Miracle-dz/UniFAR-FTUs huggingface dataset:
Genetic Control of the Variable Innate Immune Response to Asymptomatic Bacteriuria

The severity of urinary tract infection (UTI) reflects the quality and magnitude of the host response. While strong local and systemic innate immune activation occurs in patients with acute pyelonephritis, the response to asymptomatic bacteriuria (ABU) is low. The immune response repertoire in ABU has not been characterized, due to the inherent problem to distinguish bacterial differences from host-determined variation. In this study, we investigated the host response to ABU and genetic variants affecting innate immune signaling and UTI susceptibility. Patients were subjected to therapeutic urinary tract inoculation with E. coli 83972 to ensure that they were exposed to the same E. coli strain. The innate immune response repertoire was characterized in urine samples, collected from each patient before and after inoculation with bacteria or PBS, if during the placebo arm of the study. Long-term E. coli 83972 ABU was established in 23 participants, who were followed for up to twelve months and the innate immune response was quantified in 233 urine samples. Neutrophil numbers increased in all but two patients and in an extended urine cytokine/chemokine analysis (31 proteins), the chemoattractants IL-8 and GRO-α, RANTES, Eotaxin-1 and MCP-1, the T cell chemoattractant and antibacterial peptide IP-10, inflammatory regulators IL-1-α and sIL-1RA and the T lymphocyte/dendritic cell product sIL-2Rα were detected and variably increased, compared to sterile samples. IL-6, which is associated with symptomatic UTI, remained low and numerous specific immune mediators were not detected. The patients were also genotyped for UTI-associated IRF3 and TLR4 promoter polymorphisms. Patients with ABU associated TLR4 polymorphisms had low neutrophil numbers, IL-6, IP-10, MCP-1 and sIL-2Rα concentrations. Patients with the ABU-associated IRF3 genotype had lower neutrophils, IL-6 and MCP-1 responses than the remaining group. The results suggest that the host-specific, low immune response to ABU mainly includes innate immune mediators and that host genetics directly influence the magnitude of this response.
Stabilized plasmid-lipid particles for systemic gene therapy.

The structure of 'stabilized plasmid-lipid particles' (SPLP) and their properties as systemic gene therapy vectors has been investigated. We show that SPLP can be visualized employing cryo-electron microscopy to be homogeneous particles of diameter 72 +/- 5 nm consisting of a lipid bilayer surrounding a core of plasmid DNA. It is also shown that SPLP exhibit long circulation lifetimes (circulation half-life >6 h) following intravenous (i.v.) injection in a murine tumor model resulting in accumulation of up to 3% of the total injected dose and concomitant reporter gene expression at a distal (hind flank) tumor site. In contrast, i v. injection of naked plasmid DNA or plasmid DNA-cationic liposome complexes did not result in significant plasmid delivery to the tumor site or gene expression at that site. Furthermore, it is shown that high doses of SPLP corresponding to 175 microg plasmid per mouse are nontoxic as assayed by monitoring serum enzyme levels, whereas i.v. injection of complexes give rise to significant toxicity at dose levels above 20 microg plasmid per mouse. It is concluded that SPLP exhibit properties consistent with potential utility as a nontoxic systemic gene therapy vector.
Dominant resistance against plant viruses

To establish a successful infection plant viruses have to overcome a defense system composed of several layers. This review will overview the various strategies plants employ to combat viral infections with main emphasis on the current status of single dominant resistance (R) genes identified against plant viruses and the corresponding avirulence (Avr) genes identified so far. The most common models to explain the mode of action of dominant R genes will be presented. Finally, in brief the hypersensitive response (HR) and extreme resistance (ER), and the functional and structural similarity of R genes to sensors of innate immunity in mammalian cell systems will be described.
A Markov Chain Monte Carlo Cellular Automata Model to Simulate Urban Growth

This paper investigates the potential of a cellular automata (CA) model based on logistic regression (logit) and Markov Chain Monte Carlo (MCMC) to simulate the dynamics of urban growth. The model assesses urbanization likelihood based on (i) a set of urban development driving forces (calibrated based on logit) and (ii) the land-use of neighboring cells (calibrated based on MCMC). An innovative feature of this CA model is the incorporation of MCMC to automatically calibrate the CA neighborhood transition rules. The MCMC based CA model is applied to Wallonia region (Belgium) to simulate urban growth from 1990 to 2000 using Corine Land Cover data (CLC). The outcome of logit model is evaluated by the relative operating characteristic (ROC). The simulated map of 2000 is then validated against 2000 actual map based on cell-to-cell location agreement. The model outcomes are realistic and relatively accurate confirming the effectiveness of the proposed MCMC-CA approach. Keywordscellular automata; Markov chain Monte Carlo; logistic regression.
Prevalence and risk factors for sleep-disordered breathing in 8- to 11-year-old children: association with race and prematurity.

OBJECTIVES To evaluate the extent to which sleep-disordered breathing (SDB) varies with putative demographic and medical risk factors and to estimate the prevalence of undiagnosed SDB. STUDY DESIGN Prospective, cross-sectional study in a population-based cohort of 850 children (41% black, 46% preterm), 8 to 11 years of age. Participants' caretakers completed questionnaires about health and sleep. Children underwent overnight in-home cardiorespiratory recordings of airflow, respiratory effort, oximetry, and electrocardiography. SDB was identified by respiratory disturbance indices commonly applied in clinical practice. Risk factors were estimated by logistic regression. Prevalence was derived from cohort-specific estimates with birth weights from US live births data. RESULTS Using the most inclusive definition, SDB was detected in 40 (4.7%) participants, with prevalence varying widely across population subsets. Depending on the definition used, SDB was 4 to 6 times more likely in black children compared with white children and almost 3 to 5 times more likely in former preterm compared with term children. The estimated population prevalence of SDB was 2.2% (95% CI, 1.2%, 3.2%). CONCLUSIONS SDB is a relatively common condition in 8- to 11-year-old children. Potentially vulnerable subgroups, black children, and former preterm infants, are at increased risk.
Histological Analysis of γδ T Lymphocytes Infiltrating Human Triple-Negative Breast Carcinomas

Breast cancer is the leading cause of cancer death in women and the second most common cancer worldwide after lung cancer. The remarkable heterogeneity of breast cancers influences numerous diagnostic, therapeutic, and prognostic factors. Triple-negative breast carcinomas (TNBCs) lack expression of HER2 and the estrogen and progesterone receptors and often contain lymphocytic infiltrates. Most of TNBCs are invasive ductal carcinomas (IDCs) with poor prognosis, whereas prognostically more favorable subtypes such as medullary breast carcinomas (MBCs) are somewhat less frequent. Infiltrating T-cells have been associated with an improved clinical outcome in TNBCs. The prognostic role of γδ T-cells within CD3+ tumor-infiltrating T lymphocytes remains unclear. We analyzed 26 TNBCs, 14 IDCs, and 12 MBCs, using immunohistochemistry for the quantity and patterns of γδ T-cell infiltrates within the tumor microenvironment. In both types of TNBCs, we found higher numbers of γδ T-cells in comparison with normal breast tissues and fibroadenomas. The numbers of infiltrating γδ T-cells were higher in MBCs than in IDCs. γδ T-cells in MBCs were frequently located in direct contact with tumor cells, within the tumor and at its invasive border. In contrast, most γδ T-cells in IDCs were found in clusters within the tumor stroma. These findings could be associated with the fact that the patient’s prognosis in MBCs is better than that in IDCs. Further studies to characterize these γδ T-cells at the molecular and functional level are in progress.
Automatic image contrast enhancement method for liver vasculature detection

This paper presents an automatic method for image contrast enhancement necessary as a preprocessing step during vasculature detection in medical images. The method takes as input two volumetric images: one containing the original data from a computed tomography (CT) study and the other one containing segmented liver as a binary mask. The aim of the method is to enhance the contrast in the original image based on blood vessels intensities found in the organ defined by the provided mask. The methodology employs Frangi's vesselness filter and the analysis of maximal intensity projection (MIP) images to calculate the parameters of contrast enhancing function. The algorithm has been evaluated on 40 CT datasets containing liver studies in the portal phase and is being tested as a preprocessing step for automatic liver vasculature detection method being developed for a minimally-invasive liver surgery planning computer system.
A Novel Technique to Prepare Porous 3D Fluoridated Hydroxyapatite Scaffold Using Pore-forming and Foaming Agents

A novel technology using pore-forming agent and foaming agent was developed to prepare multi-porous fluoridate hydroxyapatite scaffolds. With this technology, scaffolds were produced with uniform and highly inter- connected pores in which large pores containing small ones on their walls distributing along 3-dimension. First, the precursor, FHA powder, was prepared by chemical precipitation method. Then it was used to form scaffold through heat treatments by adding ammonium bicarbonate as foaming agent and polymethyl methacrylate as pore-forming agent, and a dense frame of multi-porous structure was obtained. Investigated by X-ray diffraction (XRD), a dual-phase of FHA/β-TCP in scaffold was confirmed. The uniform morphology in scaffolds and the pore size dis- tribution of large pores (100-400 µm) containing small ones (10~50 µm) were demonstrated by SEM images. HA and β-TCP were also used to prove the universality of this method. Furthermore, the pore formation and its mecha-
Thermal inactivation and injury of Bacillus stearothermophilus spores

Aqueous spore suspensions of Bacillus stearothermophilus ATCC 12980 were heated at different temperatures for various time intervals in a resistometer, spread plated on antibiotic assay medium supplemented with 0.1% soluble starch without (AAMS) or with (AAMS-S) 0.9% NaCl, and incubated at 55 degrees C unless otherwise indicated. Uninjured spores formed colonies on AAMS and AAMS-S; injured spores formed colonies only on AAMS. Values of D, the decimal reduction time (time required at a given temperature for destruction of 90% of the cells), when survivors were recovered on AAMS were 62.04, 18.00, 8.00, 3.33, and 1.05 min at 112.8, 115.6, 118.3, 121.1, and 123.9 degrees C, respectively. Recovery on AAMS-S resulted in reduced decimal reduction time. The computed z value (the temperature change which will alter the D value by a factor of 10) for spores recovered on AAMS was 8.3 degrees C; for spores recovered on AAMS-S, it was 7.6 degrees C. The rates of inactivation and injury were similar. Injury (judged by salt sensitivity) was a linear function of the heating temperature. At a heating temperature of less than or equal to 118.3 degrees C, spore injury was indicated by the curvilinear portion of the survival curve (judged by salt sensitivity), showing that injury occurred early in the thermal treatment as well as during logarithmic inactivation (reduced decimal reduction time). Heat-injured spores showed an increased sensitivity not only to 0.9% NaCl but also to other postprocessing environmental factors such as incubation temperatures, a pH of 6.6 for the medium, and anaerobiosis during incubation.
The Evolving Role of MultiGene Tests in Breast Cancer Management

The current review by Drs. Zelnak and O’Regan aptly summarizes multi-gene tests (MGTs), their prognostic role, and how gene expression profiling has aided the definition of molecular breast cancer subtypes. However, while the current role of MGTs in the clinical care of breast cancer patients is evolving, it remains somewhat unclear. For instance, the Evaluation of Genomic Applications in Practice and Prevention (EGAPP) Working Group (EWG), established by the Centers for Disease Control and Prevention (CDC), determined in 2009 that there was “insufficient evidence to make a recommendation for or against the use of tumor gene expression profiles to improve outcomes in defined populations of women with breast cancer. ” The group stated they believed that until the TAILORx (Trial Assigning IndividuaLized Options for Treatment [Rx]) and MINDACT (Microarray In Node-Negative Disease may Avoid ChemoTherapy) trials are reported, they were not able to offer firm guidance on the use of these tests. Additionally, all of the commercial assays for breast cancer prognostication are laboratory-developed, contain proprietary information, and with the exception of the MammaPrint test that has been approved by the US Food and Drug Administration (FDA), have not been fully independently evaluated.
Title Multiscale space vehicle component identification

Vision bascd vehicle recognition systcms have an impowant role in traffic suwcillance. Most of thcsc systems however fail to distinguish velucles with similar dimcnsions dnc to Ihc lack of other details. This paper presents a new scale spacc method for idcntifying componcnts of moving vehiclcs to cnablc recognition eventually. In thc proposcd method. vehiclcs are first dividcd into multi-scale regions based on the center of gravity of the foreground vehiclc mask. It utilizes both tlic texture scale space and tlic intensity scale space to detcmiine mgions that are homogenous in texture and intensity. from wluch vehicle components are identifed based on thc relations between these regions. This method was tested on over a hundred outdoor &IC images and the results are vely promising.
An efficient algorithm to factorize sparse bivariate polynomials over the rationals

Polynomial factorization is one of the central problems and also a successful story in computer algebra. In this poster, we give a summary of an algorithm, recently presented in the authors’ manuscript [5], that uses both symbolic and numeric methods to exactly compute the irreducible factorization in Z[x, y], and therefore in Q[x, y], of any bivariate polynomial satisfying Hypothesis. On f ∈ Z[x, y] and its initial factors, we assume that (i) f is squarefree, non-constant and monic in x; (ii) f has no univariate factors; (iii) the initial factors of f are mutually coprime.
Carrier based implementation of reduced common mode voltage PWM strategies

This paper investigates the reduced common mode voltage pulse width modulation (RCMV-PWM) strategies for three-phase two-level converters in ac motor drive systems. A brief comparison of the RCMV-PWM methods is given and a conclusion is achieved that only three kinds of PWM methods are suitable for practical applications, including near state PWM (NSPWM), active zero state PWM1 (AZSPWM1) and 3-dimensional active zero state PWM (3D-AZSPWM). After that, the carrier based implementation of these three RCMV-PWM methods is studied and their modulation and carrier waves are deduced. Then a generalized active zero state PWM (GAZSPWM) is proposed. NSPWM and AZSPWM1 are found to be special cases of GAZSPWM. Actually, the proposed carrier based implementation of the three RCMV-PWM methods is found just as easy as that of the conventional PWM methods. Finally, the effects and carrier based implementation of the RCMV-PWM methods are validated through simulation and experiments.
Secure Clustering and Symmetric Key Establishment in Heterogeneous Wireless Sensor Networks

Information security in infrastructureless wireless sensor networks (WSNs) is one of the most important research challenges. In these networks, sensor nodes are typically sprinkled liberally in the field in order to monitor, gather, disseminate, and provide the sensed data to the command node. Various studies have focused on key establishment schemes in homogeneous WSNs. However, recent research has shown that achieving survivability in WSNs requires a hierarchy and heterogeneous infrastructure. In this paper, to address security issues in the heterogeneous WSNs, we propose a secure clustering scheme along with a deterministic pairwise key management scheme based on public key cryptography. The proposed security mechanism guarantees that any two sensor nodes located in the same cluster and routing path can directly establish a pairwise key without disclosing any information to other nodes. Through security performance evaluation, it is shown that the proposed scheme guarantees node-to-node authentication, high resiliency against node capture, and minimum memory space requirement.
Facial Scars after a Road Accident: Combined Treatment with Fractional Photothermolysis and Alexandrite Laser

A 37-year-old man presented to our clinic with several linear facial scars following a road accident. He was treated by a combined laser therapy with fractional photothermolysis and alexandrite laser. No side effects or complications arising from the treatment were noted. The patient presented with very good cosmetic results after treatment with this combined technique. Combined laser treatment with nonablative fractional photothermolysis and alexandrite laser can safely and effectively improve facial scars following a road accident.
Ezrin interacts with S100A4 via both its N- and C-terminal domains

Ezrin belongs to the ERM (ezrin, radixin, moesin) protein family that has a role in cell morphology changes, adhesion and migration as an organizer of the cortical cytoskeleton by linking actin filaments to the apical membrane of epithelial cells. It is highly expressed in a variety of human cancers and promotes metastasis. Members of the Ca2+-binding EF-hand containing S100 proteins have similar pathological properties; they are overexpressed in cancer cells and involved in metastatic processes. In this study, using tryptophan fluorescence and stopped-flow kinetics, we show that S100A4 binds to the N-terminal ERM domain (N-ERMAD) of ezrin with a micromolar affinity. The binding involves the F2 lobe of the N-ERMAD and follows an induced fit kinetic mechanism. Interestingly, S100A4 binds also to the unstructured C-terminal actin binding domain (C-ERMAD) with similar affinity. Using NMR spectroscopy, we characterized the complex of S100A4 with the C-ERMAD and demonstrate that no ternary complex is simultaneously formed with the two ezrin domains. Furthermore, we show that S100A4 co-localizes with ezrin in HEK-293T cells. However, S100A4 very weakly binds to full-length ezrin in vitro indicating that the interaction of S100A4 with ezrin requires other regulatory events such as protein phosphorylation and/or membrane binding, shifting the conformational equilibrium of ezrin towards the open state. As both proteins play an important role in promoting metastasis, the characterization of their interaction could shed more light on the molecular events contributing to this pathological process.
Reinforcement learning-based annotation for Deep Web data

A semantic annotation method for web database query result which is under the condition of uncertain schema information is proposed in this paper by adopting the reinforcement learning method. Using domain ontology to annotate the query result, this paper takes the mapping between domain ontology and query result as a process of finding the best strategy. By training the numeric attribute value, we can find the best strategy to match and then annotate the query result. By collecting web databases from different domains, the experiments indicate that the approach proposed can annotate the web database query result properly and improve the efficiency of annotating.
An automatic method for assessing the teaching impact of books from online academic syllabi

Scholars writing books that are widely used to support teaching in higher education may be undervalued because of a lack of evidence of teaching value. Although sales data may give credible evidence for textbooks, these data may poorly reflect educational uses of other types of books. As an alternative, this article proposes a method to search automatically for mentions of books in online academic course syllabi based on Bing searches for syllabi mentioning a given book, filtering out false matches through an extensive set of rules. The method had an accuracy of over 90% based on manual checks of a sample of 2,600 results from the initial Bing searches. Over one third of about 14,000 monographs checked had one or more academic syllabus mention, with more in the arts and humanities (56%) and social sciences (52%). Low but significant correlations between syllabus mentions and citations across most fields, except the social sciences, suggest that books tend to have different levels of impact for teaching and research. In conclusion, the automatic syllabus search method gives a new way to estimate the educational utility of books in a way that sales data and citation counts cannot.
A MODIFIED GROUND PLANE DUAL BAND COMPACT PLANAR ANTENNA FOR WIMAX APPLICATIONS

This paper presents the design of a small planar antenna with triangular patch for WiMax application. A conventional ground plane has been modified to reduce the size and increasing the bandwidth as well as to cover the WiMax band. The triangular‐shaped patch is placed on top of the substrate and parasitic patch is placed at other side. By inserting a triangular patch in the coplanar ground plane, antenna is able to radiate at two resonance frequencies simultaneously. This antenna structure has been designed for covering (3.2–3.7GHz) and (5.2 to 5.8 GHz) WiMax bands. A low dielectric constant substrate with dielectric constant of 3.38 is selected to attain a compact radiating structure that also meets the challenging bandwidth requirement. The proposed antenna is fed by a 50 ohm coplanar wave guide feed. The antenna geometry has small size of 22mm x 21mm x . 578mm and able to resonate on the 3.57 GHz and 5.23 GHz frequency with wide impedance bandwidth. This antenna provides the good return loss characteristics and the far field radiation pattern.These results indicates that this antenna have significant potential for WiMax applications. The simulation of designed antenna has been carried out by electromagnetic simulation software EMPIRE XCcel which is based on the powerful Finite Difference Time Domain method (FDTD).
PDMS microchannel regenerative peripheral nerve interface

We have fabricated a soft silicone structure to support the regeneration of a sciatic nerve. The device consists of 70 parallel (120 × 110 μm2) channels through which axons extend and then reconnect to the muscles on the other side of the device. Through histology and electrophysiology, we show that axons grow through the device and functionality of the muscle control is restored. Nerve functionality as demonstrated with stimulated electromyography (EMG) recordings is still intact at 9 months after implantation. Future work on this device will include electrodes for recording and stimulating the regenerating nerve.