bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phenotypically matched vs. traditional screen method for preparing red blood cell units in patients with abnormal placentation: a decision analysis approach
Authors: Pham H. P. , Kim C. H. , Schwartz J. 
Published: July 2014

BackgroundPatients with abnormal placentation are hospitalized approximately 21 days prior to scheduled delivery due to risk of peri‐partum bleeding. It is required to have at least one red blood cell (RBC) unit ready throughout hospitalization. This can be accomplished by performing a type and cross (T&C) every 72 h (traditional method) or providing phenotypically matched RBC units (alternative method).MethodsA Markov‐based model was created to compare the cost‐benefits between these two methods. A patient either undergoes the traditional or alternative method. If the patient already made an antibody and/or has rare phenotypes requiring frozen RBC unit at admission, then she can only enter the traditional method. All patients receive a T&C at the end of the 21st day in order to prepare RBC units for scheduled delivery. Model parameters are derived from literature and institutional experiences.ResultsSimulation was run for modelling of the 21‐day hospitalization of each patient. The expected cost per RBC unit of the traditional method is significantly higher than the alternative method (876·59 vs. 608·32 USD, P‐value <0·01). For each RBC unit, 4·85 h of technician working time is saved by the alternative method. However, to be cost‐beneficial, the alternative method should be used only if the total cost of a RBC unit is <857·67 USD.ConclusionOur model demonstrated that preparing phenotypically matched RBC units at admission is more cost‐beneficial comparing to the traditional method of T&C every 72 h if the cost for the matched unit is <857·67 USD.
Topical 5‐azacytidine accelerates skin wound healing in rats
Authors: Gomes Fabiana S. , de‐Souza Gabriela F. , Nascimento Lucas F. , Arantes Eva L. , Pedro Rafael M. , Vitorino Daniele C. , Nunez Carla E. , Melo Lima Maria H. , Velloso Lício A. , Araújo Eliana P. 
Published: July 2014

AbstractThe development of new methods to improve skin wound healing may affect the outcomes of a number of medical conditions. Here, we evaluate the molecular and clinical effects of topical 5‐azacytidine on wound healing in rats. 5‐Azacytidine decreases the expression of follistatin‐1, which negatively regulates activins. Activins, in turn, promote cell growth in different tissues, including the skin. Eight‐week‐old male Wistar rats were submitted to 8.0‐mm punch‐wounding in the dorsal region. After 3 days, rats were randomly assigned to receive either a control treatment or the topical application of a solution containing 5‐azacytidine (10 mM) once per day. Photo documentation and sample collection were performed on days 5, 9, and 15. Overall, 5‐azacytidine promoted a significant acceleration of complete wound healing (99.7% ± 0.7.0 vs. 71.2% ± 2.8 on day 15; n = 10; p < 0.01), accompanied by up to threefold reduction in follistatin expression. Histological examination of the skin revealed efficient reepithelization and cell proliferation, as evaluated by the BrdU incorporation method. 5‐Azacytidine treatment also resulted in increased gene expression of transforming growth factor‐beta and the keratinocyte markers involucrin and cytokeratin, as well as decreased expression of cytokines such as tumor necrosis factor‐alpha and interleukin‐10. Lastly, when recombinant follistatin was applied to the skin in parallel with topical 5‐azacytidine, most of the beneficial effects of the drug were lost. Thus, 5‐azacytidine acts, at least in part through the follistatin/activin pathway, to improve skin wound healing in rodents.
Species delimitation in the Chinese bamboo partridge Bambusicola thoracica (Phasianidae; Aves)
Authors: Hung Chih‐Ming , Hung Hsin‐Yi , Yeh Chia‐Fen , Fu Yi‐Qiang , Chen De , Lei Fumin , Yao Cheng‐Te , Yao Chiou‐Ju , Yang Xiao‐Jun , Lai Yu‐Ting , Li Shou‐Hsien 
Published: July 2014

Although tropical and subtropical Asia harbour a high level of species diversity, their species richness can be underestimated because species which are in fact distinct have not been separately identified. In this study, we delimit Bambusicola thoracica into two full species, the Chinese bamboo partridge (B. thoracica) in continental Asia and the Taiwanese bamboo partridge (B. sonorivox) on the island of Taiwan, using coalescent‐based multilocus division and diagnosable vocalization patterns. Isolation‐with‐migration analysis indicated that the two bamboo partridges diverged approximately 1.8 million years ago, with gene flow present most probably during the early stages of their divergence. This conclusion supports the hypothesis that diverging lowland lineages spread across the Asian mainland, and continental islands have more opportunities for secondary contact than highland ones when the sea level was low. Our results imply that conservation of biodiversity in tropical and subtropical Asia could be hindered by overlooking numerous ‘hidden’ species and highlight the importance of re‐examining the taxonomic statuses of species in this region traditionally defined as polytypic.
Random walks on projective spaces
Authors: Benoist Yves , Quint Jean-François 
Published: July 2014

AbstractLet $\def \xmlpi #1{}\def \mathsfbi #1{\boldsymbol {\mathsf {#1}}}\let \le =\leqslant \let \leq =\leqslant \let \ge =\geqslant \let \geq =\geqslant \def \Pr {\mathit {Pr}}\def \Fr {\mathit {Fr}}\def \Rey {\mathit {Re}}G$ be a connected real semisimple Lie group, $V$ be a finite-dimensional representation of $G$ and $\mu $ be a probability measure on $G$ whose support spans a Zariski-dense subgroup. We prove that the set of ergodic $\mu $-stationary probability measures on the projective space $\mathbb{P}(V)$ is in one-to-one correspondence with the set of compact $G$-orbits in $\mathbb{P}(V)$. When $V$ is strongly irreducible, we prove the existence of limits for the empirical measures. We prove related results over local fields as the finiteness of the set of ergodic $\mu $-stationary measures on the flag variety of $G$.
Matrix factorizations via Koszul duality
Authors: Tu Junwu 
Published: July 2014

AbstractIn this paper we prove a version of curved Koszul duality for $\def \xmlpi #1{}\def \mathsfbi #1{\boldsymbol {\mathsf {#1}}}\let \le =\leqslant \let \leq =\leqslant \let \ge =\geqslant \let \geq =\geqslant \def \Pr {\mathit {Pr}}\def \Fr {\mathit {Fr}}\def \Rey {\mathit {Re}}\mathbb{Z}/2\mathbb{Z}$-graded curved coalgebras and their cobar differential graded algebras. A curved version of the homological perturbation lemma is also obtained as a useful technical tool for studying curved (co)algebras and precomplexes. The results of Koszul duality can be applied to study the category of matrix factorizations $\mathsf{MF}(R,W)$. We show how Dyckerhoff’s generating results fit into the framework of curved Koszul duality theory. This enables us to clarify the relationship between the Borel–Moore Hochschild homology of curved (co)algebras and the ordinary Hochschild homology of the category $\mathsf{MF}(R,W)$. Similar results are also obtained in the orbifold case and in the graded case.
Draft Genome Sequencing of Vibrio cholerae O1 El Tor Isolates Collected in the Russian Federation from Imported Cholera Cases
Authors: Kuleshov Konstantin V. , Vodop'ianov Sergey O. , Dedkov Vladimir G. , Markelov Mikhail L. , Kermanov Anton V. , Kruglikov Vladimir D. , Vodop'ianov Alexey S. , Pisanov Ruslan V. , Chemisova Olga S. , Mazrukho Alexey B. , Titova Svetlana V. , Shipulin German A. 
Published: July 2014

ABSTRACT

We report the draft genome sequencing of five
Vibrio cholerae
O1 El Tor clinical isolates collected in the Russian Federation from imported cholera cases in 2006, 2010, and 2012. In the initial phylogenetic analysis, one isolate clustered with the Haiti/Nepal-4 group.
Draft Genome Sequence of
Deinococcus
sp. Strain RL Isolated from Sediments of a Hot Water Spring
Authors: Mahato Nitish Kumar , Tripathi Charu , Verma Helianthous , Singh Neha , Lal Rup 
Published: July 2014

ABSTRACT

Deinococcus
sp. strain RL, a moderately thermophilic bacterium, was isolated from sediments of a hot water spring in Manikaran, India. Here, we report the draft genome (2.79 Mbp) of this strain, which contains 62 contigs and 2,614 coding DNA sequences, with an average G+C content of 69.4%.
Evaluation of FilmArray and Verigene Systems for Rapid Identification of Positive Blood Cultures
Authors: Bhatti M. M. , Boonlayangoor S. , Beavis K. G. , Tesic V. 
Published: July 2014

ABSTRACT
The Verigene tests for Gram-positive and Gram-negative organisms in blood culture and the FilmArray blood culture identification panel were assessed for their ability to identify pathogens from positive blood cultures. Both platforms correctly identified bacteria in 92% of monomicrobial cultures analyzed, with times to identification that were significantly shorter than those for identification from subcultures.
Prolidase Is Required for Early Trafficking Events during Influenza A Virus Entry
Authors: Pohl Marie O. , Edinger Thomas O. , Stertz Silke 
Published: July 2014

ABSTRACT
Influenza A virus (IAV) entry is a multistep process that requires the interaction of the virus with numerous host factors. In this study, we demonstrate that prolidase (PEPD) is a cellular factor required by IAV for successful entry into target cells. PEPD was selected as a candidate during an entry screen performed on nonvalidated primary hits from previously published genome-wide small interfering RNA (siRNA) screens. siRNA-mediated depletion of PEPD resulted in the decreased growth of IAV during mono- and multicycle growth. This growth defect was independent of cell type or virus strain. Furthermore, IAV restriction was apparent as early as 3 h postinfection, and experiments in the absence of protein biosynthesis revealed that the nuclear import of viral ribonucleoprotein complexes (vRNPs) was already blocked in the absence of PEPD. These results led us to investigate which step during entry was affected. Receptor expression, IAV attachment, or IAV internalization was not dependent on the presence of PEPD. However, when looking at the distribution of incoming IAV particles in PEPD-knockdown cells, we found a localization pattern that differed from that in control cells: IAV mostly localized to the cell periphery, and consequently, viral particles displayed reduced colocalization with early and late endosome markers and fusion between viral and endosomal membranes was strongly reduced. Finally, experiments using a competitive inhibitor of PEPD catalytic activity suggested that the enzymatic function of the dipeptidase is required for its proviral effect on IAV entry. In sum, this study establishes PEPD as a novel entry factor required for early endosomal trafficking of IAV.

IMPORTANCE
Influenza A virus (IAV) continues to be a constant threat to public health. As IAV relies on its host cell for replication, the identification of host factors required by the virus is of importance. First, such studies often reveal novel functions of cellular factors and can extend our knowledge of cellular processes. Second, we can further our understanding of processes that are required for the entry of IAV into target cells. Third, the identification of host factors that contribute to IAV entry will increase the number of potential targets for the development of novel antiviral drugs that are of urgent need. Our study identifies prolidase (PEPD) to be a novel entry factor required by IAV for correct routing within the endosomal compartment following virus internalization. Thereby, we link PEPD, which has been shown to play a role during collagen recycling and growth factor signaling, to early events of viral infection.
Annexin V Incorporated into Influenza Virus Particles Inhibits Gamma Interferon Signaling and Promotes Viral Replication
Authors: Berri Fatma , Haffar Ghina , Lê Vuong Ba , Sadewasser Anne , Paki Katharina , Lina Bruno , Wolff Thorsten , Riteau Béatrice 
Published: July 2014

ABSTRACT

During the budding process, influenza A viruses (IAVs) incorporate multiple host cell membrane proteins. However, for most of them, their significance in viral morphogenesis and infectivity remains unknown. We demonstrate here that the expression of annexin V (A5) is upregulated at the cell surface upon IAV infection and that a substantial proportion of the protein is present in lipid rafts, the site of virus budding. Western blotting and immunogold analysis of highly purified IAV particles showed the presence of A5 in the virion. Significantly, gamma interferon (IFN-γ)-induced Stat phosphorylation and IFN-γ-induced 10-kDa protein (IP-10) production in macrophage-derived THP-1 cells was inhibited by purified IAV particles. Disruption of the IFN-γ signaling pathway was A5 dependent since downregulation of its expression or its blockage reversed the inhibition and resulted in decreased viral replication
in vitro
. The functional significance of these results was also observed
in vivo
. Thus, IAVs can subvert the IFN-γ antiviral immune response by incorporating A5 into their envelope during the budding process.

IMPORTANCE
Many enveloped viruses, including influenza A viruses, bud from the plasma membrane of their host cells and incorporate cellular surface proteins into viral particles. However, for the vast majority of these proteins, only the observation of their incorporation has been reported. We demonstrate here that the host protein annexin V is specifically incorporated into influenza virus particles during the budding process. Importantly, we showed that packaged annexin V counteracted the antiviral activity of gamma interferon
in vitro
and
in vivo
. Thus, these results showed that annexin V incorporated in the viral envelope of influenza viruses allow viral escape from immune surveillance. Understanding the role of host incorporated protein into virions may reveal how enveloped RNA viruses hijack the host cell machinery for their own purposes.
Rooting the Phylogenetic Tree of Middle East Respiratory Syndrome Coronavirus by Characterization of a Conspecific Virus from an African Bat
Authors: Corman Victor Max , Ithete Ndapewa Laudika , Richards Leigh Rosanne , Schoeman M. Corrie , Preiser Wolfgang , Drosten Christian , Drexler Jan Felix 
Published: July 2014

ABSTRACT

The emerging Middle East respiratory syndrome coronavirus (MERS-CoV) causes lethal respiratory infections mainly on the Arabian Peninsula. The evolutionary origins of MERS-CoV are unknown. We determined the full genome sequence of a CoV directly from fecal material obtained from a South African
Neoromicia capensis
bat (NeoCoV). NeoCoV shared essential details of genome architecture with MERS-CoV. Eighty-five percent of the NeoCoV genome was identical to MERS-CoV at the nucleotide level. Based on taxonomic criteria, NeoCoV and MERS-CoV belonged to one viral species. The presence of a genetically divergent S1 subunit within the NeoCoV
spike
gene indicated that intraspike recombination events may have been involved in the emergence of MERS-CoV. NeoCoV constitutes a sister taxon of MERS-CoV, placing the MERS-CoV root between a recently described virus from African camels and all other viruses. This suggests a higher level of viral diversity in camels than in humans. Together with serologic evidence for widespread MERS-CoV infection in camelids sampled up to 20 years ago in Africa and the Arabian Peninsula, the genetic data indicate that camels act as sources of virus for humans rather than vice versa. The majority of camels on the Arabian Peninsula is imported from the Greater Horn of Africa, where several
Neoromicia
species occur. The acquisition of MERS-CoV by camels from bats might have taken place in sub-Saharan Africa. Camelids may represent mixing vessels for MERS-CoV and other mammalian CoVs.

IMPORTANCE
It is unclear how, when, and where the highly pathogenic MERS-CoV emerged. We characterized the full genome of an African bat virus closely related to MERS-CoV and show that human, camel, and bat viruses belong to the same viral species. The bat virus roots the phylogenetic tree of MERS-CoV, providing evidence for an evolution of MERS-CoV in camels that preceded that in humans. The revised tree suggests that humans are infected by camels rather than vice versa. Although MERS-CoV cases occur mainly on the Arabian Peninsula, the data from this study together with serologic and molecular investigations of African camels indicate that the initial host switch from bats may have taken place in Africa. The emergence of MERS-CoV likely involved exchanges of genetic elements between different viral ancestors. These exchanges may have taken place either in bat ancestors or in camels acting as mixing vessels for viruses from different hosts.
Seed Sequence-Matched Controls Reveal Limitations of Small Interfering RNA Knockdown in Functional and Structural Studies of Hepatitis C Virus NS5A-MOBKL1B Interaction
Authors: Chung Hyo-Young , Gu Meigang , Buehler Eugen , MacDonald Margaret R. , Rice Charles M. 
Published: July 2014

ABSTRACT
Hepatitis C virus (HCV) is a widespread human pathogen causing liver cirrhosis and cancer. Similar to the case for other viruses, HCV depends on host and viral factors to complete its life cycle. We used proteomic and yeast two-hybrid approaches to elucidate host factors involved in HCV nonstructural protein NS5A function and found that MOBKL1B interacts with NS5A. Initial experiments with small interfering RNA (siRNA) knockdown suggesting a role in HCV replication led us to examine the interaction using biochemical and structural approaches. As revealed by a cocrystal structure of a core MOBKL1B-NS5A peptide complex at 1.95 Å, NS5A binds to a hydrophobic patch on the MOBKL1B surface. Biosensor binding assays identified a highly conserved, 18-amino-acid binding site in domain II of NS5A, which encompasses residues implicated in cyclophilin A (CypA)-dependent HCV RNA replication. However, a CypA-independent HCV variant had reduced replication in MOBKL1B knockdown cells, even though its NS5A does not interact with MOBKL1B. These discordant results prompted more extensive studies of MOBKL1B gene knockdowns, which included additional siRNAs and specifically matched seed sequence siRNA controls. We found that reduced virus replication after treating cells with MOBKL1B siRNA was actually due to off-target inhibition, which indicated that the initial finding of virus replication dependence on the MOBKL1B-NS5A interaction was incorrect. Ultimately, using several approaches, we found no relationship of the MOBKL1B-NS5A interaction to virus replication. These findings collectively serve as a reminder to investigators and scientific reviewers of the pervasive impact of siRNA off-target effects on interpretation of biological data.

IMPORTANCE
Our study illustrates an underappreciated shortcoming of siRNA gene knockdown technology. We initially identified a cellular protein, MOBKL1B, as a binding partner with the NS5A protein of hepatitis C virus (HCV). MOBKL1B siRNA, but not irrelevant RNA, treatment was associated with both reduced virus replication and the absence of MOBKL1B. Believing that HCV replication depended on the MOBKL1B-NS5A interaction, we carried out structural and biochemical analyses. Unexpectedly, an HCV variant lacking the MOBKL1B-NS5A interaction could not replicate after cells were treated with MOBKL1B siRNA. By repeating the MOBKL1B siRNA knockdowns and including seed sequence-matched siRNA instead of irrelevant siRNA as a control, we found that the MOBKL1B siRNAs utilized had off-target inhibitory effects on virus replication. Collectively, our results suggest that stricter controls must be utilized in all RNA interference (RNAi)-mediated gene knockdown experiments to ensure sound conclusions and a reliable scientific knowledge database.
Dynamic Regulation of Host Restriction Factor Expression over the Course of HIV-1 Infection
In Vivo
Authors: Raposo Rui André Saraiva , Abdel-Mohsen Mohamed , Deng Xutao , Hecht Frederick M. , Pilcher Christopher D. , Pillai Satish K. , Nixon Douglas F. 
Published: July 2014

ABSTRACT

In this study, we investigated the expression levels of host restriction factors in six untreated HIV-1-positive patients over the course of infection. We found that the host restriction factor gene expression profile consistently increased over time and was significantly associated with CD4
+
T cell activation and viral load. Our data are among the first to demonstrate the dynamic nature of host restriction factors
in vivo
over time.
The safety of intravitreal bevacizumab monotherapy in adult ophthalmic conditions: systematic review
Authors: Poku Edith , Rathbone John , Wong Ruth , Everson-Hock Emma , Essat Munira , Pandor Abdullah , Wailoo Allan 
Published: July 2014

ObjectivesTo assess the safety of intravitreal bevacizumab (IVB) as a monotherapy and to evaluate the relationship between quality of treatment and adverse events.Data sourcesCochrane Library, Ovid MEDLINE, MEDLINE in-process, Ovid EMBASE and Toxicology Literature Online (TOXLINE) from January 2009 to May 2012. Studies included in an earlier systematic review were also assessed for inclusion.Study eligibility criteria, participants and interventionsRandomised controlled trials (RCTs), controlled trials or observational studies including ≥10 participants reporting adverse events data following IVB monotherapy as a primary treatment in patients (aged 18 years or more) with any eye condition were included.Study appraisal and synthesis methodsStudy selection was undertaken independently by a minimum of two reviewers using pre-defined criteria. Data abstraction and quality assessment were performed by one reviewer, and then checked by a second reviewer. Study quality was assessed for only RCTs in accordance to the Cochrane Risk of Bias Tool. Additional items relating to safety data were also assessed. Results were tabulated or meta-analysed as appropriate.Results22 RCTs and 67 observational studies were included. Only two RCTs reported valid safety data. Rates of serious adverse events following treatment were low. There was insufficient data to explore the relationship between the incidence of adverse events and quality of IVB injection.LimitationsA majority of relevant existing studies were characterised by small sample sizes, unclear diagnostic criteria and reporting of safety outcomes.Conclusions and implications of key findingsAvailable evidence demonstrates low rates of serious local and systemic adverse events following treatment. However, the role of IVB quality in the incidence of adverse events remains unclear. Robust evidence is needed to examine the relationship between the incidence of adverse events and variables such as injection techniques, pre-existing risk factors (eg, immunosuppression, cross-contamination) and quality of IVB treatment.