bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Microbiome DNA Enrichment Method for Next‐Generation Sequencing Sample Preparation
Authors: Yigit Erbay , Feehery George R. , Langhorst Bradley W. , Stewart Fiona J. , Dimalanta Eileen T. , Pradhan Sriharsa , Slatko Barton , Gardner Andrew F. , McFarland James , Sumner Christine , Davis Theodore B. 
Published: July 2016

Abstract“Microbiome” is used to describe the communities of microorganisms and their genes in a particular environment, including communities in association with a eukaryotic host or part of a host. One challenge in microbiome analysis concerns the presence of host DNA in samples. Removal of host DNA before sequencing results in greater sequence depth of the intended microbiome target population. This unit describes a novel method of microbial DNA enrichment in which methylated host DNA such as human genomic DNA is selectively bound and separated from microbial DNA before next‐generation sequencing (NGS) library construction. This microbiome enrichment technique yields a higher fraction of microbial sequencing reads and improved read quality resulting in a reduced cost of downstream data generation and analysis. © 2016 by John Wiley & Sons, Inc.
The Importance of Titrating Antibodies for Immunocytochemical Methods
Authors: Hoffman Gloria E. , Murphy Kelley J. , Sita Luciane V. 
Published: July 2016

AbstractWhen using immunocytochemistry, investigators may not know how to optimize staining or how to troubleshoot the method when staining fails. Lacking are guides for comparing techniques and applying information derived from one staining method to another. Newer methods amplify signal detection, but will not necessarily work at the same primary antibody concentrations used for less sensitive reactions. Recommendations of optimal titers are often not accurate and are not usually accompanied by information on the method used to test those antibodies or the specifics of the assay. When the staining does not work, the investigators do not know how to determine if the antiserum is bad, the tissue is bad, or the method is inappropriate for their staining. This unit describes detailed procedures for determining optimal staining and applying that information to three common immunofluorescence methods. Lastly, a formula is provided for converting among the different methods. © 2016 by John Wiley & Sons, Inc.
Incipient sympatric speciation in Midas cichlid fish from the youngest and one of the smallest crater lakes in Nicaragua due to differential use of the benthic and limnetic habitats?
Authors: Kautt Andreas F. , Machado‐Schiaffino Gonzalo , Torres‐Dowdall Julian , Meyer Axel 
Published: July 2016

AbstractUnderstanding how speciation can occur without geographic isolation remains a central objective in evolutionary biology. Generally, some form of disruptive selection and assortative mating are necessary for sympatric speciation to occur. Disruptive selection can arise from intraspecific competition for resources. If this competition leads to the differential use of habitats and variation in relevant traits is genetically determined, then assortative mating can be an automatic consequence (i.e., habitat isolation). In this study, we caught Midas cichlid fish from the limnetic (middle of the lake) and benthic (shore) habitats of Crater Lake Asososca Managua to test whether some of the necessary conditions for sympatric speciation due to intraspecific competition and habitat isolation are given. Lake As. Managua is very small (<900 m in diameter), extremely young (maximally 1245 years of age), and completely isolated. It is inhabited by, probably, only a single endemic species of Midas cichlids,Amphilophus tolteca. We found that fish from the limnetic habitat were more elongated than fish collected from the benthic habitat, as would be predicted from ecomorphological considerations. Stable isotope analyses confirmed that the former also exhibit a more limnetic lifestyle than the latter. Furthermore, split‐brood design experiments in the laboratory suggest that phenotypic plasticity is unlikely to explain much of the observed differences in body elongation that we observed in the field. Yet, neutral markers (microsatellites) did not reveal any genetic clustering in the population. Interestingly, demographic inferences based onRAD‐seq data suggest that the apparent lack of genetic differentiation at neutral markers could simply be due to a lack of time, as intraspecific competition may only have begun a few hundred generations ago.
A model coupling the effects of soil moisture and potential evaporation on the tree transpiration of a semi‐arid larch plantation
Authors: Li Zhenhua , Yu Pengtao , Wang Yanhui , Webb Ashley A. , He Cong , Wang Yanbing , Yang Lili 
Published: July 2016

AbstractQuantifying the tree transpiration (T) response to the coupling effects of changing soil moisture and weather conditions provides insights into water use by forests, especially in dryland regions. This study was conducted in a semi‐arid pure larch (Larix principis‐rupprechtii) plantation in northwest China. The sap flow density of trees, weather conditions in open field, and soil moisture of main root zone (0–60 cm) were measured synchronously and continuously throughout a growing season in 2010. The response of daily T to the relative extractable soil water (REW) and potential evapotranspiration (PET) was analyzed. The T varied in the range of 0.08–2.18 mm/day during the study period. With increasing REW, it initially rose quickly and almost linearly; but after the REW reached a threshold, it leveled off and gradually approached its maximum (Tmax). However, Tmax positively related with PET. Based on the T‐REW and Tmax‐PET relationships, an integrated model (T = (−0.05PET2 + 0.65PET) × (1 −  exp (−5.39REW))) was developed to describe the complex T‐REW‐PET relationship and it fit the measured data well. For the whole study period, due to the limit of PET and REW, the actual T was reduced by 32% (88.6 mm) and 16% (45.0 mm) respectively, compared with potential T. Although this model cannot be widely applied until it is validated with measured data from more sites, it does provide a way to accurately estimate the daily T using REW and PET data and to quantify the coupling effects of changing REW and PET on the T.
Combined neprilysin and renin–angiotensin system inhibition in heart failure with reduced ejection fraction: a meta‐analysis
Authors: Solomon Scott D. , Claggett Brian , McMurray John J.V. , Hernandez Adrian F. , Fonarow Gregg C. 
Published: July 2016

AimsThe combined neprilysin/renin–angiotensin system (RAS) inhibitor sacubitril/valsartan reduced cardiovascular death or heart failure hospitalization, cardiovascular death, and all‐cause mortality in a large outcomes trial. While sacubitril/valsartan is the only currently available drug in its class, there are two prior clinical trials in heart failure with omapatrilat, another combined neprilysin/RAS inhibitor. Using all available evidence can inform clinicians and policy‐makers.Methods and resultsWe performed a meta‐analysis using data from three trials in heart failure with reduced EF that compared combined neprilysin/RAS inhibition with RAS inhibition alone and reported clinical outcomes: IMPRESS (n = 573), OVERTURE (n = 5770), and PARADIGM‐HF (n = 8399). We assessed the pooled hazard ratio (HR) for all‐cause death or heart failure hospitalization, and for all‐cause mortality in random‐effects models, comparing combined neprilysin/RAS inhibition with ACE inhibition alone. The composite outcome of death or heart failure hospitalization was reduced numerically in patients receiving combined neprilysin/RAS inhibition in all three trials, with a pooled HR of 0.86, 95% confidence interval (CI) 0.76–0.97, P = 0.013. For the endpoint of all‐cause mortality, the pooled HR was 0.88, 95% CI 0.80–0.98, P = 0.021. Combined neprilysin/RAS inhibition compared with ACE inhibition was associated with more hypotension, but less renal dysfunction and hyperkalaemia in all three trials.ConclusionsPooled estimates from three trials with two separate drugs of combined neprilysin/RAS inhibition support the use of combined neprilysin/RAS inhibition in heart failure with reduced EF.
Collapse assessment of moment frame buildings, considering vertical ground shaking
Authors: Harrington Cody C. , Liel Abbie B. 
Published: July 2016

SummaryWhile many cases of structural damage in past earthquakes have been attributed to strong vertical ground shaking, our understanding of vertical seismic load effects and their influence on collapse mechanisms of buildings is limited. This study quantifies ground motion parameters that are capable of predicting trends in building collapse because of vertical shaking, identifies the types of buildings that are most likely affected by strong vertical ground motions, and investigates the relationship between element level responses and structural collapse under multi‐directional shaking. To do so, two sets of incremental dynamic analyses (IDA) are run on five nonlinear building models of varying height, geometry, and design era. The first IDA is run using the horizontal component alone; the second IDA applies the vertical and horizontal motions simultaneously. When ground motion parameters are considered independently, acceleration‐based measures of the vertical shaking best predict trends in building collapse associated with vertical shaking. When multiple parameters are considered, Housner intensity (SI), computed as a ratio between vertical and horizontal components of a record (SIV/SIH), predicts the significance of vertical shaking for collapse. The building with extensive structural cantilevered members is the most influenced by vertical ground shaking, but all frame structures (with either flexural and shear critical columns) are impacted. In addition, the load effect from vertical ground motions is found to be significantly larger than the nominal value used in US building design. Copyright © 2016 John Wiley & Sons, Ltd.
Thiol oxidation of hemolymph proteins in oysters Crassostrea brasiliana as markers of oxidative damage induced by urban sewage exposure
Authors: Trevisan Rafael , Flores-Nunes Fabrício , Dolores Euler S. , Mattos Jacó J. , Piazza Clei E. , Sasaki Sílvio T. , Taniguchi Satie , Montone Rosalinda C. , Bícego Márcia C. , dos Reis Isis M. M. , Zacchi Flávia L. , Othero Bárbara N.M. , Bastolla Camila L.V. , Mello Danielle F. , Fraga Ana Paula M. , Wendt Nestor , Toledo-Silva Guilherme , Razzera Guilherme , Dafre Alcir L. , de Melo Cláudio M. R. , Bianchini Adalto , Marques Maria R. F. , Bainy Afonso C.D. 
Published: July 2016

Abstract

Urban sewage is a concerning issue worldwide, threatening both wildlife and human health. The present study investigated protein oxidation in mangrove oysters (Crassostrea brasiliana) exposed to seawater from Balneário Camboriú, an important tourist destination in Brazil that is affected by urban sewage. Oysters were exposed for 24 h to seawater collected close to the Camboriú River (CAM1) or 1 km away (CAM2). Seawater from an aquaculture laboratory was used as a reference. Local sewage input was marked by higher levels of coliforms, nitrogen, and phosphorus in seawater, as well as polycyclic aromatic hydrocarbons (PAHs), polychlorinated biphenyls (PCBs), linear alkylbenzenes (LABs), and fecal steroid in sediments at CAM1. Exposure of oysters to CAM1 caused marked bioaccumulation of LABs and decreased PAH and PCB concentrations after exposure to both CAM1 and CAM2. Protein thiol oxidation in gills, digestive gland, and hemolymph was evaluated. Lower levels of reduced protein thiols were detected in hemolymph from CAM1, and actin, segon, and dominin were identified as targets of protein thiol oxidation. Dominin susceptibility to oxidation was confirmed in vitro by exposure to peroxides and hypochlorous acid, and 2 cysteine residues were identified as potential sites of oxidation. Overall, these data indicate that urban sewage contamination in local waters has a toxic potential and that protein thiol oxidation in hemolymph could be a useful biomarker of oxidative stress in bivalves exposed to contaminants. Environ Toxicol Chem 2017;36:1833–1845. © 2016 SETAC
Novel class of collector in electrospinning device for the fabrication of 3D nanofibrous structure for large defect load‐bearing tissue engineering application
Authors: Hejazi Fatemeh , Mirzadeh Hamid , Contessi Nicola , Tanzi Maria Cristina , Faré Silvia 
Published: July 2016

AbstractAdequate porosity, appropriate pore size, and 3D‐thick shape are crucial parameters in the design of scaffolds, as they should provide the right space for cell adhesion, spreading, migration, and growth. In this work, a novel design for fabricating a 3D nanostructured scaffold by electrospinning was taken into account. Helical spring‐shaped collector was purposely designed and used for electrospinning PCL fibers. Improved morphological properties and more uniform diameter distribution of collected nanofibers on the turns of helical spring‐shaped collector are confirmed by SEM analysis. SEM images elaboration showed 3D pores with average diameter of 4 and 5.5 micrometer inx‐yplane andz‐direction, respectively. Prepared 3D scaffold possessed 99.98% porosity which led to the increased water uptake behavior in PBS at 37°C up to 10 days, and higher degradation rate compared to 2D flat structure. Uniaxial compression test on 3D scaffolds revealed an elastic modulus of 7 MPa and a stiffness of 102MPa, together with very low hysteresis area and residual strain. In vitro cytocompatibility test with MG‐63 osteoblast‐like cells using AlamarBlue™colorimetric assay, indicated a continuous increase in cell viability for the 3D structure over the test duration. SEM observation showed enhanced cells spreading and diffusion into the underneath layers for 3D scaffold. Accelerated calcium deposition in 3D substrate was confirmed by EDX analysis. Obtained morphological, physical, and mechanical properties together within vitrocytocompatibility results, suggest this novel technique as a proper method for the fabrication of 3D nanofibrous scaffolds for the regeneration of critical‐size load bearing defects. © 2017 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 105A: 1535–1548, 2017.
Outcomes after resection of occupational cholangiocarcinoma
Authors: Kubo Shoji , Takemura Shigekazu , Tanaka Shogo , Shinkawa Hiroji , Kinoshita Masahiko , Hamano Genya , Ito Tokuji , Koda Masaki , Aota Takanori , Yamamoto Takatsugu , Terajima Hiroaki , Tachiyama Gorou , Yamada Terumasa , Nakamori Shoji , Arimoto Akira , Fujikawa Masahiro , Tomimaru Yoshito , Sugawara Yasuhiko , Nakagawa Kei , Unno Michiaki , Mizuguchi Toru , Takenaka Kenji , Kimura Koichi , Shirabe Ken , Saiura Akio , Uesaka Katsuhiko , Taniguchi Hiroki , Fukuda Akira , Chong Ja‐Mun , Kuwae Yuko , Ohsawa Masahiko , Sato Yasunori , Nakanuma Yasuni 
Published: July 2016

AbstractBackgroundCholangiocarcinoma caused by exposure to 1,2‐dichloropropane and/or dichloromethane is recognized as occupational cholangiocarcinoma. The aim of this study was to investigate the outcomes after resection of occupational cholangiocarcinoma to establish a treatment strategy for this disease.MethodsClinicopathological findings and outcomes after surgical intervention in 20 patients with occupational cholangiocarcinoma were investigated.ResultsOf 20 the patients, curative resection was performed in 16 patients. Three patients underwent radiation at the stump of the bile ducts. Adjuvant chemotherapy was performed in 12 patients. Biliary intraepithelial neoplasia, intraductal papillary neoplasm of the bile duct, and/or chronic bile duct injury was detected in most subjects. Intraabdominal infection developed after surgery in nine patients. Cholangiocarcinoma recurred in 12 of the 20 patients. The recurrent tumors in five patients developed at a different part of the bile duct from the primary tumor and a second resection was performed in four of these five patients.ConclusionsThe incidence of postoperative complications including intraabdominal infection was high in patients with occupational cholangiocarcinoma. Multicentric recurrence occurred not infrequently after surgery because the bile ducts had a high potential for the development of carcinoma. The aggressive treatment including second resection for the multicentric recurrence appeared to be effective.
Fieldwork Using the Professional Development Schools Model: Developing a Social Justice Orientation and Multicultural Competency
Authors: Cook Amy L. , Krell Megan M. , Hayden Laura A. , Gracia Robert , Denitzio Kari 
Published: July 2016

Practicum fieldwork was conducted in an urban high school setting using a Professional Development Schools (PDS) model, with a focus on multicultural and social justice counseling competencies (MSJCC). Interpretative phenomenological analysis was used to analyze the journal responses of 16 counseling students to ascertain MSJCC development during fieldwork. Themes emerged related to multicultural counseling skills, self‐awareness, understanding educational inequities, and serving as agents of change. Implications of using a PDS model in counselor training are explored.Se llevó a cabo un trabajo de campo en práctica clínica en una escuela secundaria usando un modelo de Escuelas de Desarrollo Profesional (PDS, por sus siglas en inglés), con un enfoque en las competencias en consejería multicultural y de justicia social (MSJCC, por sus siglas en inglés). Se empleó un análisis fenomenológico interpretativo para analizar las respuestas registradas de 16 estudiantes de consejería para determinar el desarrollo de las MSJCC durante el trabajo de campo. Surgieron temas relacionados con las habilidades en consejería multicultural, la autoconciencia, la comprensión de desigualdades educativas, y la actuación como agentes de cambio. Se exploran las implicaciones de usar un modelo PDS en la formación de consejeros.
Needle electromyography of the frontalis muscle in patients with amyotrophic lateral sclerosis
Authors: Pan Hua , Jian Fan , Lin Jinxi , Chen Na , Zhang Zaiqiang , Wang Yongjun , Cui Liying , Kimura Jun 
Published: July 2016

ABSTRACTIntroduction: We sought to determine which muscles to choose for better assessment of the craniobulbar region in establishing the diagnosis of amyotrophic lateral sclerosis (ALS). Methods: We studied the frontalis muscle in 83 controls and compared it with the tongue, sternocleidomastoid (SCM), and trapezius muscles in 105 definite or probable ALS patients (54 bulbar, 51 nonbulbar). Results: More patients achieved complete relaxation of the frontalis muscle than the tongue or SCM. Motor unit potentials were of longer duration and higher amplitude in ALS patients than in controls (P < 0.05). The frontalis had the same frequency of spontaneous potentials as the tongue, SCM, and trapezius muscles in bulbar ALS patients, but fewer than in the trapezius in nonbulbar patients. Conclusions: Examining the frontalis provides useful information in establishing the diagnosis of ALS by identifying clinically evident or subclinical abnormalities in the craniobulbar region. Muscle Nerve 54: 1093–1096, 2016
Combined treatment with a β3‐adrenergic receptor agonist and a muscarinic receptor antagonist inhibits detrusor overactivity induced by cold stress in spontaneously hypertensive rats
Authors: Imamura Tetsuya , Ogawa Teruyuki , Minagawa Tomonori , Nagai Takashi , Suzuki Toshiro , Saito Tetsuichi , Yokoyama Hitoshi , Nakazawa Masaki , Ishizuka Osamu 
Published: July 2016

AimsThis study determined if combined treatment with the muscarinic receptor (MR) antagonist solifenacin and the β3‐adrenergic receptor (AR) agonist mirabegron could inhibit detrusor overactivity induced by cold stress in spontaneously hypertensive rats (SHRs).MethodsThirty‐two female 10‐week‐old SHRs were fed an 8% NaCl‐supplemented diet for 4 weeks. Cystometric measurements of the unanesthetized, unrestricted rats were performed at room temperature (RT, 27 ± 2°C) for 20 min. The rats were then intravenously administered vehicle, 0.1 mg/kg solifenacin alone, 0.1 mg/kg mirabegron alone, or the combination of 0.1 mg/kg mirabegron and 0.1 mg/kg solifenacin (n = 8 each group). Five minutes later, the treated rats were exposed to low temperature (LT, 4 ± 2°C) for 40 min. Finally, the rats were returned to RT. After the cystometric investigations, the β3‐ARs and M3‐MRs expressed within the urinary bladders were analyzed.ResultsJust after transfer from RT to LT, vehicle‐, solifenacin‐, and mirabegron‐treated SHRs exhibited detrusor overactivity that significantly decreased voiding interval and bladder capacity. However, treatment with the combination of solifenacin and mirabegron partially inhibited the cold stress‐induced detrusor overactivity patterns. The decreases of voiding interval and bladder capacity in the combination‐treated rats were significantly inhibited compared to other groups. Within the urinary bladders, there were no differences between expression levels of M3‐MR and β3‐AR mRNA. The tissue distribution of M3‐MRs was similar to that of the β3‐ARs.ConclusionsThis study suggested that the combination of solifenacin and mirabegron act synergistically to inhibit the cold stress‐induced detrusor overactivity in SHRs. Neurourol. Urodynam. 36:1026–1033, 2017. © 2016 The Authors. Neurourology and Urodynamics Published by Wiley Periodicals, Inc.
Severe Maternal Morbidity and Postpartum Depressive Symptomatology: A Prospective Double Cohort Comparison Study
Authors: Norhayati Mohd Noor , Nik Hazlina Nik Hussain , Aniza Abd Aziz , Asrenee Ab Razak 
Published: July 2016

AbstractThe adverse consequences to mothers of postpartum depression are well‐documented, and risk factors are of interest. There is limited evidence on postpartum depression among women with severe maternal morbidity, defined as potentially life‐threatening conditions during pregnancy, childbirth, or soon after termination of pregnancy. We compared postpartum depressive symptoms of postpartum women aged 18 and older who delivered in two tertiary referral hospitals in 2014 in Kelantan, Malaysia, and had (n = 145) or had not (n = 187) suffered severe maternal morbidity. A prospective double cohort study design was applied. Postpartum depressive symptoms were assessed at 1 and 6 months postpartum using the Malay version of the Edinburgh Postnatal Depression Scale. There was no significant difference in the mean Edinburgh Postnatal Depression Scale score changes (p = .803) between the two groups of women, after adjusting for age, social support, physical health, occupation, and education. Factors other than severe medical complications should be pursued as predictors of postpartum depressive symptomatology. © 2016 Wiley Periodicals, Inc.