bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nucleotide Substrate Specificity of Anti-Hepatitis C Virus Nucleoside Analogs for Human Mitochondrial RNA Polymerase
Authors: Ehteshami Maryam , Zhou Longhu , Amiralaei Sheida , Shelton Jadd R. , Cho Jong Hyun , Zhang Hongwang , Li Hao , Lu Xiao , Ozturk Tugba , Stanton Richard , Amblard Franck , McBrayer Tamara R. , Coats Steven J. , Schinazi Raymond F. 
Published: May 2017

ABSTRACT

Nucleoside analog inhibitors (NAIs) are an important class of antiviral agents. Although highly effective, some NAIs with activity against hepatitis C virus (HCV) can cause toxicity, presumably due to off-target inhibition of host mitochondrial RNA polymerase (POLRMT). The
in vitro
nucleotide substrate specificity of POLRMT was studied in order to explore structure-activity relationships that can facilitate the identification of nontoxic NAIs. These findings have important implications for the development of all anti-RNA virus NAIs.
Urinary Concentrations of Colistimethate and Formed Colistin after Intravenous Administration in Patients with Multidrug-Resistant Gram-Negative Bacterial Infections
Authors: Luque Sonia , Escaño Carol , Sorli Luisa , Li Jian , Campillo Nuria , Horcajada Juan Pablo , Salas Esther , Grau Santiago 
Published: May 2017

ABSTRACT

Limited information is available on the urinary excretion of colistin in infected patients. This study aimed to investigate the pharmacokinetics of colistimethate sodium (CMS) and formed colistin in urine in patients with multidrug-resistant (MDR) Gram-negative bacterial infections. A pharmacokinetic study was conducted on 12 patients diagnosed with an infection caused by an extremely drug-resistant (XDR)
P. aeruginosa
strain and treated with intravenous CMS. Fresh urine samples were collected at 2-h intervals, and blood samples were collected predose (
C
min ss
) and at the end of the CMS infusion (
C
max ss
) for measurement of concentrations of CMS and formed colistin using high-performance liquid chromatography (HPLC). CMS urinary recovery was determined as the summed amount of CMS and formed colistin recovered in urine for each 2-h interval divided by the CMS dose. There were 12 enrolled patients, 9 of whom were male (75%). Data [median (range)] were as follows: age, 65.5 (37 to 86) years; colistimethate urinary recovery 0 to 6 h, 42.6% (2.9% to 72.8%); range of concentrations of colistin in urine, <0.1 to 95.4 mg/liter;
C
min ss
and
C
max ss
of colistin in plasma, 0.9 (<0.2 to 1.4) and 0.9 (<0.2 to 1.4) mg/liter, respectively. In 6/12 (50%) patients, more than 40% of the CMS dose was recovered in the urine within the first 6 h after CMS administration. This study demonstrated rapid urinary excretion of CMS in patients within the first 6 h after intravenous administration. In all but one patient, the concentrations of formed colistin in urine were above the MIC for the most predominant isolate of
P. aeruginosa
in our hospital. Future studies are warranted for optimizing CMS dosage regimens in urinary tract infection (UTI) patients.
Plasmodium berghei PIMMS2 Promotes Ookinete Invasion of the Anopheles gambiae Mosquito Midgut
Authors: Ukegbu Chiamaka V. , Akinosoglou Karolina A. , Christophides George K. , Vlachou Dina 
Published: May 2017

ABSTRACT

Mosquito midgut stages of the malaria parasite present an attractive biological system to study host-parasite interactions and develop interventions to block disease transmission. Mosquito infection ensues upon oocyst development that follows ookinete invasion and traversal of the mosquito midgut epithelium. Here, we report the characterization of PIMMS2 (
Plasmodium
invasion of mosquito midgut screen candidate 2), a
Plasmodium berghei
protein with structural similarities to subtilisin-like proteins.
PIMMS2
orthologs are present in the genomes of all plasmodia and are mapped between the subtilisin-encoding genes
SUB1
and
SUB3
.
P. berghei
PIMMS2 is specifically expressed in zygotes and ookinetes and is localized on the ookinete surface. Loss of PIMMS2 function through gene disruption by homologous recombination leads to normal development of motile ookinetes that exhibit a severely impaired capacity to traverse the mosquito midgut and transform to oocysts. Genetic complementation of the disrupted locus with a mutated
PIMMS2
allele reveals that amino acid residues corresponding to the putative subtilisin-like catalytic triad are important but not essential for protein function. Our data demonstrate that PIMMS2 is a novel ookinete-specific protein that promotes parasite traversal of the mosquito midgut epithelium and establishment of mosquito infection.
Neutrophil Elastase and Interleukin 17 Expressed in the Pig Colon during Brachyspira hyodysenteriae Infection Synergistically with the Pathogen Induce Increased Mucus Transport Speed and Production via Mitogen-Activated Protein Kinase 3
Authors: Quintana-Hayashi Macarena P. , Navabi Nazanin , Mahu Maxime , Venkatakrishnan Vignesh , Fernandez Harvey R. , Haesebrouck Freddy , Pasmans Frank , Lindén Sara K. 
Published: May 2017

ABSTRACTBrachyspira hyodysenteriaecolonizes the pig colon, resulting in mucoid hemorrhagic diarrhea and mucus layer changes. These changes are characterized by a disorganized mucus structure and massive mucus induction withde novoexpression of MUC5AC and increased production of MUC2. To investigate the mechanisms behind this altered mucin environment, we quantified the mRNA levels of mucin pathway genes and factors from the immune system in the colons of infected and control pigs and observed upregulation ofneutrophil elastase,SPDEF,FOXA3,MAPK3/ERK1,IL-17A,IL-1β,IL-6, andIL-8expression.In vitro, colonic mucus-producing mucosal surfaces were treated with these factors along withB. hyodysenteriaeinfection and analyzed for their effect on mucin production. Neutrophil elastase and infection synergistically induced mucus production and transport speed, and interleukin 17A (IL-17A) also had similar effects, in both the presence and absence of infection. A mitogen-activated protein kinase 3 (MAPK3)/extracellular signal-regulated kinase 1 (ERK1) inhibitor suppressed these effects. Therefore, we suggest that the SPDEF, FOXA3, and MAPK3/ERK1 signaling pathways are behind the transcriptional program regulating mucin biosynthesis in the colon duringB. hyodysenteriaeinfection. In addition to furthering the knowledge on this economically important disease, this mechanism may be useful for the development of therapies aimed at conditions where enhancing mucus production may be beneficial, such as chronic inflammatory disorders of the colon.
Rv3852 (H-NS) of Mycobacterium tuberculosis Is Not Involved in Nucleoid Compaction and Virulence Regulation
Authors: Odermatt Nina T. , Sala Claudia , Benjak Andrej , Kolly Gaëlle S. , Vocat Anthony , Lupien Andréanne , Cole Stewart T. 
Published: May 2017

ABSTRACT

A handful of nucleoid-associated proteins (NAPs) regulate the vast majority of genes in a bacterial cell. H-NS, the
h
istone-like
n
ucleoid-
s
tructuring protein, is one of these NAPs and protects
Escherichia coli
from foreign gene expression. Though lacking any sequence similarity with
E. coli
H-NS, Rv3852 was annotated as the H-NS ortholog in
Mycobacterium tuberculosis
, as it resembles human histone H1. The role of Rv3852 was thoroughly investigated by immunoblotting, subcellular localization, construction of an unmarked
rv3852
deletion in the
M. tuberculosis
genome, and subsequent analysis of the resulting Δ
rv3852
strain. We found that Rv3852 was predominantly present in the logarithmic growth phase with a decrease in protein abundance in stationary phase. Furthermore, it was strongly associated with the cell membrane and not detected in the cytosolic fraction, nor was it secreted. The Δ
rv3852
strain displayed no growth defect or morphological abnormalities. Quantitative measurement of nucleoid localization in the Δ
rv3852
mutant strain compared to that in the parental H37Rv strain showed no difference in nucleoid position or spread. Infection of macrophages as well as severe combined immunodeficient (SCID) mice demonstrated that loss of Rv3852 had no detected influence on the virulence of
M. tuberculosis
. We thus conclude that
M. tuberculosis
Rv3852 is not involved in pathogenesis and is not a typical NAP. The existence of an as yet undiscovered Rv3852 ortholog cannot be excluded, although this role is likely played by the well-characterized Lsr2 protein.

IMPORTANCE
Mycobacterium tuberculosis
is the causative agent of the lung infection tuberculosis, claiming more than 1.5 million lives each year. To understand the mechanisms of latent infection, where
M. tuberculosis
can stay dormant inside the human host, we require deeper knowledge of the basic biology and of the regulatory networks. In our work, we show that Rv3852, previously annotated as H-NS, is not a typical nucleoid-associated protein (NAP) as expected from its initial annotation. Rv3852 from
M. tuberculosis
has neither influence on nucleoid shape or compaction nor a role in virulence. Our findings reduce the repertoire of identified nucleoid-associated proteins in
M. tuberculosis
to four transcription regulators and underline the importance of genetic studies to assign a function to bacterial genes.
Characterization of a Novel
cis
-3-Hydroxy-
l
-Proline Dehydratase and a
trans
-3-Hydroxy-
l
-Proline Dehydratase from Bacteria
Authors: Watanabe Seiya , Fukumori Fumiyasu , Miyazaki Mao , Tagami Shinya , Watanabe Yasuo 
Published: May 2017

ABSTRACT

Hydroxyprolines, such as
trans
-4-hydroxy-
l
-proline (T4LHyp),
trans
-3-hydroxy-
l
-proline (T3LHyp), and
cis
-3-hydroxy-
l
-proline (C3LHyp), are present in some proteins including collagen, plant cell wall, and several peptide antibiotics. In bacteria, genes involved in the degradation of hydroxyproline are often clustered on the genome (
l
-Hyp gene cluster). We recently reported that an aconitase X (AcnX)-like
hypI
gene from an
l
-Hyp gene cluster functions as a monomeric C3LHyp dehydratase (AcnX
Type I
). However, the physiological role of C3LHyp dehydratase remained unclear. We here demonstrate that
Azospirillum brasilense
NBRC 102289, an aerobic nitrogen-fixing bacterium, robustly grows using not only T4LHyp and T3LHyp but also C3LHyp as the sole carbon source. The small and large subunits of the
hypI
gene (
hypI
S
and
hypI
L
, respectively) from
A. brasilense
NBRC 102289 are located separately from the
l
-Hyp gene cluster and encode a C3LHyp dehydratase with a novel heterodimeric structure (AcnX
Type IIa
). A strain disrupted in the
hypI
S
gene did not grow on C3LHyp, suggesting its involvement in C3LHyp metabolism. Furthermore, C3LHyp induced transcription of not only the
hypI
genes but also the
hypK
gene encoding Δ
1
-pyrroline-2-carboxylate reductase, which is involved in T3LHyp,
d
-proline, and
d
-lysine metabolism. On the other hand, the
l
-Hyp gene cluster of some other bacteria contained not only the AcnX
Type IIa
gene but also two putative proline racemase-like genes (
hypA1
and
hypA2
). Despite having the same active sites (a pair of Cys/Cys) as hydroxyproline 2-epimerase, which is involved in the metabolism of T4LHyp, the dominant reaction by HypA2 was clearly the dehydration of T3LHyp, a novel type of T3LHyp dehydratase that differed from the known enzyme (Cys/Thr).

IMPORTANCE
More than 50 years after the discovery of
trans
-4-hydroxy-
l
-proline (generally called
l
-hydroxyproline) degradation in aerobic bacteria, its genetic and molecular information has only recently been elucidated.
l
-Hydroxyproline metabolic genes are often clustered on bacterial genomes. These loci frequently contain a hypothetical gene(s), whose novel enzyme functions are related to the metabolism of
trans
-3-hydroxy
l
-proline and/or
cis
-3-hydroxy
l
-proline, a relatively rare
l
-hydroxyproline in nature. Several
l
-hydroxyproline metabolic enzymes show no sequential similarities, suggesting their emergence by convergent evolution. Furthermore, transcriptional regulation by
trans
-4-hydroxy-
l
-proline,
trans
-3-hydroxy-
l
-proline, and/or
cis
-3-hydroxy-
l
-proline significantly differs between bacteria. The results of the present study show that several
l
-hydroxyprolines are available for bacteria as carbon and energy sources and may contribute to the discovery of potential metabolic pathways of another hydroxyproline(s).
Viral DNA Replication Orientation and hnRNPs Regulate Transcription of the Human Papillomavirus 18 Late Promoter
Authors: Wang Xiaohong , Liu Haibin , Ge Hui , Ajiro Masahiko , Sharma Nishi R. , Meyers Craig , Morozov Pavel , Tuschl Thomas , Klar Amar , Court Donald , Zheng Zhi-Ming 
Published: May 2017

ABSTRACT

The life cycle of human papillomaviruses (HPVs) is tightly linked to keratinocyte differentiation. Although expression of viral early genes is initiated immediately upon virus infection of undifferentiated basal cells, viral DNA amplification and late gene expression occur only in the mid to upper strata of the keratinocytes undergoing terminal differentiation. In this report, we show that the relative activity of HPV18 TATA-less late promoter P
811
depends on its orientation relative to that of the origin (Ori) of viral DNA replication and is sensitive to the eukaryotic DNA polymerase inhibitor aphidicolin. Additionally, transfected 70-nucleotide (nt)-long single-strand DNA oligonucleotides that are homologous to the region near Ori induce late promoter activity. We also found that promoter activation in raft cultures leads to production of the late promoter-associated, sense-strand transcription initiation RNAs (tiRNAs) and splice-site small RNAs (spliRNAs). Finally, a
cis
-acting AAGTATGCA core element that functions as a repressor to the promoter was identified. This element interacts with hnRNP D0B and hnRNP A/B factors. Point mutations in the core prevented binding of hnRNPs and increased the promoter activity. Confirming this result, knocking down the expression of both hnRNPs in keratinocytes led to increased promoter activity. Taking the data together, our study revealed the mechanism of how the HPV18 late promoter is regulated by DNA replication and host factors.

IMPORTANCE
It has been known for decades that the activity of viral late promoters is associated with viral DNA replication among almost all DNA viruses. However, the mechanism of how DNA replication activates the viral late promoter and what components of the replication machinery are involved remain largely unknown. In this study, we characterized the P
811
promoter region of HPV18 and demonstrated that its activation depends on the orientation of DNA replication. Using single-stranded oligonucleotides targeting the replication fork on either leading or lagging strands, we showed that viral lagging-strand replication activates the promoter. We also identified a transcriptional repressor element located upstream of the promoter transcription start site which interacts with cellular proteins hnRNP D0B and hnRNP A/B and modulates the late promoter activity. This is the first report on how DNA replication activates a viral late promoter.
In Vivo
Imaging of Influenza Virus Infection in Immunized Mice
Authors: Czakó Rita , Vogel Leatrice , Lamirande Elaine W. , Bock Kevin W. , Moore Ian N. , Ellebedy Ali H. , Ahmed Rafi , Mehle Andrew , Subbarao Kanta 
Published: May 2017

ABSTRACT

Immunization is the cornerstone of seasonal influenza control and represents an important component of pandemic preparedness strategies. Using a bioluminescent reporter virus, we demonstrate the application of noninvasive
in vivo
imaging system (IVIS) technology to evaluate the preclinical efficacy of candidate vaccines and immunotherapy in a mouse model of influenza. Sequential imaging revealed distinct spatiotemporal kinetics of bioluminescence in groups of mice passively or actively immunized by various strategies that accelerated the clearance of the challenge virus at different rates and by distinct mechanisms. Imaging findings were consistent with conclusions derived from virus titers in the lungs and, notably, were more informative than conventional efficacy endpoints in some cases. Our findings demonstrate the reliability of IVIS as a qualitative approach to support preclinical evaluation of candidate medical countermeasures for influenza in mice.

IMPORTANCE
Influenza A viruses remain a persistent threat to public health. Vaccination and immunotherapy are effective countermeasures for the control of influenza but must contend with antigenic drift and the risk of resistance to antivirals. Traditional preclinical efficacy studies for novel vaccine and pharmaceutical candidates can be time-consuming and expensive and are inherently limited in scope.
In vivo
imaging approaches offer the potential to noninvasively track virus replication in real time in animal models. In this study, we demonstrate the utility of bioluminescent imaging for tracking influenza virus replication in the lungs of immunized mice and also identify important factors that may influence the accurate interpretation of imaging results. Our findings support the potential of IVIS approaches to enhance traditional preclinical efficacy evaluation of candidate vaccines and human monoclonal antibodies for the prevention and treatment of influenza.
Developing a framework for community-based sexual health interventions for youth in the rural setting: protocol for a participatory action research study
Authors: Heslop Carl William , Burns Sharyn , Lobo Roanna , McConigley Ruth 
Published: May 2017

IntroductionThere is limited research examining community-based or multilevel interventions that address the sexual health of young people in the rural Australian context. This paper describes the Participatory Action Research (PAR) project that will develop and validate a framework that is effective for planning, implementing and evaluating multilevel community-based sexual health interventions for young people aged 16–24 years in the Australian rural setting.Methods and analysisTo develop a framework for sexual health interventions with stakeholders, PAR will be used. Three PAR cycles will be conducted, using semistructured one-on-one interviews, focus groups, community mapping and photovoice to inform the development of a draft framework. Cycle 2 and Cycle 3 will use targeted Delphi studies to gather evaluation and feedback on the developed draft framework. All data collected will be reviewed and analysed in detail and coded as concepts become apparent at each stage of the process.Ethics and disseminationThis protocol describes a supervised doctoral research project. This project seeks to contribute to the literature regarding PAR in the rural setting and the use of the Delphi technique within PAR projects. The developed framework as a result of the project will provide a foundation for further research testing the application of the framework in other settings and health areas. This research has received ethics approval from the Curtin University Human Research and Ethics Committee (HR96/2015).
Patient-reported safety incidents in older patients with long-term conditions: a large cross-sectional study
Authors: Panagioti Maria , Blakeman Thomas , Hann Mark , Bower Peter 
Published: May 2017

BackgroundIncreasing evidence suggests that patient safety is a serious concern for older patients with long-term conditions. Despite this, there is a lack of research on safety incidents encountered by this patient group. In this study, we sought to examine patient reports of safety incidents and factors associated with reports of safety incidents in older patients with long-term conditions.MethodsThe baseline cross-sectional data from a longitudinal cohort study were analysed. Older patients (n=3378 aged 65 years and over) with a long-term condition registered in general practices were included in the study. The main outcome was patient-reported safety incidents including availability and appropriateness of medical tests and prescription of wrong types or doses of medication. Binary univariate and multivariate logistic regression analyses were undertaken to examine factors associated with patient-reported safety incidents.ResultsSafety incidents were reported by 11% of the patients. Four factors were significantly associated with patient-reported safety incidents in multivariate analyses. The experience of multiple long-term conditions (OR=1.09, 95% CI 1.05 to 1.13), a probable diagnosis of depression (OR=1.36, 95% CI 1.06 to 1.74) and greater relational continuity of care (OR=1.28, 95% CI 1.08 to 1.52) were associated with increased odds for patient-reported safety incidents. Perceived greater support and involvement in self-management was associated with lower odds for patient-reported safety incidents (OR=0.95, 95% CI 0.93 to 0.97).ConclusionsWe found that older patients with multimorbidity and depression are more likely to report experiences of patient safety incidents. Improving perceived support and involvement of patients in their care may help prevent patient-reported safety incidents.
Violent injury predicts poor psychological outcomes after traumatic injury in a hard-to-reach population: an observational cohort study
Authors: Rahtz Emmylou , Bhui Kamaldeep , Smuk Melanie , Hutchison Iain , Korszun Ania 
Published: May 2017

BackgroundPeople who experience physical trauma face a range of psychosocial outcomes. These may be overlooked by busy clinicians. While some risk factors are understood, understanding of the psychological effects of violent injury remains limited, particularly in UK settings. This study compared psychological outcomes following interpersonal violence and accidental injury, including the persistence of psychological distress.MethodsA questionnaire survey was carried out at two time points of patients admitted to a large teaching hospital in London between July 2012 and April 2014. Participants were consecutive adult patients admitted to the Royal London Hospital with traumatic injuries, with 219 participants at baseline. Follow-up survey was 8  months later (n=109). Standardised measures assessed post-traumatic stress symptoms (PTSS) (Acute Stress Disorder Scale and PTSD Checklist) and depressive symptoms (Hospital Anxiety and Depression Scale).ResultsPTSS and depressive symptoms affected 27% and 33%, respectively, at baseline. At 8  months, 27% and 31% reported these symptoms for PTSS and depressive symptoms, respectively. The repeated measures were assessed with multilevel models: after adjusting for demographic factors, patients with violent injury showed more PTSS (OR 6.27, 95% CI 1.90 to 20.66) and depressive symptoms (OR 3.12, 95% CI 1.08 to 8.99).ConclusionsThere were high levels of psychological distress among traumatic injury patients. Violent injuries were associated with an increased risk of both post-traumatic and depressive symptoms. People vulnerable to distress would benefit from psychological support, and hospital admission provides a unique opportunity to engage hard-to-reach groups in interventions.
How to Predict the Consequences of a Tick Value Change? Evidence from the Tokyo Stock Exchange Pilot Program
Authors: Huang Weibing , Lehalle Charles-Albert , Rosenbaum Mathieu 
Published: May 2017

The tick value is a crucial component of market design and is often considered the most suitable tool to mitigate the effects of high frequency trading. The goal of this paper is to demonstrate that the approach introduced in [Dayri, K., and M. Rosenbaum, 2015, Large Tick Assets: Implicit Spread and Optimal Tick Size, Market Microstructure and Liquidity, 1, 1550003.] allows for an ex ante assessment of the consequences of a tick value change on the microstructure of an asset. To that purpose, we analyze the pilot program on tick value modifications started in 2014 by the Tokyo Stock Exchange in light of this methodology. We focus on forecasting the future cost of market and limit orders after a tick value change and show that our predictions are very accurate. Furthermore, for each asset involved in the pilot program, we are able to define (ex ante) an optimal tick value. This enables us to classify the stocks according to the relevance of their tick value, before and after its modification.