bluuebunny/crossref_metadata_2025_split huggingface dataset:
Simple
In Vitro
Assay To Evaluate the Incorporation Efficiency of Ribonucleotide Analog 5′-Triphosphates into RNA by Human Mitochondrial DNA-Dependent RNA Polymerase
Authors: Lu Gaofei , Bluemling Gregory R. , Mao Shuli , Hager Michael , Gurale Bharat P. , Collop Paul , Kuiper Damien , Sana Kasinath , Painter George R. , De La Rosa Abel , Kolykhalov Alexander A. 
Published: November 2017

ABSTRACT

There is a growing body of evidence suggesting that some ribonucleoside/ribonucleotide analogs may be incorporated into mitochondrial RNA by human mitochondrial DNA-dependent RNA polymerase (POLRMT) and disrupt mitochondrial RNA synthesis. An assessment of the incorporation efficiency of a ribonucleotide analog 5′-triphosphate by POLRMT may be used to evaluate the potential mitochondrial toxicity of the analog early in the development process. In this report, we provide a simple method to prepare active recombinant POLRMT. A robust
in vitro
nonradioactive primer extension assay was developed to assay the incorporation efficiency of ribonucleotide analog 5′-triphosphates. Our results show that many ribonucleotide analogs, including some antiviral compounds currently in various preclinical or clinical development stages, can be incorporated into newly synthesized RNA by POLRMT and that the incorporation of some of them can lead to chain termination. The discrimination (
D
) values of ribonucleotide analog 5′-triphosphates over those of natural ribonucleotide triphosphates (rNTPs) were measured to evaluate the incorporation efficiency of the ribonucleotide analog 5′-triphosphates by POLRMT. The discrimination values of natural rNTPs under the condition of misincorporation by POLRMT were used as a reference to evaluate the potential mitochondrial toxicity of ribonucleotide analogs. We propose the following criteria for the potential mitochondrial toxicity of ribonucleotide analogs based on
D
values: a safe compound has a
D
value of >10
5
; a potentially toxic compound has a
D
value of >10
4
but <10
5
; and a toxic compound has a
D
value of <10
4
. This report provides a simple screening method that should assist investigators in designing ribonucleoside-based drugs having lower mitochondrial toxicity.
The ABC of Biofilm Drug Tolerance: the MerR-Like Regulator BrlR Is an Activator of ABC Transport Systems, with PA1874-77 Contributing to the Tolerance of Pseudomonas aeruginosa Biofilms to Tobramycin
Authors: Poudyal Bandita , Sauer Karin 
Published: November 2017

ABSTRACT

A hallmark of biofilms is their tolerance to killing by antimicrobial agents. In
Pseudomonas aeruginosa
, biofilm drug tolerance requires the c-di-GMP-responsive MerR transcriptional regulator BrlR. However, the mechanism by which BrlR mediates biofilm drug tolerance has not been elucidated. Here, we demonstrate that BrlR activates the expression of at least 7 ABC transport systems, including the PA1874-PA1875-PA1876-PA1877 (PA1874-77) operon, with chromatin immunoprecipitation and DNA binding assays confirming BrlR binding to the promoter region of PA1874-77. Insertional inactivation of the 7 ABC transport systems rendered
P. aeruginosa
PAO1 biofilms susceptible to tobramycin or norfloxacin. Susceptibility was linked to drug accumulation, with BrlR contributing to norfloxacin accumulation in a manner dependent on multidrug efflux pumps and the PA1874-77 ABC transport system. Inactivation of the respective ABC transport system, furthermore, eliminated the recalcitrance of biofilms to killing by tobramycin but not norfloxacin, indicating that drug accumulation is not linked to biofilm drug tolerance. Our findings indicate for the first time that BrlR, a MerR-type transcriptional activator, activates genes encoding several ABC transport systems, in addition to multiple multidrug efflux pump genes. Moreover, our data confirm a BrlR target contributing to drug tolerance, likely countering the prevailing dogma that biofilm tolerance arises from a multiplicity of factors.
Integrated Resistance Analysis of CERTAIN-1 and CERTAIN-2 Studies in Hepatitis C Virus-Infected Patients Receiving Glecaprevir and Pibrentasvir in Japan
Authors: Krishnan Preethi , Schnell Gretja , Tripathi Rakesh , Beyer Jill , Reisch Thomas , Dekhtyar Tatyana , Irvin Michelle , Xie Wangang , Fu Bo , Burroughs Margaret , Redman Rebecca , Kumada Hiromitsu , Chayama Kazuaki , Collins Christine , Pilot-Matias Tami 
Published: November 2017

ABSTRACT

Glecaprevir and pibrentasvir are hepatitis C virus (HCV) pangenotypic inhibitors targeting NS3/4A protease and NS5A, respectively. This once-daily, fixed-dose combination regimen demonstrated high sustained virologic response 12 weeks postdosing (SVR
12
) rates in CERTAIN-1 and CERTAIN-2 studies in Japanese HCV-infected patients, with a low virologic failure rate (1.2%). There were no virologic failures among direct-acting antiviral (DAA)-treatment-naive genotype 1a (GT1a) (
n
= 4)-, GT1b (
n
= 128)-, and GT2 (
n
= 97)-infected noncirrhotic patients treated for 8 weeks or among GT1b (
n
= 38)- or GT2 (
n
= 20)-infected patients with compensated cirrhosis treated for 12 weeks. Two of 33 DAA-experienced and 2 of 12 GT3-infected patients treated for 12 weeks experienced virologic failure. Pooled resistance analysis, grouped by HCV subtype, treatment duration, prior treatment experience, and cirrhosis status, was conducted. Among DAA-naive GT1b-infected patients, the baseline prevalence of NS3-D168E was 1.2%, that of NS5A-L31M was 3.6%, and that of NS5A-Y93H was 17.6%. Baseline polymorphisms in NS3 or NS5A were less prevalent in GT2, with the exception of the common L/M31 polymorphism in NS5A. Among DAA-experienced GT1b-infected patients (30/32 daclatasvir plus asunaprevir-experienced patients), the baseline prevalence of NS3-D168E/T/V was 48.4%, that of NS5A-L31F/I/M/V was 81.3%, that of the NS5A P32deletion was 6.3%, and that of NS5A-Y93H was 59.4%. Common baseline polymorphisms in NS3 and/or NS5A had no impact on treatment outcomes in GT1- and GT2-infected patients; the impact on GT3-infected patients could not be assessed due to the enrollment of patients infected with diverse subtypes and the limited number of patients. The glecaprevir-pibrentasvir combination regimen allows a simplified treatment option without the need for HCV subtyping or baseline resistance testing for DAA-naive GT1- or GT2-infected patients. (The CERTAIN-1 and CERTAIN-2 studies have been registered at ClinicalTrials.gov under identifiers NCT02707952 and NCT02723084, respectively.)
Production of 1-Dodecanol, 1-Tetradecanol, and 1,12-Dodecanediol through Whole-Cell Biotransformation in Escherichia coli
Authors: Hsieh Shan-Chi , Wang Jung-Hao , Lai Yu-Chen , Su Ching-Yeuh , Lee Kung-Ta 
Published: November 2017

ABSTRACT

Medium- and long-chain 1-alkanol and α,ω-alkanediols are used in personal care products, in industrial lubricants, and as precursors for polymers synthesized for medical applications. The industrial production of α,ω-alkanediols by alkane hydroxylation primarily occurs at high temperature and pressure using heavy metal catalysts. However, bioproduction has recently emerged as a more economical and environmentally friendly alternative. Among alkane monooxygenases, CYP153A from
Marinobacter aquaeolei
VT8 (CYP153A

M.aq

; the strain is also known as
Marinobacter hydrocarbonoclasticus
VT8) possesses low overoxidation activity and high regioselectivity and thus has great potential for use in terminal hydroxylation. However, the application of CYP153A

M.aq

is limited because it is encoded by a dysfunctional operon. In this study, we demonstrated that the operon regulator AlkR

M.aq

is functional, can be induced by alkanes of various lengths, and does not suffer from product inhibition. Additionally, we identified a transposon insertion in the CYP153A

M.aq

operon. When the transposon was removed, the expression of the operon genes could be induced by alkanes, and the alkanes could then be oxyfunctionalized by the resulting proteins. To increase the accessibility of medium- and long-chain alkanes, we coexpressed a tunable alkane facilitator (AlkL) from
Pseudomonas putida
GPo1. Using a recombinant
Escherichia coli
strain, we produced 1.5 g/liter 1-dodecanol in 20 h and 2 g/liter 1-tetradecanol in 50 h by adding dodecane and tetradecane, respectively. Furthermore, in 68 h, we generated 3.76 g/liter of 1,12-dodecanediol by adding a dodecane–1-dodecanol substrate mixture. This study reports a very efficient method of producing C
12
/C
14
alkanols and C
12
1,12-alkanediol by whole-cell biotransformation.

IMPORTANCE
To produce terminally hydroxylated medium- to long-chain alkane compounds by whole-cell biotransformation, substrate permeability, enzymatic activity, and the control of overoxidability should be considered. Due to difficulties in production, small amounts of 1-dodecanol, 1-tetradecanol, and 1,12-dodecanediol are typically produced. In this study, we identified an alkane-inducible monooxygenase operon that can efficiently catalyze the conversion of alkane to 1-alkanol with no detection of the overoxidation product. By coexpressing an alkane membrane facilitator, high levels of 1-dodecanol, 1-tetradecanol, and 1,12-dodecanediol could be generated. This study is significant for the bioproduction of medium- and long-chain 1-alkanol and α,ω-alkanediols.
Quality of Irrigation Water Affects Soil Functionality and Bacterial Community Stability in Response to Heat Disturbance
Authors: Frenk Sammy , Hadar Yitzhak , Minz Dror 
Published: November 2017

ABSTRACTAnthropogenic activities alter the structure and function of a bacterial community. Furthermore, bacterial communities structured by the conditions the anthropogenic activities present may consequently reduce their stability in response to an unpredicted acute disturbance. The present mesocosm-scale study exposed soil bacterial communities to different irrigation water types, including freshwater, fertilized freshwater, treated wastewater, and artificial wastewater, and evaluated their response to a disturbance caused by heat. These effectors may be considered deterministic and stochastic forces common in agricultural operations of arid and semiarid regions. Bacterial communities under conditions of high mineral and organic carbon availability (artificial wastewater) differed from the native bacterial community and showed a proteobacterial dominance. These bacterial communities had a lower resistance to the heat treatment disturbance than soils under conditions of low resource availability (high-quality treated wastewater or freshwater). The latter soil bacterial communities showed a higher abundance of operational taxonomic units (OTUs) classified asBacilli. These results were elucidated by soil under conditions of high resource availability, which lost higher degrees of functional potential and had a greater bacterial community composition change. However, the functional resilience, after the disturbance ended, was higher under a condition of high resource availability despite the bacterial community composition shift and the decrease in species richness. The functional resilience was directly connected to the high growth rates of certainBacteroidetesand proteobacterial groups. A high stability was found in samples that supported the coexistence of both resistant OTUs and fast-growing OTUs.IMPORTANCEThis report presents the results of a study employing a hypothesis-based experimental approach to reveal the forces involved in determining the stability of a soil bacterial community to disturbance. The resultant postdisturbance bacterial community composition dynamics and functionality were analyzed. The paper demonstrates the relatedness of community structure and stability under cultivation conditions prevalent in an arid area under irrigation with water of different qualities. The use of common agricultural practices to demonstrate these features has not been described before. The combination of a fundamental theoretical issue in ecology with common and concerning disturbances caused by agricultural practice makes this study unique. Furthermore, the results of the present study have applicable importance regarding soil conservation, as it enables a better characterization and monitoring of stressed soil bacterial communities and possible intervention to reduce the stress. It will also be of valued interest in coming years, as fresh water scarcity and the use of alternative water sources are expected to rise globally.
Formation and Characterization of Early Bacterial Biofilms on Different Wood Typologies Applied in Dairy Production
Authors: Cruciata Margherita , Gaglio Raimondo , Scatassa Maria Luisa , Sala Giovanna , Cardamone Cinzia , Palmeri Marisa , Moschetti Giancarlo , La Mantia Tommaso , Settanni Luca 
Published: November 2017

ABSTRACT

The main hypothesis of this work was that Sicilian forestry resources are suitable for the production of equipment to be used in cheese making and indigenous milk lactic acid bacteria (LAB) are able to develop stable biofilms providing starter and nonstarter cultures necessary for curd fermentation and cheese ripening, respectively. Hence, the present work was carried out with deproteinized whey to evaluate LAB biofilm formation on different woods derived from tree species grown in Sicily. Microbiological and scanning electron microscopy analyses showed minimal differences in microbial levels and compositions for the neoformed biofilms. The specific investigation of
Salmonella
spp.,
Listeria monocytogenes
,
Escherichia coli
, coagulase-positive staphylococci (CPS), and sulfite-reducing anaerobes did not generate any colony for all vats before and after bacterial adhesion. LAB populations dominated all vat surfaces. The highest levels (7.63 log CFU/cm
2
) were registered for thermophilic cocci. Different colonies were characterized physiologically, biochemically, and genetically (at strain and species levels). Six species within the genera
Enterococcus
,
Lactobacillus
,
Lactococcus
, and
Streptococcus
were identified. The species most frequently present were
Lactobacillus fermentum
and
Lactococcus lactis
. LAB found on the surfaces of the wooden vats in this study showed interesting characteristics important for dairy manufacture. To thoroughly investigate the safety of the wooden vat, a test of artificial contamination on new Calabrian chestnut (control wood) vats was carried out. The results showed that LAB represent efficient barriers to the adhesion of the main dairy pathogens, probably due to their acidity and bacteriocin generation.

IMPORTANCE
This study highlights the importance of using wooden vats for traditional cheese production and provides evidence for the valorization of the Sicilian forest wood resources via the production of dairy equipment.
The effect of nut consumption on markers of inflammation and endothelial function: a systematic review and meta-analysis of randomised controlled trials
Authors: Neale Elizabeth P , Tapsell Linda C , Guan Vivienne , Batterham Marijka J 
Published: November 2017

ObjectivesTo examine the effect of nut consumption on inflammatory biomarkers and endothelial function.DesignA systematic review and meta-analysis.Data sourcesMEDLINE, PubMed, Cumulative Index to Nursing and Allied Health Literature and Cochrane Central Register of Controlled Trials (all years to 13 January 2017).Eligibility criteriaRandomised controlled trials (with a duration of 3 weeks or more) or prospective cohort designs conducted in adults; studies assessing the effect of consumption of tree nuts or peanuts on C-reactive protein (CRP), adiponectin, tumour necrosis factor alpha, interleukin-6, intercellular adhesion molecule 1, vascular cell adhesion protein 1 and flow-mediated dilation (FMD).Data extraction and analysisRelevant data were extracted for summary tables and analyses by two independent researchers. Random effects meta-analyses were conducted to explore weighted mean differences (WMD) in change or final mean values for each outcome.ResultsA total of 32 studies (all randomised controlled trials) were included in the review. The effect of nut consumption on FMD was explored in nine strata from eight studies (involving 652 participants), with consumption of nuts resulting in significant improvements in FMD (WMD: 0.79%(95% CI 0.35 to 1.23)). Nut consumption resulted in small, non-significant differences in CRP (WMD: −0.01 mg/L (95% CI −0.06 to 0.03)) (26 strata from 25 studies), although sensitivity analyses suggest results for CRP may have been influenced by two individual studies. Small, non-significant differences were also found for other biomarkers of inflammation.ConclusionsThis systematic review and meta-analysis of the effects of nut consumption on inflammation and endothelial function found evidence for favourable effects on FMD, a measure of endothelial function. Non-significant changes in other biomarkers indicate a lack of consistent evidence for effects of nut consumption on inflammation. The findings of this analysis suggest a need for more research in this area, with a particular focus on randomised controlled trials.PROSPERO registration numberCRD42016045424.
Cerebrospinal fluid biomarkers for the diagnosis and prognosis of Parkinson’s disease: protocol for a systematic review and individual participant data meta-analysis
Authors: Eusebi Paolo , Hansson Oskar , Paciotti Silvia , Orso Massimiliano , Chiasserini Davide , Calabresi Paolo , Blennow Kaj , Parnetti Lucilla 
Published: November 2017

IntroductionIdiopathic Parkinson’s disease (PD) is a progressive neurodegenerative disorder related to α-synuclein misfolding and aggregation. For this reason, it belongs to the family of ‘synucleinopathies’, which also includes some other neurological diseases. Although imaging and ancillary investigations may be helpful in the diagnostic workup, the diagnosis of PD mostly relies on the clinician’s expertise. Furthermore, there is a need today for markers that can track the disease progression in PD that might improve the evaluation of novel disease-modifying therapies. The cerebrospinal fluid (CSF) has been widely investigated with the purpose of finding useful diagnostic and prognostic biomarkers for PD.Methods and analysisThis systematic review protocol has been developed according to the Preferred Reporting Items for Systematic reviews and Meta-Analyses Protocol 2015 statement and was registered on the PROSPERO international prospective register of systematic reviews. An international collaboration will be established. We will search the Cochrane Library, Web of Science, Medline and Embase from inception, using appropriate search strategies. Individual participant data from all included studies will be merged into a single database. We will include any study assessing the diagnostic and prognostic role of CSF biomarkers in PD. To evaluate the risk of bias and applicability of primary diagnostic accuracy studies, we will use Quality Assessment of Diagnostic Accuracy Studies-2 and Quality in Prognostic Studies. We will use standard meta-analytic procedures. We will first explore the utility of each CSF biomarker in turn. For each biomarker, we will assess its diagnostic and prognostic utility by means of receiver operating characteristic analysis and regression models. We will then move towards a multivariate approach considering different panels of biomarkers.Ethics and disseminationOur study will not include confidential data, and no intervention will be involved, so ethical approval is not required. The results of the study will be reported in international peer-reviewed journals.
Core outcome research measures in anal cancer (CORMAC): protocol for systematic review, qualitative interviews and Delphi survey to develop a core outcome set in anal cancer
Authors: Fish Rebecca , Sanders Caroline , Williamson Paula R , Renehan Andrew G 
Published: November 2017

IntroductionThe incidence of anal squamous cell carcinoma (ASCC) has increased threefold in the last 30 years. Initial treatment is chemoradiotherapy, associated with short-term and long-term side effects. Future therapy innovations aim to reduce morbidity in treatment of early tumours while maintaining treatment efficacy, and to escalate treatment intensity in locally advanced tumours with acceptable quality of life (QoL). However, all phase III randomised controlled trials to-date have utilised different primary outcomes, which hinders evidence synthesis and presents challenges to the selection of optimal outcomes in future trials. No trial comprehensively assessed long-term side effects and QoL, suggesting outcomes reflecting issues important to patients are under-represented. This project aims to determine the priority outcomes for all stakeholders and reach agreement on a standardised core set of outcomes to be measured and reported on in all future ASCC trials.Methods and analysisA systematic review will identify all outcomes reported in trials and observational studies of chemoradiotherapy as primary treatment for ASCC. Outcomes of importance to patients will be identified through patient interviews. The long list of outcomes generated from the systematic review and interviews will be used to create a two-round Delphi process, including key stakeholders (patients and healthcare professionals). The results of the Delphi will be discussed at a face-to-face consensus meeting. Discussion will focus on outcomes that did not achieve consensus through the Delphi process and conclude with anonymous voting to ratify the final core outcome set (COS).Ethics and disseminationThe final COS will feed directly into the PersonaLising Anal cancer radioTherapy dOse (PLATO) national anal cancer trials and the Association of coloproctologists of Great Britain and Ireland (ACPGBI) supported national anal cancer database. Utilisation of the COS will increase the relevance of research output to all stakeholders and increase the capacity for data synthesis between trials. This study has ethical approval and is registered with the Core Outcome Measures in Effectiveness Trials (COMET) initiative.Trial registration numberPROSPERO registration ID:CRD42016036540
43 Management of acute low back pain in the ED: a systematic review
Authors: Ashbrook Jane , Rodgdakis Nikos , Goodwin Peter , Yeowell Gill , Callaghan Michael 
Published: November 2017

Study objectiveThere is no consensus on the management of low back pain in the ED and evidence suggests that these patients are likely to receive unwarranted imaging and inappropriate opioid prescription.The purpose of this study is to review the available literature pertaining to the clinical management of acute low back pain in the ED.MethodsThe Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) and Realist And Meta-narrative Evidence Syntheses: Evolving Standards (RAMESES) guidelines were observed during this review.Trials were included if the population studied were adults with acute low back pain in an emergency setting. All diagnostic tests and therapeutic interventions were evaluated.Methodological quality and risk of bias was appraised using the Downs and Black checklist.Results19 articles were identified including 1896 patients that were sub-grouped according to management.In the pharmacological subgroup corticosteroids were effective in patients with radicular pain, NSAIDs were as effective as other medication with less adverse events, Phenyramidol was not superior to placebo, promethazine and morhpine combined was not more effective than morphine alone and ketamine was no more effective than morphine but had a worse adverse effect profile.In the emergency transport group TENS and active warming both showed effects in reducing pain, anxiety and heart rate.In the physical therapy management group less pain and greater satisfaction were reported.In the adjunct interventions group showed a trend towards pain reduction in the use of heat/ice packs and short term pain relief in acupuncture and auricular acupuncture.ConclusionsMore high quality trials are needed to determine an evidence-based management protocol for the treatment of acute low back pain in the ED.