bluuebunny/crossref_metadata_2025_split huggingface dataset:
Production of 2-Hydroxyisobutyric Acid from Methanol by Methylobacterium extorquens AM1 Expressing (
R
)-3-Hydroxybutyryl Coenzyme A-Isomerizing Enzymes
Authors: Rohde Maria-Teresa , Tischer Sylvi , Harms Hauke , Rohwerder Thore 
Published: November 2016

ABSTRACT

The biotechnological production of the methyl methacrylate precursor 2-hydroxyisobutyric acid (2-HIBA) via bacterial poly-3-hydroxybutyrate (PHB) overflow metabolism requires suitable (
R
)-3-hydroxybutyryl coenzyme A (CoA)-specific coenzyme B
12
-dependent mutases (RCM). Here, we characterized a predicted mutase from
Bacillus massiliosenegalensis
JC6 as a mesophilic RCM closely related to the thermophilic enzyme previously identified in
Kyrpidia tusciae
DSM 2912 (M.-T. Weichler et al., Appl Environ Microbiol 81:4564–4572, 2015,
https://doi.org/10.1128/AEM.00716-15
). Using both RCM variants, 2-HIBA production from methanol was studied in fed-batch bioreactor experiments with recombinant
Methylobacterium extorquens
AM1. After complete nitrogen consumption, the concomitant formation of PHB and 2-HIBA was achieved, indicating that both sets of RCM genes were successfully expressed. However, although identical vector systems and incubation conditions were chosen, the metabolic activity of the variant bearing the RCM genes from strain DSM 2912 was severely inhibited, likely due to the negative effects caused by heterologous expression. In contrast, the biomass yield of the variant expressing the JC6 genes was close to the wild-type performance, and 2-HIBA titers of 2.1 g liter
−1
could be demonstrated. In this case, up to 24% of the substrate channeled into overflow metabolism was converted to the mutase product, and maximal combined 2-HIBA plus PHB yields from methanol of 0.11 g g
−1
were achieved. Reverse transcription-quantitative PCR analysis revealed that metabolic genes, such as methanol dehydrogenase and acetoacetyl-CoA reductase genes, are strongly downregulated after exponential growth, which currently prevents a prolonged overflow phase, thus preventing higher product yields with strain AM1.

IMPORTANCE
In this study, we genetically modified a methylotrophic bacterium in order to channel intermediates of its overflow metabolism to the C
4
carboxylic acid 2-hydroxyisobutyric acid, a precursor of acrylic glass. This has implications for biotechnology, as it shows that reduced C
1
substrates, such as methanol and formic acid, can be alternative feedstocks for producing today's commodities. We found that product titers and yields depend more on host physiology than on the activity of the introduced heterologous function modifying the overflow metabolism. In addition, we show that the fitness of recombinant strains substantially varies when they express orthologous genes from different origins. Further studies are needed to extend the overflow production phase in methylotrophic microorganisms for the implementation of biotechnological processes.
Three-Dimensional Structure of the Ultraoligotrophic Marine Bacterium “Candidatus Pelagibacter ubique”
Authors: Zhao Xiaowei , Schwartz Cindi L. , Pierson Jason , Giovannoni Stephen J. , McIntosh J. Richard , Nicastro Daniela 
Published: November 2016

ABSTRACT

SAR11 bacteria are small, heterotrophic, marine alphaproteobacteria found throughout the oceans. They thrive at the low nutrient concentrations typical of open ocean conditions, although the adaptations required for life under those conditions are not well understood. To illuminate this issue, we used cryo-electron tomography to study “
Candidatus
Pelagibacter ubique” strain HTCC1062, a member of the SAR11 clade. Our results revealed its cellular dimensions and details of its intracellular organization. Frozen-hydrated cells, which were preserved in a life-like state, had an average cell volume (enclosed by the outer membrane) of 0.037 ± 0.011 μm
3
. Strikingly, the periplasmic space occupied ∼20% to 50% of the total cell volume in log-phase cells and ∼50% to 70% in stationary-phase cells. The nucleoid occupied the convex side of the crescent-shaped cells and the ribosomes predominantly occupied the concave side, at a relatively high concentration of 10,000 to 12,000 ribosomes/μm
3
. Outer membrane pore complexes, likely composed of PilQ, were frequently observed in both log-phase and stationary-phase cells. Long filaments, most likely type IV pili, were found on dividing cells. The physical dimensions, intracellular organization, and morphological changes throughout the life cycle of “
Ca.
Pelagibacter ubique” provide structural insights into the functional adaptions of these oligotrophic ultramicrobacteria to their habitat.

IMPORTANCE
Bacterioplankton of the SAR11 clade (
Pelagibacterales
) are of interest because of their global biogeochemical significance and because they appear to have been molded by unusual evolutionary circumstances that favor simplicity and efficiency. They have adapted to an ecosystem in which nutrient concentrations are near the extreme limits at which transport systems can function adequately, and they have evolved streamlined genomes to execute only functions essential for life. However, little is known about the actual size limitations and cellular features of living oligotrophic ultramicrobacteria. In this study, we have used cryo-electron tomography to obtain accurate physical information about the cellular architecture of “
Candidatus
Pelagibacter ubique,” the first cultivated member of the SAR11 clade. These results provide foundational information for answering questions about the cell architecture and functions of these ultrasmall oligotrophic bacteria.
Development of a High-Efficiency Transformation Method and Implementation of Rational Metabolic Engineering for the Industrial Butanol Hyperproducer Clostridium saccharoperbutylacetonicum Strain N1-4
Authors: Herman Nicolaus A. , Li Jeffrey , Bedi Ripika , Turchi Barbara , Liu Xiaoji , Miller Michael J. , Zhang Wenjun 
Published: November 2016

ABSTRACT

While a majority of academic studies concerning acetone, butanol, and ethanol (ABE) production by
Clostridium
have focused on
Clostridium acetobutylicum
, other members of this genus have proven to be effective industrial workhorses despite the inability to perform genetic manipulations on many of these strains. To further improve the industrial performance of these strains in areas such as substrate usage, solvent production, and end product versatility, transformation methods and genetic tools are needed to overcome the genetic intractability displayed by these species. In this study, we present the development of a high-efficiency transformation method for the industrial butanol hyperproducer
Clostridium saccharoperbutylacetonicum
strain N1-4 (HMT) ATCC 27021. Following initial failures, we found that the key to creating a successful transformation method was the identification of three distinct colony morphologies (types S, R, and I), which displayed significant differences in transformability. Working with the readily transformable type I cells (transformation efficiency, 1.1 × 10
6
CFU/μg DNA), we performed targeted gene deletions in
C. saccharoperbutylacetonicum
N1-4 using a homologous recombination-mediated allelic exchange method. Using plasmid-based gene overexpression and targeted knockouts of key genes in the native acetone-butanol-ethanol (ABE) metabolic pathway, we successfully implemented rational metabolic engineering strategies, yielding in the best case an engineered strain (
Clostridium saccharoperbutylacetonicum
strain N1-4/pWIS13) displaying an 18% increase in butanol titers and 30% increase in total ABE titer (0.35 g ABE/g sucrose) in batch fermentations. Additionally, two engineered strains overexpressing aldehyde/alcohol dehydrogenases (encoded by
adh11
and
adh5
) displayed 8.5- and 11.8-fold increases (respectively) in batch ethanol production.

IMPORTANCE
This paper presents the first steps toward advanced genetic engineering of the industrial butanol producer
Clostridium saccharoperbutylacetonicum
strain N1-4 (HMT). In addition to providing an efficient method for introducing foreign DNA into this species, we demonstrate successful rational engineering for increasing solvent production. Examples of future applications of this work include metabolic engineering for improving desirable industrial traits of this species and heterologous gene expression for expanding the end product profile to include high-value fuels and chemicals.
Efficiency and productivity measurement of rural township hospitals in China: a bootstrapping data envelopment analysis
Authors: Cheng Zhaohui , Cai Miao , Tao Hongbing , He Zhifei , Lin Xiaojun , Lin Haifeng , Zuo Yuling 
Published: November 2016

ObjectiveTownship hospitals (THs) are important components of the three-tier rural healthcare system of China. However, the efficiency and productivity of THs have been questioned since the healthcare reform was implemented in 2009. The objective of this study is to analyse the efficiency and productivity changes in THs before and after the reform process.Setting and participantsA total of 48 sample THs were selected from the Xiaogan Prefecture in Hubei Province from 2008 to 2014.Outcome measuresFirst, bootstrapping data envelopment analysis (DEA) was performed to estimate the technical efficiency (TE), pure technical efficiency (PTE) and scale efficiency (SE) of the sample THs during the period. Second, the bootstrapping Malmquist productivity index was used to calculate the productivity changes over time.ResultsThe average TE, PTE and SE of the sample THs over the 7-year period were 0.5147, 0.6373 and 0.7080, respectively. The average TE and PTE increased from 2008 to 2012 but declined considerably after 2012. In general, the sample THs experienced a negative shift in productivity from 2008 to 2014. The negative change was 2.14%, which was attributed to a 23.89% decrease in technological changes (TC). The sample THs experienced a positive productivity shift from 2008 to 2012 but experienced deterioration from 2012 to 2014.ConclusionsThere was considerable space for TE improvement in the sample THs since the average TE was relatively low. From 2008 to 2014, the sample THs experienced a decrease in productivity, and the adverse alteration in TC should be emphasised. In the context of healthcare reform, the factors that influence TE and productivity of THs are complex. Results suggest that numerous quantitative and qualitative studies are necessary to explore the reasons for the changes in TE and productivity.
Feasibility study and pilot cluster-randomised controlled trial of the GoActive intervention aiming to promote physical activity among adolescents: outcomes and lessons learnt
Authors: Corder Kirsten , Brown Helen E , Schiff Annie , van Sluijs Esther M F 
Published: November 2016

ObjectivesAssess the feasibility of implementing the GoActive intervention in secondary schools, to identify improvements, test study procedures, determine preliminary effectiveness to increase moderate-to-vigorous physical activity (MVPA), and inform power calculations to establish programme effectiveness.SettingFeasibility study (1 school) and pilot cluster-randomised controlled trial (CRCT; 2 intervention; 1 control school(s)).Participants460 participants (46.6% female; 13.2 (0.4) years old).Interventions8-week intervention (2013) involved: classes choosing weekly activities encouraged by mentors (older adolescents) and in-class peer leaders. Students gain points for trying activities which are entered into an intramural competition.Primary and secondary outcome measuresPlanned quantitative (questionnaire) and qualitative (focus groups) process evaluation addressed enjoyment, confidence, participation, suggested improvements. Outcomes were assessed at baseline and follow-up (week 8) in pilot CRCT and included accelerometer-assessed MVPA; adolescent-reported activity type, well-being, peer support, shyness, sociability. Analysis of covariance was used to assess preliminary effectiveness as change in MVPA adjusted for baseline.ResultsAll year 9 students in intervention schools were exposed to the intervention; over all schools 77% of eligible students were measured. 71% boys and 74% girls found GoActive ‘fun’; 38% boys and 32% girls said it increased confidence, and 64% boys and 59% girls said they would continue with a GoActive activity. Suggested improvements included more mentorship; improved training; streamlined points recording. Pilot results indicated potential effectiveness ((adjusted mean difference (95% CI) p value; MVPA mins; 5.1 (1.1 to 9.2) p=0.014)) and suggest recruitment of 16 schools (2400 adolescents) for a full trial. Compared with control, intervention students reported greater peer support 0.5 (0.1 to 0.9) p=0.03, well-being 1.8 (0.1 to 3.4) p=0.04 but no difference in shyness/sociability. Participation in activity types approached significance (intervention group 2.3 (−0.2 to 4.7) p=0.07 more activity types).ConclusionsResults suggest feasibility and indicate potential effectiveness of GoActive to increase MVPA and support a fully powered evaluation of effectiveness and cost-effectiveness. Process evaluation data were used to refine GoActive prior to a full trial.Trial registration numberISRCTN31583496; pre-results.
Assessment of cardiac resynchronisation therapy in patients with wide QRS and non-specific intraventricular conduction delay: rationale and design of the multicentre randomised NICD-CRT study
Authors: Eschalier Romain , Ploux Sylvain , Pereira Bruno , Clémenty Nicolas , Da Costa Antoine , Defaye Pascal , Garrigue Stéphane , Gourraud Jean-Baptiste , Gras Daniel , Guy-Moyat Benoît , Leclercq Christophe , Mondoly Pierre , Bordachar Pierre 
Published: November 2016

IntroductionCardiac resynchronisation therapy (CRT) was initially developed to treat patients with left bundle branch block (LBBB). However, many patients with heart failure have a widened QRS but neither left-BBB nor right-BBB; this is called non-specific intraventricular conduction delay (NICD). It is unclear whether CRT is effective in this subgroup of patients.Methods and analysisThe NICD-CRT study is a prospective, double-blind, randomised (1:1), parallel-arm, multicentre trial comparing the effects of CRT in patients with heart failure, a reduced left ventricular ejection fraction (LVEF <35%) and NICD, who have been implanted with a device (CRT-pacemaker or CRT-defibrillator) that has or has not been activated. Enrolment began on 15 July 2015 and should finish within 3 years; 40 patients have already been randomised and 11 centres have agreed to participate. The primary end point is the comparison of the proportion of patients improved, unchanged or worsened over the subsequent 12 months. 100 patients per group are required to demonstrate a difference between groups with a statistical power of 90%, a type I error of 0.05% (two-sided) and a loss to follow-up of 10%. This trial will add substantially to the modest amount of existing data on CRT in patients with NICD and should reduce uncertainty for guidelines and clinical practice when added to the pool of current information.Ethics and disseminationLocal ethics committee authorisations have been obtained since May 2015. We will publish findings from this study in a peer-reviewed scientific journal and present results at national and international conferences.Trial registration numberNCT02454439; pre-results.
Framing of research question using the PICOT format in randomised controlled trials of venous ulcer disease: a protocol for a systematic survey of the literature
Authors: Abbade Luciana P F , Wang Mei , Sriganesh Kamath , Mbuagbaw Lawrence , Thabane Lehana 
Published: November 2016

IntroductionAlthough venous ulcers have a great social and economic impact, there is a lack of evidence from randomised controlled trials (RCTs) to support appropriate management for this disease. Framing the research question using the Population; Intervention; Comparator; Outcome; Time frame (PICOT) format in RCTs can improve the quality of the research design.ObjectivesTo evaluate how the PICOT format is used to frame a research question in reports of RCTs of venous ulcer disease and to determine the factors associated with better adherence to the PICOT format in framing the research question.Methods and analysesWe will conduct a systematic survey of RCTs on venous ulcers published in the National Institute of Health, PubMed database between January 2009 and May 2016. We will include all RCTs addressing therapeutic intervention for venous ulcer disease involving human subjects, and published in the English language. The selection process will be carried out in duplicate by two independent investigators. First, titles and abstracts will be screened, then full-text articles. We will examine whether the five elements of the PICOT format are used in formulating the research question and give a score between 0 and 5. The primary outcome will be the proportion of studies that have adequately reported all five PICOT elements.DisseminationThis will be the first survey to assess how the PICOT format is used to frame research questions on the management of venous ulcers in reports of RCTs. On completion, this review will be submitted to a peer-reviewed biomedical journal for publication and the findings will also be presented at scientific conferences.
Inter-rater reliability of the Shoulder Symptom Modification Procedure in people with shoulder pain
Authors: Lewis Jeremy S , McCreesh Karen , Barratt Eva , Hegedus Eric J , Sim Julius 
Published: November 2016

BackgroundMusculoskeletal conditions involving the shoulder are common and, because of the importance of the upper limb and hand in daily function, symptoms in this region are commonly associated with functional impairment in athletic and non-athletic populations. Deriving a definitive diagnosis as to the cause of shoulder symptoms is fraught with difficulty. Limitations have been recognised for imaging and for orthopaedic special tests. 1 solution is to partially base management on the response to tests aimed at reducing the severity of the patient's perception of symptoms. 1 (of many) such tests is the Shoulder Symptom Modification Procedure (SSMP). The reliability of this procedure is unknown.Methods37 clinician participants independently watched the videos of 11 patient participants undergoing the SSMP and recorded each patient's response as improved (partially or completely), no change or worse. Inter-rater reliability was assessed by Krippendorff's α, which ranges from 0 to 1.ResultsKrippendorff's α was found to range from 0.762 to 1.000, indicating moderate to substantial reliability. In addition, short (3-hour) and longer (1-day) durations of training were associated with similar levels of reliability across the techniques.ConclusionsDeriving a definitive structural diagnosis for a person presenting with a musculoskeletal condition involving the shoulder is difficult. The findings of the present study suggest that the SSMP demonstrates a high level of reliability. More research is needed to better understand the relevance of such procedures.Trial registration numberISRCTN95412360.
Single-nucleotide polymorphism array (SNP-A) improves the identification of chromosomal abnormalities by metaphase cytogenetics in myelodysplastic syndrome
Authors: da Silva Fernanda Borges , Machado-Neto João Agostinho , Bertini Virginia Helena Leira Lipoli , Velloso Elvira Deolinda Rodrigues Pereira , Ratis Cristina Alonso , Calado Rodrigo T , Simões Belinda Pinto , Rego Eduardo Magalhães , Traina Fabiola 
Published: November 2016

AimsThe myelodysplastic syndromes (MDS) are a heterogeneous group of clonal haematopoietic stem cell disorders characterised by inefficient haematopoiesis and risk of progression to acute myeloid leukaemia. Metaphase cytogenetics is an extremely valuable clinical tool in the management of haematological malignancies. However, metaphase cytogenetics requires cellular proliferation, its sensitivity and resolution depends on the proportion of clonal cells in the sample and size of the lesion, respectively. Single-nucleotide polymorphism array (SNP-A) does not depend on the presence of dividing cells, is able to detect copy number variations with a high resolution and to detect copy number neutral loss of heterozygosity or uniparental disomy (UPD). The aim of this study was to illustrate that the use of SNP-A can cover cryptic chromosomal lesions not identified by metaphase cytogenetics in patients with MDS.MethodsMetaphase cytogenetics was performed on bone marrow aspirate using standard methods. Genomic DNA from total bone marrow cells were submitted to SNP-A using Affymetrix Genome-Wide Human SNP CytoScan HD.ResultsIn our cohort of 15 patients with a diagnosis of MDS and related diseases, chromosomal abnormalities were found in 47% of the cases by SNP-A and in 33% by metaphase cytogenetics. SNP-A detected all lesions identified by metaphase cytogenetics, except a balanced translocation and a marker chromosome. Notably, SNP-A detected a total of 30 new lesions: 1 (3%) gain, 17 (57%) losses and 12 (40%) UPDs in 5 patients with MDS.ConclusionsSNP-A may complement metaphase cytogenetics to improve the detection of chromosomal abnormalities in myeloid neoplasms.
Treatment of posterior circulation non-saccular aneurysms with flow diverters: a single-center experience and review of 56 patients
Authors: Bhogal P , Pérez M Aguilar , Ganslandt O , Bäzner H , Henkes H , Fischer S 
Published: November 2016

Background and purposeNon-saccular aneurysms of the posterior fossa are an uncommon pathology with no clear treatment strategy. The use of flow-diverting stents (FDS) has had mixed results. We sought to evaluate our experience of FDS for the treatment of this pathology.MethodsWe retrospectively reviewed our database of prospectively collected information for all patients treated only with flow diversion for an unruptured non-saccular aneurysm of the posterior circulation between February 2009 and April 2016. The aneurysms were classified as dolichoectasia, fusiform or transitional, and imaging characteristics including maximal diameter, disease vessel segment, MRI features (intra-aneurysmal thrombus, T1 hyperintensity in the aneurysmal wall, infarctions in the territory of the posterior circulation, and mass effect) were recorded alongside clinical and follow-up data.ResultsWe identified 56 patients (45 men) with 58 aneurysms. The average age of the patients was 63.5 years. Twenty-two patients were symptomatic from the aneurysms at presentation. The majority of the lesions were vertebrobasilar in location (44.8%) with isolated vertebral lesions representing 29.3% of aneurysms. Transitional aneurysms were the most common (48.2%). The mean maximal diameter of the aneurysms was 11 mm. Angiographic exclusion of the aneurysms was seen in 57.4% of aneurysms with follow-up (n=47). During the follow-up period nine patients died.ConclusionsTreatment of non-saccular aneurysms of the posterior fossa is technically possible. Early treatment, particularly of the fusiform and transitional subtypes, is recognized, as is treatment prior to the development of symptoms. A ‘watch and wait’ strategy with regular imaging follow-up could be employed for asymptomatic dolichoectasia.