bluuebunny/crossref_metadata_2025_split huggingface dataset:
A novel TRIM family member, Trim69, regulates zebrafish development through p53‐mediated apoptosis
Authors: Han Ruiqin , Zhao Qing , Zong Shudong , Miao Shiying , Song Wei , Wang Linfang 
Published: March 2016

SUMMARYTrim69 contains the hallmark domains of a tripartite motif (TRIM) protein, including a Ring‐finger domain, B‐box domain, and coiled‐coil domain. Trim69 is structurally and evolutionarily conserved in zebrafish, mouse, rat, human, and chimpanzee. The role of this protein is unclear, however, so we investigated its function in zebrafish development. Trim69 is extensively expressed in zebrafish adults and developing embryos—particularly in the testis, brain, ovary, and heart—and its expression decreases in a time‐ and stage‐dependent manner. Loss of trim69 in zebrafish induces apoptosis and activates apoptosis‐related processes; indeed, the tp53 pathway was up‐regulated in response to the knockdown. Expression of human trim69 rescued the apoptotic phenotype, while overexpression of trim69 does not increase cellular apoptosis. Taken together, our results suggest that trim69 participates in tp53‐mediated apoptosis during zebrafish development. Mol. Reprod. Dev. 83: 442–454, 2016. © 2016 Wiley Periodicals, Inc.
ROUTE: run‐time robust reducer workload estimation for MapReduce
Authors: Liu Zhihong , Zhang Qi , Boutaba Raouf , Liu Yaping , Gong Zhenghu 
Published: March 2016

SummaryMapReduce has become a popular model for large‐scale data processing in recent years. Many works on MapReduce scheduling (e.g., load balancing and deadline‐aware scheduling) have emphasized the importance of predicting workload received by individual reducers. However, because the input characteristics and user‐specified map function of a given job are unknown to the MapReduce framework before the job starts, accurately predicting workload of reducers can be a difficult challenge. To address this challenge, we present ROUTE, a run‐time robust reducer workload estimation technique for MapReduce. ROUTE progressively samples the partition size of the early completed mappers, allowing ROUTE to perform estimation at run time yet fulfilling the accuracy requirement specified by users. Moreover, by using robust estimation and bootstrapping resampling techniques, ROUTE can achieve high applicability to a wide variety of applications. Through experiments using both real and synthetic data on an 11‐node Hadoop cluster, we show ROUTE can achieve high accuracy with error rate no more than 10.92% and an improvement of 40.6% in terms of error rate while compared with the state‐of‐the‐art solution. Besides, through simulations using synthetic data, we show that ROUTE is robust to a variety of skewed distributions. Finally, we apply ROUTE to existing load balancing and deadline‐aware scheduling frameworks and show ROUTE significantly improves the performance of these frameworks. Copyright © 2016 John Wiley & Sons, Ltd.
Unhealthy eating behaviors and weight gain: A prospective study in young and middle‐age adults
Authors: León‐Muñoz Luz M. , García‐Esquinas Esther , Soler‐Vila Hosanna , Guallar‐Castillón Pilar , Banegas José R. , Rodríguez‐Artalejo Fernando 
Published: March 2016

ObjectiveGuidelines for obesity prevention recommend reducing certain unhealthy eating behaviors (UEB). However, the association between UEB and weight gain is uncertain.MethodsProspective cohort with 1,638 individuals aged 18‐60 years was recruited in 2008‐2010. UEB assessed at baseline were: not planning how much to eat, consuming pre‐cooked/canned food, buying snacks, eating in fast‐food restaurants, not choosing low‐calorie foods, not removing visible fat from meat or skin from chicken, and eating while watching TV or seating on a sofa. Participants were followed up through 2012 to assess weight change.ResultsCompared to reporting 0‐2 UEB, the multivariate odds ratios (95% confidence interval) for gaining ≥3 kg were 0.97 (0.74‐1.28) for 3‐4 UEB and 1.61 (1.09‐2.39) for ≥5 UEB, P‐trend = 0.07. Results were similar for gaining ≥5 kg. The three UEB with the strongest associations with weight gain were: 1) not planning the amount of food to eat, 2) eating at fast‐food restaurants, and 3) eating while watching TV; compared to having none of these three behaviors, the odds ratio (95% confidence interval) for gaining ≥3 kg was 1.54 (0.77‐3.08) for 1 UEB, 1.70 (0.85‐3.37) for 2 UEB, and 2.75 (1.28‐5.90) for 3 UEB, P‐trend = 0.007. Similar results were obtained for gaining ≥5 kg.ConclusionsSeveral UEB are associated with weight gain.
High‐fat diet exacerbates pain‐like behaviors and periarticular bone loss in mice with CFA‐induced knee arthritis
Authors: Loredo‐Pérez Aleyda A. , Montalvo‐Blanco Carlos E. , Hernández‐González Luis I. , Anaya‐Reyes Maricruz , Fernández del Valle‐Laisequilla Cecilia , Reyes‐García Juan G. , Acosta‐González Rosa I. , Martínez‐Martínez Arisai , Villarreal‐Salcido Jaira C. , Vargas‐Muñoz Virginia M. , Muñoz‐Islas Enriqueta , Ramírez‐Rosas Martha B. , Jiménez‐Andrade Juan M. 
Published: March 2016

ObjectiveOur aim was to quantify nociceptive spontaneous behaviors, knee edema, proinflammatory cytokines, bone density, and microarchitecture in high‐fat diet (HFD)‐fed mice with unilateral knee arthritis.MethodsICR male mice were fed either standard diet (SD) or HFD starting at 3 weeks old. At 17 weeks, HFD and SD mice received intra‐articular injections either with Complete Freund's Adjuvant (CFA) or saline into the right knee joint every 7 days for 4 weeks. Spontaneous pain‐like behaviors and knee edema were assessed for 26 days. At day 26 post‐first CFA injection, serum levels of IL‐1β, IL‐6, and RANKL were measured by ELISA, and microcomputed tomography analysis of knee joints was performed.ResultsHFD‐fed mice injected with CFA showed greater spontaneous pain‐like behaviors of the affected extremity as well as a decrease in the weight‐bearing index compared to SD‐fed mice injected with CFA. Knee edema was not significantly different between diets. HFD significantly exacerbated arthritis‐induced bone loss at the distal femoral metaphysis but had no effect on femoral diaphyseal cortical bone. HFD did not modify serum levels of proinflammatory cytokines.ConclusionsHFD exacerbates pain‐like behaviors and significantly increases the magnitude of periarticular trabecular bone loss in a murine model of unilateral arthritis.
Preparation of alginate hydrogels containing silver nanoparticles: a facile approach for antibacterial applications
Authors: Rescignano Nicoletta , Hernandez Rebeca , Lopez Lionel D , Calvillo Inmaculada , Kenny Josè M , Mijangos Carmen 
Published: March 2016

AbstractNowadays polymer nanocomposites represent an important stake in scientific research and offer a combination of properties with respect to single components. The present work deals with nanocomposite hydrogels obtained from alginate, a biobased polymer, which is employed as a biocompatible matrix for the encapsulation of silver nanoparticles (AgNPs). Alginate nanocomposite hydrogels were obtained through crosslinking with calcium carbonate (CaCO3) and d‐glucono‐δ‐lactone (GDL) at different AgNP concentrations. The effect of the encapsulation of AgNPs within alginate hydrogels on their porous structure and the AgNP dispersion was evaluated through field‐emission scanning electron microscopy. Oscillatory rheological measurements were carried out in order to determine the alginate/AgNP ratio suitable for achieving a higher elastic modulus. Finally, nanocomposite alginate hydrogels were found to be effective against Escherichia coli and Pseudomonas aeruginosa bacteria, with inhibition zones ranging between 5 and 7 cm after 24 h of incubation at 37 °C. Therefore, the present work proposes a nanocomposite alginate hydrogel for application as bactericidal materials in the biotechnology and biomedical fields. © 2016 Society of Chemical Industry
Conservation of structural fluctuations in homologous protein kinases and its implications on functional sites
Authors: Kalaivani Raju , de Brevern Alexandre G. , Srinivasan Narayanaswamy 
Published: March 2016

ABSTRACTOur aim is to explore the similarities in structural fluctuations of homologous kinases. Gaussian Network Model based Normal Mode Analysis was performed on 73 active conformation structures in Ser/Thr/Tyr kinase superfamily. Categories of kinases with progressive evolutionary divergence, viz. (i) Same kinase with many crystal structures, (ii) Within‐Subfamily, (iii) Within‐Family, (iv) Within‐Group, and (v) Across‐Group, were analyzed. We identified a flexibility signature conserved in all kinases involving residues in and around the catalytic loop with consistent low‐magnitude fluctuations. However, the overall structural fluctuation profiles are conserved better in closely related kinases (Within‐Subfamily and Within‐family) than in distant ones (Within‐Group and Across‐Group). A substantial 65.4% of variation in flexibility was not accounted by variation in sequences or structures. Interestingly, we identified substructural residue‐wise fluctuation patterns characteristic of kinases of different categories. Specifically, we recognized statistically significant fluctuations unique to families of protein kinase A, cyclin‐dependent kinases, and nonreceptor tyrosine kinases. These fluctuation signatures localized to sites known to participate in protein‐protein interactions typical of these kinase families. We report for the first time that residues characterized by fluctuations unique to the group/family are involved in interactions specific to the group/family. As highlighted for Src family, local regions with differential fluctuations are proposed as attractive targets for drug design. Overall, our study underscores the importance of consideration of fluctuations, over and above sequence and structural features, in understanding the roles of sites characteristic of kinases. Proteins 2016; 84:957–978. © 2016 Wiley Periodicals, Inc.
Alteration of the structure and surface composition of crystalline‐amorphous porous clay heterostructures upon iron doping from metal‐organic source
Authors: Zimowska M. , Lityńska‐Dobrzyńska L. , Olejniczak Z. , Socha R.P. , Gurgul J. , Łątka K. 
Published: March 2016

Porous clay heterostructures (PCH) have been prepared through the surfactant directed assembly of organosilica in the galleries of synthetic layered clay mineral Laponite. Fe‐containing PCH nanostructures with nominal (Si + Mg)/Fe = 10 were prepared by post‐synthesis impregnation of porous clay hybrid composites with metal‐organic C6H5FeO. After impregnation, the as‐synthesized Fe–PCH samples were either directly calcined at 550 °C or, prior to calcination, hydrothermally treated in the high pressure reactor. The impact of the PCH composite doping by the trivalent (Fe3+) cations on the physicochemical properties was investigated with the use of spectroscopic methods.Detailed information on the character and lattice positions occupied by iron, the extent of its incorporation, its local structure and symmetry within samples were provided by comparing the FTIR analysis with the 57Fe Mössbauer spectroscopy and 29Si MAS NMR data. The nature of different Fe species formed after post‐synthesis treatments was determined by Mössbauer spectroscopy and HRTEM. High pressure treatment resulted in the alteration of sample morphology and better, more homogenous dispersion of the Fe species in the composite lattice. FTIR indicated slight impairment of the clay structure in the PCH network followed by surface enrichment with Mg species because of Mg cations leaching from the octahedral sheets as confirmed by XPS study. Copyright © 2016 John Wiley & Sons, Ltd.
North American megadroughts in the Common Era: reconstructions and simulations
Authors: Cook Benjamin I. , Cook Edward R. , Smerdon Jason E. , Seager Richard , Williams A. Park , Coats Sloan , Stahle David W. , Díaz José Villanueva 
Published: March 2016

During the Medieval Climate Anomaly (MCA), Western North America experienced episodes of intense aridity that persisted for multiple decades or longer. These megadroughts are well documented in many proxy records, but the causal mechanisms are poorly understood. General circulation models (GCMs) simulate megadroughts, but do not reproduce the temporal clustering of events during the MCA, suggesting they are not caused by the time history of volcanic or solar forcing. Instead, GCMs generate megadroughts through (1) internal atmospheric variability, (2) sea‐surface temperatures, and (3) land surface and dust aerosol feedbacks. While no hypothesis has been definitively rejected, and no GCM has accurately reproduced all features (e.g., timing, duration, and extent) of any specific megadrought, their persistence suggests a role for processes that impart memory to the climate system (land surface and ocean dynamics). Over the 21st century, GCMs project an increase in the risk of megadrought occurrence through greenhouse gas forced reductions in precipitation and increases in evaporative demand. This drying is robust across models and multiple drought indicators, but major uncertainties still need to be resolved. These include the potential moderation of vegetation evaporative losses at higher atmospheric [CO2], variations in land surface model complexity, and decadal to multidecadal modes of natural climate variability that could delay or advance onset of aridification over the the next several decades. Because future droughts will arise from both natural variability and greenhouse gas forced trends in hydroclimate, improving our understanding of the natural drivers of persistent multidecadal megadroughts should be a major research priority. WIREs Clim Change 2016, 7:411–432. doi: 10.1002/wcc.394This article is categorized under:

Paleoclimates and Current Trends > Paleoclimate
Climate Models and Modeling > Knowledge Generation with Models
Regulatory effects of cotranscriptional RNA structure formation and transitions
Authors: Liu Sheng‐Rui , Hu Chun‐Gen , Zhang Jin‐Zhi 
Published: March 2016

RNAs, which play significant roles in many fundamental biological processes of life, fold into sophisticated and precise structures. RNA folding is a dynamic and intricate process, which conformation transition of coding and noncoding RNAs form the primary elements of genetic regulation. The cellular environment contains various intrinsic and extrinsic factors that potentially affect RNA folding in vivo, and experimental and theoretical evidence increasingly indicates that the highly flexible features of the RNA structure are affected by these factors, which include the flanking sequence context, physiochemical conditions, cis RNA–RNA interactions, and RNA interactions with other molecules. Furthermore, distinct RNA structures have been identified that govern almost all steps of biological processes in cells, including transcriptional activation and termination, transcriptional mutagenesis, 5′‐capping, splicing, 3′‐polyadenylation, mRNA export and localization, and translation. Here, we briefly summarize the dynamic and complex features of RNA folding along with a wide variety of intrinsic and extrinsic factors that affect RNA folding. We then provide several examples to elaborate RNA structure‐mediated regulation at the transcriptional and posttranscriptional levels. Finally, we illustrate the regulatory roles of RNA structure and discuss advances pertaining to RNA structure in plants. WIREs RNA 2016, 7:562–574. doi: 10.1002/wrna.1350This article is categorized under:

RNA Structure and Dynamics > RNA Structure, Dynamics, and Chemistry
RNA Structure and Dynamics > Influence of RNA Structure in Biological Systems
Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs
Metagenomic analysis of denitrifying wastewater enrichment cultures able to transform the explosive, 3-nitro-1,2,4-triazol-5-one (NTO)
Authors: Eberly Jed O , Indest Karl J , Hancock Dawn E , Jung Carina M , Crocker Fiona H 
Published: March 2016

Abstract
Removal of 3-nitro-1,2,4-triazol-5-one (NTO) was investigated in conjunction with heterotrophic and autotrophic denitrifying growth conditions by a microbial consortium from a wastewater treatment plant. Microcosms were supplemented with molasses, methanol, or thiosulfate. Cultures were passaged twice by transferring 10 % of the culture volume to fresh media on days 11 and 21. Rates of NTO removal were 18.71 ± 0.65, 9.04 ± 2.61, and 4.34 ± 2.72 mg/L/day while rates of nitrate removal were 20.08 ± 1.13, 21.58 ± 1.20, and 24.84 ± 1.26 mg/L/day, respectively, for molasses, methanol, or thiosulfate. Metagenomic analysis showed that Proteobacteria and Firmicutes were the major phyla in the microbial communities. In molasses supplemented cultures, the community profile at the family level changed over time with Pseudomonadaceae the most abundant (67.4 %) at day 11, Clostridiaceae (65.7 %) at day 21, and Sporolactobacillaceae (35.4 %) and Clostridiaceae (41.0 %) at day 29. Pseudomonadaceae was the dominant family in methanol and thiosulfate supplemented cultures from day 21 to 29 with 76.6 and 81.6 % relative abundance, respectively.
Medial to posterior release procedure after failure of functional treatment in clubfoot: A prospective study
Authors: Bocahut Nicolas , Simon Anne-Laure , Mazda Keyvan , Ilharreborde Brice , Souchet Philippe 
Published: March 2016

Purpose Two conservative techniques for clubfoot treatment are still being debated and depend upon the institution's expertise. For >40 years, the current institution has been a pioneer in the development of the physiotherapy method; however, some severe deformities remain resistant to this method which causes pain, sprains, and difficulties wearing shoes. Therefore, a surgical approach was developed simultaneously for the treatment of these residual or recurring clubfeet. The procedure reproduces the same chronological steps by performing forefoot derotation before correcting hindfoot equinus. The aim of the current study was to assess the results of this surgical technique. Methods All clubfeet undergoing surgery between October 1995 and February 2009 were prospectively included. Initial severity was based on Dimeglio's classification and final outcomes on the International Clubfoot Study Group (ICFSG) outcome evaluation system. Last follow-up results were assessed by physical examination and radiographs. Results A total of 137 patients with severe clubfeet (mean Dimeglio score 12.0) underwent surgery. At the mean follow-up of 10.8 years, mean ICFSG score was 4.3 (range 0–23), and 12 % required revision surgery. The rate of undercorrection and overcorrection was low (17 pes-plano-valgus ft and 11 ft with undercorrection). Eight feet had a fixed deformity. Conclusions Severe deformities are more resistant to conservative techniques even for institutions with large experience. These deformities require further treatment, including surgery if necessary. The medial to posterior soft-tissue release is a valuable technique with stable results. Level of evidence Level IV.
Circle of Willis Collateral During Temporary Internal Carotid Artery Occlusion I: Observations From Digital Subtraction Angiography
Authors: Lownie Stephen P. , Larrazabal Ramiro , Kole Maximilian K. 
Published: March 2016

AbstractIntroduction: Impaired collateral circulation can lead to stroke during carotid endarterectomy. Carotid stump pressure (CSP) is used as a surrogate measure of collateral flow. The objective was to determine whether anatomical features obtained from digital subtraction angiography correlate with CSP during temporary internal carotid artery occlusion. The second objective was to use these features in combination to predict CSP. Methods: Digital subtraction angiographies from 102 patients obtained before endarterectomy were reviewed for anatomical variables including: degree of ipsilateral and contralateral carotid artery stenosis; patency of the anterior communicating artery; presence of cross-flow into ipsilateral middle cerebral artery branches; and size (< or ≥1 mm calibre) of the ipsilateral proximal anterior cerebral (A1), the contralateral A1, and the ipsilateral posterior communicating arteries. At surgery, systemic mean arterial pressure (MAP) and CSP were recorded. Multiple regression analysis was used to assess for anatomical features significantly associated with CSP. A “predicted CSP” equation was applied to 54 subsequent patients and correlated with measured CSP. Results: Variables correlating with CSP included MAP (p=0.001); the presence of severe contralateral carotid stenosis (p=0.002); patency of the anterior communicating artery (p=0.013); and the size of the contralateral A1 segment (p=0.029). Angiographic cross-flow, ipsilateral A1 size, and ipsilateral posterior communicating artery size were not significant. Predicted CSP correlated significantly with measured CSP (p<0.0001; R2=0.34). Conclusions: Anatomical features and systemic MAP are associated with carotid stump pressure during internal carotid artery occlusion and account for a significant amount of its variation.
A SAR record of early 21st century change in Greenland
Authors: JOUGHIN IAN , SMITH BEN E. , HOWAT IAN M. , MOON TWILA , SCAMBOS TED A. 
Published: March 2016

ABSTRACTGlaciers in Greenland are changing rapidly. To better understand these changes, we have produced a series of seven synthetic aperture radar (SAR) backscatter mosaics for seven winters during the period from 2000 to 2013. Six of the mosaics were created using RADARSAT Fine-Beam data and the seventh used ALOS-PALSAR Fine-Beam Single-Polarization data. The RADARSAT mosaics are radiometrically calibrated and capture changes in the backscatter coefficient related to melt and other events, particularly the strong melting in the summer of 2012. Comparison of features in the ascending-orbit ALOS mosaic and the descending-orbit RADARSAT mosaics indicate that in areas of smooth to moderate topography their locations are consistent to within a few tens of meters. The locations of features identifiable in the RADARSAT mosaics, which were collected with the same imaging parameters, generally agree to within better than the 20 m posting of the data. With such geometric accuracy, these data establish a record of change in Greenland for the early part of the 21st century, thus providing a baseline that can be compared with new radar and optical datasets.
Summary of the Joint Discussion: Atomic Data of Importance for Ultraviolet and X-Ray Astronomy
Authors: Hearn A. G. 
Published: March 2016

AbstractThis Joint Discussion is in two parts. The first part is a description of recent observations which illustrate the need for atomic data and the second part is a description of what atomic data are available or could readily be produced by the latest theoretical and experimental methods. The purpose of this summary is to highlight the immediate requirements for atomic data of current observations which are not met by our present knowledge and thereby indicate where further work is necessary in providing atomic data.Although this is a discussion of atomic data the problems of assuming local thermodynamic equilibrium have inevitably been raised. The importance of considering whether departures from LTE are significant or not in the interpretation of observations is is clearly illustrated by the work of the Harvard group on the Lyman continuum emitted by the Sun which has shown a departure coefficient as large as 200 for the ground level of hydrogen.