bluuebunny/crossref_metadata_2025_split huggingface dataset:
A knowledge‐based molecular screen uncovers a broad‐spectrum OsSWEET14 resistance allele to bacterial blight from wild rice
Authors: Hutin Mathilde , Sabot François , Ghesquière Alain , Koebnik Ralf , Szurek Boris 
Published: October 2015

SummaryTranscription activator‐like (TAL) effectors are type III‐delivered transcription factors that enhance the virulence of plant pathogenic Xanthomonas species through the activation of host susceptibility (S) genes. TAL effectors recognize their DNA target(s) via a partially degenerate code, whereby modular repeats in the TAL effector bind to nucleotide sequences in the host promoter. Although this knowledge has greatly facilitated our power to identify new S genes, it can also be easily used to screen plant genomes for variations in TAL effector target sequences and to predict for loss‐of‐function gene candidates in silico. In a proof‐of‐principle experiment, we screened a germplasm of 169 rice accessions for polymorphism in the promoter of the major bacterial blight susceptibility S gene OsSWEET14, which encodes a sugar transporter targeted by numerous strains of Xanthomonas oryzae pv. oryzae. We identified a single allele with a deletion of 18 bp overlapping with the binding sites targeted by several TAL effectors known to activate the gene. We show that this allele, which we call xa41(t), confers resistance against half of the tested Xoo strains, representative of various geographic origins and genetic lineages, highlighting the selective pressure on the pathogen to accommodate OsSWEET14 polymorphism, and reciprocally the apparent limited possibilities for the host to create variability at this particular S gene. Analysis of xa41(t) conservation across the Oryza genus enabled us to hypothesize scenarios as to its evolutionary history, prior to and during domestication. Our findings demonstrate that resistance through TAL effector‐dependent loss of S‐gene expression can be greatly fostered upon knowledge‐based molecular screening of a large collection of host plants.
Hemoglobin oxidation at functional amino acid residues during routine storage of red blood cells
Authors: Wither Matthew , Dzieciatkowska Monika , Nemkov Travis , Strop Pavel , D'Alessandro Angelo , Hansen Kirk C. 
Published: October 2015

BACKGROUNDRoutine storage of red blood cells (RBCs) results in the progressive accumulation of storage lesions. While the clinical relevance of these lesions is still a matter of debate, alterations to RBC morphology and biochemistry, especially in terms of energy and redox homeostasis, are likely to affect RBC physiology and functionality at a minimum. Identification of oxidative modifications that accumulate on key RBC proteins will help bridge the gap between storage induced alterations and post‐transfusion RBC viability.STUDY DESIGN AND METHODSFive AS‐3 units were analyzed during routine storage via one‐dimensional sodium dodecyl sulfate–polyacrylamide gel electrophoresis–nano‐high‐performance liquid chromatography coupled online with tandem mass spectrometry and advanced database searches.RESULTSWe identified oxidative modifications to functional residues of hemoglobin (Hb) beta chain, including proximal histidine, cysteine beta 94 (counting initiator methionine in the sequence), and histidine 144. Semiquantitative analysis indicates that up to approximately 20% of total Hb could be targeted by these oxidative modifications that are overlooked by standard proteomics approaches using routine database search conditions. Progressive accumulation of oxidized residues in stored RBCs and selective accumulation in vesicles was observed, further substantiating the hypothesis that vesiculation represents a self‐protective mechanism in ageing RBCs.CONCLUSIONSeveral of the oxidized residues identified play well‐established roles in heme iron coordination, 2,3‐diphosphoglycerate binding, and nitric oxide homeostasis. Further functional and structural studies are necessary to determine possible associations between these modifications and impaired gas transport homeostasis in RBCs from old units.
Pneumothorax in a dog caused by necrotizing pneumonia secondary to heatstroke
Authors: Garber Jocelyn B. , Saile Katrin , Rademacher Nathalie , Wignall James R. , McLaughlin Leslie D. , Ryan Kirk A. 
Published: October 2015

AbstractObjectiveTo describe the clinical course, diagnostic findings, medical and surgical treatments, and outcome in a dog with spontaneous pneumothorax secondary to necrotizing pneumonia thought to be a delayed complication of heatstroke.Case SummaryA 1.5‐year‐old Labrador Retriever developed spontaneous pneumothorax 12 days after an episode of exertional heat stroke. Computed tomography was performed and showed bilateral pneumothorax and multifocal pulmonary consolidation, especially at the lung periphery. A median sternotomy was performed, and multifocal, well‐demarcated areas of consolidated pulmonary tissue with purple discoloration were identified and resected from the right middle, right caudal, and accessory lung lobes. Histologic examination of the resected pulmonary tissue indicated necrotizing pneumonia, and bacteriologic culture of the tissue resulted in growth of Pseudomonas aeruginosa. Examination of tissue from a pectoral muscle biopsy performed at this time showed necrotizing myopathy. The dog was discharged 7 days after surgery and made a full recovery.New or Unique Information ProvidedThis case report describes pneumothorax and multifocal necrotizing pneumonia as a delayed complication of heatstroke, and provides the first description of the computed tomography appearance of histologically confirmed necrotizing pneumonia in a dog. Multifocal necrotizing pneumonia with or without pneumothorax should be considered in dogs that develop respiratory distress following severe systemic illness.
Cryptic diversity in a widespread land snail: revision of the genus Xanthomelon Martens, 1860 from the Australian Monsoon Tropics (Pulmonata, Camaenidae)
Authors: Köhler Frank , Burghardt Ingo 
Published: October 2015

The camaenid genus Xanthomelon is widely distributed throughout the Australian Monsoon Tropics and eastern Queensland, with nine species currently being recognised in Australia based exclusively on shell features. Due to the combination of poor taxonomic descriptions and considerable variation in shell characters, considerable confusion surrounds the number of species in the Northern Territory (NT), their key characteristics and distributions. To uncover the full taxonomic diversity of Xanthomelon in the NT, we employed molecular phylogenetics and comparative studies of morphology/anatomy. Based on the patterns of mitochondrial differentiation as well as comparative shell and penial anatomy, we demonstrate that previous studies failed to correctly delineate species. We recognise five species in the NT, of which two (X. darwinense n. sp. and X. arnhemense n. sp.) are newly described. These species have distributions that range from narrowly endemic to most widely distributed throughout most of the Australian Monsoon Tropics. The ranges of multiple species overlap extensively with each other, which is a rather unusual phenomenon amongst the Australian Camaenidae.
Development of a Multiplex PCR Assay for Rapid Molecular Serotyping of Haemophilus parasuis
Authors: Howell Kate J. , Peters Sarah E. , Wang Jinhong , Hernandez-Garcia Juan , Weinert Lucy A. , Luan Shi-Lu , Chaudhuri Roy R. , Angen Øystein , Aragon Virginia , Williamson Susanna M. , Parkhill Julian , Langford Paul R. , Rycroft Andrew N. , Wren Brendan W. , Maskell Duncan J. , Tucker Alexander W. 
Published: October 2015

ABSTRACTHaemophilus parasuiscauses Glässer's disease and pneumonia in pigs. Indirect hemagglutination (IHA) is typically used to serotype this bacterium, distinguishing 15 serovars with some nontypeable isolates. The capsule loci of the 15 reference strains have been annotated, and significant genetic variation was identified between serovars, with the exception of serovars 5 and 12. A capsule locus andin silicoserovar were identified for all but two nontypeable isolates in our collection of >200 isolates. Here, we describe the development of a multiplex PCR, based on variation within the capsule loci of the 15 serovars ofH. parasuis, for rapid molecular serotyping. The multiplex PCR (mPCR) distinguished between all previously described serovars except 5 and 12, which were detected by the same pair of primers. The detection limit of the mPCR was 4.29 × 105ng/μl bacterial genomic DNA, and high specificity was indicated by the absence of reactivity against closely related commensalPasteurellaceaeand other bacterial pathogens of pigs. A subset of 150 isolates from a previously sequencedH. parasuiscollection was used to validate the mPCR with 100% accuracy compared to thein silicoresults. In addition, the twoin silico-nontypeable isolates were typeable using the mPCR. A further 84 isolates were analyzed by mPCR and compared to the IHA serotyping results with 90% concordance (excluding those that were nontypeable by IHA). The mPCR was faster, more sensitive, and more specific than IHA, enabling the differentiation of 14 of the 15 serovars ofH. parasuis.
Evaluation of the Rapidec Carba NP Test for Detection of Carbapenemases in Enterobacteriaceae
Authors: Hombach Michael , von Gunten Barbara , Castelberg Claudio , Bloemberg Guido V. 
Published: October 2015

ABSTRACT

This study evaluated the performance of the Rapidec Carba NP test, which was introduced recently into the market for the detection of carbapenemase production in a broad spectrum of β-lactamase-producing
Enterobacteriaceae
clinical isolates. In total, 252 clinical
Enterobacteriaceae
isolates that had been genetically characterized with respect to carbapenemase, extended-spectrum β-lactamase (ESBL), and AmpC genes were analyzed; 51/252 isolates (20.2%) were genetically confirmed to be carbapenemase producers, whereas 201/252 isolates (79.8%) were genetically negative for the presence of carbapenemase genes. The Rapidec Carba NP test was applied according to the manufacturer's instructions, and results were read after 30 and 120 min of incubation. The overall sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) of the Rapidec Carba NP test were 90.2%, 100%, 100%, and 97.6%, respectively, when the manufacturer's instructions were followed. Four of 5 false-negative results occurred with OXA-48-like enzymes. After an incubation time of 30 min, the sensitivity was 49%. The sensitivity increased to 100% when the recommended bacterial inoculum was doubled and the test was read strictly after 120 min of incubation. The Rapidec Carba NP test is a useful tool for the reliable confirmation of carbapenemase-producing
Enterobacteriaceae
isolates. The test should be read strictly after 120 min of incubation and the inoculum should be larger than recommended by the manufacturer.
Intercellular Transmission of Viral Populations with Vesicles
Authors: Altan-Bonnet Nihal , Chen Ying-Han 
Published: October 2015

ABSTRACT

A common paradigm holds that during cell-to-cell transmission, viruses behave as lone soldiers. Recently, we discovered not only that enteroviruses are transmitted via vesicles as populations of viral particles but also that this type of transmission enhances their infection efficiency (Y. H. Chen et al., Cell
160:
619–630, 2015). This mechanism could be advantageous for the overall fitness of the viral population, promoting genetic interplay by enabling viral quasispecies to collectively infect a susceptible host cell. Here, we discuss these findings in the context of viral pathogenesis and also propose that this novel type of vesicular transmission is widespread among different virus families and includes populations of both viral particles and naked viral genomes.
Infection of Mouse Macrophages by Seasonal Influenza Viruses Can Be Restricted at the Level of Virus Entry and at a Late Stage in the Virus Life Cycle
Authors: Londrigan Sarah L. , Short Kirsty R. , Ma Joel , Gillespie Leah , Rockman Steven P. , Brooks Andrew G. , Reading Patrick C. 
Published: October 2015

ABSTRACT
Airway epithelial cells are susceptible to infection with seasonal influenza A viruses (IAV), resulting in productive virus replication and release. Macrophages (MΦ) are also permissive to IAV infection; however, virus replication is abortive. Currently, it is unclear how productive infection of MΦ is impaired or the extent to which seasonal IAV replicate in MΦ. Herein, we compared mouse MΦ and epithelial cells for their ability to support genomic replication and transcription, synthesis of viral proteins, assembly of virions, and release of infectious progeny following exposure to genetically defined IAV. We confirm that seasonal IAV differ in their ability to utilize cell surface receptors for infectious entry and that this represents one level of virus restriction. Following virus entry, we demonstrate synthesis of all eight segments of genomic viral RNA (vRNA) and mRNA, as well as seven distinct IAV proteins, in IAV-infected mouse MΦ. Although newly synthesized hemagglutinin (HA) and neuraminidase (NA) glycoproteins are incorporated into the plasma membrane and expressed at the cell surface, electron microscopy confirmed that virus assembly was defective in IAV-infected MΦ, defining a second level of restriction late in the virus life cycle.

IMPORTANCE
Seasonal influenza A viruses (IAV) and highly pathogenic avian influenza viruses (HPAI) infect macrophages, but only HPAI replicate productively in these cells. Herein, we demonstrate that impaired virus uptake into macrophages represents one level of restriction limiting infection by seasonal IAV. Following uptake, seasonal IAV do not complete productive replication in macrophages, representing a second level of restriction. Using murine macrophages, we demonstrate that productive infection is blocked late in the virus life cycle, such that virus assembly is defective and newly synthesized virions are not released. These studies represent an important step toward identifying host-encoded factors that block replication of seasonal IAV, but not HPAI, in macrophages.
Ultrastructural Characterization of Turnip Mosaic Virus-Induced Cellular Rearrangements Reveals Membrane-Bound Viral Particles Accumulating in Vacuoles
Authors: Wan Juan , Basu Kaustuv , Mui Jeannie , Vali Hojatollah , Zheng Huanquan , Laliberté Jean-François 
Published: October 2015

ABSTRACT

Positive-strand RNA [(+) RNA] viruses remodel cellular membranes to facilitate virus replication and assembly. In the case of turnip mosaic virus (TuMV), the viral membrane protein 6K
2
plays an essential role in endomembrane alterations. Although 6K
2
-induced membrane dynamics have been widely studied by confocal microscopy, the ultrastructure of this remodeling has not been extensively examined. In this study, we investigated the formation of TuMV-induced membrane changes by chemical fixation and high-pressure freezing/freeze substitution (HPF/FS) for transmission electron microscopy at different times of infection. We observed the formation of convoluted membranes connected to rough endoplasmic reticulum (rER) early in the infection process, followed by the production of single-membrane vesicle-like (SMVL) structures at the midstage of infection. Both SMVL and double-membrane vesicle-like structures with electron-dense cores, as well as electron-dense bodies, were found late in the infection process. Immunogold labeling results showed that the vesicle-like structures were 6K
2
tagged and suggested that only the SMVL structures were viral RNA replication sites. Electron tomography (ET) was used to regenerate a three-dimensional model of these vesicle-like structures, which showed that they were, in fact, tubules. Late in infection, we observed filamentous particle bundles associated with electron-dense bodies, which suggests that these are sites for viral particle assembly. In addition, TuMV particles were observed to accumulate in the central vacuole as membrane-associated linear arrays. Our work thus unravels the sequential appearance of distinct TuMV-induced membrane structures for viral RNA replication, viral particle assembly, and accumulation.

IMPORTANCE
Positive-strand RNA viruses remodel cellular membranes for different stages of the infection process, such as protein translation and processing, viral RNA synthesis, particle assembly, and virus transmission. The ultrastructure of turnip mosaic virus (TuMV)-induced membrane remodeling was investigated over several days of infection. The first change that was observed involved endoplasmic reticulum-connected convoluted membrane accumulation. This was followed by the formation of single-membrane tubules, which were shown to be viral RNA replication sites. Later in the infection process, double-membrane tubular structures were observed and were associated with viral particle bundles. In addition, TuMV particles were observed to accumulate in the central vacuole as membrane-associated linear arrays. This work thus unravels the sequential appearance of distinct TuMV-induced membrane structures for viral RNA replication, viral particle assembly, and accumulation.
Perceptions of data processes in mobile-based versus paper-based health information systems for maternal, newborn and child health: a qualitative study in Andhra Pradesh, India
Authors: Nguyen Lillian H , LeFevre Amnesty E , Jennings Larissa , Agarwal Smisha , Mehl Garrett , Labrique Alain B , Chava Lakshmi Durga 
Published: October 2015

BackgroundMany maternal, newborn and child health (MNCH) programmes have paired community health workers with mobile technologies to strengthen the ability of health information systems (HIS) to track women and children across time and beyond the clinical setting. However, little is known regarding the comparative effectiveness of using mobile technologies to enhance HIS data in resource-poor settings.MethodsFocus group discussions were conducted with community health workers called Health Activists (HAs; n=30), Community Organisation Leaders (n=28), HA Trainers (n=21), district and tribal area officials (n=3) and State Officials (n=4). We analysed user perceptions along seven key HIS processes: data collection, transmission, processing, analysis, display, quality checking and feedback.ResultsThe mobile-based health information system (mHIS) was found to be supportive of the MNCH continuum of care by improving the regularity and timeliness of access to robust data. Respondents noted that data errors were reduced in real time through automated error checking and data processing, which also reduced users’ workloads. The mHIS additionally enabled users to analyse both individual and aggregate data, allowing them to identify specific individuals in need of services or training as well as to identify general trends in service delivery. The system's data display and feedback mechanisms were viewed as improving data use for decision-making. The remaining challenges of the mHIS versus the paper-based HIS included resource, infrastructural and technological barriers that hindered efficient use over time.ConclusionsAs compared to paper-based HIS systems, mobile technologies can improve health information processes in resource-poor settings. More efforts are needed to ensure sufficient financial investment, training and use of mHIS data at all levels of the HIS.
German Cranial Reconstruction Registry (GCRR): protocol for a prospective, multicentre, open registry
Authors: Giese Henrik , Sauvigny Thomas , Sakowitz Oliver W , Bierschneider Michael , Güresir Erdem , Henker Christian , Höhne Julius , Lindner Dirk , Mielke Dorothee , Pannewitz Robert , Rohde Veit , Scholz Martin , Schuss Patrick , Regelsberger Jan 
Published: October 2015

IntroductionOwing to increasing numbers of decompressive craniectomies in patients with malignant middle cerebral artery infarction, cranioplastic surgery becomes more relevant. However, the current literature mainly consists of retrospective single-centre (evidence class III) studies. This leads to a wide variability of technical approaches and clinical outcomes. To improve our knowledge about the key elements of cranioplasty, which may help optimising clinical treatment and long-term outcome, a prospective multicentre registry across Germany, Austria and Switzerland will be established.MethodsAll patients undergoing cranioplastic surgery in participating centres will be invited to join the registry. Technical methods, materials, medical history, adverse events and clinical outcome measures, including modified Rankin scale and EQ-5D, will be assessed at several time points. Patients will be accessible to inclusion either at initial decompressive surgery or when cranioplasty is planned. Scheduled monitoring will be carried out at time of inclusion and subsequently at time of discharge, if any readmission is necessary, and at follow-up presentation. Cosmetic results and patient satisfaction will also be assessed. Collected data will be managed and statistically analysed by an independent biometric institute. The primary endpoint will be mortality, need for operative revision and neurological status at 3 months following cranioplasty.Ethics and disseminationEthics approval was obtained at all participating centres. The registry will provide reliable prospective evidence on surgical techniques, used materials, adverse events and functional outcome, to optimise patient treatment. We expect this study to give new insights in the treatment of skull defects and to provide a basis for future evidence-based therapy regarding cranioplastic surgery.Trial registration numberThis trial is indexed in the German Clinical Trials Register (DRKS-ID: DRKS00007931). The Universal Trial Number (UTN) is U1111-1168-7425.
Half-metallic properties of the new Ti2YPb(Y = Co, Fe) Heusler alloys
Authors: Hussain Moaid K. , Gao G. Y. , Yao Kai-Lun 
Published: October 2015

The half-metallic properties of Ti2YPb(Y = Co, Fe) Heusler alloys with a CuHg2Ti-type structure were examined within the frame of the density functional theory and the Perdew–Burke–Ernzerh of generalized gradient approximation (GGA). Analysis of the electronic band structures and density of states for Ti2YPb(Y = Co, Fe) revealed that the spin-up bands are metallic, whereas the spin-down bands exhibit gaps of 0.73 and 0.70 eV, respectively. The magnetic moments calculated for the Ti2YPb(Y = Co, Fe) alloys were found to be equal to 3 [Formula: see text]/f.u. and 2 [Formula: see text]/f.u., values which both follows the Slater–Pauling rule of [Formula: see text]. The compounds’ negative enthalpy values should encourage their experimental realization in the future. The bandgap was elucidated to be mainly determined by the bonding and antibonding states created from the hybridizations of the d states between the Ti(1)–Ti(2) coupling and the Y = Co, Fe atom. The half-metallic properties of the Ti2YPb(Y = Co, Fe) compounds were found to be insensitive to lattice distortion, with full spin polarization achievable within a large range of lattice parameter values, making the alloys suitable for use in practical applications.