consultation, medication, advice and education) or primary care management with the addition of TENS, over 6 weeks. Our primary outcome measure is average intensity of elbow pain in the past 24 hours (0-10 point numerical rating scale) at 6 weeks. Secondary outcomes include pain and limitation of function, global assessment of change, days of sick leave, illness perceptions, and overall health status. A cost-effectiveness analysis will also be performed. Patient adherence and satisfaction data will be collected at 6 weeks, 6 months and 12 months by postal questionnaire. A diary will also be completed for the first 2 weeks of treatment. Clinical effectiveness and cost-effectiveness analyses will be carried out using an intention-to-treat approach as the primary analysis.DiscussionThis paper presents detail on the rationale, design, methods and operational aspects of the trial.Trial registrationCurrent Controlled Trials. ISRCTN87141084
An improved phage-display panning method to produce an HM-1 killer toxin anti-idiotypic antibody
Authors: Kabir M Enamul , Krishnaswamy Senthilkumar , Miyamoto Masahiko , Furuichi Yasuhiro , Komiyama Tadazumi 
Published: December 2009

AbstractBackgroundPhage-display panning is an integral part of biomedical research. Regular panning methods are sometimes complicated by inefficient detachment of the captured phages from the antigen-coated solid supports, which prompted us to modify. Here, we produce an efficient antigen-specific single chain fragment variable (scFv) antibody by using a target-related molecule that favored selection ofrecombinant antibodies.ResultsTo produce more selective and specific anti-idiotypic scFv-antibodies from a cDNA library, constructed from HM-1 killer toxin (HM-1)-neutralizing monoclonal antibodies (nmAb-KT), the method was modified by using an elution buffer supplemented with HM-1 that shares structural and functional similarities with the active site of the scFv antibody. Competitive binding of HM-1 to nmAb-KT allowed easy and quick dissociation of scFv-displayed phages from immobilized nmAb-KT to select specific anti-idiotypic scFv antibodies of HM-1. After modified panning, 80% clones (40/50) showed several times higher binding affinity to nmAb-KT than regular panning. The major populations (48%) of these clones (scFv K1) were genotypically same and had strong cytocidal activity againstSaccharomycesandCandidaspecies. The scFv K1 (Kdvalue = 4.62 × 10-8M) had strong reactivity toward nmAb-KT, like HM-1 (Kdvalue = 6.74 × 10-9M) as judged by SPR analysis.ConclusionThe scFv antibodies generated after modified subtractive panning appear to have superior binding properties and cytocidal activity than regular panning. A simple modification of the elution condition in the phage-display panning protocol makes a large difference in determining success. Our method offers an attractive platform to discover potential therapeutic candidates.
The sonic hedgehog signaling pathway is reactivated in human renal cell carcinoma and plays orchestral role in tumor growth
Authors: Dormoy Valérian , Danilin Sabrina , Lindner Véronique , Thomas Lionel , Rothhut Sylvie , Coquard Catherine , Helwig Jean-Jacques , Jacqmin Didier , Lang Hervé , Massfelder Thierry 
Published: December 2009

Abstract

Background
Human clear cell renal cell carcinoma (CRCC) remains resistant to therapies. Recent advances in Hypoxia Inducible Factors (HIF) molecular network led to targeted therapies, but unfortunately with only limited clinical significance. Elucidating the molecular processes involved in kidney tumorigenesis and resistance is central to the development of improved therapies, not only for kidney cancer but for many, if not all, cancer types. The oncogenic PI3K/Akt, NF-kB and MAPK pathways are critical for tumorigenesis. The sonic hedgehog (SHH) signaling pathway is crucial to normal development.

Results
By quantitative RT-PCR and immunoblot, we report that the SHH signaling pathway is constitutively reactivated in tumors independently of the von Hippel-Lindau (VHL) tumor suppressor gene expression which is inactivated in the majority of CRCC. The inhibition of the SHH signaling pathway by the specific inhibitor cyclopamine abolished CRCC cell growth as assessed by cell counting, BrdU incorporation studies, fluorescence-activated cell sorting and β-galactosidase staining. Importantly, inhibition of the SHH pathway induced tumor regression in nude mice through inhibition of cell proliferation and neo-vascularization, and induction of apoptosis but not senescence assessed by in vivo studies, immunoblot and immunohistochemistry. Gli1, cyclin D1, Pax2, Lim1, VEGF, and TGF-β were exclusively expressed in tumors and were shown to be regulated by SHH, as evidenced by immunoblot after SHH inhibition. Using specific inhibitors and immunoblot, the activation of the oncogenic PI3K/Akt, NF-kB and MAPK pathways was decreased by SHH inhibition.

Conclusions
These findings support targeting SHH for the treatment of CRCC and pave the way for innovative and additional investigations in a broad range of cancers.
Pre-treatment preferences and characteristics among patients seeking in vitro fertilisation
Authors: Walsh Anthony PH , Collins Gary S , Le Du Monique , Walsh David J , Sills Eric Scott 
Published: December 2009

Abstract

Background
This study sought to describe patient features before beginning fertility treatment, and to ascertain their perceptions relative to risk of twin pregnancy outcomes associated with such therapy.

Methods
Data on readiness for twin pregnancy outcome from in vitro fertilisation (IVF) was gathered from men and women before initiating fertility treatment by anonymous questionnaire.

Results
A total of 206 women and 204 men were sampled. Mean (± SD) age for women and men being 35.5 ± 5 and 37.3 ± 7 yrs, respectively. At least one IVF cycle had been attempted by 27.2% of patients and 33.9% of this subgroup had initiated ≥3 cycles, reflecting an increase in previous failed cycles over five years. Good agreement was noted between husbands and wives with respect to readiness for twins from IVF (77% agreement; Cohen's K = 0.61; 95% CI 0.53 to 0.70).

Conclusion
Most patients contemplating IVF already have ideas about particular outcomes even before treatment begins, and suggests that husbands & wives are in general agreement on their readiness for twin pregnancy from IVF. However, fertility patients now may represent a more refractory population and therefore carry a more guarded prognosis. Patient preferences identified before IVF remain important, but further studies comparing pre- and post-treatment perceptions are needed.
A dose-controlled system for air-liquid interface cell exposure and application to zinc oxide nanoparticles
Authors: Lenz Anke Gabriele , Karg Erwin , Lentner Bernd , Dittrich Vlad , Brandenberger Christina , Rothen-Rutishauser Barbara , Schulz Holger , Ferron George A , Schmid Otmar 
Published: December 2009

Abstract

Background
Engineered nanoparticles are becoming increasingly ubiquitous and their toxicological effects on human health, as well as on the ecosystem, have become a concern. Since initial contact with nanoparticles occurs at the epithelium in the lungs (or skin, or eyes), in vitro cell studies with nanoparticles require dose-controlled systems for delivery of nanoparticles to epithelial cells cultured at the air-liquid interface.

Results
A novel air-liquid interface cell exposure system (ALICE) for nanoparticles in liquids is presented and validated. The ALICE generates a dense cloud of droplets with a vibrating membrane nebulizer and utilizes combined cloud settling and single particle sedimentation for fast (~10 min; entire exposure), repeatable (<12%), low-stress and efficient delivery of nanoparticles, or dissolved substances, to cells cultured at the air-liquid interface. Validation with various types of nanoparticles (Au, ZnO and carbon black nanoparticles) and solutes (such as NaCl) showed that the ALICE provided spatially uniform deposition (<1.6% variability) and had no adverse effect on the viability of a widely used alveolar human epithelial-like cell line (A549). The cell deposited dose can be controlled with a quartz crystal microbalance (QCM) over a dynamic range of at least 0.02-200 μg/cm2. The cell-specific deposition efficiency is currently limited to 0.072 (7.2% for two commercially available 6-er transwell plates), but a deposition efficiency of up to 0.57 (57%) is possible for better cell coverage of the exposure chamber.
Dose-response measurements with ZnO nanoparticles (0.3-8.5 μg/cm2) showed significant differences in mRNA expression of pro-inflammatory (IL-8) and oxidative stress (HO-1) markers when comparing submerged and air-liquid interface exposures. Both exposure methods showed no cellular response below 1 μg/cm2 ZnO, which indicates that ZnO nanoparticles are not toxic at occupationally allowed exposure levels.

Conclusion
The ALICE is a useful tool for dose-controlled nanoparticle (or solute) exposure of cells at the air-liquid interface. Significant differences between cellular response after ZnO nanoparticle exposure under submerged and air-liquid interface conditions suggest that pharmaceutical and toxicological studies with inhaled (nano-)particles should be performed under the more realistic air-liquid interface, rather than submerged cell conditions.
Impaired verbal memory in Parkinson disease: relationship to prefrontal dysfunction and somatosensory discrimination
Authors: Bohlhalter Stephan , Abela Eugenio , Weniger Dorothea , Weder Bruno 
Published: December 2009

Abstract

Objective
To study the neurocognitive profile and its relationship to prefrontal dysfunction in non-demented Parkinson's disease (PD) with deficient haptic perception.

Methods
Twelve right-handed patients with PD and 12 healthy control subjects underwent thorough neuropsychological testing including Rey complex figure, Rey auditory verbal and figural learning test, figural and verbal fluency, and Stroop test. Test scores reflecting significant differences between patients and healthy subjects were correlated with the individual expression coefficients of one principal component, obtained in a principal component analysis of an oxygen-15-labeled water PET study exploring somatosensory discrimination that differentiated between the two groups and involved prefrontal cortices.

Results
We found significantly decreased total scores for the verbal learning trials and verbal delayed free recall in PD patients compared with normal volunteers. Further analysis of these parameters using Spearman's ranking correlation showed a significantly negative correlation of deficient verbal recall with expression coefficients of the principal component whose image showed a subcortical-cortical network, including right dorsolateral-prefrontal cortex, in PD patients.

Conclusion
PD patients with disrupted right dorsolateral prefrontal cortex function and associated diminished somatosensory discrimination are impaired also in verbal memory functions. A negative correlation between delayed verbal free recall and PET activation in a network including the prefrontal cortices suggests that verbal cues and accordingly declarative memory processes may be operative in PD during activities that demand sustained attention such as somatosensory discrimination. Verbal cues may be compensatory in nature and help to non-specifically enhance focused attention in the presence of a functionally disrupted prefrontal cortex.
Look who is calling: a comparison of genotype calling algorithms
Authors: Vens Maren , Schillert Arne , König Inke R , Ziegler Andreas 
Published: December 2009

Abstract
In genome-wide association studies, high-level statistical analyses rely on the validity of the called genotypes, and different genotype calling algorithms (GCAs) have been proposed. We compared the GCAs Bayesian robust linear modeling using Mahalanobis distance (BRLMM), Chiamo++, and JAPL using the autosomal single-nucleotide polymorphisms (SNPs) from the 500 k Affymetrix Array Set data of the Framingham Heart Study as provided for the Genetic Analysis Workshop 16, Problem 2, and prepared standard quality control (sQC) for each algorithm. Using JAPL, most individuals were retained for the analysis. The lowest number of SNPs that successfully passed sQC was observed for BRLMM and the highest for Chiamo++. All three GCAs fulfilled all sQC criteria for 79% of the SNPs but at least one GCA failed for 18% of the SNPs. Previously undetected errors in strand coding were identified by comparing genotype concordances between GCAs. Concordance dropped with the number of GCAs failing sQC. We conclude that JAPL and Chiamo++ are the GCAs of choice if the aim is to keep as many subjects and SNPs as possible, respectively.
Long term outcomes of antiretroviral therapy in a large HIV/AIDS care clinic in urban South Africa: a prospective cohort study
Authors: Sanne Ian M , Westreich Daniel , Macphail Andrew P , Rubel Dennis , Majuba Pappie , Van Rie Annelies 
Published: December 2009

BackgroundClinical, immunologic and virologic outcomes at large HIV/AIDS care clinics in resource poor settings are poorly described beyond the first year of highly active antiretroviral treatment (HAART). We aimed to prospectively evaluate long‐term treatment outcomes at a large scale HIV/AIDS care clinic in South Africa.MethodsCohort study of patients initiating HAART between April 1, 2004 and March 13, 2007, and followed up until April 1, 2008 at a public HIV/AIDS care clinic in Johannesburg, South Africa. We performed time to event analysis on key treatment outcomes and program impact parameters including mortality, retention in care, CD4 count gain, virologic success and first line regimen durability.Results7583 HIV‐infected patients initiated care and contributed to 161,000 person months follow up. Overall mortality rate was low (2.9 deaths per 100 person years, 95% CI 2.6‐3.2), but high in the first three months of HAART (8.4 per 100 person years, 95% CI 7.2‐9.9). Long‐term on‐site retention in care was relatively high (74.4% at 4 years, 95%CI 73.2‐75.6). CD4 count was above 200 cells/mm3 after 6 months of treatment in almost all patients. By the fourth year of HAART, the majority (59.6%, 95%CI 57.8‐61.4) of patients had at least one first line drug (mainly stavudine) substituted. Women were twice as likely to experience drug substitution (OR 1.97, 95% CI 1.80‐2.16). By 6 months of HAART, 90.8% suppressed virus below 400 copies. Among those with initial viral suppression, 9.4% (95% CI 8.5‐10.3%) had viral rebound within one year of viral suppression, 16.8% (95% CI 15.5‐18.1) within 2 years, and 20.6% (95% CI 18.9‐22.4) within 3 years of initial suppression. Only 10% of women and 13% of men initiated second line HAART.ConclusionDespite advanced disease presentation and a very large‐scale program, high quality care was achieved as indicated by good long‐term clinical, immunologic and virologic outcomes and a low rate of second line HAART initiation. High rates of single drug substitution suggest that the public health approach to HAART could be further improved by the use of a more durable first line regimen.
Stability of serum thyroid hormones following 8–11 years of cold storage
Authors: Panesar Nirmal S. , Lit Lydia C.W. 
Published: December 2009

Abstract

Background: Ethnic differences necessitate a need for local reference intervals (RI), but establishing these can be challenging in some cultures that are reluctant to donate blood. Frozen sera are an alternative, but results can be questionable. Between 1998 and 2001, we collected blood samples from 343 healthy pregnant Chinese women (5–41 weeks' gestation), and in 2001 published gestational RI for thyrotropin thyroid stimulating hormone (TSH), free thyroxine (FT4) and free triiodothyronine (FT3) using the ACS180, now obsolete. As a pilot to re-establishing RI, TSH, FT4 and FT3 were re-assayed in archived specimens using contemporary assays.

Methods: Thirty archived specimens (–80°C) with ACS180 TSH concentrations ranging from 0.25 to 3.7 mIU/L were measured using the Roche E170, Advia Centaur and Architect i2000 TSH, FT4 and FT3 assays, along with 10 newer contemporary samples. Results were compared to the original, and examined in context of past and present methodological performances in an external quality assurance (EQA) program.

Results: All contemporary assays detected significantly lower TSH and increased FT4 and FT3 concentrations in the stored samples.

Conclusions: With reference to methodological performances in EQA, the results obtained with contemporary assays suggest analyte deterioration in specimens and thus their unsuitability for re-establishing RI.
Clin Chem Lab Med 2010;48:409–12.