bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rate and determinants of treatment response to different antiretroviral combination strategies in subjects presenting at HIV-1 diagnosis with advanced disease
Authors: Esposito Antonella , Floridia Marco , d'Ettorre Gabriella , Pastori Daniele , Fantauzzi Alessandra , Massetti Paola , Ceccarelli Giancarlo , Ajassa Camilla , Vullo Vincenzo , Mezzaroma Ivano 
Published: December 2011

AbstractBackgroundThe optimal therapeutic strategies for patients presenting with advanced disease at HIV-1 diagnosis are as yet incompletely defined.MethodsAll patients presenting at two outpatient clinics in 2000-2009 with an AIDS-defining clinical condition or a CD4+ T cell count < 200/μL at HIV-1 diagnosis were analyzed for the presence of combined immunovirological response, defined by the concomitant presence of an absolute number of CD4+ T cells > 200 cells/μL and a plasma HIV-1 RNA copy number < 50/mL after 12 months of HAART.ResultsAmong 102 evaluable patients, first-line regimens were protease inhibitors [PI]-based in 78 cases (77%) and efavirenz-based in 24 cases (23%). The overall response rate was 65% (95% CI: 55-74), with no differences by gender, age, nationality, route of transmission, hepatitis virus coinfections, presence of AIDS-defining clinical events, baseline HIV-1 viral load, or type of regimen (response rates with PI-based and efavirenz-based therapy: 63% and 71%, respectively, p = 0.474). Response rate was significantly better with higher baseline CD4+ T cell counts (78% with CD4+ ≥ 100/μL, compared to 50% with CD4+ < 100/μL; odds ratio: 3.5; 95% CI: 1.49-8.23, p = 0.003). Median time on first-line antiretroviral therapy was 24 months (interquartile range: 12-48). Switch to a second line treatment occurred in 57% of patients, mainly for simplification (57%), and was significantly more common with PI-based regimens [adjusted hazard ratios (AHR) with respect to efavirenz-based regimens: 3.88 for unboosted PIs (95% CI: 1.40-10.7, p = 0.009) and 4.21 for ritonavir-boosted PI (95%CI 1.7-10.4, p = 0.002)] and in older subjects (≥ 50 years) (AHR: 1.83; 95% CI: 1.02-3.31, p = 0.044). Overall mortality was low (3% after a median follow up of 48 months).ConclusionsOur data indicate that a favorable immunovirological response is possible in the majority of naive patients presenting at HIV-1 diagnosis with AIDS or low CD4+ T cell counts, and confirm that starting HAART with a more compromised immune system may be associated with a delayed and sometimes partial immune recovery. Simpler regimens may be preferable in this particular population.
A novel mutation in STK11 gene is associated with Peutz-Jeghers Syndrome in Chinese patients
Authors: Wang Zhiqing , Chen Yulan , Wu Baoping , Zheng Haoxuan , He Jiman , Jiang Bo 
Published: December 2011

Abstract

Background
Peutz-Jeghers syndrome (PJS) is caused by mutations in the tumor suppressor gene, STK11, and is characterized by gastrointestinal hamartomas, melanin spots on the lips, and an increased risk of developing cancer.

Methods
Blood samples were collected from two unrelated Chinese PJS families totaling 20 individuals (9 male and 11 females), including 6 PJS patients. The entire coding region of the STK11 gene was amplified by polymerase chain reaction and analyzed by direct sequencing.

Results
A novel mutation, c.904C > T, in exon 7 was identified in both families. A C > T substitution changed codon 302 from CAG (glutamine) to TAG (stop), truncating the STK11 protein, thus leading to the partial loss of the kinase domain and complete loss of the α-helix C-terminus. Furthermore, one PJS patient from each family was diagnosed with a visceral cancer, a colon cancer and a liver cancer respectively.

Conclusion
We predict that this novel mutation, p.Q302X, is most likely responsible for development of the PJS phenotype and may even contribute to malignancy.
The association between parity, infant gender, higher level of paternal education and preterm birth in Pakistan: a cohort study
Authors: Shaikh Kiran , Premji Shahirose S , Rose Marianne S , Kazi Ambreen , Khowaja Shaneela , Tough Suzanne 
Published: December 2011

Abstract

Background
High rates of antenatal depression and preterm birth have been reported in Pakistan. Self reported maternal stress and depression have been associated with preterm birth; however findings are inconsistent. Cortisol is a biological marker of stress and depression, and its measurement may assist in understanding the influence of self reported maternal stress and depression on preterm birth.

Methods
In a prospective cohort study pregnant women between 28 to 30 weeks of gestation from the Aga Khan Hospital for Women and Children completed the A-Z Stress Scale and the Centre for Epidemiology Studies Depression Scale to assess stress and depression respectively, and had a blood cortisol level drawn. Women were followed up after delivery to determine birth outcomes. Correlation coefficients and Wilcoxon rank sum test was used to assess relationship between preterm birth, stress, depression and cortisol. Logistic regression analysis was used to determine the key factors predictive of preterm birth.

Results
132 pregnant women participated of whom 125 pregnant women had both questionnaire and cortisol level data and an additional seven had questionnaire data only. Almost 20% of pregnant women (19·7%, 95% CI 13·3-27·5) experienced a high level of stress and nearly twice as many (40·9%, 95% CI 32·4-49·8%) experienced depressive symptoms. The median of cortisol level was 27·40 ug/dl (IQR 22·5-34·2). The preterm birth rate was 11·4% (95% CI 6·5-18). There was no relationship between cortisol values and stress scale or depression. There was a significant positive relationship between maternal depression and stress. Preterm birth was associated with higher parity, past delivery of a male infant, and higher levels of paternal education. Insufficient numbers of preterm births were available to warrant the development of a multivariable logistic regression model.

Conclusions
Preterm birth was associated with higher parity, past delivery of a male infant, and higher levels of paternal education. There was no relationship between stress, and depression, cortisol and preterm birth. There were high rates of stress and depression among this sample suggesting that there are missed opportunities to address mental health needs in the prenatal period. Improved methods of measurement are required to better understand the psychobiological basis of preterm birth.
Association of ADAMTS13 polymorphism with cerebral malaria
Authors: Kraisin Sirima , Naka Izumi , Patarapotikul Jintana , Nantakomol Duangdao , Nuchnoi Pornlada , Hananantachai Hathairad , Tsuchiya Naoyuki , Ohashi Jun 
Published: December 2011

Abstract

Background
Cerebral malaria is one of the most severe manifestations of Plasmodium falciparum malaria. The sequestration of parasitized red blood cells (PRBCs) to brain microvascular endothelium has been shown to contribute to the pathophysiology of cerebral malaria. Recent studies reported increased levels of von Willebrand factor (VWF) and reduced activity of VWF-cleaving protease, ADAMTS13 (a disintegrin and metalloproteinase with a thrombospondin type 1 motif, member 13), in patients with cerebral malaria.

Methods
Association of six single nucleotide polymorphisms (SNPs) of the ADAMTS13 gene with cerebral malaria was examined in 708 Thai patients with P. falciparum malaria.

Results
Among six SNPs, the derived allele of a SNP located in intron 28, rs4962153-A, was significantly associated with protection against cerebral malaria when 115 cerebral malaria patients were compared with 367 mild malaria patients (Fisher's exact P-value = 0.0057; OR = 0.27; 95% CI = 0.096-0.76). Significant association was also detected between 115 cerebral malaria and 593 non-cerebral malaria (226 non-cerebral severe malaria and 367 mild malaria) patients (Fisher's exact P-value = 0.012; OR = 0.30; 95% CI = 0.11-0.83).

Conclusions
Excessive adhesion of PRBCs to the platelet-decorated ultra-large VWF (ULVWF) appears to enhance the sequestration of PRBCs to cerebral microvascular endothelium. The genetic association observed in the present study implies that the regulation of platelet-decorated ULVWF strings by ADAMTS13 may play a role in the development of cerebral malaria.
An efficient protocol for inducing pseudopregnancy using estradiol dipropionate and follicular development associated with changes in reproductive hormones after prostaglandin F2alpha treatment in pseudopregnant sows
Authors: Noguchi Michiko , Yoshioka Koji , Suzuki Chie , Itoh Seigo , Kaneko Hiroyuki 
Published: December 2011

Abstract

Background
Utilization of estrus synchronization program in livestock industry would provide greater options for reproductive management in herd. To develop a convenient method for estrus synchronization in pigs, we determined the effective protocol using estradiol dipropionate (EDP) for the establishment of pseudopregnancy and investigated follicular development during the estrus synchronization with prostaglandin F2alpha (PGF2alpha) in association with reproductive hormone profiles in pseudopregnant sows.

Methods
In Experiment 1, the effective dose (0, 10, 20, or 30 mg) and timing (5, 8, 11 or 13 days after ovulation) of a single administration of EDP in cyclic pigs for the induction of pseudopregnancy were investigated. In Experiment 2, four pseudopregnant sows were treated with PGF2alpha twice at a 24-h interval between 24 and 28 days after EDP treatment. The changes in plasma concentrations of reproductive hormones were analyzed by time-resolved fluoroimmunoassay. Follicular development and ovulation following PGF2alpha administration were monitored by transrectal ultrasonography.

Results
High efficiency (greater than 80%) of pseudopregnancy was achieved with a single treatment with 20 mg of EDP at 8 and 11 days after ovulation (equivalent to 9-13 days after the onset of estrus). Plasma estradiol-17beta concentrations in pseudopregnant sows were significantly higher between 12 h and 7 days than before EDP treatment. Total inhibin concentrations significantly decreased following EDP treatment and remained low for 14 days. The number of small follicles was increased from 6.3 +/- 2.6 at PGF2alpha treatment to 22.8 +/- 4.8 at 3 days later; this was associated with increased plasma concentrations of inhibin. Onset of estrus was detectable in all sows on 5.3 +/- 0.3 days after PGF2alpha treatment and the number of ovulated follicles was 15.5 +/- 1.4 detected at 7.6 +/- 0.2 days after the treatment.

Conclusions
This study has defined the effective dose and timing of EDP treatment for inducing pseudopregnancy in cyclic pigs. Our results also indicated that EDP caused a lowering of inhibin concentrations during pseudopregnancy and small numbers of follicles from 20 to 28 days after EDP. In contrast, EDP-induced pseudopregnancy appears to have no adverse effect on follicular development and subsequent ovulation following PGF2alpha administration.
A methodology for multivariate phenotype-based genome-wide association studies to mine pleiotropic genes
Authors: Park Sung Hee , Lee Ji Young , Kim Sangsoo 
Published: December 2011

Abstract

Background
Current Genome-Wide Association Studies (GWAS) are performed in a single trait framework without considering genetic correlations between important disease traits. Hence, the GWAS have limitations in discovering genetic risk factors affecting pleiotropic effects.

Results
This work reports a novel data mining approach to discover patterns of multiple phenotypic associations over 52 anthropometric and biochemical traits in KARE and a new analytical scheme for GWAS of multivariate phenotypes defined by the discovered patterns. This methodology applied to the GWAS for multivariate phenotype highLDLhighTG derived from the predicted patterns of the phenotypic associations. The patterns of the phenotypic associations were informative to draw relations between plasma lipid levels with bone mineral density and a cluster of common traits (Obesity, hypertension, insulin resistance) related to Metabolic Syndrome (MS). A total of 15 SNPs in six genes (PAK7, C20orf103, NRIP1, BCL2, TRPM3, and NAV1) were identified for significant associations with highLDLhighTG. Noteworthy findings were that the significant associations included a mis-sense mutation (PAK7:R335P), a frame shift mutation (C20orf103) and SNPs in splicing sites (TRPM3).

Conclusions
The six genes corresponded to rat and mouse quantitative trait loci (QTLs) that had shown associations with the common traits such as the well characterized MS and even tumor susceptibility. Our findings suggest that the six genes may play important roles in the pleiotropic effects on lipid metabolism and the MS, which increase the risk of Type 2 Diabetes and cardiovascular disease. The use of the multivariate phenotypes can be advantageous in identifying genetic risk factors, accounting for the pleiotropic effects when the multivariate phenotypes have a common etiological pathway.
Exploring molecular links between lymph node invasion and cancer prognosis in human breast cancer
Authors: Kim Sangwoo , Nam Hojung , Lee Doheon 
Published: December 2011

Abstract

Background
Lymph node invasion is one of the most powerful clinical factors in cancer prognosis. However, molecular level signatures of their correlation are remaining poorly understood. Here, we propose a new approach, monotonically expressed gene analysis (MEGA), to correlate transcriptional patterns of lymph node invasion related genes with clinical outcome of breast cancer patients.

Results
Using MEGA, we scored all genes with their transcriptional patterns over progression levels of lymph node invasion from 278 non-metastatic breast cancer samples. Applied on 65 independent test data, our gene sets of top 20 scores (positive and negative correlations) showed significant associations with prognostic measures such as cancer metastasis, relapse and survival. Our method showed better accuracy than conventional two class comparison methods. We could also find that expression patterns of some genes are strongly associated with stage transition of pathological T and N at specific time. Additionally, some pathways including T-cell immune response and wound healing serum response are expected to be related with cancer progression from pathway enrichment and common motif binding site analyses of the inferred gene sets.

Conclusions
By applying MEGA, we can find possible molecular links between lymph node invasion and cancer prognosis in human breast cancer, supported by evidences of feasible gene expression patterns and significant results of meta-analysis tests.
Constitutive expression of a grapevine polygalacturonase-inhibiting protein affects gene expression and cell wall properties in uninfected tobacco
Authors: Alexandersson Erik , Becker John VW , Jacobson Dan , Nguema-Ona Eric , Steyn Cobus , Denby Katherine J , Vivier Melané A 
Published: December 2011

Abstract

Background
Polygalacturonase-inhibiting proteins (PGIPs) directly limit the effective ingress of fungal pathogens by inhibiting cell wall-degrading endopolygalacturonases (ePGs). Transgenic tobacco plants over-expressing grapevine (Vitis vinifera) Vvpgip1 have previously been shown to be resistant to Botrytis infection. In this study we characterized two of these PGIP over-expressing lines with known resistance phenotypes by gene expression and hormone profiling in the absence of pathogen infection.

Results
Global gene expression was performed by a cross-species microarray approach using a potato cDNA microarray. The degree of potential cross-hybridization between probes was modeled by a novel computational workflow designed in-house. Probe annotations were updated by predicting probe-to-transcript hybridizations and combining information derived from other plant species. Comparing uninfected Vvpgip1-overexpressing lines to wild-type (WT), 318 probes showed significant change in expression. Functional groups of genes involved in metabolism and associated to the cell wall were identified and consequent cell wall analysis revealed increased lignin-levels in the transgenic lines, but no major differences in cell wall-derived polysaccharides. GO enrichment analysis also identified genes responsive to auxin, which was supported by elevated indole-acetic acid (IAA) levels in the transgenic lines. Finally, a down-regulation of xyloglucan endotransglycosylase/hydrolases (XTHs), which are important in cell wall remodeling, was linked to a decrease in total XTH activity.

Conclusions
This evaluation of PGIP over-expressing plants performed under pathogen-free conditions to exclude the classical PGIP-ePG inhibition interaction indicates additional roles for PGIPs beyond the inhibition of ePGs.
Specificity Characteristics of 7 Commercial Creatinine Measurement Procedures by Enzymatic and Jaffe Method Principles
Authors: Greenberg Neil , Roberts William L , Bachmann Lorin M , Wright Elizabeth C , Dalton R Neil , Zakowski Jack J , Greg Miller W 
Published: December 2011

Abstract

BACKGROUND
Standardized calibration does not change a creatinine measurement procedure's susceptibility to potentially interfering substances.

METHODS
We obtained individual residual serum or plasma samples (n = 365) from patients with 19 different disease categories associated with potentially interfering substances and from healthy controls. Additional sera at 0.9 mg/dL (80 μmol/L) and 3.8 mg/dL (336 μmol/L) creatinine were supplemented with acetoacetate, acetone, ascorbate, and pyruvate. We measured samples by 4 enzymatic and 3 Jaffe commercially available procedures and by a liquid chromatography/isotope dilution/mass spectrometry measurement procedure against which biases were determined.

RESULTS
The number of instances when 3 or more results in a disease category had biases greater than the limits of acceptability was 28 of 57 (49%) for Jaffe and 14 of 76 (18%) for enzymatic procedures. For the aggregate group of 59 diabetes samples with increased β-hydroxybutyrate, glucose, or glycosylated hemoglobin (Hb A1c), the enzymatic procedures had 10 biased results of 236 (4.2%) compared with 89 of 177 (50.3%) for the Jaffe procedures, and these interferences were highly procedure dependent. For supplemented sera, interferences were observed in 11 of 24 (46%) of groups for Jaffe and 8 of 32 (25%) of groups for enzymatic procedures and were different at low or high creatinine concentrations.

CONCLUSIONS
There were differences in both magnitude and direction of bias among measurement procedures, whether enzymatic or Jaffe. The influence of interfering substances was less frequent with the enzymatic procedures, but no procedure was unaffected. The details of implementation of a method principle influenced its susceptibility to potential interfering substances.
Non-Equilibrium Kinetic Studies of Plasma-Assisted Combustion using Laser-Based Diagnostics
Authors: Grisch F. , Grandin G. A. , Messina D. , Attal-Tretout B. 
Published: December 2011

Abstract
Experimental investigation of nanosecond pulsed discharge in premixed CH4/air mixtures at atmospheric pressure has been carried out using laser diagnostics. Electron temperature and number density are measured using laser Thomson scattering. Temperature of neutral molecules is measured by CARS. Finally, OH, CH and CH2O are probed using PLIF to identify their role in the reduction of ignition delay and in the improvement of lean burn capability relative to conventional spark ignition. Measurements are compared with numerical simulations performed using CHEMKIN-based code.
Process Control of CVD Deposition of Nanocrystalline Diamond Films by Plasma Diagnostics
Authors: Woehrl Nicolas , Buck Volker 
Published: December 2011

Abstract
Ultrananocrystalline Diamond (UNCD) Films were deposited by MW-CVD from an Ar/H2/CH4 plasma. The plasma properties were measured in situ by optical emission spectroscopy and mass spectroscopy. The intensity of the C2 emission line was systematically varied as a key plasma parameter and a correlation with resulting film properties was found.
Single Acetone Droplets at Supercritical Pressure: Droplet Generation and Characterization of PLIFP
Authors: Weckenmann F. , Bork B. , Oldenhof E. , Lamanna G. , Weigand B. , Böhm B. , Dreizler A. 
Published: December 2011

Abstract
An experimental investigation of isolated acetone droplets under supercritical pressure is presented. An optically accessible pressure chamber was set up for pressures ranging up to 60 bar and temperatures of up to 530 K. A novel method for the generation of acetone droplets on demand in the vicinity of the critical point is presented. High speed shadowgraphy imaging revealed remarkable reproducibility of the droplet generation regarding their size and shape and the timing of the detachment.
The photo-physical properties of acetone in nitrogen as well as nitrogen-oxygen mixtures were investigated using planar laser induced fluorescence and phosphorescence (PLIFP). The measurements revealed a strong sensitivity and selectivity of the phosphorescence-fluorescence-ratio relative to the oxygen concentration. This demonstrates the potential of PLIFP to distinguish between the liquid and gaseous phase of acetone injected into mixtures of nitrogen and oxygen.
Dispersed Fluorescence Spectra of 1H- and 1D-Indazole
Authors: Nicken Hauke , Temps Friedrich , Jalviste Erko 
Published: December 2011

Abstract
Dispersed fluorescence (DF) spectra of jet-cooled indazole (Ia-h) and its singly-deuterated isotopologue (Ia-d) were recorded following excitation of the origin band of the S
1(1
A´) ← S
0(1
A´) electronic transition. The spectra were analyzed and assigned with the help of vibrational frequency calculations by density functional theory (DFT) at the TPSS/aug-cc-pVTZ level. The calculated and measured S
0 state vibrations are in agreement within ≤ 3%. The obtained results for the two Ia monomers form the basis for an analysis of the electronic spectra of the hydrogen-bonded dimers Ia2-hh, Ia2-dd and Ia2-hd and a determination of the exciton splitting in the dimer in a forthcoming paper.
Fluorescence In Situ Hybridization–Based Karyotyping of Soybean Translocation Lines
Authors: Findley Seth D , Pappas Allison L , Cui Yaya , Birchler James A , Palmer Reid G , Stacey Gary 
Published: December 2011

Abstract
Soybean (Glycine max [L.] Merr.) is a major crop species and, therefore, a major target of genomic and genetic research. However, in contrast to other plant species, relatively few chromosomal aberrations have been identified and characterized in soybean. This is due in part to the difficulty of cytogenetic analysis of its small, morphologically homogeneous chromosomes. The recent development of a fluorescence in situ hybridization –based karyotyping system for soybean has enabled our characterization of most of the chromosomal translocation lines identified to date. Utilizing genetic data from existing translocation studies in soybean, we identified the chromosomes and approximate breakpoints involved in five translocation lines.