Miracle-dz/UniFAR-FTUs huggingface dataset:
Genetic Association and Expression Studies Indicate a Role of Toll-Like Receptor 8 in Pulmonary Tuberculosis

Despite high rates of exposure, only 5–10% of people infected with Mycobacterium tuberculosis will develop active tuberculosis (TB) disease, suggesting a significant role for genetic variation in the human immune response to this infection. Here, we studied TB association and expression of 18 genes involved in the Toll-like receptor (TLR) pathways. Initially, we genotyped 149 sequence polymorphisms in 375 pulmonary TB patients and 387 controls from Indonesia. We found that four polymorphisms in the TLR8 gene on chromosome X showed evidence of association with TB susceptibility in males, including a non-synonymous polymorphism rs3764880 (Met1Val; P = 0.007, odds ratio (OR) = 1.8, 95% c.i. = 1.2–2.7). We genotyped these four TLR8 polymorphisms in an independent collection of 1,837 pulmonary TB patients and 1,779 controls from Russia and again found evidence of association in males (for rs3764880 P = 0.03, OR = 1.2, 95% c.i. = 1.02–1.48). Combined evidence for association is P = 1.2×10−3–6×10−4. In addition, a quantitative PCR analysis indicated that TLR8 transcript levels are significantly up-regulated in patients during the acute phase of disease (P = 9.36×10−5), relative to baseline levels following successful chemotherapy. A marked increase in TLR8 protein expression was also observed directly in differentiated macrophages upon infection with M. bovis bacille Calmette-Guérin (BCG). Taken together, our results provide evidence, for the first time, of a role for the TLR8 gene in susceptibility to pulmonary TB across different populations.
Optimization and Analysis of Wireless Powered Multi-Antenna Cooperative Systems

In this paper, we consider a three-node cooperative wireless powered communication system consisting of a multi-antenna hybrid access point (H-AP) and a single-antenna relay and a single-antenna user. The energy constrained relay and user first harvest energy in the downlink and then the relay assists the user using the harvested power for information transmission in the uplink. The optimal energy beamforming vector and the time split between harvest and cooperation are investigated. To reduce the computational complexity, suboptimal designs are also studied, where closed-form expressions are derived for the energy beamforming vector and the time split. For comparison purposes, we also present a detailed performance analysis in terms of the achievable outage probability and the average throughput of an intuitive energy beamforming scheme, where the H-AP directs all the energy towards the user. The findings of the paper suggest that implementing multiple antennas at the H-AP can significantly improve the system performance, and the closed-form suboptimal energy beamforming vector and time split yields near optimal performance. Also, for the intuitive beamforming scheme, a diversity order of $\frac {N+1}{2}$ can be achieved, where $N$ is the number of antennas at the H-AP.
Characterisation of microphenomena in transversely loaded composite materials

• A submitted manuscript is the author's version of the article upon submission and before peer-review. There can be important differences between the submitted version and the official published version of record. People interested in the research are advised to contact the author for the final version of the publication, or visit the DOI to the publisher's website. • The final author version and the galley proof are versions of the publication after peer review. • The final published version features the final layout of the paper including the volume, issue and page numbers.
Detection and Localization of HTML Presentation Failures Using Computer Vision-Based Techniques

An attractive and visually appealing appearance is important for the success of a website. Presentation failures in a site's web pages can negatively impact end users' perception of the quality of the site and the services it delivers. Debugging such failures is challenging because testers must visually inspect large web pages and analyze complex interactions among the HTML elements of a page. In this paper we propose a novel automated approach for debugging web page user interfaces. Our approach uses computer vision techniques to detect failures and can then identify HTML elements that are likely to be responsible for the failure. We evaluated our approach on a set of real-world web applications and found that the approach was able to accurately and quickly identify faulty HTML elements.
Neuronal plasticity and formation of new synaptic contacts follow pyramidal lesions and neutralization of Nogo‐A: A light and electron microscopic study in the pontine nuclei of adult rats

Regeneration and compensatory sprouting are limited after lesions in the mature mammalian central nervous system in contrast to the developing central nervous system (CNS). After neutralization of the growth inhibitor Nogo‐A, however, massive sprouting and rearrangements of fiber connections occurred after unilateral pyramidal tract lesions in adult rats: Corticofugal fibers from the lesioned side crossed the midline of the brainstem and innervated the contralateral basilar pontine nuclei. To determine whether these newly sprouted fibers formed synaptic contacts, we analyzed the corticofugal fibers in the basilar pontine nuclei contralateral to the lesion by light and electron microscopy 2 weeks after pyramidotomy and treatment with the Nogo‐A‐inhibiting monoclonal antibody IN‐1 (mAb IN‐1). The mAb IN‐1, but not a control antibody, led to structural changes in the basilar pons ipsilateral and contralateral to the lesion site. Fibers sprouted across the pontine midline and terminated topographically. They established asymmetric synaptic contacts with the characteristics of normal corticopontine terminals. These results show that adult CNS fibers are able to sprout and to form new synaptic contacts after a lesion when a growth‐permissive microenvironment is provided. J. Comp. Neurol. 433:426–436, 2001. © 2001 Wiley‐Liss, Inc.
Threshold Key-Establishment in Distributed Sensor Networks Using a Multivariate Scheme

Key establishment in sensor networks is not a trivial task because of the scale of the network and resource limitations of the sensor nodes. Unfortunately, the previous solutions in general networks are inapplicable to sensor networks. In this paper, we propose a novel multivariate key pre-distribution scheme (MKPS) that simultaneously provides many nice features of previous schemes without any disadvantages such as additional memory. These features include node-to-node authentication, network scalability, key compositeness, perfect secrecy up to the capture of a fraction of nodes, and network connectivity. In this scheme, every node is assigned a unique ID that is an n tuple of positive integers. Based on these IDs, the shares of multivariate polynomials are stored in the memory of every sensor node prior to their deployment. After the deployment, those nodes that are at the communication range of each other and their IDs are at the Hamming distance of one from each other can establish n − 1 common keys. The secret key between such nodes is a symmetric combination of all these n − 1 keys. Hence, the proposed MKPS is in some sense an (n − 1)-composite scheme. We will show that this feature significantly improves the security of MKPS over previous schemes. The proposed method is in the category of threshold schemes, i.e., it remains perfectly secure up to the capture of a certain fraction of sensor nodes. For example, in some instances, the scheme remains almost perfectly secure until 90% of the nodes are captured. We will also propose a procedure to choose an optimal dimension n. In contrast to previous schemes, the design criteria in our scheme are both security and network connectivity. Hence, the proposed scheme provides an opportunity to the designer to adjust the network properties according to the desired application.
The High Variability of Tibial Rotational Alignment in Total Knee Arthroplasty

Although various techniques are advocated to establish tibial rotational alignment during total knee arthroplasty, it is unknown which is most repeatable. We evaluated the precision and accuracy of five tibial rotational alignment techniques to determine whether computer-assisted navigation systems can reduce variability of tibial component rotational alignment when compared to traditional instrumentation. Eleven orthopaedic surgeons used four computer-assisted techniques that required identification of anatomical landmarks and one that used traditional extramedullary instrumentation to establish tibial rotational alignment axes on 10 cadaver legs. Two computer-assisted techniques (axes between the most medial and lateral border of the tibial plateau, and between the posterior cruciate ligament [PCL] and the anterior tibial crest) and the traditional technique were least variable, with standard deviations of 9.9°, 10.8°, and 12.1°, respectively. Computer-assisted techniques referencing the tibial tubercle (axes between the PCL and the medial border or medial ⅓ of the tubercle) were most variable, with standard deviations of 27.4° and 28.1°. The axis between the medial border of the tibial tubercle and the PCL was internally rotated compared to the other techniques. None of the techniques consistently established tibial rotational alignment, and navigation systems that establish rotational alignment by identifying anatomic landmarks were not more reliable than traditional instrumentation. Level of Evidence: Level I, diagnostic study. See Guidelines for Authors for a complete description of levels of evidence.
Functional and genetic diversity of mycorrhizal fungi from single plants of Caladenia formosa (Orchidaceae).

BACKGROUND AND AIMS Mycorrhizal associations are essential to the plant kingdom. The largest flowering plant family, the Orchidaceae, relies on mycorrhizal fungi for germination, growth and survival. Evidence suggests varying degrees of fungal-host specificity based on a single fungal isolate from a single plant. This paper shows for the first time the diversity of endophytes colonizing in a single plant over consecutive years and the functional significance of this diversity. METHODS Stem-collars of Caladenia formosa were collected in different seasons and years. Mycorrhizal fungi isolated were tested for their efficacy to induce leafing and genetically determined using ITS-RFLP and sequencing. RESULTS Multiple mycorrhizal fungi were repeatedly isolated from a single collar that displayed varying effectiveness in germination percentages and adult leaf length. Additional factors contributed to the isolation of effective mycorrhizal fungi; fungal collection season, year of collection and individual isolates. Surface sterilization only improved the number of isolated mycorrhizal fungi. Dual inoculation did not increase germination. All 59 mycorrhizal fungi effective in germinating seed belonged to one clearly defined ITS (internal transcribed spacer) clade and clustered close to Sebacina vermifera (79-89 % homology). Isolates resulting in the greatest germination were not necessarily those resulting in the greatest survival and growth 1 year after germination. CONCLUSION Single orchid plants contained multiple mycorrhizal fungal strains of one species that had diverse functional differences. These results suggest that our current knowledge of fungal-host specificity may be incomplete due to experimental and analytical limitations. It also suggests that the long-term effectiveness of a mycorrhizal fungus or fungi could only be found by germination and longer-term growth tests rather than genetically.
Protective Role of Omega-3 Polyunsaturated Fatty Acid against Lead Acetate-Induced Toxicity in Liver and Kidney of Female Rats

The present study was conducted to investigate the protective role of Omega-3 polyunsaturated fatty acids against lead acetate-induced toxicity in liver and kidney of female rats. Animals were divided into four equal groups; group 1 served as control while groups 2 and 3 were treated orally with Omega-3 fatty acids at doses of 125 and 260 mg/kg body weight, respectively, for 10 days. These groups were also injected with lead acetate (25 mg/kg body weight) during the last 5 days. Group 4 was treated only with lead acetate for 5 days and served as positive control group. Lead acetate increased oxidative stress through an elevation in MDA associated with depletion in antioxidant enzymes activities in the tissues. Moreover, the elevation of serum enzymes activities (ALT, AST, ALP, and LDH) and the levels of urea and creatinine were estimated but total proteins were decreased. Also, lead acetate-treatment induced hyperlipidemia via increasing of lipid profiles associated with decline in HDL-c level. Significant changes of Hb, PCV, RBCs, PLT, and WBCs in group 4 were recorded. The biochemical alterations of lead acetate were confirmed by histopathological changes and DNA damage. The administration of Omega-3 provided significant protection against lead acetate toxicity.
Optimal communication logics in networked control systems

This paper addresses the control of spatially distributed processes over a network that imposes bandwidth constraints and communication delays. Optimal communication policies are derived for an estimator-based networked control system architecture to reduce the communication load. These policies arise as solutions of an average cost optimization problem, which is solved using dynamic programming. The optimal policies are shown to be deterministic.
Antimalarials increase vesicle pH in Plasmodium falciparum

The asexual erythrocytic stage of the malarial parasite ingests and degrades the hemoglobin of its host red cell. To study this process, we labeled the cytoplasm of uninfected red cells with fluorescein-dextran, infected those cells with trophozoite- and schizont-rich cultures of Plasmodium falciparum, and harvested them 110-120 h later in the trophozoite stage. After lysis of the red cell cytoplasm with digitonin, the only fluorescence remaining was in small (0.5-0.9 micron) vesicles similar to the parasite's food vacuole. As measured by spectrofluorimetry, the pH of these vesicles was acid (initial pH 5.2- 5.4), and they responded to MgATP with acidification and to weak bases such as NH4Cl with alkalinization. These three properties are similar to those obtained with human fibroblasts and suggest that the endocytic vesicles of plasmodia are similar to those of mammalian cells. Each of the antimalarials tested (chloroquine, quinine, and mefloquine) as well as NH4Cl inhibited parasite growth at concentrations virtually identical to those that increased parasite vesicle pH. These results suggest two conclusions: (a) The increases in vesicle pH that we have observed in our digitonin-treated parasite preparation occur at similar concentrations of weak bases and antimalarials in cultures of parasitized erythrocytes, and (b) P. falciparum parasites are exquisitely dependent on vesicle pH during their asexual erythrocytic cycle, perhaps for processes analogous to endocytosis and proteolysis in mammalian cells, and that antimalarials and NH4Cl may act by interfering with these events.
Optogenetics reveals a role for accumbal medium spiny neurons expressing dopamine D2 receptors in cocaine-induced behavioral sensitization

Long-lasting, drug-induced adaptations within the nucleus accumbens (NAc) have been proposed to contribute to drug-mediated addictive behaviors. Here we have used an optogenetic approach to examine the role of NAc medium spiny neurons (MSNs) expressing dopamine D2 receptors (D2Rs) in cocaine-induced behavioral sensitization. Adeno-associated viral vectors encoding channelrhodopsin-2 (ChR2) were delivered into the NAc of D2R-Cre transgenic mice. This allowed us to selectively photostimulate D2R-MSNs in NAc. D2R-MSNs form local inhibitory circuits, because photostimulation of D2R-MSN evoked inhibitory postsynaptic currents (IPSCs) in neighboring MSNs. Photostimulation of NAc D2R-MSN in vivo affected neither the initiation nor the expression of cocaine-induced behavioral sensitization. However, photostimulation during the drug withdrawal period attenuated expression of cocaine-induced behavioral sensitization. These results show that D2R-MSNs of NAc play a key role in withdrawal-induced plasticity and may contribute to relapse after cessation of drug abuse.
Evaluation of digital and film hemispherical photography and spherical densiometry for measuring forest light environments.

This study presents the results of a comparison of digital and film hemispherical photography as means of characterizing forest light environments and canopy openness. We also compared hemispherical photography to spherical densiometry. Our results showed that differences in digital image quality due to the loss of resolution that occurred when images were processed for computer analysis did not affect estimates of unweighted openness. Weighted openness and total site factor estimates were significantly higher in digital images compared with film photos. The differences between the two techniques might be a result of underexposure of the film images or differences in lens optical quality and field of view. We found densiometer measurements significantly increased in consistency with user practice and were correlated with total site factor and weighted-openness estimates derived from hemispherical photography. Digital photography was effective and more convenient and inexpensive than film cameras, but unti.
Maximum likelihood estimation for compound-gaussian clutter with inverse gamma texture

The inverse gamma distributed texture is important for modeling compound-Gaussian clutter (e.g. for sea reflections), due to the simplicity of estimating its parameters. We develop maximum-likelihood (ML) and method of fractional moments (MoFM) estimates to find the parameters of this distribution. We compute the Cramer-Rao bounds (CRBs) on the estimate variances and present numerical examples. We also show examples demonstrating the applicability of our methods to real lake-clutter data. Our results illustrate that, as expected, the ML estimates are asymptotically efficient, and also that the real lake-clutter data can be very well modeled by the inverse gamma distributed texture compound-Gaussian model.
Proxemics play: understanding proxemics for designing digital play experiences

Digital games are increasingly profiting from sensing technologies. However, their focus is mostly on sensing limb movements. We propose that sensing capabilities could also be used to engage players with proxemics: the interpersonal distance between players. We further add that wireless networks offer complementary distance zones for designers, offering novel design resources for digital play. We use our own as well as other games to articulate a set of strategies on how designers can utilize both proxemics and the new wireless proxemics to facilitate novel play experiences. Ultimately, with our work, we aim to expand the range of digital play.
Antiarthritic effect of bee venom: inhibition of inflammation mediator generation by suppression of NF-kappaB through interaction with the p50 subunit.

OBJECTIVE To investigate the molecular mechanisms of the antiarthritic effects of bee venom (BV) and melittin (a major component of BV) in a murine macrophage cell line (Raw 264.7) and in synoviocytes obtained from patients with rheumatoid arthritis. METHODS We evaluated the antiarthritic effects of BV in a rat model of carrageenan-induced acute edema in the paw and in a rat model of chronic adjuvant-induced arthritis. The inhibitory effects of BV and melittin on inflammatory gene expression were measured by Western blotting, and the generation of prostaglandin E(2) (PGE(2)) and nitric oxide (NO) and the intracellular calcium level were assayed. NF-kappaB DNA binding and transcriptional activity were determined by gel mobility shift assay or by luciferase assay. Direct binding of BV and melittin to the p50 subunit of NF-kappaB was determined with a surface plasmon resonance analyzer. RESULTS BV (0.8 and 1.6 mug/kg) reduced the effects of carrageenan- and adjuvant-induced arthritis. This reducing effect was consistent with the inhibitory effects of BV (0.5, 1, and 5 mug/ml) and melittin (5 and 10 mug/ml) on lipopolysaccharide (LPS; 1 mug/ml)-induced expression of cyclooxygenase 2, cytosolic phospholipase A(2), inducible NO synthase, generation of PGE(2) and NO, and the intracellular calcium level. BV and melittin prevented LPS-induced transcriptional and DNA binding activity of NF-kappaB via the inhibition of IkappaB release and p50 translocation. BV (affinity [K(d)] = 4.6 x 10(-6)M) and melittin (K(d) = 1.2 x 10(-8)M) bound directly to p50. CONCLUSION Target inactivation of NF-kappaB by directly binding to the p50 subunit is an important mechanism of the antiarthritic effects of BV.
IndexFS: Scaling File System Metadata Performance with Stateless Caching and Bulk Insertion

The growing size of modern storage systems is expected to exceed billions of objects, making metadata scalability critical to overall performance. Many existing distributed file systems only focus on providing highly parallel fast access to file data, and lack a scalable metadata service. In this paper, we introduce a middleware design called Index FS that adds support to existing file systems such as PVFS, Lustre, and HDFS for scalable high-performance operations on metadata and small files. Index FS uses a table-based architecture that incrementally partitions the namespace on a per-directory basis, preserving server and disk locality for small directories. An optimized log-structured layout is used to store metadata and small files efficiently. We also propose two client-based storm free caching techniques: bulk namespace insertion for creation intensive workloads such as N-N check pointing, and stateless consistent metadata caching for hot spot mitigation. By combining these techniques, we have demonstrated Index FS scaled to 128 metadata servers. Experiments show our out-of-core metadata throughput out-performing existing solutions such as PVFS, Lustre, and HDFS by 50% to two orders of magnitude.
A new direct manipulation technique for aligning objects in drawing programs

Current drawing programs provide mainly three ways for carrying out object alignment: either by issuing an alignment command, or by using direct positioning with the help of gravity active points, or by making use of constraints. The first technique has limited functionality, and the other two may be mysterious for a novice. We describe here a new direct manipulation tool for alignment. We show that while direct manipulation helps to make the tool intuitive, it has through iterative design evolved into a tool that also offers functionality not found in current commercial products.
Antigen-specific T-cell factor in cell cooperation. Mapping within the I region of the H-2 complex and ability to cooperate across allogeneic barriers

Further mapping of the mouse T-cell factor specific for poly(Try,Glu)- polyD-LAla--polyLys is reported. It is shown to be a product of the I-A subregion of the H-2 complex by the use of antisera either raised specifically against or made specific, by absorption, for different regions of the H-2 complex. The factor cooperates across allogeneic barriers, e.g., when factor produced by one strian is combined with bone marrow cells of other H-2 incompatible strains.