bluuebunny/crossref_metadata_2025_split huggingface dataset:
Human Milk MicroRNA and Total RNA Differ Depending on Milk Fractionation
Authors: Alsaweed Mohammed , Hepworth Anna R. , Lefèvre Christophe , Hartmann Peter E. , Geddes Donna T. , Hassiotou Foteini 
Published: April 2015

ABSTRACTMicroRNA have been recently discovered in human milk signifying potentially important functions for both the lactating breast and the infant. Whilst human milk microRNA have started to be explored, little data exist on the evaluation of sample processing, and analysis to ensure that a full spectrum of microRNA can be obtained. Human milk comprises three main fractions: cells, skim milk, and lipids. Typically, the skim milk fraction has been measured in isolation despite evidence that the lipid fraction may contain more microRNA. This study aimed to standardize isolation of microRNA and total RNA from all three fractions of human milk to determine the most appropriate sampling and analysis procedure for future studies. Three different methods from eight commercially available kits were tested for their efficacy in extracting total RNA and microRNA from the lipid, skim, and cell fractions of human milk. Each fraction yielded different concentrations of RNA and microRNA, with the highest quantities found in the cell and lipid fractions, and the lowest in skim milk. The column‐based phenol‐free method was the most efficient extraction method for all three milk fractions. Two microRNAs were expressed and validated in the three milk fractions by qPCR using the three recommended extraction kits for each fraction. High expression levels were identified in the skim and lipid milk factions for these microRNAs. These results suggest that careful consideration of both the human milk sample preparation and extraction protocols should be made prior to embarking upon research in this area. J. Cell. Biochem. 116: 2397–2407, 2015. © 2015 The Authors. Journal of Cellular Biochemistry Published by Wiley Periodicals, Inc.
CYP2D6 predicted metabolizer status and safety in adult patients with attention‐deficit hyperactivity disorder participating in a large placebo‐controlled atomoxetine maintenance of response clinical trial
Authors: Fijal Bonnie A. , Guo Yingying , Li Si G. , Ahl Jonna , Goto Taro , Tanaka Yoko , Nisenbaum Laura K. , Upadhyaya Himanshu P. 
Published: April 2015

AbstractAtomoxetine, which is indicated for treatment of attention‐deficit hyperactivity disorder (ADHD), is predominantly metabolized by genetically polymorphic cytochrome P450 2D6 (CYP2D6). Based on identified CYP2D6 genotypes, individuals can be categorized into 4 phenotypic metabolizer groups as ultrarapid, extensive, intermediate, and poor. Previous studies have focused on observed differences between poor and extensive metabolizers, but it is not well understood whether the safety profile of intermediate metabolizers differs from that of ultrarapid and extensive metabolizers. This study compared safety and tolerability among the different CYP2D6 metabolizer groups in the 12‐week open‐label phase of an atomoxetine study in adult patients with ADHD. Genotyping identified 1039 patients as extensive/ultrarapid metabolizers, 780 patients as intermediate metabolizers, and 117 patients as poor metabolizers. Common (≥5% frequency) treatment‐emergent adverse events did not significantly differ between extensive/ultrarapid and intermediate metabolizers (odds ratios were <2.0 or >0.5). Poor metabolizers had higher frequencies of dry mouth, erectile dysfunction, hyperhidrosis, insomnia, and urinary retention compared with the other metabolizer groups. There were no significant differences between extensive/ultrarapid and intermediate metabolizers in changes from baseline in vital signs. These results suggest that data from CYP2D6 intermediate and extensive/ultrarapid metabolizers can be combined when considering safety analyses related to atomoxetine.
Soil Microbial Functions After Forest Fires Affected by the Compost Quality
Authors: Guénon René , Gros Raphaël 
Published: April 2015

AbstractComposts are frequently used to restore various degraded lands especially after fire. We investigated how different organic amendments after frequent wildfires can affect soil microbial functions. We crossed three times since fire (1, 5 and 18 years) with three different compost qualities (i.e. young, intermediate and old). After 5 months, alkaline phosphatase increased by the intermediate compost in early post‐fire chronosequence (1 and 5 year after fires). This increase was confirmed 10 months after amendment with the three composts but only for the most recent fire. The net nitrification increased 5 months after amendment under both the young and intermediate composts in the 5 and 18 years of time since fire plots. This increase was confirmed 10 months after amendment with the intermediate and old compost treatments for the 1 and 5 years of time since fire plots. In this case, compost amendment even induced positive nitrification rates for the 5 years of time since fire plots. Moreover, older composts affected catabolic diversity after 5 months, whereas at the same time, we detected an increase in biomass of cultivable bacteria. Urease activity gradually increased with the age of composts after 10 months. β‐glucosidase activity increased under the young and intermediate composts and did not change with the older. This study suggests compost addition can result in an artificial acceleration of the nutrient cycles. Thus organic amendments in burned ecosystems should be reasoned according to both the step of the Mediterranean post‐fire recovery and the quality of organic amendments. Copyright © 2015 John Wiley & Sons, Ltd.
Contrasting spatial patterns and ecological attributes of soil bacterial and archaeal taxa across a landscape
Authors: Constancias Florentin , Saby Nicolas P. A. , Terrat Sébastien , Dequiedt Samuel , Horrigue Wallid , Nowak Virginie , Guillemin Jean‐Philippe , Biju‐Duval Luc , Chemidlin Prévost‐Bouré Nicolas , Ranjard Lionel 
Published: April 2015

AbstractEven though recent studies have clarified the influence and hierarchy of environmental filters on bacterial community structure, those constraining bacterial populations variations remain unclear. In consequence, our ability to understand to ecological attributes of soil bacteria and to predict microbial community response to environmental stress is therefore limited. Here, we characterized the bacterial community composition and the various bacterial taxonomic groups constituting the community across an agricultural landscape of 12 km2, by using a 215 × 215 m systematic grid representing 278 sites to precisely decipher their spatial distribution and drivers at this scale. The bacterial and Archaeal community composition was characterized by applying 16S rRNA gene pyrosequencing directly to soil DNA from samples. Geostatistics tools were used to reveal the heterogeneous distribution of bacterial composition at this scale. Soil physical parameters and land management explained a significant amount of variation, suggesting that environmental selection is the major process shaping bacterial composition. All taxa systematically displayed also a heterogeneous and particular distribution patterns. Different relative influences of soil characteristics, land use and space were observed, depending on the taxa, implying that selection and spatial processes might be differentially but not exclusively involved for each bacterial phylum. Soil pH was a major factor determining the distribution of most of the bacterial taxa and especially the most important factor explaining the spatial patterns of α‐Proteobacteria and Planctomycetes. Soil texture, organic carbon content and quality were more specific to a few number of taxa (e.g., β‐Proteobacteria and Chlorobi). Land management also influenced the distribution of bacterial taxa across the landscape and revealed different type of response to cropping intensity (positive, negative, neutral or hump‐backed relationships) according to phyla. Altogether, this study provided valuable clues about the ecological behavior of soil bacterial and archaeal taxa at an agricultural landscape scale and could be useful for developing sustainable strategies of land management.
Development of a Chemical Methodology for the Preparation of Peptide Thioesters Applicable to Naturally Occurring Peptides Using a Sequential Quadruple Acyl Transfer System
Authors: Tsuda Yusuke , Shigenaga Akira , Tsuji Kohei , Denda Masaya , Sato Kohei , Kitakaze Keisuke , Nakamura Takahiro , Inokuma Tsubasa , Itoh Kohji , Otaka Akira 
Published: April 2015

AbstractPeptide thioesters are very useful in protein chemistry, and chemistry‐ and biochemistry‐based protocols are used for the preparation of thioesters. Among such protocols, only a few biochemistry‐based approaches have been use for naturally occurring peptide sequences. The development of chemistry‐based protocols applicable to natural sequences remains a challenge, and the development of such methods would be a major contribution to protein science. Here, we describe the preparation of peptide thioesters using innovative methodology that features nickel(II)‐mediated alcoholysis of a naturally occurring peptide sequence, followed by O−N and N−S acyl transfers. This protocol involves sequential quadruple acyl transfer, termed SQAT. Notably, the SQAT system consists of sequential chemical reactions that allow naturally occurring peptide sequences to be converted to thioesters without requiring an artificial chemical unit.
Hillslope‐Scale Variability in Seasonal Frost Depth and Soil Water Content Investigated by GPR on the Southern Margin of the Sporadic Permafrost Zone on the Tibetan Plateau
Authors: Ma Yingzhao , Zhang Yinsheng , Zubrzycki Sebastian , Guo Yanhong , Farhan Suhaib Bin 
Published: April 2015

AbstractGround temperature data show that permafrost has recently been absent at a site on the southern edge of the sporadic permafrost zone on the Tibetan Plateau (TP). A detailed survey of seasonal frost depth (SFD) and soil water content (SWC) here is significant for understanding the hydrological response to thawing permafrost. However, little is known about the spatial heterogeneity of SFD and SWC at the hillslope scale in this vulnerable permafrost region. Thus, high‐frequency ground‐penetrating radar (GPR) was applied to a field site that varied in terms of topography (slope, aspect and elevation) and surface environments (vegetation cover and stream presence). The GPR data and accompanying field observations of gravimetric water content and frost depth revealed a spatial variation at the hillslope scale in SFD and SWC, and indicated that topography, vegetation and stream distribution significantly influence the patterns observed. The average SFD was much deeper along the north‐facing slope, compared to the south‐facing slope in early May, and its thickness varied considerably with altitude along each slope. An increase in the extent of vegetation cover correlated with decreasing SFD. The SWC at shallow depth was higher along the south‐facing slope than along the north‐facing slope at the beginning of the thawing period. For slopes of both aspects, the SWC vertical profiles exhibited a similar variability, with SWC decreasing with depth, but at different rates. This study demonstrates that GPR provides an appropriate method for quantifying SWC at the hillslope scale on the TP. Copyright © 2015 John Wiley & Sons, Ltd.
The performance of fine‐grained and coarse‐grained elastic network models and its dependence on various factors
Authors: Na Hyuntae , Song Guang 
Published: April 2015

ABSTRACTIn a recent work we developed a method for deriving accurate simplified models that capture the essentials of conventional all‐atom NMA and identified two best simplified models: ssNMA and eANM, both of which have a significantly higher correlation with NMA in mean square fluctuation calculations than existing elastic network models such as ANM and ANMr2, a variant of ANM that uses the inverse of the squared separation distances as spring constants. Here, we examine closely how the performance of these elastic network models depends on various factors, namely, the presence of hydrogen atoms in the model, the quality of input structures, and the effect of crystal packing. The study reveals the strengths and limitations of these models. Our results indicate that ssNMA and eANM are the best fine‐grained elastic network models but their performance is sensitive to the quality of input structures. When the quality of input structures is poor, ANMr2 is a good alternative for computing mean‐square fluctuations while ANM model is a good alternative for obtaining normal modes. Proteins 2015; 83:1273–1283. © 2015 Wiley Periodicals, Inc.
Crystal structure of the protein At3g01520, a eukaryotic universal stress protein‐like protein from arabidopsis thaliana in complex with AMP
Authors: Kim Do Jin , Bitto Eduard , Bingman Craig A. , Kim Hyun‐Jung , Han Byung Woo , Phillips George N. 
Published: April 2015

ABSTRACTMembers of the universal stress protein (USP) family are conserved in a phylogenetically diverse range of prokaryotes, fungi, protists, and plants and confer abilities to respond to a wide range of environmental stresses. Arabidopsis thaliana contains 44 USP domain‐containing proteins, and USP domain is found either in a small protein with unknown physiological function or in an N‐terminal portion of a multi‐domain protein, usually a protein kinase. Here, we report the first crystal structure of a eukaryotic USP‐like protein encoded from the gene At3g01520. The crystal structure of the protein At3g01520 was determined by the single‐wavelength anomalous dispersion method and refined to an R factor of 21.8% (Rfree = 26.1%) at 2.5 Å resolution. The crystal structure includes three At3g01520 protein dimers with one AMP molecule bound to each protomer, comprising a Rossmann‐like α/β overall fold. The bound AMP and conservation of residues in the ATP‐binding loop suggest that the protein At3g01520 also belongs to the ATP‐binding USP subfamily members. Proteins 2015; 83:1368–1373. © 2015 The Authors. Proteins: Structure, Function, and Bioinformatics Published by Wiley Periodicals, Inc.
Corporate spinoffs and analysts' coverage decisions: The implications for diversified firms
Authors: Feldman Emilie R. 
Published: April 2015

Research summary: This paper investigates how spinoffs improve the quality of analysts' research about diversified firms, theorizing that these deals may induce analysts to revisit their earlier coverage decisions. The gains resulting from these shifts are expected to be more pronounced when a firm undertakes a legacy (rather than a non‐legacy) spinoff, which removes the business that may be constraining analysts' coverage decisions in the first place. Consistent with this argument, firms that undertake legacy spinoffs experience greater improvements in the composition and quality of their analyst coverage than their non‐legacy counterparts, and in their overall forecast accuracy and stock market performance. Taken together, these findings shed light on the relationships among the scope decisions, analyst coverage, and valuations of diversified firms.Managerial summary: Existing research has established that when companies undertake spinoffs, analysts produce more accurate forecasts about the divesting firms than they did prior to those deals, and the stock market performance of those firms also improves relative to pre‐spinoff levels. This paper explores the effects of legacy spinoffs (the spinoff of a firm's original or “legacy” business) for forecast accuracy and stock market performance. Firms that undertake legacy spinoffs are found to enjoy greater improvements in forecast accuracy and stock market performance than their non‐legacy counterparts. These findings are driven by the fact that legacy spinoffs induce analysts to revisit their existing coverage decisions to a greater extent than non‐legacy spinoffs, contributing significantly to the economic benefits of these deals for shareholders. Copyright © 2015 John Wiley & Sons, Ltd.
Pro-Insulin-Like Growth Factor-II Ameliorates Age-Related Inefficient Regenerative Response by Orchestrating Self-Reinforcement Mechanism of Muscle Regeneration
Authors: Ikemoto-Uezumi Madoka , Uezumi Akiyoshi , Tsuchida Kunihiro , Fukada So-ichiro , Yamamoto Hiroshi , Yamamoto Naoki , Shiomi Kosuke , Hashimoto Naohiro 
Published: April 2015

Abstract
Sarcopenia, age-related muscle weakness, increases the frequency of falls and fractures in elderly people, which can trigger severe muscle injury. Rapid and successful recovery from muscle injury is essential not to cause further frailty and loss of independence. In fact, we showed insufficient muscle regeneration in aged mice. Although the number of satellite cells, muscle stem cells, decreases with age, the remaining satellite cells maintain the myogenic capacity equivalent to young mice. Transplantation of young green fluorescent protein (GFP)-Tg mice-derived satellite cells into young and aged mice revealed that age-related deterioration of the muscle environment contributes to the decline in regenerative capacity of satellite cells. Thus, extrinsic changes rather than intrinsic changes in satellite cells appear to be a major determinant of inefficient muscle regeneration with age. Comprehensive protein expression analysis identified a decrease in insulin-like growth factor-II (IGF-II) level in regenerating muscle of aged mice. We found that pro- and big-IGF-II but not mature IGF-II specifically express during muscle regeneration and the expressions are not only delayed but also decreased in absolute quantity with age. Supplementation of pro-IGF-II in aged mice ameliorated the inefficient regenerative response by promoting proliferation of satellite cells, angiogenesis, and suppressing adipogenic differentiation of platelet derived growth factor receptor (PDGFR)α+ mesenchymal progenitors. We further revealed that pro-IGF-II but not mature IGF-II specifically inhibits the pathological adipogenesis of PDGFRα+ cells. Together, these results uncovered a distinctive pro-IGF-II-mediated self-reinforcement mechanism of muscle regeneration and suggest that supplementation of pro-IGF-II could be one of the most effective therapeutic approaches for muscle injury in elderly people. Stem Cells 2015;33:2456—2468
Feasibility study of ED‐XRF analysis of atmospheric particulate matter samples collected with high time resolution
Authors: Giannoni M. , Calzolai G. , Chiari M. , Lucarelli F. , Mazzinghi A. , Nava S. , Ruberto C. 
Published: April 2015

This study aims at verifying the feasibility of the analysis of particulate matter samples collected with hourly time resolution by a Streaker sampler device, using cheaper and more affordable instrumentations like energy dispersive X‐ray fluorescence (ED‐XRF) spectrometers. The ‘hourly’ samples are not analysable with the available commercial laboratory ED‐XRF spectrometers, because the aerosol deposit forms a continuous streak that has to be analysed ‘point‐by‐point’ with a collimated beam of a few mm size. For this specific application, a custom‐made compact XRF spectrometer, designed at the INFN LABEC laboratory in Florence and typically used for in‐situ analysis of cultural heritage, has been used. This ED‐XRF system is based on the combined use of two X‐ray tubes with different anodes (Mo and Ti), a 30‐mm2 silicon drift detector and a helium flow to reduce the attenuation of low energy X‐rays.A set of elemental thin standards containing elements from Na to Pb has been analysed in order to determine the best experimental conditions, the sensitivity and the detection limits of this system. The results of quantitative analysis on certified aerosol samples, on particulate matter samples collected for 24 h by a low volume sampler and on Streaker samples (‘fine’ fraction, PM2.5) are in good agreement with those obtained by PIXE and polarized optics ED‐XRF measurements. This study demonstrates that a specialized custom‐made ED‐XRF system may represent a promising solution for elemental analysis of Streaker samples, even for low‐Z elements, although PIXE technique still remains unrivalled as regards sensitivity and measurement throughput. Copyright © 2015 John Wiley & Sons, Ltd.
The prognostic value of the head-shaft angle on hip displacement in children with cerebral palsy
Authors: van der List J. P. J. , Witbreuk M. M. , Buizer A. I. , van der Sluijs J. A. 
Published: April 2015

Background Hip displacement is the second most common deformity in cerebral palsy (CP). The risk for hip displacement is related to the Gross Motor Function Classification System (GMFCS). Recently, the head-shaft angle (HSA) has been identified as a predictor for hip displacement and the aim of this study is to assess the predictive value of the HSA for hip displacement in CP. Methods In this retrospective cohort, we performed radiological measurements in 50 children on both hips. In children with GMFCS level II (30 hips), III (30 hips), IV (20 hips) and V (20 hips), we measured the HSA and migration percentage (MP) in three age intervals: age two years (T1), age four years (T2) and age seven years (T3). Results At T1, the HSA was larger (more valgus) in hips that will displace than in hips that will not displace (174° vs. 166°; p = 0.001) and was also larger in higher GMFCS levels (IV–V vs. II–III) (172° vs. 165°; p < 0.001). At T1, GMFCS [odds ratio (OR) 14.7; p = 0.001] and HSA (OR 1.102; p = 0.043) were predictors for hip displacement at T3, but at T2, MP (OR 1.071; p = 0.010) was the only predictor for hip displacement at T3. Conclusions The HSA at two years is larger in hips that will displace and larger in children with higher GMFCS levels (IV–V). At age two years, GMFCS and HSA are valuable predictors for hip displacement, but at the age of four years, only MP should be used in the prediction of hip displacement. Level of evidence Prognostic study, level II.
Multidrug-Resistant Gram-Negative Bacteria: Inter- and Intradissemination Among Nursing Homes of Residents With Advanced Dementia
Authors: D’Agata Erika M. C. , Habtemariam Daniel , Mitchell Susan 
Published: April 2015

OBJECTIVETo quantify the extent of inter– and intra–nursing home transmission of multidrug-resistant gram-negative bacteria (MDRGN) among residents with advanced dementia and characterize MDRGN colonization among these residents.DESIGNProspective cohort study.SETTINGTwenty-two nursing homes in the greater Boston, Massachusetts, area.PATIENTSResidents with advanced dementia.METHODSSerial rectal surveillance cultures for MDRGN and resident characteristics were obtained every 3 months for 12 months or until death. Molecular typing of MDRGN isolates was performed by pulsed-field gel electrophoresis.RESULTSA total of 190 MDRGN isolates from 152 residents with advanced dementia were included in the analyses. Both intra– and inter–nursing home transmission were identified. Genetically related MDRGN strains, recovered from different residents, were detected in 18 (82%) of the 22 nursing homes. The percent of clonally related strains in these nursing homes ranged from 0% to 86% (average, 35%). More than 50% of strains were clonally related in 3 nursing homes. Co-colonization with more than 1 different MDRGN species occurred among 28 residents (18.4%). A total of 168 (88.4%), 20 (10.5%), and 2 (1.0%) of MDRGN isolates were resistant to 3, 4, and 5 different antimicrobials or antimicrobial classes, respectively.CONCLUSIONSMDRGN are spread both within and between nursing homes among residents with advanced dementia. Infection control interventions should begin to target this high-risk group of nursing home residents.Infect Control Hosp Epidemiol2015;36(8):930–935