bluuebunny/crossref_metadata_2025_split huggingface dataset:
Risk of acute renal failure and mortality after surgery for a fracture of the hip
Authors: Pedersen A. B. , Christiansen C. F. , Gammelager H. , Kahlert J. , Sørensen H. T. 
Published: August 2016

Aims We examined risk of developing acute renal failure and the associated mortality among patients aged > 65 years undergoing surgery for a fracture of the hip. Patients and Methods We used medical databases to identify patients who underwent surgical treatment for a fracture of the hip in Northern Denmark between 2005 and 2011. Acute renal failure was classified as stage 1, 2 and 3 according to the Kidney Disease Improving Global Outcome criteria. We computed the risk of developing acute renal failure within five days after surgery with death as a competing risk, and the short-term (six to 30 days post-operatively) and long-term mortality (31 days to 365 days post-operatively). We calculated adjusted hazard ratios (HRs) for death with 95% confidence intervals (CIs). Results Among 13 529 patients who sustained a fracture of the hip, 1717 (12.7%) developed acute renal failure post-operatively, including 1218 (9.0%) with stage 1, 364 (2.7%) with stage 2, and 135 (1.0%) with stage 3 renal failure. The short-term mortality was 15.9% and 5.6% for patients with and without acute renal failure, respectively (HR 2.8, 95% CI 2.4 to 3.2). The long-term mortality was 25.0% and 18.3% for those with and without acute renal failure, respectively (HR 1.3, 95% CI 1.2 to 1.5). The mortality was higher in patients with an increased severity of renal failure. Conclusion Acute renal failure is a common complication of surgery in elderly patients who sustain a fracture of the hip, and is associated with increased mortality up to one year after surgery despite adjustment for coexisting comorbidity and medication before surgery. Cite this article: Bone Joint J 2016;98-B:1112–18.
Tailoring the Surface Properties of Synthetic Clays Via Intercalation, Grafting, or In Situ Incorporation of Organic Moities
Authors: Brendlé Jocelyne 
Published: August 2016

Abstract
The present chapter is devoted to recent developments in the area of surface modifications of commercially available synthetic clays by post treatments (i.e. intercalation or grafting) and by one-pot synthesis through a sol-gel process. Special attention is paid to the modifications aimed at forming pillared clays, organoclays, and organic-inorganic hybrids with a 2:1 layered structure. The different approaches are described and debated. The properties of the materials obtained are also discussed.
Sulfonic Acid-Functionalized α-Zirconium Phosphate Single-Layer Nanosheets for Catalysis and Fuel-Cell Applications
Authors: Zhou Yingjie , Hu Hang , Huang Rongcai , Ding Fuchuan , Liu Jingjing , Brittain Alex D. , Zhang Meng , Xiao Min , Meng Yuezhong , Sun Luyi 
Published: August 2016

Abstract
In this work, we explored to The grafting of thiol group- terminated chains onto single- layer α-zirconium phosphate (ZrP) nanosheets, which were subsequently oxidized to sulfonic- acid groups, was examined here. The sulfuric acid- functionalized ZrP nanosheets were thoroughly characterized extensively and the results proved that sulfonic acid group- terminated chains were successfully grafted successfully onto the ZrP nanosheets surfaces with a high significant loading density. Such Such a strong a solid acid, based on inorganic nanosheets, can be well dispersed in polar solvents, leading to high good access to the acid functional groups. The acid Meanwhile, it can also be easily separated easily from the dispersion system by centrifugation or filtration. The sulfonic acid- functionalized ZrP nanosheets can serve as an effective heterogeneous catalyst for various reactions (such as the Baeyer-Villiger oxidation). The nanosheets y were also incorporated into proton- exchange membranes to form composite membranes, which exhibited excellent performance in single- cell evaluation, showing promiseing for fuel-cell applications.
Las guías urbanas: imagen e invención del espacio de la ciudad de México
Authors: Mendoza Vargas Héctor 
Published: August 2016

<p>Este artículo analiza las guías urbanas como una producción cultural que “impone a los viajeros” una percepción espacial de la Ciudad de México (Diego, 2014:60). El análisis centra la atención en los cambios geográficos registrados en las guías bajo una amplia temporalidad de estudio, desde finales del siglo XVIII, al XIX y hasta 1940. Se presenta el espacio del andar y el descubrimiento de la ciudad en las guías hasta 1854; los primeros cambios se detectan de la función administrativa y comercial, en la guía de 1882, a los primeros itinerarios urbanos en la edición de 1891; Interesa situar el panegírico material de la ciudad y las miserias urbanas, de la guía de 1901, en el contexto de relativa paz y tranquilidad del Porfiriato. Se propone una integración interpretativa para situar el cambio de la percepción espacial en una escala temporal, entre los itinerarios urbanos de la guía de 1891 y los circuitos regionales de la guía de 1940 del Valle de México.</p><p> </p>
The production of vulnerability to landslides: the risk habitus in two landslide-prone neighborhoods in Teziutlan, Mexico
Authors: Hernández Aguilar Bertha , Ruiz Rivera Naxhelli 
Published: August 2016

Este artículo es un análisis de algunas de las condiciones que reproducen la vulnerabilidad social ante deslizamientos de ladera en dos asentamientos de la ciudad de Teziutlán, Puebla. La propuesta presentada parte del conocimiento de las percepciones, valoraciones y acciones que reproducen condiciones de riesgo a partir de la propuesta conceptual de <em>habitus de riesgo</em>, a partir de la perspectiva sociológica de Pierre Bourdieu. Este marco conceptual aporta elementos para comprender las lógicas que imperan en los habitantes de los asentamientos de Teziutlán ante situaciones potenciales de riesgo por deslizamientos de ladera. La propuesta que aquí se desarrolla busca interpretar comparativamente las condiciones que reproducen la vulnerabilidad a partir del análisis cuantitativo del capital social, cultural y simbólico (basado en redes familiares, solidaridad entre vecinos, confianza a las autoridades, las experiencias de situaciones de desastres, percepción del riesgo y el tiempo de residencia en la vivienda actual) de las dos comunidades en estudio. Los resultados muestran que las valoraciones sobre el nivel de preparación para enfrentar una situación de riesgo son determinantes para explicar su vulnerabilidad, sin importar el nivel de la exposición a la amenaza al que estén sujetos. Esto se relaciona con el alto nivel de confianza que tienen hacia las autoridades locales, así como la seguridad de que estas autoridades los ayudaran en una situación de desastre. Por otro lado, la población de ambas comunidades manifiesta expectativas altas de que sufrirán daños en condiciones similares si ocurriera un evento de desastre como en el pasado, aun cuando ambas comunidades tienen distintos niveles de exposición a deslizamientos. En ambos casos, la población cree fuertemente en su capacidad de respuesta antes deslizamientos de ladera, a pesar de que ninguna de las comunidades invierte tiempo o recursos en prevención.
CHEMICAL COMPOSITION OF WOOD ESSENTIAL OIL OF Aniba cinnamomiflora C. K. Allen FROM VENEZUELAN ANDES
Authors: Marcano Enid Esperanza , Padilla-Baretic Adriana , Rojas-Fermín Luis , Mora-Vivas Flor D. , Ferrer-Pereira Hernán 
Published: August 2016

<p><span style="font-family: Times New Roman;"><em>Aniba cinnamomiflora</em> C. K.<em> </em>Allen<strong><em> </em></strong> es una especie arbórea de la familia Lauraceae que produce aceite esencial. Se presenta un estudio sobre el producto de la hidrodestilación de partículas de madera provenientes de ramas de <em>Aniba cinnamomiflora</em>. El 0,05% de aceite esencial fue obtenido. El aceite esencial fue analizado por cromatografia de gases y espectrometria de masas. Fueron identificados quince compuestos (98.55%) del total recuperado. El principal componente (54.00%) corresponde al lípido γ-palmitolactona, seguido por 1-epi-cubenol (9.56%), δ-cadineno (6.05%), t-cadinol (5.00%) y chamazuleno (3.53%) . Este es el primer reporte del studio del aceite esencial de la madera de<strong> <em>Aniba cinnamomiflora</em>.</strong></span></p>
One-dimensional stochastic equations in layered media with semi-permeable barriers
Authors: Makhno Sergei Y. 
Published: August 2016

AbstractWe consider one-dimensional stochastic equations involving local times of unknown processes. We interpret these equations as diffusion in layered media with semi-permeable barriers and we study the limit behavior of solutions as barriers compress in one barrier. Conditions for convergence in law and limit equation are obtained.
Determination of VOCs in the Indoor Air of a New and a Renovated Apartment
Authors: Meciarova Ludmila , Vilcekova Silvia 
Published: August 2016

Abstract
This study deals with the occurrence of volatile organic compounds (VOCs) in the indoor environment of a new and a renovated apartment. Qualitative determination of VOCs was carried out with a gas chromatograph with surface acoustic wave detector (GC/SAW). Concentrations of total volatile organic compounds (TVOC) were determined by a photoionization detector with UV lamp. Simultaneously, temperature and relative humidity were monitored with a data logger. The aim of this study was to determine of TVOC concentrations, to use of GC/SAW for determination of individual VOCs in indoor air as well as to predict possible sources of VOCs in these apartments. Measurements were performed after each construction work for better resolution of the contributions of individual materials to the levels of VOC. Mean concentrations of TVOC were 624 μg/m3 in the renovated apartment and 1,686 μg/m3 in the new apartment after completion of all works. The results from the renovated apartment showed that the use of new materials can lead to lower levels of organic compounds in indoor air compared to old materials that were less environmentally friendly. Many types of VOCs were found in both apartments. After reviewing the possible sources, it seems that the main sources of these substances were applied coatings and flooring materials.
Histone H1 Limits DNA Methylation in Neurospora crassa
Authors: Seymour Michael , Ji Lexiang , Santos Alex M , Kamei Masayuki , Sasaki Takahiko , Basenko Evelina Y , Schmitz Robert J , Zhang Xiaoyu , Lewis Zachary A 
Published: August 2016

Abstract
Histone H1 variants, known as linker histones, are essential chromatin components in higher eukaryotes, yet compared to the core histones relatively little is known about their in vivo functions. The filamentous fungus Neurospora crassa encodes a single H1 protein that is not essential for viability. To investigate the role of N. crassa H1, we constructed a functional FLAG-tagged H1 fusion protein and performed genomic and molecular analyses. Cell fractionation experiments showed that H1-3XFLAG is a chromatin binding protein. Chromatin-immunoprecipitation combined with sequencing (ChIP-seq) revealed that H1-3XFLAG is globally enriched throughout the genome with a subtle preference for promoters of expressed genes. In mammals, the stoichiometry of H1 impacts nucleosome repeat length. To determine if H1 impacts nucleosome occupancy or nucleosome positioning in N. crassa, we performed micrococcal nuclease digestion in the wild-type and the ΔhH1 strain followed by sequencing (MNase-seq). Deletion of hH1 did not significantly impact nucleosome positioning or nucleosome occupancy. Analysis of DNA methylation by whole-genome bisulfite sequencing (MethylC-seq) revealed a modest but global increase in DNA methylation in the ΔhH1 mutant. Together, these data suggest that H1 acts as a nonspecific chromatin binding protein that can limit accessibility of the DNA methylation machinery in N. crassa.
Identifying Genetic Signatures of Natural Selection Using Pooled Population Sequencing in Picea abies
Authors: Chen Jun , Källman Thomas , Ma Xiao-Fei , Zaina Giusi , Morgante Michele , Lascoux Martin 
Published: August 2016

Abstract
The joint inference of selection and past demography remain a costly and demanding task. We used next generation sequencing of two pools of 48 Norway spruce mother trees, one corresponding to the Fennoscandian domain, and the other to the Alpine domain, to assess nucleotide polymorphism at 88 nuclear genes. These genes are candidate genes for phenological traits, and most belong to the photoperiod pathway. Estimates of population genetic summary statistics from the pooled data are similar to previous estimates, suggesting that pooled sequencing is reliable. The nonsynonymous SNPs tended to have both lower frequency differences and lower FST values between the two domains than silent ones. These results suggest the presence of purifying selection. The divergence between the two domains based on synonymous changes was around 5 million yr, a time similar to a recent phylogenetic estimate of 6 million yr, but much larger than earlier estimates based on isozymes. Two approaches, one of them novel and that considers both FST and difference in allele frequencies between the two domains, were used to identify SNPs potentially under diversifying selection. SNPs from around 20 genes were detected, including genes previously identified as main target for selection, such as PaPRR3 and PaGI.
Patching Holes in the Chlamydomonas Genome
Authors: Tulin Frej , Cross Frederick R 
Published: August 2016

Abstract
The Chlamydomonas genome has been sequenced, assembled, and annotated to produce a rich resource for genetics and molecular biology in this well-studied model organism. However, the current reference genome contains ∼1000 blocks of unknown sequence (‘N-islands’), which are frequently placed in introns of annotated gene models. We developed a strategy to search for previously unknown exons hidden within such blocks, and determine the sequence, and exon/intron boundaries, of such exons. These methods are based on assembly and alignment of short cDNA and genomic DNA reads, completely independent of prior reference assembly or annotation. Our evidence indicates that a substantial proportion of the annotated intronic N-islands contain hidden exons. For most of these, our algorithm recovers full exonic sequence with associated splice junctions and exon-adjacent intronic sequence. These new exons represent de novo sequence generally present nowhere in the assembled genome, and the added sequence improves evolutionary conservation of the predicted encoded peptides.
Whole-Genome Sequencing Reveals Genetic Variation in the Asian House Rat
Authors: Teng Huajing , Zhang Yaohua , Shi Chengmin , Mao Fengbiao , Hou Lingling , Guo Hongling , Sun Zhongsheng , Zhang Jianxu 
Published: August 2016

AbstractWhole-genome sequencing of wild-derived rat species can provide novel genomic resources, which may help decipher the genetics underlying complex phenotypes. As a notorious pest, reservoir of human pathogens, and colonizer, the Asian house rat, Rattus tanezumi, is successfully adapted to its habitat. However, little is known regarding genetic variation in this species. In this study, we identified over 41,000,000 single-nucleotide polymorphisms, plus insertions and deletions, through whole-genome sequencing and bioinformatics analyses. Moreover, we identified over 12,000 structural variants, including 143 chromosomal inversions. Further functional analyses revealed several fixed nonsense mutations associated with infection and immunity-related adaptations, and a number of fixed missense mutations that may be related to anticoagulant resistance. A genome-wide scan for loci under selection identified various genes related to neural activity. Our whole-genome sequencing data provide a genomic resource for future genetic studies of the Asian house rat species and have the potential to facilitate understanding of the molecular adaptations of rats to their ecological niches.
Large Deletions at the SHOX Locus in the Pseudoautosomal Region Are Associated with Skeletal Atavism in Shetland Ponies
Authors: Rafati Nima , Andersson Lisa S , Mikko Sofia , Feng Chungang , Raudsepp Terje , Pettersson Jessica , Janecka Jan , Wattle Ove , Ameur Adam , Thyreen Gunilla , Eberth John , Huddleston John , Malig Maika , Bailey Ernest , Eichler Evan E , Dalin Göran , Chowdary Bhanu , Andersson Leif , Lindgren Gabriella , Rubin Carl-Johan 
Published: August 2016

Abstract
Skeletal atavism in Shetland ponies is a heritable disorder characterized by abnormal growth of the ulna and fibula that extend the carpal and tarsal joints, respectively. This causes abnormal skeletal structure and impaired movements, and affected foals are usually killed. In order to identify the causal mutation we subjected six confirmed Swedish cases and a DNA pool consisting of 21 control individuals to whole genome resequencing. We screened for polymorphisms where the cases and the control pool were fixed for opposite alleles and observed this signature for only 25 SNPs, most of which were scattered on genome assembly unassigned scaffolds. Read depth analysis at these loci revealed homozygosity or compound heterozygosity for two partially overlapping large deletions in the pseudoautosomal region (PAR) of chromosome X/Y in cases but not in the control pool. One of these deletions removes the entire coding region of the SHOX gene and both deletions remove parts of the CRLF2 gene located downstream of SHOX. The horse reference assembly of the PAR is highly fragmented, and in order to characterize this region we sequenced bacterial artificial chromosome (BAC) clones by single-molecule real-time (SMRT) sequencing technology. This considerably improved the assembly and enabled size estimations of the two deletions to 160−180 kb and 60−80 kb, respectively. Complete association between the presence of these deletions and disease status was verified in eight other affected horses. The result of the present study is consistent with previous studies in humans showing crucial importance of SHOX for normal skeletal development.
Copy Number Profiling of Brazilian Astrocytomas
Authors: Bidinotto Lucas Tadeu , Torrieri Raul , Mackay Alan , Almeida Gisele Caravina , Viana-Pereira Marta , Cruvinel-Carloni Adriana , Spina Maria Luisa , Campanella Nathalia Cristina , Pereira de Menezes Weder , Clara Carlos Afonso , Becker Aline Paixão , Jones Chris , Reis Rui Manuel 
Published: August 2016

Abstract
Copy number alterations (CNA) are one of the driving mechanisms of glioma tumorigenesis, and are currently used as important biomarkers in the routine setting. Therefore, we performed CNA profiling of 65 astrocytomas of distinct malignant grades (WHO grade I–IV) of Brazilian origin, using array-CGH and microsatellite instability analysis (MSI), and investigated their correlation with TERT and IDH1 mutational status and clinico-pathological features. Furthermore, in silico analysis using the Oncomine database was performed to validate our findings and extend the findings to gene expression level. We found that the number of genomic alterations increases in accordance with glioma grade. In glioblastomas (GBM), the most common alterations were gene amplifications (PDGFRA, KIT, KDR, EGFR, and MET) and deletions (CDKN2A and PTEN). Log-rank analysis correlated EGFR amplification and/or chr7 gain with better survival of the patients. MSI was observed in 11% of GBMs. A total of 69% of GBMs presented TERT mutation, whereas IDH1 mutation was most frequent in diffuse (85.7%) and anaplastic (100%) astrocytomas. The combination of 1p19q deletion and TERT and IDH1 mutational status separated tumor groups that showed distinct age of diagnosis and outcome. In silico validation pointed to less explored genes that may be worthy of future investigation, such as CDK2, DMRTA1, and MTAP. Herein, using an extensive integrated analysis, we indicated potentially important genes, not extensively studied in gliomas, that could be further explored to assess their biological and clinical impact in astrocytomas.
Cilia-Associated Genes Play Differing Roles in Aminoglycoside-Induced Hair Cell Death in Zebrafish
Authors: Stawicki Tamara M , Hernandez Liana , Esterberg Robert , Linbo Tor , Owens Kelly N , Shah Arish N , Thapa Nihal , Roberts Brock , Moens Cecilia B , Rubel Edwin W , Raible David W 
Published: August 2016

Abstract
Hair cells possess a single primary cilium, called the kinocilium, early in development. While the kinocilium is lost in auditory hair cells of most species it is maintained in vestibular hair cells. It has generally been believed that the primary role of the kinocilium and cilia-associated genes in hair cells is in the establishment of the polarity of actin-based stereocilia, the hair cell mechanotransduction apparatus. Through genetic screening and testing of candidate genes in zebrafish (Danio rerio) we have found that mutations in multiple cilia genes implicated in intraflagellar transport (dync2h1, wdr35, ift88, and traf3ip), and the ciliary transition zone (cc2d2a, mks1, and cep290) lead to resistance to aminoglycoside-induced hair cell death. These genes appear to have differing roles in hair cells, as mutations in intraflagellar transport genes, but not transition zone genes, lead to defects in kinocilia formation and processes dependent upon hair cell mechanotransduction activity. These mutants highlight a novel role of cilia-associated genes in hair cells, and provide powerful tools for further study.
Placental Hypomethylation Is More Pronounced in Genomic Loci Devoid of Retroelements
Authors: Chatterjee Aniruddha , Macaulay Erin C , Rodger Euan J , Stockwell Peter A , Parry Matthew F , Roberts Hester E , Slatter Tania L , Hung Noelyn A , Devenish Celia J , Morison Ian M 
Published: August 2016

Abstract
The human placenta is hypomethylated compared to somatic tissues. However, the degree and specificity of placental hypomethylation across the genome is unclear. We assessed genome-wide methylation of the human placenta and compared it to that of the neutrophil, a representative homogeneous somatic cell. We observed global hypomethylation in placenta (relative reduction of 22%) compared to neutrophils. Placental hypomethylation was pronounced in intergenic regions and gene bodies, while the unmethylated state of the promoter remained conserved in both tissues. For every class of repeat elements, the placenta showed lower methylation but the degree of hypomethylation differed substantially between these classes. However, some retroelements, especially the evolutionarily younger Alu elements, retained high levels of placental methylation. Surprisingly, nonretrotransposon-containing sequences showed a greater degree of placental hypomethylation than retrotransposons in every genomic element (intergenic, introns, and exons) except promoters. The differentially methylated fragments (DMFs) in placenta and neutrophils were enriched in gene-poor and CpG-poor regions. The placentally hypomethylated DMFs were enriched in genomic regions that are usually inactive, whereas hypermethylated DMFs were enriched in active regions. Hypomethylation of the human placenta is not specific to retroelements, indicating that the evolutionary advantages of placental hypomethylation go beyond those provided by expression of retrotransposons and retrogenes.