bluuebunny/crossref_metadata_2025_split huggingface dataset:
Novel Benzoxazole Inhibitor of Dengue Virus Replication That Targets the NS3 Helicase
Authors: Byrd Chelsea M. , Grosenbach Douglas W. , Berhanu Aklile , Dai Dongcheng , Jones Kevin F. , Cardwell Kara B. , Schneider Christine , Yang Guang , Tyavanagimatt Shanthakumar , Harver Chris , Wineinger Kristin A. , Page Jessica , Stavale Eric , Stone Melialani A. , Fuller Kathleen P. , Lovejoy Candace , Leeds Janet M. , Hruby Dennis E. , Jordan Robert 
Published: February 2013

ABSTRACT

Dengue virus (DENV) is the predominant mosquito-borne viral pathogen that infects humans with an estimated 50 to 100 million infections per year worldwide. Over the past 50 years, the incidence of dengue disease has increased dramatically and the virus is now endemic in more than 100 countries. Moreover, multiple serotypes of DENV are now found in the same geographic region, increasing the likelihood of more severe forms of disease. Despite extensive research, there are still no approved vaccines or therapeutics commercially available to treat DENV infection. Here we report the results of a high-throughput screen of a chemical compound library using a whole-virus assay that identified a novel small-molecule inhibitor of DENV, ST-610, that potently and selectively inhibits all four serotypes of DENV replication
in vitro
. Sequence analysis of drug-resistant virus isolates has identified a single point mutation, A263T, in the NS3 helicase domain that confers resistance to this compound. ST-610 inhibits DENV NS3 helicase RNA unwinding activity in a molecular-beacon-based helicase assay but does not inhibit nucleoside triphosphatase activity based on a malachite green ATPase assay. ST-610 is nonmutagenic, is well tolerated (nontoxic) in mice, and has shown efficacy in a sublethal murine model of DENV infection with the ability to significantly reduce viremia and viral load compared to vehicle controls.
Activities of Systemically Administered Echinocandins against
In Vivo
Mature Candida albicans Biofilms Developed in a Rat Subcutaneous Model
Authors: Kucharíková Soňa , Sharma Nidhi , Spriet Isabel , Maertens Johan , Van Dijck Patrick , Lagrou Katrien 
Published: February 2013

ABSTRACT

This study addresses the effects of micafungin, caspofungin, and anidulafungin against
Candida albicans
biofilms developed in a subcutaneous catheter rat model system. Doses of 5, 10, and 30 mg/kg (of body weight)/day (the last only for micafungin) were given intravenously for 5, 7, and 10 days. All three echinocandins caused a significant reduction of the
Candida
cell numbers on the implanted catheters and are thus promising for the treatment of biofilm-related infections.
Persistence of Resistant Variants in Hepatitis C Virus-Infected Patients Treated with the NS5A Replication Complex Inhibitor Daclatasvir
Authors: Wang Chunfu , Sun Jin-Hua , O'Boyle Donald R. , Nower Peter , Valera Lourdes , Roberts Susan , Fridell Robert A. , Gao Min 
Published: February 2013

ABSTRACT

Daclatasvir (DCV; BMS-790052) is a hepatitis C virus (HCV) NS5A replication complex inhibitor (RCI) with picomolar to low nanomolar potency and broad genotypic coverage
in vitro
. Viral RNA declines have been observed in the clinic for both alpha interferon-ribavirin (IFN-α–RBV) and IFN-RBV-free regimens that include DCV. Follow-up specimens (up to 6 months) from selected subjects treated with DCV in 14-day monotherapy studies were analyzed for genotype and phenotype. Variants were detected by clonal sequencing in specimens from baseline and were readily detected by population sequencing following viral RNA breakthrough and posttreatment. The major amino acid substitutions generating resistance
in vivo
were at residues M28, Q30, L31, and Y93 for genotype 1a (GT-1a) and L31 and Y93 for GT-1b, similar to the resistance substitutions observed with the
in vitro
replicon system. The primary difference in the resistance patterns observed
in vitro
and
in vivo
was the increased complexity of linked variant combinations observed in clinical specimens. Changes in the percentage of individual variants were observed during follow-up; however, the overall percentage of variants in the total population persisted up to 6 months. Our results suggest that during the 14-day monotherapy, most wild-type virus was eradicated by DCV. After the end of DCV treatment, viral fitness, rather than DCV resistance, probably determines which viral variants emerge as dominant in populations.
Bis-(3′-5′)-Cyclic Dimeric GMP Regulates Antimicrobial Peptide Resistance in Pseudomonas aeruginosa
Authors: Chua Song Lin , Tan Sean Yang-Yi , Rybtke Morten Theil , Chen Yicai , Rice Scott A. , Kjelleberg Staffan , Tolker-Nielsen Tim , Yang Liang , Givskov Michael 
Published: February 2013

ABSTRACT

Bis-(3′-5′)-cyclic dimeric GMP (c-di-GMP) is an intracellular second messenger that controls the lifestyles of many bacteria. A high intracellular level of c-di-GMP induces a biofilm lifestyle, whereas a low intracellular level of c-di-GMP stimulates dispersal of biofilms and promotes a planktonic lifestyle. Here, we used the expression of different reporters to show that planktonic cells, biofilm cells, and cells dispersed from biofilms (DCells) had distinct intracellular c-di-GMP levels. Proteomics analysis showed that the low intracellular c-di-GMP level of DCells induced the expression of proteins required for the virulence and development of antimicrobial peptide resistance in
Pseudomonas aeruginosa
. In accordance with this,
P. aeruginosa
cells with low c-di-GMP levels were found to be more resistant to colistin than
P. aeruginosa
cells with high c-di-GMP levels. This finding contradicts the current dogma stating that dispersed cells are inevitably more susceptible to antibiotics than their sessile counterparts.
Natural History of Yersinia pestis Pneumonia in Aerosol-Challenged BALB/c Mice
Authors: Heine Henry S. , Chuvala Lara , Riggins Renaldo , Hurteau Gregory , Cirz Ryan , Cass Robert , Louie Arnold , Drusano G. L. 
Published: February 2013

ABSTRACT

After a relatively short untreated interval, pneumonic plague has a mortality approaching 100%. We employed a murine model of aerosol challenge with
Yersinia pestis
to investigate the early course of pneumonic plague in the lung, blood, and spleen. We fit a mathematical model to all data simultaneously. The model fit to the data was acceptable. The number of organisms in the lung at baseline was estimated to be 135 (median) or 1,184 (mean) CFU/g. The doubling time was estimated as 1.5 to 1.7 h. Between 1 and 12 h postexposure, counts declined, but they then increased by 24 h, a finding hypothesized to be due to innate immunity. The model predicted that innate immunity declined with a half-time of 3 to 3.8 h. The threshold for bacteremia was 6.4 × 10
4
to 1.52 × 10
6
CFU/g. By 42 to 48 h, stationary phase was obtained. Lung bacterial burdens exceeded 10 log CFU/g. Obviating early defenses allows for rapid amplification of
Y. pestis
in bacteremia, making the rapid course with high mortality understandable.
Inflammasome Components Coordinate Autophagy and Pyroptosis as Macrophage Responses to Infection
Authors: Byrne Brenda G. , Dubuisson Jean-Francois , Joshi Amrita D. , Persson Jenny J. , Swanson Michele S. 
Published: February 2013

ABSTRACT

When microbes contaminate the macrophage cytoplasm, leukocytes undergo a proinflammatory death that is initiated by nucleotide-binding-domain-, leucine-rich-repeat-containing proteins (NLR proteins) that bind and activate caspase-1. We report that these inflammasome components also regulate autophagy, a vesicular pathway to eliminate cytosolic debris. In response to infection with flagellate
Legionella pneumophila
, C57BL/6J mouse macrophages equipped with caspase-1 and the NLR proteins NAIP5 and NLRC4 stimulated autophagosome turnover. A second trigger of inflammasome assembly, K
+
efflux, also rapidly activated autophagy in macrophages that produced caspase-1. Autophagy protects infected macrophages from pyroptosis, since caspase-1-dependent cell death occurred more frequently when autophagy was dampened pharmacologically by either 3-methyladenine or an inhibitor of the Atg4 protease. Accordingly, in addition to coordinating pyroptosis, both (pro-) caspase-1 protein and NLR components of inflammasomes equip macrophages to recruit autophagy, a disposal pathway that raises the threshold of contaminants necessary to trigger proinflammatory leukocyte death.

IMPORTANCE
An exciting development in the innate-immunity field is the recognition that macrophages enlist autophagy to protect their cytoplasm from infection. Nutrient deprivation has long been known to induce autophagy; how infection triggers this disposal pathway is an active area of research. Autophagy is encountered by many of the intracellular pathogens that are known to trigger pyroptosis, an inflammatory cell death initiated when nucleotide-binding-domain-, leucine-rich-repeat-containing proteins (NLR proteins) activate caspase-1 within inflammasome complexes. Therefore, we tested the hypothesis that NLR proteins and caspase-1 also coordinate autophagy as a barrier to cytosolic infection. By exploiting classical bacterial and mouse genetics and kinetic assays of autophagy, we demonstrate for the first time that, when confronted with cytosolic contamination, primary mouse macrophages rely not only on the NLR proteins NAIP5 and NLRC4 but also on (pro-)caspase-1 protein to mount a rapid autophagic response that wards off proinflammatory cell death.
A Decade of Plague in Mahajanga, Madagascar: Insights into the Global Maritime Spread of Pandemic Plague
Authors: Vogler Amy J. , Chan Fabien , Nottingham Roxanne , Andersen Genevieve , Drees Kevin , Beckstrom-Sternberg Stephen M. , Wagner David M. , Chanteau Suzanne , Keim Paul 
Published: February 2013

ABSTRACT
A cluster of human plague cases occurred in the seaport city of Mahajanga, Madagascar, from 1991 to 1999 following 62 years with no evidence of plague, which offered insights into plague pathogen dynamics in an urban environment. We analyzed a set of 44 Mahajanga isolates from this 9-year outbreak, as well as an additional 218 Malagasy isolates from the highland foci. We sequenced the genomes of four Mahajanga strains, performed whole-genome sequence single-nucleotide polymorphism (SNP) discovery on those strains, screened the discovered SNPs, and performed a high-resolution 43-locus multilocus variable-number tandem-repeat analysis of the isolate panel. Twenty-two new SNPs were identified and defined a new phylogenetic lineage among the Malagasy isolates. Phylogeographic analysis suggests that the Mahajanga lineage likely originated in the Ambositra district in the highlands, spread throughout the northern central highlands, and was then introduced into and became transiently established in Mahajanga. Although multiple transfers between the central highlands and Mahajanga occurred, there was a locally differentiating and dominant subpopulation that was primarily responsible for the 1991-to-1999 Mahajanga outbreaks. Phylotemporal analysis of this Mahajanga subpopulation revealed a cycling pattern of diversity generation and loss that occurred during and after each outbreak. This pattern is consistent with severe interseasonal genetic bottlenecks along with large seasonal population expansions. The ultimate extinction of plague pathogens in Mahajanga suggests that, in this environment, the plague pathogen niche is tenuous at best. However, the temporary large pathogen population expansion provides the means for plague pathogens to disperse and become ecologically established in more suitable nonurban environments.

IMPORTANCE
Maritime spread of plague led to the global dissemination of this disease and affected the course of human history. Multiple historical plague waves resulted in massive human mortalities in three classical plague pandemics: Justinian (6th and 7th centuries), Middle Ages (14th to 17th centuries), and third (mid-1800s to the present). Key to these events was the pathogen’s entry into new lands by “plague ships” via seaport cities. Although initial disease outbreaks in ports were common, they were almost never sustained for long and plague pathogens survived only if they could become established in ecologically suitable habitats. Although plague pathogens’ ability to invade port cities has been essential for intercontinental spread, these regions have not proven to be a suitable long-term niche. The disease dynamics in port cities such as Mahajanga are thus critical to plague pathogen amplification and dispersal into new suitable ecological niches for the observed global long-term maintenance of plague pathogens.
Kdo Hydrolase Is Required for Francisella tularensis Virulence and Evasion of TLR2-Mediated Innate Immunity
Authors: Okan Nihal A. , Chalabaev Sabina , Kim Tae-Hyun , Fink Avner , Ross Robin A. , Kasper Dennis L. 
Published: February 2013

ABSTRACT

The highly virulent
Francisella tularensis
subsp.
tularensis
has been classified as a category A bioterrorism agent. A live vaccine strain (LVS) has been developed but remains unlicensed in the United States because of an incomplete understanding of its attenuation. Lipopolysaccharide (LPS) modification is a common strategy employed by bacterial pathogens to avoid innate immunity. A novel modification enzyme has recently been identified in
F. tularensis
and
Helicobacter pylori
. This enzyme, a two-component Kdo (3-deoxy-
d
-manno-octulosonic acid) hydrolase, catalyzes the removal of a side chain Kdo sugar from LPS precursors. The biological significance of this modification has not yet been studied. To address the role of the two-component Kdo hydrolase KdhAB in
F. tularensis
pathogenesis, a Δ
kdhAB
deletion mutant was constructed from the LVS strain. In intranasal infection of mice, the Δ
kdhAB
mutant strain had a 50% lethal dose (LD
50
) 2 log
10
units higher than that of the parental LVS strain. The levels of the proinflammatory cytokines tumor necrosis factor alpha (TNF-α) and interleukin-1β (IL-1β) in bronchoalveolar lavage fluid were significantly higher (2-fold) in mice infected with the Δ
kdhAB
mutant than in mice infected with LVS.
In vitro
stimulation of bone marrow-derived macrophages with the Δ
kdhAB
mutant induced higher levels of TNF-α and IL-1β in a TLR2-dependent manner. In addition, TLR2
−/−
mice were more susceptible than wild-type mice to Δ
kdhAB
bacterial infection. Finally, immunization of mice with Δ
kdhAB
bacteria elicited a high level of protection against the highly virulent
F. tularensis
subsp.
tularensis
strain Schu S4. These findings suggest an important role for the
Francisella
Kdo hydrolase system in virulence and offer a novel mutant as a candidate vaccine.

IMPORTANCE
The first line of defense against a bacterial pathogen is innate immunity, which slows the progress of infection and allows time for adaptive immunity to develop. Some bacterial pathogens, such as
Francisella tularensis
, suppress the early innate immune response, killing the host before adaptive immunity can mature. To avoid an innate immune response,
F. tularensis
enzymatically modifies its lipopolysaccharide (LPS). A novel LPS modification—Kdo (3-deoxy-
d
-manno-octulosonic acid) saccharide removal—has recently been reported in
F. tularensis
. We found that the ∆
kdhAB
mutant was significantly attenuated in mice. Additionally, the mutant strain induced an early innate immune response in mice both
in vitro
and
in vivo
. Immunization of mice with this mutant provided protection against the highly virulent
F. tularensis
strain Schu S4. Thus, our study has identified a novel LPS modification important for microbial virulence. A mutant lacking this modification may be used as a live attenuated vaccine against tularemia.
Translational Phase I Trial of Vorinostat (Suberoylanilide Hydroxamic Acid) Combined with Cytarabine and Etoposide in Patients with Relapsed, Refractory, or High-Risk Acute Myeloid Leukemia
Authors: Gojo Ivana , Tan Ming , Fang Hong-Bin , Sadowska Mariola , Lapidus Rena , Baer Maria R. , Carrier France , Beumer Jan H. , Anyang Bean N. , Srivastava Rakesh K. , Espinoza-Delgado Igor , Ross Douglas D. 
Published: February 2013

AbstractPurpose: To determine the maximum-tolerated dose (MTD) of the histone deacetylase inhibitor vorinostat combined with fixed doses of cytarabine (ara-C or cytosine arabinoside) and etoposide in patients with poor-risk or advanced acute leukemia, to obtain preliminary efficacy data, describe pharmacokinetics, and in vivo pharmacodynamic effects of vorinostat in leukemia blasts.Experimental Design: In this open-label phase I study, vorinostat was given orally on days one to seven at three escalating dose levels: 200 mg twice a day, 200 mg three times a day, and 300 mg twice a day. On days 11 to 14, etoposide (100 mg/m2) and cytarabine (1 or 2 g/m2 twice a day if ≥65 or &lt;65 years old, respectively) were given. The study used a standard 3+3 dose escalation design.Results: Eighteen of 21 patients with acute myelogenous leukemia (AML) treated on study completed planned therapy. Dose-limiting toxicities [hyperbilirubinemia/septic death (1) and anorexia/fatigue (1)] were encountered at the 200 mg three times a day level; thus, the MTD was established to be vorinostat 200 mg twice a day. Of 21 patients enrolled, seven attained a complete remission (CR) or CR with incomplete platelet recovery, including six of 13 patients treated at the MTD. The median remission duration was seven months. No differences in percentage S-phase cells or multidrug resistance transporter (MDR1 or BCRP) expression or function were observed in vivo in leukemia blasts upon vorinostat treatment.Conclusions: Vorinostat 200 mg twice a day can be given safely for seven days before treatment with cytarabine and etoposide. The relatively high CR rate seen at the MTD in this poor-risk group of patients with AML warrants further studies to confirm these findings. Clin Cancer Res; 19(7); 1838–51. ©2013 AACR.
Expression Defect Size among Unclassified MLH1 Variants Determines Pathogenicity in Lynch Syndrome Diagnosis
Authors: Hinrichsen Inga , Brieger Angela , Trojan Jörg , Zeuzem Stefan , Nilbert Mef , Plotz Guido 
Published: February 2013

Abstract
Purpose: Lynch syndrome is caused by a germline mutation in a mismatch repair gene, most commonly the MLH1 gene. However, one third of the identified alterations are missense variants with unclear clinical significance. The functionality of these variants can be tested in the laboratory, but the results cannot be used for clinical diagnosis. We therefore aimed to establish a laboratory test that can be applied clinically.
Experimental Design: We assessed the expression, stability, and mismatch repair activity of 38 MLH1 missense variants and determined the pathogenicity status of recurrent variants using clinical data.
Results: Four recurrent variants were classified as neutral (K618A, H718Y, E578G, V716M) and three as pathogenic (A681T, L622H, P654L). All seven variants were proficient in mismatch repair but showed defects in expression. Quantitative PCR, pulse-chase, and thermal stability experiments confirmed decreases in protein stability, which were stronger in the pathogenic variants. The minimal cellular MLH1 concentration for mismatch repair was determined, which corroborated that strongly destabilized variants can cause repair deficiency. Loss of MLH1 tumor immunostaining is consistently reported in carriers of the pathogenic variants, showing the impact of this protein instability on these tumors.
Conclusions: Expression defects are frequent among MLH1 missense variants, but only severe defects cause Lynch syndrome. The data obtained here enabled us to establish a threshold for distinguishing tolerable (clinically neutral) from pathogenic expression defects. This threshold allows the translation of laboratory results for uncertain MLH1 variants into pathogenicity statements for diagnosis, thereby improving the targeting of cancer prevention measures in affected families. Clin Cancer Res; 19(9); 2432–41. ©2013 AACR.
Determination of Extratropical Tropopause Height in an Idealized Gray Radiation Model
Authors: Zurita-Gotor Pablo , Vallis Geoffrey K. 
Published: February 2013

Abstract
This paper investigates the mechanisms that determine the extratropical tropopause height, extending previous results with a Newtonian cooling model. A primitive equation model forced by a meridional gradient of incoming solar radiation, with the outgoing infrared radiation calculated using a simple gray radiation scheme, is now used. The tropopause is defined as the top of the boundary layer over which dynamical heat transport moves the temperature away from radiative equilibrium, and its height is estimated from the isentropic mass flux. Depending on parameters, this tropopause may or may not be associated with a sharp stratification change, and it may or may not be possible to define a thermal tropopause. The mass flux and thermal tropopause display similar sensitivity to external parameters when the latter can be defined; this is a sensitivity in good agreement with predictions by a radiative constraint. In some contrast to the Newtonian model, the radiative constraint is now quite effective in preventing adjustment to marginal criticality with realistic parameters.
The meridional structure of the thermal tropopause displays a jump in height at the jet latitude, which appears to be due to the formation of a mixing barrier at the jet maximum when baroclinicity has a finite vertical scale. As meridional potential vorticity mixing is inhibited across the jet, a discontinuity is created between weakly stratified air on its warm side and strongly stratified air on its cool side. The meridional stratification contrast is created by adiabatic cooling and warming by the residual circulation, as this circulation must be deflected vertically to avoid the mixing barrier at the jet maximum.
Evaluation of CMIP3 and CMIP5 Wind Stress Climatology Using Satellite Measurements and Atmospheric Reanalysis Products
Authors: Lee Tong , Waliser Duane E. , Li Jui-Lin F. , Landerer Felix W. , Gierach Michelle M. 
Published: February 2013

AbstractWind stress measurements from the Quick Scatterometer (QuikSCAT) satellite and two atmospheric reanalysis products are used to evaluate the annual mean and seasonal cycle of wind stress simulated by phases 3 and 5 of the Coupled Model Intercomparison Project (CMIP3 and CMIP5). The ensemble CMIP3 and CMIP5 wind stresses are very similar to each other. Generally speaking, there is no significant improvement of CMIP5 over CMIP3. The CMIP ensemble–average zonal wind stress has eastward biases at midlatitude westerly wind regions (30°–50°N and 30°–50°S, with CMIP being too strong by as much as 55%), westward biases in subtropical–tropical easterly wind regions (15°–25°N and 15°–25°S), and westward biases at high-latitude regions (poleward of 55°S and 55°N). These biases correspond to too strong anticyclonic (cyclonic) wind stress curl over the subtropical (subpolar) ocean gyres, which would strengthen these gyres and influence oceanic meridional heat transport. In the equatorial zone, significant biases of CMIP wind exist in individual basins. In the equatorial Atlantic and Indian Oceans, CMIP ensemble zonal wind stresses are too weak and result in too small of an east–west gradient of sea level. In the equatorial Pacific Ocean, CMIP zonal wind stresses are too weak in the central and too strong in the western Pacific. These biases have important implications for the simulation of various modes of climate variability originating in the tropics. The CMIP as a whole overestimate the magnitude of seasonal variability by almost 50% when averaged over the entire global ocean. The biased wind stress climatologies in CMIP not only have implications for the simulated ocean circulation and climate variability but other air–sea fluxes as well.