bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comprehensive Arrayed Transposon Mutant Library of Klebsiella pneumoniae Outbreak Strain KPNIH1
Authors: Ramage Beth , Erolin Roxanne , Held Kiara , Gasper Joe , Weiss Eli , Brittnacher Mitch , Gallagher Larry , Manoil Colin 
Published: August 2017

ABSTRACT

Klebsiella pneumoniae
and other carbapenem-resistant members of the family
Enterobacteriaceae
are a major cause of hospital-acquired infections, yet the basis of their success as nosocomial pathogens is poorly understood. To help provide a foundation for genetic analysis of
K. pneumoniae
, we created an arrayed, sequence-defined transposon mutant library of an isolate from the 2011 outbreak of infections at the U.S. National Institutes of Health Clinical Center. The library is made up of 12,000 individually arrayed mutants of a carbapenemase deletion parent strain and provides coverage of 85% of the predicted genes. The library includes an average of 2.5 mutants per gene, with most insertion locations identified and confirmed in two independent rounds of Sanger sequencing. On the basis of an independent transposon sequencing assay, about half of the genes lacking representatives in this “two-allele” library are essential for growth on nutrient agar. To validate the use of the library for phenotyping, we screened candidate mutants for increased antibiotic sensitivity by using custom phenotypic microarray plates. This screening identified several mutations increasing sensitivity to β-lactams (in
acrB1
,
mcrB
,
ompR
,
phoP1
, and
slt1
) and found that two-component regulator
cpxAR
mutations increased multiple sensitivities (to an aminoglycoside, a fluoroquinolone, and several β-lactams). Strains making up the two-allele mutant library are available through a web-based request mechanism.

IMPORTANCE
K. pneumoniae
and other carbapenem-resistant members of the family
Enterobacteriaceae
are recognized as a top public health threat by the Centers for Disease Control and Prevention. The analysis of these major nosocomial pathogens has been limited by the experimental resources available for studying them. The work presented here describes a sequence-defined mutant library of a
K. pneumoniae
strain (KPNIH1) that represents an attractive model for studies of this pathogen because it is a recent isolate of the major sequence type that causes infection, the epidemiology of the outbreak it caused is well characterized, and an annotated genome sequence is available. The ready availability of defined mutants deficient in nearly all of the nonessential genes of the model strain should facilitate the genetic dissection of complex traits like pathogenesis and antibiotic resistance.
Conformational Changes That Coordinate the Activity of BamA and BamD Allowing β-Barrel Assembly
Authors: McCabe Anne L. , Ricci Dante , Adetunji Modupe , Silhavy Thomas J. 
Published: August 2017

ABSTRACT

Most integral outer membrane proteins (OMPs) of Gram-negative bacteria, such as
Escherichia coli
, assume a β-barrel structure. The β-barrel assembly machine (Bam), a five-member complex composed of β-barrel OMP BamA and four associated lipoproteins, BamB, BamC, BamD, and BamE, folds and inserts OMPs into the outer membrane. The two essential proteins BamA and BamD interact to stabilize two subcomplexes, BamAB and BamCDE, and genetic and structural evidence suggests that interactions between BamA and BamD occur via an electrostatic interaction between a conserved aspartate residue in a periplasmic domain of BamA and a conserved arginine in BamD. In this work, we characterize charge-change mutations at these key BamA and BamD residues and nearby charged residues in BamA with respect to OMP assembly and Bam complex stability. We show that Bam complex stability does not correlate with function, that BamA and BamD must adopt at least two active conformational states during OMP assembly, and that these charged residues are not required for function. Rather, these charged residues are important for coordinating the activities of BamA and BamD to allow efficient OMP assembly. We present a model of OMP assembly wherein recognition and binding of unfolded OMP substrate by BamA and BamD induce a signaling interaction between the two proteins, causing conformational changes necessary for the assembly reaction to proceed. By analogy to signal sequence recognition by SecYEG, we believe these BamA-BamD interactions ensure that both substrate and complex are competent for OMP assembly before the assembly reaction commences.

IMPORTANCE
Conformational changes in the proteins of the β-barrel assembly machine (Bam complex) are associated with the folding and assembly of outer membrane proteins (OMPs) in Gram-negative bacteria. We show that electrostatic interactions between the two essential proteins BamA and BamD coordinate conformational changes upon binding of unfolded substrate that allow the assembly reaction to proceed. Mutations affecting this interaction are lethal not because they destabilize the Bam complex but rather because they disrupt this coordination. Our model of BamA-BamD interactions regulating conformation in response to proper substrate interaction is reminiscent of conformational changes the secretory (Sec) machinery undergoes after signal sequence recognition that ensure protein quality control.
Transient clinical improvement of a mitochondrial neurogastrointestinal encephalomyopathy-like syndrome after allogeneic haematopoietic stem cell transplantation
Authors: Baker Malcolm Kevin , Schutte Clara Maria , Ranchhod Neelay , Brittain David , van Rensburg J E 
Published: August 2017

Mitochondrial neurogastrointestinal encephalopathy (MNGIE), usually an autosomal-recessive inherited condition, causes gastrointestinal dysmotility, ophthalmoplegia, ptosis, leukoencephalopathy and neuropathy. The chromosome 22 disorder, due to mutations in the nuclear gene TYMP encoding thymidine phosphorylase (TP), leads to the accumulation of thymidine and deoxyuridine, with mitochondrial dysfunction.This report describes a patient with an MNGIE-like syndrome with a heterozygous TYMP mutation who showed marked, but transient improvement postallogeneic haematopoietic stem cell transplantation (HSCT).The patient, showing ptosis and ophthalmoplegia, was initially managed for myasthenia gravis. She developed gastrointestinal symptoms, dysarthria, dysphagia and weakness, and MNGIE was considered due to its low TP levels and improvement after platelet transfusions. She underwent HSCT, with dramatic improvement, but regressed 18 months later despite normal TP levels, platelet counts and full chimerism.MNGIE may encompass a spectrum of disorders. TP deficiency alone is unlikely to explain all clinical signs, and other factors, including the possible development of anti-TP antibodies, which may play a role in the pathophysiology.
Individuals at high risk for type 2 diabetes invited to a lifestyle program: characteristics of participants versus non-participants (the HUNT Study) and 24-month follow-up of participants (the VEND-RISK Study)
Authors: Følling Ingrid Sørdal , Kulseng Bård , Midthjell Kristian , Rangul Vegar , Helvik Anne-S 
Published: August 2017

ObjectivePrevention of type 2 diabetes mellitus is possible through lifestyle programs, but the effect depends on the program's content, resources, and setting. Lifestyle programs are often confronted with high rates of non-participation and attrition. This study invited individuals at high risk for type 2 diabetes to a lifestyle program in the Norwegian primary healthcare setting. The aims were to investigate possible differences in characteristics between participants and non-participants and to study the effect of the lifestyle program at 24-month follow-up for participants.Research design and methodsIndividuals identified at high risk for type 2 diabetes during the third survey of the Nord-Trøndelag Health Study (HUNT3) from two municipalities (n=332) were invited to a lifestyle program (the VEND-RISK Study). A cross-sectional design was used to explore if the participants’ characteristics differed from non-participants. A non-randomized, single-arm, pre–post examination was used to examine the effect of the lifestyle program on participants’ characteristics at 24-month follow-up.ResultsOf all individuals at high risk for type 2 diabetes invited to the lifestyle program, 86% (287/332) declined to participate. Non-participating women had fewer years of education (p<0.001), compared with participating women. For men, no differences were seen between non-participants and participants. Among all participants (n=45) at 24-month follow-up, none had developed type 2 diabetes, and HbA1c(p<0.001) had decreased significantly. There was a small reduction in mean body mass index from baseline to 24 months that was not statistically significant. For women, waist circumference (−4.0 cm, p<0.001) decreased significantly.ConclusionsFuture research regarding individuals at high risk for type 2 diabetes in the primary healthcare lifestyle program should focus on how to promote recruitment of women with low education. Participants attending this study's lifestyle program improved their cardiometabolic markers.Clinical trials registrationNCT01135901; Results.
Polyethylene glycol intestinal lavage in addition to usual antibiotic treatment for severeClostridium difficilecolitis: a randomised controlled pilot study
Authors: McCreery Greig , Jones Philip M , Kidane Biniam , DeMelo Vanessa , Mele Tina 
Published: August 2017

IntroductionClostridium difficileinfections (CDI) are common, costly and potentially life threatening. Most CDI will respond to antibiotic therapy, but 3%–10% of all patients with CDI will progress to a severe, life-threatening course. Complete removal of the large bowel is indicated for severe CDI. However, the 30-day mortality following surgical intervention for severe CDI ranges from 20% to 70%. A less invasive approach using surgical faecal diversion and direct colonic lavage with polyethylene glycol (PEG) and vancomycin has demonstrated a relative mortality reduction of approximately 50%. As an alternative to these operative approaches, we propose to treat patients with bedside intestinal lavage with PEG and vancomycin instillation via nasojejunal tube, in addition to usual antibiotic management. Preliminary data collected by our research group are encouraging.Methods and analysisWe will conduct a 1-year, single-centre, pilot randomised controlled trial to study this new treatment strategy for patients with severe CDI and additional risk factors for fulminant or complicated infection. After informed consent, patients with severe-complicated CDI without immediate indication for surgery will be randomised to either usual antibiotic treatment or usual antibiotic treatment with the addition of 8 L of PEG lavage via nasojejunal tube. This pilot trial will evaluate our eligibility and enrolment rate, protocol compliance and adverse event rates and provide further data to inform a more robust sample size calculation and protocol modifications for a definitive multicentre trial design. Based on historical data, we anticipate enrolling approximately 24 patients during the 1-year pilot study period.As a pilot study, data will be reported in aggregate. Between-group differences will be assessed in a blinded fashion for evidence of harm, and to further refine our sample size calculation.Ethics and disseminationThis study protocol has been reviewed and approved by our local institutional review board. Results of the pilot trial and subsequent main trial will be submitted for publication in a peer-reviewed journal.Trial registration numberNCT02466698; Pre-results.
A qualitative inquiry into the barriers and facilitators to achieving home death
Authors: Sayma Meelad , Saleh Dina , Kerwat Doa’a , Jamshaid Shiraz , Ahmed Aaniya , Oyewole Folashade , Wahid Abdul Samad , Perry Claire , Cox Benita 
Published: August 2017

ObjectivesTo explore the barriers and facilitators to patients achieving death at home.MethodsIn-depth, semistructured interviews with end-of-life care experts were conducted to develop an insight into the barriers and facilitators to achieving death at home. Thirty-three interviews were conducted compromising of a mixture of face-to-face and tele interviews. Experts included healthcare professionals working in the community, hospital and policy/academic settings. Thematic analysis was undertaken on interview transcripts.ResultsThree overarching themes, further divided into a total of 12 subthemes were identified. The three themes were ‘managing people’, ‘education' and ‘planning’. The ‘managing people’ theme included subthemes of patient preferences and family influences; the ‘education’ theme encompassed knowledge and training, perceptions of death and communication and the ‘planning’ theme contained seven subthemes including ‘coordination’, ‘resources’ and ‘cost’.ConclusionsMultiple barriers and facilitators to achieving death at home were identified in this study. Of particular significance was the identification of the fear and stigma associated with death among doctors, patients and their families serving as a barrier to home death, not previously identified in the literature. Additionally, the importance of social networks and resource provision were highlighted as key in influencing patient death at home.
Tobacco companies’ use of retailer incentives after a ban on point-of-sale tobacco displays in Scotland
Authors: Stead Martine , Eadie Douglas , Purves Richard I , Moodie Crawford , Haw Sally 
Published: August 2017

IntroductionIncentives have been used by tobacco companies for many years to encourage retailers to sell and promote their products. However, few studies have examined the use of retailer incentives in countries with a ban on the open display of tobacco products in stores.MethodsAs part of the DISPLAY(Determining the Impact of Smoking Point of Sale Legislation Among Youth) study, annual qualitative interviews were conducted with 24 small retailers in four Scottish communities. This article focuses on data collected in June to July 2015 and June to July 2016 after a ban on the open display of tobacco was fully implemented in Scotland.ResultsRetailers described being offered and benefiting from a range of financial and other incentives, typically offered via tobacco company representatives (‘reps’). Most of the retailers received tobacco manufacturer support for converting their storage unit to be compliant with the new regulations, and several participated in manufacturer ‘loyalty’ or ‘reward’ schemes. Incentives were additionally offered for maintaining stock levels and availability, positioning brands in specified spaces in the public-facing storage units (even though products were covered up), increasing sales, trialling new products and participating in specific promotions, such as verbally recommending specific brands to customers.ConclusionsEven in a market where the open display of tobacco is prohibited, tobacco companies continue to incentivise retailers to sell and promote their brands and have developed new promotional strategies. For countries that have implemented tobacco display bans, or are considering doing so, one option to combat these practices would be to ban promotional communications between manufacturers and retailers.
New design of multi-band negative-index metamaterial and absorber at visible frequencies
Authors: Gong Boyi , Guo Fan , Zou Wenkang , Chen Lin , Song Kun , Zhao Xiaopeng 
Published: August 2017

A new negative-index metamaterial (NIM) structure is proposed by designing the metallic holes of traditional double-fishnet (DF) structures from uniform sizes to several different sizes. Numerical results demonstrate that the new metamaterial, as an improved variant of the DF structure, achieved a multi-band negative refractive index across a wide range of visible frequencies from 470 THz to 540 THz, which covers the red, orange, yellow, and green regions of the visible spectra. Meanwhile, a low-profile nanostrctured absorber was obtained when one side of the perforated metal layer of this multi-band NIM was substituted with a continuous metal film with the same thickness. The absorber showed the high absorption of more than 95% at multiple frequencies of 511, 520, 523, 525, and 527 THz. The behavior of multi-frequency response effectively broadened the working bandwidth. Finally, the physical mechanism of the multi-band operating characteristics of NIM and absorber was analyzed with the distributions of current intensity at different resonant frequencies.
Use of Calcium Channel Blockers and Breast Cancer Risk in the Women's Health Initiative
Authors: Brasky Theodore M. , Krok-Schoen Jessica L. , Liu Jingmin , Chlebowski Rowan T. , Freudenheim Jo L. , Lavasani Sayeh , Margolis Karen L. , Qi Lihong , Reding Kerryn W. , Shields Peter G. , Simon Michael S. , Wactawski-Wende Jean , Wang Ange , Womack Catherine , Manson JoAnn E. 
Published: August 2017

Abstract
Background: Use of calcium channel blockers (CCBs) has been associated with increased risk of breast cancer in some, but not all, studies. Differences in reported associations from prior studies may be due, in part, to inadequate control of confounding factors.
Methods: Participants were 28,561 postmenopausal women from the Women's Health Initiative who reported use of either CCBs or other antihypertensive medications (AHMs) at baseline; 1,402 incident breast cancer cases were diagnosed during 12 years of follow-up. Adjusted Cox regression models were used to estimate HRs and 95% confidence intervals (CI) for the associations between CCB use relative to other AHM use and breast cancer risk.
Results: Use of CCBs was not associated with breast cancer risk (HR, 1.06; 95% CI, 0.94–1.20) relative to use of other AHMs. Associations approximated the null value when CCBs were considered by duration of use, length of action, or drug class.
Conclusions: We provide additional evidence that CCBs do not influence breast cancer risk in postmenopausal women.
Impact: The results from this study, which includes strong control for potential confounding factors, cast doubt on increases in risk with CCBs. Cancer Epidemiol Biomarkers Prev; 26(8); 1345–8. ©2017 AACR.
Coffee and Green Tea Consumption and Subsequent Risk of Malignant Lymphoma and Multiple Myeloma in Japan: The Japan Public Health Center-based Prospective Study
Authors: Ugai Tomotaka , Matsuo Keitaro , Sawada Norie , Iwasaki Motoki , Yamaji Taiki , Shimazu Taichi , Sasazuki Shizuka , Inoue Manami , Kanda Yoshinobu , Tsugane Shoichiro 
Published: August 2017

Abstract
Background: The aim of this study was to investigate the association of coffee and green tea consumption and the risk of malignant lymphoma and multiple myeloma in a large-scale population-based cohort study in Japan.
Methods: In this analysis, a total of 95,807 Japanese subjects (45,937 men and 49,870 women; ages 40–69 years at baseline) of the Japan Public Health Center-based Prospective Study who completed a questionnaire about their coffee and green tea consumption were followed up until December 31, 2012, for an average of 18 years. HRs and 95% confidence intervals were estimated using a Cox regression model adjusted for potential confounders as a measure of association between the risk of malignant lymphoma and multiple myeloma associated with coffee and green tea consumption at baseline.
Results: During the follow-up period, a total of 411 malignant lymphoma cases and 138 multiple myeloma cases were identified. Overall, our findings showed no significant association between coffee or green tea consumption and the risk of malignant lymphoma or multiple myeloma for both sexes.
Conclusions: In this study, we observed no significant association between coffee or green tea consumption and the risk of malignant lymphoma or multiple myeloma.
Impact: Our results do not support an association between coffee or green tea consumption and the risk of malignant lymphoma or multiple myeloma. Cancer Epidemiol Biomarkers Prev; 26(8); 1352–6. ©2017 AACR.
Circulating Tumor DNA Reveals Clinically Actionable Somatic Genome of Metastatic Bladder Cancer
Authors: Vandekerkhove Gillian , Todenhöfer Tilman , Annala Matti , Struss Werner J. , Wong Amanda , Beja Kevin , Ritch Elie , Brahmbhatt Sonal , Volik Stanislav V. , Hennenlotter Jörg , Nykter Matti , Chi Kim N. , North Scott , Stenzl Arnulf , Collins Colin C. , Eigl Bernhard J. , Black Peter C. , Wyatt Alexander W. 
Published: August 2017

Abstract
Purpose: Targeted agents and immunotherapies promise to transform the treatment of metastatic bladder cancer, but therapy selection will depend on practical tumor molecular stratification. Circulating tumor DNA (ctDNA) is established in several solid malignancies as a minimally invasive tool to profile the tumor genome in real-time, but is critically underexplored in bladder cancer.
Experimental Design: We applied a combination of whole-exome sequencing and targeted sequencing across 50 bladder cancer driver genes to plasma cell-free DNA (cfDNA) from 51 patients with aggressive bladder cancer, including 37 with metastatic disease.
Results: The majority of patients with metastasis, but only 14% of patients with localized disease, had ctDNA proportions above 2% of total cfDNA (median 16.5%, range 3.9%–72.6%). Twelve percent of estimable samples had evidence of genome hypermutation. We reveal an aggressive mutational landscape in metastatic bladder cancer with 95% of patients harboring deleterious alterations to TP53, RB1, or MDM2, and 70% harboring a mutation or disrupting rearrangement affecting chromatin modifiers such as ARID1A. Targetable alterations in MAPK/ERK or PI3K/AKT/mTOR pathways were robustly detected, including amplification of ERBB2 (20% of patients) and activating hotspot mutations in PIK3CA (20%), with the latter mutually exclusive to truncating mutations in TSC1. A novel FGFR3 gene fusion was identified in consecutive samples from one patient.
Conclusions: Our study demonstrates that ctDNA provides a practical and cost-effective snapshot of driver gene status in metastatic bladder cancer. The identification of a wide spectrum of clinically informative somatic alterations nominates ctDNA as a tool to dissect disease pathogenesis and guide therapy selection in patients with metastatic bladder cancer. Clin Cancer Res; 23(21); 6487–97. ©2017 AACR.