bluuebunny/crossref_metadata_2025_split huggingface dataset:
Misidentifying Helicobacters: the
Helicobacter cinaedi
Example
Authors: Vandamme Peter , Harrington Clare S. , Jalava Katri , On Stephen L. W. 
Published: March 2020

ABSTRACT

Whole-cell protein electrophoresis and biochemical examination by means of a panel of 64 tests were used to identify 14 putative helicobacters to the species level. The results were confirmed by means of DNA-DNA hybridization experiments and were used to discuss misidentification of helicobacters based on 16S rRNA gene sequence data. The data indicated that comparison of near-complete 16S ribosomal DNA sequences does not always provide conclusive evidence for species level identification and may prove highly misleading. The data also indicated that “
Helicobacter westmeadii
” is a junior synonym of
Helicobacter cinaedi
and that
Helicobacter
sp. strain Mainz belongs to the same species.
H. cinaedi
occurs in various animal reservoirs, including hamsters, dogs, cats, rats, and foxes. Appropriate growth conditions and identification strategies will be required to establish the genuine significance of this widely distributed
Helicobacter
species.
Comparative Evaluation of Three Different Genotyping Methods for Investigation of Nosocomial Outbreaks of Legionnaires' Disease in Hospitals
Authors: Jonas Daniel , Meyer Heinz-Georg W. , Matthes Philipp , Hartung Doris , Jahn Bernhard , Daschner Franz D. , Jansen Bernd 
Published: March 2020

ABSTRACT

The increased incidence of nosocomial Legionnaires' disease in two hospitals prompted investigation of possible environmental sources. In the search for an effective DNA-typing technique for use in hospital epidemiology, the performance and convenience of three methods—
Sfi
I macrorestriction analysis (MRA), amplified fragment length polymorphism (AFLP), and arbitrarily primed PCR (AP-PCR)—were compared. Twenty-nine outbreak-associated and eight nonassociated strains of
Legionella pneumophila
with 13 MRA types and subtypes were investigated. These strains comprised isolates from bronchoalveolar lavages, from environmental, patient-related sources, and type strains. All three typing methods detected one predominant genotype associated with the outbreaks in both hospitals. All of them correctly assigned epidemiologically associated, environmental isolates to their respective patient specimens. AP-PCR was the least discriminating and least reproducible technique. In contrast, AFLP was demonstrated as being the method with the best interassay reproducibility (90%) and concordance (94%) in comparison to the genotyping standard of MRA and the epidemiological data. Analysis of AFLP fragments revealed 12 different types and subtypes. Because of its simplicity and reproducibility, AFLP proved to be the most effective technique in outbreak investigation.
Comparison of a New Colorimetric Assay with the NCCLS Broth Microdilution Method (M-27A) for Antifungal Drug MIC Determination
Authors: Li R. K. , Elie C. M. , Clayton G. E. , Ciblak M. A. 
Published: March 2020

ABSTRACT

We evaluated a new microtiter assay for antifungal susceptibility testing based on a colorimetric reaction to monitor fungal substrate utilization. This new method (rapid susceptibility assay [RSA]) provides quantitative endpoint readings in less than 8 h compared with visual determination of MIC by the National Committee for Clinical Laboratory Standards (NCCLS) broth microdilution method, which requires a minimum of 48 h of incubation. In this study, we tested clinical isolates from each of the following species:
Candida albicans
(20 isolates),
C. glabrata
(20 isolates),
C. krusei
(19 isolates),
C. tropicalis
(19 isolates), and
C. parapsilosis
(28 isolates). RSA and NCCLS broth dilution methods were used to determine the MICs of amphotericin B, fluconazole, itraconazole, and 5-flucytosine for all 106 isolates. RPMI 1640 medium buffered with morpholinopropanesulfonic acid was used for both methods; however, glucose and inoculum concentrations in the RSA were modified. RSA MICs were determined as the lowest drug concentration that prevented glucose consumption by the organism after 6 h of incubation. MICs obtained from the RSA were compared with those obtained from the NCCLS M-27A method read at 24 and 48 h. MIC pairs were considered in agreement when the difference between the pairs was within 2 twofold dilutions. For the 106 isolates tested, amphotericin B and 5-flucytosine demonstrated the highest agreement in MICs between the two methods (100 and 98%, respectively), whereas fluconazole and itraconazole produced less favorable MIC agreement (63.2 and 61.3%, respectively). The azole MIC differences between the two methods were significantly reduced when lower inocula were used with a prolonged incubation time. This preliminary comparison suggests that this rapid procedure may be a reliable tool for the in vitro determination of MICs of amphotericin B and 5-flucytosine and warrants further evaluation.
Retrospective Identification and Characterization of
Candida dubliniensis
Isolates among
Candida albicans
Clinical Laboratory Isolates from Human Immunodeficiency Virus (HIV)-Infected and Non-HIV-Infected Individuals
Authors: Jabra-Rizk M. A. , Falkler W. A. , Merz W. G. , Baqui A. A. M. A. , Kelley J. I. , Meiller T. F. 
Published: March 2020

ABSTRACT

Fungal opportunistic infections, and in particular those caused by the various
Candida
species, have gained considerable significance as a cause of morbidity and, often, mortality. The newly described species
Candida dubliniensis
phenotypically resembles
Candida albicans
so closely that it is easily misidentified as such. The present study was designed to determine the frequency at which this new species is not recognized in the clinical laboratory, to determine the patient populations with which
C. dubliniensis
is associated, to determine colonization versus infection frequency, and to assess fluconazole resistance. Over a 2-year period, 1,251 isolates that were initially identified as
C. albicans
by a hospital clinical laboratory were reevaluated for
C. dubliniensis
by inability to grow at 45°C, colony color on CHROMagar Candida medium, coaggregation assay with
Fusobacterium nucleatum
, and sugar assimilation profiles (API 20C AUX yeast identification system). A total of 15 (1.2%) isolates from 12 patients were identified as
C. dubliniensis
. Ten of the patients were found to be immunocompromised (these included patients with human immunodeficiency virus infection or AIDS, cancer patients receiving chemotherapy, and patients awaiting transplantation). Thirteen isolates were highly susceptible to fluconazole (MIC, <0.5 μg/ml). Three isolates from one patient, genotypically confirmed as the same strain, showed variable susceptibility to fluconazole. The first isolate was susceptible, whereas the other two isolates were dose-dependent susceptible (MIC, 16.0 μg/ml). These data confirm the close association of
C. dubliniensis
with immunocompromised states and that increased fluconazole MICs may develop in vivo. This study emphasizes the importance of screening germ-tube-positive yeasts for the inability to grow at 45°C followed by confirmatory tests in order to properly identify this species.
Relationship of Genetic Type of Shiga Toxin to Manifestation of Bloody Diarrhea due to Enterohemorrhagic
Escherichia coli
Serogroup O157 Isolates in Osaka City, Japan
Authors: Nishikawa Y. , Zhou Z. , Hase A. , Ogasawara J. , Cheasty T. , Haruki K. 
Published: March 2020

ABSTRACT

One hundred sixty-nine strains of enterohemorrhagic
Escherichia coli
serogroup O157 were examined for the correlation between the genotype of their Shiga toxin genes (
stx
) and manifestation of bloody diarrhea (BD). It was shown that the strains carrying only
stx2vha
were probably less virulent and caused BD less frequently.
Evaluation of meridional scans for angle closure assessment with anterior segment swept-source optical coherence tomography
Authors: Porporato Natalia , Baskaran Mani , Perera Shamira , Tun Tin A , Sultana Rehena , Tan Marcus , Quah Joanne HuiMin , Allen John C , Friedman David , Cheng Ching Yu , Aung Tin 
Published: March 2020

Background/aimsAs swept-source optical coherence tomography (SS-OCT) simultaneously obtains 128 meridional scans, it is important to identify which scans are playing the main role in classifying gonioscopic angle closure to simplify the analysis. We aimed to evaluate the diagnostic performance of every meridional scan in its ability to detect gonioscopic angle closure.MethodsObservational study with 2027 phakic subjects consecutively recruited from a community polyclinic. Gonioscopy and SS-OCT were performed. Gonioscopic angle closure was defined as non-visibility of the posterior trabecular meshwork in ≥180° of the angle, while SS-OCT was defined as iridotrabecular contact anterior to the scleral spur. The area under the receiver operating characteristic curve (AUC) was calculated to assess the diagnostic performance of each single scan, the sequential anticlockwise cumulative effect of those single scans and different combinations of them.ResultsThe AUCs of each scan ranged from 0.73 to 0.82. The single scan at 80°–260° had the highest AUC (0.82, 95% CI 0.79 to 0.84) and performed significantly better than most of the temporonasal scans (from 0° to 52° and from 153° to 179°). The superoinferior scans achieved higher AUCs compared with the temporonasal ones. When assessing the cumulative effect of adding individual scans consecutively, the peak AUC (0.80) was obtained when considering the superoinferior scans closer to 80°–85°, but no further positive cumulative effect was seen when adding the rest of the temporonasal scans of the circumference.ConclusionsIn conclusion, the single SS-OCT scan at 80°–260° had the highest diagnostic performance. Our study suggests that the 360° evaluation may not translate to better clinical utility for detection of gonioscopic angle closure.
Tackling HTLV-1 infection in ophthalmology: a nationwide survey of ophthalmic care in an endemic country, Japan
Authors: Kamoi Koju , Okayama Akihiko , Izumo Shuji , Hamaguchi Isao , Uchimaru Kaoru , Tojo Arinobu , Watanabe Toshiki , Ohno-Matsui Kyoko 
Published: March 2020

IntroductionJapan is the most endemic of the developed nations in terms of human T-lymphotropic virus type 1 (HTLV-1) infection. Japan has been tackling HTLV-1 infection and has made remarkable progress. In ophthalmology, awareness of the association between HTLV-1 infection and uveitis has been increasing since the 1990s, when the relationship was first established. Here, we describe a nationwide survey and analysis of the current state of medical care for HTLV-1-associated uveitis (HAU) at ophthalmic facilities in Japan.MethodsA questionnaire survey covered all university hospitals in Japan that were members of the Japanese Ophthalmological Society and all regional core facilities that were members of the Japanese Ocular Inflammation Society. Survey data were collected, and nationwide data on the state of medical care for HAU were tallied and analysed.ResultsOf the 115 facilities, 69 (60.0%) responded. HAU was most commonly diagnosed ‘based on blood tests and characteristic ophthalmic findings’. Overall, 86.8% of facilities perform testing for HTLV-1 antibodies during medical care for diagnosing uveitis, with 58.3% routinely performing testing. Facilities with experience in providing medical care for HAU accounted for 67.6%. The survey also revealed that 85.5% of facilities had seen no decrease in the number of patients with HAU.ConclusionsIn the two decades since the establishment of HAU as a pathological entity, the majority of facilities in Japan have started performing testing for HTLV-1 antibodies when considering differential diagnoses for uveitis. Our data suggest that providing information on HTLV-1 infection to ophthalmologists in Japan has been successfully implemented.
Cultural adaptation of a patient decision-aid for insulin therapy
Authors: Tan Ngiap Chuan , Koong Ying Leng Agnes , Phoon Kwong Yun Ian , Wang Zhen Sinead , Paulpandi Muthulakshmi , Lee Yew Kong , Furler John , Car Josip , Ng Chirk Jenn 
Published: March 2020

IntroductionPatient decision-aids (PDAs) support patients in selecting evidence-based treatment options. PDA is useful only if the user understands the content to make personalised decisions. Cultural adaptation is a process of adjusting health messages so that the information is accurate, relevant and understandable to users from a different population. A PDA has been developed to assist Malaysian patients with secondary drug failure to initiate insulin therapy to control their type 2 diabetes mellitus (T2DM). Likewise, patients with T2DM in neighbouring Singapore face similar barriers in commencing insulin treatment, which a PDA may facilitate decision-making in selecting personalised therapy.ObjectiveThe study aimed to explore the views and perceptions of Singaporean primary care providers on the Malaysia PDA to initiate insulin therapy and described the cultural adaptation process used in the design and development of a new PDA, which would be trialled in a Singapore primary healthcare institution.MethodQualitative research method was deployed to conduct one-to-one in-depth interviews of the healthcare providers at the trial site (SingHealth Polyclinics—SHP), including six primary care physicians and four nurses to gather their views and feedbacks on the Malaysian PDA. The interviews were transcribed, audited and analysed (standard content analysis) to identify themes relating to the content, layout, concerns of the original PDA and suggestions to the design of the new SHP PDA.ResultsCultural adaptation of the new PDA includes change to the overall design, graphics (including pictograms), presentation styles, additional contextualised content (personalisation, subheadings, cost and treatment option), modified phrasing of the subtitles and concerns (choice of words) relevant to the new users.ConclusionA PDA on insulin therapy underwent cultural adaptation before its implementation in another population in a neighbouring country. Its relevance and effectiveness will be evaluated in future research.
Does cannabidiol reduce severe behavioural problems in children with intellectual disability? Study protocol for a pilot single-site phase I/II randomised placebo controlled trial
Authors: Efron Daryl , Taylor Kaitlyn , Payne Jonathan M , Freeman Jeremy L , Cranswick Noel , Mulraney Melissa , Prakash Chidambaram , Lee Katherine J , Williams Katrina 
Published: March 2020

IntroductionSevere behavioural problems (SBPs) are a common contributor to morbidity and reduced quality of life in children with intellectual disability (ID). Current medication treatment for SBP is associated with a high risk of side effects. Innovative and safe interventions are urgently needed. Anecdotal reports and preliminary research suggest that medicinal cannabis may be effective in managing SBP in children with developmental disabilities. In particular, cannabidiol (CBD) may be a plausible and safe alternative to current medications. Families who are in urgent need of solutions are seeking cannabis for their ID children with SBP. However there is no evidence from randomised controlled trials to support the use of CBD for SBP. This pilot study aims to investigate the feasibility of conducting a randomised placebo-controlled trial of CBD to improve SBP in children with ID.Methods and analysisThis is a single-site, double-blind, parallel-group, randomised, placebo-controlled pilot study of 10 participants comparing 98% CBD oil with placebo in reducing SBP in children aged 8–16 years with ID. Eligible participants will be randomised 1:1 to receive either CBD 20 mg/kg/day or placebo for 8 weeks. Data will be collected regarding the feasibility and acceptability of all study components, including recruitment, drop-out rate, study visit attendance, protocol adherence and the time burden of parent questionnaires. Safety outcomes and adverse events will be recorded. All data will be reported using descriptive statistics. These data will inform the design of a full scale randomised controlled trial to evaluate the efficacy of CBD in this patient group.Ethics and disseminationThis protocol has received ethics approval from the Royal Children’s Hospital ethics committee (Human Research Ethics Committee no. 38236). Results will be disseminated through peer-reviewed journals, professional networks, conferences and social media.Trial registration numberACTRN12618001852246
Does peer education go beyond giving reproductive health information? Cohort study in Bulawayo and Mount Darwin, Zimbabwe
Authors: Mangombe Aveneni , Owiti Philip , Madzima Bernard , Xaba Sinokuthemba , Makoni Talent M , Takarinda Kudakwashe C , Timire Collins , Chimwaza Anesu , Senkoro Mbazi , Mabaya Simbarashe , Samuelson Julia , Ameyan Wole , Tapera Talent , Zwangobani Nonhlanhla , Tripathy Jaya Prasad , Kumar Ajay M V 
Published: March 2020

ObjectivePeer education is an intervention within the voluntary medical male circumcision (VMMC)–adolescent sexual reproductive health (ASRH) linkages project in Bulawayo and Mount Darwin, Zimbabwe since 2016. Little is known if results extend beyond increasing knowledge. We therefore assessed the extent of and factors affecting referral by peer educators and receipt of HIV testing services (HTS), contraception, management of sexually transmitted infections (STIs) and VMMC services by young people (10–24 years) counselled.DesignA cohort study involving all young people counselled by 95 peer educators during October–December 2018, through secondary analysis of routinely collected data.SettingAll ASRH and VMMC sites in Mt Darwin and Bulawayo.ParticipantsAll young people counselled by 95 peer educators.Outcome measuresCensor date for assessing receipt of services was 31 January 2019. Factors (clients’ age, gender, marital and schooling status, counselling type, location, and peer educators’ age and gender) affecting non-referral and non-receipt of services (dependent variables) were assessed by log-binomial regression. Adjusted relative risks (aRRs) were calculated.ResultsOf the 3370 counselled (66% men), 65% were referred for at least one service. 58% of men were referred for VMMC. Other services had 5%–13% referrals. Non-referral for HTS decreased with clients’ age (aRR: ~0.9) but was higher among group-counselled (aRR: 1.16). Counselling by men (aRR: 0.77) and rural location (aRR: 0.61) reduced risks of non-referral for VMMC, while age increased it (aRR ≥1.59). Receipt of services was high (64%–80%) except for STI referrals (39%). Group counselling and rural location (aRR: ~0.52) and male peer educators (aRR: 0.76) reduced the risk of non-receipt of VMMC. Rural location increased the risk of non-receipt of contraception (aRR: 3.18) while marriage reduced it (aRR: 0.20).ConclusionWe found varying levels of referral ranging from 5.1% (STIs) to 58.3% (VMMC) but high levels of receipt of services. Type of counselling, peer educators’ gender and location affected receipt of services. We recommend qualitative approaches to further understand reasons for non-referrals and non-receipt of services.
Holography of massive M2-brane theory with discrete torsion
Authors: Jang Dongmin , Kim Yoonbai , Kwon O-Kab , Tolla D. D. 
Published: March 2020

AbstractWe investigate the gauge/gravity duality between the $$\mathcal{N} = 6$$N=6 mass-deformed ABJ theory with $$\hbox {U}_k(N+l)\times \hbox {U}_{-k}(N)$$Uk(N+l)×U-k(N) gauge symmetry and the 11-dimensional supergravity on LLM geometries with SO(2,1) $$\times $$× SO(4)/$${\mathbb Z}_k\times $$Zk× SO(4)/$${{\mathbb {Z}}}_k$$Zk isometry and the discrete torsion l. For chiral primary operators with conformal dimensions $$\Delta =1,2$$Δ=1,2, we obtain the exact vacuum expectation values using the holographic method in 11-dimensional supergravity and show that the results depend on the shapes of droplet pictures in LLM geometries. The $$\frac{l}{\sqrt{N}}$$lN contributions from the discrete torsion l for several simple droplet pictures in the large N limit are determined in holographic vacuum expectation values. We also explore the effects of the orbifolding $${{\mathbb {Z}}}_k$$Zk and the asymptotic discrete torsion l, on the gauge/gravity duality dictionary and on the nature of the asymptotic limits of the LLM geometries.
Spectroscopy of $$\mathbf {B_c}$$ mesons and the possibility of finding exotic $$\mathbf {B_c}$$-like structures
Authors: Ortega Pablo G. , Segovia Jorge , Entem David R. , Fernández Francisco 
Published: March 2020

AbstractThe bottom-charmed ($$B_c$$Bc) mesons are more stable than their charmonium ($$c{{\bar{c}}}$$cc¯) and bottomium ($$b{{\bar{b}}}$$bb¯) partners because they cannot annihilate into gluons. However, the low production cross-sections and signal-to-background ratios avoided until now their clear identification. The recent experimental results reported by CMS and LHCb at CERN open the possibility of having a $$B_c$$Bc spectrum as complete as the ones of charmonium and bottomonium. Motivated by this expectation, we compute bottom-charmed meson masses in the region energies in which decay meson–meson thresholds are opened, looking for the analogs to the X(3872) in the $$B_c$$Bc spectroscopy. We use a constituent quark model in which quark–antiquark degrees of freedom are complemented by four-body Fock states configurations. The model has been applied to a wide range of hadronic observables, in particular to the X(3872), and thus the model parameters are completely constrained. No extra states are found in the $$J^P=0^+$$JP=0+ and $$J^P=1^+$$JP=1+ sectors. However, in the $$J^P=2^+$$JP=2+ sector we found an additional state very close to the $$D^*B^*$$D∗B∗ threshold which could be experimentally detected.
Dynamical nonextensivity or nonextensive dynamics?
Authors: Rożynek Jacek , Wilk Grzegorz 
Published: March 2020

Abstract
Dense matter is usually described using some kind of mean field theory (MFT) model based on Boltzmann–Gibbs (BG) extensive statistics. However, in many cases the conditions justifying the use of BG statistics are not fulfilled because the systems considered are explicitly nonextensive. In such cases one either enriches the original MFT by adding some dynamical elements violating extensivity (like, for example, long range correlations or intrinsic fluctuations), or one replaces the BG statistics by its nonextensive counterpart characterized by some nonextensivity parameter q ( q≠ 1 and for q → 1 one returns to the extensive situation). In this work, using a simple quasi-particle description of dense matter (with interaction modelled by effective fugacities, z) we discuss the mutual interplay of non-extensiveness and dynamics (i.e., q and z) and estimate the level of nonextensivity of the quark-gluon system described by lattice QCD.