bluuebunny/crossref_metadata_2025_split huggingface dataset:
Computational Methods for Human Microbiome Analysis
Authors: Miossec Matthieu J. , Valenzuela Sandro L. , Mendez Katterinne N. , Castro‐Nallar Eduardo 
Published: November 2017

AbstractAs the field of microbiomics advances, the burden of computational work that scientists need to perform in order to extract biological insight has grown accordingly. Likewise, while human microbiome analyses are increasingly shifting toward a greater integration of various high‐throughput data types, a core number of methods form the basis of nearly every study. In this unit, we present step‐by‐step protocols for five core stages of human microbiome research. The protocols presented in this unit provide a base case for human microbiome analysis, complete with sufficient detail for researchers to tailor certain aspects of the protocols to the specificities of their data. © 2017 by John Wiley & Sons, Inc.
Leptospira: Molecular Detection of Pathogenic Species in Natural Sources
Authors: Beigel Brittney , Verma Ashutosh 
Published: November 2017

AbstractThis protocol describes a method for the rapid detection of leptospiral DNA in environmental water. In summary, the DNA is extracted from water samples and tested in a TaqMan‐based real‐time quantitative polymerase chain reaction (qPCR) for the presence of lipl32, a gene that is present only in pathogenic Leptospira spp. The gene target used in this assay is important in that it only detects pathogenic leptospires and not the saprophytic leptospires that may be present in environmental samples. © 2017 by John Wiley & Sons, Inc.
Beyond Solar Fuels: Renewable Energy‐Driven Chemistry
Authors: Lanzafame Paola , Abate Salvatore , Ampelli Claudio , Genovese Chiara , Passalacqua Rosalba , Centi Gabriele , Perathoner Siglinda 
Published: November 2017

AbstractThe future feasibility of decarbonized industrial chemical production based on the substitution of fossil feedstocks (FFs) with renewable energy (RE) sources is discussed. Indeed, the use of FFs as an energy source has the greatest impact on the greenhouse gas emissions of chemical production. This future scenario is indicated as “solar‐driven” or “RE‐driven” chemistry. Its possible implementation requires to go beyond the concept of solar fuels, in particular to address two key aspects: i) the use of RE‐driven processes for the production of base raw materials, such as olefins, methanol, and ammonia, and ii) the development of novel RE‐driven routes that simultaneously realize process and energy intensification, particularly in the direction of a significant reduction of the number of the process steps.
Long‐term antagonistic effect of increased precipitation and nitrogen addition on soil respiration in a semiarid steppe
Authors: Han Hongyan , Du Yue , Hui Dafeng , Jiang Lin , Zhong Mingxing , Wan Shiqiang 
Published: November 2017

AbstractChanges in water and nitrogen (N) availability due to climate change and atmospheric N deposition could have significant effects on soil respiration, a major pathway of carbon (C) loss from terrestrial ecosystems. A manipulative experiment simulating increased precipitation and atmospheric N deposition has been conducted for 9 years (2005–2013) in a semiarid grassland in Mongolian Plateau, China. Increased precipitation and N addition interactively affect soil respiration through the 9 years. The interactions demonstrated that N addition weakened the precipitation‐induced stimulation of soil respiration, whereas increased precipitation exacerbated the negative impacts of N addition. The main effects of increased precipitation and N addition treatment on soil respiration were 15.8% stimulated and 14.2% suppressed, respectively. Moreover, a declining pattern and 2‐year oscillation were observed for soil respiration response to N addition under increased precipitation. The dependence of soil respiration upon gross primary productivity and soil moisture, but not soil temperature, suggests that resources C substrate supply and water availability are more important than temperature in regulating interannual variations of soil C release in semiarid grassland ecosystems. The findings indicate that atmospheric N deposition may have the potential to mitigate soil C loss induced by increased precipitation, and highlight that long‐term and multi‐factor global change studies are critical for predicting the general patterns of terrestrial C cycling in response to global change in the future.
Weak whole‐plant trait coordination in a seasonally dry South American stressful environment
Authors: Silva José L. A. , Souza Alexandre F. , Caliman Adriano , Voigt Eduardo L. , Lichston Juliana E. 
Published: November 2017

AbstractA core question involving both plant physiology and community ecology is whether traits from different organs are coordinated across species, beyond pairwise trait correlations. The strength of within‐community trait coordination has been hypothesized to increase along gradients of environmental harshness, due to the cost of adopting ecological strategies out of the viable niche space supported by the abiotic conditions. We evaluated the strength of trait relationship and coordination in a stressful environment using 21 leaf and stem traits of 21 deciduous and evergreen woody species from a heath vegetation growing on coastal sandy plain in northeastern South America. The study region faces marked dry season, high soil salinity and acidity, and poor nutritional conditions. Results from multiple factor analyses supported two weak and independent axes of trait coordination, which accounted for 25%–29% of the trait variance using phylogenetically independent contrasts. Trait correlations on the multiple factor analyses main axis fit well with the global plant economic spectrum, with species investing in small leaves and dense stems as opposed to species with softer stems and large leaves. The species’ positions on the main functional axis corresponded to the competitor‐stress‐tolerant side of Grime's CSR triangle of plant strategies. The weak degree of trait coordination displayed by the heath vegetation species contradicted our expectation of high trait coordination in stressful environmental habitats. The distinct biogeographic origins of the species occurring in the study region and the prevalence of a regional environmental filter coupled with local homogeneous conditions could account for prevalence of trait independence we observed.
Evolution and comparative ecology of parthenogenesis in haplodiploid arthropods
Authors: van der Kooi Casper J. , Matthey-Doret Cyril , Schwander Tanja 
Published: November 2017

AbstractChanges from sexual reproduction to female-producing parthenogenesis (thelytoky) have great evolutionary and ecological consequences, but how many times parthenogenesis evolved in different animal taxa is unknown. We present the first exhaustive database covering 765 cases of parthenogenesis in haplodiploid (arrhenotokous) arthropods, and estimate frequencies of parthenogenesis in different taxonomic groups. We show that the frequency of parthenogenetic lineages extensively varies among groups (0–38% among genera), that many species have both sexual and parthenogenetic lineages and that polyploidy is very rare. Parthenogens are characterized by broad ecological niches: parasitoid and phytophagous parthenogenetic species consistently use more host species, and have larger, polewards extended geographic distributions than their sexual relatives. These differences did not solely evolve after the transition to parthenogenesis. Extant parthenogens often derive from sexual ancestors with relatively broad ecological niches and distributions. As these ecological attributes are associated with large population sizes, our results strongly suggests that transitions to parthenogenesis are more frequent in large sexual populations and/or that the risk of extinction of parthenogens with large population sizes is reduced. The species database presented here provides insights into the maintenance of sex and parthenogenesis in natural populations that are not taxon specific and opens perspectives for future comparative studies.
Synthesis of descriptive sensory attributes and hedonic rankings of dried persimmon (Diospyros kaki sp.)
Authors: Milczarek Rebecca R. , Woods Rachelle D. , LaFond Sean I. , Breksa Andrew P. , Preece John E. , Smith Jenny L. , Sedej Ivana , Olsen Carl W. , Vilches Ana M. 
Published: November 2017

AbstractThis work aimed to characterize the sensory attributes of hot air‐dried persimmon (Diospyros kaki) chips, correlate these attributes with consumer hedonic information, and, by doing so, present recommendations for cultivars that are most suitable for hot‐air drying. A trained sensory panel evaluated dried persimmon samples (representing 40 cultivars) for flavor, taste/aftertaste, and texture. In addition, in each of two tests conducted in different years, more than 100 consumers provided hedonic evaluations of 21 unique samples in a ranking task with a balanced incomplete block design. A partial least squares regression model correlating the mean hedonic ranking to the trained panel data was developed using the data from the first consumer panel. The predictions from the model were correlated with the second panel to verify the model. It was found that including taste, aftertaste, and texture data (but not specific flavor attribute data) produced a predictive model (Spearman's ρ=0.83). This indicates that flavor is likely secondary to taste and texture in dried persimmon chips. Using the validated predictive model, 6 of the 40 persimmon cultivars tested are recommended for a dried chip product; these cultivars are ‘Fuyu’, ‘Lycopersicon’, ‘Maekawa Jiro’, ‘Nishimura Wase’, ‘Tishihtzu’, and ‘Yotsumizo’.
Changing the shift system in a mining company: An intervention study
Authors: Castellucci H. I. , Altamirano I. 
Published: November 2017

AbstractThe aim of this study is to determine the shift system that allows for sustainable time management, considering the characteristics of the mining company analyzed. Regarding the methodology, the Standard Shiftwork Index was used to characterize the workers perceptions of the shift system. In order to increase the chances of changing the shift system, the Besiak method of shifts was applied to the following: modified 4 × 4 (current shift); 6 × 6 modified and 7 × 7. Furthermore, with input from company representatives, the method seeks to jointly identify the company's strengths, weaknesses, opportunities, and threats of the different shift systems. The main results show that the level in which the shift system (modified 4 × 4) interferes with leisure, social, and domestic life is associated with the city of residence. The application of Besiak concluded that the order of the highest risk to the lowest risk is as follows: 7 × 7, modified 6 × 6, and modified 4 × 4. Once the 7 × 7 shift work was discarded, a second level of analysis was performed between the two remaining shift work systems. Both have strengths, but the worker's place of residence on the days off became the determining factor. Hence, the 6 × 6 modified model met the biopsychosocial factors and favored residence in other cities during the days off. Finally, it was clear that during the shift system change, it is very important to involve workers, labor unions, and managers in the process of designing and introducing a new shift system.
Impaired expression of CXCL5 and matrix metalloproteinases in the lungs of mice with high susceptibility to Streptococcus pneumoniae infection
Authors: Mancuso Rubia I. , Miyaji Eliane N. , Silva Cristiane C.F. , Portaro Fernanda V. , Soares‐Schanoski Alessandra , Ribeiro Orlando G. , Oliveira Maria Leonor S. 
Published: November 2017

AbstractIntroductionStreptococcus pneumoniae colonizes the nasopharynx of healthy individuals establishing a commensal relationship with the host. In some conditions, bacteria invade the lower respiratory tract and innate immune responses are crucial to avoid diseases such as pneumonia, sepsis, or meningitis.MethodsHere, we compared the susceptibility to pneumococcal respiratory infection of two outbred mouse lines, AIRmin and AIRmax, selected for low or high acute inflammatory responses, respectively.ResultsAIRmin mice showed increased susceptibility to infection with different pneumococcal serotypes, when compared to AIRmax. Significant higher numbers of alveolar macrophages expressing the CD206 mannose receptor were observed in AIRmin mice when compared to AIRmax mice. Despite this difference, secretion of several cytokines and chemokines in the respiratory tract of AIRmin and AIRmax mice, after infection, was similar. The only exception was CXCL5, which was highly induced after pneumococcal infection in AIRmax mice but not in AIRmin mice. Reduced expression of the matrix metalloproteinases (MMP) 2, 3, 8, and 9, as well as reduced activities of MMPs were also observed in the lungs of AIRmin mice, after infection. Such impaired responses may have contributed to the low influx of neutrophils observed in the airways of these mice. Finally, high percentages of macrophages and neutrophils in apoptosis or necrosis, at the site of infection, were also observed in AIRmin mice, suggesting that leukocyte functionality is also compromised.ConclusionsOur results indicate that CXCL5 and MMPs contribute to the resistance to pneumococcal infection in mice.
FATHER PLAY: IS IT SPECIAL?
Authors: Cabrera Natasha J. , Roggman Lori 
Published: November 2017

ABSTRACTBoth mothers and fathers play with their children, but research on parent–child play interactions is conducted with mothers three times more often than it is with fathers. The articles in this special issue address this gap by focusing on the nature and quality of father–child play, across cultural contexts, and considering whether father play offers something unique and special for early human development, in infancy or early childhood. The studies show that fathers can be just as developmentally supportive as are mothers in terms of being playful and engaged with their children in ways that are related to greater child socioemotional competence, emotion regulation, and vocabulary, and to less aggression, anxiety, and negativity. We encourage future research to examine the cultural influences, family system dynamics, and specificity of timing and types of father–child play in relation to children's developmental competence.
Assessment of hydrogels for bioprinting of endothelial cells
Authors: Benning Leo , Gutzweiler Ludwig , Tröndle Kevin , Riba Julian , Zengerle Roland , Koltay Peter , Zimmermann Stefan , Stark G. Björn , Finkenzeller Günter 
Published: November 2017

AbstractIn tissue engineering applications, vascularization can be accomplished by coimplantation of tissue forming cells and endothelial cells (ECs), whereby the latter are able to form functional blood vessels. The use of three‐dimensional (3D) bioprinting technologies has the potential to improve the classical tissue engineering approach because these will allow the generation of scaffolds with high spatial control of endothelial cell allocation. This study focuses on a side by side comparison of popular commercially available bioprinting hydrogels (Matrigel, fibrin, collagen, gelatin, agarose, Pluronic F‐127, alginate, and alginate/gelatin) in the context of their physicochemical parameters, their swelling/degradation characteristics, their biological effects on vasculogenesis‐related EC parameters and their printability. The aim of this study was to identify the most suitable hydrogel or hydrogel combination for inkjet printing of ECs to build prevascularized tissue constructs. Most tested hydrogels displayed physicochemical characteristics suitable for inkjet printing. However, Pluronic F‐127 and the alginate/gelatin blend were rapidly degraded when incubated in cell culture medium. Agarose, Pluronic F‐127, alginate and alginate/gelatin hydrogels turned out to be unsuitable for bioprinting of ECs because of their non‐adherent properties and/or their incapability to support EC proliferation. Gelatin was able to support EC proliferation and viability but was unable to support endothelial cell sprouting. Our experiments revealed fibrin and collagen to be most suitable for bioprinting of ECs, because these hydrogels showed acceptable swelling/degradation characteristics, supported vasculogenesis‐related EC parameters and showed good printability. Moreover, ECs in constructs of preformed spheroids survived the printing process and formed capillary‐like cords. © 2017 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 106A: 935–947, 2018.
Palovarotene Inhibits Osteochondroma Formation in a Mouse Model of Multiple Hereditary Exostoses
Authors: Inubushi Toshihiro , Lemire Isabelle , Irie Fumitoshi , Yamaguchi Yu 
Published: November 2017

ABSTRACT

Multiple hereditary exostoses (MHE), also known as multiple osteochondromas (MO), is an autosomal dominant disorder characterized by the development of multiple cartilage-capped bone tumors (osteochondromas). The large majority of patients with MHE carry loss-of-function mutations in the EXT1 or EXT2 gene, which encodes a glycosyltransferase essential for heparan sulfate (HS) biosynthesis. Increasing evidence suggests that enhanced bone morphogenetic protein (BMP) signaling resulting from loss of HS expression plays a role in osteochondroma formation in MHE. Palovarotene (PVO) is a retinoic acid receptor γ selective agonist, which is being investigated as a potential drug for fibrodysplasia ossificans progressiva (FOP), another genetic bone disorder with features that overlap with those of MHE. Here we show that PVO inhibits osteochondroma formation in the Fsp1Cre;Ext1flox/flox model of MHE. Four-week daily treatment with PVO starting at postnatal day (P) 14 reduced the number of osteochondromas that develop in these mice by up to 91% in a dose-dependent manner. An inhibition of long bone growth observed in animals treated from P14 was almost entirely abrogated by delaying the initiation of treatment to P21. We also found that PVO attenuates BMP signaling in Fsp1Cre;Ext1flox/flox mice and that aberrant chondrogenic fate determination of Ext1-deficient perichondrial progenitor cells in these mice is restored by PVO. Together, the present data support further preclinical and clinical investigations of PVO as a potential therapeutic agent for MHE. © 2017 American Society for Bone and Mineral Research.
Nutritional status is associated with the return home in a long‐term care health facility
Authors: Nishida Yuri , Wakabayashi Hidetaka , Maeda Keisuke , Nishioka Shinta 
Published: November 2017

AbstractBackgroundThe purpose of this study was to determine the association between nutritional status and the return home of older people living in a long‐term care health facility (LCHF).MethodsA nested case control study was performed in 116 people ≥65 years of age in a single LCHF. Nutritional status was assessed using the Mini Nutritional Assessment Short Form (MNA‐SF) and activities of daily living by the Functional Independence Measure (FIM). The return home, duration of rehabilitation, and the family wanting the patient to return home were obtained from clinical records. Multivariate logistic regression analysis was used to assess whether malnutrition had independent effects on the return home.ResultsThe participants included 36 males and 80 females with a mean age of 82 years. Thirty‐seven people returned home while 79 did not. The MNA‐SF showed that 80 subjects were malnourished. Sixty‐six of the participants received rehabilitation for longer than 1 hour per week, while 50 received rehabilitation for <1 hour. The proportion of subjects with malnutrition who returned home was significantly lower (P = .003) than in participants who did not return home. Multivariate logistic regression analysis showed that malnutrition (adjusted odds ratio [AOR], 0.23; 95% confidence interval [CI], 0.08‐0.65; P = .006), total FIM score (AOR, 1.03; 95% CI, 1.01‐1.06; P = .012), and the family wanting the patient to return home (AOR, 9.46; 95% CI, 3.19‐28.12; P < .001) were independently associated with the return home.ConclusionsNutritional status is associated with the return home in older people living in LCHF.
Ultrasound Features of Breast Cancer for Predicting Axillary Lymph Node Metastasis
Authors: Guo Qiang , Dong Zhiwu , Zhang Lei , Ning Chunping , Li Ziyao , Wang Dongmo , Liu Chong , Zhao Ming , Tian Jiawei 
Published: November 2017

ObjectivesThe purpose of this study was to assess the clinical value of ultrasound (US) features of breast lesions for predicting the risk of axillary lymph node metastasis in patients with breast cancer.MethodsIn this retrospective study, 425 patients with breast cancer were recruited, and their preoperative US features and postoperative pathologic results were collected. The association of these US features of breast cancer with axillary lymph node metastasis was determined by univariate and multivariate analyses.ResultsAmong the 425 patients, 200 (47.1%) had axillary lymph node metastasis, and 225 (52.9%) did not. The parameters of tumor shape, color Doppler flow imaging grades, histologic grade, and E‐cadherin level were significantly and independently associated with axillary lymph node metastasis (P < .05 for all).ConclusionsAxillary lymph node metastasis was prone to happen in patients with US features of an irregular tumor shape and higher color Doppler flow imaging grades. Ultrasound imaging provides a promising tool for predicting axillary lymph node metastasis in patients with breast cancer.
Community Health Workers Supporting Clinical Pharmacists in Diabetes Management: A Randomized Controlled Trial
Authors: Sharp Lisa K. , Tilton Jessica J. , Touchette Daniel R. , Xia Yinglin , Mihailescu Daniel , Berbaum Michael L. , Gerber Ben S. 
Published: November 2017

ObjectivesTo evaluate the effectiveness of clinical pharmacists and community health workers (CHWs) in improving glycemic control within a low‐income ethnic minority population.MethodsIn a two‐arm 2‐year crossover trial, 179 African‐American and 65 Hispanic adult patients with uncontrolled diabetes mellitus (hemoglobin A1c [HbA1C] of 8% or higher) were randomized to CHW support either during the first or second year of the study. All participants received clinical pharmacist support for both years of the study. The primary outcome was change in HbA1C over 1 and 2 years.ResultsSimilar HbA1C declines were noted after receiving the 1 year of CHW support: −0.45% (95% confidence interval [CI] −0.96 to 0.05) with CHW versus −0.42% (95% CI −0.93 to 0.08) without CHW support. In addition, no differences were noted in change on secondary outcome measures including body mass index, systolic blood pressure, high‐density lipoprotein and low‐density lipoprotein cholesterol, quality of life, and perceived social support. A difference in diastolic blood pressure change was noted: 0.80 mm Hg (95% CI −1.92 to 3.53) with CHW versus −1.85 mm Hg (95% CI −4.74 to 1.03) without CHW support (p=0.0078). Patients receiving CHW support had more lipid‐lowering medication intensifications (0.39 [95% CI 0.27–0.52]) compared with those without CHW support (0.26 [95% CI 0.14–0.38], p<0.0001). However, no significant differences in intensification of antihyperglycemic and antihypertensive medications were observed between patients receiving CHW support and those without CHW support. Patients with low health literacy completed significantly more encounters with the pharmacist and CHW than those with high health literacy, although outcomes were comparable.ConclusionsNo significant differences were noted between a clinical pharmacist–CHW team and clinical pharmacist alone in improving glycemic control within a low‐income ethnic minority population.