bluuebunny/crossref_metadata_2025 huggingface dataset:
Chemical Warfare Agent Simulants in Gamble’s Fluid: Is the Fluid Toxic? Can It Be Made Safer by Inclusion of Solid Nanocrystalline Metal Oxides?
Authors: Karote Dennis , Walker Brandon , Dai Huaien , Krishnamoorthi Ramaswamy , Voo Janis , Rajagopalan Shyamala
Published: December 2012

The reactions of chemical warfare agent simulants, 2‐chloroethyl ethyl sulfide (2‐CEES) and di‐i‐propyl fluoro phosphate (DFP), in fluids have been investigated. Data analyses confirm the major degradation pathway to be hydrolysis of 2‐CEES to 2‐hydroxyethyl ethyl sulfide, along with minor self‐condensation products. Among the three fluids examined, 2‐CEES degradation was the fastest in Gamble’s fluid during a 96 h period. Upon addition of Exceptional Hazard Attenuation Materials (EHAMs) to 2‐CEES containing Gamble’s fluid, degradation was generally improved during the first 24 h period. The 96 h outcome was similar for fluid samples with or without EHAM 2 and EHAM 4. EHAM 1‐added fluid contained only one degradation product, 2‐nitroethyl ethyl sulfide. DFP degradation was the slowest in Gamble’s fluid, but was enhanced by the addition of EHAMs. FTIR and solid state 31P NMR confirm the destructive adsorption of 2‐CEES and DFP by the EHAMs. The results collectively demonstrate that 2‐CEES and DFP decompose to various extents in Gamble’s fluid over a 96 h period but the fluid still contains a considerable amount of intact simulant. EHAM 1 appears to be promising for 2‐CEES and DFP mitigation while EHAM 2 and EHAM 4 work well for early on concentration reduction of 2‐CEES and DFP.
A Comparison of the Language Skills of ELLs and Monolinguals Who Are Poor Decoders, Poor Comprehenders, or Normal Readers
Authors: Geva Esther , Massey-Garrison Angela
Published: December 2012

The overall objective of this article is to examine how oral language abilities relate to reading profiles in English language learners (ELLs) and English as a first language (EL1) learners, and the extent of similarities and differences between ELLs and EL1s in three reading subgroups: normal readers, poor decoders, and poor comprehenders. The study included 100 ELLs and 50 EL1s in Grade 5. The effect of language group (ELL/EL1) and reading group on cognitive and linguistic skills was examined. Except for vocabulary, there was no language group effect on any measure. However, within ELL and EL1 alike, significant differences were found between reading groups: Normal readers outperformed the two other groups on all the oral language measures. Distinct cognitive and linguistic profiles were associated with poor decoders and poor comprehenders, regardless of language group. The ELL and EL1 poor decoders outperformed the poor comprehenders on listening comprehension and inferencing. The poor decoders displayed phonological-based weaknesses, whereas the poor comprehenders displayed a more generalized language processing weakness that is nonphonological in nature. Regardless of language status, students with poor decoding or comprehension problems display difficulties with various aspects of language.
Surface Electromyography Recording of Spontaneous Eyeblinks
Authors: Frigerio Alice , Brenna Stefano , Cavallari Paolo
Published: December 2012

Objective

We are designing an implantable neuroprosthesis for the treatment of unilateral facial paralysis. The envisioned biomimetic device paces artificial blinks in the paretic eyelid when activity in the healthy orbicularis oculi (orbicularis) muscle is detected. The present article focuses on electromyography (EMG)–based eyeblink detection.

Study Design

A pilot clinical study was performed in healthy volunteers who were intended to represent individuals with facial paralysis. Spontaneous eyeblinks were detected by a surface EMG recording. Blink detection accuracy was tested at rest and during voluntary smiling and chewing.

Setting

Fifteen participants were asked to wear surface recording electrodes on the left side of their face, detecting the orbicularis oculi, the masseter, and the zygomatic muscle EMG activity.

Subjects and Methods

Participants were asked to look ahead, voluntarily smile, and chew according to an experimental protocol. Custom software was designed with the purpose of selectively filtering the multichannel EMG recordings and triggering a digital output.

Results

The software filter allowed elimination of spurious artificial eyeblinks and thus increased the accuracy of the EMG recording apparatus for the spontaneous blinking.

Conclusion

Orbicularis oculi EMG recording worked as a real‐time eyeblink‐detecting system. Moreover, the multichannel EMG recording coupled to a proper digital signal processing was very effective in specifically detecting the spontaneous blinking during other facial muscle activities. With regard to closed‐loop biomimetic devices for the pacing of the eyeblink, the EMG signal represents a valid option for the recording side.
Distortion‐Product Otoacoustic Emission Tests Evaluate Cochlear Function and Differentiate Cochlear and Vestibular Schwannoma
Authors: Kagoya Ryoji , Shinogami Masanobu , Kohno Michihiro , Yamasoba Tatsuya
Published: December 2012

Objectives

(1) To investigate cochlear function in patients with acoustic neuroma by distortion‐product otoacoustic emission tests and (2) to evaluate the utility of this method for identifying the nerve origin of acoustic neuroma.

Study Design

Diagnostic test assessment.

Setting

Community hospital.

Methods

The study included 196 patients with unilateral acoustic neuroma who were surgically treated in our hospital between April 2008 and March 2011. In all patients, pure‐tone audiometry and distortion‐product otoacoustic emission tests were conducted before surgery, and tumor size was measured on magnetic resonance imaging.

Results

Superior vestibular schwannoma (n = 112), inferior vestibular schwannoma (n = 80), and cochlear schwannoma (n = 4) were observed. Positive results of distortion‐product otoacoustic emission tests were observed in 11 patients with superior vestibular schwannoma, 14 with inferior vestibular schwannoma, and 3 with cochlear schwannoma. They were predictive of cochlear schwannoma, with 75.0% sensitivity (95% confidence interval [CI], 30.6‐95.4) and 87.0% specificity (95% CI, 86.1‐87.4). Retrocochlear hearing loss was detected in 5 patients with inferior vestibular schwannoma and 1 with cochlear schwannoma. It was also predictive of cochlear schwannoma. This criterion showed 25.0% sensitivity (95% CI, 4.7‐66.1) and 97.4% specificity (95% CI, 97.0‐98.3).

Conclusion

Percentages of patients with positive results on distortion‐product otoacoustic emission tests and those with retrocochlear hearing loss differed by nerve origin. Distortion‐product otoacoustic emission tests can be of some assistance in differentiating cochlear and vestibular schwannoma.
The Systemic Effects of Platelet-Rich Plasma Injection
Authors: Wasterlain Amy S. , Braun Hillary J. , Harris Alex H.S. , Kim Hyeon-Joo , Dragoo Jason L.
Published: December 2012

Background:

Platelet-rich plasma (PRP) is an autologous blood product used to treat acute and chronic tendon, ligament, and muscle injuries in over 86,000 athletes in the United States annually. The World Anti-Doping Agency (WADA) banned intramuscular PRP injections in competitive athletes in 2010 because of concerns that it may increase performance-enhancing growth factors. The ban on PRP was removed in 2011 because of limited evidence for a systemic ergogenic effect of PRP, but the growth factors within PRP remain prohibited.

Purpose:

To quantify the effect of PRP injection on systemic growth factors with performance-enhancing effects and to identify molecular markers to detect treated athletes.

Study Design:

Descriptive laboratory study.

Methods:

Six ergogenic growth factors monitored by WADA—human growth hormone (hGH), insulin-like growth factor–1 (IGF-1), insulin-like growth factor binding protein–3 (IGFBP-3), basic fibroblast growth factor (bFGF or FGF-2), vascular endothelial growth factor (VEGF), and platelet-derived growth factor–BB (PDGF-BB)—were measured in 25 patients before (baseline) and at 0.25, 3, 24, 48, 72, and 96 hours after intratendinous leukocyte-rich PRP injection. Eating and exercise were prohibited for 3 hours before testing. Growth factors were quantified by enzyme-linked immunosorbent assay, and the change relative to each patient’s baseline was calculated.

Results:

Relative to serum, PRP contained significantly more bFGF (226 vs 5 pg/mL), VEGF (1426 vs 236 pg/mL), and PDGF-BB (26,285 vs 392 pg/mL), but IGF-1 and hGH were not elevated. Serum levels increased significantly for IGF-1 at 24 and 48 hours, for bFGF at 72 and 96 hours, and for VEGF at 3, 24, 48, 72, and 96 hours after PRP injection. Additionally, VEGF was increased in all 25 patients after PRP treatment.

Conclusion:

Serum IGF-1, VEGF, and bFGF levels are significantly elevated after PRP injection, supporting a possible ergogenic effect of PRP. An indirect marker for hGH doping, the product of IGFBP-3 × IGF-1, also significantly increased after PRP. Platelet-rich plasma appears to trigger an increase in circulating growth factors through activating biological pathways rather than by serving as a vehicle for the direct delivery of presynthesized growth factors. Elevated VEGF was observed in all patients after PRP, and ≥88% of patients had elevated VEGF at each time point from 3 to 96 hours after PRP, suggesting that VEGF may be a sensitive molecular marker to detect athletes recently treated with PRP.

Clinical Relevance:

This is the first and only adequately powered study of the systemic effects of PRP. We present evidence that PRP contains and may trigger systemic increases in substances currently banned in competitive athletes. Finally, we provide evidence that VEGF could serve as a useful molecular marker to detect athletes treated with PRP.
Sleep-Wake Behavior in the Rat
Authors: Stephenson Richard , Lim Joonbum , Famina Svetlana , Caron Aimee M. , Dowse Harold B.
Published: December 2012

Ultradian rhythms are a prominent but little-studied feature of mammalian sleep-wake and rest-activity patterns. They are especially evident in long-term records of behavioral state in polyphasic animals such as rodents. However, few attempts have been made to incorporate ultradian rhythmicity into models of sleep-wake dynamics, and little is known about the physiological mechanisms that give rise to ultradian rhythms in sleep-wake state. This study investigated ultradian dynamics in sleep and wakefulness in rats entrained to a 12-h:12-h light-dark cycle (LD) and in rats whose circadian rhythms were suppressed and free-running following long-term exposure to uninterrupted bright light (LL). We recorded sleep-wake state continuously for 7 to 12 consecutive days and used time-series analysis to quantify the dynamics of net cumulative time in each state (wakefulness [WAKE], rapid eye movement sleep [REM], and non-REM sleep [NREM]) in each animal individually. Form estimates and autocorrelation confirmed the presence of significant ultradian and circadian rhythms; maximum entropy spectral analysis allowed high-resolution evaluation of multiple periods within the signal, and wave-by-wave analysis enabled a statistical evaluation of the instantaneous period, peak-trough range, and phase of each ultradian wave in the time series. Significant ultradian periodicities were present in all 3 states in all animals. In LD, ultradian range was approximately 28% of circadian range. In LL, ultradian range was slightly reduced relative to LD, and circadian range was strongly attenuated. Ultradian rhythms were found to be quasiperiodic in both LD and LL. That is, ultradian period varied randomly around a mean of approximately 4 h, with no relationship between ultradian period and time of day.
Modelling laminar transport phenomena in a Casson rheological fluid from a horizontal circular cylinder with partial slip
Authors: Prasad V Ramachandra , Rao A Subba , Reddy N Bhaskar , Vasu B , Bég O Anwar
Published: December 2012

The laminar boundary layer flow and heat transfer of Casson non-Newtonian fluid from a permeable horizontal cylinder in the presence of thermal and hydrodynamic slip conditions is analysed. The cylinder surface is maintained at a constant temperature. The boundary layer conservation equations, which are parabolic in nature, are normalised into non-similar form and then solved numerically with the well-tested, efficient, implicit, stable Keller–Box finite-difference scheme. Increasing velocity slip induces acceleration in the flow near the cylinder surface and the reverse effect further from the surface. Increasing velocity slip consistently enhances temperatures throughout the boundary layer regime. An increase in thermal slip parameter strongly decelerates the flow and also reduces temperatures in the boundary layer regime. An increase in Casson rheological parameter acts to elevate considerably the skin friction (non-dimensional wall shear stress) and this effect is pronounced at higher values of tangential coordinate. Temperatures are however very slightly decreased with increasing values of Casson rheological parameter. Increasing mass flow injection (blowing) at the cylinder surface causes a strong acceleration, whereas increasing suction is found to induce the opposite effect. The study finds applications in rheological chocolate food processing.
Learning from young people and from our own experiences in Barrio San Jorge
Authors: Hardoy Jorgelina , Sierra Guadalupe , Tammarazio Andrea , Ledesma Gabriela , Ledesma Lucas , García Carolina
Published: December 2012

This paper brings together the perceptions of three youths from Barrio San Jorge, a low-income settlement located in the municipality of San Fernando in the Buenos Aires Metropolitan Area, and the more technical views of three adult researchers working in the same barrio with the Instituto Internacional de Medio Ambiente y Desarrollo—América Latina (IIED—AL). It highlights youth’s perceptions and aspirations within a context of neighbourhood upgrading and transformation, and discusses some ideas on how best to approach and work with youth, addressing the challenges of integration, participation and commitment.
Increasing autism prevalence in metropolitan New Jersey
Authors: Zahorodny Walter , Shenouda Josephine , Howell Sandra , Rosato Nancy Scotto , Peng Bo , Mehta Uday
Published: December 2012

High baseline autism spectrum disorder prevalence estimates in New Jersey led to a follow-up surveillance. The objectives were to determine autism spectrum disorder prevalence in the year 2006 in New Jersey and to identify changes in the prevalence of autism spectrum disorder or in the characteristics of the children with autism spectrum disorder, between 2002 and 2006. The cohorts included 30,570 children, born in 1998 and 28,936 children, born in 1994, residing in Hudson, Union, and Ocean counties, New Jersey. Point prevalence estimates by sex, ethnicity, autism spectrum disorder subtype, and previous autism spectrum disorder diagnosis were determined. For 2006, a total of 533 children with autism spectrum disorder were identified, consistent with prevalence of 17.4 per 1000 (95% confidence interval = 15.9–18.9), indicating a significant increase in the autism spectrum disorder prevalence (p < 0.001), between 2002 (10.6 per 1000) and 2006. The rise in autism spectrum disorder was broad, affecting major demographic groups and subtypes. Boys with autism spectrum disorder outnumbered girls by nearly 5:1. Autism spectrum disorder prevalence was higher among White children than children of other ethnicities. Additional studies are needed to specify the influence of better awareness of autism spectrum disorder prevalence estimates and to identify possible autism spectrum disorder risk factors. More resources are necessary to address the needs of individuals affected by autism spectrum disorder.
Generating trust? Sport and community participation
Authors: Brown Kevin M. , Hoye Russell , Nicholson Matthew
Published: December 2012

This article explores the claim that generalized trust and community participation are positively associated and reports results from a survey that collected data on individuals’ involvement in sport and non-sport community organizations. Data were collected on levels of involvement in community sport and other non-profit community organizations, selected demographic variables and the standard measure of generalized trust. The analysis included an estimation of the direction of causality between involvement and trust and indicated that sport membership led to trust elevation. The findings support the arguments of Stolle and others: that joining community organizations creates heightened trust. Further, sport membership was a strong and significant predictor of trust. The findings have implications both for policy-related social capital interventions and the theory of social capital and trust generation.
Toward Standardization (Part 2)
Authors: Moulton Patricia L. , Wiebusch Pamela L. , Cleary Brenda L. , Brunell Mary Lou , Napier Duane F. , Bienemy Cynthia , LeVasseur Sandra A. , Cimiotti Jeannie P.
Published: December 2012

With the passage of the Affordable Care Act and the development of a National Workforce Commission, multiple entities have increased their interest in collecting standardized health care workforce data at the state and national levels. In a tight budget environment, developing data sets which collect the minimum needed information that is necessary for workforce planning and supply/demand projections has become critically needed. This article represents the second of a two part series describing the work that the Forum of State Nursing Workforce Centers has undertaken during the last 3 years toward standardizing nursing workforce data. Part I described the initial steps that informed the development of national nursing workforce minimum data sets. Part II describes the consensus model used to develop the minimum data sets as well as an update on the implementation of the minimum data sets in individual states including challenges and barriers encountered.
Surgical Wound Infection by Streptococcus pneumoniae After a Cat-Scratch Disease
Authors: Savini Vincenzo , Cecinati Valerio , Onofrillo Daniela , Consilvio Nicola Pietro , Polilli Ennio , Crescenzi Carlo , Fazii Paolo , D’Antonio Domenico
Published: December 2012

Streptococcus pneumoniae (pneumococcus) is mostly known as an agent of meningitis and pneumonia. We present what is believed to be a previously unreported case of pneumococcal disease, involving an inguinal wound. A 10-year-old male patient underwent surgical removal of a cat-scratch disease-related enlarged groin lymph node; infection of the wound was soon observed, with multidrug-resistant S pneumoniae growing from the lesion discharge. This communication expands the spectrum of skin ulcer–infecting pathogens; in fact, although pneumococcus has been known to mostly affect central nervous system and airways, we observed a surgical wound infection by this organism.
The Benefits of Breakfast Consumption to Combat Obesity and Diabetes in Young People
Authors: Leidy Heather J.
Published: December 2012

The obesity epidemic, particularly in young people, is the greatest threat to public health this century. Several dietary factors have recently been identified to play a critical role in the etiology of this disease. Of particular interest is the common dietary habit of skipping breakfast, which has been strongly associated with obesity. Cross-sectional studies indicate that young people who habitually eat breakfast have a higher-quality diet, eat fewer unhealthy snacks, and have better body weight management compared with those who skip breakfast. Additionally, breakfast consumers also exhibit better glucose control throughout the day compared with those who skip the morning meal. These data lend support for the addition of breakfast to reduce factors contributing to obesity and diabetes in young people. Although evidence exists illustrating the benefits of cereal-based breakfast compared with skipping the morning meal, less is known with respect to the consumption of other breakfast foods, namely those rich in dietary protein. This article provides clinical evidence documenting the strong protective effect of breakfast consumption to prevent and/or treat obesity/type 2 diabetes and promote overall health in young people.
Stem cell transplantation can provide durable disease control in blastic plasmacytoid dendritic cell neoplasm: a retrospective study from the European Group for Blood and Marrow Transplantation
Authors: Roos-Weil Damien , Dietrich Sascha , Boumendil Ariane , Polge Emmanuelle , Bron Dominique , Carreras Enric , Iriondo Atienza Arturo , Arcese William , Beelen Dietrich W. , Cornelissen Jan J. , Kröger Nicolaus , Milone Giuseppe , Rossi Giuseppe , Jardin Fabrice , Peters Christina , Rocha Vanderson , Sureda Anna , Mohty Mohamad , Dreger Peter
Published: December 2012

Patients with blastic plasmacytoid dendritic cell neoplasm (BPDCN) have a poor prognosis with conventional chemotherapy. In the present study, we retrospectively analyzed the outcome of patients with BPDCN who underwent allogeneic stem cell transplantation (allo-SCT) or autologous stem cell transplantation (auto-SCT). A total of 39 patients (allo-SCT, n = 34; auto-SCT, n = 5) were identified in the European Group for Blood and Marrow Transplantation registry. The 34 allo-SCT patients had a median age of 41 years (range, 10-70) and received transplantations from sibling (n = 11) or unrelated donors (n = 23) between 2003 and 2009. MAC was used in 74% of patients. Nineteen allo-SCT patients (56%) received transplantations in first complete remission. The 3-year cumulative incidence of relapse, disease-free survival, and overall survival was 32%, 33%, and 41%, respectively. By univariate comparison, being in first remission at allo-SCT favorably influenced survival, whereas age, donor source, and chronic GVHD had no significant impact. We conclude that high-dose therapy followed by allo-SCT from related or unrelated donors can provide durable remission even in elderly patients with BPDCN. However, it remains to be shown if graft-versus-malignancy effects can contribute significantly to BPDCN control after allo-SCT.
In vitro substrate phosphorylation by Ca2+/calmodulin-dependent protein kinase kinase using guanosine-5′-triphosphate as a phosphate donor
Authors: Yurimoto Saki , Fujimoto Tomohito , Magari Masaki , Kanayama Naoki , Kobayashi Ryoji , Tokumitsu Hiroshi
Published: December 2012

Background

Ca2+/calmodulin-dependent protein kinase kinase (CaMKK) phosphorylates and activates particular downstream protein kinases — including CaMKI, CaMKIV, and AMPK— to stimulate multiple Ca2+-signal transduction pathways. To identify previously unidentified CaMKK substrates, we used various nucleotides as phosphate donors to develop and characterize an in vitro phosphorylation assay for CaMKK.

Results

Here, we found that the recombinant CaMKK isoforms were capable of utilizing Mg-GTP as a phosphate donor to phosphorylate the Thr residue in the activation-loop of CaMKIα (Thr177) and of AMPK (Thr172) in vitro. Kinetic analysis indicated that the K
m values of CaMKK isoforms for GTP (400-500 μM) were significantly higher than those for ATP (~15 μM), and a 2- to 4-fold decrease in V
max was observed with GTP. We also confirmed that an ATP competitive CaMKK inhibitor, STO-609, also competes with GTP to inhibit the activities of CaMKK isoforms. In addition, to detect enhanced CaMKI phosphorylation in brain extracts with Mg-GTP and recombinant CaMKKs, we found potential CaMKK substrates of ~45 kDa and ~35 kDa whose Ca2+/CaM-induced phosphorylation was inhibited by STO-609.

Conclusions

These results indicated that screens that use STO-609 as a CaMKK inhibitor and Mg-GTP as a CaMKK-dependent phosphate donor might be useful to identify previously unidentified downstream target substrates of CaMKK.
Uninformative polymorphisms bias genome scans for signatures of selection
Authors: Roesti Marius , Salzburger Walter , Berner Daniel
Published: December 2012

Background

With the establishment of high-throughput sequencing technologies and new methods for rapid and extensive single nucleotide (SNP) discovery, marker-based genome scans in search of signatures of divergent selection between populations occupying ecologically distinct environments are becoming increasingly popular.

Methods and Results

On the basis of genome-wide SNP marker data generated by RAD sequencing of lake and stream stickleback populations, we show that the outcome of such studies can be systematically biased if markers with a low minor allele frequency are included in the analysis. The reason is that these ‘uninformative’ polymorphisms lack the adequate potential to capture signatures of drift and hitchhiking, the focal processes in ecological genome scans. Bias associated with uninformative polymorphisms is not eliminated by just avoiding technical artifacts in the data (PCR and sequencing errors), as a high proportion of SNPs with a low minor allele frequency is a general biological feature of natural populations.

Conclusions

We suggest that uninformative markers should be excluded from genome scans based on empirical criteria derived from careful inspection of the data, and that these criteria should be reported explicitly. Together, this should increase the quality and comparability of genome scans, and hence promote our understanding of the processes driving genomic differentiation.
The Corynebacterium pseudotuberculosis in silico predicted pan-exoproteome
Authors: Santos Anderson R , Carneiro Adriana , Gala-García Alfonso , Pinto Anne , Barh Debmalya , Barbosa Eudes , Aburjaile Flávia , Dorella Fernanda , Rocha Flávia , Guimarães Luis , Zurita-Turk Meritxell , Ramos Rommel , Almeida Sintia , Soares Siomar , Pereira Ulisses , Abreu Vinícius C , Silva Artur , Miyoshi Anderson , Azevedo Vasco
Published: December 2012

Background

Pan-genomic studies aim, for instance, at defining the core, dispensable and unique genes within a species. A pan-genomics study for vaccine design tries to assess the best candidates for a vaccine against a specific pathogen. In this context, rather than studying genes predicted to be exported in a single genome, with pan-genomics it is possible to study genes present in different strains within the same species, such as virulence factors. The target organism of this pan-genomic work here presented isCorynebacterium pseudotuberculosis, the etiologic agent of caseous lymphadenitis (CLA) in goat and sheep, which causes significant economic losses in those herds around the world. Currently, only a few antigens against CLA are known as being the basis of commercial and still ineffective vaccines. In this regard, the here presented work analyses,in silico, fiveC. pseudotuberculosisgenomes and gathers data to predict common exported proteins in all five genomes. These candidates were also compared to two recentC. pseudotuberculosis in vitroexoproteome results.

Results

The complete genome of fiveC. pseudotuberculosisstrains (1002, C231, I19, FRC41 and PAT10) were submitted to pan-genomics analysis, yielding 306, 59 and 12 gene sets, respectively, representing the core, dispensable and uniquein silicopredicted exported pan-genomes. These sets bear 150 genes classified as secreted (SEC) and 227 as potentially surface exposed (PSE). Our findings suggest that the mainC. pseudotuberculosis in vitroexoproteome could be greater, appended by a fraction of the 35 proteins formerly predicted as making part of the variantin vitroexoproteome. These genomes were manually curated for correct methionine initiation and redeposited with a total of 1885 homogenized genes.

Conclusions

Thein silicoprediction of exported proteins has allowed to define a list of putative vaccine candidate genes present in all five completeC. pseudotuberculosisgenomes. Moreover, it has also been possible to define thein silicopredicted dispensable and uniqueC. pseudotuberculosisexported proteins. These results providein silicoevidence to further guide experiments in the areas of vaccines, diagnosis and drugs. The work here presented is the first wholeC. pseudotuberculosis in silicopredicted pan-exoproteome completed till today.
Methods for high-throughput MethylCap-Seq data analysis
Authors: Rodriguez Benjamin AT , Frankhouser David , Murphy Mark , Trimarchi Michael , Tam Hok-Hei , Curfman John , Huang Rita , Chan Michael WY , Lai Hung-Cheng , Parikh Deval , Ball Bryan , Schwind Sebastian , Blum William , Marcucci Guido , Yan Pearlly , Bundschuh Ralf
Published: December 2012

Background

Advances in whole genome profiling have revolutionized the cancer research field, but at the same time have raised new bioinformatics challenges. For next generation sequencing (NGS), these include data storage, computational costs, sequence processing and alignment, delineating appropriate statistical measures, and data visualization. Currently there is a lack of workflows for efficient analysis of large, MethylCap-seq datasets containing multiple sample groups.

Methods

The NGS application MethylCap-seq involves the in vitro capture of methylated DNA and subsequent analysis of enriched fragments by massively parallel sequencing. The workflow we describe performs MethylCap-seq experimental Quality Control (QC), sequence file processing and alignment, differential methylation analysis of multiple biological groups, hierarchical clustering, assessment of genome-wide methylation patterns, and preparation of files for data visualization.

Results

Here, we present a scalable, flexible workflow for MethylCap-seq QC, secondary data analysis, tertiary analysis of multiple experimental groups, and data visualization. We demonstrate the experimental QC procedure with results from a large ovarian cancer study dataset and propose parameters which can identify problematic experiments. Promoter methylation profiling and hierarchical clustering analyses are demonstrated for four groups of acute myeloid leukemia (AML) patients. We propose a Global Methylation Indicator (GMI) function to assess genome-wide changes in methylation patterns between experimental groups. We also show how the workflow facilitates data visualization in a web browser with the application Anno-J.

Conclusions

This workflow and its suite of features will assist biologists in conducting methylation profiling projects and facilitate meaningful biological interpretation.
The experience of puberty in Iranian adolescent girls: a qualitative content analysis
Authors: Golchin Nayereh Azam Hagikhani , Hamzehgardeshi Zeinab , Fakhri Moloud , Hamzehgardeshi Leila
Published: December 2012

Background

Adolescence is an important stage in human life span. Physiologic changes associated with puberty manifest themselves in often complex and bizarre ways to which girls show different reactions. This study aims to explore to puberty experiences in adolescent girls who live in the city of Sari in Iran.

Methods

The present study is a qualitative study of content analysis. Sampling took place in the city of Sari, Iran and was objective focused in accordance with qualitative studies. Participants were 38 girls of 12–20 years old who had at least experienced 3 menstrual cycles. Data was collected by means of focus group and in-depth interviews.

Results

As follows, Seven main themes were extracted from the interviews are follows: Menarche as the most unpleasant event in puberty, getting nervous about and ashamed of bodily changes, psychological changes, discordance with parents, sexual orientation and the need for education on this issue, scholastic dysfunction and religious considerations.

Conclusion

The results showed that for the majority of the participants puberty was an unpleasant experience. Most of them were in need of education on how to go about the issues surrounding puberty. The society, families and of course the adolescents themselves are responsible to work together in order to create an atmosphere in which correct information on puberty and the associated issues are readily accessible.
Early outcomes of colon laparoscopic resection in the elderly patients compared with the younger
Authors: Bottino Vincenzo , Esposito Maria Grazia , Mottola Arianna , Marte Giampaolo , Di Maio Vittorio , Sciascia Valerio , Nunziante Marco , Fregola Giovanni , Cuzzovaglia Salvatore , Galante Francesco , Andreoli Federica , Breglia Alfredo , Giuliano Maria Elena , Papaleo Domenico , Della Rocca Paola , Maida Pietro
Published: December 2012

Background

The aim of this study was to define any benefits in terms of early outcome for laparoscopic colectomy in patients over 75 years old (OP) compared with the outcomes of a younger populations (YP).

Methods

Forty elderly patients undergoing laparoscopic colectomy for colorectal cancer between 2007-2011 were studied, the patients are divided for gender, age, year of surgery, site of cancer, and comorbidity on admission and compared with 40 younger patients.

Results and discussion

Mean (standard deviation) age was 81.3 in OP and 68.3 YP Conversion rate was the same between the two groups. There was no difference in operative mean time . The overall mortality rate was 0% percent. The surgical morbidity rate was the same but there was an increased in cardiologic e bronchopneumonia complications in older population. Patients treated with laparoscopic approach had a faster recovery of bowel function and a significant reduction of the mean length of hospital stay not age related. Laparoscopy allowed a better preservation of postoperative independence status.

Conclusions

Laparoscopic colectomy for cancer in elderly patients is safe and beneficial including preservation of postoperative independence and a reduction of length of hospital stay.
Student perceptions of evaluation in undergraduate medical education: A qualitative study from one medical school
Authors: Schiekirka Sarah , Reinhardt Deborah , Heim Susanne , Fabry Götz , Pukrop Tobias , Anders Sven , Raupach Tobias
Published: December 2012

Background

Evaluation is an integral part of medical education. Despite a wide use of various evaluation tools, little is known about student perceptions regarding the purpose and desired consequences of evaluation. Such knowledge is important to facilitate interpretation of evaluation results. The aims of this study were to elicit student views on the purpose of evaluation, indicators of teaching quality, evaluation tools and possible consequences drawn from evaluation data.

Methods

This qualitative study involved 17 undergraduate medical students in Years 3 and 4 participating in 3 focus group interviews. Content analysis was conducted by two different researchers.

Results

Evaluation was viewed as a means to facilitate improvements within medical education. Teaching quality was believed to be dependent on content, process, teacher and student characteristics as well as learning outcome, with an emphasis on the latter. Students preferred online evaluations over paper-and-pencil forms and suggested circulating results among all faculty and students. Students strongly favoured the allocation of rewards and incentives for good teaching to individual teachers.

Conclusions

In addition to assessing structural aspects of teaching, evaluation tools need to adequately address learning outcome. The use of reliable and valid evaluation methods is a prerequisite for resource allocation to individual teachers based on evaluation results.
Development of a decision aid to inform patients’ and families’ renal replacement therapy selection decisions
Authors: Ameling Jessica M , Auguste Priscilla , Ephraim Patti L , Lewis-Boyer LaPricia , DePasquale Nicole , Greer Raquel C , Crews Deidra C , Powe Neil R , Rabb Hamid , Boulware L Ebony
Published: December 2012

Background

Few educational resources have been developed to inform patients’ renal replacement therapy (RRT) selection decisions. Patients progressing toward end stage renal disease (ESRD) must decide among multiple treatment options with varying characteristics. Complex information about treatments must be adequately conveyed to patients with different educational backgrounds and informational needs. Decisions about treatment options also require family input, as families often participate in patients’ treatment and support patients’ decisions. We describe the development, design, and preliminary evaluation of an informational, evidence-based, and patient-and family-centered decision aid for patients with ESRD and varying levels of health literacy, health numeracy, and cognitive function.

Methods

We designed a decision aid comprising a complementary video and informational handbook. We based our development process on data previously obtained from qualitative focus groups and systematic literature reviews. We simultaneously developed the video and handbook in “stages.” For the video, stages included (1) directed interviews with culturally appropriate patients and families and preliminary script development, (2) video production, and (3) screening the video with patients and their families. For the handbook, stages comprised (1) preliminary content design, (2) a mixed-methods pilot study among diverse patients to assess comprehension of handbook material, and (3) screening the handbook with patients and their families.

Results

The video and handbook both addressed potential benefits and trade-offs of treatment selections. The 50-minute video consisted of demographically diverse patients and their families describing their positive and negative experiences with selecting a treatment option. The video also incorporated health professionals’ testimonials regarding various considerations that might influence patients’ and families’ treatment selections. The handbook was comprised of written words, pictures of patients and health care providers, and diagrams describing the findings and quality of scientific studies comparing treatments. The handbook text was written at a 4th to 6th grade reading level. Pilot study results demonstrated that a majority of patients could understand information presented in the handbook. Patient and families screening the nearly completed video and handbook reviewed the materials favorably.

Conclusions

This rigorously designed decision aid may help patients and families make informed decisions about their treatment options for RRT that are well aligned with their values.
Cost comparison of MRSA screening and management – a decision tree analysis
Authors: Tübbicke Andrea , Hübner Claudia , Hübner Nils-Olaf , Wegner Christian , Kramer Axel , Fleßa Steffen
Published: December 2012

Background

Methicillin-resistant Staphylococcus aureus (MRSA) infections represent a serious challenge for health-care institutions. Rapid and precise identification of MRSA carriers can help to reduce both nosocomial transmissions and unnecessary isolations and associated costs. The practical details of MRSA screenings (who, how, when and where to screen) remain a controversial issue.

Methods

Aim of this study was to determine which MRSA screening and management strategy causes the lowest expected cost for a hospital. For this cost analysis a decision analytic cost model was developed, primary based on data from peer-reviewed literature. Single and multiplex sensitivity analyses of the parameters “costs per MRSA case per day”, “costs for pre-emptive isolation per day”, “MRSA rate of transmission not in isolation per day” and “MRSA prevalence” were conducted.

Results

The omission of MRSA screening was identified as the alternative with the highest risk for the hospital. Universal MRSA screening strategies are by far more cost-intensive than targeted screening approaches. Culture confirmation of positive PCR results in combination with pre-emptive isolation generates the lowest costs for a hospital. This strategy minimizes the chance of false-positive results as well as the possibility of MRSA cross transmissions and therefore contains the costs for the hospital. These results were confirmed by multiplex and single sensitivity analyses. Single sensitivity analyses have shown that the parameters “MRSA prevalence” and the “rate of MRSA of transmission per day of non-isolated patients” exert the greatest influence on the choice of the favorite screening strategy.

Conclusions

It was shown that universal MRSA screening strategies are far more cost-intensive than the targeted screening approaches. In addition, it was demonstrated that all targeted screening strategies produce lower costs than not performing a screening at all.
Lyn is involved in CD24-induced ERK1/2 activation in colorectal cancer
Authors: Su Ning , Peng Liang , Xia Bingqing , Zhao Yingying , Xu Angao , Wang Jing , Wang Xinying , Jiang Bo
Published: December 2012

Background and aim

CD24 expression is associated with human colorectal cancer (CRC). Our previous data indicated that CD24 promoted the proliferation and invasion of colorectal cancer cells through the activation of ERK1/2. Since Src family kinases are frequently deregulated in CRC and closely related to the MAPK signaling pathway, we investigated the impact of Lyn, an important member of SFKs, on CD24-induced ERK1/2 activation in CRC.

Methods and Results

The interaction of CD24 and Lyn was identified by co-immunoprecipitation (Co-IP) and ectopic expression of CD24-induced Lyn activation. Inhibition of Lyn activation by phosphatase PP2 in SW480CD24cells abrogated CD24-induced invasion. The results of the Co-IP and immunofluorescence assay revealed that overexpression of CD24 enhanced the interaction of Lyn and ERK1/2 and induced the nuclear translocation of Lyn. However, inhibition of Lyn activity attenuated CD24-induced ERK1/2 activation, and depletion of CD24 disrupted Lyn-ERK1/2 interaction. Immunohistochemistry analysis for 202 cases of CRC showed that the expression of both CD24 and Lyn was positively correlated with tumor grade, stage, lymph node and distant metastasis. Patients with lower expression of CD24 or Lyn had a higher survival rate. The Cox multivariate analysis showed that CD24 expression, but not Lyn expression, was an independent prognostic factor of CRC.

Conclusions

Our results suggest that Lyn is involved in CD24-induced ERK1/2 activation in CRC. The expression of CD24 is associated with activation of Lyn and ERK1/2, which might be a novel mechanism related to CD24-mediated regulation of CRC development.
Using association rules mining to explore pattern of Chinese medicinal formulae (prescription) in treating and preventing breast cancer recurrence and metastasis
Authors: He Yanhua , Zheng Xiao , Sit Cindy , Loo Wings TY , Wang ZhiYu , Xie Ting , Jia Bo , Ye Qiaobo , Tsui Kamchuen , Chow Louis WC , Chen Jianping
Published: December 2012

Background

Chinese herbal medicine is increasingly widely used as a complementary approach for control of breast cancer recurrence and metastasis. In this paper, we examined the implicit prescription patterns behind the Chinese medicinal formulae, so as to explore the Chinese medicinal compatibility patterns or rules in the treatment or control of breast cancer recurrence and metastasis.

Methods

This study was based on the herbs recorded in Pharmacopoeia of the People’s Republic of China, and the literature sources from Chinese Journal Net and China Master Dissertations Full-text Database (1990 – 2010) to analyze the compatibility rule of the prescription. Each Chinese herb was listed according to the selected medicinal formulae and the added information was organized to establish a database. The frequency and the association rules of the prescription patterns were analyzed using the SPSS Clenmentine Data Mining System. An initial statistical analysis was carried out to categorize the herbs according to their medicinal types and dosage, natures, flavors, channel tropism, and functions. Based on the categorization, the frequencies of occurrence were computed.

Results

The main prescriptive features from the selected formulae of the mining data are: (1) warm or cold herbs in the Five Properties category; sweet or bitter herbs in the Five Flavors category and with affinity to the liver meridian are the most frequently prescribed in the 96 medicinal formulae; (2) herbs with tonifying and replenishing, blood-activating and stasis-resolving, spleen-strengthening and dampness-resolving or heat-clearing and detoxicating functions that are frequently prescribed; (3) herbs with blood-tonifying, yin-tonifying, spleen-strengthening and dampness-resolving, heat-clearing and detoxicating, and blood-activating with stasis-resolving functions that are interrelated and prescribed in combination with qi-tonifying herbs.

Conclusions

The results indicate that there is a close relationship between recurrence and metastasis of breast cancer with liver dysfunctions. These prescriptions focus on the herbs for nourishing the yin-blood, and emolliating and regulating the liver which seems to be the key element in the treatment process. Meanwhile, the use of qi-tonifying and spleen-strengthening herbs also forms the basis of prescription patterns.
Low-temperature poly-Si nanowire junctionless devices with gate-all-around TiN/Al2O3 stack structure using an implant-free technique
Authors: Su Chun-Jung , Tsai Tzu-I , Lin Horng-Chih , Huang Tiao-Yuan , Chao Tien-Sheng
Published: December 2012

In this work, we present a gate-all-around (GAA) low-temperature poly-Si nanowire (NW) junctionless device with TiN/Al2O3 gate stack using an implant-free approach. Since the source/drain and channel regions are sharing one in situ phosphorous-doped poly-Si material, the process flow and cost could be efficiently reduced. Owing to the GAA configuration and small volume of NW channels, the fabricated devices with heavily doped channels display superior switching behaviors and excellent immunity to short-channel effects. Besides, the negative fixed charges in Al2O3 are found to be helpful to obtain desirable positive threshold voltages for the n+-poly-Si channel devices. Thus, the simple and low-cost fabrication method along with excellent device characteristics makes the proposed GAA NW transistor a promising candidate for future 3-D electronics and system-on-panel applications.
Large size self-assembled quantum rings: quantum size effect and modulation on the surface diffusion
Authors: Tong Cunzhu , Yoon Soon Fatt , Wang Lijun
Published: December 2012

We demonstrate experimentally the submicron size self-assembled (SA) GaAs quantum rings (QRs) by quantum size effect (QSE). An ultrathin In0.1 Ga0.9As layer with different thickness is deposited on the GaAs to modulate the surface nucleus diffusion barrier, and then the SA QRs are grown. It is found that the density of QRs is affected significantly by the thickness of inserted In0.1 Ga0.9As, and the diffusion barrier modulation reflects mainly on the first five monolayer . The physical mechanism behind is discussed. The further analysis shows that about 160 meV decrease in diffusion barrier can be achieved, which allows the SA QRs with density of as low as one QR per 6 μm2. Finally, the QRs with diameters of 438 nm and outer diameters of 736 nm are fabricated using QSE.