bluuebunny/crossref_metadata_2025_split huggingface dataset:
Polar localization of Escherichia coli chemoreceptors requires an intact Tol–Pal complex
Authors: Santos Thiago M. A. , Lin Ti‐Yu , Rajendran Madhusudan , Anderson Samantha M. , Weibel Douglas B. 
Published: April 2014

SummarySubcellular biomolecular localization is critical for the metabolic and structural properties of the cell. The functional implications of the spatiotemporal distribution of protein complexes during the bacterial cell cycle have long been acknowledged; however, the molecular mechanisms for generating and maintaining their dynamic localization in bacteria are not completely understood. Here we demonstrate that the trans‐envelope Tol–Pal complex, a widely conserved component of the cell envelope of Gram‐negative bacteria, is required to maintain the polar positioning of chemoreceptor clusters in Escherichia coli. Localization of the chemoreceptors was independent of phospholipid composition of the membrane and the curvature of the cell wall. Instead, our data indicate that chemoreceptors interact with components of the Tol–Pal complex and that this interaction is required to polarly localize chemoreceptor clusters. We found that disruption of the Tol–Pal complex perturbs the polar localization of chemoreceptors, alters cell motility, and affects chemotaxis. We propose that the E. coli Tol–Pal complex restricts mobility of the chemoreceptor clusters at the cell poles and may be involved in regulatory mechanisms that co‐ordinate cell division and segregation of the chemosensory machinery.
Developments in the correction of presbyopia II: surgical approaches
Authors: Charman W. Neil 
Published: April 2014

AbstractPurposeTo discuss the various static and dynamic surgical approaches which attempt to give presbyopes good vision at far, intermediate and near viewing distances.ContentStatic methods broadly adopt the same optical techniques as those used in presbyopic contact lens correction and aim to satisfy the needs of the presbyope by increasing binocular depth‐of‐focus, often using monovision as well as simultaneous‐imagery. Dynamic methods generally attempt to make use of at least some of the still‐active elements of the accommodation system. They include procedures which are supposed to modify the relative geometry of the ciliary muscle and lens, or which reduce the stiffness of the presbyopic lens either by replacing it with other natural or man‐made material or by subjecting it to femtosecond laser treatment. Alternatively the natural lens may be replaced by some form of intraocular lens which changes power as a result of forces derived from the still‐active ciliary muscle, zonule and capsule, or other sources.ConclusionsAt present, multifocal intraocular lenses appear to offer the most consistent and reliable surgical approach to surgical presbyopic correction. They have obvious advantages in convenience and stability over optically‐similar, simultaneous‐image presbyopic contact lenses but this must be balanced against their relative inflexibility in cases of patient dissatisfaction. Dynamic methods remain largely experimental. Although some approaches show promise, as yet no method has demonstrated a reliable, long‐term ability to correct distance refractive error and to appropriately change ocular power in response to changes in viewing distance over the normal range of interest.
Deciphering the molecular bases for drought tolerance in Arabidopsis autotetraploids
Authors: DEL POZO JUAN C. , RAMIREZ‐PARRA ELENA 
Published: April 2014

AbstractWhole genome duplication (autopolyploidy) is common in many plant species and often leads to better adaptation to adverse environmental conditions. However, little is known about the physiological and molecular mechanisms underlying these adaptations. Drought is one of the major environmental conditions limiting plant growth and development. Here, we report that, in Arabidopsis thaliana, tetraploidy promotes alterations in cell proliferation and organ size in a tissue‐dependent manner. Furthermore, it potentiates plant tolerance to salt and drought stresses and decreases transpiration rate, likely through controlling stomata density and closure, abscisic acid (ABA) signalling and reactive oxygen species (ROS) homeostasis. Our transcriptomic analyses revealed that tetraploidy mainly regulates the expression of genes involved in redox homeostasis and ABA and stress response. Taken together, our data have shed light on the molecular basis associated with stress tolerance in autopolyploid plants.
Trade Liberalization and Firm Productivity: Evidence from Chinese Manufacturing Industries
Authors: Hu Albert Guangzhou , Liu Zhengning 
Published: April 2014

AbstractThis paper examines the impact of tariff reduction following China's World Trade Organization (WTO) entry on the productivity of Chinese manufacturing firms using a firm‐level panel database that comprises all of China's manufacturing firms with an annual turnover above 5 million yuan and that spans the period of 2000–2006. An instrumental variable estimator is used to account for the endogeneity of the tariff reduction. The results indicate that China's trade liberalization in the five years following its WTO entry has led to a 0.94% annual increase in total factor productivity for Chinese manufacturing firms. However, the overall productivity gain from the tariff reduction is a net result of a productivity depressing effect of output tariff reduction and a productivity enhancing effect of input tariff reduction. Both effects have diminished in magnitude over the years after China joined the WTO. Firm heterogeneity and turnover plays an important role in generating gains from trade liberalization. The surviving firms have managed to cope with and take advantage of lower tariffs. The extent to which the tariff reduction affects Chinese firms' productivity is also dependent on the ownership structure of the firms with foreign‐invested firms being the clear winner.
Local Influence Analysis in AB–BA Crossover Designs
Authors: Hao Chengcheng , von Rosen Dietrich , von Rosen Tatjana 
Published: April 2014

ABSTRACTThe aim of this article is to develop methodology for detecting influential observations in crossover models with random individual effects. Various case‐weighted perturbations are performed. We obtain the influence of the perturbations on each parameter estimator and on their dispersion matrices. The obtained results exhibit the possibility to obtain closed‐form expressions of the influence using the residuals in mixed linear models. Some graphical tools are also presented.
Agricultural Biotechnology in Central and Eastern Europe: Determinants of Cultivation Bans
Authors: Tosun Jale 
Published: April 2014

AbstractBy the joining of the European Union (EU), the Central and Eastern European states had to align their agricultural biotechnology regulations to EU standards. In some cases, this meant the adoption of stricter regulations such as for the co‐existence of genetically modified organisms (GMOs) and conventional crops. In other cases, harmonisation with EU rules entailed the need to give up more restrictive national regulation, for example: to allow the cultivation of a limited number of GMOs. This article examines why some Central and Eastern European states joined the group of Western European countries that instituted bans on the commercial cultivation of GMOs in the EU. This study contributes to the literature in two ways. First, it contends that the prohibition of the commercial cultivation of GMOs in some Central and Eastern European member states must be interpreted in light of the EU‐wide public and political contestation of GMOs. Second, this piece of research shows that the ideological composition of governments matters in explaining the regulation of agricultural biotechnology. This second contribution allows for going beyond the predominant focus on public opinion when analysing the regulation of GMOs in the EU.
Understanding noncompliance with selective donor deferral criteria for high‐risk behaviors in Australian blood donors
Authors: Lucky Tarana T.A. , Seed Clive R. , Waller Daniel , Lee June F. , McDonald Ann , Wand Handan , Wroth Stephen , Shuttleworth Glen , Keller Anthony J. , Pink Joanne , Wilson David P. 
Published: April 2014

BackgroundUsing a predonation screening questionnaire, potential blood donors are screened for medical or behavioral factors associated with an increased risk for transfusion‐transmissible infection. After disclosure of these risks, potential donors are deferred from donating. Understanding the degree of failure to disclose full and truthful information (termed noncompliance) is important to determine and minimize residual risk. This study estimates the prevalence of, and likely reasons for, noncompliance among Australian donors with the deferrals for injecting drug use, sex with an injecting drug user, male‐to‐male sex, sex worker activity or contact, and sex with a partner from a high‐HIV‐prevalence country.Study Design and MethodsAn anonymous, online survey of a nationally representative sample of Australian blood donors was conducted. Prevalence of noncompliance with deferrable risk categories was estimated. Factors associated with noncompliance were determined using unadjusted and adjusted odds ratios.ResultsOf 98,044 invited donors, 30,790 donors completed the survey. The estimated prevalence of overall noncompliance (i.e., to at least one screening question) was 1.65% (95% confidence interval CI, 1.51%‐1.8%). Noncompliance with individual deferrals ranged from 0.05% (sex work) to 0.54% (sex with an injecting drug user). The prevalences of the disclosed exclusionary risk behaviors were three to 14 times lower than their estimated prevalence in the general population.ConclusionThe prevalence of noncompliance is relatively low but our estimate is likely to be a lower bound. The selected high‐risk behaviors were substantially less common in blood donors compared to the general population suggesting that self‐deferral is effective. Nevertheless, a focus on further minimization should improve the blood safety.
Mapping the Cellular Response to Small Molecules Using Chemogenomic Fitness Signatures
Authors: Lee Anna Y. , St.Onge Robert P. , Proctor Michael J. , Wallace Iain M. , Nile Aaron H. , Spagnuolo Paul A. , Jitkova Yulia , Gronda Marcela , Wu Yan , Kim Moshe K. , Cheung-Ong Kahlin , Torres Nikko P. , Spear Eric D. , Han Mitchell K. L. , Schlecht Ulrich , Suresh Sundari , Duby Geoffrey , Heisler Lawrence E. , Surendra Anuradha , Fung Eula , Urbanus Malene L. , Gebbia Marinella , Lissina Elena , Miranda Molly , Chiang Jennifer H. , Aparicio Ana Maria , Zeghouf Mahel , Davis Ronald W. , Cherfils Jacqueline , Boutry Marc , Kaiser Chris A. , Cummins Carolyn L. , Trimble William S. , Brown Grant W. , Schimmer Aaron D. , Bankaitis Vytas A. , Nislow Corey , Bader Gary D. , Giaever Guri 
Published: April 2014

Yeasty HIPHOPIn order to identify how chemical compounds target genes and affect the physiology of the cell, tests of the perturbations that occur when treated with a range of pharmacological chemicals are required. By examining the haploinsufficiency profiling (HIP) and homozygous profiling (HOP) chemogenomic platforms,Leeet al.(p.208) analyzed the response of yeast to thousands of different small molecules, with genetic, proteomic, and bioinformatic analyses. Over 300 compounds were identified that targeted 121 genes within 45 cellular response signature networks. These networks were used to extrapolate the likely effects of related chemicals, their impact upon genetic pathways, and to identify putative gene functions.
Comparison of Tetrazolium Salt Assays for Evaluation of Drug Activity against Leishmania spp
Authors: Ginouves Marine , Carme Bernard , Couppie Pierre , Prevot Ghislaine 
Published: April 2014

ABSTRACT

In French Guiana, leishmaniasis is an essentially cutaneous infection. It constitutes a major public health problem, with a real incidence of 0.2 to 0.3%.
Leishmania guyanensis
is the causal species most frequently encountered in French Guiana. The treatment of leishmaniasis is essentially drug based, but the therapeutic compounds available have major side effects (e.g., liver damage and diabetes) and must be administered parenterally or are costly. The efficacy of some of these agents has declined due to the emergence of resistance in certain strains of
Leishmania
. There is currently no vaccine against leishmaniasis, and it is therefore both necessary and urgent to identify new compounds effective against
Leishmania
. The search for new drugs requires effective tests for evaluations of the leishmanicidal activity of a particular molecule or extract. Microculture tetrazolium assays (MTAs) are colorimetric tests based on the use of tetrazolium salts. We compared the efficacies of three tetrazolium salts—3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT), 2,3-bis-(2-methoxy-4-nitro-5-sulfophenyl)-2
H
-tetrazolium-5-carboxanilide (XTT), and 2-(2-methoxy-4-nitrophenyl)-3-(4-nitrophenyl)-5-(2,4-disulfophenyl)-2
H
-tetrazolium (WST-8)—for quantification of the promastigotes of various species of
Leishmania
. We found that the capacity of
Leishmania
to metabolize a tetrazolium salt depended on the salt used and the species of
Leishmania
. WST-8 was the tetrazolium salt best metabolized by
L. guyanensis
and gave the best sensitivity.
Simplified Microarray System for Simultaneously Detecting Rifampin, Isoniazid, Ethambutol, and Streptomycin Resistance Markers in Mycobacterium tuberculosis
Authors: Linger Yvonne , Kukhtin Alexander , Golova Julia , Perov Alexander , Lambarqui Amine , Bryant Lexi , Rudy George B. , Dionne Kim , Fisher Stefanie L. , Parrish Nicole , Chandler Darrell P. 
Published: April 2014

ABSTRACT

We developed a simplified microarray test for detecting and identifying mutations in
rpoB
,
katG
,
inhA
,
embB
, and
rpsL
and compared the analytical performance of the test to that of phenotypic drug susceptibility testing (DST). The analytical sensitivity was estimated to be at least 110 genome copies per amplification reaction. The microarray test correctly detected 95.2% of mutations for which there was a sequence-specific probe on the microarray and 100% of 96 wild-type sequences. In a blinded analysis of 153 clinical isolates, microarray sensitivity for first-line drugs relative to phenotypic DST (true resistance) was 100% for rifampin (RIF) (14/14), 90.0% for isoniazid (INH) (36/40), 70% for ethambutol (EMB) (7/10), and 89.1% (57/64) combined. Microarray specificity (true susceptibility) for first-line agents was 95.0% for RIF (132/139), 98.2% for INH (111/113), and 98.6% for EMB (141/143). Overall microarray specificity for RIF, INH, and EMB combined was 97.2% (384/395). The overall positive and negative predictive values for RIF, INH, and EMB combined were 84.9% and 98.3%, respectively. For the second-line drug streptomycin (STR), overall concordance between the agar proportion method and microarray analysis was 89.5% (137/153). Sensitivity was 34.8% (8/23) because of limited microarray coverage for STR-conferring mutations, and specificity was 99.2% (129/130). All false-susceptible discrepant results were a consequence of DNA mutations that are not represented by a specific microarray probe. There were zero invalid results from 220 total tests. The simplified microarray system is suitable for detecting resistance-conferring mutations in clinical
M. tuberculosis
isolates and can now be used for prospective trials or integrated into an all-in-one, closed-amplicon consumable.
Direct Detection of Indirect Transmission of Streptobacillus moniliformis Rat Bite Fever Infection
Authors: Mackey Joseph R. , Melendez Elsa L. Vazquez , Farrell John J. , Lowery Kristin S. , Rounds Megan A. , Sampath Rangarajan , Bonomo Robert A. 
Published: April 2014

ABSTRACT

We describe the evaluation of culture-negative synovial fluid from a 3-year-old boy by PCR and electrospray ionization followed by mass spectrometry (PCR/ESI-MS). Our patient developed a diffuse rash and fever with systemic signs and symptoms of sepsis, but four sets of blood cultures obtained prior to initiation of antibiotics were negative. After 1 week of illness, he developed right-knee swelling. Analysis of synovial fluid was consistent with infection, but cultures of specimens obtained following initiation of antimicrobial treatment were negative for growth. PCR/ESI-MS detected
Streptobacillus moniliformis
in the synovial fluid sample. Our patient completed an appropriate course of antibiotic treatment and remained completely asymptomatic in follow-up evaluation. This unique case suggests that PCR/ESI-MS may be a useful diagnostic tool for direct detection of unusual or unexpected pathogens directly from clinical specimens, particularly when samples have been obtained from patients following initiation of antibiotic therapy.
Reduction in False-Positive Aspergillus Serum Galactomannan Enzyme Immunoassay Results Associated with Use of Piperacillin-Tazobactam in the United States
Authors: Vergidis Paschalis , Razonable Raymund R. , Wheat L. Joseph , Estes Lynn , Caliendo Angela M. , Baden Lindsey R. , Wingard John R. , Baddley John , Assi Maha , Norris Steven , Chandrasekar Pranatharthi , Shields Ryan , Nguyen Hong , Freifeld Alison , Kohler Richard , Kleiman Martin , Walsh Thomas J. , Hage Chadi A. 
Published: April 2014

ABSTRACT

Piperacillin-tazobactam (PTZ) is known to cause false-positive results in the Platelia
Aspergillus
enzyme-linked immunoassay (EIA), due to contamination with galactomannan (GM). We tested 32 lots of PTZ and 27 serum specimens from patients receiving PTZ. GM was not detected in the lots of PTZ; one serum specimen (3.7%) was positive. PTZ formulations commonly used in the United States today appear to be a rare cause for false-positive GM results.
Integrative Analysis of Salmonellosis in Israel Reveals Association of Salmonella enterica Serovar 9,12:l,v:− with Extraintestinal Infections, Dissemination of Endemic S. enterica Serovar Typhimurium DT104 Biotypes, and Severe Underreporting of Outbreaks
Authors: Marzel Alex , Desai Prerak T. , Nissan Israel , Schorr Yosef Ilan , Suez Jotham , Valinsky Lea , Reisfeld Abraham , Agmon Vered , Guard Jean , McClelland Michael , Rahav Galia , Gal-Mor Ohad 
Published: April 2014

ABSTRACT

Salmonella enterica
is the leading etiologic agent of bacterial food-borne outbreaks worldwide. This ubiquitous species contains more than 2,600 serovars that may differ in their host specificity, clinical manifestations, and epidemiology. To characterize salmonellosis epidemiology in Israel and to study the association of nontyphoidal
Salmonella
(NTS) serovars with invasive infections, 48,345
Salmonella
cases reported and serotyped at the National
Salmonella
Reference Center between 1995 and 2012 were analyzed. A quasi-Poisson regression was used to identify irregular clusters of illness, and pulsed-field gel electrophoresis in conjunction with whole-genome sequencing was applied to molecularly characterize strains of interest. Three hundred twenty-nine human salmonellosis clusters were identified, representing an annual average of 23 (95% confidence interval [CI], 20 to 26) potential outbreaks. We show that the previously unsequenced
S. enterica
serovar 9,12:l,v:− belongs to the B clade of
Salmonella enterica
subspecies
enterica
, and we show its frequent association with extraintestinal infections, compared to other NTS serovars. Furthermore, we identified the dissemination of two prevalent
Salmonella enterica
serovar Typhimurium DT104 clones in Israel, which are genetically distinct from other global DT104 isolates. Accumulatively, these findings indicate a severe underreporting of
Salmonella
outbreaks in Israel and provide insights into the epidemiology and genomics of prevalent serovars, responsible for recurring illness.
Detection of Prosthetic Joint Infection by Use of PCR-Electrospray Ionization Mass Spectrometry Applied to Synovial Fluid
Authors: Melendez Dante P. , Uhl James R. , Greenwood-Quaintance Kerryl E. , Hanssen Arlen D. , Sampath Rangarajan , Patel Robin 
Published: April 2014

ABSTRACT
PCR coupled with electrospray ionization mass spectrometry applied to synovial fluid specimens had an 81% sensitivity and a 95% specificity for the diagnosis of prosthetic joint infection.
Fungal DNA Detected in Blood Samples of Patients Who Received Contaminated Methylprednisolone Injections Reveals Increased Complexity of Causative Agents
Authors: Zhao Yanan , Armeanu Emilian , DiVerniero Richard , Lewis Terri A. , Dobson Richard C. , Kontoyiannis Dimitrios P. , Roilides Emmanuel , Walsh Thomas J. , Perlin David S. 
Published: April 2014

ABSTRACT

Using
Exserohilum rostratum
-specific and panfungal real-time PCR, we studied 24 blood samples and 2 synovial fluid specimens from 20 patients with persistent or worsening pain following injections of contaminated methylprednisolone. Seven blood specimens from 6 patients were significantly positive for fungal DNA by panfungal PCR, with multiple fungal species identified.
hnRNP L and NF90 Interact with Hepatitis C Virus 5′-Terminal Untranslated RNA and Promote Efficient Replication
Authors: Li You , Masaki Takahiro , Shimakami Tetsuro , Lemon Stanley M. 
Published: April 2014

ABSTRACT
The 5′-terminal sequence of the hepatitis C virus (HCV) positive-strand RNA genome is essential for viral replication. Critical host factors, including a miR-122/Ago2 complex and poly(rC)-binding protein 2 (PCBP2), associate with this RNA segment. We used a biotinylated RNA pulldown approach to isolate host factors binding to the HCV 5′ terminal 47 nucleotides and, in addition to Ago2 and PCBP2, identified several novel proteins, including IGF2BP1, hnRNP L, DHX9, ADAR1, and NF90 (ILF3). PCBP2, IGF2BP1, and hnRNP L bound single-stranded RNA, while DHX9, ADAR1, and NF90 bound a cognate double-stranded RNA bait. PCBP2, IGF2BP1, and hnRNP L binding were blocked by preannealing the single-stranded RNA bait with miR-122, indicating that they bind the RNA in competition with miR-122. However, IGF2BP1 binding was also inhibited by high concentrations of heparin, suggesting that it bound the bait nonspecifically. Among these proteins, small interfering RNA-mediated depletion of hnRNP L and NF90 significantly impaired viral replication and reduced infectious virus yields without substantially affecting HCV internal ribosome entry site-mediated translation. hnRNP L and NF90 were found to associate with HCV RNA in infected cells and to coimmunoprecipitate with NS5A in an RNA-dependent manner. Both also associate with detergent-resistant membranes where viral replication complexes reside. We conclude that hnRNP and NF90 are important host factors for HCV replication, at least in cultured cells, and may be present in the replication complex.

IMPORTANCE
Although HCV replication has been intensively studied in many laboratories, many aspects of the viral life cycle remain obscure. Here, we use a novel RNA pulldown strategy coupled with mass spectrometry to identify host cell proteins that interact functionally with regulatory RNA elements located at the extreme 5′ end of the positive-strand RNA genome. We identify two, primarily nuclear RNA-binding proteins, hnRNP L and NF90, with previously unrecognized proviral roles in HCV replication. The data presented add to current understanding of the replication cycle of this pathogenic human virus.