bluuebunny/crossref_metadata_2025_split huggingface dataset:
Microfluidic Studies of Biofilm Formation in Dynamic Environments
Authors: Yawata Yutaka , Nguyen Jen , Stocker Roman , Rusconi Roberto 
Published: June 2016

ABSTRACT
The advent of microscale technologies, such as microfluidics, has revolutionized many areas of biology yet has only recently begun to impact the field of bacterial biofilms. By enabling accurate control and manipulation of physical and chemical conditions, these new microscale approaches afford the ability to combine important features of natural and artificial microbial habitats, such as fluid flow and ephemeral nutrient sources, with an unprecedented level of flexibility and quantification. Here, we review selected case studies to exemplify this potential, discuss limitations, and suggest that this approach opens new vistas into biofilm research over traditional setups, allowing us to expand our understanding of the formation and consequences of biofilms in a broad range of environments and applications.
Seminal Plasma Promotes Neisseria gonorrhoeae Aggregation and Biofilm Formation
Authors: Anderson Mark T. , Byerly Luke , Apicella Michael A. , Seifert H. Steven 
Published: June 2016

ABSTRACT

Neisseria gonorrhoeae
causes the human-specific disease gonorrhea and is transmitted from person to person primarily via sexual contact. During transmission,
N. gonorrhoeae
is often exposed to seminal fluid and must adapt to this change in environment. Previous work demonstrated that seminal fluid facilitates
N. gonorrhoeae
motility and alters epithelial cell interactions. In this study, exposure to seminal fluid was found to decrease surface adherence of gonococci in a manner that was independent of Opa adhesin proteins or type IV pilus retraction. Semen was also shown to cause dispersal of bacteria that had previously established surface adherence. Although surface adherence decreased, interbacterial interactions were increased by seminal plasma both in long-term static culture and on a cell-to-cell basis over shorter time periods. The result of increased bacterium-bacterium interactions resulted in the formation of microcolonies, an important step in the
N. gonorrhoeae
infectious process. Seminal fluid also facilitated increased bacterial aggregation in the form of shear-resistant three-dimensional biofilms. These results emphasize the importance of the gonococcal response to the influx of seminal fluid within the genital niche. Further characterization of the
N. gonorrhoeae
response to semen will advance our understanding of the mechanisms behind the establishment of infection in naive hosts and the process of transmission.

IMPORTANCE
N. gonorrhoeae
is the causative agent of the globally prevalent sexually transmitted infection gonorrhea. An understudied aspect of this human-adapted pathogen is the change in bacterial physiology that occurs during sexual transmission.
N. gonorrhoeae
encounters semen when transmitted from host to host, and it is known that, when
N. gonorrhoeae
is exposed to seminal fluid, alterations in bacterial motility and type IV pilus arrangement occur. This work extends our previous observations on this modulation of gonococcal physiology by seminal fluid and demonstrates that seminal plasma decreases surface adherence, promotes interbacterial interactions, and enhances biofilm formation.
The
SMUL_1544
Gene Product Governs Norcobamide Biosynthesis in the Tetrachloroethene-Respiring Bacterium Sulfurospirillum multivorans
Authors: Keller Sebastian , Treder Aaron , von Reuss Stephan H. , Escalante-Semerena Jorge C. , Schubert Torsten 
Published: June 2016

ABSTRACT

The tetrachloroethene (PCE)-respiring bacterium
Sulfurospirillum multivorans
produces a unique cobamide, namely, norpseudo-B
12
, which, in comparison to other cobamides, e.g., cobalamin and pseudo-B
12
, lacks the methyl group in the linker moiety of the nucleotide loop. In this study, the protein SMUL_1544 was shown to be responsible for the formation of the unusual linker moiety, which is most probably derived from ethanolamine-phosphate (EA-P) as the precursor. The product of the
SMUL_1544
gene successfully complemented a
Salmonella enterica
Δ
cobD
mutant. The
cobD
gene encodes an
l
-threonine-
O
-3-phosphate (
l
-Thr-P) decarboxylase responsible for the synthesis of (
R
)-1-aminopropan-2-ol
O
-2-phosphate (AP-P), required specifically for cobamide biosynthesis. When SMUL_1544 was produced in the heterologous host lacking CobD, norpseudo-B
12
was formed, which pointed toward the formation of EA-P rather than AP-P. Guided cobamide biosynthesis experiments with minimal medium supplemented with
l
-Thr-P supported cobamide biosynthesis in
S. enterica
producing SMUL_1544 or
S. multivorans
. Under these conditions, both microorganisms synthesized pseudo-B
12
. This observation indicated a flexibility in the SMUL_1544 substrate spectrum. From the formation of catalytically active PCE reductive dehalogenase (PceA) in
S. multivorans
cells producing pseudo-B
12
, a compatibility of the respiratory enzyme with the cofactor was deduced. This result might indicate a structural flexibility of PceA in cobamide binding. Feeding of
l
-[3-
13
C]serine to cultures of
S. multivorans
resulted in isotope labeling of the norpseudo-B
12
linker moiety, which strongly supports the hypothesis of EA-P formation from
l
-serine-
O
-phosphate (
l
-Ser-P) in this organism.

IMPORTANCE
The identification of the gene product SMUL_1544 as a putative
l
-Ser-P decarboxylase involved in norcobamide biosynthesis in
S. multivorans
adds a novel module to the assembly line of cobamides (complete corrinoids) in prokaryotes. Selected cobamide-containing enzymes (e.g., reductive dehalogenases) showed specificity for their cobamide cofactors. It has recently been proposed that the structure of the linker moiety of norpseudo-B
12
and the mode of binding of the EA-P linker to the PceA enzyme reflect the high specificity of the enzyme for its cofactor. Data reported herein do not support this idea. In fact, norpseudo-B
12
was functional in the cobamide-dependent methionine biosynthesis of
S. enterica
, raising questions about the role of norcobamides in nature.
Essential Genes Predicted in the Genome of Rubrivivax gelatinosus
Authors: Curtis Patrick D. 
Published: June 2016

ABSTRACT

Rubrivivax gelatinosus
is a betaproteobacterium with impressive metabolic diversity. It is capable of phototrophy, chemotrophy, two different mechanisms of sugar metabolism, fermentation, and H
2
gas production. To identify core essential genes,
R. gelatinosus
was subjected to saturating transposon mutagenesis and high-throughput sequencing (TnSeq) analysis using nutrient-rich, aerobic conditions. Results revealed that virtually no primary metabolic genes are essential to the organism and that genomic redundancy only explains a portion of the nonessentiality, but some biosynthetic pathways are still essential under nutrient-rich conditions. Different essentialities of different portions of the Pho regulatory pathway suggest that overexpression of the regulon is toxic and hint at a larger connection between phosphate regulation and cellular health. Lastly, various essentialities of different tRNAs hint at a more complex situation than would be expected for such a core process. These results expand upon research regarding cross-organism gene essentiality and further enrich the study of purple nonsulfur bacteria.

IMPORTANCE
Microbial genomic data are increasing at a tremendous rate, but physiological characterization of those data lags far behind. One mechanism of high-throughput physiological characterization is TnSeq, which uses high-volume transposon mutagenesis and high-throughput sequencing to identify all of the essential genes in a given organism's genome. Here TnSeq was used to identify essential genes in the metabolically versatile betaproteobacterium
Rubrivivax gelatinosus
. The results presented here add to the growing TnSeq field and also reveal important aspects of
R. gelatinosus
physiology, which are applicable to researchers working on metabolically flexible organisms.
Validation of the Kinyarwanda-version Short-Form Leeds Dyspepsia Questionnaire and Short-Form Nepean Dyspepsia Index to assess dyspepsia prevalence and quality-of-life impact in Rwanda
Authors: Nkurunziza Arcade , Dusabejambo Vincent , Everhart Kelly , Bensen Steve , Walker Tim 
Published: June 2016

ObjectivesWe aimed to develop and validate Kinyarwanda versions of Short-Form Leeds Dyspepsia Questionnaire (SF-LDQ) and Short-Form Nepean Dyspepsia Index (SF-NDI) to measure the frequency and severity of dyspepsia and associated quality-of-life impact in Rwanda.SettingA single, tertiary care centre in Rwanda.Participants200 consecutive Kinyarwanda-speaking patients referred to endoscopy (100 patients) or medical outpatients (100 patients).InterventionsKinyarwanda versions of the SF-LDQ and SF-NDI were developed from English versions by translation, with back translation, crosschecking and pilot testing. Study participants completed these questionnaires at enrolment (time 1), and then completed the surveys again with blinded phone interviewers 3 days later (time 2). 20 randomly selected participants, diagnosed with a peptic ulcer on index endoscopy, completed a third survey by phone at day 30 (time 3), after therapy.Primary outcome measuresInternal consistency at time 1 (by Cronbach's α) and test–retest reliability between time 1 and time 2 (Spearman's correlation coefficient) for translated SF-LDQ and SF-NDI; validity versus clinical diagnosis (by receiver operating characteristic (ROC) curve) and responsiveness to treatment for SF-LDQ (by change in mean score). All outcomes were measured as per protocol.ResultsCronbach's α of the translated SF-LDQ was 0.93, showing high internal consistency. Spearman's correlation coefficient comparing time 1 and time 2 was 0.978 (p<0.001), demonstrating high reliability. Cronbach's α for the translated SF-NDI was 0.92. A cut-off score of 16 on the SF-LDQ showed a sensitivity of 97% and a specificity of 71% for the diagnosis of dyspepsia, correctly classifying 89% of patients. In the responsiveness analysis, the mean SF-LDQ score was reduced from 20.1 prior to treatment to 13.9 after 30 days of treatment (p=0.003).ConclusionsThe Kinyarwanda versions of the SF-LDQ and SF-NDI were valid, reliable and responsive to treatment.
Clinical outcomes at 12 months and risk of inflammatory bowel disease in patients with an intermediate raised fecal calprotectin: a ‘real-world’ view
Authors: McFarlane Michael , Chambers Samantha , Malik Ahmad , Lee Bee , Sung Edmond , Nwokolo Chuka , Waugh Norman , Arasaradnam Ramesh 
Published: June 2016

ObjectivesA recent systematic review confirmed the usefulness of fecal calprotectin (FC) in distinguishing organic (inflammatory bowel disease (IBD)) from non-organic gastrointestinal disease (irritable bowel syndrome (IBS)). FC levels <50 μg/g have a negative predictive value >92% to exclude organic gastrointestinal (GI) disease. Levels >250 μg/g correlate with endoscopic IBD disease activity; sensitivity 90%. We aimed to determine clinical outcomes in intermediate raised FC results (50–250 μg/g).SettingPrimary care general practices in Coventry and Warwickshire, and 3 secondary care hospitals.Participants443 FC results in adults (>16 years old) were reviewed from July 2012 to October 2013. Clinical data was collected from hospital databases and general practitioners. Long-term clinical data was available in 41 patients (out of 48).Primary and secondary outcome measuresThe number of new diagnoses of IBD, IBS and other diagnoses for the intermediate group. The number referred and discharged from secondary care.ResultsA new IBD diagnosis was made in 19% (n=8) of intermediate results (1% of normal and 38% of raised results). 5% (n=2) of intermediate results had known IBD in remission. A new IBS diagnosis was made in 27% (n=11) of intermediate results, while 34% (n=14) remained undiagnosed, although 8 of these were not referred to secondary care.ConclusionsFC testing remains useful in aiding diagnosis of organic GI conditions. However, unlike negative and strongly positive FC results, intermediate FC results lead to a mixture of diagnoses. The OR of a new diagnosis of IBD for an intermediate result compared to normal FC result was 26.6, while an intermediate FC result gave an OR of 0.54 for a new IBS diagnosis compared to normal FC. For intermediate FC results, 1 in 3 patients remained in secondary care after 12 months with an OR of 3.6 compared to a normal FC result.
Effect of affordable technology on physical activity levels and mobility outcomes in rehabilitation: a protocol for the Activity and MObility UsiNg Technology (AMOUNT) rehabilitation trial
Authors: Hassett Leanne , van den Berg Maayken , Lindley Richard I , Crotty Maria , McCluskey Annie , van der Ploeg Hidde P , Smith Stuart T , Schurr Karl , Killington Maggie , Bongers Bert , Howard Kirsten , Heritier Stephane , Togher Leanne , Hackett Maree , Treacy Daniel , Dorsch Simone , Wong Siobhan , Scrivener Katharine , Chagpar Sakina , Weber Heather , Pearson Ross , Sherrington Catherine 
Published: June 2016

IntroductionPeople with mobility limitations can benefit from rehabilitation programmes that provide a high dose of exercise. However, since providing a high dose of exercise is logistically challenging and resource-intensive, people in rehabilitation spend most of the day inactive. This trial aims to evaluate the effect of the addition of affordable technology to usual care on physical activity and mobility in people with mobility limitations admitted to inpatient aged and neurological rehabilitation units compared to usual care alone.Methods and analysisA pragmatic, assessor blinded, parallel-group randomised trial recruiting 300 consenting rehabilitation patients with reduced mobility will be conducted. Participants will be individually randomised to intervention or control groups. The intervention group will receive technology-based exercise to target mobility and physical activity problems for 6 months. The technology will include the use of video and computer games/exercises and tablet applications as well as activity monitors. The control group will not receive any additional intervention and both groups will receive usual inpatient and outpatient rehabilitation care over the 6-month study period. The coprimary outcomes will be objectively assessed physical activity (proportion of the day spent upright) and mobility (Short Physical Performance Battery) at 6 months after randomisation. Secondary outcomes will include: self-reported and objectively assessed physical activity, mobility, cognition, activity performance and participation, utility-based quality of life, balance confidence, technology self-efficacy, falls and service utilisation. Linear models will assess the effect of group allocation for each continuously scored outcome measure with baseline scores entered as a covariate. Fall rates between groups will be compared using negative binomial regression. Primary analyses will be preplanned, conducted while masked to group allocation and use an intention-to-treat approach.Ethics and disseminationThe protocol has been approved by the relevant Human Research Ethics Committees and the results will be disseminated widely through peer-reviewed publication and conference presentations.Trial registration numberACTRN12614000936628. Pre-results.
Using lean methodology to improve efficiency of electronic order set maintenance in the hospital
Authors: Idemoto Lori , Williams Barbara , Blackmore Craig 
Published: June 2016

Order sets, a series of orders focused around a diagnosis, condition, or treatment, can reinforce best practice, help eliminate outdated practice, and provide clinical guidance. However, order sets require regular updates as evidence and care processes change. We undertook a quality improvement intervention applying lean methodology to create a systematic process for order set review and maintenance.Root cause analysis revealed challenges with unclear prioritization of requests, lack of coordination between teams, and lack of communication between producers and requestors of order sets. In March of 2014, we implemented a systematic, cyclical order set review process, with a set schedule, defined responsibilities for various stakeholders, formal meetings and communication between stakeholders, and transparency of the process.We first identified and deactivated 89 order sets which were infrequently used. Between March and August 2014, 142 order sets went through the new review process. Processing time for the build duration of order sets decreased from a mean of 79.6 to 43.2 days (p<.001, CI=22.1, 50.7).Applying Lean production principles to the order set review process resulted in significant improvement in processing time and increased quality of orders. As use of order sets and other forms of clinical decision support increase, regular evidence and process updates become more critical.
Standardised incidence ratios (SIRs) for cancer after renal transplant in systemic lupus erythematosus (SLE) and non-SLE recipients
Authors: Ramsey-Goldman Rosalind , Brar Amarpali , Richardson Carrie , Salifu Moro O , Clarke Ann , Bernatsky Sasha , Stefanov Dimitre G , Jindal Rahul M 
Published: June 2016

ObjectiveWe investigated malignancy risk after renal transplantation in patients with and without systemic lupus erythematosus (SLE).MethodsUsing the United States Renal Data System from 2001 to 2009, 143 652 renal transplant recipients with and without SLE contributed 585 420 patient-years of follow-up to determine incident cancers using Medicare claims codes. We calculated standardised incidence ratios (SIRs) of cancer by group using age, sex, race/ethnicity-specific and calendar year-specific cancer rates compared with the US population.Results10 160 cancers occurred at least 3 months after renal transplant. Overall cancer risk was increased in both SLE and non-SLE groups compared with the US general population, SIR 3.5 (95% CI 2.1 to 5.7) and SIR 3.7 (95% CI 2.4 to 5.7), respectively. Lip/oropharyngeal, Kaposi, neuroendocrine, thyroid, renal, cervical, lymphoma, liver, colorectal and breast cancers were increased in both groups, whereas only melanoma was increased in SLE and lung cancer was increased in non-SLE. In Cox regression analysis, SLE status (HR 1.1, 95% CI 0.9 to 1.3) was not associated with increased risk of developing cancer, adjusted for other independent risk factors for developing cancer in renal transplant recipients. We found that smoking (HR 2.2, 95% CI 1.2 to 4.0), cytomegalovirus positivity at time of transplant (HR 1.3, 95% CI 1.2 to 1.4), white race (HR 1.2, 95% CI 1.2 to 1.3) and older recipient age at time of transplantation (HR 1.0 95% CI 1.0 to 1.2) were associated with an increased risk for development of cancer, whereas shorter time on dialysis, Epstein-Barr virus or HIV were associated with a lower risk for development of cancer.ConclusionsCancer risk in renal transplant recipients appeared similar in SLE and non-SLE subjects, aside from melanoma. Renal transplant recipients may need targeted counselling regarding surveillance and modifiable risk factors.
High-Frequency Trading Meets Online Learning
Authors: Fernandez-Tapia Joaquin 
Published: June 2016

We propose an optimization framework for market-making in a limit order book, based on the theory of stochastic approximation. The idea is to take advantage of the iterative nature of the process of updating bid and ask quotes in order to make the algorithm optimize its strategy on a trial-and-error basis (i.e., online learning) using a variation of the stochastic gradient-descent algorithm. An advantage of this approach is that the exploration of the system by the algorithm is performed in run-time, so explicit specifications of price dynamics are not necessary, as is the case in the stochastic-control approach [(Gueant et al., 2013, Dealing with the Inventory Risk: A Solution to the Market Making Problem, Mathematics and Financial Economics 7(4), 477–507)]. For price/liquidity modeling, we consider a discrete-time variant of the Avellaneda–Stoikov model [(Avellaneda, M. and S. Stoikov, 2008, Liquidation in Limit Order Books with Controlled Intensity, Mathematical Finance 24(4), 627–650)] similar to its developent in the paper of Laruelle et al. [(Laruelle et al., 2013, Optimal Posting Price of Limit Orders: Learning by trading, Mathematics and Financial Economics 7(3), 359–403)] in the context of optimal liquidation tactics. Our aim is to set the ground for more advanced reinforcement learning techniques and to argue that the rationale of our method is generic enough to be extended to other classes of trading problems besides market-making.
Dynamic Stability Analysis of Generator with Power System Stabilizers Using Matlab Simulink
Authors: Sulaiman Marizan , Hussein Hayfaa Mohammed , Omar Rosli , Salleh Zulhisyam 
Published: June 2016

<p> The dynamics in single machine been connected to an infinite power system bus is analyzed in this paper. This analysis requires certain amount of system modeling level. The main components of the system models are excitation system, synchronous machine and the Power System Stabilizer. The Simulink /Matlab are used as the programming tool for analyzing this system performance. Design optimization arobust PSS based on Genetic Algorithm (GA) approach has been improvement. A proper design is required for this Power System Stabilizer (PSS) performance using the Particle Swarm Optimization (PSO) to archieve this. Then the implemented of the model and response of the dynamic system is been analyzed. The designed without PSS showed an unacceptable system response since as shown in the simulation results, system response with PSS proven to have improvements and PSS succeeding in stabilizing an unstable system. Therefore this leads to stability of the performance of the generator.</p>