bluuebunny/crossref_metadata_2025_split huggingface dataset:
Thermal and Solvent Stress Cross-Tolerance Conferred to Corynebacterium glutamicum by Adaptive Laboratory Evolution
Authors: Oide Shinichi , Gunji Wataru , Moteki Yasuhiro , Yamamoto Shogo , Suda Masako , Jojima Toru , Yukawa Hideaki , Inui Masayuki 
Published: January 2015

ABSTRACTReinforcing microbial thermotolerance is a strategy to enable fermentation with flexible temperature settings and thereby to save cooling costs. Here, we report on adaptive laboratory evolution (ALE) of the amino acid-producing bacteriumCorynebacterium glutamicumunder thermal stress. After 65 days of serial passage of the transgenic strain GLY3, in which the glycolytic pathway is optimized for alanine production under oxygen deprivation, three strains adapted to supraoptimal temperatures were isolated, and all the mutations they acquired were identified by whole-genome resequencing. Of the 21 mutations common to the three strains, one large deletion and two missense mutations were found to promote growth of the parental strain under thermal stress. Additive effects on thermotolerance were observed among these mutations, and the combination of the deletion with the missense mutation onotsA, encoding a trehalose-6-phosphate synthase, allowed the parental strain to overcome the upper limit of growth temperature. Surprisingly, the three evolved strains acquired cross-tolerance for isobutanol, which turned out to be partly attributable to the genomic deletion associated with the enhanced thermotolerance. The deletion involved loss of two transgenes,pfkandpyk, encoding the glycolytic enzymes, in addition to six native genes, and elimination of the transgenes, but not the native genes, was shown to account for the positive effects on thermal and solvent stress tolerance, implying a link between energy-producing metabolism and bacterial stress tolerance. Overall, the present study provides evidence that ALE can be a powerful tool to refine the phenotype ofC. glutamicumand to investigate the molecular bases of stress tolerance.
Novel Hypovirulence-Associated RNA Mycovirus in the Plant-Pathogenic Fungus Botrytis cinerea: Molecular and Biological Characterization
Authors: Yu Lin , Sang Wen , Wu Ming-De , Zhang Jing , Yang Long , Zhou Ying-Jun , Chen Wei-Dong , Li Guo-Qing 
Published: January 2015

ABSTRACT

Botrytis cinerea
is a pathogenic fungus causing gray mold on numerous economically important crops and ornamental plants. This study was conducted to characterize the biological and molecular features of a novel RNA mycovirus, Botrytis cinerea RNA virus 1 (BcRV1), in the hypovirulent strain BerBc-1 of
B. cinerea
. The genome of BcRV1 is 8,952 bp long with two putative overlapped open reading frames (ORFs), ORF1 and ORF2, coding for a hypothetical polypeptide (P1) and RNA-dependent RNA polymerase (RdRp), respectively. A −1 frameshifting region (designated the KNOT element) containing a shifty heptamer, a heptanucleotide spacer, and an H-type pseudoknot was predicted in the junction region of ORF1 and ORF2. The −1 frameshifting role of the KNOT element was experimentally confirmed through determination of the production of the fusion protein red fluorescent protein (RFP)-green fluorescent protein (GFP) by the plasmid containing the construct
dsRed-
KNOT-
eGFP
in
Escherichia coli
. BcRV1 belongs to a taxonomically unassigned double-stranded RNA (dsRNA) mycovirus group. It is closely related to grapevine-associated totivirus 2 and Sclerotinia sclerotiorum nonsegmented virus L. BcRV1 in strain BerBc-1 was found capable of being transmitted vertically through macroconidia and horizontally to other
B. cinerea
strains through hyphal contact. The presence of BcRV1 was found to be positively correlated with hypovirulence in
B. cinerea
, with the attenuation effects of BcRV1 on mycelial growth and pathogenicity being greatly affected by the accumulation level of BcRV1.
Identification and Characterization of LFD-2, a Predicted Fringe Protein Required for Membrane Integrity during Cell Fusion in Neurospora crassa
Authors: Palma-Guerrero Javier , Zhao Jiuhai , Gonçalves A. Pedro , Starr Trevor L. , Glass N. Louise 
Published: January 2015

ABSTRACT

The molecular mechanisms of membrane merger during somatic cell fusion in eukaryotic species are poorly understood. In the filamentous fungus
Neurospora crassa
, somatic cell fusion occurs between genetically identical germinated asexual spores (germlings) and between hyphae to form the interconnected network characteristic of a filamentous fungal colony. In
N. crassa
, two proteins have been identified to function at the step of membrane fusion during somatic cell fusion: PRM1 and LFD-1. The absence of either one of these two proteins results in an increase of germling pairs arrested during cell fusion with tightly appressed plasma membranes and an increase in the frequency of cell lysis of adhered germlings. The level of cell lysis in Δ
Prm1
or Δ
lfd-1
germlings is dependent on the extracellular calcium concentration. An available transcriptional profile data set was used to identify genes encoding predicted transmembrane proteins that showed reduced expression levels in germlings cultured in the absence of extracellular calcium. From these analyses, we identified a mutant (
lfd-2
, for

l

ate

f

usion

d

efect-2
) that showed a calcium-dependent cell lysis phenotype.
lfd-2
encodes a protein with a Fringe domain and showed endoplasmic reticulum and Golgi membrane localization. The deletion of an additional gene predicted to encode a low-affinity calcium transporter,
fig1
, also resulted in a strain that showed a calcium-dependent cell lysis phenotype. Genetic analyses showed that LFD-2 and FIG1 likely function in separate pathways to regulate aspects of membrane merger and repair during cell fusion.
Molecular Characterization of Hap Complex Components Responsible for Methanol-Inducible Gene Expression in the Methylotrophic Yeast Candida boidinii
Authors: Oda Saori , Yurimoto Hiroya , Nitta Nobuhisa , Sasano Yu , Sakai Yasuyoshi 
Published: January 2015

ABSTRACT

We identified genes encoding components of the Hap complex,
CbHAP2
,
CbHAP3
, and
CbHAP5
, as transcription factors regulating methanol-inducible gene expression in the methylotrophic yeast
Candida boidinii
. We found that the
Cbhap2
Δ,
Cbhap3
Δ, and
Cbhap5
Δ gene-disrupted strains showed severe growth defects on methanol but not on glucose and nonfermentable carbon sources such as ethanol and glycerol. In these disruptants, the transcriptional activities of methanol-inducible promoters were significantly decreased compared to those of the wild-type strain, indicating that CbHap2p, CbHap3p, and CbHap5p play indispensable roles in methanol-inducible gene expression. Further molecular and biochemical analyses demonstrated that CbHap2p, CbHap3p, and CbHap5p localized to the nucleus and bound to the promoter regions of methanol-inducible genes regardless of the carbon source, and heterotrimer formation was suggested to be necessary for binding to DNA. Unexpectedly, distinct from
Saccharomyces cerevisiae
, the Hap complex functioned in methanol-specific induction rather than glucose derepression in
C. boidinii
. Our results shed light on a novel function of the Hap complex in methanol-inducible gene expression in methylotrophic yeasts.
A FACS-Optimized Screen Identifies Regulators of Genome Stability in Candida albicans
Authors: Loll-Krippleber Raphaël , Feri Adeline , Nguyen Marie , Maufrais Corinne , Yansouni Jennifer , d'Enfert Christophe , Legrand Mélanie 
Published: January 2015

ABSTRACT

Loss of heterozygosity (LOH) plays important roles in genome dynamics, notably, during tumorigenesis. In the fungal pathogen
Candida albicans
, LOH contributes to the acquisition of antifungal resistance. In order to investigate the mechanisms that regulate LOH in
C. albicans
, we have established a novel method combining an artificial heterozygous locus harboring the blue fluorescent protein and green fluorescent protein markers and flow cytometry to detect LOH events at the single-cell level. Using this fluorescence-based method, we have confirmed that elevated temperature, treatment with methyl methanesulfonate, and inactivation of the Mec1 DNA damage checkpoint kinase triggered an increase in the frequency of LOH. Taking advantage of this system, we have searched for
C. albicans
genes whose overexpression triggered an increase in LOH and identified four candidates, some of which are known regulators of genome dynamics with human homologues contributing to cancer progression. Hence, the approach presented here will allow the implementation of new screens to identify genes that are important for genome stability in
C. albicans
and more generally in eukaryotic cells.
Electroencephalography as a clinical tool for diagnosing and monitoring attention deficit hyperactivity disorder: a cross-sectional study
Authors: Helgadóttir Halla , Gudmundsson Ólafur Ó , Baldursson Gísli , Magnússon Páll , Blin Nicolas , Brynjólfsdóttir Berglind , Emilsdóttir Ásdís , Gudmundsdóttir Gudrún B , Lorange Málfrídur , Newman Paula K , Jóhannesson Gísli H , Johnsen Kristinn 
Published: January 2015

ObjectivesThe aim of this study was to develop and test, for the first time, a multivariate diagnostic classifier of attention deficit hyperactivity disorder (ADHD) based on EEG coherence measures and chronological age.SettingThe participants were recruited in two specialised centres and three schools in Reykjavik.ParticipantsThe data are from a large cross-sectional cohort of 310 patients with ADHD and 351 controls, covering an age range from 5.8 to 14 years. ADHD was diagnosed according to the Diagnostic and Statistical Manual of Mental Disorders fourth edition (DSM-IV) criteria using the K-SADS-PL semistructured interview. Participants in the control group were reported to be free of any mental or developmental disorders by their parents and had a score of less than 1.5 SDs above the age-appropriate norm on the ADHD Rating Scale-IV. Other than moderate or severe intellectual disability, no additional exclusion criteria were applied in order that the cohort reflected the typical cross section of patients with ADHD.ResultsDiagnostic classifiers were developed using statistical pattern recognition for the entire age range and for specific age ranges and were tested using cross-validation and by application to a separate cohort of recordings not used in the development process. The age-specific classification approach was more accurate (76% accuracy in the independent test cohort; 81% cross-validation accuracy) than the age-independent version (76%; 73%). Chronological age was found to be an important classification feature.ConclusionsThe novel application of EEG-based classification methods presented here can offer significant benefit to the clinician by improving both the accuracy of initial diagnosis and ongoing monitoring of children and adolescents with ADHD. The most accurate possible diagnosis at a single point in time can be obtained by the age-specific classifiers, but the age-independent classifiers are also useful as they enable longitudinal monitoring of brain function.
Establishment of a prospective cohort of mechanically ventilated patients in five intensive care units in Lima, Peru: protocol and organisational characteristics of participating centres
Authors: Denney Joshua A , Capanni Francesca , Herrera Phabiola , Dulanto Augusto , Roldan Rollin , Paz Enrique , Jaymez Amador A , Chirinos Eduardo E , Portugal Jose , Quispe Rocio , Brower Roy G , Checkley William ,   INTENSIVOS Cohort Study
Published: January 2015

IntroductionMechanical ventilation is a cornerstone in the management of critically ill patients worldwide; however, less is known about the clinical management of mechanically ventilated patients in low and middle income countries where limitation of resources including equipment, staff and access to medical information may play an important role in defining patient-centred outcomes. We present the design of a prospective, longitudinal study of mechanically ventilated patients in Peru that aims to describe a large cohort of mechanically ventilated patients and identify practices that, if modified, could result in improved patient-centred outcomes and lower costs.Methods and analysisFive Peruvian intensive care units (ICUs) and the Medical ICU at the Johns Hopkins Hospital were selected for this study. Eligible patients were those who underwent at least 24 h of invasive mechanical ventilation within the first 48 h of admission into the ICU. Information on ventilator settings, clinical management and treatment were collected daily for up to 28 days or until the patient was discharged from the unit. Vital status was assessed at 90 days post enrolment. A subset of participants who survived until hospital discharge were asked to participate in an ancillary study to assess vital status, and physical and mental health at 6, 12, 24 and 60 months after hospitalisation, Primary outcomes include 90-day mortality, time on mechanical ventilation, hospital and ICU lengths of stay, and prevalence of acute respiratory distress syndrome. In subsequent analyses, we aim to identify interventions and standardised care strategies that can be tailored to resource-limited settings and that result in improved patient-centred outcomes and lower costs.Ethics and disseminationWe obtained ethics approval from each of the four participating hospitals in Lima, Peru, and at the Johns Hopkins School of Medicine, Baltimore, USA. Results will be disseminated as several separate publications in different international journals.
Detection for pathway effect contributing to disease in systems epidemiology with a case–control design
Authors: Ji Jiadong , Yuan Zhongshang , Zhang Xiaoshuai , Li Fangyu , Xu Jing , Liu Ying , Li Hongkai , Wang Jia , Xue Fuzhong 
Published: January 2015

ObjectivesIdentification of pathway effects responsible for specific diseases has been one of the essential tasks in systems epidemiology. Despite some advance in procedures for distinguishing specific pathway (or network) topology between different disease status, statistical inference at a population level remains unsolved and further development is still needed. To identify the specific pathways contributing to diseases, we attempt to develop powerful statistics which can capture the complex relationship among risk factors.Setting and participantsAcute myeloid leukaemia (AML) data obtained from 133 adults (98 patients and 35 controls; 47% female).ResultsSimulation studies indicated that the proposed Pathway Effect Measures (PEM) were stable; bootstrap-based methods outperformed the others, with bias-corrected bootstrap CI method having the highest power. Application to real data of AML successfully identified the specific pathway (Treg→TGFβ→Th17) effect contributing to AML with p values less than 0.05 under various methods and the bias-corrected bootstrap CI (−0.214 to −0.020). It demonstrated that Th17–Treg correlation balance was impaired in patients with AML, suggesting that Th17–Treg imbalance potentially plays a role in the pathogenesis of AML.ConclusionsThe proposed bootstrap-based PEM are valid and powerful for detecting the specific pathway effect contributing to disease, thus potentially providing new insight into the underlying mechanisms and ways to study the disease effects of specific pathways more comprehensively.
Differentiation between mycoplasma and viral community-acquired pneumonia in children with lobe or multi foci infiltration: a retrospective case study
Authors: Guo Wan-liang , Wang Jian , Zhu Li-yuan , Hao Chuang-li 
Published: January 2015

ObjectivesTo analyse the clinical features, inflammatory markers and radiographs of community-acquired pneumonia (CAP) cases with lobe or multi foci infiltration; with a special focus on factors which allow the differential diagnosis of viral and mycoplasma pneumonia.SettingRetrospective chart review of CAP cases in a large university teaching hospital.Participants126 paediatric CAP cases, with lobe or multi foci infiltration, presenting between May 2012 and April 2013. Demographic data, clinical presentation on admission or referral, laboratory tests, prior history, and radiography were collected for each case if available.Primary and secondary outcome measuresWe used univariate and multivariate logistic regression to determine the significant factors which allow the differential diagnosis of viral and mycoplasma CAP with lobe or multi foci infiltration.ResultsThere were 71 (56%) male and 55 (44%) female CAP cases with lobar or multi foci infiltration. 70 pneumonia cases were caused byMycoplasma pneumoniaeand 18 by viruses. Univariate analysis of the mycoplasma and viral causes of the CAP revealed that increased respiratory rate, wheeze, male gender and lymphocyte percentage were the factors associated with the differentiation of mycoplasma and viral aetiologies of pneumonia (p<0.05). A stepwise logistic regression analysis was performed to assess independent factors which allow the differential diagnosis of viral and mycoplasma pneumonia. Increased respiratory rate, wheeze, and lymphocyte percentage were reliable independent factors which allow the differential diagnosis of viral and mycoplasma CAP with lobar or multi foci infiltration.ConclusionsWhether the CAP with lobar or multi foci infiltration was caused by mycoplasma species or viruses could not be inferred from the radiological patterns. Wheeze, lymphocyte percentage and respiratory rate were independent factors which allowed the differential diagnosis of viral and mycoplasma CAP with lobar or multi foci infiltration.
The impact of a streamlined funding application process on application time: two cross-sectional surveys of Australian researchers
Authors: Barnett Adrian G , Graves Nicholas , Clarke Philip , Herbert Danielle 
Published: January 2015

ObjectiveTo examine if streamlining a medical research funding application process saved time for applicants.DesignCross-sectional surveys before and after the streamlining.SettingThe National Health and Medical Research Council (NHMRC) of Australia.ParticipantsResearchers who submitted one or more NHMRC Project Grant applications in 2012 or 2014.Main outcome measuresAverage researcher time spent preparing an application and the total time for all applications in working days.ResultsThe average time per application increased from 34 working days before streamlining (95% CI 33 to 35) to 38 working days after streamlining (95% CI 37 to 39; mean difference 4 days, bootstrap p value <0.001). The estimated total time spent by all researchers on applications after streamlining was 614 working years, a 67-year increase from before streamlining.ConclusionsStreamlined applications were shorter but took longer to prepare on average. Researchers may be allocating a fixed amount of time to preparing funding applications based on their expected return, or may be increasing their time in response to increased competition. Many potentially productive years of researcher time are still being lost to preparing failed applications.
Pneumococcal conjugate vaccines PREVenar13 and SynflorIX in sequence or alone in high-risk Indigenous infants (PREV-IX_COMBO): protocol of a randomised controlled trial
Authors: Leach Amanda Jane , Mulholland Edward Kim , Santosham Mathu , Torzillo Paul John , Brown Ngiare Joy , McIntyre Peter , Smith-Vaughan Heidi , Skull Sue , Balloch Anne , Andrews Ross , Carapetis Jonathan , McDonnell Joseph , Krause Vicki , Morris Peter Stanley 
Published: January 2015

IntroductionOtitis media (OM) starts within weeks of birth in almost all Indigenous infants living in remote areas of the Northern Territory (NT). OM and associated hearing loss persist from infancy throughout childhood and often into adulthood. Educational and social opportunities are greatly compromised.Pneumococcusand non-typeableHaemophilus influenzae(NTHi) are major OM pathogens that densely colonise the nasopharynx and infect the middle ear from very early in life. Our hypothesis is that compared to current single vaccine schedules, a combination of vaccines starting at 1 month of age, may provide earlier, broadened protection.Methods and analysesThis randomised outcome assessor, blinded controlled trial will recruit 425 infants between 28 and 38 days of age and randomly allocate them (1:1:1) to one of three pneumococcal conjugate vaccine (PCV) schedules: Synflorix at 2, 4, 6 months of age, Prevenar13 at 2, 4 and 6 months of age, or an investigational schedule of Synflorix at 1, 2 and 4 months plus Prevenar13 at 6 months of age. The blinded primary outcomes at 7 months of age are immunogenicity of specific vaccine antigens (geometric mean concentration (GMC) and proportion of participants with above threshold GMC of 0.35 µg/L). Secondary outcomes at all timepoints are additional immunogenicity measures and proportion of participants with nasopharyngeal carriage of vaccine-type pneumococci and NTHi, and any OM, including any tympanic membrane perforation. Parental interviews will provide data on common risk factors for OM.Ethics and disseminationEthical approval has been obtained from NT Department of Health and Menzies HREC (EC00153), Central Australian HREC (EC00155) and West Australian Aboriginal Health Ethics Committee (WAAHEC- 377-12/2011). Final trial results, data analyses, interpretation and conclusions will be presented in appropriate written and oral formats to parents and guardians, participating communities, local, national and international conferences, and published in peer-reviewed open access journals.Trial registration numbersACTRN12610000544077 andNCT01174849.
Improving the quality of initial management of self harm and suicide patients in A+E at the James Paget Hospital
Authors: Cracknell Ben 
Published: January 2015

AbstractOur objective was to improve the initial management and documentation of suicide risk assessment in the notes of patients attending A+E with a suicide attempt or self harm.An initial audit was carried out in 2012 looking at the notes of 50 patients who attended the James Paget Hospital accident and emergency (A+E) department following a suicide attempt or self harm episode. Compliance to the NICE guidelines on the initial management of self harm was assessed and was found to be low in certain areas. A significant number of these patients are discharged without evidence of a satisfactory suicide risk assessment being documented. This is dangerous practice for the patients and puts the doctor at risk medico-legally.A number of interventions were introduced to raise compliance to the NICE guidelines. These changes included adaptation to the self harm pro-forma to better conform to the NICE guidelines, departmental teaching sessions, and posters of the pro-forma put up in A+E at the doctors stations. In addition, a "see and greet" nurse was involved in the triage and administration of activated charcoal.The audit was repeated in 2013 and 2014. It was found that the interventions led to an increase in compliance to the NICE guidelines and better documentation in the notes of patients who present with a suicide attempt or self harm episode.