bluuebunny/crossref_metadata_2025_split huggingface dataset:
CYP2B6*6 is an independent determinant of inferior response to fludarabine plus cyclophosphamide in chronic lymphocytic leukemia
Authors: Johnson Gillian G. , Lin Ke , Cox Trevor F. , Oates Melanie , Sibson David R. , Eccles Richard , Lloyd Bryony , Gardiner Laura-Jayne , Carr Daniel F. , Pirmohamed Munir , Strefford Jonathan C. , Oscier David G. , Gonzalez de Castro David , Else Monica , Catovsky Daniel , Pettitt Andrew R. 
Published: October 2013

Key Points
Therapeutic response in CLL can be influenced by host pharmacogenetics.
Dynamical modelling of phenotypes in a genome-wide RNAi live-cell imaging assay
Authors: Pau Gregoire , Walter Thomas , Neumann Beate , Hériché Jean-Karim , Ellenberg Jan , Huber Wolfgang 
Published: October 2013

Abstract

Background
The combination of time-lapse imaging of live cells with high-throughput perturbation assays is a powerful tool for genetics and cell biology. The Mitocheck project employed this technique to associate thousands of genes with transient biological phenotypes in cell division, cell death and migration. The original analysis of these data proceeded by assigning nuclear morphologies to cells at each time-point using automated image classification, followed by description of population frequencies and temporal distribution of cellular states through event-order maps. One of the choices made by that analysis was not to rely on temporal tracking of the individual cells, due to the relatively low image sampling frequency, and to focus on effects that could be discerned from population-level behaviour.

Results
Here, we present a variation of this approach that employs explicit modelling by dynamic differential equations of the cellular state populations. Model fitting to the time course data allowed reliable estimation of the penetrance and time of appearance of four types of disruption of the cell cycle: quiescence, mitotic arrest, polynucleation and cell death. Model parameters yielded estimates of the duration of the interphase and mitosis phases. We identified 2190 siRNAs that induced a disruption of the cell cycle at reproducible times, or increased the durations of the interphase or mitosis phases.

Conclusions
We quantified the dynamic effects of the siRNAs and compiled them as a resource that can be used to characterize the role of their target genes in cell death, mitosis and cell cycle regulation. The described population-based modelling method might be applicable to other large-scale cell-based assays with temporal readout when only population-level measures are available.
RETRACTED ARTICLE: Coffee component hydroxyl hydroquinone (HHQ) as a putative ligand for PPAR gamma and implications in breast cancer
Authors: Shashni Babita , Sharma Karun , Singh Rumani , Sakharkar Kishore R , Dhillon Sarinder K , Nagasaki Yukio , Sakharkar Meena K 
Published: October 2013

Abstract
Background
Coffee contains several compounds that have the potential to influence breast cancer risk and survival. However, epidemiologic data on the relation between coffee compounds and breast cancer survival are sparse and inconsistent.

Results
We show that coffee component HHQ has significant apoptotic effect on MDA-MB-231 and MCF-7 cells in vitro, and that ROS generation, change in mitochondrial membrane permeability, upregulation of Bax and Caspase-8 as well as down regulation of PGK1 and PKM2 expression may be important apoptosis-inducing mechanisms. The results suggest that PPARγ ligands may serve as potential therapeutic agents for breast cancer therapy. HHQ was also validated as a ligand for PPARγ by docking procedure.

Conclusion
This is the first report on the anti-breast cancer (in vitro) activity of HHQ.
Influence of zoledronic acid on disseminated tumor cells in bone marrow and survival: results of a prospective clinical trial
Authors: Banys Malgorzata , Solomayer Erich-Franz , Gebauer Gerhard , Janni Wolfgang , Krawczyk Natalia , Lueck Hans-Joachim , Becker Sven , Huober Jens , Kraemer Bernhard , Wackwitz Birgit , Hirnle Peter , Wallwiener Diethelm , Fehm Tanja 
Published: October 2013

Abstract

Background
The presence of disseminated tumor cells (DTC) in bone marrow (BM) of breast cancer patients is associated with reduced clinical outcome. Bisphosphonate treatment was shown to eradicate DTC from BM in several studies. This controlled randomized open-label multi-center study aimed to investigate the influence of zoledronic acid (ZOL) on DTC and survival of breast cancer patients (Clinical Trial Registration Number: NCT00172068).

Methods
Patients with primary breast cancer and DTC-positive bone marrow were randomized to treatment with ZOL plus adjuvant systemic therapy (n = 40) or adjuvant systemic therapy alone (n = 46) between 03/2002 and 12/2004. DTC were identified by immunocytochemistry using the pancytokeratin antibody A45B/B3 and by cytomorphology. The change in DTC numbers at 12 months and 24 months versus baseline, as well as patient outcomes were evaluated.

Results
86 patients could be included into survival analysis (median follow-up: 88 months, range: 8–108 mths). Patients in the control group were more likely to die during follow-up than those in the ZOL-group (11% vs. 2%, p = 0.106). 15% of patients in the control group presented with relapse whereas only 8% of ZOL group patients developed metastatic or recurrent disease during follow-up (p = 0.205). At 24 months, 16% of patients from the control group were still DTC positive, whereas all patients treated with ZOL became DTC negative (p = 0.032). Patients presenting with persistent DTC 12 months after diagnosis had significantly shorter overall survival (p = 0.011).

Conclusions
Bisphosphonate therapy contributes to eradication of disseminated tumor cells. The positive influence of bisphosphonates on survival in the adjuvant setting may be due to their effects on DTC.

Trial registration
ClinicalTrials.gov Identifier: NCT00172068 [Zoledronic Acid in the Treatment of Breast Cancer With Minimal Residual Disease in the Bone Marrow (MRD-1)].
Clinical and microbiological profile of infectious keratitis in children
Authors: Chirinos-Saldaña Patricia , Bautista de Lucio Victor Manuel , Hernandez-Camarena Julio Cesar , Navas Alejandro , Ramirez-Miranda Arturo , Vizuet-Garcia Lizet , Ortiz-Casas Mariana , Lopez-Espinosa Nadia , Gaona-Juarez Carolina , Bautista-Hernandez Luis Antonio , Graue-Hernandez Enrique O 
Published: October 2013

AbstractBackgroundInfectious keratitis is a sight-threatening condition for children. The purpose of this study was to describe the clinical profile, risk factors and microbiological profile of infectious keratitis in children.MethodsRetrospective review of clinical records of patients under 16 years of age with history of microbial keratitis seen at a tertiary referral center. Clinical characteristics, risk factors, visual and surgical outcomes as well as the microbiological profile are analyzed.ResultsForty-one eyes of 41 patients. Mean age was 8.7 years. Time between the onset of symptoms and ophthalmological examination was 12.7 days. Predisposing factors were found in 78%; ocular trauma was the most common (25%). Visual acuity equal or worse than 20/200 at admission correlated positively with a poorer visual outcome, p=0.002. Positivity of cultures was 34%. Gram-positive bacteria were isolated in 78.5%;Staphylococcus epidermidis(28.6%) was the most common microorganism.ConclusionsOur study emphasizes the importance of a prompt diagnosis and treatment of infectious corneal ulcers in children. Trauma and contact lenses were the main predisposing factors. Gram-positive organisms were isolated in the vast majority of cases and visual outcomes are usually poor.
Two polymorphisms (rs699947, rs2010963) in the VEGFA gene and diabetic retinopathy: an updated meta-analysis
Authors: Lu Yan , Ge Yirui , Shi Yuhua , Yin Jie , Huang Zhenping 
Published: October 2013

Abstract

Background
The vascular endothelial growth factor (VEGFA) gene has been suggested to play an important role in the pathogenesis of diabetic retinopathy (DR). However, the results have been inconsistent. In this study, we performed a meta-analysis to clarify the associations between VEGFA polymorphisms and DR risk.

Methods
Published literature from PubMed, EMBASE, Web of Science and Google Scholar were retrieved. Pooled odds ratios (ORs) with 95% confidence intervals (CIs) were calculated using fixed- or random-effects model.

Results
A total of eight studies (1204 cases and 1198 controls) for rs699947 polymorphism and ten studies (1666 cases and 1782 controls) for rs2010963 polymorphism were included in the meta-analysis. The results suggested that rs699947 polymorphism was marginally associated with DR under a homogeneous co-dominant model (AA vs. CC: OR = 1.69, 95% CI = 1.03-2.77, p = 0.040) and a dominant model (AA + AC vs. CC: OR = 1.38, 95% CI = 1.01-1.90, p = 0.040), whereas the association between rs2010963 polymorphism and DR was not significant under all genetic models (all p > 0.05). In the subgroup analysis, the effect size for rs699947 polymorphism was only marginally significant among European populations under a dominant model (OR = 1.47, 95% CI = 1.07–2.02, p = 0.018), but not among East Asians. After exclusion of outliers which were the source of between-study heterogeneity, there was significant association between rs699947 polymorphism and DR under a homogeneous co-dominant model (OR = 1.64, 95% CI = 1.18-2.28, p = 0.003), even after multiple comparison correction.

Conclusions
Our meta-analysis confirmed the significant association between rs699947 polymorphism and DR after exclusion of outliers, and rs2010963 polymorphism might be not associated with DR.
A case–control study of maternal bathing habits and risk for birth defects in offspring
Authors: Agopian AJ , Waller D Kim , Lupo Philip J , Canfield Mark A , Mitchell Laura E 
Published: October 2013

Abstract

Background
Nearly all women shower or take baths during early pregnancy; however, bathing habits (i.e., shower and bath length and frequency) may be related to the risk of maternal hyperthermia and exposure to water disinfection byproducts, both of which are suspected to increase risk for multiple types of birth defects. Thus, we assessed the relationships between bathing habits during pregnancy and the risk for several nonsyndromic birth defects in offspring.

Methods
Data for cases with one of 13 types of birth defects and controls from the National Birth Defects Prevention Study delivered during 2000–2007 were evaluated. Logistic regression analyses were conducted separately for each type of birth defect.

Results
There were few associations between shower frequency or bath frequency or length and risk for birth defects in offspring. The risk for gastroschisis in offspring was increased among women who reported showers lasting ≥15 compared to <15 minutes (adjusted odds ratio: 1.43, 95% confidence interval: 1.18-1.72). In addition, we observed modest increases in the risk for spina bifida, cleft lip with or without cleft palate, and limb reduction defects in offspring of women who showered ≥15 compared to <15 minutes. The results of comparisons among more specific categories of shower length (i.e., <15 minutes versus 15–19, 20–29, and ≥ 30 minutes) were similar.

Conclusions
Our findings suggest that shower length may be associated with gastroschisis, but the modest associations with other birth defects were not supported by analyses of bath length or bath or shower frequency. Given that showering for ≥15 minutes during pregnancy is very common, further evaluation of the relationship between maternal showering habits and birth defects in offspring is worthwhile.
Exposure to aircraft and road traffic noise and associations with heart disease and stroke in six European countries: a cross-sectional study
Authors: Floud Sarah , Blangiardo Marta , Clark Charlotte , de Hoogh Kees , Babisch Wolfgang , Houthuijs Danny , Swart Wim , Pershagen Göran , Katsouyanni Klea , Velonakis Manolis , Vigna-Taglianti Federica , Cadum Ennio , Hansell Anna L 
Published: October 2013

Abstract

Background
Although a number of studies have found an association between aircraft noise and hypertension, there is a lack of evidence on associations with other cardiovascular disease. For road traffic noise, more studies are available but the extent of possible confounding by air pollution has not been established.

Methods
This study used data from the Hypertension and Environmental Noise near Airports (HYENA) study. Cross-sectional associations between self-reported ‘heart disease and stroke’ and aircraft noise and road traffic noise were examined using data collected between 2004 and 2006 on 4712 participants (276 cases), who lived near airports in six European countries (UK, Germany, Netherlands, Sweden, Greece, Italy). Data were available to assess potential confounding by NO2 air pollution in a subsample of three countries (UK, Netherlands, Sweden).

Results
An association between night-time average aircraft noise and ‘heart disease and stroke’ was found after adjustment for socio-demographic confounders for participants who had lived in the same place for ≥ 20 years (odds ratio (OR): 1.25 (95% confidence interval (CI) 1.03, 1.51) per 10 dB (A)); this association was robust to adjustment for exposure to air pollution in the subsample. 24 hour average road traffic noise exposure was associated with ‘heart disease and stroke’ (OR: 1.19 (95% CI 1.00, 1.41), but adjustment for air pollution in the subsample suggested this may have been due to confounding by air pollution. Statistical assessment (correlations and variance inflation factor) suggested only modest collinearity between noise and NO2 exposures.

Conclusions
Exposure to aircraft noise over many years may increase risks of heart disease and stroke, although more studies are needed to establish how much the risks associated with road traffic noise may be explained by air pollution.
Expression of epidermal growth factor receptor is an independent prognostic factor for esophageal squamous cell carcinoma
Authors: Wang Qifeng , Zhu Hongxia , Xiao Zefen , Zhang Wencheng , Liu Xiao , Zhang Xun , He Jie , Sun Kelin , Wang Lvhua , Xu Ningzhi 
Published: October 2013

Abstract

Background
The overall survival of patients with esophageal squamous cell carcinoma (ESCC) remains poor. Prognostic predictions in ESCC are usually based on histological assessment of tumor invasion and lymph node metastasis, but a biomarker with better predictive accuracy could be more useful. Because overexpression of epidermal growth factor receptor (EGFR) has been associated with poor prognosis, this study investigated whether EGFR is an independent prognostic factor for overall survival and disease-free survival of ESCC patients.

Methods
ESCC tissue specimens from 243 patients obtained during surgical resection between 1980 and 1997 were retrieved for immunohistochemical analysis of EGFR expression.

Results
The data showed that EGFR protein was overexpressed in 187 of 243 (77%) ESCC tissues. Elevated expression was associated with higher pathologic tumor stages (P = 0.001), lymph node metastasis (P = 0.002), and higher Union for International Cancer Control (UICC) stage (P <0.0001), as well as poorer disease-free survival and overall survival of ESCC patients (P <0.0001). A multivariate analysis showed that overexpression of EGFR protein was an independent factor for disease-free survival (P = 0.003) and overall survival (P = 0.001) of these patients. Subgroup analysis of patients with stage IIA (UICC 2002) showed that EGFR overexpression was associated with poorer disease-free survival (P = 0.007) and overall survival (P = 0.010) of the patients in univariate analyses.

Conclusions
The current study demonstrated that EGFR overexpression was an independent prognostic factor for overall survival and disease-free survival of ESCC patients. However, targeting of EGFR activity using gefitinib or erlotinib could be useful for clinical treatment of ESCC patients.
Expression profile of host restriction factors in HIV-1 elite controllers
Authors: Abdel-Mohsen Mohamed , Raposo Rui André Saraiva , Deng Xutao , Li Manqing , Liegler Teri , Sinclair Elizabeth , Salama Mohamed S , Ghanem Hussam El-din A , Hoh Rebecca , Wong Joseph K , David Michael , Nixon Douglas F , Deeks Steven G , Pillai Satish K 
Published: October 2013

Abstract

Background
Several host-encoded antiviral factors suppress HIV-1 replication in a cell-autonomous fashion in vitro. The relevance of these defenses to the control of HIV-1 in vivo remains to be elucidated. We hypothesized that cellular restriction of HIV-1 replication plays a significant role in the observed suppression of HIV-1 in "elite controllers", individuals who maintain undetectable levels of viremia in the absence of antiretroviral therapy (ART). We comprehensively compared the expression levels of 34 host restriction factors and cellular activation levels in CD4+ T cells and sorted T cell subsets between elite controllers, HIV-1-infected (untreated) non-controllers, ART-suppressed, and uninfected individuals.

Results
Expression of schlafen 11, a codon usage-based inhibitor of HIV-1 protein synthesis, was significantly elevated in CD4+ T cells from elite controllers as compared to both non-controllers (p = 0.048) and ART-suppressed individuals (p = 0.024), with this effect most apparent in central memory CD4+ T cells. Schlafen 11 expression levels were comparable between controllers and uninfected individuals. Cumulative restriction factor expression was positively correlated with CD4+ T cell activation (r2 = 0.597, p < 0.0001), viral load (r2 = 0.34, p = 0.015), and expression of ISG15 (r2 = 0.73, p < 0.0001), a marker of interferon exposure. APOBEC3C, APOBEC3D, CTR9, TRIM26, and TRIM32 were elevated in elite controllers with respect to ART-suppressed individuals, while levels were comparable to uninfected individuals and non-controllers.

Conclusions
Host restriction factor expression typically scales with cellular activation levels. However, the elevated mRNA and protein expression of schlafen 11, despite low activation and viral load, violates the global pattern and may be a signature characteristic of HIV-1 elite control.
Distribution and genetic diversity of Southern rice black-streaked dwarf viru s in China
Authors: Cheng Zhaobang , Li Shuo , Gao Ruizhen , Sun Feng , Liu Wancai , Zhou Guohui , Wu Jianxiang , Zhou Xueping , Zhou Yijun 
Published: October 2013

Abstract

Background
Rice and maize dwarf diseases caused by the newly introduced Southern rice black-streaked dwarf virus (SRBSDV) have led to severe economic losses in South China in recent years. The distribution and diversity of SRBSDV have not been investigated in the main rice and maize growing areas in China. In this study, the distribution of SRBSDV in China was determined by using reverse transcription-polymerase chain reaction (RT-PCR).

Results
Between 2009 and 2010, 2404 plant samples (2294 rice, 110 maize samples, and more than 300 cultivars) with dwarf symptoms were collected from fields in 194 counties of 17 provinces in China and SRBSDV was detected. The results indicated that 1545 (64.27%) of samples (both rice and maize) were infected with SRBSDV. SRBSDV was detected widely in Hainan, Guangdong, Guangxi, Yunnan, Guizhou, Chongqing, Fujian, Jiangxi, Hunan, Hubei, Anhui, Jiangsu, and Zhejiang provinces, which suggests SRBSDV is an important pathogen causing rice dwarfing diseases in South China. Phylogenetic analysis of 15 representative virus isolates revealed that SRBSDV isolates in China had high levels of nucleotide and amino acid sequence identities (>97.8%).

Conclusions
SRBSDV spreads naturally in Yangtze River basin and south region, the location of the major rice production areas. In comparison, the virus rarely spreads north of Yangtze River in North China. Distribution of SRBSDV is consistent with the migrating and existing ranges of its vector WBPH, suggesting that SRBSDV might be introduced into South China along with the migration of viruliferous WBPH.
Restrictions on antimicrobial use in food animal production: an international regulatory and economic survey
Authors: Maron Dina Fine , Smith Tyler JS , Nachman Keeve E 
Published: October 2013

Abstract

Background
The administration of antimicrobial drugs to food animals at low doses for extended durations for growth promotion and disease prevention has been linked to the global health crisis of antimicrobial resistance. Internationally, multiple jurisdictions have responded by restricting antimicrobial use for these purposes, and by requiring a veterinary prescription to use these drugs in food animals. Opponents of these policies have argued that restrictions have been detrimental to food animal production where they have been adopted.

Methods
We surveyed the antimicrobial use policies of 17 political jurisdictions outside of the United States with respect to growth promotion, disease prevention, and veterinary oversight, and reviewed the available evidence regarding their production impacts, including measures of animal health. Jurisdictions were included if they were a top-five importer of a major U.S. food animal product in 2011, as differences between the policies of the U.S. and other jurisdictions may lead to trade barriers to U.S. food animal product exports. Jurisdictions were also included if information on their policies was publicly available in English. We searched the peer-reviewed and grey literatures and corresponded with jurisdictions’ U.S. embassies, regulators, and local experts.

Results
Jurisdictions were categorized by whether they prohibit use of antimicrobials for growth promotion and/or use of antimicrobials without a veterinary prescription. Of the 17 jurisdictions surveyed, six jurisdictions have prohibited both types of use, five jurisdictions have prohibited one use but not the other use, and five jurisdictions have not prohibited either use, while information was not available for one jurisdiction. Data on the production impacts of these prohibitions were limited, although available data, especially from Denmark and Sweden, suggest that restrictions on growth promotion use can be implemented with minimal production consequences.

Conclusions
A majority of leading U.S. trade partners have more stringent policies regarding antibiotic use and veterinary oversight in food animal production. Available data suggest that restrictions on growth promotion may not be detrimental to production in the long run, although additional research could be useful. There is evidence that discordance between the U.S. and other jurisdictions with respect to antimicrobial use in food animals may be detrimental to U.S. access to export markets for food animal products. The available economic evidence strengthens the rationale for restricting antimicrobial use in U.S. food animals.