Miracle-dz/UniFAR-FTUs huggingface dataset:
Different Roles of EIIABMan and EIIGlc in Regulation of Energy Metabolism, Biofilm Development, and Competence in Streptococcus mutans

ABSTRACT The phosphoenolpyruvate:sugar phosphotransferase system (PTS) is the major carbohydrate transport system in oral streptococci. The mannose-PTS of Streptococcus mutans, which transports mannose and glucose, is involved in carbon catabolite repression (CCR) and regulates the expression of known virulence genes. In this study, we investigated the role of EIIGlc and EIIABMan in sugar metabolism, gene regulation, biofilm formation, and competence. The results demonstrate that the inactivation of ptsG, encoding a putative EIIGlc, did not lead to major changes in sugar metabolism or affect the phenotypes of interest. However, the loss of EIIGlc was shown to have a significant impact on the proteome and to affect the expression of a known virulence factor, fructan hydrolase (fruA). JAM1, a mutant strain lacking EIIABMan, had an impaired capacity to form biofilms in the presence of glucose and displayed a decreased ability to be transformed with exogenous DNA. Also, the lactose- and cellobiose-PTSs were positively and negatively regulated by EIIABMan, respectively. Microarrays were used to investigate the profound phenotypic changes displayed by JAM1, revealing that EIIABMan of S. mutans has a key regulatory role in energy metabolism, possibly by sensing the energy levels of the cells or the carbohydrate availability and, in response, regulating the activity of transcription factors and carbohydrate transporters.
Gaussian Ring Basis Functions for the Analysis of Modulated Metasurface Antennas

This paper presents a novel type of basis functions, whose spectral-and space-domain properties can be exploited for the efficient method of moments (MoM) analysis of planar metasurface (MTS) antennas. The effect of the homogenized MTS is introduced in the integral equation as an impedance boundary condition (IBC). The proposed basis functions are shaped as Gaussian-type rings with small width and linear azimuthal phase. The analytical form of the spectrum of the Gaussian ring basis allows for a closed-form evaluation of the MoM impedance matrix's entries. Moreover, these basis functions account for the global evolution of the surface current density in an effective manner, reducing the size of the MoM system of equations with respect to the case of subdomain basis functions. These features allow one to carry out a direct solution for problems with a diameter of up to 15 wavelengths in less than 1 min using a conventional laptop. The applicability on practical antennas has been tested through the full-wave analysis of MTS antennas implemented with small printed elements.
Rejected, Excluded, Ignored: The Perception of Social Rejection and Mental Disorders - A Review

Summary This article presents an overview of the impact of rejec- tion sensitivity on subclinical syndromes and mental dis- orders. Rejection sensitivity is the tendency to anxiously expect, readily perceive and overreact to rejection. From 1075 articles, we selected those 21 studies that investi- gate rejection sensitivity using the rejection sensitivity questionnaire (RSQ) in clinical and non-clinical samples, showing different aspects of the relationship between re- jection sensitivity and various subclinical syndromes and mental disorders. The results suggest an overall role of rejection sensitivity for the etiology as well as the main- tenance of mental problems. Positive associations have been found between rejection sensitivity and borderline symptoms, depressive symptoms, social anxiety and ag- gressive behavior, whereas the attention deficit hyperac- tivity disorder (ADHD) and psychotic symptoms did not show any relationship with rejection sensitivity. Recom- mendations for research and practice are discussed.
Improvement of PAPR and BER in OFDM Using Combination of SLM and Clipping Techniques

Orthogonal Frequency Division Multiplexing (OFDM) is high speed data transmission scheme. It has got various advantages like easy and efficient in dealing with multi-path, robust against narrow-band interference, supports various modulation schemes and perfect for MIMO etc. In spite of having various advantages it has got one major drawback of high Peak to Average Power Ratio (PAPR). One of the common technique for reducing the PAPR is Clipping, in this method a threshold value of the amplitude is set and any sub-carrier having amplitude more than that value is clipped. Advantage of clipping is that PAPR reduction is obtained without any redundancy and no side information is needed to transmit. Another technique is Selective Mapping (SLM), where M number of random phase sequences are multiplied with the actual data to be transmitted and out of M stream one stream is selected which have less PAPR, in SLM Bit Error Rate (BER) is improved compared to Clipping and SLM both. In this paper clipping and SLM both are combined to improve PAPR as well as BER. Simulation results show that PAPR and BER both are improved for combination as compared to clipping and SLM.
Self-adaptive pattern formation with battery-powered robot swarms

This paper presents a distributed, energy-aware algorithm for an autonomous deployment of battery-powered robots in a specified pattern. While each robot gradually discharges and leaves the formation to recharge, the algorithm presented in this paper assures that the formation pattern is preserved. This is achieved by defining the desired pattern as a point cloud where each point is occupied by a robot. The point cloud is transformed into a tree model that is shared among all robots. This model is used by each robot independently to govern its behavior, resulting in a self-adaptive network of robots which automatically generate paths for joining the formation and leaving it to recharge. Robots which leave the formation are replaced by neighbors to preserve the formation pattern. To demonstrate our algorithm we use a physics-based simulator and evaluate the persistence of the pattern formation formed by a robot swarm in an environment without global positioning, using only range and bearing.
Expanded protein information at SGD: new pages and proteome browser

The recent explosion in protein data generated from both directed small-scale studies and large-scale proteomics efforts has greatly expanded the quantity of available protein information and has prompted the Saccharomyces Genome Database (SGD; ) to enhance the depth and accessibility of protein annotations. In particular, we have expanded ongoing efforts to improve the integration of experimental information and sequence-based predictions and have redesigned the protein information web pages. A key feature of this redesign is the development of a GBrowse-derived interactive Proteome Browser customized to improve the visualization of sequence-based protein information. This Proteome Browser has enabled SGD to unify the display of hidden Markov model (HMM) domains, protein family HMMs, motifs, transmembrane regions, signal peptides, hydropathy plots and profile hits using several popular prediction algorithms. In addition, a physico-chemical properties page has been introduced to provide easy access to basic protein information. Improvements to the layout of the Protein Information page and integration of the Proteome Browser will facilitate the ongoing expansion of sequence-specific experimental information captured in SGD, including post-translational modifications and other user-defined annotations. Finally, SGD continues to improve upon the availability of genetic and physical interaction data in an ongoing collaboration with BioGRID by providing direct access to more than 82 000 manually-curated interactions.
Experimental evaluation of upper bounds of reachability index for set of solutions of 2-D positive system

Obtaining an upper bound of the local reachability index for 2-D systems is one of unsolved problems for which it is still not determined what tool could be used to solve it. In this paper there is presented the use of computational tool for calculating the reachability index for all possible solution sets of given characteristic polynomial belonging to specific class. Obtained results are illustrated with detailed numerical example, compared to theoretical state-of-the-art proposals for calculating an upper bound of reachability index and discussed.
Bandwidth efficient error resilience scheme for wavelet based video transmission

In this paper, a bandwidth efficient error resilience scheme aiming to protect region of interest (ROI) in frame based on Wyner-Ziv(WZ) coding for wavelet based video transmission is proposed. By utilizing additional WZ coding, all the corresponding wavelet coefficients related to ROI will be specially protected during transmission on error prone channel and eventually ROI area can be better reconstructed. Comparing to FEC algorithm fully applied to all wavelet coefficients to realize protection, the proposed scheme has distinct advantages in saving bandwidth and robust transmission.
Staffing Multiskill Call Centers via Linear Programming and Simulation

We study an iterative cutting-plane algorithm on an integer program for minimizing the staffing costs of a multiskill call center subject to service-level requirements that are estimated by simulation. We solve a sample average version of the problem, where the service levels are expressed as functions of the staffing for a fixed sequence of random numbers driving the simulation. An optimal solution of this sample problem is also an optimal solution to the original problem when the sample size is large enough. Several difficulties are encountered when solving the sample problem, especially for large problem instances, and we propose practical heuristics to deal with these difficulties. We report numerical experiments with examples of different sizes. The largest example corresponds to a real-life call center with 65 types of calls and 89 types of agents (skill groups).
Energy yield losses due to emulated inertial response with wind turbines

In several countries, the wind power penetration increased tremendously in recent years. As the current wind turbines do not participate in inertial response nor primary control, this may compromise the proper functioning of the power system. This paper discusses the emulated inertial response with wind turbines. In literature, several strategies to provide inertial response with wind turbines are available. However, if they are operated in their maximum power point, emulated inertial response results in energy yield losses. These are caused by the suboptimal operation of the wind turbines during the inertial response. This paper focuses on the calculation of the energy yield losses for different cases. In this way, it is possible to estimate their importance and the loss of revenue for the operator of the wind turbine. It is shown that the energy yield losses are very low for both strategies, for all simulated cases. This is an important result, as it shows that the different inertial response strategies only have a minor effect on the total energy yield of the turbine.
Cross-covariance functions for multivariate random fields based on latent dimensions

The problem of constructing valid parametric cross-covariance functions is challenging. We propose a simple methodology, based on latent dimensions and existing covariance models for univariate random fields, to develop flexible, interpretable and computationally feasible classes of cross-covariance functions in closed form. We focus on spatio-temporal cross-covariance functions that can be nonseparable, asymmetric and can have different covariance structures, for instance different smoothness parameters, in each component. We discuss estimation of these models and perform a small simulation study to demonstrate our approach. We illustrate our methodology on a trivariate spatio-temporal pollution dataset from California and demonstrate that our cross-covariance performs better than other competing models. Copyright 2010, Oxford University Press.
Cell Type-specific Autoregulation of theCaudal-related Homeobox Gene Cdx-2/3 *

The caudal-related homeobox geneCdx-2/3 is a critical “master” control gene in embryogenesis. Mice heterozygous for a null mutation inCdx-2/3 exhibit multiple malfunctions including tail abnormalities, stunted growth, a homeotic shift in vertebrae, and the development of multiple intestinal adenomatous polyps, indicating thatCdx-2/3 is haplo-insufficient. In vitro studies have identified more than a half-dozen downstream target genes expressed in pancreatic and intestinal cells for this transcription factor. We have examined the transcriptional properties of the mouseCdx-2/3 promoter. This promoter could be autoregulated in pancreatic and intestinal cells that express endogenous Cdx-2/3. In contrast, Cdx-2/3 transfection represses the Cdx-2/3promoter in fibroblasts, which do not express endogenous Cdx-2/3. Since Cdx-2/3 activates proglucagon gene promoter in both pancreatic and intestinal cells and in fibroblasts, we suggest that some, yet to be identified, cell type-specific components are required for activating selected target gene promoters of Cdx-2/3, including the Cdx-2/3 promoter itself. Cdx-2/3 binds to the TATA box and another AT-rich motif, designated as DBS, within an evolutionarily conserved proximal element of the Cdx-2/3 promoter. The DBS motif is critical for the autoregulation, whereas the TATA box may act as an attenuating element for the autoregulatory loop. Finally, overexpression of Cdx-2/3 in a pancreatic cell line activated the expression of the endogenous Cdx-2/3. Taken together, our results indicate that the dose-dependent phenotype of Cdx-2/3 expression on its downstream targets in vivo could be regulated initially via a transcriptional network involving cell type-specific autoregulation of the Cdx-2/3 promoter.
Prospective, open‐label safety study of intravenous recombinant tissue plasminogen activator in wake‐up stroke

It is estimated that one of four ischemic strokes are noticed upon awakening and are not candidates for intravenous recombinant tissue plasminogen activator (rtPA) because their symptoms are >3 hours from last seen normal (LSN). We tested the safety of rtPA in a multicenter, single‐arm, prospective, open‐label study (NCT01183533) in patients with wake‐up stroke (WUS).
Patterns of deterioration in senile dementia of the Alzheimer type.

OBJECTIVE To determine rates of decline in Alzheimer's disease. DESIGN A longitudinal review of patients diagnosed as having dementia during life, tested serially with the Extended Scale for Dementia, and confirmed by autopsy as having Alzheimer's disease. SUBJECTS AND SETTING Twenty-nine dead patients with Alzheimer's disease from the participants in the University of Western Ontario Dementia Study Project, confirmed at autopsy as having Alzheimer's disease. METHODS Analysis of the Extended Scale for Dementia data according to a trilinear model. FINDINGS In the middle phase of the trilinear model, there was a mean annual change of 13% (range, 2.5% to 51.7%). CONCLUSIONS It is likely that the common method of averaging a group of different individual scores from the initial and middle phases of observation of Alzheimer's disease collapses together individuals at different stages of the disorder, some of whom are in the initial plateau phase and whose conditions are not declining rapidly. The trilinear model of decline avoids this difficulty and the present study provides postmortem confirmed figures on rate of change.
Integrated Lithographic Molding for Microneedle-Based Devices

This paper presents a new fabrication method consisting of lithographically defining multiple layers of high aspect-ratio photoresist onto preprocessed silicon substrates and release of the polymer by the lost mold or sacrificial layer technique, coined by us as lithographic molding. The process methodology was demonstrated fabricating out-of-plane polymeric hollow microneedles. First, the fabrication of needle tips was demonstrated for polymeric microneedles with an outer diameter of 250 mum, through-hole capillaries of 75-mum diameter and a needle shaft length of 430 mum by lithographic processing of SU-8 onto simple v-grooves. Second, the technique was extended to gain more freedom in tip shape design, needle shaft length and use of filling materials. A novel combination of silicon dry and wet etching is introduced that allows highly accurate and repetitive lithographic molding of a complex shape. Both techniques consent to the lithographic integration of microfluidic back plates forming a patch-type device. These microneedle-integrated patches offer a feasible solution for medical applications that demand an easy to use point-of-care sample collector, for example, in blood diagnostics for lithium therapy. Although microchip capillary electrophoresis glass devices were addressed earlier, here, we show for the first time the complete diagnostic method based on microneedles made from SU-8.
Scrimshaw: A Language for Document Queries and Transformations

SUMMARY We present a new language for tree pattern matching and transformation called Scrimshaw. It extends to trees the familiar notions of regular expressions, pattern matching, and pattern replacement for strings. As we show by examples, it serves well as both a structured document query language and as a language for expressing document transformations. Scrimshaw has been implemented in a C-like language and is in ongoing use.
Colimit completions and the effective topos

The family of readability toposes, of which the effective topos is the best known, was discovered by Martin Hyland in the late 1970's. Since then these toposes have been used for several purposes. The effective topos itself was originally intended as a category in which various recursion-theoretic or effective constructions would live as natural parts of the higher-order type structure. For example the hereditary effective operators become the higher types over N (Hyland [1982]), and effective domains become the countably-based domains in the topos (McCarty [1984], Rosolini [1986]). However, following the discovery by Moggi and Hyland that it contained nontrivial small complete categories, the effective topos has also been used to provide natural models of polymorphic type theories, up to and including the theory of constructions (Hyland [1987], Hyland, Robinson and Rosolini [1987], Scedrov [1987], Bainbridge et al. [1987]). Over the years there have also been several different constructions of the topos. The original approach, as in Hyland [1982], was to construct the topos by first giving a notion of Pω-valued set. A Pω-valued set is a set X together with a function =x: X × X → Pω. The elements of X are to be thought of as codes, or as expressions denoting elements of some “real underlying” set in the topos. Given a pair (x,x′) of elements of X, the set =x (x,x′) (generally written ) is the set of codes of proofs that the element denoted by x is equal to the element denoted by x′.
The impacts of errors in individual genotyping and DNA pooling on association studies

Case‐control association studies using unrelated individuals may offer an effective approach for identifying genetic variants that have small to moderate disease risks. In general, two different strategies may be employed to establish associations between genotypes and phenotypes: (1) collecting individual genotypes or (2) quantifying allele frequencies in DNA pools. These two technologies have their respective advantages. Individual genotyping gathers more information, whereas DNA pooling may be more cost effective. Recent technological advances in DNA pooling have generated great interest in using DNA pooling in association studies. In this article, we investigate the impacts of errors in genotyping or measuring allele frequencies on the identification of genetic associations with these two strategies. We find that, with current technologies, compared to individual genotyping, a larger sample is generally required to achieve the same power using DNA pooling. We further consider the use of DNA pooling as a screening tool to identify candidate regions for follow‐up studies. We find that the majority of the positive regions identified from DNA pooling results may represent false positives if measurement errors are not appropriately considered in the design of the study. Genet Epidemiol 26:1–10, 2004. © 2003 Wiley‐Liss, Inc.
Risk Externalities, Wildfire Hazard, and Private Investment to Mitigate Wildfire Risk in the Wildland-Urban Interface

Homeowners in areas adjacent to wildlands – in the Wildland-Urban Interface (WUI) – can mitigate the risk that their home will be damaged in a wildfire by creating “defensible space” on their property. This article explores homeowners’ incentives to invest in defensible space using a unique data set on 35 WUI communities in Nevada. This is the first study to analyze homeowners’ incentives to invest in defensible space, comparing across both forested (alpine forest) and non-forested (sagebrush rangeland, pinyon pine and juniper woodland, grassland) communities. This article explores two explanations for perceived homeowner underinvestment in defensible space: (i) homeowners’ misjudging their wildfire risk and (ii) spatial interdependencies between neighbor’s defensible space investments due to risk externalities. We find no evidence to suggest that homeowners’ systematically misjudge their wildfire risk, though we do find evidence of strategic complementarities in defensible space investments due to risk externalities in certain communities, depending on predominant vegetation. Our results suggest that wildland fire policy to promote defensible space should focus on financial and regulatory barriers to investment in defensible space, rather than on educational programs, and that “tipping policies” to encourage early adopters to invest in defensible space may be appropriate in communities where the majority of homeowners have not invested in defensible space and whose predominant vegetation suggests the presence of strategic complementarities.
Cellular Sources of Noncollagenous Matrix Proteins: Role of Fat-Storing Cells in Fibrogenesis

The main types of noncollagenous ECM proteins in liver are FN, laminin, PGs and elastin. Also present is a pure carbohydrate polymer, hyaluronic acid. Their concentrations increase during fibrogenesis in a specific sequence and spatial distribution. FN is among the first to appear. The accumulation of matrix proteins in the space of Disse (perisinusoidal fibrosis) is most important for some clinical consequences of fibrosis. Perisinusoidal FSC are the cell type responsible for exaggerated ECM formation at sites of tissue injury, since these cells synthesize at a high rate in vitro all the noncollagenous matrix components occurring in fibrotic liver matrix (FN, laminin, dermatan sulfate, chondroitin sulfate, hyaluronic acid) and since FSC proliferate and transform into myofibroblast-like cells with an enhanced matrix protein synthesis rate. Recent experimental data suggest strong cellular cooperation of these cells with activated liver macrophages or Kupffer cells, platelets, and regenerating hepatocytes, which leads via a paracrine mechanism involving TGF beta, TGF alpha/EGF, PDGF, and probably other cytokines to stimulated proteoglycan synthesis, proliferation, and transformation into myofibroblast-like cells. The latter cell type has the potential of auto-stimulation (by an autocrine process) involving secretion of TGF beta and TGF alpha/EGF. Based on these findings, a model of FSC activation is proposed (Fig. 10).