bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cryptic binding sites become accessible through surface reconstruction of the type I collagen fibril
Authors: Zhu Jie , Hoop Cody L. , Case David A. , Baum Jean 
Published: November 2018

AbstractCollagen fibril interactions with cells and macromolecules in the extracellular matrix drive numerous cellular functions. Binding motifs for dozens of collagen-binding proteins have been determined on fully exposed collagen triple helical monomers. However, when the monomers are assembled into the functional collagen fibril, many binding motifs become inaccessible, and yet critical cellular processes occur. Here, we have developed an early stage atomic model of the smallest repeating unit of the type I collagen fibril at the fibril surface that provides a novel framework to address questions about these functionally necessary yet seemingly obstructed interactions. We use an integrative approach by combining molecular dynamics (MD) simulations with atomic force microscopy (AFM) experiments and show that reconstruction of the collagen monomers within the complex fibril play a critical role in collagen interactions. In particular, the fibril surface shows three major conformational changes, which allow cryptic binding sites, including an integrin motif involved in platelet aggregation, to be exposed. The observed dynamics and reconstruction of the fibril surface promote its role as a “smart fibril” to keep certain binding sites cryptic, and to allow accessibility of recognition domains when appropriate.
Implications of high rates of sexual recruitment in driving rapid reef recovery in Mo’orea, French Polynesia
Authors: Edmunds Peter J. 
Published: November 2018

AbstractCoral abundance continues to decline on tropical reefs around the world, and this trend suggests that coral reefs may not persist beyond the current century. In contrast, this study describes the near-complete mortality of corals on the outer reef (10 m and 17 m depth) of the north shore of Mo’orea, French Polynesia, from 2005 to 2010, followed by unprecedented recovery from 2011 to 2017. Intense corallivory and a cyclone drove coral cover from 33–48% to <3% by 2010, but over the following seven years, recovery occurred through rapid population growth (up to 12% cover y−1) to 25–74% cover by 2017. The thirteen-year, U-shape trajectory of coral cover over time created by the loss and replacement of millions of corals through sexual reproduction underscores the potential for beneficial genetic responses to environmental conditions for at least one genus, Pocillopora. The high ecological resilience of this coral community appears to have been enhanced by variation among genera in the susceptibility to declining cover, and the capacity for population growth (i.e., response diversity). These results suggest that the outer coral communities of Mo’orea may be poised for genetic changes that could affect their capacity to persistence.
Unlocking conserved and diverged metabolic characteristics in cassava carbon assimilation via comparative genomics approach
Authors: Siriwat Wanatsanan , Kalapanulak Saowalak , Suksangpanomrung Malinee , Saithong Treenut 
Published: November 2018

AbstractGlobally, cassava is an important source of starch, which is synthesized through carbon assimilation in cellular metabolism whereby harvested atmospheric carbon is assimilated into macromolecules. Although the carbon assimilation pathway is highly conserved across species, metabolic phenotypes could differ in composition, type, and quantity. To unravel the metabolic complexity and advantage of cassava over other starch crops, in terms of starch production, we investigated the carbon assimilation mechanisms in cassava through genome-based pathway reconstruction and comparative network analysis. First, MeRecon — the carbon assimilation pathway of cassava was reconstructed based upon six plant templates: Arabidopsis, rice, maize, castor bean, potato, and turnip. MeRecon, available at http://bml.sbi.kmutt.ac.th/MeRecon, comprises 259 reactions (199 EC numbers), 1,052 proteins (870 genes) and 259 metabolites in eight sub-metabolisms. Analysis of MeRecon and the carbon assimilation pathways of the plant templates revealed the overall topology is highly conserved, but variations at sub metabolism level were found in relation to complexity underlying each biochemical reaction, such as numbers of responsible enzymatic proteins and their evolved functions, which likely explain the distinct metabolic phenotype. Thus, this study provides insights into the network characteristics and mechanisms that regulate the synthesis of metabolic phenotypes of cassava.
Species richness and taxonomic composition of trawl macrofauna of the North Pacific and its adjacent seas
Authors: Volvenko Igor V. , Orlov Alexei M. , Gebruk Andrey V. , Katugin Oleg N. , Vinogradov Georgy M. , Maznikova Olga A. 
Published: November 2018

AbstractA checklist is presented of animal species obtained in 68,903 trawl tows during 459 research surveys performed by the Pacific Research Fisheries Center (TINRO-Center) over an area measuring nearly 25 million km2 in the Chukchi and Bering seas, Sea of Okhotsk, Sea of Japan and North Pacific Ocean in 1977–2014 at depths of 5 to 2,200 m. The checklist comprises 949 fish species, 588 invertebrate species, and four cyclostome species (some specimens were identified only to genus or family level). For each species details are given on the type of trawl (benthic and/or pelagic) and basins where the species was found. Comprehensiveness of data, taxonomic composition of catches, dependence of species richness on the survey area, sample size, and habitat, are considered. Ratios of various taxonomic groups of trawl macrofauna in pelagic and benthic zones and in different basins are analysed. Basins are compared based on species composition.
Divergent short-chain fatty acid production and succession of colonic microbiota arise in fermentation of variously-sized wheat bran fractions
Authors: Tuncil Yunus E. , Thakkar Riya D. , Marcia Arianna D. Romero , Hamaker Bruce R. , Lindemann Stephen R. 
Published: November 2018

AbstractThough the physical structuring of insoluble dietary fiber sources may strongly impact their processing by microbiota in the colon, relatively little mechanistic information exists to explain how these aspects affect microbial fiber fermentation. Here, we hypothesized that wheat bran fractions varying in size would be fermented differently by gut microbiota, which would lead to size-dependent differences in metabolic fate (as short-chain fatty acids; SCFAs) and community structure. To test this hypothesis, we performed an in vitro fermentation assay in which wheat bran particles from a single source were separated by sieving into five size fractions and inoculated with fecal microbiota from three healthy donors. SCFA production, measured by gas chromatography, uncovered size fraction-dependent relationships between total SCFAs produced as well as the molar ratios of acetate, propionate, and butyrate. 16S rRNA sequencing revealed that these size-dependent metabolic outcomes were accompanied by the development of divergent microbial community structures. We further linked these distinct results to subtle, size-dependent differences in chemical composition. These results suggest that physical context can drive differences in microbiota composition and function, that fiber-microbiota interaction studies should consider size as a variable, and that manipulating the size of insoluble fiber-containing particles might be used to control gut microbiome composition and metabolic output.
Analysis of the Genome and Metabolome of Marine Myxobacteria Reveals High Potential for Biosynthesis of Novel Specialized Metabolites
Authors: Amiri Moghaddam Jamshid , Crüsemann Max , Alanjary Mohammad , Harms Henrik , Dávila-Céspedes Antonio , Blom Jochen , Poehlein Anja , Ziemert Nadine , König Gabriele M. , Schäberle Till F. 
Published: November 2018

AbstractComparative genomic/metabolomic analysis is a powerful tool to disclose the potential of microbes for the biosynthesis of novel specialized metabolites. In the group of marine myxobacteria only a limited number of isolated species and sequenced genomes is so far available. However, the few compounds isolated thereof so far show interesting bioactivities and even novel chemical scaffolds; thereby indicating a huge potential for natural product discovery. In this study, all marine myxobacteria with accessible genome data (n = 5), including Haliangium ochraceum DSM 14365, Plesiocystis pacifica DSM 14875, Enhygromyxa salina DSM 15201 and the two newly sequenced species Enhygromyxa salina SWB005 and SWB007, were analyzed. All of these accessible genomes are large (~10 Mb), with a relatively small core genome and many unique coding sequences in each strain. Genome analysis revealed a high variety of biosynthetic gene clusters (BGCs) between the strains and several resistance models and essential core genes indicated the potential to biosynthesize antimicrobial molecules. Polyketides (PKs) and terpenes represented the majority of predicted specialized metabolite BGCs and contributed to the highest share between the strains. BGCs coding for non-ribosomal peptides (NRPs), PK/NRP hybrids and ribosomally synthesized and post-translationally modified peptides (RiPPs) were mostly strain specific. These results were in line with the metabolomic analysis, which revealed a high diversity of the chemical features between the strains. Only 6–11% of the metabolome was shared between all the investigated strains, which correlates to the small core genome of these bacteria (13–16% of each genome). In addition, the compound enhygrolide A, known from E. salina SWB005, was detected for the first time and structurally elucidated from Enhygromyxa salina SWB006. The here acquired data corroborate that these microorganisms represent a most promising source for the detection of novel specialized metabolites.
Targeting CD40 enhances antibody- and CD8-mediated protection against respiratory syncytial virus infection
Authors: Muralidharan Abenaya , Russell Marsha , Larocque Louise , Gravel Caroline , Li Changgui , Chen Wangxue , Cyr Terry , Lavoie Jessie R. , Farnsworth Aaron , Rosu-Myles Michael , Wang Lisheng , Li Xuguang 
Published: November 2018

AbstractRespiratory Syncytial Virus (RSV) infects almost all children under the age of one and is the leading cause of hospitalization among infants. Despite several decades of research with dozens of candidate vaccines being vigorously evaluated in pre-clinical and clinical studies, there is no licensed vaccine available to date. Here, the RSV fusion protein (F) was fused with CD40 ligand and delivered by an adenoviral vector into BALB/c mice where the CD40 ligand serves two vital functions as a molecular adjuvant and an antigen-targeting molecule. In contrast to a formaldehyde-inactivated vaccine, the vectored vaccine effectively protected animals against RSV without inducing enhanced respiratory disease. This protection involved a robust induction of neutralizing antibodies and memory CD8 T cells, which were not observed in the inactivated vaccine group. Finally, the vectored vaccine was able to elicit long-lasting protection against RSV, one of the most challenging issues in RSV vaccine development. Further studies indicate that the long lasting protection elicited by the CD40 ligand targeted vaccine was mediated by increased levels of effector memory CD8 T cell 3 months post-vaccination.
A Research on Preparation and Application of the Monolithic Catalyst with Interconnecting Pore Structure
Authors: Tsai Sang-Bing , Ma Hailing 
Published: November 2018

AbstractIn recent years, the monolithic material has been developed increasingly in the high performance liquid phase field, and it could also be applied in the field of catalyst, as a monolithic catalyst carrier, since it has a large specific surface area, and could be customized based on the mould. The monolithic catalyst is characterized with many advantages such as low bed pressure, high physical efficiency and small amplification effect. The most impotant part refers to the preparation of copper-based catalyst. The impregnation method is used to produce CuO-ZnO monolithic catalyst and CuO-ZnO-ZrO2 monolithic catalyst with the prepared monolithic silica-alumina carrier. The fixed bed microreactor is used to investigate the effect of copper-based catalyst on the process in which carbon dioxide is used to produce methanol through hydrogenation. The metal salt is added into the sol-gel process, which could form the M-O-Si bond, thus make the metal-containing catalytic material obtain good mechanical strength, and make it possible to be introduced into the acidic center generally. The metal-containing catalytic material carrier also has macropores and mesopores. The presence of large pores could make the molecular mass transfer more effective, while the presence of mesopores could increase the specific surface area of the material. In this paper, the experimental study has been conducted on the production of methanol through hydrogenation of CO2 under different catalysts, to mainly investigate the effect of catalysts with different catalytic performance on the reaction.
Sympatric Ixodes-tick species: pattern of distribution and pathogen transmission within wild rodent populations
Authors: Cayol Claire , Jääskeläinen Anu , Koskela Esa , Kyröläinen Sami , Mappes Tapio , Siukkola Anja , Kallio Eva R. 
Published: November 2018

AbstractThe generalist tick Ixodes ricinus is the most important vector for tick-borne pathogens (TBP), including Borrelia burgdorferi sensu lato, in Europe. However, the involvement of other sympatric Ixodes ticks, such as the specialist vole tick I. trianguliceps, in the enzootic circulations of TBP remains unclear. We studied the distribution of I. ricinus and I. trianguliceps in Central Finland and estimated the TBP infection likelihood in the most common rodent host in relation with the abundance of the two tick species. Ixodes trianguliceps was encountered in all 16 study sites whereas I. ricinus was frequently observed only at a quarter of the study sites. The abundance of I. ricinus was positively associated with open water coverage and human population density around the study sites. Borrelia burgdorferi s. l.-infected rodents were found only in sites where I. ricinus was abundant, whereas the occurrence of other TBP was independent of I. ricinus presence. These results suggest that I. trianguliceps is not sufficient, at least alone, in maintaining the circulation of B. burgdorferi s. l. in wild hosts. In addition, anthropogenic factors might affect the distribution of I. ricinus ticks and, hence, their pathogens, thus shaping the landscape of tick-borne disease risk for humans.
Head inversion technique to restore physiological conjunctival structure for surgical treatment of primary pterygium
Authors: Yoshitomi Fumiaki , Oshika Tetsuro 
Published: November 2018

AbstractWe describe a new surgical technique to treat primary pterygium, the head inversion technique, with its surgical outcomes. Seventy-five eyes of 75 consecutive patients with primary pterygium undergoing surgical treatment were included. The pterygium head and body were bluntly separated from the cornea and inverted onto the nasal conjunctival area. By injecting a balanced salt solution subconjunctivally, the conjunctiva was ballooned and smoothed. Two or three interrupted 8–0 virgin silk sutures were placed to secure the inverted conjunctiva in place. No adjunctive therapy was used during and after surgery. Postoperatively, one eye showed pterygium recurrence at 233 days, in which an unintended conjunctival hole was made during surgery. The Kaplan-Meier analysis showed that the recurrence rate at 1 year was 2.4%. In 43 eyes which were followed up for longer than 6 months, the vascular loop, which is characteristic of normal limbal structure, appeared on the nasal conjunctiva in 41 eyes (95.3%). The palisades of Vogt were found on the nasal limbus postoperatively in 13 eyes (30.2%). The pterygium head inversion technique was an effective treatment for primary pterygium. By separating the pterygium from the cornea and inverting the intact pterygium head onto the nasal conjunctival site, the conjunctiva restored near physiological status after surgery.
Unusual indication of Cell therapy for hip osteonecrosis after pregnancy
Authors: Hernigou Philippe , Rigoulot Guillaume , Auregan Jean Charles , Housset Victor , Bastard Claire , Dubory Arnaud , Lachaniette Charles Henri Flouzat 
Published: November 2018

Purpose: Osteonecrosis is a rare event during or after pregnancy. Due to the low number of cases, there is no report of long-term results after conservative surgery in this population.
Method: From 1992 to 2010, 145 consecutive female patients with unilateral symptomatic (94 stage I and 51 stage II) left hip osteonecrosis (ON) related to pregnancy were treated between 4 and 16 months after delivery with percutaneous mesenchymal stem cell (MSC) injection obtained from bone marrow concentration. The average total number of MSCs (counted as number of colonies forming units-fibroblast) injected in the hip was 185 000 ± 65 000 cells (range 95 000–240 000 cells).
Results: At the most recent follow-up (average 15 years after hip surgery, range 8–25 years), among the 145 hips included in the study, 4 hips (2.7%) had collapsed and were treated with total hip arthroplasty (THA). Thirty-two of the 94 stage I had progressed to stage II; and 4 of the 51 stage II had progressed to stage III and collapse. The other 141 hips (97.3%) were without collapse and pain free. On MRI, as percentage of the volume of the femoral head, the osteonecrosis had decreased from 34.5% pre-operatively to 6% at the most recent follow-up. For women who had other children after treatment, a subsequent pregnancy was not associated with osteonecrosis.
Conclusion: Patients with hip osteonecrosis following pregnancy had a low conversion rate to THA when treated early with cell therapy.
Effektive Einarbeitung
Authors: Weiß Claudia , Zoller Richard 
Published: November 2018

ZusammenfassungDie Digitalisierung von Informationssystemen macht auch vor Kliniken nicht Halt.
Die Einarbeitung der Pflegefachkräfte in die Funktionsweise und Anwendung eines
Patientendatenmanagementsystems verläuft in aller Regel parallel zum
Stationsalltag. Am Beispiel des Universitätsklinikums Bonn schildern die beiden
Autoren, wie den Mitarbeitern der Einstieg erleichtert und der Umgang mit dem
System effektiv gestaltet werden kann.
Normocalcemic Primary Hyperparathyroidism: A Comparison with the Hypercalcemic Form in a Tertiary Referral Population
Authors: Pierreux Jan , Bravenboer Bert 
Published: November 2018

AbstractNormocalcemic primary hyperparathyroidism (NPHPT) is a formally recognized variant of primary hyperparathyroidism (PHPT), characterized by normal total and ionized serum calcium concentrations and elevated parathyroid hormone (PTH) levels, in the absence of secondary causes for hyperparathyroidism. NPHPT has been studied previously, but data are limited and confounded. We aimed to compare the clinical and biochemical data of normocalcemic and hypercalcemic subjects in a hospital-based population.We retrospectively analysed the medical records of 131 subjects diagnosed with PHPT at the university hospital Brussels (UZ Brussel) between January 1st 2007 and December 31st 2016, including 25 normocalcemic and 106 hypercalcemic subjects.The mean values of age, BMI, sex, serum 25-OH vitamin D levels and urinary phosphate excretion were comparable between both groups. Subjects diagnosed with NPHPT had significantly lower plasma PTH levels, lower urinary calcium excretion and lower serum creatinine levels compared to the hypercalcemic subjects with PHPT. Corresponding eGFR values were higher in the normocalcemic group. Normocalcemic subjects (NPHPT) presented with a high prevalence of nephrolithiasis (36%), fragility fractures (12%) and osteoporosis (25%). Clinical manifestations and BMD measurements revealed no statistically significant differences between both groups.Our data show a relative prevalence of 19% NPHPT in PHPT. NPHPT may present the earliest form of PHPT with an extension in time, but is not an indolent disease state. Normocalcemic subjects should be managed as hypercalcemic subjects with PHPT. Further research regarding the pathophysiology and natural course of NPHPT is required.
Association Between Plasma Concentration of Klotho Protein, Osteocalcin, Leptin, Adiponectin, and Bone Mineral Density in Patients with Chronic Kidney Disease
Authors: Marchelek-Mysliwiec Małgorzata , Wisniewska Magda , Nowosiad-Magda Monika , Safranow Krzysztof , Kwiatkowska Ewa , Banach Bolesław , Dołegowska Barbara , Dołegowska Katarzyna , Stepniewska Joanna , Domanski Leszek , Pawlik Andrzej , Ciechanowski Kazimierz 
Published: November 2018

AbstractPatients with early-stage chronic kidney disease (CKD) are susceptible to changes in metabolic processes. Partial loss of kidney function leads to homoeostatic disturbances in bone and fatty tissue. The aim of this study was to investigate the association between plasma concentrations of Klotho protein, FGF23, leptin, adiponectin, osteocalcin, and bone mineral density (BMD) in patients with CKD in the pre-dialysis period. The study involved 52 patients with CKD and 23 patients with no kidney disease. In both groups, BMD, body mass index and serum or plasma concentrations of lipids, glucose, creatinine, calcium, phosphorus, parathormone, leptin, adiponectin, osteocalcin, Klotho, and FGF23 were measured. The group with CKD had statistically significant higher concentrations of leptin (p<0.001), parathormone (p<0.001), and osteocalcin (p<0.001) in comparison with the control group. Patients with CKD also had statistically significant lower BMD in the femoral neck in comparison with the control group. Osteocalcin correlated negatively with BMD. The results of our study suggest that elevated osteocalcin is the most sensitive marker of decreased bone mass in patients with CKD. Osteocalcin correlated negatively with BMD and GFR. The loss of bone mass in CKD patients was greatest in the femoral neck.