bluuebunny/crossref_metadata_2025_split huggingface dataset:
Acorn cotyledons are larger than their seedlings' need: evidence from artificial cutting experiments
Authors: Yi Xianfeng , Wang Zhenyu , Liu Changqu , Liu Guoqiang , Zhang Mingming 
Published: January 2015

AbstractAlthough the consequences of cotyledon removal have been widely studied in oaks producing large acorns, we have little knowledge of at what level cotyledons can be removed without affecting acorn survival and seedling development. In this study, we aimed to test the hypothesis that the amount of energy reserves in cotyledons is more than the demands of seedlings and that large acorns can tolerate seed predation and/or attract seed predators for seed dispersal. Acorn germination rates were not affected even when 60% of cotyledons were cut off at the basal end, suggesting that the energy reserves contained in cotyledons are not essential for acorn survival. Post-cut acorn mass, more than initial acorn mass, appear to be a better predictor of seedling performance, indicating that the energy reserves in cotyledons are sufficient for seedlings. Acorns with large masses sustained cotyledon damage better than small ones with respect to seedling performance. Large acorns were more likely to be dispersed and cached by animals, implying that producing large acorns is more important for oaks to manipulate seed predators and dispersers rather than provide a seedling with cotyledonary reserves.
Molecular evolution and functional divergence of zebrafish (Danio rerio) cryptochrome genes
Authors: Liu Chao , Hu Jia , Qu Chunxiang , Wang Lin , Huang Guodong , Niu Pengfei , Zhong Zhaomin , Hong Fashui , Wang Guanghui , Postlethwait John H. , Wang Han 
Published: January 2015

AbstractCryptochromes function in animal circadian regulation. Zebrafish are known to have six cryptochrome (cry) genes but their evolutionary relationships are not yet fully resolved. Here, comparative genomic analyses revealed that a local duplication of ancestral chordate Cry occurred likely before the first round of vertebrate genome duplication (VGD); following two successive rounds of VGD and subsequent gene losses, coelacanths retained cry1a, cry1b, cry2 and cry3; and following the third-round teleost genome duplication (TGD) and subsequent gene losses, zebrafish retained six cry genes, renamed as cry1aa (zcry1a in the old nomenclature), cry1ab (zcry1b), cry1ba (zcry2a), cry1bb (zcry2b), cry2 (zcry3) and cry3 (zcry4). Molecular evolutionary analyses suggested that zebrafish cry genes have evolved divergent functions, which is further supported by their distinct and rhythmic expression patterns as shown by both in situ hybridization and quantitative real-time PCR. Systematic cell transfection assays divided six Cry proteins into repressive Cry1aa, Cry1ab, Cry1ba and Cry1bb and non-repressive Cry2 and Cry3. Cry2 is non-repressive because it lacks an effective protein-protein interaction domain although it does possess a nuclear localization signal (NLS) motif, whilst Cry3 lacks both an NLS motif and a protein-protein interaction domain. These findings provide a better understanding of evolution of zebrafish cry genes.
FXR antagonism of NSAIDs contributes to drug-induced liver injury identified by systems pharmacology approach
Authors: Lu Weiqiang , Cheng Feixiong , Jiang Jing , Zhang Chen , Deng Xiaokang , Xu Zhongyu , Zou Shien , Shen Xu , Tang Yun , Huang Jin 
Published: January 2015

AbstractNon-steroidal anti-inflammatory drugs (NSAIDs) are worldwide used drugs for analgesic, antipyretic and anti-inflammatory therapeutics. However, NSAIDs often cause several serious liver injuries, such as drug-induced liver injury (DILI) and the molecular mechanisms of DILI have not been clearly elucidated. In this study, we developed a systems pharmacology approach to explore the mechanism-of-action of NSAIDs. We found that the Farnesoid X Receptor (FXR) antagonism of NSAIDs is a potential molecular mechanism of DILI through systematic network analysis and in vitro assays. Specially, the quantitative real-time PCR assay reveals that indomethacin and ibuprofen regulate FXR downstream target gene expression in HepG2 cells. Furthermore, the western blot shows that FXR antagonism by indomethacin induces the phosphorylation of STAT3 (signal transducer and activator of transcription 3), promotes the activation of caspase9 and finally causes DILI. In summary, our systems pharmacology approach provided novel insights into molecular mechanisms of DILI for NSAIDs, which may propel the ways toward the design of novel anti-inflammatory pharmacotherapeutics.
Crustal thickness control on Sr/Y signatures of recent arc magmas: an Earth scale perspective
Authors: Chiaradia Massimo 
Published: January 2015

AbstractArc magmas originate in subduction zones as partial melts of the mantle, induced by aqueous fluids/melts liberated by the subducted slab. Subsequently, they rise through and evolve within the overriding plate crust. Aside from broadly similar features that distinguish them from magmas of other geodynamic settings (e.g., mid-ocean ridges, intraplate), arc magmas display variably high Sr/Y values. Elucidating the debated origin of high Sr/Y signatures in arc magmas, whether due to mantle-source, slab melting or intracrustal processes, is instrumental for models of crustal growth and ore genesis. Here, using a statistical treatment of >23000 whole rock geochemical data, I show that average Sr/Y values and degree of maturation (MgO depletion at peak Sr/Y values) of 19 out of 22 Pliocene-Quaternary arcs correlate positively with arc thickness. This suggests that crustal thickness exerts a first order control on the Sr/Y variability of arc magmas through the stabilization or destabilization of mineral phases that fractionate Sr (plagioclase) and Y (amphibole ± garnet). In fact, the stability of these mineral phases is function of the pressure at which magma evolves, which depends on crustal thickness. The data presented show also that high Sr/Y Pliocene-Quaternary intermediate-felsic arc rocks have a distinct origin from their Archean counterparts.
PhenomeExpress: A refined network analysis of expression datasets by inclusion of known disease phenotypes
Authors: Soul Jamie , Hardingham Timothy E. , Boot-Handford Raymond P. , Schwartz Jean-Marc 
Published: January 2015

AbstractWe describe a new method, PhenomeExpress, for the analysis of transcriptomic datasets to identify pathogenic disease mechanisms. Our analysis method includes input from both protein-protein interaction and phenotype similarity networks. This introduces valuable information from disease relevant phenotypes, which aids the identification of sub-networks that are significantly enriched in differentially expressed genes and are related to the disease relevant phenotypes. This contrasts with many active sub-network detection methods, which rely solely on protein-protein interaction networks derived from compounded data of many unrelated biological conditions and which are therefore not specific to the context of the experiment. PhenomeExpress thus exploits readily available animal model and human disease phenotype information. It combines this prior evidence of disease phenotypes with the experimentally derived disease data sets to provide a more targeted analysis. Two case studies, in subchondral bone in osteoarthritis and in Pax5 in acute lymphoblastic leukaemia, demonstrate that PhenomeExpress identifies core disease pathways in both mouse and human disease expression datasets derived from different technologies. We also validate the approach by comparison to state-of-the-art active sub-network detection methods, which reveals how it may enhance the detection of molecular phenotypes and provide a more detailed context to those previously identified as possible candidates.
Automated Analysis of Cell-Matrix Adhesions in 2D and 3D Environments
Authors: Broussard Joshua A. , Diggins Nicole L. , Hummel Stephen , Georgescu Walter , Quaranta Vito , Webb Donna J. 
Published: January 2015

AbstractCell-matrix adhesions are of great interest because of their contribution to numerous biological processes, including cell migration, differentiation, proliferation, survival, tissue morphogenesis, wound healing and tumorigenesis. Adhesions are dynamic structures that are classically defined on two-dimensional (2D) substrates, though the need to analyze adhesions in more physiologic three-dimensional (3D) environments is being increasingly recognized. However, progress has been greatly hampered by the lack of available tools to analyze adhesions in 3D environments. To address this need, we have developed a platform for the automated analysis, segmentation and tracking of adhesions (PAASTA) based on an open source MATLAB framework, CellAnimation. PAASTA enables the rapid analysis of adhesion dynamics and many other adhesion characteristics, such as lifetime, size and location, in 3D environments and on traditional 2D substrates. We manually validate PAASTA and utilize it to quantify rate constants for adhesion assembly and disassembly as well as adhesion lifetime and size in 3D matrices. PAASTA will be a valuable tool for characterizing adhesions and for deciphering the molecular mechanisms that regulate adhesion dynamics in 3D environments.
Simple and mild biomolecule‐assisted green route to nanosheet‐built zinc indium sulphide microspheres
Authors: Cai Wen , Wang Aiwu , Rao Tingke , Hu Jie , Fu Li , Zhong Jiasong , Xiang Weidong 
Published: January 2015

A simple and mild green route has been developed to synthesise zinc indium sulphide nanopowders with L‐cysteine as the sulphur source and complexing agent under hydrothermal conditions at 160 °C for 12 h. The crystal structure, morphologies and chemical composition of the obtained nanopowders are conﬁrmed by X‐ray powder diffraction, field‐emission scanning electron microscopy, energy dispersive spectrometry, transmission electron microscopy and selected area electron diffraction. Results reveal that the synthesised nanopowder is comprised of microspheres with nanosheets and the diameter of the microspheres and the thickness of the nanosheets are 100 nm–2 μm and 10–50 nm, respectively. Moreover, a possible formation mechanism for the zinc indium sulphide product is briefly discussed. The present route would provide an alternative strategy to prepare other II–III–VI ternary metal sulphide nanocrystals.
An Introduction to Free Geographic Information Systems in Fisheries Science
Authors: Neely Ben C. , Eder Brandon L. 
Published: January 2015

Abstract
Geographic information systems (GIS) are powerful tools for analysis and interpretation of spatial data commonly encountered in fisheries science. We presented details of GIS use in fisheries management in a prior study and found cost to be a factor limiting GIS use. This article introduces fisheries managers to free or open-source GIS. Free or open-source GIS are readily available, powerful tools capable of performing a variety of spatial analyses. We strongly encourage managers wishing to perform spatial analyses, but who are unable to purchase software, to consider free GIS.
Los Sistemas de Información Geográfica (GIS) son una herramienta poderosa para el análisis e interpretación de datos espaciales comúnmente encontrados en la ciencia pesquera. Se presentan los detalles del uso del GIS en el manejo de pesquerías aplicado en un estudio previo, encontrando que el costo era un factor que limitaba el uso del GIS. En este artículo se introduce a los manejadores de pesquerías un GIS gratuito o de acceso abierto. Este GIS gratuito ya está disponible y contiene herramientas poderosas, capaces de realizar una variedad de análisis espaciales. Se recomienda ampliamente a los manejadores que deseen realizar análisis espaciales, pero no puedan comprar el software, a que consideren el GIS gratuito.
Guiding Principles for Development of Effective Commercial Fishery Monitoring Programs
Authors: Zollett Erika A. , Trumble Robert J. , Swasey Jill H. , Stebbins Shawn B. 
Published: January 2015

Abstract
Monitoring of fishing activities is an essential component of successful fisheries management that can provide verifiable fishery-dependent data on fishing activities and help assess performance and success of fisheries management plans. Fishery managers and stakeholders have often struggled in developing and implementing effective monitoring programs due to lack of information, funding, and peer-to-peer learning from existing monitoring programs. This article draws on the experience of over 25 national and international monitoring experts and reflects the most important lessons learned from commercial fisheries regarding the development and implementation of effective monitoring programs. The article discusses a set of “guiding principles,” developed in consultation with the monitoring experts, which provide fishery managers and stakeholders with cumulative knowledge and references to more easily develop comprehensive, appropriate, and effective monitoring approaches.
El monitoreo de actividades pesqueras es un componente esencial en las pesquerías manejadas adecuadamente y puede ofrecer datos verificables, dependientes de la pesquería, acerca de las actividades de pesca y ayuda a evaluar el desempeño y éxito de los planes de manejo. Manejadores e involucrados en las pesquerías suelen batallar con el desarrollo e implementación de programas efectivos de monitoreo debido a la falta de información, fondos y aprendizaje por parte de otros pares que participan en programas ya existentes de monitoreo. Este artículo muestra la experiencia de 25 expertos nacionales e internacionales y refleja las lecciones aprendidas más relevantes en lo concerniente al desarrollo e implementación de programas efectivos de monitoreo. También se discute una serie de “directrices” derivadas de la consulta con expertos en monitoreo, que brindan a manejadores e involucrados el conocimiento acumulado y las referencias que permiten más fácilmente desarrollar enfoques de monitoreo sistemáticos, adecuados y efectivos.
Snapshot on carbapenemase-producing Pseudomonas aeruginosa and Acinetobacter baumannii in Bucharest hospitals reveals unusual clones and novel genetic surroundings for blaOXA-23
Authors: Gheorghe Irina , Novais Ângela , Grosso Filipa , Rodrigues Carla , Chifiriuc Mariana Carmen , Lazar Veronica , Peixe Luísa 
Published: January 2015

Abstract

Objectives
The present study was designed to provide a snapshot on carbapenemase-producing Pseudomonas aeruginosa (n = 11) and Acinetobacter baumannii (n = 7) isolates in hospitalized patients (November 2011, January–March 2012) from two main hospitals in Bucharest, south Romania.

Methods
Clonality among isolates was established by PFGE, MLST and Fourier transform infrared spectroscopy. Carbapenemases were screened by the Blue-Carba test, PCR and sequencing. Transferability of blaOXA-23 was tested by conjugation and plasmid typing (number, size and identity) was assessed by S1-PFGE, replicon typing, hybridization and PCR mapping.

Results
All P. aeruginosa isolates carried chromosomally located blaVIM-2, associated with a common class 1 integron (aacA7-blaVIM-2) or an atypical configuration (aacA7-blaVIM-2-dfrB5-tniC). These isolates belonged to unusual lineages; mostly ST233 disseminated in one hospital unit, with ST364 and ST1074 also being detected. A. baumannii isolates carried blaOXA-23 in Tn2008, which was found truncating a TnaphA6 transposon located in a common 60 kb GR6 (aci6) pABKp1-like conjugative plasmid in highly related CC92 clones (ST437, ST764 and ST765), where CC stands for clonal complex.

Conclusions
Our results show the spread of VIM-2-producing P. aeruginosa and OXA-23-producing A. baumannii clinical isolates in two hospitals from Bucharest and highlight a peculiar population structure in this Eastern European country. Also, we demonstrate the dissemination of a common and conjugative aci6 pABKp1-like plasmid scaffold in different A. baumannii clones and we report the first known identification of Tnaph6-carrying pACICU2-like plasmids in Europe.
ST-246 is a key antiviral to inhibit the viral F13L phospholipase, one of the essential proteins for orthopoxvirus wrapping
Authors: Duraffour Sophie , Lorenzo María M. , Zöller Gudrun , Topalis Dimitri , Grosenbach Doug , Hruby Dennis E. , Andrei Graciela , Blasco Rafael , Meyer Hermann , Snoeck Robert 
Published: January 2015

AbstractObjectivesST-246 is one of the key antivirals being developed to fight orthopoxvirus (OPV) infections. Its exact mode of action is not completely understood, but it has been reported to interfere with the wrapping of infectious virions, for which F13L (peripheral membrane protein) and B5R (type I glycoprotein) are required. Here we monitored the appearance of ST-246 resistance to identify its molecular target.MethodsVaccinia virus (VACV), cowpox virus (CPXV) and camelpox virus (CMLV) with reduced susceptibility to ST-246 were selected in cell culture and further characterized by antiviral assays and immunofluorescence. A panel of recombinant OPVs was engineered and a putative 3D model of F13L coupled with molecular docking was used to visualize drug–target interaction. The F13L gene of 65 CPXVs was sequenced to investigate F13L amino acid heterogeneity.ResultsAmino acid substitutions or insertions were found in the F13L gene of six drug-resistant OPVs and production of four F13L-recombinant viruses confirmed their role(s) in the occurrence of ST-246 resistance. F13L, but not B5R, knockout OPVs showed resistance to ST-246. ST-246 treatment of WT OPVs delocalized F13L- and B5R-encoded proteins and blocked virus wrapping. Putative modelling of F13L and ST-246 revealed a probable pocket into which ST-246 penetrates. None of the identified amino acid changes occurred naturally among newly sequenced or NCBI-derived OPV F13L sequences.ConclusionsBesides demonstrating that F13L is a direct target of ST-246, we also identified novel F13L residues involved in the interaction with ST-246. These findings are important for ST-246 use in the clinic and crucial for future drug-resistance surveillance programmes.
Risk factors for ambulatory urinary tract infections caused by high-MIC fluoroquinolone-susceptible Escherichia coli in women: results from a large case–control study
Authors: Rattanaumpawan Pinyo , Nachamkin Irving , Bilker Warren B. , Roy Jason A. , Metlay Joshua P. , Zaoutis Theoklis E. , Lautenbach Ebbing 
Published: January 2015

Abstract

Objectives
The prevalence of high-MIC fluoroquinolone-susceptible Escherichia coli (FQSEC) has been increasing. These isolates are one step closer to full fluoroquinolone (FQ) resistance and may lead to delayed response to FQ therapy. Our study aimed to investigate the epidemiology of high-MIC FQSEC in ambulatory urinary tract infections (UTIs).

Patients and methods
A case–control study was conducted at outpatient services within the University of Pennsylvania Health System, Philadelphia. All female subjects with non-recurrent UTI caused by FQSEC (levofloxacin MIC &lt; 4 mg/L) were enrolled. Cases were subjects with high-MIC FQSEC UTI (levofloxacin MIC &gt;0.12 but &lt; 4 mg/L) and controls were subjects with low-MIC FQSEC UTI (levofloxacin MIC ≤0.12 mg/L). Data on microbiology results and baseline characteristics were extracted from electronic medical records.

Results
During the 3 year study period (May 2008–April 2011), 11 287 episodes of E. coli bacteriuria were identified. The prevalence of FQSEC, FQ-intermediate susceptible E. coli and FQ-resistant E. coli was 75.0%, 0.4% and 24.6%, respectively. A total of 2001 female subjects with FQSEC UTI were enrolled into our study (165 cases and 1836 controls). Independent risk factors for high-MIC FQ susceptibility included Asian race (OR = 2.92; 95% CI = 1.29–6.58; P = 0.02), underlying renal disease (OR = 2.18; 95% CI = 1.15–4.14; P = 0.02) and previous nitrofurantoin exposure (OR = 8.86; 95% CI = 1.95–40.29; P = 0.005).

Conclusions
Asian race, underlying renal disease and previous exposure to nitrofurantoin were identified as independent risk factors for high-MIC FQSEC. There may be some factors that are more common in Asians, which may result in the selection of high-MIC FQSEC. Further studies are necessary to explore these findings.
Pharmacokinetic profile of raltegravir, elvitegravir and dolutegravir in plasma and mucosal secretions in rhesus macaques
Authors: Massud Ivana , Martin Amy , Dinh Chuong , Mitchell James , Jenkins Leecresia , Heneine Walid , Pau Chou-Pong , García-Lerma J. Gerardo 
Published: January 2015

Abstract

Objectives
Pharmacokinetic studies in animal models are important for assessing the prophylactic potential of antiretroviral drugs for HIV prevention. This study sought to identify clinically relevant doses of the marketed integrase inhibitors raltegravir, elvitegravir and dolutegravir in macaques and investigate drug penetration and antiviral activity in mucosal secretions.

Methods
Macaques received one oral dose of raltegravir, elvitegravir or dolutegravir alone or in combination with emtricitabine and tenofovir disoproxil fumarate followed by drug level measurements in blood and rectal and vaginal secretions. Antiviral activity was investigated in TZM-bl cells exposed to SHIV162p3 in the presence of rectal secretions collected from treated animals.

Results
Plasma drug concentrations with 50 mg/kg raltegravir or elvitegravir were within the range seen in humans receiving 400–800 mg of raltegravir or 800 mg of unboosted elvitegravir but lower than with 150 mg of elvitegravir boosted with cobicistat. AUC0–24 values for dolutegravir increased proportionally with the dose, with a calculated human-equivalent dose of 20 mg/kg. Elvitegravir showed the highest penetration in rectal and vaginal fluids despite the absence of pharmacological boosting, followed by raltegravir and dolutegravir. Rectal secretions collected at 24 h from treated macaques blocked infection of TZM-bl cells by 50% at dilutions of 1/1000 (raltegravir), 1/800 (dolutegravir) and &gt;1/30 000 (elvitegravir).

Conclusions
We defined macaque doses of HIV integrase inhibitors that recapitulate human clinical doses, which will facilitate efficacy and dose escalation studies in macaques. High and sustained drug concentrations and activity in mucosal secretions suggest that integrase inhibitors are promising candidates for HIV prevention.
Emergence of azole-resistant invasive aspergillosis in HSCT recipients in Germany
Authors: Steinmann J. , Hamprecht A. , Vehreschild M. J. G. T. , Cornely O. A. , Buchheidt D. , Spiess B. , Koldehoff M. , Buer J. , Meis J. F. , Rath P.-M. 
Published: January 2015

Abstract

Objectives
Aspergillus fumigatus is the most common agent of invasive aspergillosis (IA). In recent years, resistance to triazoles, the mainstay of IA therapy, has emerged in different countries worldwide. IA caused by azole-resistant A. fumigatus (ARAF) shows an exceedingly high mortality. In this study, IA due to ARAF isolates in HSCT recipients in Germany was investigated.

Methods
The epidemiology of azole resistance in IA was analysed in two German haematology departments. Between 2012 and 2013, 762 patients received HSCT in Essen (n = 388) and Cologne (n = 374). Susceptibility testing of A. fumigatus isolates was performed by Etest, followed by EUCAST broth microdilution testing if elevated MICs were recorded. In all ARAF isolates the cyp51A gene was sequenced and the genotype was determined by microsatellite typing using nine short tandem repeats.

Results
In total, A. fumigatus was recovered from 27 HSCT recipients. Eight patients had azole-resistant IA after HSCT, and seven of the cases were fatal (88%). All except one patient received antifungal prophylaxis (in five cases triazoles). TR34/L98H was the most common mutation (n = 5), followed by TR46/Y121F/T289A (n = 2). In one resistant isolate no cyp51A mutation was detected. Genotyping revealed genetic diversity within the German ARAF isolates and no clustering with resistant isolates from the Netherlands, India and France.

Conclusions
This report highlights the emergence of azole-resistant IA with TR34/L98H and TR46/Y121F/T289A mutations in HSCT patients in Germany and underscores the need for systematic antifungal susceptibility testing of A. fumigatus.