bluuebunny/crossref_metadata_2025_split huggingface dataset:
Understanding the basis of antibiotic resistance: a platform for drug discovery
Authors: Piddock Laura J. V. 
Published: August 2014

There are numerous genes in Salmonella enterica serovar Typhimurium that can confer resistance to fluoroquinolone antibiotics, including those that encode topoisomerase proteins, the primary targets of this class of drugs. However, resistance is often multifactorial in clinical isolates and it is not uncommon to also detect mutations in genes that affect the expression of proteins involved in permeability and multi-drug efflux. The latter mechanism, mediated by tripartite efflux systems, such as that formed by the AcrAB–TolC system, confers inherent resistance to many antibiotics, detergents and biocides. Genetic inactivation of efflux genes gives multi-drug hyper-susceptibility, and in the absence of an intact AcrAB–TolC system some chromosomal and transmissible antibiotic resistance genes no longer confer clinically relevant levels of resistance. Furthermore, a functional multi-drug resistance efflux pump, such as AcrAB–TolC, is required for virulence and the ability to form a biofilm. In part, this is due to altered expression of virulence and biofilm genes being sensitive to efflux status. Efflux pump expression can be increased, usually due to mutations in regulatory genes, and this confers resistance to clinically useful drugs such as fluoroquinolones and β-lactams. Here, I discuss some of the work my team has carried out characterizing the mechanisms of antibiotic resistance in Salmonella enterica serovar Typhimurium from the late 1980s to 2014.
A video of this Prize Lecture, presented at the Society for General Microbiology Annual Conference 2014, can be viewed via this link: https://www.youtube.com/watch?v=MCRumMV99Yw.
Shadow enhancers enable Hunchback bifunctionality in the Drosophila embryo
Authors: Staller Max V. , Vincent Ben J. , Bragdon Meghan D.J. , Zeba Wunderlich Tara Lydiard-Martin , Estrada Javier , DePace Angela H. 
Published: August 2014

AbstractHunchback (Hb) is a bifunctional transcription factor that activates and represses distinct enhancers. Here, we investigate the hypothesis that Hb can activate and repress the same enhancer. Computational models predicted that Hb bifunctionally regulates the even-skipped (eve) stripe 3+7 enhancer (eve3+7) in Drosophila blastoderm embryos. We measured and modeled eve expression at cellular resolution under multiple genetic perturbations and found that the eve3+7 enhancer could not explain endogenous eve stripe 7 behavior. Instead, we found that eve stripe 7 is controlled by two enhancers: the canonical eve3+7 and a sequence encompassing the minimal eve stripe 2 enhancer (eve2+7). Hb bifunctionally regulates eve stripe 7, but it executes these two activities on different pieces of regulatory DNA–it activates the eve2+7 enhancer and represses the eve3+7 enhancer. These two “shadow enhancers” use different regulatory logic to create the same pattern.Significance statementEnhancers are regions of regulatory DNA that control gene expression and cell fate decisions during development. Enhancers compute the expression pattern of their target gene by reading the concentrations of input regulatory proteins. Many developmental genes contain multiple enhancers that control the same output pattern, but it is unclear if these enhancers all compute the pattern in the same way. We use measurements in single cells and computational models inDrosophilaembryos to demonstrate that two enhancers that encode the same gene expression pattern compute differently: the same regulatory protein represses one enhancer and activates the other. Pairs of enhancers that output the same pattern by performing different computations may impart special properties to developmental systems.
Comparison of the Microbiological Quality of Environmentally Friendly and Conventionally Grown Vegetables Sold at Retail Markets in Korea
Authors: Ryu Jee‐Hoon , Kim Minju , Kim Eun‐Gyeong , Beuchat Larry R. , Kim Hoikyung 
Published: August 2014

AbstractFresh produce is usually eaten raw without cooking or heating, which may increase the probability of foodborne infection. The microbiological quality of 11 types of fresh, raw vegetables (romaine lettuce, sesame leaves, crown daisy, garlic chives, iceberg lettuce, cabbage, broccoli, leek, chili pepper, capsicum, and zucchini) purchased at retail markets in Iksan, Korea as affected by cultivation method (environmentally friendly vegetables [organic, pesticide‐free, and low‐pesticide vegetables] and conventionally grown vegetables) and harvest season was determined. Escherichia coli O157:H7 and Salmonella were not detected in all samples of vegetables tested. Aerobic mesophiles (>6 log cfu/g) were detected in environmentally friendly romaine lettuce and crown daisy and environmentally friendly and conventionally grown garlic chives, which also contained coliforms (>3 log cfu/g). Sesame leaf and crown daisy (regardless of cultivation method), as well as conventionally grown romaine lettuce and leek, contained >1 log cfu/g of E. coli. The overall microbiological quality of environmentally friendly and conventionally grown vegetables was not significantly different (P > 0.05). However, there were seasonal effects on populations of coliforms and generic E. coli on vegetables. The greatest numbers of microorganisms were isolated from environmentally friendly or conventionally grown vegetables purchased in winter. The vegetables, regardless of cultivation method or season, should be subjected to appropriate antimicrobial treatment to enhance their microbial safety.
An Improved and Validated Sample Cleanup Method for Analysis of Ethyl Carbamate in Chinese Liquor
Authors: Xia Qiang , Yuan Huawei , Wu Chongde , Zheng Jia , Zhang Suyi , Shen Caihong , Yi Bin , Zhou Rongqing 
Published: August 2014

AbstractEthyl carbamate (EC) is a potential human carcinogen widely existing in fermented foods and alcoholic beverages. The solid‐phase extraction (SPE) coupled to gas chromatography mass spectrometry is a widely‐used method to determine EC levels, but the accuracy varies with sample matrix and the effects of operation parameters are rarely examined. In this study, the influence factors involved in EC determination were investigated using Chinese liquor as sample matrix, and the improved method was further applied. Three types of SPE columns, including diatomite, Florisil, and primary‐secondary amine, were compared in extraction efficiency, and the diatomite column exhibited the highest extraction efficiency. The optimal volumes of elution solvents with diatomite column were 15 mL for 3‐mL samples solution loaded. In addition, the alcoholic strength for EC determination should be diluted below 20% (v/v) to avoid the enhancement of matrix‐induced chromatographic response. Moreover, the pH neutralization could help improve EC recovery and peak resolution, reducing interfering effects. Based on these results, the improved method showed that the limit of detection, the limit of quantification, and average recoveries were 1.10 μg/L, 3.65 μg/L, and 93.06%, respectively. To further elucidate the underlying factors related to EC accumulation, partial least square regression analysis was conducted, and the results suggested that EC levels had the closest relationship with alcoholic strength among the remaining precursors.
Four types of Bifidobacteria trigger autophagy response in intestinal epithelial cells
Authors: Lin Rong , Jiang Ye , Zhao Xin Yan , Guan Yang , Qian Wei , Fu Xiao Chao , Ren Hun Yu , Hou Xiao Hua 
Published: August 2014

ObjectivesTo investigate the influence of gut microbiota on autophagy activation in intestinal epithelial cells (IEC) and to evaluate the IEC autophagy response to different types of Bifidobacteria.MethodsIEC‐18 cells were treated with lipopolysaccharide (LPS) derived from enteropathogenic Escherichia coli (EPEC) O127:B8 and culture medium supernatants of four types of Bifidobacteria. Transepithelial electrical resistance (TEER) was measured using an epithelial voltohmmeter. Autophagy was determined by transmission electron microscopy (TEM), the ratio of LC3‐II to LC3‐I and the persistence of both green fluorescent protein (GFP) and mCherry signals using a tandem mCherry‐GFP‐LC3 construct. The expression of Atg12–Atg5–Atg16 complex was measured by quantitative real‐time polymerase chain reaction.ResultsEPEC‐LPS significantly diminished the TEER of IEC compared with untreated controls by 45–55%. This reduction was not observed after treated with Bifidobacteria at all time points. Bifidobacteria could initiate the activation of autophagy in IEC, based on both the ratio of LC3‐II to LC3‐I and TEM. There was no difference in the influence of the four types of Bifidobacteria on the autophagy response. Compared with Bifidobacteria, IEC reacted to EPEC‐LPS much more intensively by autophagy accumulation. More mCherry+LC3 autophagic puncta and increased expressions of autophagy genes Atg5, Atg12 and Atg16 could be detected after being treated with Bifidobacteria and EPEC‐LPS.ConclusionsBifidobacteria initiate autophagy activation in IEC. The Atg12–Atg5–Atg16 multimeric complex might participate in the activation of Bifidobacteria‐induced cell autophagy.
Dessiné d'après nature: Renditions from Life in the Journal des Dames et des Modes, 1798‐9
Authors: Bissonnette Anne 
Published: August 2014

AbstractThis paper examines the strengths and limitations of late Directoire Journal des Dames et des Modes fashion plates. It observes the phenomenon of ‘drawn‐from‐life’ sub‐captioned plates from 1798 to 1799, which provide contextualising factual information. The research questions the assumed omnipresence of the sheer, white, short‐sleeved, columnal Directoire dress. The Journal's plates tell a different story, where certain traditions persist and a much broader range of dress styles, silhouettes and colours subsist. The study demonstrates the limits of broad generalisation and seeks to expand our understanding of classicism's influence on dress and embodiment practices in the late eighteenth century.
Patient Safety Training in Pediatric Emergency Medicine: A National Survey of Program Directors
Authors: Wolff Margaret , Macias Charles G. , Garcia Estevan , Stankovic Curt 
Published: August 2014

AbstractObjectivesThe Accreditation Council for Graduate Medical Education requires training in patient safety and medical errors but does not provide specification for content or methods. Pediatric emergency medicine (EM) fellowship directors were surveyed to characterize current training of pediatric EM fellows in patient safety and to determine the need for additional training.Methods From June 2013 to August 2013, pediatric EM fellowship directors were surveyed via e‐mail.Results Of the 71 eligible survey respondents, 57 (80.3%) completed surveys. A formal curriculum was present in 24.6% of programs, with a median of 6 hours (range = 1 to 18 hours) dedicated to the curriculum. One program evaluated the efficacy of the curriculum. Nearly 91% of respondents without formal programs identified lack of local faculty expertise or interest as the primary barrier to implementing patient safety curricula. Of programs without formal curricula, 93.6% included at least one component of patient safety training in their fellowship programs. The majority of respondents would implement a standardized patient safety curriculum for pediatric EM if one was available.ConclusionsDespite the importance of patient safety training and requirements to train pediatric EM fellows in patient safety and medical errors, there is a lack of formal curriculum and local faculty expertise. The majority of programs have introduced components of patient safety training and desire a standardized curriculum.
Lower subcortical gray matter volume in both younger smokers and established smokers relative to non‐smokers
Authors: Hanlon Colleen A. , Owens Max M. , Joseph Jane E. , Zhu Xun , George Mark S. , Brady Kathleen T , Hartwell Karen J. 
Published: August 2014

AbstractAlthough established adult smokers with long histories of nicotine dependence have lower neural tissue volume than non‐smokers, it is not clear if lower regional brain volume is also observed in younger, less established smokers. The primary goal of this study was to investigate neural tissue volume in a large group of smokers and non‐smokers, with a secondary goal of measuring the impact of age on these effects. We used voxel‐based morphometry to compare regional gray matter volume in 118 individuals (59 smokers, 59 age‐ and gender‐matched non‐smokers). Younger smokers had significantly lower gray matter volume in the left thalamus and the left amygdala than their non‐smoking peers (family‐wise error‐corrected clusters, P < 0.05). There was no correlation between smoking use variables and tissue volume among younger smokers. Established smokers had significantly lower gray matter volume than age‐matched non‐smokers in the insula, parahippocampal gyrus and pallidum. Medial prefrontal cortex gray matter volume was negatively correlated with pack‐years of smoking among the established smokers, but not the younger smokers. These data reveal that regional tissue volume differences are not limited exclusively to established smokers. Deficits in young adults indicate that cigarette smoking may either be deleterious to the thalamus and amygdala at an earlier age than previously reported, or that pre‐existing differences in these areas may predispose individuals to the development of nicotine dependence.
Synergistic effects of temperature, diet and colony size on the competitive ability of two ant species
Authors: Barbieri Rafael F. , Grangier Julien , Lester Philip J. 
Published: August 2014

AbstractMultiple biotic and abiotic factors influence species coexistence and co‐occurrence patterns. In a competitive environment, for example, temperature and diet variation may modify both foraging behaviour and aggression, thereby changing competitive interactions and species co‐occurrence patterns. In New Zealand, two endemic ant species (Prolasius advenus and Monomorium antarcticum) often form allopatric distributions; though also periodically do co‐occur in the same habitat. Here, we performed a long‐term laboratory experiment in an attempt to understand how diet, colony size and environmental conditions may influence these co‐occurrence patterns. The consequences of temperature and diet variation differed between P. advenus and M. antarcticum. Colonies of P. advenus exhibited increased aggression and foraging activities at higher temperatures. In addition, P. advenus colonies augmented their foraging activities when deprived of a carbohydrate‐rich food source. Conversely, small M. antarcticum colonies exhibited higher aggression than when in large colonies, and increased their foraging activities at lower temperatures. The modulation of aggression and foraging behaviour may influence the likelihood of small P. advenus and M. antarcticum colonies persisting in the long term. Our results are compatible with the hypothesis that the environment is likely to be a strong filter for the negative co‐occurrence patterns we observe between P. advenus and M. antarcticum in New Zealand. Furthermore, this study provides a mechanistic explanation for potential impacts of climate warming on community structure. Environmental modification of aggression and foraging behaviour could potentially alter competitive interactions and influence community assembly.
The Women's Squad in Ukraine's protests: Feminism, nationalism, and militarism on the Maidan
Authors: PHILLIPS SARAH D. 
Published: August 2014

ABSTRACTAlthough women and men participated in nearly equal numbers in Ukraine's 2013–14 Maidan protests, women were excluded from some of the more dangerous activities and their contributions went largely unrecognized. I examine women's modes of participation in and their exclusion from the Maidan and the creative responses of feminists to this exclusion, including creation of so‐called Women's Squads. The protests generated important feminist initiatives and discussions about women's roles in Ukraine's past and future, which were partially couched in discourses of nationalism and militarism. Examining debates about women's roles during and after the protests suggests that the Maidan provided Ukraine's feminists with opportunities to articulate divergent yet reconcilable perspectives on women's activism, social change, and national sovereignty. Their creative responses to the challenges of the protests have potentially paved the way for broadening the base of Ukrainian feminism, introducing women's rights principles to segments of the population previously reluctant to embrace feminism.
The social unit of debt: Gender and creditworthiness in Paraguayan microfinance
Authors: SCHUSTER CAROLINE E. 
Published: August 2014

ABSTRACTParaguayan microcredit poverty‐alleviation programs are built around instrumentalizing women's economic ties through group‐based loans guaranteed by no more than the promise of women's solidarity and joint liability for their collective loan repayment. I track the production and regulation of the social unit of borrowing in different aspects of microcredit, drawing on examples of individual loans, loans to “committees of women entrepreneurs,” credit scores, and a short‐lived program of “men's committees.” I illustrate how the institutionalized management of creditworthiness actually produces the very flexible and relational feminized borrowers to which microcredit initiatives seek to appeal and, in so doing, creates certain kinds of gendered sociality by enacting and embodying different social units of debt.
“Fraternal” nations and challenges to sovereignty in Ukraine: The politics of linguistic and religious ties
Authors: WANNER CATHERINE 
Published: August 2014

ABSTRACTVladimir Putin's recent assertions that Russian “compatriots” were suffering in Ukraine contributed to a rapid escalation of instability and violence in this borderland country that defines the margins of Europe and the edge of Eurasia. After 23 years of independence, Ukraine retains significant regional diversity and strong local identities. At the same time, social differences understood in terms of ethnicity, language choice, and religious affiliation have become less defined, as Ukrainians have embraced fluid linguistic and religious practices that defy easy characterization. On the basis of long‐term fieldwork in Ukraine, I argue that “non‐accommodating bilingualism” and “ambient faith” characterize everyday linguistic and religious practices in this postcolonial, post‐Soviet‐socialist space. This flexibility is adaptive domestically. Paradoxically, it contributes to the vulnerability of Ukrainian sovereignty when polarizing, politicized categories based on supposedly identifiable cultural attributes inject a spurious precision into everyday practices with the aim of redefining state sovereignty.
Neuroaxonal dystrophy in Merino‐Border Leicester × Polled Dorset lambs
Authors: Finnie JW , Jerrett IV , Manavis J , Cave J 
Published: August 2014

Case reportThe clinicopathological features of neuroaxonal dystrophy (NAD) in 2 lambs are described. Of 40 Merino‐Border Leicester × Polled Dorset lambs on a property in north‐eastern Victoria, 4 presented with marked ataxia and listlessness, and 2 affected animals (2 days and 2 weeks of age, respectively) of both sexes were necropsied. Numerous axonal swellings (spheroids) were found in the central nervous system, particularly in brainstem nuclei and spinal cord grey matter, and there was severe spinal cord demyelination.ConclusionsThis is the first report of NAD in such crossbred lambs; the affected animals were much younger than in previously described cases of ovine NAD and myelin loss was of much greater magnitude than previously reported.
Identifying optimal biomarker combinations for treatment selection via a robust kernel method
Authors: Huang Ying , Fong Youyi 
Published: August 2014

SummaryTreatment‐selection markers predict an individual's response to different therapies, thus allowing for the selection of a therapy with the best predicted outcome. A good marker‐based treatment‐selection rule can significantly impact public health through the reduction of the disease burden in a cost‐effective manner. Our goal in this article is to use data from randomized trials to identify optimal linear and nonlinear biomarker combinations for treatment selection that minimize the total burden to the population caused by either the targeted disease or its treatment. We frame this objective into a general problem of minimizing a weighted sum of 0‐1 loss and propose a novel penalized minimization method that is based on the difference of convex functions algorithm (DCA). The corresponding estimator of marker combinations has a kernel property that allows flexible modeling of linear and nonlinear marker combinations. We compare the proposed methods with existing methods for optimizing treatment regimens such as the logistic regression model and the weighted support vector machine. Performances of different weight functions are also investigated. The application of the proposed method is illustrated using a real example from an HIV vaccine trial: we search for a combination of Fc receptor genes for recommending vaccination in preventing HIV infection.
Hypoalbuminaemia is associated with mortality in patients undergoing cytoreductive nephrectomy
Authors: Corcoran Anthony T. , Kaffenberger Samuel D. , Clark Peter E. , Walton John , Handorf Elizabeth , Piotrowski Zack , Tomaszewski Jeffery J. , Ginzburg Serge , Mehrazin Reza , Plimack Elizabeth , Chen David Y.T. , Smaldone Marc C. , Uzzo Robert G. , Morgan Todd M. , Kutikov Alexander 
Published: August 2014

ObjectiveTo evaluate whether poor nutrition is associated with mortality in patients undergoing cytoreductive nephrectomy (CN) for metastatic renal cell carcinoma (mRCC).Patients and MethodsA multi‐institutional review of prospective databases identified 246 patients meeting inclusion criteria who underwent CN for mRCC from 1993 to 2012. Nutritional markers evaluated were: body mass index <18.5 kg/m2, serum albumin <3.5 g/dL, or preoperative weight loss of ≥5% of body weight. Primary outcomes were overall (OS) and disease‐specific survival (DSS). Secondary outcome was ‘early mortality’ defined as death at ≤6 months of surgery. Survival curves were estimated using the Kaplan–Meier product‐limit method and multivariate analysis using logistic regression was used to test associations between nutritional markers and survival outcomes.ResultsIn all, 119 patients (median follow‐up 17 months) were categorised as having any abnormal nutrition parameter (48%). Hypoalbuminaemia was the only independent predictor of OS and DSS (OS: median 8 vs 23 months, P < 0.001; DSS: 11 vs 33 months, P < 0.001). On multivariate analysis, hypoalbuminaemia remained a significant predictor of death for both overall [hazard ratio (HR) 2, 95% confidence interval (CI) 1.4–2.8; P < 0.001) and disease‐specific mortality (HR 2.2, 95% CI 1.4–3.3; P < 0.001). Hypoalbuminaemia was also associated with early mortality (overall: P < 0.001 and disease specific: P = 0.002).ConclusionPatients with mRCC and hypoalbuminaemia undergoing CN have decreased OS and CSS, and increased risk of all‐cause and disease‐specific early mortality. As such, serum albumin may help risk stratify patients selected as candidates for CN. Furthermore, future work should evaluate whether nutritional depletion is a modifiable risk factor.