bluuebunny/crossref_metadata_2025_split huggingface dataset:
Gliding Motility of Mycoplasma mobile on Uniform Oligosaccharides
Authors: Kasai Taishi , Hamaguchi Tasuku , Miyata Makoto 
Published: July 2015

ABSTRACT

The binding and gliding of
Mycoplasma mobile
on a plastic plate covered by 53 uniform oligosaccharides were analyzed. Mycoplasmas bound to and glided on only 21 of the fixed sialylated oligosaccharides (SOs), showing that sialic acid is essential as the binding target. The affinities were mostly consistent with our previous results on the inhibitory effects of free SOs and suggested that
M. mobile
recognizes SOs from the nonreducing end with four continuous sites as follows. (i and ii) A sialic acid at the nonreducing end is tightly recognized by tandemly connected two sites. (iii) The third site is recognized by a loose groove that may be affected by branches. (iv) The fourth site is recognized by a large groove that may be enhanced by branches, especially those with a negative charge. The cells glided on uniform SOs in manners apparently similar to those of the gliding on mixed SOs. The gliding speed was related inversely to the mycoplasma's affinity for SO, suggesting that the detaching step may be one of the speed determinants. The cells glided faster and with smaller fluctuations on the uniform SOs than on the mixtures, suggesting that the drag caused by the variation in SOs influences gliding behaviors.

IMPORTANCE
Mycoplasma is a group of bacteria generally parasitic to animals and plants. Some
Mycoplasma
species form a protrusion at a pole, bind to solid surfaces, and glide in the direction of the protrusion. These procedures are essential for parasitism. Usually, mycoplasmas glide on mixed sialylated oligosaccharides (SOs) derived from glycoprotein and glycolipid. Since gliding motility on uniform oligosaccharides has never been observed, this study gives critical information about recognition and interaction between receptors and SOs.
DNA Processing Proteins Involved in the UV-Induced Stress Response of Sulfolobales
Authors: van Wolferen Marleen , Ma Xiaoqing , Albers Sonja-Verena 
Published: July 2015

ABSTRACT

The
ups
operon of
Sulfolobus
species is highly induced upon UV stress. Previous studies showed that the pili encoded by this operon are involved in cellular aggregation, which is essential for subsequent DNA exchange between cells, resulting in homologous recombination. The presence of this pilus system increases the fitness of
Sulfolobus
cells under UV light-induced stress conditions, as the transfer of DNA takes place in order to repair UV-induced DNA lesions via homologous recombination. Four conserved genes (
saci_1497
to
saci_1500
) which encode proteins with putative DNA processing functions are present downstream of the
ups
operon. In this study, we show that after UV treatment the cellular aggregation of strains with
saci_1497
,
saci_1498
, and
saci_1500
deletions is similar to that of wild-type strains; their survival rates, however, were reduced and similar to or lower than those of the pilus deletion strains, which could not aggregate anymore. DNA recombination assays indicated that
saci_1498
, encoding a ParB-like protein, plays an important role in DNA transfer. Moreover, biochemical analysis showed that the endonuclease III encoded by
saci_1497
nicks UV-damaged DNA. In addition, RecQ-like helicase Saci_1500 is able to unwind homologous recombination intermediates, such as Holliday junctions. Interestingly, a
saci_1500
deletion mutant was more sensitive to UV light but not to the replication-stalling agents hydroxyurea and methyl methanesulfonate, suggesting that Saci_1500 functions specifically in the UV damage pathway. Together these results suggest a role of Saci_1497 to Saci_1500 in the repair or transfer of DNA that takes place after UV-induced damage to the genomic DNA of
Sulfolobus acidocaldarius
.

IMPORTANCE
Sulfolobales
species increase their fitness after UV stress by a UV-inducible pilus system that enables high rates of DNA exchange between cells. Downstream of the pilus operon, three genes that seem to play a role in the repair or transfer of the DNA between
Sulfolobus
cells were identified, and their possible functions are discussed. Next to the previously described role of UV-inducible pili in the exchange of DNA, we have thereby increased our knowledge of DNA transfer at the level of DNA processing. This paper therefore contributes to the overall understanding of the DNA exchange mechanism among
Sulfolobales
cells.
Systematic Nomenclature for GGDEF and EAL Domain-Containing Cyclic Di-GMP Turnover Proteins of Escherichia coli
Authors: Hengge Regine , Galperin Michael Y. , Ghigo Jean-Marc , Gomelsky Mark , Green Jeffrey , Hughes Kelly T. , Jenal Urs , Landini Paolo 
Published: July 2015

ABSTRACT

In recent years,
Escherichia coli
has served as one of a few model bacterial species for studying cyclic di-GMP (c-di-GMP) signaling. The widely used
E. coli
K-12 laboratory strains possess 29 genes encoding proteins with GGDEF and/or EAL domains, which include 12 diguanylate cyclases (DGC), 13 c-di-GMP-specific phosphodiesterases (PDE), and 4 “degenerate” enzymatically inactive proteins. In addition, six new GGDEF and EAL (GGDEF/EAL) domain-encoding genes, which encode two DGCs and four PDEs, have recently been found in genomic analyses of commensal and pathogenic
E. coli
strains. As a group of researchers who have been studying the molecular mechanisms and the genomic basis of c-di-GMP signaling in
E. coli
, we now propose a general and systematic
dgc
and
pde
nomenclature for the enzymatically active GGDEF/EAL domain-encoding genes of this model species. This nomenclature is intuitive and easy to memorize, and it can also be applied to additional genes and proteins that might be discovered in various strains of
E. coli
in future studies.
Development of a computerised decisions support system for renal risk drugs targeting primary healthcare
Authors: Helldén Anders , Al-Aieshy Fadiea , Bastholm-Rahmner Pia , Bergman Ulf , Gustafsson Lars L , Höök Hans , Sjöviker Susanne , Söderström Anders , Odar-Cederlöf Ingegerd 
Published: July 2015

ObjectivesTo assess general practitioners (GPs) experience from the implementation and use of a renal computerised decision support system (CDSS) for drug dosing, developed for primary healthcare, integrated into the patient’s electronic health record (EHR), and building on estimation of the patient's creatinine clearance (ClCG).DesignQualitative research design by a questionnaire and a focus group discussion.Setting and participantsEight GPs at two primary healthcare centres (PHCs).InterventionsThe GP at PHC 1, and the project group, developed and tested the technical solution of the CDSS. Proof-of-concept was tested by seven GPs at PHC 2. They also participated in a group discussion and answered a questionnaire. A web window in the EHR gave drug and dosage in relation to ClCG. Each advice was according to three principles: If? Why? Because.Outcome measures(1) The GPs’ experience of ‘easiness to use’ and ‘perceived usefulness’ at PHC 2, based on loggings of use, answers from a questionnaire using a 5-point Likert scale, and answers from a focus group discussion. (2) The number of patients aged 65 years and older with an estimation of ClCGbefore and after the implementation of the CDSS.ResultsThe GPs found the CDSS fast, simple and easy to use. They appreciated the automatic presentation of the CICGstatus on opening the medication list, and the ability to actively look up specific drug recommendations in two steps. The CDSS scored high on the Likert scale. All GPs wanted to continue the use of the CDSS and to recommend it to others. The number of patients with an estimated ClCGincreased 1.6-fold.ConclusionsAcceptance of the simple graphical interface of this push and pull renal CDSS was high among the primary care physicians evaluating this proof of concept. The graphical model should be useful for further development of renal decision support systems.
How effective are patient safety initiatives? A retrospective patient record review study of changes to patient safety over time
Authors: Baines Rebecca , Langelaan Maaike , de Bruijne Martine , Spreeuwenberg Peter , Wagner Cordula 
Published: July 2015

ObjectivesTo assess whether, compared with previous years, hospital care became safer in 2011/2012, expressing itself in a fall in preventable adverse event (AE) rates alongside patient safety initiatives.DesignRetrospective patient record review at three points in time.SettingIn three national AE studies, patient records of 2004, 2008 and 2011/2012 were reviewed in, respectively, 21 hospitals in 2004, 20 hospitals in 2008 and 20 hospitals in 2011/2012. In each hospital, 400, 200 and 200 patient records were sampled, respectively.ParticipantsIn total, 15 997 patient admissions were included in the study, 7926 patient admissions from 2004, 4023 from 2008 and 4048 from 2011/2012.InterventionsThe main patient safety initiatives in hospital care at a national level between 2004 and 2012 have been small as well as large-scale multifaceted programmes.Main outcome measuresRates of both AEs and preventable AEs.ResultsUncorrected crude overall AE rates showed no change in 2011/2012 in comparison with 2008, whereas preventable AE rates showed a reduction of 45%. After multilevel corrections, the decrease in preventable AE rate in 2011/2012 was still clearly visible with a decrease of 30% in comparison to 2008 (p=0.10). In 2011/2012, fewer preventable AEs were found in older age groups, or related to the surgical process, in comparison with 2008.ConclusionsOur study shows some improvements in preventable AEs in the areas that were addressed during the comprehensive national safety programme. There are signs that such a programme has a positive impact on patient safety.
Potential of Quantum Finite Automata with Exact Acceptance
Authors: Gruska Jozef , Qiu Daowen , Zheng Shenggen 
Published: July 2015

The potential of the exact quantum information processing is an interesting, important and intriguing issue. For examples, it has been believed that quantum tools can provide significant, that is larger than polynomial, advantages in the case of exact quantum computation only, or mainly, for problems with very special structures. We will show that this is not the case.In this paper the potential of quantum finite automata producing outcomes not only with a (high) probability, but with certainty (so called exactly) is explored in the context of their uses for solving promise problems and with respect to the size of automata. It is shown that for solving particular classes [Formula: see text] of promise problems, even those without some very special structure, that succinctness of the exact quantum finite automata under consideration, with respect to the number of (basis) states, can be very small (and constant) though it grows proportional to [Formula: see text] in the case deterministic finite automata (DFAs) of the same power are used. This is here demonstrated also for the case that the component languages of the promise problems solvable by DFAs are non-regular. The method used can be applied in finding more exact quantum finite automata or quantum algorithms for other promise problems.
Hazard mitigation and crisis management during major flank eruptions at Etna volcano: reporting on real experience
Authors: Bonaccorso Alessandro , Calvari Sonia , Boschi Enzo 
Published: July 2015

Abstract
Etna volcano is characterized by frequent effusive eruptions from the summit craters or from flank fissures, and these have often threatened villages, infrastructures and tourist facilities. Considerable experience of lava-flow mitigation has been gained by scientists working on this volcano, and in this paper we principally discuss the problems arising from lava flows emplaced during the 2002–03 flank eruption, when eruptive fissures opened both on the northern and southern flanks of the volcano, feeding lava flows towards several villages, tourist facilities and forests. We highlight the importance of the monitoring system to follow the spreading of eruptive fissures and predict when they stopped propagating. We illustrate the value of thermal mapping in identifying active lava flows, in measuring effusion rates to estimate the maximum distance that flows can travel, and in obtaining reliable lava-flow simulations in real time in order to predict possible paths of the lava flow and to adopt the most appropriate solutions to limit its damage. Collaborations between scientists from different institutions and fields once again proved essential to understand and model the eruptive processes, to mitigate hazards and to obtain the best results.
TERTPolymorphism rs2736100-C Is Associated with EGFR Mutation–Positive Non–Small Cell Lung Cancer
Authors: Wei Rongrong , Cao Lan , Pu Hengying , Wang Hongwei , Zheng Yonglan , Niu Xiaomin , Weng Xiaoling , Zhang Hong , Favus Murray J. , Zhang Lanjun , Jia Weihua , Zeng Yixin , Amos Christopher I. , Lu Shun , Wang Hui-Yun , Liu Yun , Liu Wanqing 
Published: July 2015

AbstractPurpose: EGF receptor (EGFR) mutation–positive (EGFRmut+) non–small cell lung cancer (NSCLC) may be a unique orphan disease. Previous studies suggested that the telomerase reverse transcriptase (TERT) gene polymorphism is associated with demographic and clinical features strongly associated with EGFR mutations, for example, adenocarcinoma histology, never-smoking history, and female gender. We aim to test the association between TERT polymorphism and EGFRmut+ NSCLC.Experimental Design: We conducted a genetic association study in Chinese patients with NSCLC (n = 714) and healthy controls (n = 2,520), between the rs2736100 polymorphism and EGFRmut+ NSCLC. We further tested the association between the EGFR mutation status and mean leukocyte telomere length (LTL). The potential function of rs2736100 in lung epithelial cells was also explored.Results: The rs2736100-C allele was significantly associated with EGFRmut+ NSCLC [OR, 1.52; 95% confidence interval (CI), 1.28–1.80; P = 1.6 × 10−6] but not EGFRmut− NSCLC (OR = 1.07, 95% CI, 0.92–1.24, P = 0.4). While patients with NSCLC as a whole have significantly longer LTL than healthy controls (P ≤ 10−13), the EGFRmut+ patients have even longer LTL than EGFRmut− patients (P = 0.008). Meanwhile, rs2736100 was significantly associated with TERT mRNA expression in both normal and tumor lung tissues. All results remained significant after controlling for age, gender, smoking status, and histology (P &lt; 0.05 for all tests). Moreover, the rs2736100 DNA sequence has an allele-specific affinity to nuclear proteins extracted from lung epithelial cells, which led to an altered enhancer activity of the sequence in vitro.Conclusions: Our study suggests that telomerase and telomere function may be essential for carcinogenesis of EGFRmut+ NSCLC. Further investigation for the underlying mechanism is warranted. Clin Cancer Res; 21(22); 5173–80. ©2015 AACR.
Mass Media Campaigns’ Influence on Prehospital Behavior for Acute Coronary Syndromes: An Evaluation of the Australian Heart Foundation's Warning Signs Campaign
Authors: Bray Janet E. , Stub Dion , Ngu Philip , Cartledge Susie , Straney Lahn , Stewart Michelle , Keech Wendy , Patsamanis Harry , Shaw James , Finn Judith 
Published: July 2015

Background

The aim of this study was to examine the awareness of a recent mass media campaign, and its influence on knowledge and prehospital times, in a cohort of acute coronary syndrome (
ACS
) patients admitted to an Australian hospital.

Methods and Results

We conducted 199 semistructured interviews with consecutive
ACS
patients who were aged 35 to 75 years, competent to provide consent, and English speaking. Questions addressed the factors known to predict prehospital delay, awareness of the campaign, and whether it increased knowledge and influenced actions. Multivariable logistic regression was used to examine the association between campaign awareness and a 1‐hour delay in deciding to seek medical attention (patient delay) and a 2‐hour delay in presenting to hospital (prehospital delay). The median age was 62 years (
IQR
=53 to 68 years), and 68% (n=136) were male. Awareness of the campaign was reported by 127 (64%) patients, with most of these patients stating the campaign (1) increased their understanding of what is a heart attack (63%), (2) increased their awareness of the signs and symptoms of heart attack (68%), and (3) influenced their actions in response to symptoms (43%). After adjustment for other predictors, awareness of the campaign was significantly associated with patient delay time of ≤1 hour (adjusted odds ratio [
AOR
]=2.25, 95%
CI
: 1.03 to 4.91,
P
=0.04) and prehospital delay time ≤2 hours (
AOR
=3.11, 95%
CI
: 1.36 to 7.08,
P
=0.007).

Conclusions
Our study showed reasonably high awareness of the warning signs campaign, which was significantly associated with shorter prehospital decision‐making and faster presentation to hospital.
Sex Disparities in Stroke: Women Have More Severe Strokes but Better Survival Than Men
Authors: Dehlendorff Christian , Andersen Klaus Kaae , Olsen Tom Skyhøj 
Published: July 2015

Background
Uncertainty remains about whether stroke affects men and women similarly. We studied differences between men and women with regard to stroke severity and survival.

Methods and Results
We used the Danish Stroke Registry, with information on all hospital admissions for stroke in Denmark between 2003 and 2012 (N=79 617), and the Danish Register of Causes of Death. Information was available on age, sex, marital status, stroke severity, stroke subtype, socioeconomic status, and cardiovascular risk profile. We studied only deaths due to the index stroke, with the assumption that death reported on death certificates as due to stroke was related to the index stroke if death occurred within the first week or month after stroke. Multivariate Cox regression analysis and multiple imputation were applied. Stroke was the cause of death for 4373 and 5512 of the 79 617 patients within 1 week (5.5%) or 1 month (6.9%), respectively. After the age of 60 years, women had more severe strokes than men. Up to ages in the mid‐60s, no difference in the risk of death from stroke was seen between the 2 sexes. For people aged >65 years, however, the risk gradually became greater in men than in women and significantly so (>15%) from the mid‐70s (adjusted for age, marital status, stroke severity, stroke subtype, socioeconomic status, and cardiovascular risk factors). Results were essentially the same when analyzing deaths within 1 week, 1 month and ischemic and hemorrhagic stroke separately.

Conclusions
Stroke affects women and men differently. Elderly women were affected more severely than elderly men but were more likely to survive.
The Early Codex Book
Authors: Stanley Timothy 
Published: July 2015

In 1933 Frederic Kenyon was one of the first to note the early Christian addiction to codex books. As later scholars confirmed, Christian communities reproduced their sacred literature in a way that differed from the largely scrolled Greco-Roman bibliographic cultures of the first centuries of the Common Era. Book historians and scholars of biblical literature alike have developed a range of competing theories in order to better understand this peculiarity. By evaluating their claims, a number of clarifications can be made in order to demonstrate the codex’s sensitivity to Jewish scribal practices as well as its capacity to include a cosmopolitan diversity of texts. Through these clarifications the codex book form itself can provide vital interpretative insights into early biblical literature and the longer history of the book today.
Redescription of Clitocybe umbrinopurpurascens (Basidiomycota, Agaricales) and revision of Neohygrophorus and Pseudoomphalina
Authors: Lavorato Carmine , Vizzini Alfredo , Ge Zai-Wei , Contu Marco 
Published: July 2015

Clitocybe umbrinopurpurascens, a rare species thus far known only from Morocco, is redescribed based on fresh collections made in Calabria (South Italy). Photographs of fresh material and drawings of the main micromorphological features of the species are provided. The type collection, in poor condition and not suitable for molecular analysis, was restudied macro- and micromorphologically and was found fully identical with the collections from Calabria. Based on molecular data, this species belongs to the genus Pseudoomphalina (type Omphalia kalchbrenneri) and the genus Neohygrophorus is treated as a synonym of Pseudoomphalina. A collection from Calabria is chosen as an epitype for P. umbrinopurpurascens. Our morphological and molecular revision of other Pseudoomphalina species did not provide evidence supporting the placement of Agaricus pachyphyllus in Pseudomphalina, or any other of the allied genera, therefore, for this species the new genus Pseudolaccaria is introduced. As there are no extant original herbarium specimens, a lectotype and epitype for Omphalia kalchbrenneri and a neotype for Agaricus pachyphyllus are designated.
Reestablishment of Hymenaea travassii (Leguminosae, Caesalpinioideae), a species endemic to the Bolivian Chaco
Authors: Pinto Rafael Barbosa , Mansano Vidal De Freitas , Tozzi Ana Maria Goulart de Azevedo 
Published: July 2015

In Lee & Langenheim’s taxonomic revision of the genus Hymenaea (Leguminosae, Caesalpinioideae), the species Hymenaea travassii was considered a species of dubious status. A detailed analysis of the type material and additional specimens, clearly indicates, however, that this is a distinct species, endemic to the Bolivian “chaco”. The species can be distinguished by a combination of its habit, the texture of the bark and the shape and size of its leaflets. This study proposes the reestablishment of Hymenaea travassii as a distinct species, based on morphology. A species description, a key to distinguish Hymenaea travassii from related species, and a summary of its geographical distribution are presented, together with an illustration.
The Relationship between the Pacific–North American Teleconnection Pattern, the Great Plains Low-Level Jet, and North Central U.S. Heavy Rainfall Events*
Authors: Harding Keith J. , Snyder Peter K. 
Published: July 2015

Abstract
This study demonstrates the relationship between the Pacific–North American (PNA) teleconnection pattern and the Great Plains low-level jet (GPLLJ). The negative phase of the PNA, which is associated with lower heights over the Great Plains and ridging in the southeastern United States, enhances the GPLLJ by increasing the pressure gradient within the GPLLJ on 6-hourly to monthly time scales. Strong GPLLJ events predominantly occur when the PNA is negative. Warm-season strong GPLLJ events with a very negative PNA (&lt;−1) are associated with more persistent, longer wavelength planetary waves that increase the duration of GPLLJ events and enhance precipitation over the north central United States. When one considers the greatest 5-day north central U.S. precipitation events, a large majority occur when the PNA is negative, with most exhibiting a very negative PNA. Stronger moisture transport during heavy rainfall events with a very negative PNA decreases the precipitation of locally derived moisture compared to events with a very positive PNA. The PNA becomes negative 2–12 days before heavy rainfall events and is very negative within two weeks of 78% of heavy rainfall events in the north central United States, a finding that could be used to improve medium-range forecasts of heavy rainfall events.