bluuebunny/crossref_metadata_2025_split huggingface dataset:
Alcoholytic Cleavage of Polyhydroxyalkanoate Chains by Class IV Synthases Induced by Endogenous and Exogenous Ethanol
Authors: Hyakutake Manami , Tomizawa Satoshi , Mizuno Kouhei , Abe Hideki , Tsuge Takeharu 
Published: December 2013

ABSTRACT

Polyhydroxyalkanoate (PHA)-producing
Bacillus
strains express class IV PHA synthase, which is composed of the subunits PhaR and PhaC. Recombinant
Escherichia coli
expressing PHA synthase from
Bacillus cereus
strain YB-4 (PhaRC
YB-4
) showed an unusual reduction of the molecular weight of PHA produced during the stationary phase of growth. Nuclear magnetic resonance analysis of the low-molecular-weight PHA revealed that its carboxy end structure was capped by ethanol, suggesting that the molecular weight reduction was the result of alcoholytic cleavage of PHA chains by PhaRC
YB-4
induced by endogenous ethanol. This scission reaction was also induced by exogenous ethanol in both
in vivo
and
in vitro
assays. In addition, PhaRC
YB-4
was observed to have alcoholysis activity for PHA chains synthesized by other synthases. The PHA synthase from
Bacillus megaterium
(PhaRC
Bm
) from another subgroup of class IV synthases was also assayed and was shown to have weak alcoholysis activity for PHA chains. These results suggest that class IV synthases may commonly share alcoholysis activity as an inherent feature.
Lineage-Specific Distribution of Insertion Sequence Excision Enhancer in Enterotoxigenic Escherichia coli Isolated from Swine
Authors: Kusumoto Masahiro , Fukamizu Dai , Ogura Yoshitoshi , Yoshida Eiji , Yamamoto Fumiko , Iwata Taketoshi , Ooka Tadasuke , Akiba Masato , Hayashi Tetsuya 
Published: December 2013

ABSTRACT

Insertion sequences (ISs) are the simplest transposable elements and are widely distributed in bacteria; however, they also play important roles in genome evolution. We recently identified a protein called IS excision enhancer (IEE) in enterohemorrhagic
Escherichia coli
(EHEC) O157. IEE promotes the excision of IS elements belonging to the IS
3
family, such as IS
629
, as well as several other families. IEE-mediated IS excision generates various genomic deletions that lead to the diversification of the bacterial genome. IEE has been found in a broad range of bacterial species; however, among sequenced
E. coli
strains, IEE is primarily found in EHEC isolates. In this study, we investigated non-EHEC pathogenic
E. coli
strains isolated from domestic animals and found that IEE is distributed in specific lineages of enterotoxigenic
E. coli
(ETEC) strains of serotypes O139 or O149 isolated from swine. The
iee
gene is located within integrative elements that are similar to SpLE1 of EHEC O157. All
iee
-positive ETEC lineages also contained multiple copies of IS
629
, a preferred substrate of IEE, and their genomic locations varied significantly between strains, as observed in O157. These data suggest that IEE may have been transferred among EHEC and ETEC in swine via SpLE1 or SpLE1-like integrative elements. In addition, IS
629
is actively moving in the ETEC O139 and O149 genomes and, as in EHEC O157, is promoting the diversification of these genomes in combination with IEE.
Assessing the Mechanisms Responsible for Differences between Nitrogen Requirements of Saccharomyces cerevisiae Wine Yeasts in Alcoholic Fermentation
Authors: Brice Claire , Sanchez Isabelle , Tesnière Catherine , Blondin Bruno 
Published: December 2013

ABSTRACTNitrogen is an essential nutrient forSaccharomyces cerevisiaewine yeasts during alcoholic fermentation, and its abundance determines the fermentation rate and duration. The capacity to ferment under conditions of nitrogen deficiency differs between yeasts. A characterization of the nitrogen requirements of a set of 23 strains revealed large differences in their fermentative performances under nitrogen deficiency, and these differences reflect the nitrogen requirements of the strains. We selected and compared two groups of strains, one with low nitrogen requirements (LNRs) and the other with high nitrogen requirements (HNRs). A comparison of various physiological traits indicated that the differences are not related to the ability to store nitrogen or the protein content. No differences in protein synthesis activity were detected between strains with different nitrogen requirements. Transcriptomic analysis revealed expression patterns specific to each of the two groups of strains, with an overexpression of stress genes in HNR strains and a stronger expression of biosynthetic genes in LNR strains. Our data suggest that differences in glycolytic flux may originate from variations in nitrogen sensing and signaling under conditions of starvation.
Comparative Phylogenomics and Evolution of the Brucellae Reveal a Path to Virulence
Authors: Wattam Alice R. , Foster Jeffrey T. , Mane Shrinivasrao P. , Beckstrom-Sternberg Stephen M. , Beckstrom-Sternberg James M. , Dickerman Allan W. , Keim Paul , Pearson Talima , Shukla Maulik , Ward Doyle V. , Williams Kelly P. , Sobral Bruno W. , Tsolis Renee M. , Whatmore Adrian M. , O'Callaghan David 
Published: December 2013

ABSTRACT

Brucella
species include important zoonotic pathogens that have a substantial impact on both agriculture and human health throughout the world. Brucellae are thought of as “stealth pathogens” that escape recognition by the host innate immune response, modulate the acquired immune response, and evade intracellular destruction. We analyzed the genome sequences of members of the family
Brucellaceae
to assess its evolutionary history from likely free-living soil-based progenitors into highly successful intracellular pathogens. Phylogenetic analysis split the genus into two groups: recently identified and early-dividing “atypical” strains and a highly conserved “classical” core clade containing the major pathogenic species. Lateral gene transfer events brought unique genomic regions into
Brucella
that differentiated them from
Ochrobactrum
and allowed the stepwise acquisition of virulence factors that include a type IV secretion system, a perosamine-based O antigen, and systems for sequestering metal ions that are absent in progenitors. Subsequent radiation within the core
Brucella
resulted in lineages that appear to have evolved within their preferred mammalian hosts, restricting their virulence to become stealth pathogens capable of causing long-term chronic infections.
Two Small (p)ppGpp Synthases in Staphylococcus aureus Mediate Tolerance against Cell Envelope Stress Conditions
Authors: Geiger Tobias , Kästle Benjamin , Gratani Fabio Lino , Goerke Christiane , Wolz Christiane 
Published: December 2013

ABSTRACT

The stringent response is a conserved global regulatory mechanism that is related to the synthesis of (p)ppGpp nucleotides. Gram-positive bacteria, such as
Staphylococcus aureus
, possess three (p)ppGpp synthases: the bifunctional RSH (RelA/SpoT homolog) protein, which consists of a (p)ppGpp synthase and a (p)ppGpp hydrolase domain, and two truncated (p)ppGpp synthases, designated RelP and RelQ. Here, we characterized these two small (p)ppGpp synthases. Biochemical analyses of purified proteins and
in vivo
studies revealed a stronger synthetic activity for RelP than for RelQ. However, both enzymes prefer GDP over GTP as the pyrophosphate recipient to synthesize ppGpp. Each of the enzymes was shown to be responsible for the essentiality of the (p)ppGpp hydrolase domain of the RSH protein. The staphylococcal RSH-hydrolase is an efficient enzyme that prevents the toxic accumulation of (p)ppGpp. Expression of (p)ppGpp synthases in a hydrolase-negative background leads not only to growth arrest but also to cell death. Transcriptional analyses showed that
relP
and
relQ
are strongly induced upon vancomycin and ampicillin treatments. Accordingly, mutants lacking
relP
and
relQ
showed a significantly reduced survival rate upon treatments with cell wall-active antibiotics. Thus, RelP and RelQ are active (p)ppGpp synthases in
S. aureus
that are induced under cell envelope stress to mediate tolerance against these conditions.
Characteristics of urinary tract infection pathogens and their in vitro susceptibility to antimicrobial agents in China: data from a multicenter study
Authors: Qiao Lu-Dong , Chen Shan , Yang Yong , Zhang Kai , Zheng Bo , Guo Hong-Feng , Yang Bo , Niu Yuan-Jie , Wang Yi , Shi Ben-Kang , Yang Wei-Min , Zhao Xiao-Kun , Gao Xiao-Feng , Chen Ming , Tian Ye 
Published: December 2013

ObjectiveThis study assessed the characteristics of pathogens identified in clinical isolates from patients with urinary tract infection (UTI) and their in vitro sensitivity to commonly used antibiotics in the clinical setting in China.Design and settingMulticenter study was conducted between January and December 2011 in 12 hospitals in China.ParticipantsUrine samples were collected from 356 symptomatic patients treated in the study hospitals for acute uncomplicated cystitis, recurrent UTI or complicated UTI.Primary and secondary outcome measuresMinimal inhibitory concentrations (MICs) were measured using broth microdilution according to the Clinical and Laboratory Standards Institute 2011 guidelines. Thirteen antimicrobial agents were tested: fosfomycin tromethamine, levofloxacin, moxifloxacin, cefdinir, cefixime, cefaclor, cefprozil, cefuroxime, amoxicillin/clavulanic acid, cefotaxime, azithromycin, nitrofurantoin and oxacillin.Escherichia coliisolates were screened and extended spectrum β-lactamases (ESBL) production was confirmed by a double-disk synergy test.Results198 urine samples were culture-positive and 175 isolates were included in the final analysis.E coliwas detected in 50% of cultures, followed byStaphylococcus epidermidis(9%),Enterococcus faecalis(9%) andKlebsiella pneumoniae(5%). The detection rate of ESBL-producingE coliwas 53%. Resistance to levofloxacin was the most common among all the isolates. Nitrofurantoin and fosfomycin tromethamine had the greatest activity againstE coli; overall, 92% and 91% of isolates were susceptible to these antimicrobials.E faecalishad the highest susceptibility rates to fosfomycin tromethamine (100%).ConclusionsThe most frequently identified pathogens in our patients were ESBL-producingEcoliandE faecalis. Fosfomycin tromethamine and nitrofurantoin showed a good antimicrobial activity against UTI pathogens. They may represent good options for the empiric treatment of patients with UTI.
Errors in after-hours phone consultations: a simulation study
Authors: Joffe Erel , Turley James P , Hwang Kevin O , Johnson Todd R , Johnson Craig W , Bernstam Elmer V 
Published: December 2013

BackgroundAfter-hours out-of-hospital phone consultations require physicians to make decisions based on information provided by a nurse over the phone.MethodsWe conducted a simulation study to evaluate physicians’ actions following communication of key information. 22 nurses were asked to call physicians with six cases based on the six most common reasons for after-hours phone calls. We evaluated physicians’ actions following the communication of key clinical information: Asituation cuedescribed a patient's problem (eg, confusion). Abackground cuedescribed a specific clinical finding regarding the cause of the problem (eg, patient's sodium is low). For each cue we defined a list of indicators, based on the medical literature, to ascertain whether physicians acted upon the provided information (which was defined as addressing at least one of the indicators).ResultsA total of 108 phone consultations (containing 88 situation and 93 background cues) were analysed. Situation cues were communicated in 90% (79/88) of the calls and background cues in 33% (31/93). Physician acted upon the provided information in 57% (45/79) and 48% (15/31) of the communicated situation and background cues, respectively. When the background cues were not communicated, physicians asked questions expected to elicit the cue in 12% of the cases. Responding to the situation cue was associated with longer conversations and active inquiry by the physician.ConclusionsAfter-hours phone calls are error prone. Both nurse communication and physician decision-making are problematic. Efforts to improve patient safety in this setting must address both communication and decision-making.
Interactive questioning in critical care during handovers: a transcript analysis of communication behaviours by physicians, nurses and nurse practitioners
Authors: Rayo Michael F , Mount-Campbell Austin F , O'Brien James M , White Susan E , Butz Alexandra , Evans Kris , Patterson Emily S 
Published: December 2013

ObjectiveAlthough there is a growing recognition of the importance of active communication behaviours from the incoming clinician receiving a patient handover, there are currently no agreed-upon measures to objectively describe those behaviours. This study sought to identify differences in incoming clinician communication behaviours across levels of clinical training for physicians and nurses.MethodsHandover observations were conducted during shift changes for attending physicians, resident physicians, registered nurses and nurse practitioners in three medical intensive care units from July 2011 to August 2012. Measures were the number of interjections from the incoming clinician and the communication mode of those interjections. Each collaborative cross-check, a specific type of interactive question, was subsequently classified by level of assertiveness.Results133 patient handovers were analysed. Statistical differences were found in both measures. Higher levels of training were associated with fewer interjections, and a higher proportion of interactive questioning to detect erroneous assessments and actions by the incoming provider. All groups were observed to use the least assertive level of a collaborative cross-check, which contributed to misunderstandings. Nurses used less assertive collaborative cross-checks than physicians.ConclusionsDifferences across clinician type and levels of clinical training were found in both measures during patient handovers. The findings suggest that training could enable physicians and nurses to learn communication competencies during patient handovers which were used more frequently by more experienced practitioners, including interjecting less frequently and using interactive questioning strategies to clarify understanding, and assertively question the appropriateness of diagnoses, treatment plans and prognoses. Accompanying cultural change initiatives might be required to routinely employ these strategies in the clinical setting, particularly for nursing personnel.
Correlation of caecal intubation rate to volume: colonoscopists should undertake at least 120 procedures per year
Authors: Verma Ajay M , Dixon Andrew D , Chilton Andrew P 
Published: December 2013

IntroductionThe measurement of the quality of colonoscopy has been in the vanguard of quality improvement. The Joint Advisory Group on Gastrointestinal endoscopy (JAG) has issued guidance for practitioners to achieve caecal intubation rates (CIR) of ≥90% and to undertake ≥100 colonoscopies per annum. The British Society of Gastroenterology National Colonoscopy Audit published in 2012–2013 demonstrated a combined CIR of 92.3%. In 2012, we published data from 16 064 colonoscopies showing a combined CIR of 90.57%—both meeting JAG's standard. Analysis of our audit looked at the relationship of volume and outcome. CIR of operators performing ≥100 procedures per annum was 91.76%; those performing <100 was 87.77%. The 2-year data we collected involved 120+ operators. This provided an opportunity to study the correlation between volume and CIR in detail.MethodsWe analysed 129 operator records who had undertaken 20–399 procedures per annum (total 12 594). Each operator's volume was plotted against CIR as individuals and groups of operators undertaking a similar annual volume. 9859 procedures (78.3%) were performed by operators undertaking 20–199 procedures per annum (120 operators); this subgroup was further analysed.ResultsWhen plotting individuals and groups of individuals who have undertaken a similar annual volume against CIR, the trend-lines cross a 90% CIR at a volume of 120–125 procedures. The subgroup analysis showed the trend-line crossing at 110–120 procedures.ConclusionsThis detailed analysis of 12 594 colonoscopies over 2 years suggests that JAG should advise operators to undertake ≥120 procedures per annum to support the quality standard for CIR of ≥90%.
Perspectives and attitudes of young patients with inflammatory bowel disease: symptoms, burden of disease and communication with their healthcare professionals
Authors: Alexakis C , Davies G , Stephens J , Clark S , Rogers S , Poullis A 
Published: December 2013

IntroductionInflammatory bowel disease (IBD) affects a significant proportion of young patients in the UK. The role of the healthcare professional, and their relationship with the young patient is particularly important at this difficult stage of their life, when education, social integration and career planning, can be dramatically affected by this consuming condition.ObjectivesTo address the attitudes, experiences and erspectives of young patients suffering from IBD, focusing particularly on the relationship between sufferer and healthcare provider.MethodsCrohn's and Colitis UK invited its young members to respond to a detailed internet based questionnaire addressing various aspects of patients' disease and their relationship with respective healthcare workers.Results1081 patients aged 29 years or less responded. Self reported burden of illness was high with only 12% respondents free from a disease flare in the previous 12 months with almost half being hospitalised in the same period. Quality of ommunication with healthcare providers was generally high, with three-quarters of patients feeling appropriately empowered in their healthcare decisions. The IBD nurse specialist was highlighted as a particularly valuable member of the team, scoring the highest of the professional groups in communication comfort scores, as well as being nominated by the patients as the preferred professional group to discuss their disease with.ConclusionsThe results emphasize the considerable impact of the disease that this group is encumbered with, and identifies areas in the patient-professional relationship that can be augmented to improve the overall healthcare of this complex and fragile subgroup of patients.
The preventive effect of the Nordic hamstring exercise on hamstring injuries in amateur soccer players: study protocol for a randomised controlled trial
Authors: van der Horst Nick , Smits Dirk Wouter , Petersen Jesper , Goedhart Edwin A , Backx Frank J G 
Published: December 2013

BackgroundHamstring injuries are the most common muscle injury in male amateur soccer players and have a high rate of recurrence, often despite extensive treatment and long rehabilitation periods. Eccentric strength and flexibility are recognised as important modifiable risk factors, which have led to the development of eccentric hamstring exercises, such as the Nordic hamstring exercise. As the effectiveness of the Nordic hamstring exercise in reducing hamstring injuries has never been investigated in amateur soccer players, the aim of this study is to investigate the effect of this exercise on the incidence and severity of hamstring injuries in male amateur soccer players. An additional aim is to determine whether flexibility is associated with hamstring injuries.Study designCluster-randomised controlled trial with soccer teams as the unit of cluster.MethodsDutch male amateur soccer players, aged 18–40 years, were allocated to an intervention or control group. Both study groups continued regular soccer training during 2013, but the intervention group additionally performed the Nordic hamstring exercise (25 sessions over 13 weeks). Primary outcomes are the incidence of initial and recurrent hamstring injury and injury severity. Secondary outcomes are hamstring-and-lower-back flexibility and compliance. Compliance to the intervention protocol was also monitored.DiscussionEccentric hamstring strength exercises are hypothesised to reduce the incidence of hamstring injury among male amateur soccer players by 70%. The prevention of such injuries will be beneficial to soccer players, clubs, football associations, health insurance companies and society.Trial RegistrationNTR3664.
Cross-sectional study: CagA–positiveHelicobacter pyloriinfection, acute coronary artery disease and systemic levels of B-type natriuretic peptide
Authors: Figura Natale , Palazzuoli Alberto , Vaira Dino , Campagna Mariastella , Moretti Elena , Iacoponi Francesca , Giordano Nicola , Clemente Salvatore , Nuti Ranuccio , Ponzetto Antonio 
Published: December 2013

BackgroundB-type natriuretic peptide (BNP) determination is routinely used to evaluate the severity of congestive heart failure, a possible consequence of coronary artery disease (CAD). CAD originates from vascular atherosclerotic processes and is stimulated by inflammatory events, which may also be triggered by chronic bacterial infections.AimTo explore the effect ofHelicobacter pyloriinfection upon systemic BNP, tumour necrosis factor-α (TNF-α) and interleukin-6 (IL-6) levels and linear homology between cardiac peptides andH pylori.MethodsA group of 103 consecutive patients with a diagnosis of non-ST elevation acute CAD (ACAD) and no other concomitant pathology was examined. BNP was measured by a commercial solid-phase sandwich immunoradiometric assay.H pyloriinfection, CagA serological status and circulating levels of IL-6 and TNF-α, were determined by ELISA assays. Amino acid sequence homology between human cardiac andH pyloripeptides was investigated by Basic Local Alignment Search Tool (BLAST) analysis.ResultsCirculating levels of BNP and IL-6, in pg/mL (interquartile difference), among infected patients with anti-CagA serum antibodies, respectively 781 (1899) and 37.7 (137.6), were significantly increased in respect to those measured in uninfected patients, respectively 325 (655) and 7.7 (23.5), (p<0.01 and p=0.025), and, with regard to BNP alone, also in patients infected by CagA negativeH pyloristrains, 305 (593), (p<0.01). TNF-α levels were raised in CagA positive in respect to uninfected patients. Tropomyosin and Ca2+ transporting ATPases showed strong similarities toH pyloriproteins, suggesting the existence of molecular mimicry phenomena.ConclusionsChronic infection byH pyloriexpressing CagA correlates with high circulating levels of BNP and IL-6 in patients with ACAD.