bluuebunny/crossref_metadata_2025_split huggingface dataset:
ESEA: Discovering the Dysregulated Pathways based on Edge Set Enrichment Analysis
Authors: Han Junwei , Shi Xinrui , Zhang Yunpeng , Xu Yanjun , Jiang Ying , Zhang Chunlong , Feng Li , Yang Haixiu , Shang Desi , Sun Zeguo , Su Fei , Li Chunquan , Li Xia 
Published: August 2015

AbstractPathway analyses are playing an increasingly important role in understanding biological mechanism, cellular function and disease states. Current pathway-identification methods generally focus on only the changes of gene expression levels; however, the biological relationships among genes are also the fundamental components of pathways and the dysregulated relationships may also alter the pathway activities. We propose a powerful computational method, Edge Set Enrichment Analysis (ESEA), for the identification of dysregulated pathways. This provides a novel way of pathway analysis by investigating the changes of biological relationships of pathways in the context of gene expression data. Simulation studies illustrate the power and performance of ESEA under various simulated conditions. Using real datasets from p53 mutation, Type 2 diabetes and lung cancer, we validate effectiveness of ESEA in identifying dysregulated pathways. We further compare our results with five other pathway enrichment analysis methods. With these analyses, we show that ESEA is able to help uncover dysregulated biological pathways underlying complex traits and human diseases via specific use of the dysregulated biological relationships. We develop a freely available R-based tool of ESEA. Currently, ESEA can support pathway analysis of the seven public databases (KEGG; Reactome; Biocarta; NCI; SPIKE; HumanCyc; Panther).
Transcriptomic and metabolomic analyses identify a role for chlorophyll catabolism and phytoalexin during Medicago nonhost resistance against Asian soybean rust
Authors: Ishiga Yasuhiro , Rao Uppalapati Srinivasa , Gill Upinder S. , Huhman David , Tang Yuhong , Mysore Kirankumar S. 
Published: August 2015

AbstractAsian soybean rust (ASR) caused byPhakopsora pachyrhiziis a devastating foliar disease affecting soybean production worldwide. Understanding nonhost resistance against ASR may provide an avenue to engineer soybean to confer durable resistance against ASR. We characterized aMedicago truncatula-ASR pathosystem to study molecular mechanisms of nonhost resistance. Although urediniospores formed appressoria and penetrated into epidermal cells ofM. truncatula,P. pachyrhizifailed to sporulate. Transcriptomic analysis revealed the induction of phenylpropanoid, flavonoid and isoflavonoid metabolic pathway genes involved in the production of phytoalexin medicarpin inM. truncatulaupon infection withP. pachyrhizi. Furthermore, genes involved in chlorophyll catabolism were induced during nonhost resistance. We further characterized one of the chlorophyll catabolism genes,Stay-green(SGR) and demonstrated that theM. truncatula sgrmutant and alfalfaSGR-RNAi lines showed hypersensitive-response-like enhanced cell death upon inoculation withP. pachyrhizi. Consistent with transcriptomic analysis, metabolomic analysis also revealed the accumulation of medicarpin and its intermediate metabolites.In vitroassay showed that medicarpin inhibited urediniospore germination and differentiation. In addition, several triterpenoid saponin glycosides accumulated inM. truncatulaupon inoculation withP. pachyrhizi. In summary, using multi-omic approaches, we identified a correlation between phytoalexin production andM. truncatuladefense responses against ASR.
Inflammation-induced microvascular insulin resistance is an early event in diet-induced obesity
Authors: Zhao Lina , Fu Zhuo , Wu Jing , Aylor Kevin W. , Barrett Eugene J. , Cao Wenhong , Liu Zhenqi 
Published: August 2015

Endothelial dysfunction and vascular insulin resistance usually coexist and chronic inflammation engenders both. In the present study, we investigate the temporal relationship between vascular insulin resistance and metabolic insulin resistance. We assessed insulin responses in all arterial segments, including aorta, distal saphenous artery and the microvasculature, as well as the metabolic insulin responses in muscle in rats fed on a high-fat diet (HFD) for various durations ranging from 3 days to 4 weeks with or without sodium salicylate treatment. Compared with controls, HFD feeding significantly blunted insulin-mediated Akt (protein kinase B) and eNOS [endothelial nitric oxide (NO) synthase] phosphorylation in aorta in 1 week, blunted vasodilatory response in small resistance vessel in 4 weeks and microvascular recruitment in as early as 3 days. Insulin-stimulated whole body glucose disposal did not begin to progressively decrease until after 1 week. Salicylate treatment fully inhibited vascular inflammation, prevented microvascular insulin resistance and significantly improved muscle metabolic responses to insulin. We conclude that microvascular insulin resistance is an early event in diet-induced obesity and insulin resistance and inflammation plays an essential role in this process. Our data suggest microvascular insulin resistance contributes to the development of metabolic insulin resistance in muscle and muscle microvasculature is a potential therapeutic target in the prevention and treatment of diabetes and its related complications.
Stripline‐fed aperture‐coupled patch array antenna with reduced sidelobe
Authors: Cheon Yonghun , Kim Yonghoon 
Published: August 2015

An aperture‐coupled patch array antenna with a reduced sidelobe level (SLL) at the 28 GHz frequency band is presented. The feeding line consists of an asymmetric stripline with a stripline‐to‐waveguide transition. The array antenna is serially fed in the E‐plane, the excitation of which is tapered by controlling the aperture sizes, and is fed through a power divider in the H‐plane. The experimental results show a SLL of <−20 dB and a gain of ∼20 dBi for a frequency band in the range of 27.5–28.5 GHz.
Selenium Supplementation and the Effects on Reproductive Outcomes, Biomarkers of Inflammation, and Oxidative Stress in Women with Polycystic Ovary Syndrome
Authors: Razavi M. , Jamilian M. , Kashan Z. Fakhrieh , Heidar Z. , Mohseni M. , Ghandi Y. , Bagherian T. , Asemi Z. 
Published: August 2015

AbstractSelenium supplementation could be effective on reproductive outcomes, biomarkers of inflammation, and oxidative stress among women with polycystic ovary syndrome (PCOS). The aim of the study was to determine the effects of selenium supplementation on reproductive outcomes, biomarkers of inflammation, and oxidative stress in PCOS patients. The present randomized double-blind, placebo-controlled trial was conducted on 64 women aged 18–40 years old with PCOS at the clinic affiliated to Ardabil University of Medical Sciences, Ardabil, Iran. The participants were randomly assigned to 2 groups receiving either 200 μg selenium daily (n=32) or placebo (n=32) for 8 weeks. Hormonal profiles, biomarkers of inflammation, and oxidative stress were measured and compared both before and after the treatment. After 8 weeks of intervention, pregnancy rate in the selenium group was higher than in the placebo group: 18.8 (6/32) vs. 3.1% (1/32), p=0.04. In addition, alopecia (40.6 vs. 9.4%, p=0.004) and acne (46.9 vs. 12.5 %, p=0.003) decreased following the consumption of selenium supplements compared with placebo. Additionally, patients who received selenium supplements had significantly decreased serum dehydroepiandrosterone (DHEA) levels (p=0.02), hirsutism (modified Ferriman–Gallwey scores) (p<0.001), serum high sensitivity C-reactive protein (hs-CRP) (p=0.02), and plasma malondialdehyde (MDA) levels (p=0.01) compared with placebo. We did not observe any significant effects of taking selenium supplements on other hormonal profiles, nitric oxide (NO), and other biomarkers of oxidative stress. Taken together, selenium supplementation for 8 weeks among PCOS women had beneficial effects on reproductive outcomes, DHEA, hs-CRP, and MDA levels.
Characterization of Adult Pacific Lamprey Swimming Behavior in Relation to Environmental Conditions within Large‐Dam Fishways
Authors: Kirk Mark A. , Caudill Christopher C. , Johnson Eric L. , Keefer Matthew L. , Clabough Tami S. 
Published: August 2015

AbstractUnderstanding the migration behaviors of adult Pacific Lamprey Entosphenus tridentatus inside fishways is critical to resolving why the species has low passage rates at hydropower dams. We used an acoustic camera to make in situ observations on the swimming behaviors of Pacific Lampreys at two large Columbia River dams (Bonneville and John Day) and to develop inferences regarding potential mechanisms influencing passage within lower fishway sections (entrances, collection channels, transition areas). Pacific Lampreys were primarily free‐swimming in the middle and upper water column at both the high‐velocity entrance (>1 m/s) and the low‐velocity transition area (<1 m/s) of Bonneville Dam. In contrast, Pacific Lampreys in the high‐velocity fishway channel at John Day Dam were more likely to orient to the fishway floor at the entrance and in the collection channel. Pacific Lampreys exhibited no interaction with diffuser grating along the fishway floor at Bonneville Dam and were observed free‐swimming above these structures. Behavior in the Bonneville Dam transition area appeared to be affected by poor attraction flow and the presence of predatory White Sturgeon Acipenser transmontanus. Higher Pacific Lamprey tail‐beat frequencies and lower ground speeds were observed at the fishway entrances of both dams and in the John Day Dam collection channel, indicating that Pacific Lampreys were exerting greater effort to achieve upstream progress under the high water velocities at these locations. High tail‐beat frequencies and low ground speeds support the hypothesis that fishway entrances may act as short‐distance, high‐velocity barriers for Pacific Lampreys, while passage through the lower John Day Dam fishway may be limited by the endurance requirements for passing a long‐distance (~80 m), high‐velocity challenge (collection channel). Similar in situ applications offer the potential for understanding and improving the passage of migratory fish at anthropogenic barriers.
Performance characteristics of Parkour practitioners: Who are the traceurs?
Authors: Grosprêtre Sidney , Lepers Romuald 
Published: August 2015

AbstractParkour is a modern physical activity that consists of using the environment, mostly urban, as a playground of obstacles. The aims of this study were (i) to investigate age, anthropometric and training characteristics of Parkour practitioners, called ‘traceurs’ and (ii) to assess jump performances and muscular characteristics of traceurs, compared to those of gymnasts and power athletes. The mean age of the population of traceurs studied (n = 130) was 19.4 ± 4.3 years, women represented 12.4% of the total field and mean training volume was 8.1 ± 0.5 hours/week. Vertical and long jump performances were analysed on smaller samples of participants (four groups, n = 15 per group); and eccentric (−90° s−1, −30° s−1), concentric (30° s−1, 90° s−1) and isometric knee extensors torques were evaluated by means of an isokinetic dynamometer. Traceurs showed greater (P < .01) drop jump performance (64.9 ± 1.5 cm) than gymnasts (60.9 ± 1.1 cm) and greater (P < .001) counter movement jump with arms (59.2 ± 1.5 cm) than power athletes (53.0 ± 1.4 cm). Standing long jump performances were greater (P < .05) for traceurs (282.7 ± 5.2 cm) compared to other athletes (gymnasts: 273.9 ± 7.3 cm; power athletes: 261.3 ± 6.7 cm). Eccentric knee extension torques were greater (P < .05) for traceurs compared to other athletes. This study revealed that Parkour training induces major development of jump and muscular skills. The use of such training has several practical applications as it provides a better resistance to high eccentric load and helps reinforce musculoskeletal structures.
Momentum sequence and environmental climate influence levels of perceived psychological momentum within a sport competition
Authors: Briki Walid , Markman Keith D. , Coudevylle Guillaume , Sinnapah Stéphane , Hue Olivier 
Published: August 2015

AbstractThe present study examined the influence of momentum sequence (positive vs. negative) and environmental climate (hot–wet vs. neutral) on supporters’ (i.e. virtual observers’) reported levels of perceived psychological momentum (PM) during a simulated cycling competition. Participants supported one of two competing cyclists involved in a race that was displayed on a screen in a lecture hall. The race scenario was manipulated so that the supported cyclist appeared to undergo either a positive or negative momentum sequence. In addition, participants were either exposed to a hot–wet environmental climate or to a neutral environmental climate while observing the race scenario. According to the results, reported levels of PM were higher in the positive momentum sequence condition than in the negative momentum sequence condition, consistent with the notion that supporters’ PM is influenced by a positivity bias, and reported levels of PM were also found to be higher in the hot–wet climate condition than in the neutral climate condition, consistent with the notion that environmental climate is a contextual factor that influences PM through the operation of a causal augmenting mechanism.
Muscle activation, blood lactate, and perceived exertion responses to changing resistance training programming variables
Authors: Hiscock Daniel J. , Dawson Brian , Donnelly Cyril J. , Peeling Peter 
Published: August 2015

AbstractRatings of perceived exertion (RPE: 0–10) during resistance training with varying programming demands were examined. Blood lactate (BLa) and muscle activation (using surface electromyography: EMG) were measured as potential mediators of RPE responses. Participants performed three sets of single arm (preferred side) bicep curls at 70% of 1 repetition maximum over 4 trials: Trial (A) 3 sets × 8 repetitions × 120 s recovery between sets; (B) 3 sets × 8 repetitions × 240 s recovery; (C) 3 sets × maximum number of repetitions (MNR) × 120 s recovery; (D) 3 sets × MNR × 240 s recovery. Overall body (RPE‐O) and active muscle (RPE‐AM) perceptual responses were assessed following each set in each trial. Biceps brachii and brachioradialis muscle EMG was measured during each set for each trial. RPE‐O and RPE‐AM were not different between Trial A (3.5 ± 1 and 6 ± 1, respectively) and Trial B (3.5 ± 1 and 5.5 ± 1, respectively) (p < .05). However, RPE‐AM was significantly greater in Trial C (7.5 ± 1.5) and Trial D (7.5 ± 1.5) than in Trial B (p < .05). There were no significant differences in muscle activation or BLa between trials; however, work rate (tonnage/min) was greater in Trials C and D compared to Trial B. In conclusion, BLa and muscle activation were not related to RPE, but resistance training variables, such as work rate, may impact on RPE when intensity (%1RM) and the number of sets completed remain constant.
Evaluation of Cytokine Profile and HLA Association in Benznidazole Related Cutaneous Reactions in Patients With Chagas Disease
Authors: Salvador Fernando , Sánchez-Montalvá Adrián , Martínez-Gallo Mónica , Sala-Cunill Anna , Viñas Laura , García-Prat Marina , Aparicio Gloria , Sao Avilés Augusto , Artaza Mª Ángeles , Ferrer Berta , Molina Israel 
Published: August 2015

Abstract
Background.  Benznidazole is the drug of choice for Chagas disease. The major drawback of this drug is the high adverse events rate, being cutaneous reactions the most frequent one, leading to definitive withdrawal of treatment in 15%–30% of patients.
Methods.  Prospective observational study where adult Chagas disease patients accepting to receive benznidazole (100 mg/8 hours for 60 days) were included. The objective was to characterize the skin toxicity of benznidazole in patients with Chagas disease, determine the serum cytokine profile, and evaluate the potential association with specific HLA alleles and benznidazole concentration. Serum cytokine levels were measured at day 0, 15, and 60 of treatment. Class I and II HLA alleles were determined. When cutaneous reaction was detected, a skin biopsy was performed. Serum benznidazole concentration was determined at the time of cutaneous reaction, or at day 15 of treatment.
Results.  Fifty-two patients were included, 20(38.5%) had cutaneous reaction, and median time of appearance was 9 days. Skin biopsies showed histopathological findings consistent with drug eruption. Patients with cutaneous drug-reaction had higher proportion of eosinophilia during treatment, and higher interleukin (IL)-5 and IL-10 serum concentrations at day 15 of treatment than those without cutaneous reaction. Treatment interruption (that included moderate-severe cutaneous reactions) was more frequent in patients carrying HLA-B*3505 allele (45.5% vs 15.4%, P = .033). No differences in benznidazole serum concentration were found.
Conclusions.  Benznidazole related cutaneous reaction rate is high, and it was produced by a delayed hypersensitivity reaction with a Th2 response. Carrying HLA-B*3505 allele could be associated with moderate-severe cutaneous reaction.
Effect of zooplankton on fish larval abundance and distribution: a long-term study on North Sea herring (Clupea harengus)
Authors: Alvarez-Fernandez S. , Licandro P. , van Damme C. J. G. , Hufnagl M. 
Published: August 2015

Abstract
During the last decade, North Sea autumn spawning herring (Clupea harengus) has gone through consecutive years of low recruitment despite high spawning-stock biomass. Although several mechanisms, such as reduced larval growth and high early larvae mortality, have been identified as co-occurring during these years, the causes behind them have not been identified. In this study, we analyse a long-term dataset of larval distribution, obtained during the International Bottom Trawl Survey, in relation to environmental conditions during winter and zooplankton abundances, obtained from the continuous plankton recorder. These analyses assessed the potential influence of these factors on the reduced survival of larval stages. Generalized additive mixed models on 30 years of data showed the abundance of Pseudocalanus sp. during winter to have a strong relationship with larval distribution and abundance, suggesting that predator–prey processes are behind the low recruitment in recent years. According to our models, the direct effect of temperature on larval abundances was less than the effect of zooplankton abundances.
Association Between Outpatient Antibiotic Prescribing Practices and Community-Associated Clostridium difficile Infection
Authors: Dantes Raymund , Mu Yi , Hicks Lauri A. , Cohen Jessica , Bamberg Wendy , Beldavs Zintars G. , Dumyati Ghinwa , Farley Monica M. , Holzbauer Stacy , Meek James , Phipps Erin , Wilson Lucy , Winston Lisa G. , McDonald L. Clifford , Lessa Fernanda C. 
Published: August 2015

Abstract
Background.  Antibiotic use predisposes patients to Clostridium difficile infections (CDI), and approximately 32% of these infections are community-associated (CA) CDI. The population-level impact of antibiotic use on adult CA-CDI rates is not well described.
Methods.  We used 2011 active population- and laboratory-based surveillance data from 9 US geographic locations to identify adult CA-CDI cases, defined as C difficile-positive stool specimens (by toxin or molecular assay) collected from outpatients or from patients ≤3 days after hospital admission. All patients were surveillance area residents and aged ≥20 years with no positive test ≤8 weeks prior and no overnight stay in a healthcare facility ≤12 weeks prior. Outpatient oral antibiotic prescriptions dispensed in 2010 were obtained from the IMS Health Xponent database. Regression models examined the association between outpatient antibiotic prescribing and adult CA-CDI rates.
Methods.  Healthcare providers prescribed 5.2 million courses of antibiotics among adults in the surveillance population in 2010, for an average of 0.73 per person. Across surveillance sites, antibiotic prescription rates (0.50–0.88 prescriptions per capita) and unadjusted CA-CDI rates (40.7–139.3 cases per 100 000 persons) varied. In regression modeling, reducing antibiotic prescribing rates by 10% among persons ≥20 years old was associated with a 17% (95% confidence interval, 6.0%–26.3%; P = .032) decrease in CA-CDI rates after adjusting for age, gender, race, and type of diagnostic assay. Reductions in prescribing penicillins and amoxicillin/clavulanic acid were associated with the greatest decreases in CA-CDI rates.
Conclusions and Relevance.  Community-associated CDI prevention should include reducing unnecessary outpatient antibiotic use. A modest reduction of 10% in outpatient antibiotic prescribing can have a disproportionate impact on reducing CA-CDI rates.
Opportunities and barriers to cardiopulmonary resuscitation training in English secondary schools
Authors: Lockey Andrew S. , Barton Katherine , Yoxall Heather 
Published: August 2015

Objectives
Cardiopulmonary resuscitation rates and survival from out-of-hospital cardiac arrest are poor in the UK compared with areas abroad that deliver mandatory training to all school children. We sought to identify barriers to training and develop a strategy to enable delivery of this training.

Methods
Qualitative analysis, comprising semistructured interviews and group discussions, covering 14 schools in the metropolitan borough of Calderdale in West Yorkshire.

Results
Only three schools out of 14 were delivering training to entire year groups. Barriers include lack of resources, lack of training for teachers and difficulty in initiating a programme. Strategies were developed to overcome these barriers with the result that four additional schools are now teaching a whole year group. There is no single solution and bespoke plans may be needed for each school.

Conclusion
The establishment of cardiopulmonary resuscitation training in secondary schools in the UK is achievable. The commonly perceived barriers to establishment of training are all surmountable, but solving them does not necessarily ensure universal coverage. Support from healthcare professionals, in particular public health, is essential to ensure that the training is as widespread as possible. Mandatory inclusion of this training on the school curriculum, as seen in other countries, would result in significantly improved survival rates from out-of-hospital cardiorespiratory arrest. Solutions to improve training have been proposed, which could be used in other parts of Europe where such training is not a mandatory requirement.