bluuebunny/crossref_metadata_2025_split huggingface dataset:
Similarity measurement of lung masses for medical image retrieval using kernel based semisupervised distance metric
Authors: Wei Guohui , Ma He , Qian Wei , Qiu Min 
Published: November 2016

Purpose:To develop a new algorithm to measure the similarity between the query lung mass and reference lung mass data set for content‐based medical image retrieval (CBMIR).Methods:A lung mass data set including 746 mass regions of interest (ROIs) was assembled. Among them, 375 ROIs depicted malignant lesions and 371 depicted benign lesions. Each mass ROI is represented by a vector of 26 texture features. A kernel function was employed to map the original data in input space to a feature space. In this space, a semisupervised distance metric was learned, which used differential scatter discriminant criterion to represent the semantic relevance, and the regularization term to represent the visual similarity. The learned distance metric can measure the similarity of the query mass and reference mass data set. The clustering accuracy is used to configure the parameters. The retrieval accuracy and classification accuracy are used as the performance assessment index.Results:After configuring the parameters, a mean clustering accuracy of 0.87 can be achieved. For retrieval accuracy, our algorithm achieves better performance than other state‐of‐the‐art retrieval algorithms when applying a leave‐one‐out validation method to the testing data set. For classification accuracy, the area under the ROC curve of our algorithm can be achieved as 0.941 ± 0.006. The running times of 346 query images with the proposed algorithm are 5.399 and 6.0 s, respectively.Conclusions:The study results demonstrated the proposed algorithm outperforms the compared algorithms, when taking the semantic relevant and visual similarity into account in kernel space. The algorithm can be used in a CBMIR system for a query mass to retrieve similarity masses, which can help doctors make better decisions.
Detection of Isoniazid-, Fluoroquinolone-, Amikacin-, and Kanamycin-Resistant Tuberculosis in an Automated, Multiplexed 10-Color Assay Suitable for Point-of-Care Use
Authors: Chakravorty Soumitesh , Roh Sandy S. , Glass Jennifer , Smith Laura E. , Simmons Ann Marie , Lund Kevin , Lokhov Sergey , Liu Xin , Xu Peng , Zhang Guolong , Via Laura E. , Shen Qingyu , Ruan Xianglin , Yuan Xing , Zhu Hong Zhu , Viazovkina Ekaterina , Shenai Shubhada , Rowneki Mazhgan , Lee Jong Seok , Barry Clifton E. , Gao Qian , Persing David , Kwiatkawoski Robert , Jones Martin , Gall Alexander , Alland David 
Published: November 2016

ABSTRACT

Extensively drug-resistant (XDR) tuberculosis (TB) cannot be easily or quickly diagnosed. We developed a rapid, automated assay for the detection of XDR-TB plus resistance to the drug isoniazid (INH) for point-of-care use. Using a simple filter-based cartridge with an integrated sample processing function, the assay identified a wide selection of wild-type and mutant sequences associated with XDR-TB directly from sputum. Four new large-Stokes-shift fluorophores were developed. When these four Stokes-shift fluorophores were combined with six conventional fluorophores, 10-color probe detection in a single PCR tube was enabled. A new three-phase, double-nested PCR approach allowed robust melting temperature analysis with enhanced limits of detection (LODs). Finally, newly designed sloppy molecular beacons identified many different mutations using a small number of probes. The assay correctly distinguished wild-type sequences from 32 commonly occurring mutant sequences tested in
gyrA
,
gyrB
,
katG
, and
rrs
genes and the promoters of
inhA
and
eis
genes responsible for resistance to INH, the fluoroquinolone (FQ) drugs, amikacin (AMK), and kanamycin (KAN). The LOD was 300 CFU of
Mycobacterium tuberculosis
in 1 ml sputum. The rate of detection of heteroresistance by the assay was equivalent to that by Sanger sequencing. In a blind study of 24 clinical sputum samples, resistance mutations were detected in all targets with 100% sensitivity, with the specificity being 93.7 to 100%. Compared to the results of phenotypic susceptibility testing, the sensitivity of the assay was 75% for FQs and 100% each for INH, AMK, and KAN and the specificity was 100% for INH and FQ and 94% for AMK and KAN. Our approach could enable testing for XDR-TB in point-of-care settings, potentially identifying highly drug-resistant TB more quickly and simply than currently available methods.
Comparison of Clostridium difficile Ribotypes Circulating in Australian Hospitals and Communities
Authors: Furuya-Kanamori Luis , Riley Thomas V. , Paterson David L. , Foster Niki F. , Huber Charlotte A. , Hong Stacey , Harris-Brown Tiffany , Robson Jenny , Clements Archie C. A. 
Published: November 2016

ABSTRACT

Clostridium difficile
infection (CDI) is becoming less exclusively a health care-associated CDI (HA-CDI). The incidence of community-associated CDI (CA-CDI) has increased over the past few decades. It has been postulated that asymptomatic toxigenic
C. difficile
(TCD)-colonized patients may play a role in the transfer of
C. difficile
between the hospital setting and the community. Thus, to investigate the relatedness of
C. difficile
across the hospital and community settings, we compared the characteristics of symptomatic and asymptomatic host patients and the pathogens from these patients in these two settings over a 3-year period. Two studies were simultaneously conducted; the first study enrolled symptomatic CDI patients from two tertiary care hospitals and the community in two Australian states, while the second study enrolled asymptomatic TCD-colonized patients from the same tertiary care hospitals. A total of 324 patients (96 with HA-CDI, 152 with CA-CDI, and 76 colonized with TCD) were enrolled. The predominant
C. difficile
ribotypes isolated in the hospital setting corresponded with those isolated in the community, as it was found that for 79% of the
C. difficile
isolates from hospitals, an isolate with a matching ribotype was isolated in the community, suggesting that transmission between these two settings is occurring. The toxigenic
C. difficile
strains causing symptomatic infection were similar to those causing asymptomatic infection, and patients exposed to antimicrobials prior to admission were more likely to develop a symptomatic infection (odds ratio, 2.94; 95% confidence interval, 1.20 to 7.14). Our findings suggest that the development of CDI symptoms in a setting without establishment of hospital epidemics with binary toxin-producing
C. difficile
strains may be driven mainly by host susceptibility and exposure to antimicrobials, rather than by
C. difficile
strain characteristics.
Impact of High Diversity of Achromobacter Populations within Cystic Fibrosis Sputum Samples on Antimicrobial Susceptibility Testing
Authors: Dupont Chloé , Jumas-Bilak Estelle , Michon Anne-Laure , Chiron Raphaël , Marchandin Hélène 
Published: November 2016

ABSTRACT

Chronic colonization by opportunistic environmental bacteria is frequent in the airways of cystic fibrosis (CF) patients. Studies of
Pseudomonas aeruginosa
evolution during persistence have highlighted the emergence of pathoadaptive genotypes and phenotypes, leading to complex and diversified inpatient colonizing populations also observed at the intraspecimen level. Such diversity, including heterogeneity in resistance profiles, has been considered an adaptive strategy devoted to host persistence. Longitudinal genomic diversity has been shown for the emergent opportunistic pathogen
Achromobacter
, but phenotypic and genomic diversity has not yet been studied within a simple CF sputum sample. Here, we studied the genomic diversity and antimicrobial resistance heterogeneity of 132
Achromobacter
species strains (8 to 27 strains of identical or distinct colonial morphotypes per specimen) recovered from the sputum samples of 9 chronically colonized CF patients. We highlighted the high within-sample and within-morphotype diversity of antimicrobial resistance (disk diffusion) and genomic (pulsed-field gel electrophoresis) profiles. No sputum sample included strains with identical pulsotypes or antibiotic susceptibility patterns. Differences in clinical categorization were observed for the 9 patients and concerned 3 to 11 antibiotics, including antibiotics recommended for use against
Achromobacter
. Within-sample antimicrobial resistance heterogeneity, not predictable from colonial morphology, suggested that it may represent a selective advantage against antibiotics in an
Achromobacter
persisting population and potentially compromise the antibiotic management of CF airway infections.
Optimal Periprosthetic Tissue Specimen Number for Diagnosis of Prosthetic Joint Infection
Authors: Peel Trisha N. , Spelman Tim , Dylla Brenda L. , Hughes John G. , Greenwood-Quaintance Kerryl E. , Cheng Allen C. , Mandrekar Jayawant N. , Patel Robin 
Published: November 2016

ABSTRACT

We recently demonstrated improved sensitivity of prosthetic joint infection (PJI) diagnosis using an automated blood culture bottle system for periprosthetic tissue culture [T. N. Peel et al., mBio 7(1):e01776-15, 2016,
https://doi.org/10.1128/mBio.01776-15
]. This study builds on the prior research by examining the optimal number of periprosthetic tissue specimens required for accurate PJI diagnosis. Current guidelines recommend five to six, which is impractical. We applied Bayesian latent class modeling techniques for estimating diagnostic test properties of conventional culture techniques (aerobic and anaerobic agars and thioglycolate broth) compared to inoculation into blood culture bottles. Conventional, frequentist receiver operating characteristic curve analysis was conducted as a sensitivity analysis. The study was conducted at Mayo Clinic, Rochester, MN, from August 2013 through April 2014 and included 499 consecutive patients undergoing revision arthroplasty from whom 1,437 periprosthetic tissue samples were collected and processed. For conventional periprosthetic tissue culture techniques, the greatest accuracy was observed when four specimens were obtained (91%; 95% credible interval, 77 to 100%), whereas when using inoculation of periprosthetic tissues into blood culture bottles, the greatest accuracy of diagnosis was observed when three specimens were cultured (92%; 95% credible intervals, 79 to 100%). Results of this study show that the greatest accuracy of PJI diagnosis is obtained when three periprosthetic tissue specimens are obtained and inoculated into blood culture bottles or four periprosthetic tissue specimens are obtained and cultured using standard plate and broth cultures. Increasing the number of specimens to five or more, per current recommendations, does not improve accuracy of PJI diagnosis.
Virion Background and Efficiency of Virion Incorporation Determine Susceptibility of Simian Immunodeficiency Virus Env-Driven Viral Entry to Inhibition by IFITM Proteins
Authors: Wrensch Florian , Hoffmann Markus , Gärtner Sabine , Nehlmeier Inga , Winkler Michael , Pöhlmann Stefan 
Published: November 2016

ABSTRACT
Interferon-induced transmembrane proteins (IFITMs) can inhibit the cellular entry of several enveloped viruses, including simian immunodeficiency virus (SIV). The blockade of SIV by IFITMs is isolate specific, raising the question of which parameters impact sensitivity to IFITM. We show that the virion context in which SIV-Env is presented and the efficiency of virion incorporation determine Env susceptibility to inhibition by IFITMs. Thus, determinants other than the nature of the envelope protein can impact the IFITM sensitivity of viral entry.

IMPORTANCE
The host cell-encoded IFITM proteins can block viral entry and are an important component of the innate defenses against viral infection. However, the determinants controlling whether a virus is susceptible to blockade by IFITM proteins are incompletely understood. Our study shows that the amount of envelope proteins incorporated into virions as well as the nature of the virion particle itself can impact the sensitivity of viral entry to IFITMs. These results show for the first time that determinants other than the viral envelope protein can impact sensitivity to IFITM and have implications for the interpretation of previously published data on inhibition of viruses by IFITM proteins. Moreover, our findings might help to define the mechanism underlying the antiviral activity of IFITM proteins.
Porcine Epidemic Diarrhea Virus 3C-Like Protease-Mediated Nucleocapsid Processing: Possible Link to Viral Cell Culture Adaptability
Authors: Jaru-Ampornpan Peera , Jengarn Juggragarn , Wanitchang Asawin , Jongkaewwattana Anan 
Published: November 2016

ABSTRACT

Porcine epidemic diarrhea virus (PEDV) causes severe diarrhea and high mortality rates in newborn piglets, leading to massive losses to the swine industry worldwide during recent epidemics. Intense research efforts are now focusing on defining viral characteristics that confer a growth advantage, pathogenicity, or cell adaptability in order to better understand the PEDV life cycle and identify suitable targets for antiviral or vaccine development. Here, we report a unique phenomenon of PEDV nucleocapsid (N) cleavage by the PEDV-encoded 3C-like protease (3Cpro) during infection. The identification of the 3Cpro cleavage site at the C terminus of N supported previous observations that PEDV 3Cpro showed a substrate requirement slightly different from that of severe acute respiratory syndrome coronavirus (SARS-CoV) 3Cpro and revealed a greater flexibility in its substrate recognition site. This cleavage motif is present in the majority of cell culture-adapted PEDV strains but is missing in emerging field isolates. Remarkably, reverse-genetics-derived cell culture-adapted PEDV
AVCT12
harboring uncleavable N displayed growth retardation in Vero E6-APN cells compared to the wild-type virus. These observations altogether shed new light on the investigation and characterization of the PEDV nucleocapsid protein and its possible link to cell culture adaptation.

IMPORTANCE
Recurrent PEDV outbreaks have resulted in enormous economic losses to swine industries worldwide. To gain the upper hand in combating this disease, it is necessary to understand how this virus replicates and evades host immunity. Characterization of viral proteins provides important clues to mechanisms by which viruses survive and spread. Here, we characterized an intriguing phenomenon in which the nucleocapsids of some PEDV strains are proteolytically processed by the virally encoded main protease. Growth retardation in recombinant PEDV carrying uncleavable N suggests a replication advantage provided by the cleavage event, at least in the cell culture system. These findings may direct us to a more complete understanding of PEDV replication and pathogenicity.
The Microminipig as an Animal Model for Influenza A Virus Infection
Authors: Iwatsuki-Horimoto Kiyoko , Nakajima Noriko , Shibata Masatoshi , Takahashi Kenta , Sato Yuko , Kiso Maki , Yamayoshi Seiya , Ito Mutsumi , Enya Satoko , Otake Masayoshi , Kangawa Akihisa , da Silva Lopes Tiago Jose , Ito Hirotaka , Hasegawa Hideki , Kawaoka Yoshihiro 
Published: November 2016

ABSTRACT
Pigs are considered a mixing vessel for the generation of novel pandemic influenza A viruses through reassortment because of their susceptibility to both avian and human influenza viruses. However, experiments to understand reassortment in pigs in detail have been limited because experiments with regular-sized pigs are difficult to perform. Miniature pigs have been used as an experimental animal model, but they are still large and require relatively large cages for housing. The microminipig is one of the smallest miniature pigs used for experiments. Introduced in 2010, microminipigs weigh around 10 kg at an early stage of maturity (6 to 7 months old) and are easy to handle. To evaluate the microminipig as an animal model for influenza A virus infection, we compared the receptor distribution of 10-week-old male pigs (Yorkshire Large White) and microminipigs. We found that both animals have SAα2,3Gal and SAα2,6Gal in their respiratory tracts, with similar distributions of both receptor types. We further found that the sensitivity of microminipigs to influenza A viruses was the same as that of larger miniature pigs. Our findings indicate that the microminipig could serve as a novel model animal for influenza A virus infection.

IMPORTANCE
The microminipig is one of the smallest miniature pigs in the world and is used as an experimental animal model for life science research. In this study, we evaluated the microminipig as a novel animal model for influenza A virus infection. The distribution of influenza virus receptors in the respiratory tract of the microminipig was similar to that of the pig, and the sensitivity of microminipigs to influenza A viruses was the same as that of miniature pigs. Our findings suggest that microminipigs represent a novel animal model for influenza A virus infection.
‘Now I care’: a qualitative study of how overweight adolescents managed their weight in the transition to adulthood
Authors: Sweeting Helen , Smith Emily , Neary Joanne , Wright Charlotte 
Published: November 2016

ObjectivesA qualitative study of recalled experiences of early adolescent overweight/obesity revealed low levels of weight-related concern. This further analysis aimed to explore weight-related concern and weight-loss efforts as participants transitioned into adulthood.Design, participants and methodsParticipants were 35 young adults from a population-based cohort study who had body mass index (BMI) >95th centile between ages 11 and 15 and participated in semistructured interviews aged 24. At age 24, they were categorised as: ‘slimmers’ (N=13) who had lower BMI Z-scores at 24 than their adolescent peak and were not obese (BMI<30 kg/m2); ‘relapsers’ (N=8, of whom 2 were morbidly obese (BMI>35 kg/m2) at age 24); ‘stable’ (N=3, of whom 1 morbidly obese); and ‘gainers’ (N=11, of whom 5 morbidly obese). Themes were identified and coded using NVivo qualitative data analysis software, blind to participants’ current weight status.ResultsContrasting with the lack of concern recalled in respect of earlier adolescence, weight-related concerns and/or desire to lose weight generally increased around the time of school leaving and almost all participants described some form of exercise (formal/informal) and dietary weight-control strategies. Among ‘slimmers’, there was some (subtle) evidence of more consistent use of exercise, self-monitoring of diet and exercise and of lifestyle changes becoming habitual and/or part of identity. Few participants had accessed professional support. Diet clubs seemed to have been used most by ‘gainers’, some only recently. Labour-market and housing transitions were strong influences, described as facilitating weight losses by some, but increases by others. For some participants, it appeared that weight loss was simply a by-product of these transitions.ConclusionsIn contrast to earlier adolescence, even the heaviest participants tended to show actual weight loss action or preparation for action. The transition to adulthood could thus be a key life stage for interventions.
How do community health committees contribute to capacity building for maternal and child health? A realist evaluation protocol
Authors: Gilmore Brynne , McAuliffe Eilish , Larkan Fiona , Conteh Magnus , Dunne Nicola , Gaudrault Michele , Mollel Henry , Tumwesigye Nazarius Mbona , Vallières Frédérique 
Published: November 2016

IntroductionThe proposed research is part of ongoing operations research within World Vision's Access: Infant and Maternal Health Programme. This study aims to identify key context features and underlying mechanisms through which community health committees build community capacity within the field of maternal and child health. This may help to improve programme implementation by providing contextually informed and explanatory findings forhowcommunity health committees work,whatworks best and forwhomdo they work for best for. Though frequently used within health programmes, little research is carried out on such committees’ contribution to capacity building—a frequent goal or proposed outcome of these groups.Methods and analysisThe scarce information that does exist often fails to explain ‘how, why, and for whom’ these committees work best. Since such groups typically operate within or as components of complex health interventions, they require a systems thinking approach and design, and thus so too does their evaluation. Using a mixed methods realist evaluation with intraprogramme case studies, this protocol details a proposed study on community health committees in rural Tanzania and Uganda to better understand underlying mechanisms through which these groups work (or do not) to build community capacity for maternal and child health. This research protocol follows the realist evaluation methodology of eliciting initial programme theories, to inform the field study design, which are detailed within. Thus far, the methodology of a realist evaluation has been well suited to the study of community health committees within these contexts. Implications for its use within these contexts are discussed within.Ethics and disseminationInstitutional Review Boards and the appropriate research clearance bodies within Ireland, Uganda and Tanzania have approved this study. Planned dissemination activities include via academic and programme channels, as well as feedback to the communities in which this work occurs.
Are housing tenure and car access still associated with health? A repeat cross-sectional study of UK adults over a 13-year period
Authors: Ellaway A , Macdonald L , Kearns A 
Published: November 2016

BackgroundIt is usually assumed that housing tenure and car access are associated with health simply because they are acting as markers for social class or income and wealth. However, previous studies conducted in the late 1990s found that these household assets were associated with health independently of social class and income. Here, we set out to examine if this is still the case.MethodsWe use data from our 2010 postal survey of a random sample of adults (n=2092) in 8 local authority areas in the West of Scotland. Self-reported health measures included limiting longstanding illness (LLSI), general health over the last year and the Hospital Anxiety and Depression Scale.ResultsWe found a statistically significant relationship between housing tenure and all 4 health measures, regardless of the inclusion of social class or income as controls. Compared with owner occupiers, social renters were more likely to report ill-health (controlling for social class—LLSI OR: 3.24, general health OR: 2.82, anxiety η2: 0.031, depression η2: 0.048, controlling for income—LLSI OR: 3.28, general health OR: 2.82, anxiety η2: 0.033, depression η2: 0.057) (p<0.001 for all models). Car ownership was independently associated with depression and anxiety, with non-owners at higher risk of both (controlling for income—anxiety η2: 0.010, depression η2: 0.023, controlling for social class—anxiety η2: 0.013, depression η2: 0.033) (p<0.001 for all models).ConclusionsOur results show that housing tenure and car ownership are still associated with health, after taking known correlates (age, sex, social class, income) into account. Further research is required to unpack some of the features of these household assets such as the quality of the dwelling and access to and use of different forms of transport to determine what health benefits or disbenefits they may be associated with in different contexts.