bluuebunny/crossref_metadata_2025 huggingface dataset:
Speeding up the product release: a second‐sphere contribution from Tyr191 to the reactivity of l‐lactate oxidase revealed in crystallographic and kinetic studies of site‐directed variants
Authors: Stoisser Thomas , Klimacek Mario , Wilson David K. , Nidetzky Bernd
Published: August 2015

Among α‐hydroxy acid‐oxidizing flavoenzymes l‐lactate oxidase (LOX) is unique in featuring a second‐sphere tyrosine (Tyr191 in Aerococcus viridans LOX; avLOX) at the binding site for the substrate's carboxylate group. Y191F, Y191L and Y191A variants of avLOX were constructed to affect a hydrogen‐bond network connecting Tyr191 to the carboxylate of the bound ligand via the conserved Tyr40 and to examine consequent effects on enzymatic reactivity. Kinetic studies at 20 °C and pH 6.5 revealed that release of pyruvate product was decreased 4.7‐fold (Y191F), 19‐fold (Y191L) and 28‐fold (Y191A) compared with wild‐type enzyme (~ 141 s−1) and thus became mainly rate limiting for l‐lactate oxidation by the variants at a steady‐state under air‐saturated conditions. In the Y191L and the Y191A variants, but not in the Y191F variant, l‐lactate binding was also affected strongly by the site‐directed substitution. Reduction of the flavin cofactor by l‐lactate and its reoxidation by molecular oxygen were, however, comparatively weakly affected by the replacements of Tyr191. Unlike the related lactate monooxygenase, which prevents the fast dissociation of pyruvate to promote its oxidative decarboxylation by H2O2 into acetate, CO2 and water as final reaction products, all avLOX variants retained their native oxidase activity where catalytic turnover results in the equivalent formation of H2O2. The 1.9 Å crystal structure of the Y191F variant bound with FMN and pyruvate revealed a strictly locally disruptive effect of the site‐directed substitution. Product off‐rates appear to be dictated by partitioning of residues including Tyr191 from an active‐site lid loop into bulk solvent and modulation of the hydrogen bond strength that links Tyr40 with the pyruvate's carboxylate group. Overall, this study emphasizes the possibly high importance of contributions from second‐sphere substrate‐binding residues to the fine‐tuning of reactivity in α‐hydroxy acid‐oxidizing flavoenzymes, requiring that the catalytic steps of flavin reduction and oxidation are properly timed with the physical step of α‐keto acid product release.

Database

The structure of Y191F variant of A. viridans l‐lactate oxidase was deposited in the wwPDB under the accession code 4YL2.
Response surface methodology in β‐glucan wheat rolls production using microwave convection
Authors: Kurek Marcin Andrzej , Wyrwisz Jarosław , Wierzbicka Agnieszka
Published: August 2015

The aim of research was to test the response surface methodology for optimising the β‐glucan content (BG) and microwave power (MV) during baking the wheat bread rolls. The increasing content of BG in wheat bread rolls caused the shortening the time of baking. The firmness of breadcrumbs was significantly influenced by the BG content in linear terms (P ≤ 0.05) and not influenced by the MV. The content of BG in the final product was highest in the products obtained with the middle range of MV. The response surface methodology was employed for optimising the BG and MV to produce the best quality product.
Characterization of acute‐on‐chronic liver failure and prediction of mortality in Asian patients with active alcoholism
Authors: Kim Hwi Young , Chang Young , Park Jae Yong , Ahn Hongkeun , Cho Hyeki , Han Seung Jun , Oh Sohee , Kim Donghee , Jung Yong Jin , Kim Byeong Gwan , Lee Kook Lae , Kim Won
Published: August 2015

Background and Aims

Alcoholic liver diseases often evolve to acute‐on‐chronic liver failure (ACLF), which increases the risk of (multi‐)organ failure and death. We investigated the development and characteristics of alcohol‐related ACLF and evaluated prognostic scores for prediction of mortality in Asian patients with active alcoholism.

Methods

A total of 205 patients who were hospitalized with severe alcoholic liver disease were included in this retrospective cohort study, after excluding those with serious cardiovascular diseases, malignancy, or co‐existing viral hepatitis. The Chronic Liver Failure (CLIF) Consortium Organ Failure score was used in the diagnosis and grading of ACLF, and the CLIF Consortium ACLF score (CLIF‐C ACLFs) was used to predict mortality.

Results

Patients with ACLF had higher Maddrey discriminant function, model for end‐stage liver disease (MELD), and MELD‐sodium scores than those without ACLF. Infections were more frequently documented in patients with ACLF (33.3% vs 53.0%; P = 0.004). Predictive factors for ACLF development were systemic inflammatory response syndrome (odds ratio [OR], 2.239; P < 0.001), serum sodium level (OR, 0.939; P = 0.029), and neutrophil count (OR, 1.000; P = 0.021). For prediction of mortality at predefined time points (28‐day and 90‐day) in patients with ACLF, areas under the receiver‐operating characteristic were significantly greater for the CLIF‐C ACLFs than for Child–Pugh, MELD, and MELD‐sodium scores.

Conclusions

Infection and systemic inflammatory response syndrome play an important role in the development of alcohol‐related ACLF in Asian patients with active alcoholism. The CLIF‐C ACLFs may be more useful for predicting mortality in ACLF cases than liver‐specific scoring systems.
The reliability, validity, sensitivity, specificity and predictive values of the Chinese version of the Rowland Universal Dementia Assessment Scale
Authors: Chen Chia‐Wei , Chu Hsin , Tsai Chia‐Fen , Yang Hui‐Ling , Tsai Jui‐Chen , Chung Min‐Huey , Liao Yuan‐Mei , Chi Mei‐ju , Chou Kuei‐Ru
Published: August 2015

Aims and objectives

The purpose of this study was to translate the Rowland Universal Dementia Assessment Scale into Chinese and to evaluate the psychometric properties (reliability and validity) and the diagnostic properties (sensitivity, specificity and predictive values) of the Chinese version of the Rowland Universal Dementia Assessment Scale.

Background

The accurate detection of early dementia requires screening tools with favourable cross‐cultural linguistic and appropriate sensitivity, specificity, and predictive values, particularly for Chinese‐speaking populations.

Design

This was a cross‐sectional, descriptive study.

Methods

Overall, 130 participants suspected to have cognitive impairment were enrolled in the study. A test‐retest for determining reliability was scheduled four weeks after the initial test. Content validity was determined by five experts, whereas construct validity was established by using contrasted group technique. The participants' clinical diagnoses were used as the standard in calculating the sensitivity, specificity, positive predictive value and negative predictive value.

Results

The study revealed that the Chinese version of the Rowland Universal Dementia Assessment Scale exhibited a test‐retest reliability of 0·90, an internal consistency reliability of 0·71, an inter‐rater reliability (kappa value) of 0·88 and a content validity index of 0·97. Both the patients and healthy contrast group exhibited significant differences in their cognitive ability. The optimal cut‐off points for the Chinese version of the Rowland Universal Dementia Assessment Scale in the test for mild cognitive impairment and dementia were 24 and 22, respectively; moreover, for these two conditions, the sensitivities of the scale were 0·79 and 0·76, the specificities were 0·91 and 0·81, the areas under the curve were 0·85 and 0·78, the positive predictive values were 0·99 and 0·83 and the negative predictive values were 0·96 and 0·91 respectively.

Conclusion

The Chinese version of the Rowland Universal Dementia Assessment Scale exhibited sound reliability, validity, sensitivity, specificity and predictive values.

Relevance to clinical practice

This scale can help clinical staff members to quickly and accurately diagnose cognitive impairment and provide appropriate treatment as early as possible.
Inflammation and plaque vulnerability
Authors: Hansson G. K. , Libby P. , Tabas I.
Published: August 2015

Atherosclerosis is a maladaptive, nonresolving chronic inflammatory disease that occurs at sites of blood flow disturbance. The disease usually remains silent until a breakdown of integrity at the arterial surface triggers the formation of a thrombus. By occluding the lumen, the thrombus or emboli detaching from it elicits ischaemic symptoms that may be life‐threatening. Two types of surface damage can cause atherothrombosis: plaque rupture and endothelial erosion. Plaque rupture is thought to be caused by loss of mechanical stability, often due to reduced tensile strength of the collagen cap surrounding the plaque. Therefore, plaques with reduced collagen content are thought to be more vulnerable than those with a thick collagen cap. Endothelial erosion, on the other hand, may occur after injurious insults to the endothelium instigated by metabolic disturbance or immune insults. This review discusses the molecular mechanisms involved in plaque vulnerability and the development of atherothrombosis.
The DTI Challenge: Toward Standardized Evaluation of Diffusion Tensor Imaging Tractography for Neurosurgery
Authors: Pujol Sonia , Wells William , Pierpaoli Carlo , Brun Caroline , Gee James , Cheng Guang , Vemuri Baba , Commowick Olivier , Prima Sylvain , Stamm Aymeric , Goubran Maged , Khan Ali , Peters Terry , Neher Peter , Maier‐Hein Klaus H. , Shi Yundi , Tristan‐Vega Antonio , Veni Gopalkrishna , Whitaker Ross , Styner Martin , Westin Carl‐Fredrik , Gouttard Sylvain , Norton Isaiah , Chauvin Laurent , Mamata Hatsuho , Gerig Guido , Nabavi Arya , Golby Alexandra , Kikinis Ron
Published: August 2015

BACKGROUND AND PURPOSE

Diffusion tensor imaging (DTI) tractography reconstruction of white matter pathways can help guide brain tumor resection. However, DTI tracts are complex mathematical objects and the validity of tractography‐derived information in clinical settings has yet to be fully established. To address this issue, we initiated the DTI Challenge, an international working group of clinicians and scientists whose goal was to provide standardized evaluation of tractography methods for neurosurgery. The purpose of this empirical study was to evaluate different tractography techniques in the first DTI Challenge workshop.

METHODS

Eight international teams from leading institutions reconstructed the pyramidal tract in four neurosurgical cases presenting with a glioma near the motor cortex. Tractography methods included deterministic, probabilistic, filtered, and global approaches. Standardized evaluation of the tracts consisted in the qualitative review of the pyramidal pathways by a panel of neurosurgeons and DTI experts and the quantitative evaluation of the degree of agreement among methods.

RESULTS

The evaluation of tractography reconstructions showed a great interalgorithm variability. Although most methods found projections of the pyramidal tract from the medial portion of the motor strip, only a few algorithms could trace the lateral projections from the hand, face, and tongue area. In addition, the structure of disagreement among methods was similar across hemispheres despite the anatomical distortions caused by pathological tissues.

CONCLUSIONS

The DTI Challenge provides a benchmark for the standardized evaluation of tractography methods on neurosurgical data. This study suggests that there are still limitations to the clinical use of tractography for neurosurgical decision making.
Effect of dietary vanadium and vitamin C on egg quality and antioxidant status in laying hens
Authors: Wang J. P. , He K. R. , Ding X. M. , Luo Y. H. , Bai S. P. , Zeng Q. F. , Su Z. W. , Xuan Y. , Zhang K. Y.
Published: August 2015

This study assessed the effect of dietary vanadium (V) and vitamin C (VC) on production performance, egg quality and antioxidant status in laying hens. A total of 360 laying hens (31‐week‐old) were randomly allotted into a 3 × 3 factorial arrangement treatments (four replicates and 10 chicks per replicate) with three levels of dietary V (0, 5 and 10 mg/kg) and three levels of vitamin C (0, 50 and 100 mg/kg) for 12 weeks. The effect of V and VC did not alter egg production, egg weight, average daily feed intake and feed conversion ratio during 1–12 week. Albumen height and Haugh unit value were linearly decreased (p < 0.001) by addition of V, whereas the effect of 100 mg/kg VC was observed to counteract (p < 0.05) this effect in V‐containing treatments during 1–12 week. Hens fed V‐containing diet laid lighter (linear effect, p < 0.05) coloured eggs (higher lightness value, lower redness and yellowness value), and the VC exerted no influence on it during 1–12 week. The serum superoxide dismutase (SOD), catalase (CAT) and glutathione peroxidase (GSH‐Px) activities, ability to inhibit hydroxyl radical, were significantly decreased, and the malondialdehyde (MDA) and V contents were increased (p < 0.05) by effect of V during 4, 8 and 12 week. The effect of VC alone and the interactive effect between VC and V were shown to increase serum (p < 0.05) SOD activity in 4 week and decrease MAD levels in 12 week. The result indicate that V decreased the egg quality and caused the oxidative stress at level of 5 mg/kg and 10 mg/kg, and the addition of 100 mg/kg vitamin C can alleviate its egg quality reduction effect and can mitigate the oxidative stress to some extent.
Expression of the Helicobacter pylori virulence factor vacuolating cytotoxin A (vacA) is influenced by a potential stem‐loop structure in the 5′ untranslated region of the transcript
Authors: Amilon Karin R. , Letley Darren P. , Winter Jody A. , Robinson Karen , Atherton John C.
Published: August 2015

The vacuolating cytotoxin, VacA, is an important virulence factor secreted by the gastric pathogen Helicobacter pylori. Certain vacA genotypes are strongly associated with disease risk, but the association is not absolute. The factors determining vacA gene expression are not fully understood, and the mechanisms of its regulation are elusive. We have identified a potential mRNA stem‐loop forming structure in the 5′ untranslated region (UTR) of the vacA transcript. Using site‐directed mutagenesis, we found that disruption of the stem‐loop structure reduced steady‐state mRNA levels between two‐ and sixfold (P = 0.0005) and decreased mRNA half‐life compared with wild type (P = 0.03). This led to a marked reduction in VacA protein levels and overall toxin activity. Additionally, during stressful environmental conditions of acid pH or high environmental salt concentrations, when general transcription of vacA was decreased or increased respectively, the stabilising effects of the stem‐loop were even more pronounced. Our results suggest that the stem‐loop structure in the vacA 5′ UTR is an important determinant of vacA expression through stabilisation of the vacA mRNA transcript and that the stabilising effect is of particular importance during conditions of environmental stress.
Different faces of Nocardia infection in renal transplant recipients
Authors: Shrestha Shailendra , Kanellis John , Korman Tony , Polkinghorne Kevan R , Brown Fiona , Yii Ming , Kerr Peter G , Mulley William
Published: August 2015

Aim

Nocardia infections are an uncommon but important cause of morbidity and mortality in renal transplant recipients. The present study was carried out to determine the spectrum of Nocardia infections in a renal transplant centre in Australia.

Methods

A retrospective chart analysis of all renal transplants performed from 2008 to 2014 was conducted to identify cases of culture proven Nocardia infection. The clinical course for each patient with nocardiosis was examined.

Results

Four of the 543 renal transplants patients developed Nocardia infection within 2 to 13 months post‐transplant. All patients were judged at high immunological risk of rejection pre‐transplant and had received multiple sessions of plasmaphoeresis and intravenous immunoglobulin before the onset of the infection. Two patients presented with pulmonary nocardiosis and two with cerebral abscesses. One case of pulmonary nocardiosis was complicated by pulmonary aspergillosis and the other by cytomegalovirus pneumonia. All four patients improved with combination antibiotic therapy guided by drug susceptibility testing. At the time of Nocardia infection all four patients were receiving primary prophylaxis with trimethoprim/sulphamethoxazole (TMP/SMX) 160/800 mg, twice weekly.

Conclusion

Plasmaphoeresis may be risk factor for Nocardia infection and need further study. Nocardia infection may coexist with other opportunistic infections. Identification of the Nocardia species and drug susceptibility testing is essential in guiding the effective management of patients with Nocardia. Intermittent TMP‐SMX (one double strength tablet, twice a week) appears insufficient to prevent Nocardia infection in renal transplant recipients.
Arabidopsis COPPER MODIFIED RESISTANCE1/PATRONUS1 is essential for growth adaptation to stress and required for mitotic onset control
Authors: Juraniec Michal , Heyman Jefri , Schubert Veit , Salis Pietrino , De Veylder Lieven , Verbruggen Nathalie
Published: August 2015

The mitotic checkpoint (MC) guards faithful sister chromatid segregation by monitoring the attachment of spindle microtubules to the kinetochores. When chromosome attachment errors are detected, MC delays the metaphase‐to‐anaphase transition through the inhibition of the anaphase‐promoting complex/cyclosome (APC/C) ubiquitin ligase. In contrast to yeast and mammals, our knowledge on the proteins involved in MC in plants is scarce.

Transient synchronization of root tips as well as promoter–reporter gene fusions were performed to analyze temporal and spatial expression of COPPER MODIFIED RESISTANCE1/PATRONUS1 (CMR1/PANS1) in developing Arabidopsis thaliana seedlings. Functional analysis of the gene was carried out, including CYCB1;2 stability in CMR1/PANS1 knockout and overexpressor background as well as metaphase–anaphase chromosome status.

CMR1/PANS1 is transcriptionally active during M phase. Its deficiency provokes premature cell cycle exit and in consequence a rapid consumption of the number of meristematic cells in particular under stress conditions that are known to affect spindle microtubules. Root growth impairment is correlated with a failure to delay the onset of anaphase, resulting in anaphase bridges and chromosome missegregation. CMR1/PANS1 overexpression stabilizes the mitotic CYCB1;2 protein.

Likely, CMR1/PANS1 coordinates mitotic cell cycle progression by acting as an APC/C inhibitor and plays a key role in growth adaptation to stress.
An RNA‐Seq‐based reference transcriptome for Citrus
Authors: Terol Javier , Tadeo Francisco , Ventimilla Daniel , Talon Manuel
Published: August 2015

Previous RNA‐Seq studies in citrus have been focused on physiological processes relevant to fruit quality and productivity of the major species, especially sweet orange. Less attention has been paid to vegetative or reproductive tissues, while most Citrus species have never been analysed. In this work, we characterized the transcriptome of vegetative and reproductive tissues from 12 Citrus species from all main phylogenetic groups. Our aims were to acquire a complete view of the citrus transcriptome landscape, to improve previous functional annotations and to obtain genetic markers associated with genes of agronomic interest. 28 samples were used for RNA‐Seq analysis, obtained from 12 Citrus species: C. medica, C. aurantifolia, C. limon, C. bergamia, C. clementina, C. deliciosa, C. reshni, C. maxima, C. paradisi, C. aurantium, C. sinensis and Poncirus trifoliata. Four different organs were analysed: root, phloem, leaf and flower. A total of 3421 million Illumina reads were produced and mapped against the reference C. clementina genome sequence. Transcript discovery pipeline revealed 3326 new genes, the number of genes with alternative splicing was increased to 19 739, and a total of 73 797 transcripts were identified. Differential expression studies between the four tissues showed that gene expression is overall related to the physiological function of the specific organs above any other variable. Variants discovery analysis revealed the presence of indels and SNPs in genes associated with fruit quality and productivity. Pivotal pathways in citrus such as those of flavonoids, flavonols, ethylene and auxin were also analysed in detail.
Mycobacterium tuberculosis nucleic acid amplification tests reduce nosocomial tuberculosis exposure in intensive care units: A nationwide cohort study
Authors: Wang Jann‐Yuan , Lee Ming‐Chia , Chang Jer‐Hwa , Yu Ming‐Chih , Wu Vin‐Cent , Huang Kuo‐Liang , Su Chiu‐Ping , Chao Kun‐Mao , Lee Chih‐Hsin
Published: August 2015

Background and objective

This retrospective national surveillance study investigated the burden of and risk factors for nosocomial exposure of pulmonary tuberculosis (TB) in intensive care units.

Methods

Patients admitted to intensive care units were identified from the National Health Insurance Research Database. During 2004–2009, there were 1 387 707 intensive care unit admissions of 900 562 adult patients. Pulmonary tuberculosis association was considered if the patient was diagnosed with pulmonary tuberculosis during admission or within 3 months after discharge. Nosocomial transmissible period was calculated based on the length of anti‐tuberculosis treatment and negative‐pressure isolation during admission.

Results

Pulmonary tuberculosis was associated with 1.20% of all intensive care unit admissions and 6731 (38.9%) started anti‐TB treatment during admission. For the other 10 583 admissions, the diagnosis was made after discharge and anti‐TB treatment was not prescribed during admission. The probability paralleled the regional tuberculosis incidence. On average, 2794 pulmonary tuberculosis associated intensive care unit admissions contributed to 42 999–44 062 days of nosocomial exposure per year. The length of nosocomial transmissible period decreased with the gradual implementation of Mycobacterium tuberculosis nucleic acid amplification tests in intensive care practice. Multivariate linear regression analysis revealed that the length of nosocomial transmissible period was inversely associated with male gender, airway symptoms prior to admission and performing M. tuberculosis nucleic acid amplification tests and mycobacterial culture.

Conclusions

Nosocomial tuberculosis exposure is not uncommon in intensive care units. Performing rapid molecular diagnostic tests in those suspected of tuberculosis is recommended to reduce the risk of nosocomial exposure.
2015 proceedings of the National Heart, Lung, and Blood Institute's State of the Science in Transfusion Medicine symposium
Authors: Spitalnik Steven L. , Triulzi Darrell , Devine Dana V. , Dzik Walter H. , Eder Anne F. , Gernsheimer Terry , Josephson Cassandra D. , Kor Daryl J. , Luban Naomi L. C. , Roubinian Nareg H. , Mondoro Traci , Welniak Lisbeth A. , Zou Shimian , Glynn Simone ,   for the State of the Science in Transfusion Medicine Working Groups
Published: August 2015

On March 25 and 26, 2015, the National Heart, Lung, and Blood Institute sponsored a meeting on the State of the Science in Transfusion Medicine on the National Institutes of Health (NIH) campus in Bethesda, Maryland, which was attended by a diverse group of 330 registrants. The meeting's goal was to identify important research questions that could be answered in the next 5 to 10 years and which would have the potential to transform the clinical practice of transfusion medicine. These questions could be addressed by basic, translational, and/or clinical research studies and were focused on four areas: the three “classical” transfusion products (i.e., red blood cells, platelets, and plasma) and blood donor issues. Before the meeting, four working groups, one for each area, prepared five major questions for discussion along with a list of five to 10 additional questions for consideration. At the meeting itself, all of these questions, and others, were discussed in keynote lectures, small‐group breakout sessions, and large‐group sessions with open discourse involving all meeting attendees. In addition to the final lists of questions, provided herein, the meeting attendees identified multiple overarching, cross‐cutting themes that addressed issues common to all four areas; the latter are also provided. It is anticipated that addressing these scientific priorities, with careful attention to the overarching themes, will inform funding priorities developed by the NIH and provide a solid research platform for transforming the future practice of transfusion medicine.
Simulation‐Based Learning as a Tactic for Teaching Evidence‐Based Practice
Authors: Raurell‐Torredà Marta , Romero‐Collado Àngel
Published: August 2015

This column shares the best evidence‐based strategies and innovative ideas on how to facilitate the learning of EBP principles and processes by clinicians as well as nursing and interprofessional students. Guidelines for submission are available at http://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1741‐6787
Computational Modeling of Rolling Wave-Energy Converters in a Viscous Fluid1
Authors: Jiang Yichen , Yeung Ronald W.
Published: August 2015

The performance of an asymmetrical rolling cam as an ocean-wave energy extractor was studied experimentally and theoretically in the 70s. Previous inviscid-fluid theory indicated that energy-absorbing efficiency could approach 100% in the absence of real-fluid effects. The way viscosity alters the performance is examined in this paper for two distinctive rolling-cam shapes: a smooth “Eyeball Cam (EC)” with a simple mathematical form and a “Keeled Cam (KC)” with a single sharp-edged keel. Frequency-domain solutions in an inviscid fluid were first sought for as baseline performance metrics. As expected, without viscosity, both shapes, despite their differences, perform exceedingly well in terms of extraction efficiency. The hydrodynamic properties of the two shapes were then examined in a real fluid, using the solution methodology called the free-surface random-vortex method (FSRVM). The added inertia and radiation damping were changed, especially for the KC. With the power-take-off (PTO) damping present, nonlinear time-domain solutions were developed to predict the rolling motion, the effects of PTO damping, and the effects of the cam shapes. For the EC, the coupled motion of sway, heave and roll in waves was investigated to understand how energy extraction was affected.
Facile technique for the removal of metal contamination from graphene
Authors: Wells George H. , Hunt Michael R. C. , Hopf Toby , Vassilevski Konstantin V. , Escobedo-Cousin Enrique , Horsfall Alton B. , Goss Jonathan P. , O'Neill Anthony
Published: August 2015

Metal contamination deposited on few-layer graphene (3 ± 1 monolayers) grown on SiC(0001) was successfully removed from the surface, using low cost adhesive tape. More than 99% of deposited silver contamination was removed from the surface via peeling, causing minimal damage to the graphene. A small change in the adhesion of graphene to the SiC(0001) substrate was indicated by changes observed in pleat defects on the surface; however, atomic resolution images show the graphene lattice remains pristine. Thin layers of contamination deposited via an electron gun during Auger electron spectroscopy/low energy electron diffraction measurements were also found to be removable by this technique. This contamination showed similarities to “roughened” graphene previously reported in the literature.
Constitutive and Inducible Expression of the rRNA Methylase Gene
erm
(B) in Campylobacter
Authors: Deng Fengru , Shen Jianzhong , Zhang Maojun , Wu Congming , Zhang Qijing , Wang Yang
Published: August 2015

Macrolides are the antimicrobials of choice for treating human campylobacteriosis. The recent emergence of
erm
(B) in
Campylobacter
bacteria threatens the utility of this class of antibiotics. Here we report the constitutive and inducible expression of
erm
(B) in
Campylobacter
isolates derived from diarrheal patients and food-producing animals. Constitutive expression of
erm
(B) was associated with insertion and deletion in the regulatory region of the gene, providing the first documentation of the differential expression of
erm
(B) in
Campylobacter
bacteria.
Candida parapsilosis Resistance to Fluconazole: Molecular Mechanisms and
In Vivo
Impact in Infected Galleria mellonella Larvae
Authors: Souza Ana Carolina R. , Fuchs Beth Burgwyn , Pinhati Henrique M. S. , Siqueira Ricardo A. , Hagen Ferry , Meis Jacques F. , Mylonakis Eleftherios , Colombo Arnaldo L.
Published: August 2015

Candida parapsilosis
is the main non-
albicans Candida
species isolated from patients in Latin America. Mutations in the
ERG11
gene and overexpression of membrane transporter proteins have been linked to fluconazole resistance. The aim of this study was to evaluate the molecular mechanisms in fluconazole-resistant strains of
C. parapsilosis
isolated from critically ill patients. The identities of the nine collected
C. parapsilosis
isolates at the species level were confirmed through molecular identification with a TaqMan qPCR assay. The clonal origin of the strains was checked by microsatellite typing. The
Galleria mellonella
infection model was used to confirm
in vitro
resistance. We assessed the presence of
ERG11
mutations, as well as the expression of
ERG11
and two additional genes that contribute to antifungal resistance (
CDR1
and
MDR1
), by using real-time quantitative PCR. All of the
C. parapsilosis
(
sensu stricto
) isolates tested exhibited fluconazole MICs between 8 and 16 μg/ml. The
in vitro
data were confirmed by the failure of fluconazole in the treatment of
G. mellonella
infected with fluconazole-resistant strains of
C. parapsilosis
. Sequencing of the
ERG11
gene revealed a common mutation leading to a Y132F amino acid substitution in all of the isolates, a finding consistent with their clonal origin. After fluconazole exposure, overexpression was noted for
ERG11
,
CDR1
, and
MDR1
in 9/9, 9/9, and 2/9 strains, respectively. We demonstrated that a combination of molecular mechanisms, including the presence of point mutations in the
ERG11
gene, overexpression of
ERG11
, and genes encoding efflux pumps, are involved in fluconazole resistance in
C. parapsilosis
.
Identification of NDM-1 in a Putatively Novel Acinetobacter Species (“NB14”) Closely Related to Acinetobacter pittii
Authors: Espinal Paula , Mosqueda Noraida , Telli Murat , van der Reijden Tanny , Rolo Dora , Fernández-Orth Dietmar , Dijkshoorn Lenie , Roca Ignasi , Vila Jordi
Published: August 2015

In this study, we describe the molecular characterization of a plasmid-located
bla
NDM-1
harbored by an
Acinetobacter
clinical isolate recovered from a patient in Turkey that putatively constitutes a novel
Acinetobacter
species, as shown by its distinct ARDRA (amplified 16S ribosomal DNA restriction analysis) profile and molecular sequencing techniques.
bla
NDM-1
was carried by a conjugative plasmid widespread among non-
baumannii Acinetobacter
isolates, suggesting its potential for dissemination before reaching more clinically relevant
Acinetobacter
species.
Coculture of Escherichia coli O157:H7 with a Nonpathogenic E. coli Strain Increases Toxin Production and Virulence in a Germfree Mouse Model
Authors: Goswami Kakolie , Chen Chun , Xiaoli Lingzi , Eaton Kathryn A. , Dudley Edward G.
Published: August 2015

Escherichia coli
O157:H7 is a notorious foodborne pathogen due to its low infectious dose and the disease symptoms it causes, which include bloody diarrhea and severe abdominal cramps. In some cases, the disease progresses to hemorrhagic colitis (HC) and hemolytic uremic syndrome (HUS), due to the expression of one or more Shiga toxins (Stx). Isoforms of Stx, including Stx2a, are encoded within temperate prophages. In the presence of certain antibiotics, phage induction occurs, which also increases the expression of toxin genes. Additionally, increased Stx2 accumulation has been reported when O157:H7 was cocultured with phage-susceptible nonpathogenic
E. coli
. This study characterized an
E. coli
O157:H7 strain, designated PA2, that belongs to the hypervirulent clade 8 cluster. Stx2a levels after ciprofloxacin induction were lower for PA2 than for the prototypical outbreak strains Sakai and EDL933. However, during coculture with the nonpathogenic strain
E. coli
C600, PA2 produced Stx2a levels that were 2- to 12-fold higher than those observed during coculture with EDL933 and Sakai, respectively. Germfree mice cocolonized by PA2 and C600 showed greater kidney damage, increased Stx2a accumulation in feces, and more visible signs of disease than mice given PA2 or C600 alone. These data suggest one mechanism by which microorganisms associated with the colonic microbiota could enhance the virulence of
E. coli
O157:H7, particularly a subset of clade 8 strains.
Streptococcus gordoniiprosthetic joint infection in the setting of vigorous dental flossing
Authors: Klein Rick , Dababneh Ala S , Palraj Bharath Raj Varatharaj
Published: August 2015

A 65-year-old woman with osteoarthritis, who underwent knee replacement 5 years prior, developed sudden onset knee pain and swelling. She had voluntarily starting a vigorous dental flossing regimen prior to the onset of symptoms. The patient underwent right knee arthrotomy, irrigation and debridement of right total knee arthroplasty and exchange of polyethylene with retention of the prosthesis. Intraoperative cultures grewStreptococcus gordonii. She was treated with 6 weeks of ceftriaxone and was later placed on oral antibiotic suppression.
A Neural Network Ensemble Classifier for Effective Intrusion Detection Using Fuzzy Clustering and Radial Basis Function Networks
Authors: Amini Mohammad , Rezaeenour Jalal , Hadavandi Esmaeil
Published: August 2015

Intrusion Detection Systems have considerable importance in preventing security threats and protecting computer networks against attackers. So far, various classification approaches using data mining and machine learning techniques have been proposed to the problem of intrusion detection. However, using single classifier systems for intrusion detection suffers from some limitations including lower detection rate for low-frequent attacks, detection instability, and complexity in training process. Ensemble classifier systems combine several individual classifiers and obtain a classifier with higher performance. In this paper, we propose a new ensemble classifier using Radial Basis Function (RBF) neural networks and fuzzy clustering in order to increase detection accuracy and stability, reduce false positives, and provide higher detection rate for low-frequent attacks. We also use a hybrid combination method to aggregate the individual predictions of the base classifiers, which helps to increase detection accuracy. The experimental results on NSL-KDD data set demonstrate that our proposed system has a higher detection accuracy compared to other wellknown classification systems. It also performs more effectively for detection of low-frequent attacks. Furthermore, the proposed ensemble method offers better performance compared to popular ensemble methods.
Tabu Search to Solve the Shape from Shading Ambiguity
Authors: Abada Lyes , Aouat Saliha
Published: August 2015

The three-dimensional reconstruction of an object from one gray-scale image is a basic problem in computer vision. This problem is known by Shape From Shading. It is considered as an ill-posed due to the ambiguity of the convexity or the concavity of the surface to be reconstructed. A method of solving the ambiguity based on the singular points of the image was proposed in this paper. It uses tabu search to determine the optimal solution of the solution space. The proposed method determines all 3D objects for an image in a short time. The proposed method has been tested on synthetic and real images, it was compared with another method of resolution.
Breakdown of the equivalence between gravitational mass and energy for a quantum body: Theory and suggested experiments
Authors: Lebed Andrei G.
Published: August 2015

In this paper, we review recent theoretical results, obtained for the equivalence between gravitational mass and energy of a composite quantum body as well as for its breakdown at macroscopic and microscopic levels. In particular, we discuss that the expectation values of passive and active gravitational mass operators are equivalent to the expectation value of energy for electron stationary quantum states in hydrogen atom. On the other hand, for superpositions of the stationary quantum states, inequivalence between the gravitational masses and energy appears at a macroscopic level. It reveals itself as time-dependent oscillations of the expectation values of passive and active gravitational masses, which can be, in principle, experimentally measured. Inequivalence between passive gravitational mass and energy at a microscopic level can be experimentally observed as unusual electromagnetic radiation, emitted by a macroscopic ensemble of the atoms. We propose the corresponding experiment, which can be done on the Earth's orbit, using small spacecraft. If such experiment is done it would be the first direct observation of quantum effects in general relativity.
On injective envelopes of semimodules over semirings
Authors: Il’in S. N.
Published: August 2015

As is well-known, every module over a ring has an injective envelope; however, that fact does not hold, in general, for semimodules over semirings. We study the problem of existence of injective envelopes with respect to several types of semimodules, in particular, we consider simple semimodules, modules, additively idempotent semimodules, and additively regular semimodules. We completely describe semirings whose all semimodules of these types have injective envelopes.
CONSEQUENCES AND ANTECEDENTS OF ABSORPTIVE CAPACITY IN A CROSS-CULTURAL CONTEXT
Authors: ADAMS DANIEL ROBERT , FLATTEN TESSA CHRISTINA , BRINKMANN HELGE , BRETTEL MALTE
Published: August 2015

Continuous innovation is one of the key challenges businesses are currently facing, which makes organisational absorptive capacity (ACAP) — a firms ability to explore and exploit external knowledge — a highly relevant topic. This study addresses ACAPs consequences and antecedents in an international context by analysing data from 549 small and medium-sized companies in Austria, Brazil, Germany, India, Singapore, and the US First, we reveal that both potential and realised ACAP have an equally strong positive impact on firm performance around the world. Second, we assess that the relationship between organisational structure and potential ACAP is not moderated by national cultural values. Furthermore, we show that the role a formalised organisational structure plays with regard to realised ACAP is positively moderated by the national cultural characteristic of power distance and negatively by the national cultural trait of masculinity. In contrast, masculinity positively moderates the relationship between specialisation and realised ACAP. Overall, with our study, we advance research on the consequences as well as the antecedents of ACAP and provide managers with mechanisms to support corporate knowledge absorption and innovation generation throughout the world.
Privacy in the Genomic Era
Authors: Naveed Muhammad , Ayday Erman , Clayton Ellen W. , Fellay Jacques , Gunter Carl A. , Hubaux Jean-Pierre , Malin Bradley A. , Wang Xiaofeng
Published: August 2015

Genome sequencing technology has advanced at a rapid pace and it is now possible to generate highly-detailed genotypes inexpensively. The collection and analysis of such data has the potential to support various applications, including personalized medical services. While the benefits of the genomics revolution are trumpeted by the biomedical community, the increased availability of such data has major implications for personal privacy; notably because the genome has certain essential features, which include (but are not limited to)
(i)
an association with traits and certain diseases,
(ii)
identification capability (e.g., forensics), and
(iii)
revelation of family relationships. Moreover, direct-to-consumer DNA testing increases the likelihood that genome data will be made available in less regulated environments, such as the Internet and for-profit companies. The problem of genome data privacy thus resides at the crossroads of computer science, medicine, and public policy. While the computer scientists have addressed data privacy for various data types, there has been less attention dedicated to genomic data. Thus, the goal of this paper is to provide a systematization of knowledge for the computer science community. In doing so, we address some of the (sometimes erroneous) beliefs of this field and we report on a survey we conducted about genome data privacy with biomedical specialists. Then, after characterizing the genome privacy problem, we review the state-of-the-art regarding privacy attacks on genomic data and strategies for mitigating such attacks, as well as contextualizing these attacks from the perspective of medicine and public policy. This paper concludes with an enumeration of the challenges for genome data privacy and presents a framework to systematize the analysis of threats and the design of countermeasures as the field moves forward.
Degradation Effect of Sulfa Antibiotics by Potassium Ferrate Combined with Ultrasound (Fe(VI)-US)
Authors: Zhang Kejia , Luo Zhang , Zhang Tuqiao , Gao Naiyun , Ma Yan
Published: August 2015

Sulfa antibiotics are a family of typical broad-spectrum antibiotics, which have become one of the most frequently detected antibiotics in water, posing a great threat to human health and ecosystem. Potassium ferrate is a new type of high-efficiency multifunctional water treatment agent, collecting the effects of oxidation, adsorption, flocculation, coagulation, sterilization, and deodorization. Performance and mechanism of degradation of typical broad-spectrum antibiotics by Fe(VI)-US were further studied, investigating the degradation effect of sulfa antibiotics by single ultrasound, single potassium ferrate, and potassium ferrate-ultrasound (Fe(VI)-US). It was found that Fe(VI)-US technology had a significant role in promoting the degradation of sulfa antibiotics via orthogonal experiments. Factors evaluated included sulfa antibiotics type, pH value, potassium ferrate dosage, ultrasonic frequency, and ultrasonic power, with the pH value and potassium ferrate dosage being affected most significantly. One reason for synergy facilitating the degradation is the common oxidation of potassium ferrate and ultrasound, and the other is that Fe(III) produced promotes the degradation rate. According to the product analysis and degradation pathways of three sulfa antibiotics, ferrate-sonication sulfa antibiotics are removed by hydroxyl radical oxidation.
Application of Neutron Activation Analysis for Determination of As, Cr, Hg, and Se in Mosses in the Metropolitan Area of the Valley of Toluca, Mexico
Authors: Mejía-Cuero R. , García-Rosales G. , Longoria-Gándara L. C. , López-Reyes M. C. , Ávila-Pérez P.
Published: August 2015

This research presents a study of environmental monitoring at different sampling sites from the Metropolitan Area of the Valley of Toluca (MAVT), Mexico, using mosses (Leskea angustata(Tayl.) andFabronia ciliaris(Brid.)) and soil samples. The epiphytic mosses and soils were sampled in two campaigns within two periods of the year, a rainy and dry-cold season. The selected sampling sites included urban regions (UR), transitional regions (TR), and protected natural areas (PA). The samples were analyzed by the Instrumental Neutron Activation Analysis (INAA) to determine As, Cr, Hg, and Se principally. However, due to the versatility of the analytic technique used, other elements including Cs, Co, Sc, Sb, Rb, Ce, La, Eu, and Yb were also detected. Statistical analysis (As, Cr, Hg, and Se) was carried out with principal components and cluster analysis methods; this revealed that a good correlation exists between metal content in mosses and the degree of pollution in the areas sampled. The obtained results in mosses showed that the concentrations of As, Cr, Co, Cs, Rb, Ce, La, and Yb increased with respect to the concentrations obtained during the first sampling, whereas Se, Sc, Sb and Eu, concentrations were decreased. For As and Hg, the concentrations were similar in both sampling periods. The soil samples present the most significant concentration.
Complete Bilateral Teleoperation System for a Rotorcraft UAV with Time-Varying Delay
Authors: Salinas Lucio R. , Slawiñski Emanuel , Mut Vicente A.
Published: August 2015

This paper proposes the use of simple proportional plus damping injection (P+d) controllers for delayed bilateral teleoperation of a rotorcraft UAV. The proposed control scheme involves P+d remote and local controllers, considers master and slave dynamics, and takes into account asymmetric time-varying delays. The stability of the proposed teleoperation system is analyzed using Lyapunov-Krasovskii functionals and delay-dependent stability criteria are obtained under linear-matrix-inequalities conditions. The performance of the teleoperation scheme is tested driving a virtual nonlinear 6DOF dynamic model of a minihelicopter in a human-in-the-loop simulation.
Correlation Properties of (Discrete) Fractional Gaussian Noise and Fractional Brownian Motion
Authors: Delignières Didier
Published: August 2015

The fractional Gaussian noise/fractional Brownian motion framework (fGn/fBm) has been widely used for modeling and interpreting physiological and behavioral data. The concept of 1/fnoise, reflecting a kind of optimal complexity in the underlying systems, is of central interest in this approach. It is generally considered that fGn and fBm represent a continuum, punctuated by the boundary of “ideal” 1/fnoise. In the present paper, we focus on the correlation properties of discrete-time versions of these processes (dfGn and dfBm). We especially derive a new analytical expression of the autocorrelation function (ACF) of dfBm. We analyze the limit behavior of dfGn and dfBm when they approach their upper and lower limits, respectively. We show that, asHapproaches 1, the ACF of dfGn tends towards 1 at all lags, suggesting that dfGn series tend towards straight line. Conversely, asHapproaches 0, the ACF of dfBm tends towards 0 at all lags, suggesting that dfBm series tend towards white noise. These results reveal a severe breakdown of correlation properties around the 1/fboundary and challenge the idea of a smooth transition between dfGn and dfBm processes. We discuss the implications of these findings for the application of the dfGn/dfBm model to experimental series, in terms of theoretical interpretation and modeling.
SP140L, an Evolutionarily Recent Member of the SP100 Family, Is an Autoantigen in Primary Biliary Cirrhosis
Authors: Saare Mario , Hämarik Uku , Venta Rainis , Panarina Marina , Zucchelli Chiara , Pihlap Maire , Remm Anu , Kisand Kai , Toots Urve , Möll Kaidi , Salupere Riina , Musco Giovanna , Uibo Raivo , Peterson Pärt
Published: August 2015

The SP100 family members comprise a set of closely related genes on chromosome 2q37.1. The widely expressed SP100 and the leukocyte-specific proteins SP110 and SP140 have been associated with transcriptional regulation and various human diseases. Here, we have characterized the SP100 family member SP140L. The genome sequence analysis showed the formation ofSP140Lgene through rearrangements of the two neighboring genes,SP100andSP140, during the evolution of higher primates. TheSP140Lexpression is interferon-inducible with high transcript levels in B cells and other peripheral blood mononuclear cells. Subcellularly, SP140L colocalizes with SP100 and SP140 in nuclear structures that are devoid of SP110, PML, or p300 proteins. Similarly to SP100 and SP140 protein, we detected serum autoantibodies to SP140L in patients with primary biliary cirrhosis using luciferase immunoprecipitation system and immunoblotting assays. In conclusion, our results show that SP140L is phylogenetically recent member of SP100 proteins and acts as an autoantigen in primary biliary cirrhosis patients.