Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification of two genes, kpsM and kpsT, in region 3 of the polysialic acid gene cluster of Escherichia coli K1

The polysialic acid capsule of Escherichia coli K1, a causative agent of neonatal septicemia and meningitis, is an essential virulence determinant. The 17-kb kps gene cluster, which is divided into three functionally distinct regions, encodes proteins necessary for polymer synthesis and expression at the cell surface. The central region, 2, encodes products required for synthesis, activation, and polymerization of sialic acid, while flanking regions, 1 and 3, are thought to be involved in polymer assembly and transport. In this study, we identified two genes in region 3, kpsM and kpsT, which encode proteins with predicted sizes of 29.6 and 24.9 kDa, respectively. The hydrophobicity profile of KpsM suggests that it is an integral membrane protein, while KpsT contains a consensus ATP-binding domain. KpsM and KpsT belong to a family of prokaryotic and eukaryotic proteins involved with a variety of biological processes, including membrane transport. A previously described kpsT chromosomal mutant that accumulates intracellular polysialic acid was characterized and could be complemented in trans. Results of site-directed mutagenesis of the putative ATP-binding domain of KpsT are consistent with the view that KpsT is a nucleotide-binding protein. KpsM and KpsT have significant similarity to BexB and BexA, two proteins that are essential for polysaccharide capsule expression in Haemophilus influenzae type b. We propose that KpsM and KpsT constitute a system for transport of polysialic acid across the cytoplasmic membrane.
The flagellar apparatus of the glaucophyte Cyanophora cuspidata

Glaucophytes are a kingdom‐scale lineage of unicellular algae with uniquely underived plastids. The genus Cyanophora is of particular interest because it is the only glaucophyte that is a flagellate throughout its life cycle, making its morphology more directly comparable than other glaucophytes to other eukaryote flagellates. The ultrastructure of Cyanophora has already been studied, primarily in the 1960s and 1970s. However, the usefulness of that work has been undermined by its own limitations, subsequent misinterpretations, and a recent taxonomic revision of the genus. For example, Cyanophora's microtubular roots have been widely reported as cruciate, with rotationally symmetrical wide and thin roots, although the first ultrastructural work described it as having three wide and one narrow root. We examine Cyanophora cuspidata using scanning and transmission electron microscopy, and construct a model of its cytoskeleton using serial‐section TEM. We confirm the earlier model, with asymmetric roots. We describe previously unknown and unsuspected features of its microtubular roots, including (i) a rearrangement of individual microtubules within the posterior right root, (ii) a splitting of the posterior left root into two subroots, and (iii) the convergence and termination of the narrow roots against wider ones in both the anterior and posterior subsystems of the flagellar apparatus. We also describe a large complement of nonmicrotubular components of the cytoskeleton, including a substantial connective between the posterior right root and the anterior basal body. Our work should serve as the starting point for a re‐examination of both internal glaucophyte diversity and morphological evolution in eukaryotes.
An efficient destination-based data management policy for vehicular networks

The Vehicular Ad hoc Network (VANET) takes the advantage of the relative mobility of the vehicles to opportunistically share dynamic information when they meet, aiming to avoid accidents and traffic jams, get local information of the nearby places, enjoy entertainment applications among others. However, the shared information must be handled properly, saving bandwidth and tackling the unnecessary duplication of data, preventing the scalability problem and congestion. The current solutions of these problems incorporate the concept of Relevance to share the information in a clever way but they do not exploit the advantage of knowing the destination of the vehicles and context-aware services to follow behavior patterns. Therefore, we propose an efficient destination-based data management policy, which follows the vehicular behavior and context to determine the relevance or importance of the information using a publisher/subscriber model and cluster-based dissemination. In order to demonstrate the feasibility of the proposal we implemented sets of simulation in which the results reported an outstanding performance in terms of congestion and delivery ratio.
Enhancing an elevator efficiency by using supercapacitor

In the elevator drives, there is a wastage of a huge amount of energy in a breaking resistor which need to be controlled. The extra energy being generated by different ways required to be stored for some duration to be used later for the efficient operation of an elevator. Aim of this paper is to present how the supercapacitor can be used for enhancing elevator efficiency by saving the energy. The dc-dc converter has been used to interface the voltage level of different sources. The regenerated energy which is normally wasted during braking is stored temporarily into supercapacitor energy storage device and reutilized it when the more energy is requested by an elevator motor. For elucidation of the operation of an overall system, the simulation results have been discussed. (Abstract)
2 DCJ operation on linear chromosome and graphs 2 . 1

The double-cut-and-join (DCJ) operation, introduced by Yancopoulos et al., allows minimum edit distance to be computed by modeling all possible classical rearrangement operations, such as inversions, fusions, fissions, translocations and transpositions, in linear-time between two genomes. However, there is lack of visualization tool that can effectively present DCJ operations that will help biologists to use DCJ operation. In this paper, a new visualization program is introduced, DCJVis, to create a diagram of each DCJ operation necessary to transform between the genomes of two distinct organisms by describing a possible sequence of genome graphs based on the selected gene adjacency on the source genome for the DCJ operation. Our program is the first visualization tool for DCJ operations using circular layout. Specifically, the genomes of Saccharomyces cerevisiae and Candida albicans are used to demonstrate the functionality of this program and provide an example of the type of problem this program can solve for biologists.
Suboptimal use of HIV drug resistance testing in a universal health-care setting

Abstract HIV drug resistance testing is recommended as routine part of clinical practice in HIV/AIDS treatment and care. Our objective is to assess the determinants of accessing HIV drug resistance testing and examine the factors associated with resistance testing prior to or after starting highly active antiretroviral therapy (HAART) in a setting where access to HIV care is free and universal. The Longitudinal Investigation into Supportive and Ancillary health services (LISA) study is an open prospective cohort of HIV-positive persons on HAART in British Columbia (BC), Canada. Non-clinical data were collected through an interviewer-administered survey and clinical data were obtained through the BC Centre for Excellence in HIV/AIDS Drug Treatment Program. Independent associations between key explanatory variables and resistance testing were analyzed using logistic regression. We restricted our post-HAART analyses to those patients who met the criteria for resistance testing after HAART initiation. Of 359 LISA participants who started HAART after 2000 and at a time when resistance testing was available free of charge, almost half did not receive a baseline resistance test. Post-HAART initiation, 165 of 359 study subjects met the criteria for resistance testing based on current therapeutic guidelines due to virological failure. About 37.6% of them remain untested for resistance. Multivariable analyses show that baseline testing was less likely performed for persons of Aboriginal ethnicity and more likely performed for patients initiating HAART in 2004 or after. Additionally, persons initiating HAART in 2004 or after were less likely to have received a resistance test after virologic failure. Our results show that despite existing clinical guidelines, resistance testing is underused, even in an environment where the service is available free of charge. Further, resistance testing is particularly underutilized among vulnerable populations. Urgent efforts are needed to ensure the optimal use of resistance testing at baseline and at the time of virologic failure as recommended by current guidelines.
Multiscale BerEp4 Molecular Imaging of Microtumor Phantoms: Toward Theranostics for Basal Cell Carcinoma

Basal cell carcinoma (BCC), the most common cancer in humans, appears macroscopically and microscopically similar to many other skin lesions, which makes differential diagnosis difficult. We are developing an approach for quantitative molecular imaging of BerEP4, a transmembrane biomarker for BCC, with the goal of increasing the precision and accuracy of diagnosis. This pilot study was conducted to assess the affinity and selectivity of BerEp4 antibody and assess its possible use in designing theranostic probes for BCC. We provide evidence that our photon-counting fluorescence macrodetection system can recover specific signal increases from a film/pellet phantom. Additionally, we show that a two-photon excited fluorescence /backscatter confocal microscopy system can image BerEP4 antibody/antigen complex on the surface of BerEP4-expressing cancer cells in three dimensions. Based on the initial results, BerEP4 seems to be a promising biomarker for molecular imaging of BCC. To prepare BerEP4 for eventual theranostic use, we examined the feasibility of a combined macro-/micro-optical approach to imaging BCC with various histologies. These optical methods, endowed with the ability to monitor treatment in real time, may open an opportunity for noninvasive diagnosis, treatments, and follow-up.
Disturbed communication in schizophrenia: the role of poor pragmatics and poor mind-reading

Background. Disturbed speech in schizophrenia may reflect pragmatic deficits of expressive language. Pragmatic comprehension deficits also occur in schizophrenia. This study investigated whether poor ‘mind-reading’ (i.e. a general difficulty with inferring and monitoring other people's thoughts) causes pragmatic language impairments of both expression and comprehension in patients with schizophrenia. Method. Mind-reading (or theory of mind) was tested in patients with schizophrenia and in healthy controls using a false-belief picture-sequencing task. Pragmatic comprehension skills were assessed using a test of non-literal speech interpretation. Clinical ratings of formal thought disorder (FTD) indexed the expressive language deficits of patients. To control for possible contributory effects of executive dysfunction, inhibitory control was tested using capture picture-sequences and executive-planning was tested using the Tower of London task. Results. False-belief picture-sequencing, understanding of irony and understanding of metaphors were all selectively impaired in the patients. Poor mind-reading (indexed by high error rate in sequencing false-belief stories) was associated with poor understanding of irony, but was unrelated to poor understanding of metaphors. Whereas poor appreciation of irony and poor mind-reading were associated with high ratings of positive formal thought disorder, high ratings of negative formal thought disorder were associated with poor understanding of metaphors and executive dysfunction. Conclusions. Whereas poor mind-reading may contribute to positive aspects of formal thought disorder and impaired appreciation of irony in patients with schizophrenia; negative features of formal thought disorder and poor understanding of metaphors appear better explained by abnormal semantics. Overall, the findings of this study support the view that the functional basis of formal thought disorder in schizophrenia is not unitary.
Prediction of Human Pharmacokinetics Using Physiologically Based Modeling: A Retrospective Analysis of 26 Clinically Tested Drugs

The aim of this study was to evaluate different physiologically based modeling strategies for the prediction of human pharmacokinetics. Plasma profiles after intravenous and oral dosing were simulated for 26 clinically tested drugs. Two mechanism-based predictions of human tissue-to-plasma partitioning (Ptp) from physicochemical input (method Vd1) were evaluated for their ability to describe human volume of distribution at steady state (Vss). This method was compared with a strategy that combined predicted and experimentally determined in vivo rat Ptp data (method Vd2). Best Vss predictions were obtained using method Vd2, providing that rat Ptp input was corrected for interspecies differences in plasma protein binding (84% within 2-fold). Vss predictions from physicochemical input alone were poor (32% within 2-fold). Total body clearance (CL) was predicted as the sum of scaled rat renal clearance and hepatic clearance projected from in vitro metabolism data. Best CL predictions were obtained by disregarding both blood and microsomal or hepatocyte binding (method CL2, 74% within 2-fold), whereas strong bias was seen using both blood and microsomal or hepatocyte binding (method CL1, 53% within 2-fold). The physiologically based pharmacokinetics (PBPK) model, which combined methods Vd2 and CL2 yielded the most accurate predictions of in vivo terminal half-life (69% within 2-fold). The Gastroplus advanced compartmental absorption and transit model was used to construct an absorption-disposition model and provided accurate predictions of area under the plasma concentration-time profile, oral apparent volume of distribution, and maximum plasma concentration after oral dosing, with 74%, 70%, and 65% within 2-fold, respectively. This evaluation demonstrates that PBPK models can lead to reasonable predictions of human pharmacokinetics.
Single real transformation matrix application for asymmetrical three-phase line transient analyses

Single real transformation matrices can change the Z and Y matrices into diagonal ones for transposed three-phase lines. Considering non-transposed non-symmetrical three-phase lines, the errors between the Clarkepsilas matrix application results (called quasi-modes) and the eigenvectors are negligible. In this text, some other analyses are performed for two line designs. So, the arithmetic media among error curves tends to zero for every design. The non-diagonal elements of the quasi-mode matrix are compared to the correspondent eigenvalues. There are non-diagonal elements that present significant relative values when compared to the eigenvalues. Using all these analyses, it is suggested the hypothesis that the interactions among the Clarkepsilas matrix application, the non-symmetrical line characteristics and propagated signal spectrum can be maximizing the error of the proposed single real transformation matrix application. Because of this, in future development, correction procedures should be applied to Clarkepsilas matrix searching for minimizing the non-diagonal elements of the quasi-mode matrices.
Comparative Genomic Analyses of 17 Clinical Isolates of Gardnerella vaginalis Provide Evidence of Multiple Genetically Isolated Clades Consistent with Subspeciation into Genovars

ABSTRACT Gardnerella vaginalis is associated with a spectrum of clinical conditions, suggesting high degrees of genetic heterogeneity among stains. Seventeen G. vaginalis isolates were subjected to a battery of comparative genomic analyses to determine their level of relatedness. For each measure, the degree of difference among the G. vaginalis strains was the highest observed among 23 pathogenic bacterial species for which at least eight genomes are available. Genome sizes ranged from 1.491 to 1.716 Mb; GC contents ranged from 41.18% to 43.40%; and the core genome, consisting of only 746 genes, makes up only 51.6% of each strain's genome on average and accounts for only 27% of the species supragenome. Neighbor-grouping analyses, using both distributed gene possession data and core gene allelic data, each identified two major sets of strains, each of which is composed of two groups. Each of the four groups has its own characteristic genome size, GC ratio, and greatly expanded core gene content, making the genomic diversity of each group within the range for other bacterial species. To test whether these 4 groups corresponded to genetically isolated clades, we inferred the phylogeny of each distributed gene that was present in at least two strains and absent in at least two strains; this analysis identified frequent homologous recombination within groups but not between groups or sets. G. vaginalis appears to include four nonrecombining groups/clades of organisms with distinct gene pools and genomic properties, which may confer distinct ecological properties. Consequently, it may be appropriate to treat these four groups as separate species.
The COX-2 inhibitor nimesulide suppresses superoxide and 8-hydroxy-deoxyguanosine formation, and stimulates apoptosis in mucosa during early colonic inflammation in rats.

As we have shown previously [Tardieu,D. , Jaeg,J.P., Cadet,J., Embvani,E. , Corpet,D.E. and Petit,C. (1998) Cancer Lett, 134, 1-5], a 48-h treatment of 6% dextran sodium sulphate (DSS) in drinking water led to a reproducible 2-fold increase of the mutagenic oxidative lesion 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodGuo) in colonic mucosa DNA of rats in vivo. The aim of this study was to test the effect of nimesulide, a preferential COX-2 inhibitor, on the DSS-induced 8-oxodGuo increase. We show that nimesulide when administered orally, simultaneously with DSS at 5 mg/kg/day, not only totally prevents 8-oxodGuo formation but also suppresses the 5-fold increase of superoxide induced by DSS in the colonic mucosa. This was measured by in vivo formazan blue precipitation (P < 0.01 in the Wilcoxon test). Moreover, nimesulide enhances apoptosis by approximately 30% as compared with the already high level induced by DSS treatment (P < 0.01). It is suggested that the significant increase in mutagenic oxidative DNA damage, produced by mild acute colonic inflammation, could be important in the initiation of colon cancer in both animals and man. These effects may explain at least partly the well-documented protective action towards colon cancer by preferential COX-2 inhibitors, either xenobiotics such as nimesulide or natural nutrients.
Money and Pay-As-You-Go Pension

This paper presents examination of how a pension policy affects income growth and the inflation rate in a utility model. Even if the contribution rate of pension increases because of an aging society, an aging society increases income growth and the inflation rate. Moreover, this paper presents examination of the optimal growth rate of the money supply. Because of the pension policy, the optimal growth rate of money stock changes. This result is intuitive because a pay-as-you-go pension changes capital accumulation. Therefore, the income growth rate should be changed to raise the welfare of all generations.
Discretionary Accruals: Earnings Management ... Or Not?

This paper discusses some limitations of discretionary accruals measures. While discretionary accruals are acknowledged to be noisy proxies for earnings management, they are still widely used in the literature. This paper attempts to explain from basic econometrics how discretionary accruals are estimated, and in doing so why they are inappropriate measures for earnings management. It is shown that decisions of peer firms will influence the regression coefficients, and hence residuals, in accruals models, which may lead to false conclusions about earnings management in other firms. This point is emphasized using an artificially constructed firm with no changes in its fundamental performance, and hence no discretion in its accruals. I also note concerns about the inferences, which are commonly not acknowledged in research. Finally, using Accounting and Auditing Enforcement Releases and Enron as examples, I demonstrate how discretionary accruals do not capture what literature often claims.
AFEE or AFIT: Which Represents Institutional Economics?

It is difficult to know what to think of institutional economics. There are those who continue to maintain that it is dead and buried. Others think it lives, and they struggle to identify its principles and protagonists. Still others, not concerned with labels, have been willing to accept the activities of the Association for Evolutionary Economics as representing institutional economics. But the recent formation of an organization calling itself the Association for Institutional Thought (AFIT) makes more urgent than ever the question of what institutional economics is and which group represents it. Many scholars who hope to develop an influential alternative to orthodox economics view the new organizational with misgivings. They sense a criticism of AFEE in its very formation, and they fear that fragmenting the already small and weak heterodox movement will produce negative results. As far as results to date are concerned, probably members of both associations would agree on the present situation: Although AFEE has existed for thirteen years, there is today neither a recognized or growing body of institutional principles nor a group of institutional economists influential in policy formulation. In short, institutional economics is not a viable alternative to mainstream economics. Whether AFEE could or
Pattern synthesis of stub-loaded half-mode substrate-integrated leaky-wave antenna

A pattern synthesis technique for a periodically stub-loaded half-mode substrate-integrated waveguide (HMSIW) leaky-wave antenna (LWA) is studied in this paper. In this structure, the waveguide host, i.e. the HMSIW, has a fixed cross-section whilst the stub lengths in each unit-cell are varied to control the propagation constant along the guided-wave direction. The results show that pattern synthesis at a fixed frequency with minimized sidelobe level (SLL) is achievable with a main beam steering in the forward direction. Since the stub length can be effectively tuned with a varactor, this preliminary study shows the potential for designing a reconfigurable fixed-frequency beam scanning with a high degree of flexible control on the radiation patterns.
The effect of fibrin(ogen) on thrombin generation and decay

Summary Defibrination causes a ~30% decrease of thrombin generation (TG) which can be restored by adding native fibrinogen in its original concentration (3 mg/ml). The fibrinogen variant γA/γ′, which binds thrombin with high affinity, is over four times more efficient in this respect than the more common γA/γA form. By using high tissue factor concentrations we accelerated prothrombin conversion so as to obtain a descending part of the TG curve that was governed by thrombin decay only. From that part we calculated the antithrombin (AT)- and α2-macroglobulin- dependent decay constants at a series of concentrations of native, γA/γA and γA/γ′ fibrinogen. We found that the increase of TG in the presence of fibrinogen is primarily due to a dose-dependent decrease of thrombin inactivation by α2-macroglobulin, where the γA/γ′ form is much more active than the γA/γA form. AT-dependent decay is somewhat decreased by γA/γ′ fibrinogen but hardly by the γA/γA form. We assume that binding of thrombin to fibrin(ogen) interferes with its binding to inhibitors. Attenuation of decay only in part explains the stimulating effect of fibrinogen on TG, as fibrinogen stimulates prothrombin conversion, regardless of the fibrinogen variant. Note: Part of this work was presented at the ISTH meeting in 2013.