Miracle-dz/UniFAR-FTUs huggingface dataset:
TLR–Dependent Control of Francisella tularensis Infection and Host Inflammatory Responses

Background Francisella tularensis is the causative agent of tularemia and is classified as a Category A select agent. Recent studies have implicated TLR2 as a critical element in the host protective response to F. tularensis infection, but questions remain about whether TLR2 signaling dominates the response in all circumstances and with all species of Francisella and whether F. tularensis PAMPs are predominantly recognized by TLR2/TLR1 or TLR2/TLR6. To address these questions, we have explored the role of Toll-like receptors (TLRs) in the host response to infections with F. tularensis Live Vaccine Strain (LVS) and F. tularensis subspecies (subsp.) novicida in vivo. Methodology/Principal Findings C57BL/6 (B6) control mice and TLR– or MyD88-deficient mice were infected intranasally (i.n.) or intradermally (i.d.) with F. tularensis LVS or with F. tularensis subsp. novicida. B6 mice survived >21 days following infection with LVS by both routes and survival of TLR1−/−, TLR4−/−, and TLR6−/− mice infected i.n. with LVS was equivalent to controls. Survival of TLR2−/− and MyD88−/− mice, however, was significantly reduced compared to B6 mice, regardless of the route of infection or the subspecies of F. tularensis. TLR2−/− and MyD88−/− mice also showed increased bacterial burdens in lungs, liver, and spleen compared to controls following i.n. infection. Primary macrophages from MyD88−/− and TLR2−/− mice were significantly impaired in the ability to secrete TNF and other pro-inflammatory cytokines upon ex vivo infection with LVS. TNF expression was also impaired in vivo as demonstrated by analysis of bronchoalveolar lavage fluid and by in situ immunofluorescent staining. Conclusions/Significance We conclude from these studies that TLR2 and MyD88, but not TLR4, play critical roles in the innate immune response to F. tularensis infection regardless of the route of infection or the subspecies. Moreover, signaling through TLR2 does not depend exclusively on TLR1 or TLR6 during F. tularensis LVS infection.
The Effect of Altered Loading on Mandibular Condylar Cartilage

Objective The purpose of this study was to delineate the cellular, mechanical and morphometric effects of altered loading on the mandibular condylar cartilage (MCC) and subchondral bone. We hypothesized that altered loading will induce differentiation of cells by accelerating the lineage progression of the MCC. Materials and Methods Four-week-old male Dkk3 XCol2A1XCol10A1 mice were randomly divided into two groups: (1) Loaded-Altered loading of MCC was induced by forced mouth opening using a custom-made spring; (2) Control-served as an unloaded group. Mice were euthanized and flow cytometery based cell analysis, micro-CT, gene expression analysis, histology and morphometric measurements were done to assess the response. Results Our flow cytometery data showed that altered loading resulted in a significant increase in a number of Col2a1-positive (blue) and Col10a1-positive (red) expressing cells. The gene expression analysis showed significant increase in expression of BMP2, Col10a1 and Sox 9 in the altered loading group. There was a significant increase in the bone volume fraction and trabecular thickness, but a decrease in the trabecular spacing of the subchondral bone with the altered loading. Morphometric measurements revealed increased mandibular length, increased condylar length and increased cartilage width with altered loading. Our histology showed increased mineralization/calcification of the MCC with 5 days of loading. An unexpected observation was an increase in expression of tartrate resistant acid phosphatase activity in the fibrocartilaginous region with loading. Conclusion Altered loading leads to mineralization of fibrocartilage and drives the lineage towards differentiation/maturation.
Localization of PDZD7 to the Stereocilia Ankle-Link Associates this Scaffolding Protein with the Usher Syndrome Protein Network

Usher syndrome is the leading cause of genetic deaf–blindness. Monoallelic mutations in PDZD7 increase the severity of Usher type II syndrome caused by mutations in USH2A and GPR98, which respectively encode usherin and GPR98. PDZ domain-containing 7 protein (PDZD7) is a paralog of the scaffolding proteins harmonin and whirlin, which are implicated in Usher type 1 and type 2 syndromes. While usherin and GPR98 have been reported to form hair cell stereocilia ankle-links, harmonin localizes to the stereocilia upper tip-link density and whirlin localizes to both tip and ankle-link regions. Here, we used mass spectrometry to show that PDZD7 is expressed in chick stereocilia at a comparable molecular abundance to GPR98. We also show by immunofluorescence and by overexpression of tagged proteins in rat and mouse hair cells that PDZD7 localizes to the ankle-link region, overlapping with usherin, whirlin, and GPR98. Finally, we show in LLC-PK1 cells that cytosolic domains of usherin and GPR98 can bind to both whirlin and PDZD7. These observations are consistent with PDZD7 being a modifier and candidate gene for USH2, and suggest that PDZD7 is a second scaffolding component of the ankle-link complex.
Dictionary Learning for Noisy and Incomplete Hyperspectral Images

We consider analysis of noisy and incomplete hyperspectral imagery, with the objective of removing the noise and inferring the missing data. The noise statistics may be wavelength dependent, and the fraction of data missing (at random) may be substantial, including potentially entire bands, offering the potential to significantly reduce the quantity of data that need be measured. To achieve this objective, the imagery is divided into contiguous three-dimensional (3D) spatio-spectral blocks of spatial dimension much less than the image dimension. It is assumed that each such 3D block may be represented as a linear combination of dictionary elements of the same dimension, plus noise, and the dictionary elements are learned in situ based on the observed data (no a priori training). The number of dictionary elements needed for representation of any particular block is typically small relative to the block dimensions, and all the image blocks are processed jointly (“collaboratively") to infer the underlying dictionary. We address dictionary learning from a Bayesian perspective, considering two distinct means of imposing sparse dictionary usage. These models allow inference of the number of dictionary elements needed as well as the underlying wavelength-dependent noise statistics. It is demonstrated that drawing the dictionary elements from a Gaussian process prior, imposing structure on the wavelength dependence of the dictionary elements, yields significant advantages, relative to the more conventional approach of using an independent and identically distributed Gaussian prior for the dictionary elements; this advantage is particularly evident in the presence of noise. The framework is demonstrated by processing hyperspectral imagery with a significant number of voxels missing uniformly at random, with imagery at specific wavelengths missing entirely, and in the presence of substantial additive noise.
Routing with QoS information aggregation in hierarchical networks

In this paper, we consider the problem of routing with two additive constraints in the hierarchical networks, such as the Internet. In order for scalability, the supported QoS information in the hierarchical networks has to be aggregated. We propose a novel method for aggregating the QoS information. To the best of our knowledge, our approach is the first study to use the area-minimization optimization, the de facto optimization problem of the QoS information aggregation. We use a set of real numbers to approximate the supported QoS between different domains. The size of the set is predefined so that advertisement overhead and the space requirement will not grow exponentially as the network size grows. The simulation results show that the proposed method outperforms the existing methods.
The role of agricultural commercialization for smallholders productivity and food security

For the past few decades, continuing economic and demographic change across the world has brought an excess demand for different types of agricultural products. As a result, policy makers and international institutions have been advocating several policy instruments aimed to boost agricultural production and food security. In most cases, however, the potential role of smallholder commercialization has not been given due attention despite its importance. Therefore, this research assesses the potential role of commercialization for smallholder agricultural productivity and food security in Ethiopian farm households. Econometric model based on stochastic frontier analysis is used as the main technique in addressing the predetermined research questions. As a data set, the 2009 Ethiopian rural household survey compiled by International Food Policy Research Institute is used. Findings show that farmers are only 40.2 percent efficient relative to the most efficient farmers in the sample using the current input level. The variables related to educational level, access for radio, access for cell phone and level of commercialization are positively linked with technical efficiency. Results imply that output can be increased up to 59.8 percent by improving the existing input mixes used in the production process. Furthermore, estimated results for the determinants of farmers’ commercialization identified different types of market as the main statistically significant variables. Besides, the amount of households' budget share allocated for food consumption expenditure is indirectly associated with level of commercialization suggesting possibility of substantial influence on quality and quantity of households' food consumption. Finally, with respect to policy recommendations, the overall results suggested that policy makers and international donors should prioritize their effort on increasing smallholders' degree of market participation as one of the main instrument in improving agricultural productivity and food security.
A Low-Cost Jitter Measurement Technique for BIST Applications

In this paper, we present a BIST technique that measures the RMS value of a Gaussian distribution period jitter. In the proposed approach, the signal under test is delayed by two different delay values and the probabilities it leads the two delayed signals are measured. The RMS jitter can then be derived from the probabilities and the delay values. Behavior and circuit simulations are performed to validate the proposed technique and analyze the design tradeoffs, and preliminary measurement results on FPGA are also presented.
Visual odometry for road vehicles—feasibility analysis

Estimating the global position of a road vehicle without using GPS is a challenge that many scientists look forward to solving in the near future. Normally, inertial and odometry sensors are used to complement GPS measures in an attempt to provide a means for maintaining vehicle odometry during GPS outage. Nonetheless, recent experiments have demonstrated that computer vision can also be used as a valuable source to provide what can be denoted as visual odometry. For this purpose, vehicle motion can be estimated using a non-linear, photogrametric approach based on RAndom SAmple Consensus (RANSAC). The results prove that the detection and selection of relevant feature points is a crucial factor in the global performance of the visual odometry algorithm. The key issues for further improvement are discussed in this letter.
Using Inertial Data to Enhance Image Segmentation - Knowing Camera Orientation Can Improve Segmentation of Outdoor Scenes

In the context of semantic image segmentation, we show that knowledge of world-centric camera orientation (from an inertial sensor) can be used to improve classification accuracy. This works because certain structural classes (such as the ground) tend to appear in certain positions relative to the viewer. We show that orientation information is useful in conjunction with typical image-based features, and that fusing the two results in substantially better classification accuracy than either alone – we observed an increase from 61% to 71% classification accuracy, over the six classes in our test set, when orientation information was added. The method is applied to segmentation using both points and lines, and we also show that combining points with lines further improves accuracy. This work is done towards our intended goal of visually guided locomotion for either an autonomous robot or human.
Satisfaction with amplification in daily life (SADL) in different types and degrees of hearing loss

Introduction: The aim of this study is to determine the satisfaction level of hearing aids users in different types and degrees of hearing loss using the satisfaction with amplification in daily life (SADL) questionnaire. Methods: 35 hearing aid users with different types of hearing loss who sought help from the International Islamic University, Malaysia (IIUM) Hearing and Speech Clinic at Jalan Hospital Campus, Kuantan, IIUM Medical Specialist Centre and private hearing aid centres were involved in this study. The data was collected from the participants who filled in the Malay SADL questionnaires. Results: Among the thirty-five (31) participants, most of the hearing aid users were satisfied with their hearing aids regardless of their different types of hearing loss. However, there was no significant difference between the different types of hearing loss and their satisfaction level in the SADL global score and each of the subscales. It was found that satisfaction level with the hearing aids may depend on several factors such as cosmetic preference, cost of hearing aid and audiologist competence. Meanwhile, in terms of degrees of hearing loss, majority of the users were relatively satisfied with their hearing aids. Yet, there was no correlation between hearing aid users’ satisfaction level and their degrees of hearing loss for all subscales and SADL global score. Conclusions: This study indicates that some hearing aid users are not satisfied in terms of feedback, telephone use, cosmetic appearance and costs of hearing aid. The findings of this study can benefit the audiologists, as they would be able to use the information to help future patients understand and adapt to the use of the hearing aids better.
A unified model for the evolution of galaxies and quasars

We incorporate a simple scheme for the growth of supermassive black holes into semi-analytic models that follow the formation and evolution of galaxies in a cold dark matter-dominated Universe. We assume that supermassive black holes are formed and fuelled during major mergers. If two galaxies of comparable mass merge, their central black holes coalesce and a few per cent of the gas in the merger remnant is accreted by the new black hole over a time-scale of a few times 107 yr. With these simple assumptions, our model not only fits many aspects of the observed evolution of galaxies, but also reproduces quantitatively the observed relation between bulge luminosity and black hole mass in nearby galaxies, the strong evolution of the quasar population with redshift, and the relation between the luminosities of nearby quasars and those of their host galaxies. The strong decline in the number density of quasars from z∼2 to z=0 is a result of the combination of three effects: (i) a decrease in the merging rate; (ii) a decrease in the amount of cold gas available to fuel black holes, and (iii) an increase in the time-scale for gas accretion. The predicted decline in the total content of cold gas in galaxies is consistent with that inferred from observations of damped Lyα systems. Our results strongly suggest that the evolution of supermassive black holes, quasars and starburst galaxies is inextricably linked to the hierarchical build-up of galaxies.
DESIGN OF SECOND ORDER SIGMA-DELTA MODULATOR FOR AUDIO APPLICATIONS

The paper includes the design of second order sigma-delta modulator. A comparative study between a first order and second order sigma-delta modulator is carried out. The second order is preferred over the first order sigma-delta modulator due to its better signal-to-noise ratio (SNR). The comparative study between the modulators is done in Matlab, the second-order sigma-delta modulator is designed and modelled in Verilog-A and simulated in Cadence SpectreS. The second order sigma-delta modulator provides an enhancement of 27% in SNR as compared to the first order sigma-delta modulator.
Hermite polynomials for signal reconstruction from zero-crossings. 1. One-dimensional signals

Generalised Hermite polynomials are employed for the reconstruction of an unknown signal from a knowledge of its zero-crossings, under certain conditions on its spatial/spectral width, but dispensing with the assumption of bandlimitedness. A computational implementation of the proposed method is given for one-variable (or one-dimensional) signals, featuring an application of simulated annealing for optimal reconstruction.
Comparison of various active impedance control approaches, modeling, implementation, passivity, stability and trade-offs

Impedance control, as method to improve the interaction ability of robotic systems, has gained great attention by the robotic community and a large number of different implementations have been reported in the literature. Most implementations are based on an outer impedance loop and a number of nested inner loops. In this paper, various active Impedance Control (IC) schemes are designed, analyzed and tested based on different inner control loops, namely velocity, position and torque. IC on link and motor side are considered. Stability, passivity, safety and performance of the different IC schemes are presented. All the IC schemes are evaluated and tested on a 1-dof series elastic actuator. The system dynamics are modeled including gearbox meshing friction and harmonic drive torque ripple. Simulation and experimental results are compared.
Force-directed scheduling for the behavioral synthesis of ASICs

A general scheduling methodology is presented that can be integrated into specialized or general-purpose high-level synthesis systems. An initial version of the force-directed scheduling algorithm at the heart of this methodology was originally presented by the authors in 1987. The latest implementation of the logarithm introduced here reduces the number of functional units, storage units, and buses required by balancing the concurrency of operations assigned to them. The algorithm supports a comprehensive set of constraint types and scheduling modes. These include multicycle and chained operations; mutually exclusive operations; scheduling under fixed global timing constraints with minimization of functional unit costs, minimization of register costs, and minimization of global interconnect requirements; scheduling with local time constraints (on operation pairs); scheduling under fixed hardware resource constraints; functional pipelining; and structural pipeline (use of pipeline functional units). Examples from current literature, one of which was chosen as a benchmark for the 1988 High-Level Synthesis Workshop, are used to illustrate the effectiveness of the approach. >
Lessons Learned from a Collaborative Self-Study in International Teacher Education: Visiones, Preguntas, y Desafíos

Sometimes I feel like a fraud and a failure.at least that ́s what I felt after the last class. I guess that the old phrase to go abroad helps you to make the strange familiar and the familiar strange has allowed me time to really think about what I teach and how I teach. I know that asking questions about why things haven ́t been as successful as they might is a difficult and painful road on which to embark. But embark I must. If only for my sense of professional growth and for my own sense that I really, really tried to understand. (Francisco, personal journal, 3/05)
Dietary Cholesterol Reduces Plasma Triacylglycerol in Apolipoprotein E-Null Mice: Suppression of Lipin-1 and -2 in the Glycerol-3-Phosphate Pathway

Background Cholesterol metabolism is tightly regulated by both cholesterol and its metabolites in the mammalian liver, but the regulatory mechanism of triacylglycerol (TG) synthesis remains to be elucidated. Lipin, which catalyzes the conversion of phosphatidate to diacylglycerol, is a key enzyme involved in de novo TG synthesis in the liver via the glycerol-3-phosphate (G3P) pathway. However, the regulatory mechanisms for the expression of lipin in the liver are not well understood. Methodology/Principal Findings Apolipoprotein E-knock out (apoE-KO) mice were fed a chow supplemented with 1.25% cholesterol (high-Chol diet). Cholesterol and bile acids were highly increased in the liver within a week. However, the amount of TG in very low-density lipoprotein (VLDL), but not in the liver, was reduced by 78%. The epididymal adipose tissue was almost eradicated in the long term. DNA microarray and real-time RT-PCR analyses revealed that the mRNA expression of all the genes in the G3P pathway in the liver was suppressed in the high-Chol diet apoE-KO mice. In particular, the mRNA and protein expression of lipin-1 and lipin-2 was markedly decreased, and peroxisome proliferator-activated receptor-γ coactivator-1α (PGC-1α), which up-regulates the transcription of lipin-1, was also suppressed. In vitro analysis using HepG2 cells revealed that the protein expression of lipin-2 was suppressed by treatment with taurocholic acid. Conclusions/Significance These data using apoE-KO mice indicate that cholesterol and its metabolites are involved in regulating TG metabolism through a suppression of lipin-1 and lipin-2 in the liver. This research provides evidence for the mechanism of lipin expression in the liver.
Insights from Web 3.0: Is it Time for a New Scientific Publishing Methodology?

Scientific publishing almost hasn't changed for the last few centuries. Conferences and Journals are the only two ways to publish scientific information. On the other hand publishing technology has advanced from ordinary typography and it is ironic that scientific institutions, which should be the primers in using advanced technologies, still use traditional (often black and white) paper publishing. Today's Web interfaces to journals act mainly as a digital archive of non-digital papers. Technology allows us to use multimedia systems, software applications, social and semantic web facilities that could tremendously improve publishing quality and allow for more scientific interaction. In order to show some of the possibilities of these new technologies, the TaOPis system will be presented. TaOPis is a social semantic web application for self-organizing communities providing suitable tools like semantic wiki systems, forums, blogs, ranking mechanisms, content filtering, tagging etc. The system has been used for more than three years for various purposes, but most projects deal with knowledge management due to the fact that the system is used in a knowledge management course at the Faculty of organization and informatics. Especially its semantic wiki subsystem is of special interest since it accumulates metainformation which is of great importance to finding relevant information. It shall be shown that a semantic wiki system (provided with some additional functionality based on social network analysis) can be used for a scientific publishing system that is self-organizing and facilitates the autopoiesis of the scientific social system.