bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular Pathways: Targeting Resistance in the Androgen Receptor for Therapeutic Benefit
Authors: Mostaghel Elahe A. , Plymate Stephen R. , Montgomery Bruce 
Published: December 2013

Abstract
Androgen receptor signaling is critical in the development and progression of prostate cancer, leading to intensive efforts to elucidate all potential points of inflection for therapeutic intervention. These efforts have revealed new mechanisms of resistance and raise the possibility that known mechanisms may become even more relevant in the context of effective androgen receptor suppression. These mechanisms include tumoral appropriation of alternative androgen sources, alterations in androgen receptor expression, androgen receptor mutations, truncated androgen receptor variants, alterations and cross-talk in recruitment of cofactors to androgen receptor binding sites in the genome, and androgen receptor–driven oncogenic gene fusions. New agents such as enzalutamide, EPI-001, androgen receptor–specific peptidomimetics, novel HSP90 inhibitors, and PARP inhibitors, as well as new approaches to cotargeting the androgen receptor pathway, point to the potential for more complete and durable control of androgen receptor–mediated growth. Clin Cancer Res; 20(4); 791–8. ©2013 AACR.
Cost-effectiveness of a Genetic Test for Breast Cancer Risk
Authors: Folse Henry J. , Green Linda E. , Kress Andrea , Allman Richard , Dinh Tuan A. 
Published: December 2013

Abstract
Genetic testing of seven single-nucleotide polymorphisms (7SNP) can improve estimates of risk of breast cancer relative to the Gail risk test alone, for the purpose of recommending MRI screening for women at high risk. A simulation of breast cancer and health care processes was used to conduct a virtual trial comparing the use of the 7SNP test with the Gail risk test to categorize patients by risk. Average-risk patients received annual mammogram, whereas high-risk patients received annual MRI. Cancer incidence was based on Surveillance, Epidemiology, and End Results data and validated to Cancer Prevention Study II Nutrition Cohort data. Risk factor values were drawn from National Health and Nutrition Examination Survey (NHANES-4) and Prostate, Lung, Colorectal, and Ovarian Cancer Screening Trial data. Mammogram characteristics were derived from Breast Cancer Surveillance Consortium data. The test was most cost-effective when given to patients at an intermediate lifetime risk of breast cancer. For patients with a risk of 16% to 28%, it resulted in a 1.91% reduction in cancer deaths, saving 0.005 quality-adjusted life years per person at a cost of $163,264 per QALY. These results were sensitive to the age at which the test is given, the discount rate, and the costs of the genetic test and MRI. The cost effectiveness of using the 7SNP test for patients with intermediate Gail risk is similar to that of other recommended strategies, including annual MRI for patients with a lifetime risk greater than 20% or BRCA1/2 mutations. Cancer Prev Res; 6(12); 1328–36. ©2013 AACR.
Association of mean platelet volume with risk of venous thromboembolism and mortality in patients with cancer
Authors: Riedl Julia , Kaider Alexandra , Reitter Eva-Maria , Marosi Christine , Jäger Ulrich , Schwarzinger Ilse , Zielinski Christoph , Pabinger Ingrid , Ay Cihan 
Published: December 2013

SummaryVenous thromboembolism (VTE) is a frequent complication in cancer patients. Mean platelet volume (MPV) has been associated with arterial and venous thrombosis in patients without cancer. We analysed MPV in cancer patients and investigated the association of MPV with risk of VTE and mortality. MPV was routinely determined in the Vienna Cancer and Thrombosis Study, a prospective, observational cohort study of patients with newly diagnosed or progressive cancer after remission. Study endpoints were occurrence of symptomatic VTE or death during a maximum follow-up of two years. Out of 1,544 included patients, 114 (7.4%) developed VTE and 573 (37.1%) died during a median observation time of 576 days. High MPV ≥75th percentile of the study population; ≥10.8 fL) was associated with decreased risk of VTE compared to MPV below the 75th percentile (HR [95% CI]: 0.59 [0.37–0.95], p=0.031). In multivariable analysis, including age, sex, cancer groups, newly diagnosed vs recurrent disease, platelet count and soluble P-selectin, this association remained statistically significant (0.65 [0.37–0.98], p=0.041). Mortality of patients with MPV (≥75th percentile was significantly decreased compared to those with lower MPV (0.72 [0.59–0.88], p=0.001). Two-year probability of VTE and overall survival was 5.5% and 64.7% in patients with high MPV compared to 9% and 55.7% in those with lower MPV. In conclusion, high MPV is associated with decreased VTE risk and improved survival in cancer patients. This finding is contrary to results observed in patients without cancer. Further studies are needed to confirm our results and elucidate underlying mechanisms.Previous presentations of this manuscript: Data from this study were presented in part at the Annual Spring Meeting of the Austrian Society for Haematology and Oncology (OeGHO) in Linz, Austria, and as an oral presentation at the XXIV. Congress of the International Society on Thrombosis and Haemostasis (ISTH) 2013 in Amsterdam, the Netherlands.
Information Content and Uncertainties in Thermodynamic Profiles and Liquid Cloud Properties Retrieved from the Ground-Based Atmospheric Emitted Radiance Interferometer (AERI)
Authors: Turner D. D. , Löhnert U. 
Published: December 2013

AbstractThe Atmospheric Emitted Radiance Interferometer (AERI) observes spectrally resolved downwelling radiance emitted by the atmosphere in the infrared portion of the electromagnetic spectrum. Profiles of temperature and water vapor, and cloud liquid water path and effective radius for a single liquid cloud layer, are retrieved using an optimal estimation–based physical retrieval algorithm from AERI-observed radiance data. This algorithm provides a full error covariance matrix for the solution, and both the degrees of freedom for signal and the Shannon information content. The algorithm is evaluated with both synthetic and real AERI observations. The AERI is shown to have approximately 85% and 70% of its information in the lowest 2 km of the atmosphere for temperature and water vapor profiles, respectively. In clear-sky situations, the mean bias errors with respect to the radiosonde profiles are less than 0.2 K and 0.3 g kg−1 for heights below 2 km for temperature and water vapor mixing ratio, respectively; the maximum root-mean-square errors are less than 1 K and 0.8 g kg−1. The errors in the retrieved profiles in cloudy situations are larger, due in part to the scattering contribution to the downwelling radiance that was not accounted for in the forward model. Scattering is largest in one of the spectral regions used in the retrieval, however, and removing this spectral region results in a slight reduction of the information content but a considerable improvement in the accuracy of the retrieved thermodynamic profiles.
Consistent Trends in a Modified Climate Extremes Index in the United States, Europe, and Australia
Authors: Gallant Ailie J. E. , Karoly David J. , Gleason Karin L. 
Published: December 2013

AbstractThe utility of a combined modified climate extremes index (mCEI) is presented for monitoring coherent trends in multiple types of climate extremes across large regions. Its usefulness lies in its ability to distill complex spatiotemporal fields into a simple, flexible nonparametric index.Two versions of the mCEI are computed that incorporate changes in several annual- or daily-scale temperature-related and moisture-related extremes. Applying data from the contiguous United States, Europe, and Australia detects consistent and statistically significant increases in the spatial prevalence of climate extremes from 1950 to 2012. All three continental-scale regions show increasingly widespread warm annual- and daily-scale minimum and maximum temperature extremes, a decreasing spatial extent of cool annual- and daily-scale minimum and maximum temperature extremes, and increasing areas where the proportion of annual total precipitation falls on heavy-rain days. There were no statistically significant trends toward more widespread, annual-scale drought or moisture surplus in any region.The dependence of annual extremes on the frequency of daily-scale extremes is highlighted by the strong covariations between annual- and daily-scale extremes in all regions. By the nature of construction of the combined indices, the differences in the trends of the mCEI and daily-scale mCEI (dmCEI) suggest that extremes in more areas are changing primarily because of a shift of temperature and daily rainfall distributions toward warm extremes and heavy-rainfall extremes.
The Observed North Atlantic Meridional Overturning Circulation: Its Meridional Coherence and Ocean Bottom Pressure
Authors: Elipot Shane , Frajka-Williams Eleanor , Hughes Chris W. , Willis Josh K. 
Published: December 2013

Abstract
Analyses of meridional transport time series from the Rapid Climate Change–Meridional Overturning Circulation (RAPID MOC) array at 26°N and from Argo float and altimetry data at 41°N reveal that, at semiannual and longer time scales, the contribution from the western boundary dominates the variability of the North Atlantic meridional overturning circulation (MOC), defined as the transport in the upper 1000 m of the ocean. Because the variability of the western boundary contribution is associated with a geostrophic overturning, it is reflected in independent estimates of transports from gradient of ocean bottom pressure (OBP) relative to and below 1000 m on the continental slope of the western boundary at three nominal latitudes (26°, 39°, and 42.5°N). Time series of western meridional transports relative to and below 1000 m derived from the OBP gradient, or equivalently derived from the transport shear profile, exhibit approximately the same phase relationship between 26° and 39°–42.5°N as the western contribution to the geostrophic MOC time series do: the western geostrophic MOC at 41°N precedes the MOC at 26°N by approximately a quarter of an annual cycle, resulting in a zero correlation at this time scale. This study therefore demonstrates how OBP gradients on basin boundaries can be used to monitor the MOC and its meridional coherence.
A Case Study of the Interaction of a Mesoscale Gravity Wave with a Mesoscale Convective System
Authors: Ruppert James H. , Bosart Lance F. 
Published: December 2013

Abstract
This study documents the high-amplitude mesoscale gravity wave (MGW) event of 7 March 2008 in which two MGWs strongly impacted the sensible weather over a large portion of the Southeast United States. These MGWs exhibited starkly contrasting character despite propagating within similar environments. The primary (i.e., long lived) MGW was manifest by a solitary wave of depression associated with rapid sinking motion and adiabatic warming, while the secondary (short lived) MGW was manifest by a solitary wave of elevation (“MGWEL”), dominated by rising motion and moist adiabatic cooling. Genesis of the primary MGW occurred as a strong cold front arrived at the foot of Mexico’s high terrain and perturbed the appreciable overriding flow. The resulting gravity wave became ducted in the presence of a low-level frontal stable layer, and caused surface pressure falls up to ~4 hPa. The MGW later amplified as it became coupled with a stratiform precipitation system, which led to its evolution into an intense mesohigh–wake low couplet. This couplet propagated as a ducted MGW attached to a stratiform system for ~12 h thereafter, and induced rapid surface pressure falls of ≥10 hPa (including a fall of 6.7 hPa in 10 min), rapid wind vector changes (e.g., 17 m s−1 in 25 min), and high wind gusts (e.g., 20 m s−1) across several states. MGWEL appeared within the remnants of a squall line, and was manifest by a sharp pressure ridge of ~6 hPa with a narrow embedded rainband following the motion of a surface cold front. MGWEL bore resemblance to previously documented gravity waves formed by density currents propagating through stable environments.
Endovenous saphenous vein ablation in patients with acute isolated superficial-vein thrombosis
Authors: Gradman Wayne S 
Published: December 2013

Objective: The possible benefits of endovenous saphenous ablation (EVSA) as initial treatment in patients presenting with isolated superficial-vein thrombosis (SVT) and saphenous vein reflux include: (1) definitive treatment of the underlying pathology and (2) elimination of the saphenous vein as a path for pulmonary emboli, which (3) may eliminate the need for anticoagulation. Methods: In a ten-year review of 115 limbs presenting with acute isolated SVT, 72 limbs (71 patients) with saphenous reflux were given a choice of two treatments following an explanation of the risks and benefits of each. Group I limbs ( n = 41) were treated with office EVSA using radiofrequency or laser with or without thrombophlebectomy if performed within 45 days of diagnosis. Post-treatment anticoagulants were not given. Group II limbs ( n = 31) were treated with compression hose and repeat Duplex within one week, with added anticoagulants if SVT extended into the thigh. Results: In group I, mean interval from diagnosis to treatment was 13.7 days. One calf deep vein thrombosis was noted. In group II no complications were noted. In late follow-up of group II patients, 12/29 underwent EVSA more than 45 days after initial presentation. Conclusions: The safety and efficacy of EVSA and thrombophlebectomy appear indistinguishable from conservative measures and may be offered as initial treatment to patients presenting with SVT and saphenous reflux.
A preliminary association study of fat mass and obesity associated gene polymorphisms and degenerative disc disease in a Chinese Han population
Authors: Lao Lifeng , Zhong Guibin , Li Xinfeng , Liu Zude 
Published: December 2013

Objective To assess whether polymorphisms of the fat mass and obesity associated gene ( FTO) are associated with the presence and severity of degenerative disc disease (DDD) in a Chinese Han population. Methods In this case–control study, patients with DDD and controls matched for age, sex and body mass index were genotyped for six single nucleotide polymorphisms (SNPs) of FTO. Disease severity was measured using the Japanese Orthopaedic Association score. Allelic, genotypic and genotype–phenotype association analyses were performed. Results A total of 80 patients with DDD and 80 controls were studied. All six SNPs were in Hardy–Weinberg equilibrium. The frequencies of allele G and genotype G/G of the SNP rs11076008 were significantly associated with DDD after Bonferroni correction. No associations were shown between the SNPs studied and sex or disease severity. Conclusion The SNP rs11076008 of FTO may play an important role in the development of DDD in a Chinese Han population. The G/G genotype and/or G allele may be a risk factor for DDD. These results suggest that FTO is a DDD predisposition gene and may support a close relationship between obesity and DDD.
The role of in vivo confocal microscopy in the diagnosis of hidden corneal foreign bodies
Authors: Xu Zhongzhong , Yu Xiaofei , Li Zhijie , Wang Liya 
Published: December 2013

Objective To investigate in vivo confocal microscopy (IVCM) to diagnose hidden corneal foreign bodies. Methods Male Kunming mice ( n = 25; 12 weeks old) were anaesthetized prior to the insertion of five different materials (spiny wood, rusty iron, sharp stone, sharp glass fragment and human hair fragment) into the cornea by different traumatic processes. A separate mouse was used for each corneal foreign body. The corneas of the mice were scanned 24 h later by a laser scanning IVCM to establish the characteristics (shape, reflectivity and depth in the cornea) of each foreign body. These findings were used to help screen and identify corneal foreign bodies in patients. Corneal smears and scraping cultures were performed in cases of probable corneal infection. Results Animal models for the five different foreign particles were established successfully, with each showing distinctive characteristics. These animal results were used to diagnose 41 patients with suspected corneal foreign bodies who were negative by slit lamp examination, but positive by IVCM (observational case series). The most prevalent type of hidden foreign body was plant material (51.2%), followed by metal (29.3%). Ten patients with corneal foreign bodies developed fungal keratitis, found using IVCM. Conclusions Laser IVCM is an effective and reliable tool for the diagnosis of hidden corneal foreign bodies.
Politiques de lutte contre le paludisme en Casamance, Sénégal: une activité de santé publique soumise aux contextes de conflit et de décentralisation
Authors: Faye Sylvain Landry , le Marcis Frédéric , Samb Fatoumata , Badji Mouhamed 
Published: December 2013

Cet article analyse, à partir d’une ethnographie menée à Oussouye (Casamance), la manière dont s’incarnent et se traduisent les politiques nationales sanitaires, dans des contextes locaux spécifiques. Il discute des contraintes que rencontre une politique globalisante, ou plus exactement des points aveugles de cette politique pas suffisamment à l’écoute du contexte, c’est-à-dire, des spécificités régionales et géopolitiques. Les résultats indiquent que le contexte de la décentralisation et du conflit casamançais ont eu des effets sur le financement, la gestion des activités promotionnelles et la domestication des recommandations officielles de la lutte contre le paludisme. Par ailleurs, celles antérieures laissent des traces, qui s’expriment dans les discours des acteurs et structurent la façon dont ils pensent la lutte aujourd’hui, alors même que cette dernière est supposée s’inscrire dans un autre paradigme. Enfin la dissonance de la prescription d’antipaludiques à Mlomp et Elinkine fait penser à l’existence de « territoires » locaux de la santé où les recommandations nationales cèdent la place aux spécificités contextuelles et locales. Les politiques de santé ne peuvent faire l’économie ni des acteurs, ni des contextes locaux, cependant la prise en compte de la spécificité ne doit certainement pas se faire au détriment d’une certaine notion de « l’être ensemble ».
Analysis of sea-island cotton and upland cotton in response to Verticillium dahliaeinfection by RNA sequencing
Authors: Sun Quan , Jiang Huaizhong , Zhu Xiaoyan , Wang Weina , He Xiaohong , Shi Yuzhen , Yuan Youlu , Du Xiongming , Cai Yingfan 
Published: December 2013

Abstract

Background
Cotton Verticillium wilt is a serious soil-borne vascular disease that causes great economic loss each year. However, due to the lack of resistant varieties of upland cotton, the molecular mechanisms of resistance to this disease, especially to the pathogen Verticillium dahliae, remain unclear.

Results
We used the RNA-seq method to research the molecular mechanisms of cotton defence responses to different races of Verticillium dahliae by comparing infected sea-island cotton and upland cotton. A total of 77,212 unigenes were obtained, and the unigenes were subjected to BLAST searching and annotated using the GO and KO databases. Six sets of digital gene expression data were mapped to the reference transcriptome. The gene expression profiles of cotton infected with Verticillium dahliae were compared to those of uninfected cotton; 44 differentially expressed genes were identified. Regarding genes involved in the phenylalanine metabolism pathway, the hydroxycinnamoyl transferase gene (HCT) was upregulated in upland cotton whereas PAL, 4CL, CAD, CCoAOMT, and COMT were upregulated in sea-island cotton. Almost no differentially expressed genes in this pathway were identified in sea-island cotton and upland cotton when they were infected with V. dahliae V991 and V. dahliae D07038, respectively.

Conclusions
Our comprehensive gene expression data at the transcription level will help elucidate the molecular mechanisms of the cotton defence response to V. dahliae. By identifying the genes involved in the defence response of each type of cotton to V. dahliae, our data not only provide novel molecular information for researchers, but also help accelerate research on genes involved in defences in cotton.
A platform independent RNA-Seq protocol for the detection of transcriptome complexity
Authors: Calabrese Claudia , Mangiulli Marina , Manzari Caterina , Paluscio Anna Maria , Caratozzolo Mariano Francesco , Marzano Flaviana , Kurelac Ivana , D’Erchia Anna Maria , D’Elia Domenica , Licciulli Flavio , Liuni Sabino , Picardi Ernesto , Attimonelli Marcella , Gasparre Giuseppe , Porcelli Anna Maria , Pesole Graziano , Sbisà Elisabetta , Tullo Apollonia 
Published: December 2013

Abstract

Background
Recent studies have demonstrated an unexpected complexity of transcription in eukaryotes. The majority of the genome is transcribed and only a little fraction of these transcripts is annotated as protein coding genes and their splice variants. Indeed, most transcripts are the result of antisense, overlapping and non-coding RNA expression. In this frame, one of the key aims of high throughput transcriptome sequencing is the detection of all RNA species present in the cell and the first crucial step for RNA-seq users is represented by the choice of the strategy for cDNA library construction. The protocols developed so far provide the utilization of the entire library for a single sequencing run with a specific platform.

Results
We set up a unique protocol to generate and amplify a strand-specific cDNA library representative of all RNA species that may be implemented with all major platforms currently available on the market (Roche 454, Illumina, ABI/SOLiD). Our method is reproducible, fast, easy-to-perform and even allows to start from low input total RNA. Furthermore, we provide a suitable bioinformatics tool for the analysis of the sequences produced following this protocol.

Conclusion
We tested the efficiency of our strategy, showing that our method is platform-independent, thus allowing the simultaneous analysis of the same sample with different NGS technologies, and providing an accurate quantitative and qualitative portrait of complex whole transcriptomes.