Miracle-dz/UniFAR-FTUs huggingface dataset:
Fast-growing, non-infectious and intracellularly surviving drug-resistant Mycobacterium aurum: a model for high-throughput antituberculosis drug screening.

OBJECTIVES Enoyl acyl-carrier-protein reductase (InhA), the primary endogenous target for isoniazid and ethionamide, is crucial to type-II fatty acid biosynthesis (FAS-II). The objectives of this study were first to generate InhA mutants of Mycobacterium aurum, secondly to characterize InhA-mediated isoniazid and ethionamide resistance mechanisms across those mutants and finally to investigate the interaction of InhA with enzymes in the FAS-II pathway in M. aurum. METHODS Spontaneous mutants were generated by isoniazid overdose and limited broth dilution, while for genetically modified mutants sense-antisense DNA technology was used. Southern hybridization and immunoprecipitation were both used to identify the InhA homologue in M. aurum. The latter method was further used to compare the level of InhA expression in M. aurum with that in corresponding mutants. Isoniazid/ethionamide susceptibility modulation was examined in vitro and ex vivo using a resazurin assay as well as by cfu counting. In addition, circular dichroism and the bacterial two-hybrid system were exploited to investigate the interaction of InhA with other enzymes of the FAS-II pathway. RESULTS A Mycobacterium tuberculosis InhA homologue was detected in M. aurum. Susceptibility to isoniazid/ethionamide was significantly altered in genetically modified mutants and simultaneously InhA was overexpressed in both spontaneous and genetically modified mutants. InhA interacts with other FAS-II enzymes of M. aurum in vivo. CONCLUSION Close resemblance of isoniazid/ethionamide action on InhA between M. tuberculosis and M. aurum further supports the use of fast-growing and intracellularly surviving drug-resistant M. aurum to substitute for highly virulent, extremely slow-growing M. tuberculosis strains in the early stage of antituberculosis inhibitor screening.
Deregulation of lipid metabolism pathway genes in nasopharyngeal carcinoma cells

Nasopharyngeal carcinoma (NPC) is a unique tumour of epithelial origin with a distinct geographical distribution, closely associated with the Epstein-Barr virus (EBV). EBV-encoded RNAs (EBERs) are small non-polyadenylated RNAs that are abundantly expressed in latent EBV-infected NPC cells. To study the role of EBERs in NPC, we established stable expression of EBERs in HK1, an EBV-negative NPC cell line. Cells expressing EBERs consistently exhibited an increased growth rate. However, EBERs did not confer resistance towards cisplatin-induced apoptosis or promote migration or invasion ability in the cells tested. Using microarray gene expression profiling, we identified potential candidate genes that were deregulated in NPC cells expressing EBERs. Gene Ontology analysis of the data set revealed that EBERs upregulate the cellular lipid metabolic process. Upregulation of low-density lipoprotein receptor (LDLR) and fatty acid synthase (FASN) was observed in EBER-expressing cells. NPC cells exhibited LDL-dependent cell proliferation. In addition, a polyphenolic flavonoid compound, quercetin, known to inhibit FASN, was found to inhibit proliferation of NPC cells.
Role of Articular Disc in Condylar Regeneration of the Mandible

The articular disc in the temporomandibular joint plays an important role in mandibular growth. Functional appliances induce regeneration of the condyle even after condylectomy. The aim of this study was to examine the role of the articular disc in regeneration of the condyle after unilateral condylectomy with use of a functional appliance in growing rats. Fifty growing rats were subjected to unilateral condylectomy and then half of them underwent discectomy. The functional appliance was applied to half of the rats in each group to induce regeneration of the condyle. Four and eight weeks later, morphometric and histologic analyses of the mandible were performed. Regeneration of the condyle was demonstrated in the two condylectomy groups. In the condylectomy+appliance group, the shape and cartilage of the condyle were equivalent to a normal condyle. However, regeneration of the condyle was not observed in the two discectomy groups even with the use of the functional appliance. The articular disc appears to be crucial in the regeneration of a damaged condyle, suggesting that defects or damage to the articular disc may influence mandibular growth and regeneration or repair of the condyle.
Suppression of neural fate and control of inner ear morphogenesis by Tbx1

Inner ear sensory organs and VIIIth cranial ganglion neurons of the auditory/vestibular pathway derive from an ectodermal placode that invaginates to form an otocyst. We show that in the mouse otocyst epithelium, Tbx1 suppresses neurogenin 1-mediated neural fate determination and is required for induction or proper patterning of gene expression related to sensory organ morphogenesis (Otx1 and Bmp4, respectively). Tbx1 loss-of-function causes dysregulation of neural competence in otocyst regions linked to the formation of either mechanosensory or structural sensory organ epithelia. Subsequently, VIIIth ganglion rudiment form is duplicated posteriorly, while the inner ear is hypoplastic and shows neither a vestibular apparatus nor a coiled cochlear duct. We propose that Tbx1 acts in the manner of a selector gene to control neural and sensory organ fate specification in the otocyst.
Modeling and Performance Comparison of Privacy Approaches for Location Based Services

In pervasive computing environment, Location Based Services (LBSs) are getting popularity among users because of their usefulness in day-to-day life. LBSs are information services that use geospatial data of mobile device and smart phone users to provide information, entertainment and security in real time. A key concern in such pervasive computing environment is the need to reveal the user's exact location which may allow an adversary to infer private information about the user. To address the privacy concerns of LBS users, a large number of security approaches have been proposed based on the concept of k-anonymity. The central idea in location k-anonymity is to find a set of k-1 users confined in a given geographical area of the actual user, such that the location of these k users are indistinguishable from one another, thus protecting the identity of the user. Although a number of performance parameters like success rate, amount of privacy achieved are used to measure the performance of the k-anonymity approaches, they make the implicit, unrealistic assumption that the k-1 users are readily available. As such these approaches ignore the turnaround time to process a user request, which is crucial for a real-time application like LBS. In this work, we model the k-anonymity approaches using queuing theory to compute the average sojourn time of users and queue length of the system. To demonstrate that queuing theory can be used to model all k-anonymity approaches, we consider graph-based k-anonymity approaches. The proposed analytical model is further validated with experimental results.
Cell cycle control of c-kit+IL-7R+ B precursor cells by two distinct signals derived from IL-7 receptor and c-kit in a fully defined medium

An important goal for the investigation of the proliferation of mammalian cells is to establish a fully defined condition for culturing them in vitro. Here, we report establishment of a fully defined culture condition that supports the primary culture of normal c-kit+IL-7 receptor (IL-7R)+ B precursor cells without the aid of stromal cell lines. This defined culture condition contains IL-7, the ligand for c- kit, transferrin, insulin, and bovine serum albumin as protein components. By using the cell lines derived from RAG2(-/-) mice, which do not differentiate into c-kit- stage, we have evaluated the role of each protein in the cell cycle progression of c-kit+IL-7R+ B precursor cells. Since B precursor cells can grow without insulin, c-kit remains a sole functional receptor tyrosine kinase for their growth. While both c-kit ligand (KL) and IL-7 are the requisite molecules for sustained proliferation of B precursor cells, each molecule plays distinct roles. IL-7 starvation results in prompt arrest of the cells at G1. An accumulation of the cells in the mitotic phase was also detected. Thus, the major role of IL-7 is to regulate the G1/S transition and the process of cytokinesis of B precursor cells. Although prolonged KL starvation over 48 h resulted in accumulation of G1 cells, its effect could not be detected within 24 h, which is long enough for all the cells to complete one cell cycle. This suggests that KL might be involved in the cell cycle progression of B precursor cells in a manner that its signal could still be effective in the one or two cell cycles that follow. Although molecular nature of the signals underlying the present observation awaits future investigation, the method described in this report would provide a useful model system for investigating the signaling pathways that are involved in the cell cycle progression of B precursor cells.
Automating joiners

Pictures taken from different view points cannot be stitched into a geometrically consistent mosaic, unless the structure of the scene is very special. However, geometrical consistency is not the only criterion for success: incorporating multiple view points into the same picture may produce compelling and informative representations. A multi viewpoint form of visual expression that has recently become highly popular is that of joiners (a term coined by artist David Hockney). Joiners are compositions where photographs are layered on a 2D canvas, with some photographs occluding others and boundaries fully visible. Composing joiners is currently a tedious manual process, especially when a great number of photographs is involved. We are thus interested in automating their construction. Our approach is based on optimizing a cost function encouraging image-to-image consistency which is measured on point-features and along picture boundaries. The optimization looks for consistency in the 2D composition rather than 3D geometrical scene consistency and explicitly considers occlusion between pictures. We illustrate our ideas with a number of experiments on collections of images of objects, people, and outdoor scenes.
The prevalence and source of methicillin-resistant Staphylococcus aureus (MRSA) in the community in Hong Kong

Although reports of isolation of methicillin-resistant Staphylococcus aureus (MRSA) from patients admitted from the community have increased, few studies have investigated colonization of healthy subjects. This study aimed to determine community levels of MRSA in Hong Kong. Nasal swabs from a cross section of young adults and family units were cultured for MRSA. Antibiotic sensitivities and risk factors for carriage were determined and clonal relationships were investigated by pulsed-field gel electrophoresis (PFGE). Overall carriage was low (1·4%), and associated with health-care exposures (OR 13·56, 95% CI 1·11–165·21). Subjects working in health care yielded multi-resistant MRSA strains, but isolates from non-hospital-exposed subjects were methicillin-resistant only. Strains indistinguishable by PFGE were carried by subjects working together, and some spread to other contacts was observed. MRSA colonization in the community is rare in Hong Kong and is largely associated with working in health care. Community-acquired staphylococcal infections may be treated with agents effective against methicillin-sensitive strains.
Conservative Management of Vestibular Schwannoma: Expectations Based on the Length of the Observation Period

Objective Evaluate long-term prevalence of tumor growth and need for further treatment in patients with a vestibular schwannoma treated with conservative management. Study Design Retrospective chart review. Setting Private neurotologic tertiary referral center. Patients Vestibular schwannoma patients undergoing conservative management and previously studied (N = 114). Mean time to last magnetic resonance imaging was 4.8 years and to last follow-up was 6.4 years (maximum, 18.5 yr). Intervention Serial gadolinium-enhanced magnetic resonance imaging with size measurement. Main Outcome Measures Change in maximum tumor dimension of 2 mm or higher (growth), further treatment, audiologic measures—pure-tone average, word recognition, AAO-HNS (American Academy of Otolaryngology-Head and Neck Surgery) hearing class. Results Thirty-eight percent of tumors demonstrated growth; an average of 6.5 mm (SD, 3.8) at a mean rate of 3.1 mm per year. Of patients with no growth at 1 year or less, 20% grew by last follow-up. Overall, 31% had further treatment after a mean of 3.8 years (SD, 3.5; maximum, 18.5 yr). Of those followed for 5 to 10 years, 18% eventually had further treatment. Only 56% of growing tumors had further treatment by last follow-up; 14.8% with nongrowing tumors also had further treatment. Pure-tone average declined more in tumors that grew (mean &Dgr; = 28.8 dB) than those that did not (mean &Dgr; = 16.5 dB) (p ⩽ 0.025), but there was no correlation between the amount of change in hearing and in the size of the tumor. Of patients with an initial AAO-HNS hearing Class A, 85.7% retained serviceable hearing. Conclusion For patients electing an observation approach to treatment of vestibular schwannoma, about 31% may eventually undergo further treatment. Of those followed for 5 to 10 years, 18% eventually had further treatment. However, some patients are followed with radiologic evaluations for many years without necessity for further treatment.
The Mineral Question: How Energy and Technology Will Determine the Future of Mining

Almost 150 years after that William Stanley Jevons published his paper “The Coal Question” (Jevons, 1866) the debate on mineral depletion has been ongoing between two main schools of thought: one that sees depletion as an important problem for the near future and another that sees technology and human ingenuity as the most important factors in making depletion a problem for the remote future. Today, however, we have created intellectual tools that permit us to frame the problem on the basis of physical factors, in particular on the basis of thermodynamics. The present paper examines the problem of mineral depletion from a broad viewpoint, with a specific view on the role of energy in the mining and production processes. The conclusion is that energy is a fundamental factor in determining how long we can expect the supply of mineral resources to last at the present prices and production levels. The rapid depletion of our main energy resources, fossil fuels, is creating a serious supply problem that is already being felt in terms of high prices of all mineral commodities. Technology can mitigate the problem, but not solve it. In a non remote future, the world's industrial system will have to undergo fundamental changes in order to adapt to a reduced supply of mineral commodities.
Temperature-Dependent Characteristics of SiC Devices: Performance Evaluation and Loss Calculation

Silicon Carbide (SiC) devices have obvious advantages compared with conventional Si devices, and especially so at high temperatures. This paper aims at developing a method for the characterization of SiC JFET conduction and switching losses at high temperatures as well as the calculation of semiconductor losses in SiC JFET-based converters. To this end, the steady-state performance of SiC JFET and Schottky diodes at different temperatures is studied, and an improved conduction loss evaluation is proposed considering the bidirectional conduction paths of the JFET. Specifically, a SiC JFET bridge test bed is built to measure the switching losses at different temperatures with and without antiparallel diodes, where experimental results show that using SiC Schottky diodes in antiparallel eliminates the reverse recovery of the JFET body diode, improving the switching behavior and reducing the losses of the devices. Further, these test results are used to estimate the losses of a 10-kW ac-dc-ac converter, which shows that the use of Schottky diodes as freewheeling devices helps reduce both conduction and switching losses, presenting an even greater reduction at higher operating temperatures.
MediaEval 2014 Visual Privacy Task: Geometrical Privacy Protection Tool

This paper describes EPFL privacy protection tool for the MediaEval 2014 Visual Privacy task. The goal of the task is to obscure faces, body silhouettes, and personal items of people in the provided surveillance clips to preserve their personal privacy. The EPFL privacy protection tool mainly relies on two privacy protection filters: a warping-based reversible filter to obscure features with low visual details (body silhouettes) by distorting them with randomized warping and morphing-based reversible filter to obscure features with high visual details (faces and personal items) by ‘replacing’ them with a graphical representation. The aim of this tool is to achieve an acceptable balance between privacy (how well the privacy is protected) and intelligibility (how well the surveillance task can still be performed), as well as, privacy and pleasantness (how pleasant is the protection). The results of three types of subjective evaluations, via crowdsourcing, practitioners, and stakeholders, provided by the organizers of the task demonstrates that EPFL privacy protection tool achieves a great overall balance between privacy, intelligibility, and pleasantness, while being secure and reversible in the same time.
Leporine-Derived Adipose Precursor Cells Exhibit In Vitro Osteogenic Potential

Adipose-derived stem cells (ASCs) possess osteogenic potential and have been shown to undergo in vitro osteoblastic differentiation and promote bone regeneration in vivo. In this study, we describe the isolation and osteoblastic differentiation of rabbit ASCs and their behavior on a gelatin foam scaffold. These studies will form the basis of future in vivo studies of the osteogenic potential of rabbit ASCs for calvarial defect repair. Adipose-derived stem cells were isolated from New Zealand White rabbits and cultured in osteogenic medium ± bone morphogenetic protein 2. Osteoblastic differentiation was assessed via histochemical stains for alkaline phosphatase (AP) and extracellular matrix (ECM) calcification. Reverse transcriptase polymerase chain reaction was performed to evaluate the expression of AP and the osteogenic transcription factor Runx2. Adipose-derived stem cells were seeded onto gelatin foam scaffolds at various densities, and cell proliferation was measured fluorometrically. Cells isolated from rabbit adipose tissue exhibited classic ASC morphology. Adipose-derived stem cells cultured in osteogenic medium exhibited more robust staining for AP and ECM calcification compared with ASCs in control medium. Furthermore, this staining was more marked in male ASCs versus female ASCs and also enhanced by bone morphogenetic protein 2. mRNA for AP and Runx2 were also increased in the osteoinduced cells. Theoptimal seeding density was 1 × 105 ASCs on an 8-mm gelatin foam scaffold. We have shown that rabbit ASCs have in vitro osteogenic potential and are compatible with a gelatin foam scaffold. Characteristic features of osteoblasts, such as ECM mineralization and expression of osteogenic genes, were demonstrated in this cell population. In vitro osteoblastic differentiation and scaffold studies are necessary before in vivo trials. The mechanism underlying the sex-based variation in osteoblastic differentiation is unknown but may involve signaling via factors such as estrogen.
Spatial coherence properties of an LED-based illumination system for mask-aligner lithography

A high-power LED-based illumination system has been developed as a replacement for the mercury arc lamps used in mask-aligner lithography. LEDs are arranged in a grid array and placed in the entrance aperture of individual reflectors. Those reflectors decrease the angular extent of the light. With this multisource approach, different groups of LEDs can be switched on independently. The illumination patterns created determine the illumination angles and the spatial coherence in the mask plane. The spatial coherence is measured in the mask plane by using a circular double slits approach. The interference pattern for different illumination patterns are measured, showing the effect of the asymmetry and size of the angular extent of the illumination light. The effect of the different illumination patterns on the quality of the prints are also illustrated with print tests.
Privacy and security requirements framework for the internet of things (IoT)

Capturing privacy and security requirements in the very early stages is essential for creating sufficient public confidence in order to facilitate the adaption of novel systems such as the Internet of Things (IoT). However, traditional requirements engineering methods and frameworks might not be sufficiently effective when dealing with new types of IoT heterogeneous systems. Therefore, building a methodological framework to model the privacy and security requirements specifications for IoT is necessary in order to deal with its mission critical nature. The purpose of this project is to develop such a requirements engineering framework in order to ensure proper development of IoT with security and privacy taken into account from the earliest stages.
Take advantage of time in your experiments: a guide to simple, informative kinetics assays

Understanding virtually any process in cellular and molecular biology depends on knowledge of the rates of the biochemical reactions, so it is regrettable that few cellular and molecular biologists take advantage of kinetics experiments in their work. Fortunately, the kinetics experiments that are most useful for understanding cellular systems are within reach for everyone whose research would benefit from this information. This essay describes simple methods to measure the valuable kinetic parameters that characterize the dynamics of life processes. These “transient-state” methods not only differ in concept from traditional approaches used to analyze enzyme reactions at steady state, but they are also applicable to learning about the dynamics of any biological process.
Further Reliability, Convergent and Discriminant Validity of Overall Defensive Functioning

The reliability, convergent and discriminant validity of the Defensive Functioning Scale (DFS) and the overall defensive functioning score (ODF) has been previously examined. This study aims to address gaps in the literature as well as to replicate and extend the initial positive clinical validity data emerging on the DFS (Blais et al., 1996;Hoglend and Perry, 1998;Lingiardi et al., 1999;Perry 2001;Perry and Hoglend, 1998;Perry et al., 1998). Fifty-three outpatient clients were rated by clinicians trained on the DFS. The relationship between the ODF with both clinician-rated and self-report measures of psychopathology was examined. The mean interrater reliability for the DFS levels rated in this study was found to be moderate to high, and reliability for the ODF score was found to be excellent. Coefficient alpha of individual defense levels as well as across the entire DFS indicated high levels of internal consistency. Factor analysis revealed that the ODF represents a construct different from various aspects of patient self-report and clinician ratings of psychopathology. These results provide further support for the clinical application and relevance of the DFS system.