bluuebunny/crossref_metadata_2025_split huggingface dataset:
Candida auris: a Review of the Literature
Authors: Jeffery-Smith Anna , Taori Surabhi K. , Schelenz Silke , Jeffery Katie , Johnson Elizabeth M. , Borman Andrew ,   Candida auris Incident Management Team, Manuel Rohini , Brown Colin S. 
Published: November 2017

SUMMARY

The emerging pathogen
Candida auris
has been associated with nosocomial outbreaks on five continents. Genetic analysis indicates the simultaneous emergence of separate clades of this organism in different geographical locations. Invasive infection and colonization have been detected predominantly in patients in high-dependency settings and have garnered attention due to variable antifungal resistance profiles and transmission within units instituting a range of infection prevention and control measures. Issues with the identification of
C. auris
using both phenotypic and molecular techniques have raised concerns about detecting the true scale of the problem. This review considers the literature available on
C. auris
and highlights the key unknowns, which will provide direction for further work in this field.
Occurrence and Nature of Double Alleles in Variable-Number Tandem-Repeat Patterns of More than 8,000 Mycobacterium tuberculosis Complex Isolates in The Netherlands
Authors: Jajou Rana , Kamst Miranda , van Hunen Rianne , de Zwaan Carolina Catherina , Mulder Arnout , Supply Philip , Anthony Richard , van der Hoek Wim , van Soolingen Dick 
Published: November 2017

ABSTRACT

Since 2004, variable-number tandem-repeat (VNTR) typing of
Mycobacterium tuberculosis
complex isolates has been applied on a structural basis in The Netherlands to study the epidemiology of tuberculosis (TB). Although this technique is faster and technically less demanding than the previously used restriction fragment length polymorphism (RFLP) typing, reproducibility remains a concern. In the period from 2004 to 2015, 8,532 isolates were subjected to VNTR typing in The Netherlands, with 186 (2.2%) of these exhibiting double alleles at one locus. Double alleles were most common in loci 4052 and 2163b. The variables significantly associated with double alleles were urban living (odds ratio [OR], 1.503; 95% confidence interval [CI], 1.084 to 2.084;
P
= 0.014) and pulmonary TB (OR, 1.703; 95% CI, 1.216 to 2.386;
P
= 0.002). Single-colony cultures of double-allele strains were produced and revealed single-allele profiles; a maximum of five single nucleotide polymorphisms (SNPs) was observed between the single- and double-allele isolates from the same patient when whole-genome sequencing (WGS) was applied. This indicates the presence of two bacterial populations with slightly different VNTR profiles in the parental population, related to genetic drift. This observation is confirmed by the fact that secondary cases from TB source cases with double-allele isolates sometimes display only one of the two alleles present in the source case. Double alleles occur at a frequency of 2.2% in VNTR patterns in The Netherlands. They are caused by biological variation rather than by technical aberrations and can be transmitted either as single- or double-allele variants.
Autographa californica Nucleopolyhedrovirus AC141 (Exon0), a Potential E3 Ubiquitin Ligase, Interacts with Viral Ubiquitin and AC66 To Facilitate Nucleocapsid Egress
Authors: Biswas Siddhartha , Willis Leslie G. , Fang Minggang , Nie Yingchao , Theilmann David A. 
Published: November 2017

ABSTRACT

During the infection cycle of Autographa californica multiple nucleopolyhedrovirus (AcMNPV), two forms of virions are produced, budded virus (BV) and occlusion-derived virus (ODV). Nucleocapsids that form BV have to egress from the nucleus, whereas nucleocapsids that form ODV remain inside the nucleus. The molecular mechanism that determines whether nucleocapsids remain inside or egress from the nucleus is unknown. AC141 (a predicted E3 ubiquitin ligase) and viral ubiquitin (vUbi) have both been shown to be required for efficient BV production. In this study, it was hypothesized that vUbi interacts with AC141, and in addition, that this interaction was required for BV production. Deletion of both
ac141
and
vubi
restricted viral infection to a single cell, and BV production was completely eliminated. AC141 was ubiquitinated by either vUbi or cellular Ubi, and this interaction was required for optimal BV production. Nucleocapsids in BV, but not ODV, were shown to be specifically ubiquitinated by vUbi, including a 100-kDa protein, as well as high-molecular-weight conjugates. The viral ubiquitinated 100-kDa BV-specific nucleocapsid protein was identified as AC66, which is known to be required for BV production and was shown by coimmunoprecipitation and mass spectrometry to interact with AC141. Confocal microscopy also showed that AC141, AC66, and vUbi interact at the nuclear periphery. These results suggest that ubiquitination of nucleocapsid proteins by vUbi functions as a signal to determine if a nucleocapsid will egress from the nucleus and form BV or remain in the nucleus to form ODV.

IMPORTANCE
Baculoviruses produce two types of virions called occlusion-derived virus (ODV) and budded virus (BV). ODVs are required for oral infection, whereas BV enables the systemic spread of virus to all host tissues, which is critical for killing insects. One of the important steps for BV production is the export of nucleocapsids out of the nucleus. This study investigated the molecular mechanisms that enable the selection of nucleocapsids for nuclear export instead of being retained within the nucleus, where they would become ODV. Our data show that ubiquitination, a universal cellular process, specifically tags nucleocapsids of BV, but not those found in ODV, using a virus-encoded ubiquitin (vUbi). Therefore, ubiquitination may be the molecular signal that determines if a nucleocapsid is destined to form a BV, thus ensuring lethal infection of the host.
Refactoring the Genetic Code for Increased Evolvability
Authors: Pines Gur , Winkler James D. , Pines Assaf , Gill Ryan T. 
Published: November 2017

ABSTRACT
The standard genetic code is robust to mutations during transcription and translation. Point mutations are likely to be synonymous or to preserve the chemical properties of the original amino acid. Saturation mutagenesis experiments suggest that in some cases the best-performing mutant requires replacement of more than a single nucleotide within a codon. These replacements are essentially inaccessible to common error-based laboratory engineering techniques that alter a single nucleotide per mutation event, due to the extreme rarity of adjacent mutations. In this theoretical study, we suggest a radical reordering of the genetic code that maximizes the mutagenic potential of single nucleotide replacements. We explore several possible genetic codes that allow a greater degree of accessibility to the mutational landscape and may result in a hyperevolvable organism that could serve as an ideal platform for directed evolution experiments. We then conclude by evaluating the challenges of constructing such recoded organisms and their potential applications within the field of synthetic biology.

IMPORTANCE
The conservative nature of the genetic code prevents bioengineers from efficiently accessing the full mutational landscape of a gene via common error-prone methods. Here, we present two computational approaches to generate alternative genetic codes with increased accessibility. These new codes allow mutational transitions to a larger pool of amino acids and with a greater extent of chemical differences, based on a single nucleotide replacement within the codon, thus increasing evolvability both at the single-gene and at the genome levels. Given the widespread use of these techniques for strain and protein improvement, along with more fundamental evolutionary biology questions, the use of recoded organisms that maximize evolvability should significantly improve the efficiency of directed evolution, library generation, and fitness maximization.
Non-acid gastro-oesophageal reflux is associated with squamous cell carcinoma of the oesophagus
Authors: Kgomo Mpho , Mokoena Taole R , Ker James A 
Published: November 2017

IntroductionSquamous cell carcinoma of the oesophagus is a common cancer among South Africans. Due to the absence of effective screening and surveillance programme for early detection and late presentation, squamous cell carcinoma of the oesophagus is usually diagnosed at an advanced stage or when metastasis has already occurred. The 5-year survival is often quoted at 5%–10%, which is poor.ObjectivesTo determine the association between oesophageal squamous cell carcinoma (OSCC) and non-acid gastro-oesophageal reflux disease.MethodsStudy designA cross-sectional case–control analytical study of patients referred to the Gastroenterology Division of Steve Biko Academic Hospital in Pretoria, South Africa. All patients had combined multichannel impedance and pH studies done and interpreted after upper gastroscopy using the American College of Gastroenterology guidelines by two clinicians.ResultsThirty-two patients with OSCC were recruited: non-acid reflux was found in 23 patients (73%), acid reflux in 2 patients (6%) and 7 patients (22%) had normal multichannel impedance and pH studies.Forty-nine patients matched by age, gender and race were recruited as a control group. Non-acid reflux was found in 11 patients (22%), acid reflux in 31 patients (63%) and 7 patients (14%) had normal multichannel impedance and pH monitoring study.ConclusionThe significance of the association between non-acid reflux and OSCC was tested using χ2, and simple logistic regression was used to adjust for the effects of potential confounders.The OR of developing OSCC in patients with non-acid gastro-oesophageal reflux was 8.8 (95% CI 3.2 to 24.5, P<0.0001) in this South African group.Alcohol and smoking had no effect on these results.
Prevalence of non-communicable disease risk factors among poor shantytown residents in Dhaka, Bangladesh: a community-based cross-sectional survey
Authors: Khalequzzaman Md , Chiang Chifa , Choudhury Sohel Reza , Yatsuya Hiroshi , Al-Mamun Mohammad Abdullah , Al-Shoaibi Abubakr Ahmed Abdullah , Hirakawa Yoshihisa , Hoque Bilqis Amin , Islam Syed Shariful , Matsuyama Akiko , Iso Hiroyasu , Aoyama Atsuko 
Published: November 2017

ObjectivesThis study aims to describe the prevalence of non-communicable disease (NCD) risk factors among the urban poor in Bangladesh.DesignWe conducted a community-based cross-sectional epidemiological study.SettingThe study was conducted in a shantytown in the city of Dhaka. There were 8604 households with 34 170 residents in the community. Those households were categorised into two wealth strata based on the housing structure.ParticipantsThe study targeted residents aged 18–64 years. A total of 2986 eligible households with one eligible individual were selected by simple random sampling stratified by household wealth status. A total of 2551 residents completed the questionnaire survey, and 2009 participated in the subsequent physical and biochemical measurements.Outcome measuresA modified WHO survey instrument was used for assessing behavioural risk factors and physical and biochemical measurements, including glycated haemoglobin (HbA1c). The prevalence of NCD risk factors, such as tobacco use, fruit and vegetable intake, overweight/obesity, hypertension, diabetes (HbA1c ≥6.5%) and dyslipidaemia, was described according to household wealth status and gender differences.ResultsThe prevalence of current tobacco use was 60.4% in men and 23.5% in women. Most of them (90.8%) consumed more than 1 serving of fruits and vegetables per day; however, only 2.1% consumed more than 5 servings. Overweight/obesity was more common in women (39.2%) than in men (18.9%), while underweight was more common in men (21.0%) than in women (7.1%). The prevalence of hypertension was 18.6% in men and 20.7% in women. The prevalence of diabetes was 15.6% in men and 22.5% in women, which was much higher than the estimated national prevalence (7%). The prevalence of raised total cholesterol (≥190 mg/dL) was 25.7% in men and 34.0% in women.ConclusionThe study identified that tobacco use, both overweight and underweight, diabetes, hypertension and dyslipidaemia were prevalent among the urban poor in Bangladesh.
Current status of postnatal depression smartphone applications available on application stores: an information quality analysis
Authors: Zhang Melvyn WB , Ho Roger CM , Loh Alvona , Wing Tracey , Wynne Olivia , Chan Sally Wai Chi , Car Josip , Fung Daniel Shuen Sheng 
Published: November 2017

ObjectivesIt is the aim of the current research to identify some common functionalities of postnatal application, and to determine the quality of the information content of postnatal depression application using validated scales that have been applied for applications in other specialties.Settings and participantsTo determine the information quality of the postnatal depression smartphone applications, the two most widely used smartphone application stores, namely Apple iTunes as well as Google Android Play store, were searched between 20May and 31 May. No participants were involved. The inclusion criteria for the application were that it must have been searchable using the keywords ‘postnatal’, ‘pregnancy’, ‘perinatal’, ‘postpartum’ and ‘depression’, and must be in English language.InterventionThe Silberg Scale was used in the assessment of the information quality of the smartphone applications.Primary and secondary outcomes measureThe information quality score was the primary outcome measure.ResultsOur current results highlighted that while there is currently a myriad of applications, only 14 applications are specifically focused on postnatal depression. In addition, the majority of the currently available applications on the store have only disclosed their last date of modification as well as ownership. There remain very limited disclosures about the information of the authors, as well as the references for the information included in the application itself. The average score for the Silberg Scale for the postnatal applications we have analysed is 3.0.ConclusionsThere remains a need for healthcare professionals and developers to jointly conceptualise new applications with better information quality and evidence base.
Effect of iron and zinc-biofortified pearl millet consumption on growth and immune competence in children aged 12–18 months in India: study protocol for a randomised controlled trial
Authors: Mehta Saurabh , Finkelstein Julia L , Venkatramanan Sudha , Huey Samantha L , Udipi Shobha A , Ghugre Padmini , Ruth Caleb , Canfield Richard L , Kurpad Anura V , Potdar Ramesh D , Haas Jere D 
Published: November 2017

IntroductionBiofortified crops represent a sustainable agricultural solution for the widespread micronutrient malnutrition in India and other resource-limited settings. This study aims to investigate the effect of the consumption of foods prepared with iron- and zinc-biofortified pearl millet (FeZn-PM) by children on biomarkers of iron and zinc status, growth, and immune function.Methods and analysisWe will conduct a randomised controlled feeding trial in identified slums of Mumbai, India among 200 children aged between 12 and 18 months. Children will be randomised to receive foods prepared with the biofortified PM (FeZn-PM, ICTP8203-Fe) or non-biofortified PM. Anthropometric and morbidity data will be gathered every month for 9 months. Biological samples will be collected at baseline, midline and endline to assess iron and zinc status, including haemoglobin, serum ferritin, serum transferrin receptor, serum zinc, C-reactive protein and alpha-1 acid glycoprotein. Biological samples will be archived for future analyses. The midline measurement will be a random serial sample between baseline and endline. Immune function will be assessed at each time point by the measurement of T cell counts and vaccine responses in a subset, respectively.Ethics and disseminationThis study has obtained clearance from the Health Ministry Screening Committee of the Indian Council of Medical Research. Ethical clearance has been obtained from Cornell University’s Institutional Review Board, the Inter System Biomedica Ethics Committee and St John’s Research Institute’s Institutional Ethics Review Board. The results of this study will be disseminated at several research conferences and as published articles in peer-reviewed journals.Trial registration numberClinical trial registration numberNCT02233764. CTRI registration number REF/2014/10/007731.
Inflammatory natalizumab-associated PML: baseline characteristics, lesion evolution and relation with PML-IRIS
Authors: Wattjes Mike P , Wijburg Martijn T , van Eijk Jeroen , Frequin Stephan , Uitdehaag Bernard M J , Barkhof Frederik , Warnke Clemens , Killestein Joep 
Published: November 2017

Background and objectiveNatalizumab-associated progressive multifocal leukoencephalopathy (NTZ-PML) patients may show imaging signs suggestive of inflammation at diagnosis (‘inflammatory PML’), reminiscent of PML-immune reconstitution inflammatory syndrome (PML-IRIS). We investigated the imaging characteristics of inflammatory NTZ-PML lesions and PML-IRIS to determine differentiating and overlapping features.MethodsWe scored the presence, localisation and pattern of imaging characteristics of inflammation on brain MRI scans of inflammatory NTZ-PML patients. The imaging characteristics were followed up until the occurrence of PML-IRIS.ResultsTen out of the 44 NTZ-PML patients included showed signs suggestive of inflammation at the time of diagnosis. The inflammation pattern at diagnosis was similar to the pattern seen at PML-IRIS, with contrast enhancement representing the most frequent sign of inflammation (90% at diagnosis, 100% at PML-IRIS). However, the severity of inflammation differed, with absence of swelling and low frequency of perilesional oedema (10%) at diagnosis, as compared with the PML-IRIS stage (40%).ConclusionPatterns of inflammation at the time of PML diagnosis and at the PML-IRIS stage overlap but differ in their severity of inflammation. This supports histopathological evidence that the inflammation seen at both stages of the same disease shares a similar underlying pathophysiology, representing the immune response to the JC virus to a variable extend.
Illness representations of systemic lupus erythematosus and systemic sclerosis: a comparison of patients, their rheumatologists and their general practitioners
Authors: Arat Seher , Lenaerts Jan L , De Langhe Ellen , Verschueren Patrick , Moons Philip , Vandenberghe Joris , Taelman Veerle , Westhovens Rene 
Published: November 2017

ObjectiveDiscrepancies in illness representations between patients and physicians result in treatment difficulties, decreased well-being of patients and misunderstandings and disrupted communication. Hence, the objective of this study was to compare illness perceptions of individual patients with systemic lupus erythematosus (SLE) and systemic sclerosis (SSc), their rheumatologists and their general practitioners (GPs) and explore potential differences.MethodsThis study has a cross-sectional design. Patients with SLE and SSc, who were followed at the rheumatology department of the University Hospitals Leuven (Belgium), completed the revised Illness Perception Questionnaire which measures patients’ perceptions of their condition and captures nine dimensions. Physicians completed the Revised Illness Perception Questionnaire for Healthcare Professionals which consists of seven dimensions and measures perceptions of the healthcare professional regarding the disease of their patients. Intraclass correlation was performed to examine relationships between pairs of respondents; Cohen’s d was used for estimating the magnitude of the difference.ResultsQuestionnaires were sent to 284 patients of whom 241 (113 SSc and 128 SLE patients) were included. Five rheumatologists and 160 GPs participated. For both diseases, positive correlations were found for ‘consequences’, ‘illness coherence’ and ‘emotional representations’ among patients, rheumatologists and GPs. GPs scored higher on the ‘consequences’ of these diseases for the patient (d=0.71 for SLE; d=0.80 for SSc). Differences between rheumatologists and GPs were small for SSc and moderate to large for ‘consequences’ (d=0.56) and ‘timeline acute/chronic’ (d=0.95) in SLE with higher scores for GPs.ConclusionsFor both diseases and among the three groups, significant correlations are detected for the dimensions ‘consequences’, ‘illness coherence’ and ‘emotional representations’. Differences between rheumatologists and GPs were mainly detected in the case of SLE patients. This can have implications for the collaboration between these two groups of physicians in daily clinical practice.Clinical trial registrationNCT02655640; Pre-results.
Experimental determination of the field shift factor and the mass shift coefficient for the 1S0–3P1 spin-forbidden transition at 791 nm in neutral barium
Authors: Yu Geng-Hua , Yan Hui , Zhong Jia-Qi , Liu Hong , Zhu Xiao-Ling , Yang Wei 
Published: November 2017

The experimental measurements of the isotope shifts (ISs) for the 1S0–3P1 spin-forbidden transition at 791 nm in neutral barium have been carried out with a thermal barium atom beam. The hyperfine structure (HFS) constants a and b of the odd isotopes [Formula: see text]Ba and [Formula: see text]Ba for this transition have been extracted from the experimental results: a([Formula: see text]Ba) = 1149.9(1.0) MHz, b([Formula: see text]Ba)= −41.6(0.5) MHz, a([Formula: see text]Ba) = 1028.0(1.0) MHz, b([Formula: see text]Ba) = −27.5(0.5) MHz. The measured IS results with the reference isotope [Formula: see text]Ba are 183.7(1.0) MHz ([Formula: see text]Ba–[Formula: see text]Ba), 108.5(0.3) MHz ([Formula: see text]Ba–[Formula: see text]Ba) and 218.9(1.0) MHz ([Formula: see text]Ba–[Formula: see text]Ba). Our IS measurements are in good agreement with the previous experiments. The field shift (FS) factor [Formula: see text] and the mass shift (MS) coefficient [Formula: see text] for this spin-forbidden transition have be determined experimentally as −3.19(4) GHz ⋅ fm[Formula: see text] and −242(20) GHz ⋅ amu, respectively. The results provided herein could be used for further checks theoretically and experimentally, and could also contribute to the study on the nuclear structure of the barium isotopic nuclei.