bluuebunny/crossref_metadata_2025 huggingface dataset:
Tolling and Economic Efficiency
Authors: Swan Peter F. , Belzer Michael H.
Published: September 2012

This article uses crash data, highway classification, and traffic statistics to estimate the crash cost per truck vehicle mile traveled (VMT) from 2002 to 2006 for trucks that diverted from the Ohio Turnpike to avoid paying higher toll rates imposed by the Ohio Turnpike Authority. The data show that the truck crash cost per VMT is lowest for rural interstates such as the Turnpike and highest for the roads to which truck traffic diverted. Using the elasticity of demand for truck use of toll roads, we then estimate that the crash cost of trucks diverted from the Ohio Turnpike to other roads during 2004 at more than US$38 million, which far exceeds the revenue benefit. The article discusses implications of these results for road infrastructure pricing.
Comparing Neuropsychological Profiles Between Girls With Asperger’s Disorder and Girls With Learning Disabilities
Authors: McKnight Megan E. , Culotta Vincent P.
Published: September 2012

Research examining neuropsychological profiles of girls with Asperger’s disorder (AD) is sparse. In this study, we sought to characterize neurocognitive profiles of girls with AD compared to girls with learning disabilities (LD). Two groups of school-age girls referred for neuropsychological assessment participated in the study. A total of 23 girls with AD were compared to 50 girls with LD using intellectual, academic, neuropsychological, and behavioral assessments. Standard two-tailed t-tests revealed statistically significant discrepancies in a number of areas, and results were interpreted to conclude that the participants with AD had a more severe cognitive and behavioral presentation than same-age girls with LD. The severity of these discrepancies indicates the need for routine neuropsychological and behavioral screening to promote early diagnosis and intervention. Based on this study, we challenge the idea that girls present with a more benign expression of AD than boys.
Intensive Behavioral Treatment of Urinary Incontinence of Children With Autism Spectrum Disorders
Authors: Hanney Nicole M. , Jostad Candice M. , LeBlanc Linda A. , Carr James E. , Castile Allison J.
Published: September 2012

LeBlanc, Crossett, Bennett, Detweiler, and Carr (2005) described an outpatient model for conducting intensive toilet training with young children with autism using a modified Azrin and Foxx, protocol. In this article, we summarize the use of the protocol in an outpatient setting and the outcomes achieved with a large sample of children with autism spectrum disorders. Thirty archival clinical records were coded for several variables related to treatment implementation and outcome. The majority of participants achieved full continence in an average of approximately 2 weeks. Details on the typical implementation and course of treatment are presented to provide a profile for future practitioners.
How Does Fidelity of Implementation Matter? Using Multilevel Models to Detect Relationships Between Participant Outcomes and the Delivery and Receipt of Treatment
Authors: Zvoch Keith
Published: September 2012

Multilevel modeling techniques facilitated examination of relationships between fidelity indicators and outcomes associated with a summer literacy intervention. Three-level growth models were specified to capture the extent to which students experienced instruction and to demonstrate the ways in which dosage–response relationships manifest in program evaluation contexts. The observation that outcome-related deviations from program protocol occurred both at the provider and at the recipient levels suggests that evaluators will often need to conceptualize, measure, and model “treatment fidelity” as a multilevel, multidimensional construct.
Measuring Relative Cue Strength as a Means of Validating an Inventory of Expert Offender Profiling Cues
Authors: Morrison Ben W. , Wiggins Mark W. , Bond Nigel W. , Tyler Michael D.
Published: September 2012

Cues have been identified as important precursors to successful diagnoses among expert practitioners. However, current approaches to the identification of expert cues typically rely on subjective methods, making the validity of cues difficult to establish. The present research examined the utility of a Paired-Concept Association Task (P-CAT) as a basis for discriminating expert and novice cue activation in the context of offender profiling. Three studies are reported: 1A employed a cognitive interview for the acquisition of cue-based concepts used by experts and novices; 1B presented pairs of concepts as part of the P-CAT, which recorded response latency; and, 1C employed a survey to further gauge participants’ perceptions of the concepts. The results revealed differences between experts and novices in the cue-based associations activated, and in the response latencies associated with the P-CAT, across expertise. The P-CAT accurately discriminated expert from novice cue activation and consequently offers a new method for objectively validating expert cue use.
Scapular Stress Fracture in Water Polo
Authors: Donaldson Laurie D.
Published: September 2012

Water polo is an intense sport with extreme physical contact and repetitive shoulder motion that predisposes to injury. The continuous scapular motion and recruitment of the scapular stabilizers to maintain buoyancy expose water polo athletes to the risk of scapular stress fracture. Suspicion should arise when evaluating water polo athletes presenting with shoulder pain.
“One Question Before You Get Gone. . .”
Authors: Gau Jacinta M. , Brunson Rod K.
Published: September 2012

The use of consent searches in the war on drugs has brought this type of search to the forefront of the racial profiling debate. Studies using official traffic-stop data have attempted to determine whether minority drivers are more likely than White drivers to be asked for consent to search. This analytic strategy, though informative, does not account for the perceptual nature of racial profiling and the damage that might be done to drivers’ attitudes toward police if they react negatively to being asked for consent. The present study, using the theories of procedural justice and expectancy disconfirmation, analyzes the impact of officers’ requests for consent to search on drivers’ perceptions about the legitimacy of the stops themselves. Interaction effects are also modeled by breaking the sample down by race. Results suggest that consent search requests significantly damage perceived stop legitimacy only among White drivers; the effect is marginally significant among Black drivers and nonsignificant for Hispanics. This finding is interpreted within the bounds of expectancy theory, whereby minority drivers’ expectations for the way officers will treat them are lower from the outset than Whites’ are, so Whites, then, are particularly affronted by search requests. This suggests that perceived racial profiling is a complex, nuanced phenomenon and that race is more symbolic than predictive of stopped drivers’ attitudes toward police.
Focal Nodular Hyperplasia
Authors: McCann Chelsey N. , Penny Steven M.
Published: September 2012

Focal nodular hyperplasia (FNH) is the second most common benign hepatic mass. The primary purpose of this article is to provide a relevant case study and offer a review of the recent literature related to FNH with a discussion of both the clinical and imaging findings of this classically benign hepatic lesion. Although magnetic resonance imaging is considered the gold standard of FNH imaging, the sonographic and computed tomography appearance also is offered in this article. Furthermore, contrast-enhanced ultrasound, which boasts a 96% success rate at differentiating FNH from other hepatic tumors, is analyzed. The historical treatment options, including medical and possible surgical intervention, are provided as well. Last, this article offers an analysis of the prognosis for the patient diagnosed with FNH.
The p53 pathway in hematopoiesis: lessons from mouse models, implications for humans
Authors: Pant Vinod , Quintás-Cardama Alfonso , Lozano Guillermina
Published: September 2012

Aberrations in the p53 tumor suppressor pathway are associated with hematologic malignancies. p53-dependent cell cycle control, senescence, and apoptosis functions are actively involved in maintaining hematopoietic homeostasis under normal and stress conditions. Whereas loss of p53 function promotes leukemia and lymphoma development in humans and mice, increased p53 activity inhibits hematopoietic stem cell function and results in myelodysplasia. Thus, exquisite regulation of p53 activity is critical for homeostasis. Most of our understanding of p53 function in hematopoiesis is derived from genetically engineered mice. Here we summarize some of these models, the various mechanisms that disrupt the regulation of p53 activity, and their relevance to human disease.
Self-antigen recognition by follicular lymphoma B-cell receptors
Authors: Sachen Kacey L. , Strohman Michael J. , Singletary Jonathan , Alizadeh Ash A. , Kattah Nicole H. , Lossos Chen , Mellins Elizabeth D. , Levy Shoshana , Levy Ronald
Published: September 2012

Follicular lymphoma is a monoclonal B-cell malignancy with each patient's tumor expressing a unique cell surface immunoglobulin (Ig), or B-cell receptor (BCR), that can potentially recognize antigens and/or transduce signals into the tumor cell. Here we evaluated the reactivity of tumor derived Igs for human tissue antigens. Self-reactivity was observed in 26% of tumor Igs (25 of 98). For one follicular lymphoma patient, the recognized self-antigen was identified as myoferlin. This patient's tumor cells bound recombinant myoferlin in proportion to their level of BCR expression, and the binding to myoferlin was preserved despite ongoing somatic hypermutation of Ig variable regions. Furthermore, BCR-mediated signaling was induced after culture of tumor cells with myoferlin. These results suggest that antigen stimulation may provide survival signals to tumor cells and that there is a selective pressure to preserve antigen recognition as the tumor evolves.
Expression of Myc, but not pSTAT3, is an adverse prognostic factor for diffuse large B-cell lymphoma treated with epratuzumab/R-CHOP
Authors: Gupta Mamta , Maurer Matthew J. , Wellik Linda E. , Law Mark E. , Han Jing Jing , Ozsan Nazan , Micallef Ivana N. , Dogan Ahmet , Witzig Thomas E.
Published: September 2012

STAT3 regulates cell growth by up-regulating downstream targets, such as Myc. The frequency of phosphorylated STAT3 (pSTAT3) and Myc expression and their prognostic relevance is unknown within diffuse large B-cell lymphoma (DLBCL) germinal center B-cell (GCB) and non-GCB subtypes. pSTAT3 and Myc were studied by immunohistochemistry (IHC) on tumors from 40 DLBCL patients uniformly treated on a clinical trial of epratuzumab/rituximab-CHOP. A total of 35% of cases were pSTAT3-positive, and pSTAT3 positivity was more frequent in the non-GCB (P = .06) type but did not correlate with event-free survival (EFS). Myc expression was observed in 50% of cases and was more frequent in non-GCB type (P = .07). Myc-positive cases had inferior EFS in all patients, including the GCB and pSTAT3-positive cases, were more likely to express Myc (P = .06). Myc translocations involving the major breakpoint regions were found in 10% (3 of 29) of cases, and all 3 cases were GCB and had an inferior EFS (P = .09). pSTAT3, but not Myc expression, was correlated with elevated pretreatment serum cytokines, such as IL-10 (P = .05), G-CSF (P = .03), and TNF-α (P = .04). pSTAT3 IHC in DLBCL tumors has the potential to identify patients for STAT3 pathway–directed therapy; Myc IHC is a potential marker for inferior EFS in GCB patients.
γ9 and δ2CDR3 domains regulate functional avidity of T cells harboring γ9δ2TCRs
Authors: Gründer Cordula , van Dorp Suzanne , Hol Samantha , Drent Esther , Straetemans Trudy , Heijhuurs Sabine , Scholten Kirsten , Scheper Wouter , Sebestyen Zsolt , Martens Anton , Strong Roland , Kuball Jürgen
Published: September 2012

Immunotherapy with innate immune cells has recently evoked broad interest as a novel treatment option for cancer patients. γ9δ2T cells in particular are emerging as an innate cell population with high frequency and strong antitumor reactivity, which makes them and their receptors promising candidates for immune interventions. However, clinical trials have so far reported only limited tumor control by adoptively transferred γ9δ2T cells. As a potential explanation for this lack of efficacy, we found unexpectedly high variability in tumor recognition within the physiologic human γ9δ2T-cell repertoire, which is substantially regulated by the CDR3 domains of individual γ9δ2TCRs. In the present study, we demonstrate that the reported molecular requirements of CDR3 domains to interact with target cells shape the physiologic γ9δ2T-cell repertoire and, most likely, limit the protective and therapeutic antitumor efficacy of γ9δ2T cells. Based on these findings, we propose combinatorial-γδTCR-chain exchange as an efficient method for designing high-affinity γ9δ2TCRs that mediate improved antitumor responses when expressed in αβT cells both in vitro and in vivo in a humanized mouse model.
BMP9 regulates endoglin-dependent chemokine responses in endothelial cells
Authors: Young Kira , Conley Barbara , Romero Diana , Tweedie Eric , O'Neill Christine , Pinz Ilka , Brogan Louise , Lindner Volkhard , Liaw Lucy , Vary Calvin P. H.
Published: September 2012

BMP9 signaling has been implicated in hereditary hemorrhagic telangiectasia (HHT) and vascular remodeling, acting via the HHT target genes, endoglin and ALK1. This study sought to identify endothelial BMP9-regulated proteins that could affect the HHT phenotype. Gene ontology analysis of cDNA microarray data obtained after BMP9 treatment of primary human endothelial cells indicated regulation of chemokine, adhesion, and inflammation pathways. These responses included the up-regulation of the chemokine CXCL12/SDF1 and down-regulation of its receptor CXCR4. Quantitative mass spectrometry identified additional secreted proteins, including the chemokine CXCL10/IP10. RNA knockdown of endoglin and ALK1 impaired SDF1/CXCR4 regulation by BMP9. Because of the association of SDF1 with ischemia, we analyzed its expression under hypoxia in response to BMP9 in vitro, and during the response to hindlimb ischemia, in endoglin-deficient mice. BMP9 and hypoxia were additive inducers of SDF1 expression. Moreover, the data suggest that endoglin deficiency impaired SDF1 expression in endothelial cells in vivo. Our data implicate BMP9 in regulation of the SDF1/CXCR4 chemokine axis in endothelial cells and point to a role for BMP9 signaling via endoglin in a switch from an SDF1-responsive autocrine phenotype to an SDF1 nonresponsive paracrine state that represses endothelial cell migration and may promote vessel maturation.
Quantitative biomedical annotation using medical subject heading over-representation profiles (MeSHOPs)
Authors: Cheung Warren A , Ouellette BF Francis , Wasserman Wyeth W
Published: September 2012

Background

MEDLINE®/PubMed® indexes over 20 million biomedical articles, providing curated annotation of its contents using a controlled vocabulary known as Medical Subject Headings (MeSH). The MeSH vocabulary, developed over 50+ years, provides a broad coverage of topics across biomedical research. Distilling the essential biomedical themes for a topic of interest from the relevant literature is important to both understand the importance of related concepts and discover new relationships.

Results

We introduce a novel method for determining enriched curator-assigned MeSH annotations in a set of papers associated to a topic, such as a gene, an author or a disease. We generate MeSH Over-representation Profiles (MeSHOPs) to quantitatively summarize the annotations in a form convenient for further computational analysis and visualization. Based on a hypergeometric distribution of assigned terms, MeSHOPs statistically account for the prevalence of the associated biomedical annotation while highlighting unusually prevalent terms based on a specified background. MeSHOPs can be visualized using word clouds, providing a succinct quantitative graphical representation of the relative importance of terms. Using the publication dates of articles, MeSHOPs track changing patterns of annotation over time. Since MeSHOPs are quantitative vectors, MeSHOPs can be compared using standard techniques such as hierarchical clustering. The reliability of MeSHOP annotations is assessed based on the capacity to re-derive the subset of the Gene Ontology annotations with equivalent MeSH terms.

Conclusions

MeSHOPs allows quantitative measurement of the degree of association between any entity and the annotated medical concepts, based directly on relevant primary literature. Comparison of MeSHOPs allows entities to be related based on shared medical themes in their literature. A web interface is provided for generating and visualizing MeSHOPs.
Variation in the genomic locations and sequence conservation of STAR elements among staphylococcal species provides insight into DNA repeat evolution
Authors: Purves Joanne , Blades Matthew , Arafat Yasrab , Malik Salman A , Bayliss Christopher D , Morrissey Julie A
Published: September 2012

Background

Staphylococcus aureus Repeat (STAR) elements are a type of interspersed intergenic direct repeat. In this study the conservation and variation in these elements was explored by bioinformatic analyses of published staphylococcal genome sequences and through sequencing of specific STAR element loci from a large set of S. aureus isolates.

Results

Using bioinformatic analyses, we found that the STAR elements were located in different genomic loci within each staphylococcal species. There was no correlation between the number of STAR elements in each genome and the evolutionary relatedness of staphylococcal species, however higher levels of repeats were observed in both S. aureus and S. lugdunensis compared to other staphylococcal species. Unexpectedly, sequencing of the internal spacer sequences of individual repeat elements from multiple isolates showed conservation at the sequence level within deep evolutionary lineages of S. aureus. Whilst individual STAR element loci were demonstrated to expand and contract, the sequences associated with each locus were stable and distinct from one another.

Conclusions

The high degree of lineage and locus-specific conservation of these intergenic repeat regions suggests that STAR elements are maintained due to selective or molecular forces with some of these elements having an important role in cell physiology. The high prevalence in two of the more virulent staphylococcal species is indicative of a potential role for STAR elements in pathogenesis.
Adenylate kinase 2 (AK2) promotes cell proliferation in insect development
Authors: Chen Ru-Ping , Liu Chun-Yan , Shao Hong-Lian , Zheng Wei-Wei , Wang Jin-Xing , Zhao Xiao-Fan
Published: September 2012

Background

Adenylate kinase 2 (AK2) is a phosphotransferase that catalyzes the reversible reaction 2ADP(GDP) ↔ ATP(GTP) + AMP and influences cellular energy homeostasis. However, the role of AK2 in regulating cell proliferation remains unclear because AK2 has been reported to be involved in either cell proliferation or cell apoptosis in different cell types of various organisms.

Results

This study reports AK2 promotion of cell proliferation using the lepidopteran insect Helicoverpa armigera and its epidermal cell line HaEpi as models. Western blot analysis indicates that AK2 constitutively expresses in various tissues during larval development. Immunocytochemistry analysis indicates that AK2 localizes in the mitochondria. The recombinant expressed AK2 in E. coli promotes cell growth and viability of HaEpi cell line by 3-(4, 5-Dimethylthiazol-2-yl)-2, 5-diphenyltetrazolium bromide (MTT) assay. AK2 knockdown in larvae by RNA interference causes larval growth defects, including body weight decrease and development delay. AK2 knockdown in larvae also decreases the number of circulating haemocytes. The mechanism for such effects might be the suppression of gene transcription involved in insect development caused by AK2 knockdown.

Conclusion

These results show that AK2 regulates cell growth, viability, and proliferation in insect growth and development.
Divergent patterns of endogenous small RNA populations from seed and vegetative tissues of Glycine max
Authors: Zabala Gracia , Campos Edhilvia , Varala Kranthi K , Bloomfield Sean , Jones Sarah I , Win Hlaing , Tuteja Jigyasa H , Calla Bernarda , Clough Steven J , Hudson Matthew , Vodkin Lila O
Published: October 2012

Background

Small non-coding RNAs (smRNAs) are known to have major roles in gene regulation in eukaryotes. In plants, knowledge of the biogenesis and mechanisms of action of smRNA classes including microRNAs (miRNAs), short interfering RNAs (siRNAs), and trans-acting siRNAs (tasiRNAs) has been gained mostly through studies with Arabidopsis. In recent years, high throughput sequencing of smRNA populations has enabled extension of knowledge from model systems to plants with larger, more complex genomes. Soybean (Glycine max) now has many genomics resources available including a complete genome sequence and predicted gene models. Relatively little is known, however, about the full complement of its endogenous smRNAs populations and the silenced genes.

Results

Using Illumina sequencing and computational analysis, we characterized eight smRNA populations from multiple tissues and organs of soybean including developing seed and vegetative tissues. A total of 41 million raw sequence reads collapsed into 135,055 unique reads were mapped to the soybean genome and its predicted cDNA gene models. Bioinformatic analyses were used to distinguish miRNAs and siRNAs and to determine their genomic origins and potential target genes. In addition, we identified two soybean TAS3 gene homologs, the miRNAs that putatively guide cleavage of their transcripts, and the derived tasiRNAs that could target soybean genes annotated as auxin response factors. Tissue-differential expression based on the flux of normalized miRNA and siRNA abundances in the eight smRNA libraries was evident, some of which was confirmed by smRNA blotting. Our global view of these smRNA populations also revealed that the size classes of smRNAs varied amongst different tissues, with the developing seed and seed coat having greater numbers of unique smRNAs of the 24-nt class compared to the vegetative tissues of germinating seedlings. The 24-nt class is known to be derived from repetitive elements including transposons. Detailed analysis of the size classes associated with ribosomal RNAs and transposable element families showed greater diversity of smRNAs in the 22- and 24-nt size classes.

Conclusions

The flux of endogenous smRNAs within multiple stages and tissues of seed development was contrasted with vegetative tissues of soybean, one of the dominant sources of protein and oil in world markets. The smRNAs varied in size class, complexity of origins, and possible targets. Sequencing revealed tissue-preferential expression for certain smRNAs and expression differences among closely related miRNA family members.
Variation in dengue virus plaque reduction neutralization testing: systematic review and pooled analysis
Authors: Rainwater-Lovett Kaitlin , Rodriguez-Barraquer Isabel , Cummings Derek AT , Lessler Justin
Published: September 2012

Background

The plaque reduction neutralization test (PRNT) remains the gold standard for the detection of serologic immune responses to dengue virus (DENV). While the basic concept of the PRNT remains constant, this test has evolved in multiple laboratories, introducing variation in materials and methods. Despite the importance of laboratory-to-laboratory comparability in DENV vaccine development, the effects of differing PRNT techniques on assay results, particularly the use of different dengue strains within a serotype, have not been fully characterized.

Methods

We conducted a systematic review and pooled analysis of published literature reporting individual-level PRNT titers to identify factors associated with heterogeneity in PRNT results and compared variation between strains within DENV serotypes and between articles using hierarchical models.

Results

The literature search and selection criteria identified 8 vaccine trials and 25 natural exposure studies reporting 4,411 titers from 605 individuals using 4 different neutralization percentages, 3 cell lines, 12 virus concentrations and 51 strains. Of 1,057 titers from primary DENV exposure, titers to the exposure serotype were consistently higher than titers to non-exposure serotypes. In contrast, titers from secondary DENV exposures (n = 628) demonstrated high titers to exposure and non-exposure serotypes. Additionally, PRNT titers from different strains within a serotype varied substantially. A pooled analysis of 1,689 titers demonstrated strain choice accounted for 8.04% (90% credible interval [CrI]: 3.05%, 15.7%) of between-titer variation after adjusting for secondary exposure, time since DENV exposure, vaccination and neutralization percentage. Differences between articles (a proxy for inter-laboratory differences) accounted for 50.7% (90% CrI: 30.8%, 71.6%) of between-titer variance.

Conclusions

As promising vaccine candidates arise, the lack of standardized assays among diagnostic and research laboratories make unbiased inferences about vaccine-induced protection difficult. Clearly defined, widely accessible reference reagents, proficiency testing or algorithms to adjust for protocol differences would be a useful first step in improving dengue PRNT comparability and quality assurance.
Picking transplant glomerulopathy out of the CAN: evidence from a clinico-pathological evaluation
Authors: Sun Qiquan , Huang Xianghua , Jiang Song , Zeng Caihong , Liu Zhihong
Published: September 2012

Background

Since the term chronic allograft nephropathy (CAN) was removed from the Banff scheme in 2005, transplant glomerulopathy (TG) has been regarded as a clinicopathological entity that is one of the major causes of graft loss. To assess the distinction between CAN and TG, we performed a comprehensive evaluation comparing TG with traditional CAN.

Methods

We compared the clinicopathological features of 43 cases of TG with 43 matched cases of non-TG CAN (non-TG group) after renal transplantation. TG was diagnosed by light microscopy based on the double contours of the glomerular basement membranes, and the Banff 97 classification system was used to score TG severity (cg0-3).

Results

Compared to the control group, we found a significantly higher incidence of positivity for human leukocyte antigen class-I and II antibodies, a higher incidence of hepatitis C virus (HCV) infection, and poorer graft survival in TG patients. Clinically, TG was associated with a higher prevalence of proteinuria, hematuria, anaemia and hypoalbuminemia. Histologically, TG strongly correlated with antibody related microcirculatory injuries, including glomerulitis, peritubular capillaritis and peritubular capillary (PTC) C4d deposition. Interestingly, the TG patients showed a significantly higher incidence of IgA deposition than the control patients. C4d-positive TG was correlated with higher TG and PTC scores, and PTC C4d deposition was correlated with a more rapid progression to graft dysfunction. TG accompanied by HCV infection was associated with heavier proteinuria, higher TG and C4d scores, and poorer graft survival.

Conclusions

TG presents clinicopathological features that are distinct from non-TG cases and leads to poorer outcomes. PTC C4d deposition is related to a more rapid progression to graft loss, suggesting ongoing antibody reactivity. HCV-positive TG is a more severe sub-entity, that requires further investigation.
Characterizing sexual histories of women before formal sex-work in south India from a cross-sectional survey: implications for HIV/STI prevention
Authors: Mishra Sharmistha , Ramanaik Satyanarayana , Blanchard James F , Halli Shiva , Moses Stephen , Raghavendra T , Bhattacharjee Parinita , Lorway Rob , Becker Marissa
Published: September 2012

Background

Interventions designed to prevent HIV and STIs in female sex-workers (FSWs) reach women after they formally enter the sex-trade. We aimed to characterize the pattern of sexual behaviour among FSWs from first-sex to when they identify as sex-workers (transition period) in a region with traditional (historically characterized by dedication into sex-work at first-sex) and non-traditional forms of sex-work.

Methods

We conducted a cross-sectional survey of 246 traditional and 765 non-traditional FSWs across three districts in Karnataka, India. We performed univariate and multivariate logistic regression to profile FSWs most likely to engage in a commercial first-sex before identifying as a sex-worker. Sexual life-course patterns were distinguished using univariate and multivariate linear regression based on key events associated with length of transition period.

Results

Overall, 266 FSWs experienced a commercial first-sex, of whom 45.9% (95% CI: 38.2,53.7) continued a long-term relationship with the first partner. In adjusted analysis, traditional FSWs were more likely to experience a commercial first-sex (AOR 52.5, 95% CI: 27.4,100.7). The average transition time was 8.8 years (SD 3.9), but there was considerable variability between respondents. Among women who experienced a commercial first-sex, a slower transition was independently associated with non-traditional sex-work, the presence of long-term partnerships during the transition period, and ongoing partnerships at time of entry into sex-work. In the absence of a commercial first-sex, a faster transition was associated with traditional sex-work and the dissolution of long-term partnerships, while a slower transition was associated with the presence of long-term partnerships and widowhood. Only 18.5% (95% CI: 12.7,26.2) and 47.3% (95% CI: 32.7,62.3) of women reported ‘always’ condom use with their long-term and occasional partners during the transition period, respectively.

Conclusions

FSWs identify as sex-workers several years after becoming sexually active, even when the first-sex is commercial in nature. Long-term partnerships are common after a commercial first-sex, and are associated with a delay in formally entering the sex-trade. The findings call for a better understanding of HIV/STI risk before FSWs identify as sex-workers, and an adaptive programme to reach this period of vulnerability.
Experiences with Surgical treatment of chronic lower limb ulcers at a Tertiary hospital in northwestern Tanzania: A prospective review of 300 cases
Authors: Mbunda Fidelis , Mchembe Mabula D , Chalya Phillipo L , Rambau Peter , Mshana Stephen E , Kidenya Benson R , Gilyoma Japhet M
Published: September 2012

Background

Chronic lower limb ulcers constitute a major public health problem of great important all over the world and contribute significantly to high morbidity and long-term disabilities. There is paucity of information regarding chronic lower limb ulcers in our setting; therefore it was necessary to conduct this study to establish the patterns and outcome of chronic lower limb ulcers and to identify predictors of outcome in our local setting.

Methods

This was a descriptive prospective study of patients with chronic lower limb ulcers conducted at Bugando Medical Centre between November 2010 and April 2012. Ethical approval to conduct the study was sought from relevant authorities. Statistical data analysis was done using SPSS version 17.0 and STATA version 11.0.

Results

A total of 300 patients were studied. Their ages ranged from 3 months to 85 years (median 32 years). The male to female ratio was 2:1. The median duration of illness was 44 days. Traumatic ulcer was the most frequent type of ulcer accounting for 60.3% of patients. The median duration of illness was 44 days. The leg was commonly affected in 33.7% of cases and the right side (48.7%) was frequently involved. Out of 300 patients, 212 (70.7%) had positive aerobic bacterial growth within 48 hours of incubation.Pseudomonas aeruginosa(25.5%) was the most frequent gram negative bacteria isolated, whereas gram positive bacteria commonly isolated wasStaphylococcus aureus(13.7%). Twenty (6.7%) patients were HIV positive with a median CD4+ count of 350 cells/μl. Mycological investigation was not performed. Bony involvement was radiologically reported in 83.0% of cases. Histopathological examination performed in 56 patients revealed malignancy in 20 (35.7%) patients, of which malignant melanoma (45.0%) was the most common histopathological type. The vast majority of patients, 270 (90.0%) were treated surgically, and surgical debridement was the most common surgical procedure performed in 24.1% of cases. Limb amputation rate was 8.7%. Postoperative complication rate was 58.3% of which surgical site infection (77.5%) was the most common post-operative complications. The median length of hospital stay was 23 days. Mortality rate was 4.3%. Out of the two hundred and eighty-seven (95.7%) survivors, 253 (91.6%) were treated successfully and discharged well (healed). After discharge, only 35.5% of cases were available for follow up at the end of study period.

Conclusion

Chronic lower limb ulcers remain a major public health problem in this part of Tanzania. The majority of patients in our environment present late when the disease is already in advanced stages. Early recognition and aggressive treatment of the acute phase of chronic lower limb ulcers at the peripheral hospitals and close follow-up are urgently needed to improve outcomes of these patients in our environment.
Structural and mechanistic investigations on Salmonella typhimurium acetate kinase (AckA): identification of a putative ligand binding pocket at the dimeric interface
Authors: Chittori Sagar , Savithri Handanahal S , Murthy Mathur RN
Published: October 2012

Background

Bacteria such as Escherichia coli and Salmonella typhimurium can utilize acetate as the sole source of carbon and energy. Acetate kinase (AckA) and phosphotransacetylase (Pta), key enzymes of acetate utilization pathway, regulate flux of metabolites in glycolysis, gluconeogenesis, TCA cycle, glyoxylate bypass and fatty acid metabolism.

Results

Here we report kinetic characterization of S. typhimurium AckA (St AckA) and structures of its unliganded (Form-I, 2.70 Å resolution) and citrate-bound (Form-II, 1.90 Å resolution) forms. The enzyme showed broad substrate specificity with k

cat
/K

m
in the order of acetate > propionate > formate. Further, the K

m
for acetyl-phosphate was significantly lower than for acetate and the enzyme could catalyze the reverse reaction (i.e. ATP synthesis) more efficiently. ATP and Mg2+ could be substituted by other nucleoside 5′-triphosphates (GTP, UTP and CTP) and divalent cations (Mn2+ and Co2+), respectively. Form-I St AckA represents the first structural report of an unliganded AckA. St AckA protomer consists of two domains with characteristic βββαβαβα topology of ASKHA superfamily of proteins. These domains adopt an intermediate conformation compared to that of open and closed forms of ligand-bound Methanosarcina thermophila AckA (Mt AckA). Spectroscopic and structural analyses of StAckA further suggested occurrence of inter-domain motion upon ligand-binding. Unexpectedly, Form-II St AckA structure showed a drastic change in the conformation of residues 230–300 compared to that of Form-I. Further investigation revealed electron density corresponding to a citrate molecule in a pocket located at the dimeric interface of Form-II St AckA. Interestingly, a similar dimeric interface pocket lined with largely conserved residues could be identified in Form-I St AckA as well as in other enzymes homologous to AckA suggesting that ligand binding at this pocket may influence the function of these enzymes.

Conclusions

The biochemical and structural characterization of St AckA reported here provides insights into the biochemical specificity, overall fold, thermal stability, molecular basis of ligand binding and inter-domain motion in AckA family of enzymes. Dramatic conformational differences observed between unliganded and citrate-bound forms of St AckA led to identification of a putative ligand-binding pocket at the dimeric interface of St AckA with implications for enzymatic function.
Predicting necrosis in residual mass analysis after retroperitoneal lymph node dissection: a retrospective study
Authors: Miranda Eduardo de Paula , Abe Daniel Kanda , Nesrallah Adriano João , dos Reis Sabrina Thalita , Crippa Alexandre , Srougi Miguel , Dall’Oglio Marcos Francisco
Published: September 2012

Background

Recent studies have demonstrated that pathological analysis of retroperitoneal residual masses of patients with testicular germ cell tumors revealed findings of necrotic debris or fibrosis in up to 50% of patients. We aimed at pursuing a clinical and pathological review of patients undergoing post chemotherapy retroperitoneal lymph node dissection (PC-RPLND) in order to identify variables that may help predict necrosis in the retroperitoneum.

Methods

We performed a retrospective analysis of all patients who underwent PC-RPLND at the University Hospital of the University of São Paulo and Cancer Institute of Sao Paulo between January 2005 and September 2011. Clinical and pathological data were obtained and consisted basically of: measures of retroperitoneal masses, histology of the orchiectomy specimen, serum tumor marker and retroperitoneal nodal size before and after chemotherapy.

Results

We gathered a total of 32 patients with a mean age of 29.7; pathological analysis in our series demonstrated that 15 (47%) had necrosis in residual retroperitoneal masses, 15 had teratoma (47%) and 2 (6.4%) had viable germ cell tumors (GCT). The mean size of the retroperitoneal mass was 4.94 cm in our sample, without a difference between the groups (P = 0.176). From all studied variables, relative changes in retroperitoneal lymph node size (P = 0.04), the absence of teratoma in the orchiectomy specimen (P = 0.03) and the presence of choriocarcinoma in the testicular analysis after orchiectomy (P = 0.03) were statistically significant predictors of the presence of necrosis. A reduction level of 35% was therefore suggested to be the best cutoff for predicting the absence of tumor in the retroperitoneum with a sensitivity of 73.3% and specificity of 82.4%.

Conclusions

Even though retroperitoneal lymph node dissection remains the gold standard for patients with residual masses, those without teratoma in the primary tumor and a shrinkage of 35% or more in retroperitoneal mass have a considerably smaller chance of having viable GCT or teratoma in the retroperitoneum and a surveillance program could be considered.
Study of the oxygen vacancy influence on magnetic properties of Fe- and Co-doped SnO2 diluted alloys
Authors: Borges Pablo D , Scolfaro Luisa M R , Alves Horacio W Leite , da Silva Eronides F , Assali Lucy V C
Published: September 2012

Transition-metal (TM)-doped diluted magnetic oxides (DMOs) have attracted attention from both experimental and theoretical points of view due to their potential use in spintronics towards new nanostructured devices and new technologies. In the present work, we study the magnetic properties of Sn0.96TM0.04O2 and Sn0.96TM0.04O1.98(V
O)0.02, where TM = Fe and Co, focusing in particular in the role played by the presence of O vacancies nearby the TM. The calculated total energy as a function of the total magnetic moment per cell shows a magnetic metastability, corresponding to a ground state, respectively, with 2 and 1 μB/cell, for Fe and Co. Two metastable states, with 0 and 4 μB/cell were found for Fe, and a single value, 3 μB/cell, for Co. The spin-crossover energies (E
S) were calculated. The values are E
S
0/2 = 107 meV and E
S
4/2 = 25 meV for Fe. For Co, E
S
3/1 = 36 meV. By creating O vacancies close to the TM site, we show that the metastablity and E
S change. For iron, a new state appears, and the state with zero magnetic moment disappears. The ground state is 4 μB/cell instead of 2 μB/cell, and the energy E
S
2/4 is 30 meV. For cobalt, the ground state is then found with 3 μB/cell and the metastable state with 1 μB/cell. The spin-crossover energy E
S
1/3 is 21 meV. Our results suggest that these materials may be used in devices for spintronic applications that require different magnetization states.
Antibacterial performance of Ag nanoparticles and AgGO nanocomposites prepared via rapid microwave-assisted synthesis method
Authors: Chook Soon Wei , Chia Chin Hua , Zakaria Sarani , Ayob Mohd Khan , Chee Kah Leong , Huang Nay Ming , Neoh Hui Min , Lim Hong Ngee , Jamal Rahman , Rahman RahaMohdFadhilRajaAbdul
Published: September 2012

Silver nanoparticles and silver-graphene oxide nanocomposites were fabricated using a rapid and green microwave irradiation synthesis method. Silver nanoparticles with narrow size distribution were formed under microwave irradiation for both samples. The silver nanoparticles were distributed randomly on the surface of graphene oxide. The Fourier transform infrared and thermogravimetry analysis results showed that the graphene oxide for the AgNP-graphene oxide (AgGO) sample was partially reduced during the in situ synthesis of silver nanoparticles. Both silver nanoparticles and AgGO nanocomposites exhibited stronger antibacterial properties against Gram-negative bacteria (Salmonella typhi and Escherichia coli) than against Gram-positive bacteria (Staphyloccocus aureus and Staphyloccocus epidermidis). The AgGO nanocomposites consisting of approximately 40 wt.% silver can achieve antibacterial performance comparable to that of neat silver nanoparticles.
Three-dimensional AlZnO/Al2O3/AlZnO nanocapacitor arrays on Si substrate for energy storage
Authors: Li Lian-Jie , Zhu Bao , Ding Shi-Jin , Lu Hong-Liang , Sun Qing-Qing , Jiang Anquan , Zhang David Wei , Zhu Chunxiang
Published: October 2012

High density three-dimensional AZO/Al2O3/AZO nanocapacitor arrays have been fabricated for energy storage applications. Using atomic layer deposition technique, the stack of AZO/Al2O3/AZO has been grown in the porous anodic alumina template which is directly formed on the Si substrate. The fabricated capacitor shows a high capacitance density of 15.3 fF/μm2 at 100 kHz, which is nearly 2.5 times over the planar capacitor under identical conditions in theory. Further, the charge-discharge characteristics of the capacitor are characterized, indicating that the resistance-capacitance time constants are equal to 300 ns for the charging and discharging processes, and have no dependence on the voltage supply. This reflects good power characteristics of the electrostatic capacitor.
Rapid production of antigen-specific monoclonal antibodies from a variety of animals
Authors: Kurosawa Nobuyuki , Yoshioka Megumi , Fujimoto Rika , Yamagishi Fuminori , Isobe Masaharu
Published: September 2012

Background

Although a variety of animals have been used to produce polyclonal antibodies against antigens, the production of antigen-specific monoclonal antibodies from animals remains challenging.

Results

We propose a simple and rapid strategy to produce monoclonal antibodies from a variety of animals. By staining lymph node cells with an antibody against immunoglobulin and a fluorescent dye specific for the endoplasmic reticulum, plasma/plasmablast cells were identified without using a series of antibodies against lineage markers. By using a fluorescently labeled antigen as a tag for a complementary cell surface immunoglobulin, antigen-specific plasma/plasmablast cells were sorted from the rest of the cell population by fluorescence-activated cell sorting. Amplification of cognate pairs of immunoglobulin heavy and light chain genes followed by DNA transfection into 293FT cells resulted in the highly efficient production of antigen-specific monoclonal antibodies from a variety of immunized animals.

Conclusions

Our technology eliminates the need for both cell propagation and screening processes, offering a significant advantage over hybridoma and display strategies.
A checkpoints capturing timing-robust Boolean model of the budding yeast cell cycle regulatory network
Authors: Hong Changki , Lee Minho , Kim Dongsup , Kim Dongsan , Cho Kwang-Hyun , Shin Insik
Published: September 2012

Background

Cell cycle process of budding yeast (Saccharomyces cerevisiae) consists of four phases: G1, S, G2 and M. Initiated by stimulation of the G1 phase, cell cycle returns to the G1 stationary phase through a sequence of the S, G2 and M phases. During the cell cycle, a cell verifies whether necessary conditions are satisfied at the end of each phase (i.e., checkpoint) since damages of any phase can cause severe cell cycle defect. The cell cycle can proceed to the next phase properly only if checkpoint conditions are met. Over the last decade, there have been several studies to construct Boolean models that capture checkpoint conditions. However, they mostly focused on robustness to network perturbations, and the timing robustness has not been much addressed. Only recently, some studies suggested extension of such models towards timing-robust models, but they have not considered checkpoint conditions.

Results

To construct a timing-robust Boolean model that preserves checkpoint conditions of the budding yeast cell cycle, we used a model verification technique, ‘model checking’. By utilizing automatic and exhaustive verification of model checking, we found that previous models cannot properly capture essential checkpoint conditions in the presence of timing variations. In particular, such models violate the M phase checkpoint condition so that it allows a division of a budding yeast cell into two before the completion of its full DNA replication and synthesis. In this paper, we present a timing-robust model that preserves all the essential checkpoint conditions properly against timing variations. Our simulation results show that the proposed timing-robust model is more robust even against network perturbations and can better represent the nature of cell cycle than previous models.

Conclusions

To our knowledge this is the first work that rigorously examined the timing robustness of the cell cycle process of budding yeast with respect to checkpoint conditions using Boolean models. The proposed timing-robust model is the complete state-of-the-art model that guarantees no violation in terms of checkpoints known to date.
Electronic health records: what does your signature signify?
Authors: Victoroff MD Michael S
Published: September 2012

Electronic health records serve multiple purposes, including clinical communication, legal documentation, financial transaction capture, research and analytics. Electronic signatures attached to entries in EHRs have different logical and legal meanings for different users. Some of these are vestiges from historic paper formats that require reconsideration. Traditionally accepted functions of signatures, such as identity verification, attestation, consent, authorization and non-repudiation can become ambiguous in the context of computer-assisted workflow processes that incorporate functions like logins, auto-fill and audit trails. This article exposes the incompatibility of expectations among typical users of electronically signed information.