bluuebunny/crossref_metadata_2025_split huggingface dataset:
Two forward genetic screens for vein density mutants in sorghum converge on a cytochrome P450 gene in the brassinosteroid pathway
Authors: Rizal Govinda , Thakur Vivek , Dionora Jacqueline , Karki Shanta , Wanchana Samart , Acebron Kelvin , Larazo Nikki , Garcia Richard , Mabilangan Abigail , Montecillo Florencia , Danila Florence , Mogul Reychelle , Pablico Paquito , Leung Hei , Langdale Jane A. , Sheehy John , Kelly Steven , Quick William Paul 
Published: September 2015

SummaryThe specification of vascular patterning in plants has interested plant biologists for many years. In the last decade a new context has emerged for this interest. Specifically, recent proposals to engineer C4 traits into C3 plants such as rice require an understanding of how the distinctive venation pattern in the leaves of C4 plants is determined. High vein density with Kranz anatomy, whereby photosynthetic cells are arranged in encircling layers around vascular bundles, is one of the major traits that differentiate C4 species from C3 species. To identify genetic factors that specify C4 leaf anatomy, we generated ethyl methanesulfonate‐ and γ‐ray‐mutagenized populations of the C4 species sorghum (Sorghum bicolor), and screened for lines with reduced vein density. Two mutations were identified that conferred low vein density. Both mutations segregated in backcrossed F2 populations as homozygous recessive alleles. Bulk segregant analysis using next‐generation sequencing revealed that, in both cases, the mutant phenotype was associated with mutations in the CYP90D2 gene, which encodes an enzyme in the brassinosteroid biosynthesis pathway. Lack of complementation in allelism tests confirmed this result. These data indicate that the brassinosteroid pathway promotes high vein density in the sorghum leaf, and suggest that differences between C4 and C3 leaf anatomy may arise in part through differential activity of this pathway in the two leaf types.
Cross‐Border Mergers and Upstreaming
Authors: Beladi Hamid , Chakrabarti Avik , Hollas Daniel 
Published: September 2015

AbstractGlobal forces of fragmentation continue to distance (upstream) a product's conception from its end use. A concurrent flow of cross‐border mergers and upstreaming, by multinational corporations, dominates the fashion of doing international business. We investigate if there is any link between cross‐country variations in upstreaming within firms, apparent in international data, and mergers between firms across borders. Our empirical analysis reveals a significantly positive association between country upstreamness and cross‐border mergers. We build on Neary as well as Beladi et al. to provide a theoretical explanation of our findings in terms of the incentives in business strategic decision‐making to realise the gains from cross‐border mergers and upstreaming through the pricing mechanism of intermediate inputs in a vertically related oligopolistic industry.
Economic Integration, Corporate Tax Incidence and Fiscal Compensation
Authors: Exbrayat Nelly , Geys Benny 
Published: September 2015

AbstractHigher corporate taxes are often argued to depress wages (a tax incidence effect), while higher wages may require compensation via lower corporate tax rates (a fiscal compensation effect). Yet, existing empirical evidence ignores that (i) both effects are likely to occur simultaneously (necessitating a joint estimation approach), and (ii) capital mobility might play a critical moderating role for the strength of both effects. Using a panel data set comprising 24 OECD countries over the period 1982–2007, we address both these deficiencies. This clearly illustrates the simultaneous existence of tax incidence and fiscal compensation effects. Moreover, capital mobility (and the ensuing relative bargaining power of economic agents) has a significant influence on both the prevalence and strength of these effects.
Feline discrete high‐grade gastrointestinal lymphoma treated with surgical resection and adjuvantCHOP‐based chemotherapy: retrospective study of 20 cases
Authors: Gouldin E. D. , Mullin C. , Morges M. , Mehler S. J. , de Lorimier L.‐P. , Oakley C. , Risbon R. , May L. , Kahn S. A. , Clifford C. 
Published: September 2015

AbstractThe aim of this retrospective study was to evaluate the outcome of cats treated with surgical intervention for a discrete intermediate‐/high‐grade gastrointestinal lymphoma prior toCHOP‐based chemotherapy. Variables including sex, breed, haematocrit, white blood cell count, serum albumin concentration, clinical stage of disease, gastrointestinal obstruction and peritonitis were assessed for their effect on survival. Twenty cats met the inclusion criteria with three cats still alive at the time of data analysis. The overall median survival time (MST) was 417 days (range: 12–2962 days). The disease‐free interval (DFI) was 357 days (range: 0–1585 days) with six cats still deemed in remission prior to death. Only clinical stage had a significant effect on bothMSTandDFI. Cats with discrete intermediate/high‐grade gastrointestinal lymphoma that undergo surgical resection followed by adjuvantCHOPchemotherapy may achieve acceptable overall survival times.
The PapilloCheck Assay for Detection of High-Grade Cervical Intraepithelial Neoplasia
Authors: Crosbie Emma J. , Bailey Andrew , Sargent Alex , Gilham Clare , Peto Julian , Kitchener Henry C. 
Published: September 2015

ABSTRACT

Human papillomavirus (HPV) testing is used in primary cervical screening, as an adjunct to cervical cytology for the management of low grade abnormal cytology, and in a test of cure. PapilloCheck (Greiner Bio-One) is a PCR-based DNA microarray system that can individually identify 24 HPV types, including the 13 high-risk (HR) types identified by Hybrid Capture 2 (HC2). Here, we compare PapilloCheck with HC2 for the detection of high-grade cervical intraepithelial neoplasia (CIN2+) in a total of 8,610 cervical cytology samples from the ARTISTIC population-based cervical screening study. We performed a retrospective analysis of 3,518 cytology samples from round 1 ARTISTIC enriched for underlying CIN2+ (
n
= 723) and a prospective analysis of 5,092 samples from round 3 ARTISTIC. Discrepant results were tested using the Roche reverse line blot (RLB) or Linear Array (LA) assay. The relative sensitivity and specificity of HR PapilloCheck compared with that of HC2 for the detection of CIN2+ in women aged over 30 years were 0.94 (95% confidence interval [CI], 0.91, 0.97) and 1.05 (95% CI, 1.04, 1.05), respectively. HC2 missed 44/672 (7%) CIN2+ lesions, while HR PapilloCheck missed 74/672 (11%) CIN2+ lesions. Thirty-six percent of HC2-positive normal cytology samples were HR HPV negative by both PapilloCheck and RLB/LA, indicating that the use of HR PapilloCheck rather than HC2 in population-based primary screening would reduce the number of additional tests required (e.g., reflex cytology) in women where underlying CIN2+ is extremely unlikely. HR PapilloCheck could be a suitable HPV detection assay for use in the cervical screening setting.
Evaluation of the “Dip Effect” Phenomenon in Antifungal Susceptibility Testing of Candida spp. against Echinocandins by Use of Gradient Concentration Strips
Authors: Siopi Maria , Tsala Marilena , Siafakas Nikolaos , Zerva Loukia , Meletiadis Joseph 
Published: September 2015

ABSTRACT

The “dip effect” phenomenon complicates antifungal susceptibility testing with gradient concentration strips. Of 60
Candida
isolates tested with the three echinocandins, this phenomenon was observed only for caspofungin with most (>90%)
Candida albicans
,
Candida glabrata
, and
Candida tropicalis
isolates and for isolates with CLSI MICs of ≤0.25 mg/liter. In order to facilitate MIC determination, a practical approach was developed using the inhibition zones at 32, 8, 2, and 1 mg/liter, increasing the agreement with the CLSI method >86%.
Tracking the Fate of Genetically Distinct Vesicular Stomatitis Virus Matrix Proteins Highlights the Role for Late Domains in Assembly
Authors: Soh Timothy K. , Whelan Sean P. J. 
Published: September 2015

ABSTRACT
Vesicular stomatitis virus (VSV) assembly requires condensation of the viral ribonucleoprotein (RNP) core with the matrix protein (M) during budding from the plasma membrane. The RNP core comprises the negative-sense genomic RNA completely coated by the nucleocapsid protein (N) and associated by a phosphoprotein (P) with the large polymerase protein (L). To study the assembly of single viral particles, we tagged M and P with fluorescent proteins. We selected from a library of viruses with insertions in the M gene a replication-competent virus containing a fluorescent M and combined that with our previously described virus containing fluorescent P. Virus particles containing those fusions maintained the same bullet shape appearance as wild-type VSV but had a modest increase in particle length, reflecting the increased genome size. Imaging of the released particles revealed a variation in the amount of M and P assembled into the virions, consistent with a flexible packaging mechanism. We used the recombinants to further study the importance of the late domains in M, which serve to recruit the endosomal sorting complex required for transport (ESCRT) machinery during budding. Mutations in late domains resulted in the accumulation of virions that failed to pinch off from the plasma membrane. Imaging of single virions released from cells that were coinfected with M tagged with enhanced green fluorescent protein and M tagged with mCherry variants in which the late domains of one virus were inactivated by mutation showed a strong bias against the incorporation of the late-domain mutant into the released virions. In contrast, the intracellular expression and membrane association of the two variants were unaltered. These studies provide new tools for imaging particle assembly and enhance our resolution of existing models for assembly of VSV.

IMPORTANCE
Assembly of vesicular stomatitis virus (VSV) particles requires the separate trafficking of the viral replication machinery, a matrix protein (M) and a glycoprotein, to the plasma membrane. The matrix protein contains a motif termed a “late domain” that engages the host endosomal sorting complex required for transport (ESCRT) machinery to facilitate the release of viral particles. Inactivation of the late domains through mutation results in the accumulation of virions arrested at the point of release. In the study described here, we developed new tools to study VSV assembly by fusing fluorescent proteins to M and to a constituent of the replication machinery, the phosphoprotein (P). We used those tools to show that the late domains of M are required for efficient incorporation into viral particles and that the particles contain a variable quantity of M and P.
Viral Small-RNA Analysis of Bombyx mori Larval Midgut during Persistent and Pathogenic Cytoplasmic Polyhedrosis Virus Infection
Authors: Zografidis Aris , Van Nieuwerburgh Filip , Kolliopoulou Anna , Apostolou-Karampelis Konstantinos , Head Steven R. , Deforce Dieter , Smagghe Guy , Swevers Luc 
Published: September 2015

ABSTRACT

The lepidopteran innate immune response against RNA viruses remains poorly understood, while in other insects several studies have highlighted an essential role for the exo-RNAi pathway in combating viral infection. Here, by using deep-sequencing technology for viral small-RNA (vsRNA) assessment, we provide evidence that exo-RNAi is operative in the silkworm
Bombyx mori
against both persistent and pathogenic infection of
B. mori
cytoplasmic polyhedrosis virus (BmCPV) which is characterized by a segmented double-stranded RNA (dsRNA) genome. Further, we show that Dicer-2 predominantly targets viral dsRNA and produces 20-nucleotide (nt) vsRNAs, whereas an additional pathway is responsive to viral mRNA derived from segment 10. Importantly, vsRNA distributions, which define specific hot and cold spot profiles for each viral segment, to a considerable degree overlap between Dicer-2-related (19 to 21 nt) and Dicer-2-unrelated vsRNAs, suggesting a common origin for these profiles. We found a degenerate motif significantly enriched at the cut sites of vsRNAs of various lengths which link an unknown RNase to the origins of vsRNAs biogenesis and distribution. Accordingly, the indicated RNase activity may be an important early factor for the host's antiviral defense in Lepidoptera.

IMPORTANCE
This work contributes to the elucidation of the lepidopteran antiviral response against infection of segmented double-stranded RNA (dsRNA) virus (CPV;
Reoviridae
) and highlights the importance of viral small-RNA (vsRNA) analysis for getting insights into host-pathogen interactions. Three vsRNA pathways are implicated in antiviral defense. For dsRNA, two pathways are proposed, either based on Dicer-2 cleavage to generate 20-nucleotide vsRNAs or based on the activity of an uncharacterized endo-RNase that cleaves the viral RNA substrate at a degenerate motif. The analysis also indicates the existence of a degradation pathway that targets the positive strand of segment 10.
The Genome of a Tortoise Herpesvirus (Testudinid Herpesvirus 3) Has a Novel Structure and Contains a Large Region That Is Not Required for Replication
In Vitro
or Virulence
In Vivo
Authors: Gandar Frédéric , Wilkie Gavin S. , Gatherer Derek , Kerr Karen , Marlier Didier , Diez Marianne , Marschang Rachel E. , Mast Jan , Dewals Benjamin G. , Davison Andrew J. , Vanderplasschen Alain F. C. 
Published: September 2015

ABSTRACT

Testudinid herpesvirus 3 (TeHV-3) is the causative agent of a lethal disease affecting several tortoise species. The threat that this virus poses to endangered animals is focusing efforts on characterizing its properties, in order to enable the development of prophylactic methods. We have sequenced the genomes of the two most studied TeHV-3 strains (1976 and 4295). TeHV-3 strain 1976 has a novel genome structure and is most closely related to a turtle herpesvirus, thus supporting its classification into genus
Scutavirus
, subfamily
Alphaherpesvirinae
, family
Herpesviridae
. The sequence of strain 1976 also revealed viral counterparts of cellular interleukin-10 and semaphorin, which have not been described previously in members of subfamily
Alphaherpesvirinae
. TeHV-3 strain 4295 is a mixture of three forms (m1, m2, and M), in which, in comparison to strain 1976, the genomes exhibit large, partially overlapping deletions of 12.5 to 22.4 kb. Viral subclones representing these forms were isolated by limiting dilution assays, and each replicated in cell culture comparably to strain 1976. With the goal of testing the potential of the three forms as attenuated vaccine candidates, strain 4295 was inoculated intranasally into Hermann's tortoises (
Testudo hermanni
). All inoculated subjects died, and PCR analyses demonstrated the ability of the m2 and M forms to spread and invade the brain. In contrast, the m1 form was detected in none of the organs tested, suggesting its potential as the basis of an attenuated vaccine candidate. Our findings represent a major step toward characterizing TeHV-3 and developing prophylactic methods against it.

IMPORTANCE
Testudinid herpesvirus 3 (TeHV-3) causes a lethal disease in tortoises, several species of which are endangered. We have characterized the viral genome and used this information to take steps toward developing an attenuated vaccine. We have sequenced the genomes of two strains (1976 and 4295), compared their growth
in vitro
, and investigated the pathogenesis of strain 4295, which consists of three deletion mutants. The major findings are that (i) TeHV-3 has a novel genome structure, (ii) its closest relative is a turtle herpesvirus, (iii) it contains interleukin-10 and semaphorin genes (the first time these have been reported in an alphaherpesvirus), (iv) a sizeable region of the genome is not required for viral replication
in vitro
or virulence
in vivo
, and (v) one of the components of strain 4295, which has a deletion of 22.4 kb, exhibits properties indicating that it may serve as the starting point for an attenuated vaccine.
Molecular Determinants of Virulence and Stability of a Reporter-Expressing H5N1 Influenza A Virus
Authors: Zhao Dongming , Fukuyama Satoshi , Yamada Shinya , Lopes Tiago J. S. , Maemura Tadashi , Katsura Hiroaki , Ozawa Makoto , Watanabe Shinji , Neumann Gabriele , Kawaoka Yoshihiro 
Published: September 2015

ABSTRACT
We previously reported that an H5N1 virus carrying the Venus reporter gene, which was inserted into the NS gene segment from the A/Puerto Rico/8/1934(H1N1) virus (Venus-H5N1 virus), became more lethal to mice, and the reporter gene was stably maintained after mouse adaptation compared with the wild-type Venus-H5N1 (WT-Venus-H5N1) virus. However, the basis for this difference in virulence and Venus stability was unclear. Here, we investigated the molecular determinants behind this virulence and reporter stability by comparing WT-Venus-H5N1 virus with a mouse-adapted Venus-H5N1 (MA-Venus-H5N1) virus. To determine the genetic basis for these differences, we used reverse genetics to generate a series of reassortants of these two viruses. We found that reassortants with PB2 from MA-Venus-H5N1 (MA-PB2), MA-PA, or MA-NS expressed Venus more stably than did WT-Venus-H5N1 virus. We also found that a single mutation in PB2 (V25A) or in PA (R443K) increased the virulence of the WT-Venus-H5N1 virus in mice and that the presence of both of these mutations substantially enhanced the pathogenicity of the virus. Our results suggest roles for PB2 and PA in the stable maintenance of a foreign protein as an NS1 fusion protein in influenza A virus.

IMPORTANCE
The ability to visualize influenza viruses has far-reaching benefits in influenza virus research. Previously, we reported that an H5N1 virus bearing the Venus reporter gene became more pathogenic to mice and that its reporter gene was more highly expressed and more stably maintained after mouse adaptation. Here, we investigated the molecular determinants behind this enhanced virulence and reporter stability. We found that mutations in PB2 (V25A) and PA (R443K) play crucial roles in the stable maintenance of a foreign protein as an NS1 fusion protein in influenza A virus and in the virulence of influenza virus in mice. Our findings further our knowledge of the pathogenicity of influenza virus in mammals and will help advance influenza virus-related live-imaging studies
in vitro
and
in vivo
.
Circadian Rhythms in Cyanobacteria
Authors: Cohen Susan E. , Golden Susan S. 
Published: September 2015

SUMMARY

Life on earth is subject to daily and predictable fluctuations in light intensity, temperature, and humidity created by rotation of the earth. Circadian rhythms, generated by a circadian clock, control temporal programs of cellular physiology to facilitate adaptation to daily environmental changes. Circadian rhythms are nearly ubiquitous and are found in both prokaryotic and eukaryotic organisms. Here we introduce the molecular mechanism of the circadian clock in the model cyanobacterium
Synechococcus elongatus
PCC 7942. We review the current understanding of the cyanobacterial clock, emphasizing recent work that has generated a more comprehensive understanding of how the circadian oscillator becomes synchronized with the external environment and how information from the oscillator is transmitted to generate rhythms of biological activity. These results have changed how we think about the clock, shifting away from a linear model to one in which the clock is viewed as an interactive network of multifunctional components that are integrated into the context of the cell in order to pace and reset the oscillator. We conclude with a discussion of how this basic timekeeping mechanism differs in other cyanobacterial species and how information gleaned from work in cyanobacteria can be translated to understanding rhythmic phenomena in other prokaryotic systems.
Healthcare provider perceptions of clinical prediction rules
Authors: Richardson Safiya , Khan Sundas , McCullagh Lauren , Kline Myriam , Mann Devin , McGinn Thomas 
Published: September 2015

ObjectivesTo examine internal medicine and emergency medicine healthcare provider perceptions of usefulness of specific clinical prediction rules.SettingThe study took place in two academic medical centres. A web-based survey was distributed and completed by participants between 1 January and 31 May 2013.ParticipantsMedical doctors, doctors of osteopathy or nurse practitioners employed in the internal medicine or emergency medicine departments at either institution.Primary and secondary outcome measuresThe primary outcome was to identify the clinical prediction rules perceived as most useful by healthcare providers specialising in internal medicine and emergency medicine. Secondary outcomes included comparing usefulness scores of specific clinical prediction rules based on provider specialty, and evaluating associations between usefulness scores and perceived characteristics of these clinical prediction rules.ResultsOf the 401 healthcare providers asked to participate, a total of 263 (66%), completed the survey. The CHADS2 score was chosen by most internal medicine providers (72%), and Pulmonary Embolism Rule-Out Criteria (PERC) score by most emergency medicine providers (45%), as one of the top three most useful from a list of 24 clinical prediction rules. Emergency medicine providers rated their top three significantly more positively, compared with internal medicine providers, as having a better fit into their workflow (p=0.004), helping more with decision-making (p=0.037), better fitting into their thought process when diagnosing patients (p=0.001) and overall, on a 10-point scale, more useful (p=0.009). For all providers, the perceived qualities of useful at point of care, helps with decision making, saves time diagnosing, fits into thought process, and should be the standard of clinical care correlated highly (≥0.65) with overall 10-point usefulness scores.ConclusionsHealthcare providers describe clear preferences for certain clinical prediction rules, based on medical specialty.
Impact of physical frailty on disability in community-dwelling older adults: a prospective cohort study
Authors: Makizako Hyuma , Shimada Hiroyuki , Doi Takehiko , Tsutsumimoto Kota , Suzuki Takao 
Published: September 2015

ObjectiveTo examine the relationship between physical frailty and risk of disability, and to identify the component(s) of frailty with the most impact on disability in community-dwelling older adults.DesignProspective cohort study.SettingA Japanese community.Participants4341 older adults aged ≥65 living in the community participated in a baseline assessment from 2011 to 2012 and were followed for 2 years.Main outcome measuresCare-needs certification in the national long-term care insurance (LTCI) system of Japan, type of physical frailty (robust, prefrail, frail) and subitems (slowness, weakness, exhaustion, low activity, weight loss), adjusted for several potential confounders such as demographic characteristics, analysed with Kaplan-Meier survival curves for incidence of disability by frailty phenotype.ResultsDuring the 2-year follow-up period, 168 participants (3.9%) began using the LTCI system for incidence of disability. Participants classified as frail (HR 4.65, 95% CI 2.63 to 8.22) or prefrail (2.52, 1.56 to 4.07) at the baseline assessment had an increased risk of disability incidence compared with robust participants. Analyses for subitems of frailty showed that slowness (2.32, 1.62 to 3.33), weakness (1.90, 1.35 to 2.68) and weight loss (1.61, 1.13 to 2.31) were related to increased risk of disability incidence. In stratified analyses, participants who were classified as frail and who had lower cognitive function had the highest percentage (30.3%) of disability incidence during the 2 years after baseline assessment.ConclusionsPhysical frailty, even being prefrail, had a strong impact on the risk of future disability. Some components of frailty, such as slowness, weakness and weight loss, are strongly associated with incident disability in community-dwelling older adults.