bluuebunny/crossref_metadata_2025_split huggingface dataset:
Draft Genome Assemblies of Xylose-Utilizing
Candida tropicalis
and
Candida boidinii
with Potential Application in Biochemical and Biofuel Production
Authors: Somani Abhishek , Smith Daniel , Hegarty Matthew , Fernandez-Fuentes Narcis , Ravella Sreenivas R. , Gallagher Joe A. , Bryant David N. 
Published: February 2018

ABSTRACT

Non-
albicans Candida
species are growing in prominence in industrial biotechnology due to their ability to utilize hemicellulose. Here, we present the draft genome sequences of an inhibitor-tolerant
Candida tropicalis
strain (Y6604) and
Candida boidinii
NCAIM Y01308
T
.
Complete Genome Sequence of
Mycobacterium
sp. Strain 4858
Authors: Bouam Amar , Levasseur Anthony , Bonnet Maryline , Borand Laurence , Van Goethem Charles , Drancourt Michel , Godreuil Sylvain 
Published: February 2018

ABSTRACT

Mycobacterium
sp. strain 4858 is a nontuberculous mycobacterium isolated from sputum in a Cambodian patient with a pulmonary infection. We report the first complete 5.6-Mbp-long genome sequence of
Mycobacterium
strain 4858, with 68.24% GC content, carrying 5,255 protein-coding genes, 47 tRNAs, and 3 rRNA genes.
Complete Genome Sequences of Five Human Respiratory Syncytial Virus Isolates Collected in Brazil
Authors: Di Paola Nicholas , Cunha Marielton dos Passos , Durigon Giuliana Stravinskas , Berezin Eitan Naaman , Durigon Edison , Oliveira Danielle Bruna Leal de , Zanotto Paolo Marinho de Andrade 
Published: February 2018

ABSTRACT
Here, we present the complete genome sequences of five human respiratory syncytial virus isolates collected from hospitalized infants suffering from acute respiratory disease. These are the first five complete genome sequences of human respiratory syncytial virus to originate from Brazil.
Absence of Receptor Guanylyl Cyclase C Enhances Ileal Damage and Reduces Cytokine and Antimicrobial Peptide Production during Oral Salmonella enterica Serovar Typhimurium Infection
Authors: Majumdar Shamik , Mishra Vishwas , Nandi Somesh , Abdullah Mudabir , Barman Anaxee , Raghavan Abinaya , Nandi Dipankar , Visweswariah Sandhya S. 
Published: February 2018

ABSTRACTNontyphoidalSalmonelladisease contributes toward significant morbidity and mortality across the world. Host factors, including gamma interferon, tumor necrosis factor alpha, and gut microbiota, significantly influence the outcome ofSalmonellapathogenesis. However, the entire repertoire of host protective mechanisms contributing toSalmonellapathogenicity is not completely appreciated. Here, we investigated the roles of receptor guanylyl cyclase C (GC-C), which is predominantly expressed in the intestine and regulates intestinal cell proliferation and fluid-ion homeostasis. Mice deficient in GC-C (Gucy2c−/−) displayed accelerated mortality compared with that for wild-type mice following infection via the oral route, even though both groups possessed comparable systemicSalmonellainfection burdens. Survival following intraperitoneal infection remained similar in both groups, indicating that GC-C offered protection via a gut-mediated response. The serum cortisol level was higher inGucy2c−/−mice than wild-type (Gucy2c+/+) mice, and an increase in infection-induced thymic atrophy with a loss of immature CD4+CD8+double-positive thymocytes was observed. Accelerated and enhanced damage in the ileum, including submucosal edema, epithelial cell damage, focal tufting, and distortion of the villus architecture, was seen inGucy2c−/−mice concomitantly with a larger number of ileal tissue-associated bacteria. Transcription of key mediators ofSalmonella-induced inflammation (interleukin-22/Reg3β) was altered inGucy2c−/−mice in comparison to that inGucy2c+/+mice. A reduction in fecal lactobacilli, which are protective againstSalmonellainfection, was observed inGucy2c−/−mice.Gucy2c−/−mice cohoused with wild-type mice continued to show reduced amounts of lactobacilli and increased susceptibility to infection. Our study, therefore, suggests that the receptor GC-C confers a survival advantage during gut-mediatedSalmonella entericaserovar Typhimurium pathogenesis, presumably by regulatingSalmonellaeffector mechanisms and maintaining a beneficial microbiome.
Differential Contributions of Specimen Types, Culturing, and 16S rRNA Sequencing in Diagnosis of Prosthetic Joint Infections
Authors: Larsen Lone Heimann , Khalid Vesal , Xu Yijuan , Thomsen Trine Rolighed , Schønheyder Henrik C. , Christensen Poul Hedevang , Jørgensen Mogens Brouw , Kappel Andreas , Laursen Mogens Berg , Nielsen Poul Torben , Pedersen Christian , Rasmussen Sten , Riis Jess Tvede , Simonsen Ole , Aleksyniene Ramune , Bertelsen Henrik , Fisker Rune , Frost Majbritt , Kubik Magdalene , Iyer Victor , Ørsted Iben , Jordal Peter Lüttge , Kyneb Majbritt Hauge , Lorenzen Jan , Nielsen Kaare Lehmann , Nilsen Jeppe Lund , Nielsen Per Halkjær , Pedersen Kristian Kjær , Nielsen Lars Arendt 
Published: February 2018

ABSTRACT

Prosthetic joint failure is mainly caused by infection, aseptic failure (AF), and mechanical problems. Infection detection has been improved with modified culture methods and molecular diagnostics. However, comparisons between modified and conventional microbiology methods are difficult due to variations in specimen sampling. In this prospective, multidisciplinary study of hip or knee prosthetic failures, we assessed the contributions of different specimen types, extended culture incubations, and 16S rRNA sequencing for diagnosing prosthetic joint infections (PJI). Project specimens included joint fluid (JF), bone biopsy specimens (BB), soft-tissue biopsy specimens (STB), and swabs (SW) from the prosthesis, collected
in situ
, and sonication fluid collected from prosthetic components (PC). Specimens were cultured for 6 (conventional) or 14 days, and 16S rRNA sequencing was performed at study completion. Of the 156 patients enrolled, 111 underwent 114 surgical revisions (cases) due to indications of either PJI (
n
= 43) or AF (
n
= 71). Conventional tissue biopsy cultures confirmed PJI in 28/43 (65%) cases and refuted AF in 3/71 (4%) cases; one case was not evaluable. Based on these results, minor diagnostic adjustments were made. Fourteen-day cultures of JF, STB, and PC specimens confirmed PJI in 39/42 (93%) cases, and 16S rRNA sequencing confirmed PJI in 33/42 (83%) cases. One PJI case was confirmed with 16S rRNA sequencing alone and five with cultures of project specimens alone. These findings indicated that JF, STB, and PC specimen cultures qualified as an optimal diagnostic set. The contribution of sequencing to diagnosis of PJI may depend on patient selection; this hypothesis requires further investigation.
Retrospective Review of Treponema pallidum PCR and Serology Results: Are Both Tests Necessary?
Authors: Brischetto Anna , Gassiep Ian , Whiley David , Norton Robert 
Published: February 2018

ABSTRACT

There has been a resurgence of syphilis diagnoses in Australia. We investigated whether our
Treponema pallidum
PCR test provides any additional diagnostic information over syphilis serology (chemiluminescence immunoassay [CMIA],
Treponema pallidum
particle agglutination [TPPA] assay, and the rapid plasma reagin [RPR] flocculation test). A retrospective audit of all
T. pallidum
PCR requests that came through our laboratory from January 2010 to June 2017 was conducted; data collected included age, gender, site of swab, and results from
T. pallidum
PCR, syphilis serology, and herpes simplex virus 1 (HSV-1) and HSV-2 PCRs. A total of 441
T. pallidum
PCR tests were performed; on average, 3
T. pallidum
PCRs per month were requested in 2011, and this rate increased to 17.2 requests per month in 2017. A total of 323 patients had both
T. pallidum
PCR and syphilis serology performed, with 67% of swabs taken from the genitals.
T. pallidum
PCR gave positive results for 61/323 (19%) patients; of these 61 patients, 59 (97%) also had positive syphilis serology results (
T. pallidum
PCR sensitivity, 68%; specificity, 99%; positive predictive value, 97%; negative predictive value, 89%). Syphilis serology was positive for 91/323 patients (28%); of these 91 patients, 61 (66%) were also
T. pallidum
PCR positive (syphilis serology sensitivity, 97%; specificity, 88%; positive predictive value, 60%; negative predictive value, 99%). The Cohen's kappa value was 0.74, indicating substantial agreement between the two tests. Our results show that most patients with positive
T. pallidum
PCR results also had positive syphilis serology. Therefore,
T. pallidum
PCR adds little clinical value over serology for the diagnosis of syphilis in certain clinical settings.
Assessment of the societal and individual preferences for fertility treatment in Australia: study protocol for stated preference discrete choice experiments
Authors: Botha Willings , Donnolley Natasha , Shanahan Marian , Chambers Georgina M 
Published: February 2018

IntroductionIn Australia, societal and individual preferences for funding fertility treatment remain largely unknown. This has resulted in a lack of evidence about willingness to pay (WTP) for fertility treatment by either the general population (the funders) or infertile individuals (who directly benefit). Using a stated preference discrete choice experiment (SPDCE) approach has been suggested as a more appropriate method to inform economic evaluations of fertility treatment. We outline the protocol for an ongoing study which aims to assess fertility treatment preferences of both the general population and infertile individuals, and indirectly estimate their WTP for fertility treatment.Methods and analysisTwo separate but related SPDCEs will be conducted for two population samples—the general population and infertile individuals—to elicit preferences for fertility treatment to indirectly estimate WTP. We describe the qualitative work to be undertaken to design the SPDCEs. We will use D-efficient fractional experimental designs informed by prior coefficients from the pilot surveys. The mode of administration for the SPDCE is also discussed. The final results will be analysed using mixed logit or latent class model.Ethics and disseminationThis study is being funded by the Australian National Health and Medical Research Council (NHMRC) project grant AP1104543 and has been approved by the University of New South Wales Human Research Ethics Committee (HEC 17255) and a fertility clinic’s ethics committee. Findings of the study will be disseminated in peer-reviewed journals and presented at various conferences. A lay summary of the results will be made publicly available on the University of New South Wales National Perinatal Epidemiology and Statistics Unit website. Our results will contribute to the development of an evidence-based policy framework for the provision of cost-effective and patient-centred fertility treatment in Australia.
Air-drop blood supply in the French Army
Authors: Javaudin Olivier , Baillon A , Varin N , Martinaud C , Pouget T , Civadier C , Clavier B , Sailliol A 
Published: February 2018

BackgroundHaemorrhagic shock remains the leading cause of preventable death in overseas and austere settings. Transfusion of blood components is critical in the management of this kind of injury. For French naval and ground military units, this supply often takes too long considering the short shelf-life of red blood cell concentrates (RBCs) and the limited duration of transport in cooling containers (five to six days). Air-drop supply could be an alternative to overcome these difficulties on the condition that air-drop does not cause damage to blood units.MethodsAfter a period of study and technical development of packaging, four air-drops at medium and high altitudes were performed with an aircraft of the French Air Force. After this, one air-drop was carried out at medium altitude with 10 RBCs and 10 French lyophilised plasma (FLYP). A second air-drop was performed with a soldier carrying one FLYP unit at 12 000 feet. For these air-drops real blood products were used, and quality control testing and temperature monitoring were performed.ResultsThe temperatures inside the containers were within the normal ranges. Visual inspection indicated that transfusion packaging and dumped products did not undergo deterioration. The quality control data on RBCs and FLYP, including haemostasis, suggested no difference before and after air-drop.DiscussionThe operational implementation of the air-drop of blood products seems to be one of the solutions for the supply of blood products in military austere settings or far forward on battlefield, allowing safe and early transfusion.
Efficacy of multicomponent culturally tailored HIV/ STI prevention interventions targeting foreign female entertainment workers: a quasi-experimental trial
Authors: Lim Raymond B T , Cheung Olive N Y , Tai Bee Choo , Chen Mark I-C , Chan Roy K W , Wong Mee Lian 
Published: February 2018

ObjectivesWe assessed the efficacy of a multicomponent culturally tailored HIV/STI prevention intervention programme on consistent condom use and STI incidence among foreign Thai and Vietnamese female entertainment workers (FEWs) in Singapore.MethodsWe conducted a quasi-experimental pretest and post-test intervention trial with a comparison group. We recruited 220 participants (115 Vietnamese and 105 Thai) for the comparison group, followed by the intervention group (same number) from the same sites which were purposively selected after a 3-month interval period. Both groups completed a self-administered anonymous questionnaire and STI testing for cervical gonorrhoea and Chlamydia, as well as pharyngeal gonorrhoea at baseline and 6-week follow-up. The peer-led intervention consisted of behavioural (HIV/STI education and condom negotiation skills), biomedical (STI screening and treatment services) and structural components (access to free condoms). We used the mixed effects Poisson regression model accounting for clustering by establishment venue to compute the adjusted risk ratio (aRR) of the outcomes at follow-up.ResultsAt follow-up, the intervention group was more likely than the comparison group to report consistent condom use for vaginal sex with paid (aRR 1.77; 95% CI 1.71 to 1.83) and casual (aRR 1.81; 95% CI 1.71 to 1.91) partners. For consistent condom use for oral sex, this was aRR 1.50; 95% CI 1.23 to 1.82 with paid and aRR 1.54; 95% CI 1.22 to 1.95 with casual partners. STI incidence at follow-up was significantly lower in the intervention (6.8 per 100 FEWs) than the comparison (14.8 per 100 FEWs) group (aRR 0.42; 95% CI 0.32 to 0.55).ConclusionsThis trial was effective in promoting consistent condom use for vaginal and oral sex as well as reducing STI incidence among the foreign Thai and Vietnamese FEWs in Singapore. The feasibility of scaling up the interventions to all entertainment establishments in Singapore should be assessed.
Direct intertectal inputs are an integral component of the bilateral sensorimotor circuit for behavior in Xenopus tadpoles
Authors: Gambrill Abigail C. , Faulkner Regina L. , Cline Hollis T. 
Published: February 2018

The circuit controlling visually guided behavior in nonmammalian vertebrates, such as Xenopus tadpoles, includes retinal projections to the contralateral optic tectum, where visual information is processed, and tectal motor outputs projecting ipsilaterally to hindbrain and spinal cord. Tadpoles have an intertectal commissure whose function is unknown, but it might transfer information between the tectal lobes. Differences in visual experience between the two eyes have profound effects on the development and function of visual circuits in animals with binocular vision, but the effects on animals with fully crossed retinal projections are not clear. We tested the effect of monocular visual experience on the visuomotor circuit in Xenopus tadpoles. We show that cutting the intertectal commissure or providing visual experience to one eye (monocular visual experience) is sufficient to disrupt tectally mediated visual avoidance behavior. Monocular visual experience induces asymmetry in tectal circuit activity across the midline. Repeated exposure to monocular visual experience drives maturation of the stimulated retinotectal synapses, seen as increased AMPA-to-NMDA ratios, induces synaptic plasticity in intertectal synaptic connections, and induces bilaterally asymmetric changes in the tectal excitation-to-inhibition ratio (E/I). We show that unilateral expression of peptides that interfere with AMPA or GABAA receptor trafficking alters E/I in the transfected tectum and is sufficient to degrade visuomotor behavior. Our study demonstrates that monocular visual experience in animals with fully crossed visual systems produces asymmetric circuit function across the midline and degrades visuomotor behavior. The data further suggest that intertectal inputs are an integral component of a bilateral visuomotor circuit critical for behavior. NEW & NOTEWORTHY The developing optic tectum of Xenopus tadpoles represents a unique circuit in which laterally positioned eyes provide sensory input to a circuit that is transiently monocular, but which will be binocular in the animal’s adulthood. We challenge the idea that the two lobes of tadpole optic tectum function independently by testing the requirement of interhemispheric communication and demonstrate that unbalanced sensory input can induce structural and functional plasticity in the tectum sufficient to disrupt function.
Phase reorganization leads to transient β-LFP spatial wave patterns in motor cortex during steady-state movement preparation
Authors: Rule Michael E. , Vargas-Irwin Carlos , Donoghue John P. , Truccolo Wilson 
Published: February 2018

Previous studies on the origin and properties of spatial patterns in motor cortex β-local field potential (β-LFP) oscillations have focused on planar traveling waves. However, it is unclear 1) whether β-LFP waves are limited to plane waves, or even 2) whether they are propagating waves of excito-excitatory activity, i.e., primarily traveling waves in excitable media; they could reflect, instead, reorganization in the relative phases of transient oscillations at different spatial sites. We addressed these two problems in β-LFPs recorded via microelectrode arrays implanted in three adjacent motor cortex areas of nonhuman primates during steady-state movement preparation. Our findings are fourfold: 1) β-LFP wave patterns emerged as transient events, despite stable firing rates of single neurons concurrently recorded during the same periods. 2) β-LFP waves showed a richer variety of spatial dynamics, including rotating and complex waves. 3) β-LFP wave patterns showed no characteristic wavelength, presenting instead a range of scales with global zero-lag phase synchrony as a limiting case, features surprising for purely excito-excitatory waves but consistent with waves in coupled oscillator systems. 4) Furthermore, excito-excitatory traveling waves induced by optogenetic stimulation in motor cortex showed, in contrast, a characteristic wavelength and reduced phase synchrony. Overall, β-LFP wave statistics differed from those of induced traveling waves in excitable media recorded under the same microelectrode array setup. Our findings suggest phase reorganization in neural coupled oscillators contribute significantly to the origin of transient β-LFP spatial dynamics during preparatory steady states and outline important constraints for spatially extended models of β-LFP dynamics in motor cortex. NEW & NOTEWORTHY We show that a rich variety of transient β-local field potential (β-LFP) wave patterns emerge in motor cortex during preparatory steady states, despite stable neuronal firing rates. Furthermore, unlike optogenetically induced traveling waves, β-LFP waves showed no characteristic wavelength, presenting instead a range of scales with global phase synchrony as a limiting case. Overall, our statistical analyses suggest that transient phase reorganization in neural coupled oscillators, beyond purely excito-excitatory traveling waves, contribute significantly to the origin of motor cortex β-LFP wave patterns.
Progression of convulsive and nonconvulsive seizures during epileptogenesis after pilocarpine-induced status epilepticus
Authors: Smith Zachariah Z. , Benison Alexander M. , Bercum Florencia M. , Dudek F. Edward , Barth Daniel S. 
Published: February 2018

Although convulsive seizures occurring during pilocarpine-induced epileptogenesis have received considerable attention, nonconvulsive seizures have not been closely examined, even though they may reflect the earliest signs of epileptogenesis and potentially guide research on antiepileptogenic interventions. The definition of nonconvulsive seizures based on brain electrical activity alone has been controversial. Here we define and quantify electrographic properties of convulsive and nonconvulsive seizures in the context of the acquired epileptogenesis that occurs after pilocarpine-induced status epilepticus (SE). Lithium-pilocarpine was used to induce the prolonged repetitive seizures characteristic of SE; when SE was terminated with paraldehyde, seizures returned during the 2-day period after pilocarpine treatment. A distinct latent period ranging from several days to >2 wk was then measured with continuous, long-term video-EEG. Nonconvulsive seizures dominated the onset of epileptogenesis and consistently preceded the first convulsive seizures but were still present later. Convulsive and nonconvulsive seizures had similar durations. Postictal depression (background suppression of the EEG) lasted for >100 s after both convulsive and nonconvulsive seizures. Principal component analysis was used to quantify the spectral evolution of electrical activity that characterized both types of spontaneous recurrent seizures. These studies demonstrate that spontaneous nonconvulsive seizures have electrographic properties similar to convulsive seizures and confirm that nonconvulsive seizures link the latent period and the onset of convulsive seizures during post-SE epileptogenesis in an animal model. Nonconvulsive seizures may also reflect the earliest signs of epileptogenesis in human acquired epilepsy, when intervention could be most effective. NEW & NOTEWORTHY Nonconvulsive seizures usually represent the first bona fide seizure following a latent period, dominate the early stages of epileptogenesis, and change in severity in a manner consistent with the progressive nature of epileptogenesis. This analysis demonstrates that nonconvulsive and convulsive seizures have different behavioral outcomes but similar electrographic signatures. Alternatively, epileptiform spike-wave discharges fail to recapitulate several key seizure features and represent a category of electrical activity separate from nonconvulsive seizures in this model.