Miracle-dz/UniFAR-FTUs huggingface dataset:
Staging prostate cancer with dynamic contrast-enhanced endorectal MR imaging prior to radical prostatectomy: experienced versus less experienced readers.

PURPOSE To prospectively determine the accuracy of experienced and less experienced readers in the interpretation of combined T2-weighted fast spin-echo (SE) magnetic resonance (MR) images and dynamic contrast material-enhanced MR images compared with T2-weighted fast SE alone, with respect to differentiation of stage T2 versus stage T3 prostate carcinoma, with histologic analysis serving as the reference standard. MATERIALS AND METHODS Institutional review board approval and informed consent were obtained, and 124 consecutive men (age range, 42-74 years; median age, 63 years) with biopsy-proved prostate cancer underwent MR imaging and were candidates for radical prostatectomy. T2-weighted fast SE MR images and multisection dynamic contrast-enhanced MR images with a 2-second time resolution for the whole prostate were obtained. The T2-weighted and fused color-coded parametric dynamic contrast-enhanced MR images with T2-weighted images were evaluated prospectively and scored with regard to local extent by one experienced reader and evaluated retrospectively by two less experienced readers working in consensus by using a five-point scale; images with a score greater than or equal to four were considered indicative of T3 disease. Results were correlated with whole-mount section histopathologic findings, and receiver operating characteristics analysis was performed. RESULTS Twenty-five patients were excluded because of positive findings in the lymph nodes (n = 16), preoperative biopsy-proved seminal vesicle invasion (n = 5), and an absent dynamic dataset (n = 4). Ninety-nine patients were included in this study. The overall sensitivity, specificity, and accuracy of MR staging performance in prostate cancer with dynamic contrast-enhanced MR imaging was 69% (24 of 35 patients), 97% (62 of 64 patients), and 87% (86 of 99 patients), respectively, for the experienced reader. This difference was not significant (P = .48) when results were compared with results from the T2-weighted images. Staging performance for the less experienced readers with parametric dynamic contrast-enhanced MR imaging, however, resulted in significant improvement of the area under the receiver operating characteristics curve (A(z)) compared with T2-weighted MR imaging alone (A(z) = . 66 and . 82, respectively; P = . 01). CONCLUSION The use of multisection dynamic contrast-enhanced MR imaging in staging prostate cancer showed significant improvement in staging performance for the less experienced readers but had no benefit for the experienced reader.
Anterior-Posterior Ground Reaction Forces as a Measure of Paretic Leg Contribution in Hemiparetic Walking

Background and Purpose— Walking after stroke is characterized by slow gait speed, poor endurance, reduced quality and adaptability of walking patterns, and an inability to coordinate the legs. Estimates based on mechanical work calculations have suggested that the paretic leg does 30% to 40% of the total mechanical work over the gait cycle, regardless of hemiparetic severity, but these work estimates may not describe the contribution of each leg to forward propulsion. The purpose of this study was to establish a quantifiable link between hemiparetic severity and paretic leg contribution to propulsion during walking, which we propose to quantify using a measure based on the anterior-posterior ground reaction forces (A-P GRFs). Methods— A total of 47 participants with chronic hemiparesis walked at self-selected speeds to collect spatiotemporal parameters and 3D GRFs. A 16-person subset also participated in a pedaling protocol to compare A-P GRF measures to established measures of paretic leg output. Results— A-P GRF measures were correlated with both walking speed and hemiparetic severity. These measures were also strongly correlated with positive work and net work values obtained during the pedaling task. The percentage of total propulsion generated by the paretic leg (PP) was calculated and found to be 16%, 36%, and 49% for those with high, moderate, and low hemiparetic severity, respectively. Conclusion— PP was found to provide a quantitative measure of the coordinated output of the paretic leg. Further research on this measure of forward propulsion may lead to the provision of an effective tool for distinguishing functional compensation from physiological restitution.
A meta-analysis of the validity of FFQ targeted to adolescents

Abstract Objective The present work is aimed at meta-analysing validity studies of FFQ for adolescents, to investigate their overall accuracy and variables that can affect it negatively. Design A meta-analysis of sixteen original articles was performed within the ASSO Project (Adolescents and Surveillance System in the Obesity prevention). Setting The articles assessed the validity of FFQ for adolescents, compared with food records or 24 h recalls, with regard to energy and nutrient intakes. Subjects Pearson’s or Spearman’s correlation coefficients, means/standard deviations, kappa agreement, percentiles and mean differences/limits of agreement (Bland–Altman method) were extracted. Pooled estimates were calculated and heterogeneity tested for correlation coefficients and means/standard deviations. A subgroup analysis assessed variables influencing FFQ accuracy. Results An overall fair/high correlation between FFQ and reference method was found; a good agreement, measured through the intake mean comparison for all nutrients except sugar, carotene and K, was observed. Kappa values showed fair/moderate agreement; an overall good ability to rank adolescents according to energy and nutrient intakes was evidenced by data of percentiles; absolute validity was not confirmed by mean differences/limits of agreement. Interviewer administration mode, consumption interval of the previous year/6 months and high number of food items are major contributors to heterogeneity and thus can reduce FFQ accuracy. Conclusions The meta-analysis shows that FFQ are accurate tools for collecting data and could be used for ranking adolescents in terms of energy and nutrient intakes. It suggests how the design and the validation of a new FFQ should be addressed.
Novel Antigens of Helicobacter pylori Correspond to Ulcer-Related Antibody Pattern of Sera from Infected Patients

ABSTRACT Recently, we reported that the patterns of antibodies to Helicobacter pylori protein antigens in serum may be useful for screening patients at high risk for ulcers (P. Aucher et al., J. Clin. Microbiol. 36:931-936, 1998). Here we report the identification, by a combination of electrophoretic, immunochemical, and protein sequencing methods, of five antigens that correspond to this antibody pattern: groEL, catalase A, flagellin A, beta-ketoacyl-acyl carrier protein synthase I (β-ketoacyl-ACP S), and peptidyl prolyl cis-trans isomerase (PPiase). β-Ketoacyl-ACP S and PPiase are reported for the first time as antigens of diagnostic interest in infections by H. pylori. The antigenicity of the five antigens, together with those of CagA and VacA, was tested in an immunoblot assay with water-soluble protein extracts from two H. pylori pathogenic strains (HP 141 and ATCC 43579) and panels of sera from H. pylori-positive patients with gastroduodenal ulcers (GDU), nonulcer dyspepsia (NUD), as well as sera from H. pylori-negative healthy volunteers. For catalase A, groEL, and flagellin A antigens, no overall statistically important values were found making it possible to discriminate between patients with GDU and NUD. For both H. pylori strains, the mean performance indices (MPI) presenting percentages of correctly classified patients with GDU and NUD showed that the most significant antibody patterns were as follows: anti-VacA + anti-β-ketoacyl-ACP S (MPI = 76.1), anti-VacA + anti-PPiase (MPI = 71.8), and anti-CagA + anti-VacA + anti-β-ketoacyl-ACP S (MPI = 70.5). Antibody patterns detected with these antigen profiles may therefore be useful in developing a diagnostic test designed to predict the clinical severity of the H. pylori infection within the adult population of France.
Exercise Training-Induced Regulation of Mitochondrial Quality

Mitochondria are dynamic organelles in skeletal muscle critical in physical performance and disease. The mitochondrial life cycle spans biogenesis, maintenance, and clearance. Exercise training may promote each of these processes, conferring positive impacts on skeletal muscle contractile and metabolic functions. This review focuses on the regulation of these processes by endurance exercise and discusses potential benefits in health and disease.
Using Pervasive Computing to Deliver Elder Care

The Elite Care Information Technology Group has deployed a system with many elements of pervasive computing, including portable and wearable devices and wireless networking, to create intelligent and responsive work and living spaces for the elderly in a residential setting. Elite Care based the setting's layout on an apartment complex rather than a hospital with its hallways and rooms. By using a social care model that has the staff making house calls rather than doctors making rounds, the residents continue to live as normally as they can. In this scheme, pervasive sensors and staff assist residents in maintaining their independence, offering assistance as necessary and using the pervasive sensors to monitor vital signs and health indicators. Elite Care has harnessed the technology in direct and important ways to construct a more humane and human world for its residents and staff.
Factors affecting natural resource conservation investments of residents in the Lower Big Walnut Creek watershed, Ohio

Data were collected from adults living in households within the Lower Big Walnut Creek watershed in central Ohio to assess psychosocial orientations of local property owners toward natural resources issues within the watershed and to evaluate their willingness to allocate economic resources to implement soil and water conservation programs on their properties. Unlike adoption studies that have examined attitudes toward nonpoint source pollution issues using managers of agricultural land holdings, this study was designed to assess orientations of suburban residents who live adjacent to an environmentally sensitive stream in the largest metropolitan area of Ohio. Study participants were chosen using databases that contained descriptions of residential land holdings within the Big Walnut Watershed. All land owners with residential property equal to or greater than 2 ac (0.8 ha) within the watershed were defined as being eligible to participate in the study. A total of 386 single family residential land holdings were identified as meeting these criteria, and a structured questionnaire was mailed to all identified property owners during the fall of 2005 and early winter of 2006. Thirty-eight subjects could not be located, which reduced the sampling frame to 348. A total of 149 questionnaires were returned that were sufficiently completed for use in statistical modeling. This constitutes a response rate of 41.8%, which is considered good for mail questionnaire studies using contemporary social science research standards. Study findings revealed that watershed residents were positive toward natural resources conservation within the watershed. Multi-variate binary logistic regression analysis revealed that the theoretical model used to guide the investigation was useful for predicting which respondents would be willing to allocate personal resources to address natural resources conservation problems on their properties. Study findings are basically consistent with hypotheses derived from theoretical modeling based on the traditional diffusion model. Findings are discussed in the context of future natural resources conservation initiatives among watershed residents.
Le financement des très petites entreprises urbaines : étude d'impact d'un projet de micro-finance à Antananarivo (Madagascar)

(english) This article highlights the main findings of an evaluation report on the impact of a microfinance program based in Antananarivo. It first provides background information on microfinance programs in Madagascar and on the market-demand for micro-loans. It then describes the main characteristics of the participants to the microfinance program under concern. It finally presents the results of the economic impact analysis of the program on the clients' microenterprises, using the matching estimators' method. The analysis is based on two original surveys conducted in 2001, which were administered to a large representative sample of microenterprises in Antananarivo and to a representative sample of clients respectively. The results suggest that the gains from microborrowing accrued to participants are large. Productivity, production levels and turnover are all found to have significantly increased thanks to credit. However, the accrued benefits from microfinance are likely to be small at a more aggregate level, as microfinance programs have a very low coverage in urban areas. In terms of targeting, the results show that the microfinance program does exclusively benefit small unregistered production units but only the better-off ones. _________________________________ (francais) Cet article expose les principaux resultats d'une etude d'impact d'une institution de micro-finance operant a Antananarivo. Il debute par un etat des lieux de la micro-finance a Madagascar et une presentation des besoins en financement des unites de production informelles. Il s'attache ensuite a decrire la clientele de l'institution de micro-finance (IMF) concernee par l'etude. Il presente enfin les resultats de l'analyse de l'impact des financements accordes par cette institution a sa clientele, en mobilisant la methode des groupes apparies. L'ensemble de l'expose repose sur les resultats de deux enquetes ad hoc realisees en 2001 : l'une sur un echantillon representatif de 1 000 unites de production informelles de l'agglomeration d'Antananarivo, l'autre sur un echantillon representatif de 200 clients de l'IMF. Les resultats obtenus suggerent que d'un point de vue strictement micro-economique, l'impact des financements accordes est largement positif. Les performances des micro-entreprises clientes semblent en effet avoir fortement evolue avec le recours au credit, que ce soit en termes de productivite par travailleur ou par nombre d'heures travaillees, ou en termes de volume de production ou de chiffre d'affaires. Toutefois, en raison du tres faible taux de penetration des IMF a Antananarivo, il est vraisemblable que l'impact significatif et substantiel a l'echelle micro-economique soit extremement faible a l'echelle macro-economique. En terme de ciblage, l'analyse des caracteristiques des beneficiaires montre que si l'IMF, conformement a sa mission, touche bien une clientele de petites entreprises urbaines du secteur informel, elle ne s'adresse qu'a la frange "superieure" de ce secteur.
Early Identification of Violent Criminal Gang Members

Gang violence is a major problem in the United States accounting for a large fraction of homicides and other violent crime. In this paper, we study the problem of early identification of violent gang members. Our approach relies on modified centrality measures that take into account additional data of the individuals in the social network of co-arrestees which together with other arrest metadata provide a rich set of features for a classification algorithm. We show our approach obtains high precision and recall (0.89 and 0.78 respectively) in the case where the entire network is known and out-performs current approaches used by law-enforcement to the problem in the case where the network is discovered overtime by virtue of new arrests - mimicking real-world law-enforcement operations. Operational issues are also discussed as we are preparing to leverage this method in an operational environment.
Volume Reconstruction Based on Non-rigid Registration

Volume reconstruction is one of the key problems in 3D image rendering and analysis. Inter slice interpolation methods have been widely discussed in the literature and object-based algorithms have been shown to well behave. In this paper, we present a non-rigid registration based strategy to improve the volume reconstruction. A level set evolution technique is proposed to yield the deformation between adjacent slices. A modified bilinear interpolation method is then designed to generate propagating image. A multi-resolution scheme is applied to decrease the computation time and support large deformation. The resulting images show good results on regions enclosing different anatomic structures.
Low voltage CMOS op-amp with rail-to-rail input/output swing

As the supply voltage to a standard CMOS op-amp is reduced, the input common mode range and the output swing get reduced drastically. Special biasing circuits have to be used to raise them up to rail-to-rail supply voltage. Three low voltage op-amps with new biasing circuits have been proposed in this paper and their performance evaluated. The op-amp design is focused on dynamic range and high drive capability.
Induction of glial glutamate transporters in adult mesenchymal stem cells

Adult bone marrow mesenchymal stem cells are multipotent cells that can differentiate into a variety of mesodermal tissues. Recent studies have reported on their ability to also evolve into non‐mesodermal cells, especially neural cells. While most of these studies revealed that manipulating these cells triggers the expression of typical neurone markers, less is known about the induction of neuronal‐ or glial‐related physiological properties. The present study focused on the characterisation of glutamate transporters expression and activity in rat mesenchymal stem cells grown in culture conditions favouring their differentiation into astroglial cells. Ten days exposure of the cells to the culture supplement G5 was found to increase the expression of nestin (neuro‐epithelial stem cell intermediate filament), an intermediate filament protein expressed by neural stem cells. Simultaneously, a robust induction of the high‐affinity glutamate transporter GLT‐1 (and GLAST) expression was detected by RT‐PCR and immunocytochemistry. This expression was correlated with a highly significant increase in the Na+‐dependent [3H]d‐aspartate uptake. Finally, while glial fibrillary acidic protein immunoreactivity could not be detected, the induced expression of the astrocytic enzyme glutamine synthetase was demonstrated. These results indicate that in vitro differentiation of adult mesenchymal stem cells in neural precursors coincides with the induction of functional glutamate transport systems. Although the astrocytic nature of these cells remains to be confirmed, this observation gives support to the study of mesenchymal stem cells as a promising tool for the treatment of neurological diseases involving glutamate excitoxicity.
Dual coding in alternative reading frames correlates with intrinsic protein disorder

Numerous human genes display dual coding within alternatively spliced regions, which give rise to distinct protein products that include segments translated in more than one reading frame. To resolve the ensuing protein structural puzzle, we identified 67 human genes with alternative splice variants comprising a dual-coding region at least 75 nucleotides in length and analyzed the structural status of the protein segments they encode. The inspection of their amino acid composition and predictions by the IUPred and PONDR® VSL2 algorithms suggest a high propensity for structural disorder in dual-coding regions. In the case of +1 frameshifts, the average level of disorder in the two frames is similarly high (47.2% in the ancestral frame, 58.2% in the derived frame, with the average level of disorder in human proteins being approximately 30%), whereas in the case of -1 frameshifts, there is a significant tendency to become more disordered upon shifting the frame (16.7% in the ancestral frame, 56.3% in the derived frame). The regions encoded by the derived frame are mostly disordered (disorder percentage > 50%) in 39 out of 62 cases, which strongly suggests that structural disorder enables these protein products to exist and function without the need of a highly evolved 3D fold. The potential advantages are also demonstrated by the appearance of novel functions and the high incidence of transcripts escaping nonsense-mediated decay. By discussing several examples, we demonstrate that dual coding may be an effective mechanism for the evolutionary appearance of novel intrinsically disordered regions with new functions.
Refining laboratory rodent husbandry-recent advances

The three Rs of animal research Replacement, Reduction, Refinement first put forward by Russell and Birch (1959) have provided the foundation on which many of the advances in laboratory animal welfare have been built. The desired end-state is the complete replacement of animals in research, however until scientific advances make this feasible, efforts should be taken to refine husbandry procedures in order to minimise pain and distress for the animals involved. This paper will discuss a number of recent studies aimed at addressing some of the welfare concerns associated with laboratory rodents in terms of environmental enrichment, reduction of intermale aggression, and humane euthanasia.
Substrate Recognition and Molecular Mechanism of Fatty Acid Hydroxylation by Cytochrome P450 from Bacillus subtilis

Cytochrome P450 isolated from Bacillus subtilis (P450BSβ; molecular mass, 48 kDa) catalyzes the hydroxylation of a long-chain fatty acid (e.g. myristic acid) at the α- and β-positions using hydrogen peroxide as an oxidant. We report here on the crystal structure of ferric P450BSβ in the substrate-bound form, determined at a resolution of 2.1 Å. P450BSβ exhibits a typical P450 fold. The substrate binds to a specific channel in the enzyme and is stabilized through hydrophobic interactions of its alkyl side chain with some hydrophobic residues on the enzyme as well as by electrostatic interaction of its terminal carboxylate with the Arg242 guanidium group. These interactions are responsible for the site specificity of the hydroxylation site in which the α- and β-positions of the fatty acid come into close proximity to the heme iron sixth site. The fatty acid carboxylate group interacts with Arg242 in the same fashion as has been reported for the active site of chloroperoxidase, His105-Glu183, which is an acid-base catalyst in the peroxidation reactions. On the basis of these observations, a possible mechanism for the hydroxylation reaction catalyzed by P450BSβ is proposed in which the carboxylate of the bound-substrate fatty acid assists in the cleavage of the peroxide O-O bond.
A C35 Carotenoid Biosynthetic Pathway

ABSTRACT Upon coexpression with Erwinia geranylgeranyldiphosphate (GGDP) synthase in Escherichia coli, C30 carotenoid synthase CrtM from Staphylococcus aureus produces novel carotenoids with the asymmetrical C35 backbone. The products of condensation of farnesyldiphosphate and GDP, C35 structures comprise 40 to 60% of total carotenoid accumulated. Carotene desaturases and carotene cyclases from C40 or C30 pathways accepted and converted the C35 substrate, thus creating a C35 carotenoid biosynthetic pathway in E. coli. Directed evolution to modulate desaturase step number, together with combinatorial expression of the desaturase variants with lycopene cyclases, allowed us to produce at least 10 compounds not previously described. This result highlights the plastic and expansible nature of carotenoid pathways and illustrates how combinatorial biosynthesis coupled with directed evolution can rapidly access diverse chemical structures.