Miracle-dz/UniFAR-FTUs huggingface dataset:
Cryptococcus neoformans Virulence Gene Discovery through Insertional Mutagenesis

ABSTRACT Insertional mutagenesis was applied to Cryptococcus neoformans to identify genes associated with virulence attributes. Using biolistic transformation, we generated 4,300 nourseothricin (NAT)-resistant strains, of which 590 exhibited stable resistance. We focused on mutants with defects in established virulence factors and identified two with reduced growth at 37°C, four with reduced production of the antioxidant pigment melanin, and two with an increased sensitivity to nitric oxide (NO). The NAT insertion and mutant phenotypes were genetically linked in five of eight mutants, and the DNA flanking the insertions was characterized. For the strains with altered growth at 37°C and altered melanin production, mutations were in previously uncharacterized genes, while the two NO-sensitive strains bore insertions in the flavohemoglobin gene FHB1, whose product counters NO stress. Because of the frequent instability of nourseothricin resistance associated with biolistic transformation, Agrobacterium-mediated transformation was tested. This transkingdom DNA delivery approach produced 100% stable nourseothricin-resistant transformants, and three melanin-defective strains were identified from 576 transformants, of which 2 were linked to NAT in segregation analysis. One of these mutants contained a T-DNA insertion in the promoter of the LAC1 (laccase) gene, which encodes a key enzyme required for melanin production, while the second contained an insertion in the promoter of the CLC1 gene, encoding a voltage-gated chloride channel. Clc1 and its homologs are required for ion homeostasis, and in their absence Cu+ transport into the secretory pathway is compromised, depriving laccase and other Cu+-dependent proteins of their essential cofactor. The NAT resistance cassette was optimized for cryptococcal codon usage and GC content and was then used to disrupt a mitogen-activated protein kinase gene, a predicted gene, and two putative chloride channel genes to analyze their contributions to fungal physiology. Our findings demonstrate that both insertional mutagenesis methods can be applied to gene identification, but Agrobacterium-mediated transformation is more efficient and generates exclusively stable insertion mutations.
RITA displays anti-tumor activity in medulloblastomas independent of TP53 status

Current therapy of medulloblastoma, the most common malignant brain tumor of childhood, achieves 40–70% survival. Secondary chemotherapy resistance contributes to treatment failure, where TP53 pathway dysfunction plays a key role. MDM2 interaction with TP53 leads to its degradation. Reactivating TP53 functionality using small-molecule inhibitors, such as RITA, to disrupt TP53-MDM2 binding may have therapeutic potential. We show here that RITA decreased viability of all 4 analyzed medulloblastoma cell lines, regardless of TP53 functional status. The decrease in cell viability was accompanied in 3 of the 4 medulloblastoma cell lines by accumulation of TP53 protein in the cells and increased CDKN1A expression. RITA treatment in mouse models inhibited medulloblastoma xenograft tumor growth. These data demonstrate that RITA treatment reduces medulloblastoma cell viability in both in vitro and in vivo models, and acts independently of cellular TP53 status, identifying RITA as a potential therapeutic agent to treat medulloblastoma.
Requirement of SpOtx in cell fate decisions in the sea urchin embryo and possible role as a mediator of beta-catenin signaling.

We show here that the homeodomain transcription factor SpOtx is required for endoderm and aboral ectoderm formation during sea urchin embryogenesis. SpOtx target genes were repressed by fusing the SpOtx homeodomain to an active repression domain of Drosophila Engrailed. The Engrailed-SpOtx fusion protein reduced the expression of endoderm- and aboral ectoderm-specific genes and inhibited the formation of endoderm and aboral ectoderm cell types. Coexpressing activated beta-catenin with Engrailed-SpOtx did not overcome the inhibition of endoderm and aboral ectoderm formation, suggesting that SpOtx functioned either downstream of or parallel to nuclear beta-catenin. Embryos expressing C-cadherin, which blocks nuclear translocation of beta-catenin, have defects in endoderm and aboral ectoderm formation. Coexpressing SpOtx with C-cadherin restored aboral ectoderm-specific gene expression and aboral ectoderm morphology, but with C-cadherin present, SpOtx was not sufficient for endoderm formation. Our results show that SpOtx plays a key role in the activation of aboral ectoderm- and endoderm-specific gene expression and, in addition, suggest that SpOtx mediates some of beta-catenin's functions in endoderm and aboral ectoderm formation.
USEQ: A Short Questionnaire for Satisfaction Evaluation of Virtual Rehabilitation Systems

New emerging technologies have proven their efficacy in aiding people in their rehabilitation. The tests that are usually used to evaluate usability (in general) or user satisfaction (in particular) of this technology are not specifically focused on virtual rehabilitation and patients. The objective of this contribution is to present and evaluate the USEQ (User Satisfaction Evaluation Questionnaire). The USEQ is a questionnaire that is designed to properly evaluate the satisfaction of the user (which constitutes part of usability) in virtual rehabilitation systems. Forty patients with balance disorders completed the USEQ after their first session with ABAR (Active Balance Rehabilitation), which is a virtual rehabilitation system that is designed for the rehabilitation of balance disorders. Internal consistency analysis and exploratory factor analysis were carried out to identify the factor structure of the USEQ. The six items of USEQ were significantly associated with each other, and the Cronbach alpha coefficient for the questionnaire was 0.716. In an analysis of the principal components, a one-factor solution was considered to be appropriate. The findings of the study suggest that the USEQ is a reliable questionnaire with adequate internal consistency. With regard to patient perception, the patients found the USEQ to be an easy-to-understand questionnaire with a convenient number of questions.
Functional exploratory data analysis for high‐resolution measurements of urban particulate matter

In this work we propose the use of functional data analysis (FDA) to deal with a very large dataset of atmospheric aerosol size distribution resolved in both space and time. Data come from a mobile measurement platform in the town of Perugia (Central Italy). An OPC (Optical Particle Counter) is integrated on a cabin of the Minimetrò, an urban transportation system, that moves along a monorail on a line transect of the town. The OPC takes a sample of air every six seconds and counts the number of particles of urban aerosols with a diameter between 0.28 μ m and 10 μ m and classifies such particles into 21 size bins according to their diameter. Here, we adopt a 2D functional data representation for each of the 21 spatiotemporal series. In fact, space is unidimensional since it is measured as the distance on the monorail from the base station of the Minimetrò. FDA allows for a reduction of the dimensionality of each dataset and accounts for the high space‐time resolution of the data. Functional cluster analysis is then performed to search for similarities among the 21 size channels in terms of their spatiotemporal pattern. Results provide a good classification of the 21 size bins into a relatively small number of groups (between three and four) according to the season of the year. Groups including coarser particles have more similar patterns, while those including finer particles show a more different behavior according to the period of the year. Such features are consistent with the physics of atmospheric aerosol and the highlighted patterns provide a very useful ground for prospective model‐based studies.
Genetic Requirements for RAD51- andRAD54-Independent Break-Induced Replication Repair of a Chromosomal Double-Strand Break

ABSTRACT Broken chromosomes can be repaired by several homologous recombination mechanisms, including gene conversion and break-induced replication (BIR). In Saccharomyces cerevisiae, an HO endonuclease-induced double-strand break (DSB) is normally repaired by gene conversion. Previously, we have shown that in the absence ofRAD52, repair is nearly absent and diploid cells lose the broken chromosome; however, in cells lacking RAD51, gene conversion is absent but cells can repair the DSB by BIR. We now report that gene conversion is also abolished when RAD54, RAD55, and RAD57 are deleted but BIR occurs, as withrad51Δ cells. DSB-induced gene conversion is not significantly affected when RAD50, RAD59, TID1(RDH54), SRS2, or SGS1 is deleted. Various double mutations largely eliminate both gene conversion and BIR, including rad51Δ rad50Δ, rad51Δ rad59Δ, andrad54Δ tid1Δ. These results demonstrate that there is aRAD51- and RAD54-independent BIR pathway that requires RAD59, TID1, RAD50, and presumablyMRE11 and XRS2. The similar genetic requirements for BIR and telomere maintenance in the absence of telomerase also suggest that these two processes proceed by similar mechanisms.
Guiding ziplock snakes with a priori information

Active contour models, or snakes, are effective and robust in contour extraction. In most papers on snakes, an initialization close to the desired contour is assumed to be provided, which is inappropriate in many cases. The ziplock snake model presented by Neuenschwander et al. (1997), however, needs only two user-supplied endpoints. The optimization process for a ziplock snake starts from the two endpoints and progresses towards the center of the snake. In this paper, we present a method to combine a grammatical model that encodes a priori shape information with the ziplock snakes. A competing mechanism is adopted to take advantage of the shape models without inducing excessive computation. The resulting model-based ziplock snakes have many advantages over the original model: They can accurately locate contour features, produce more refined results, and deal with multiple contours, missing image cues and noise.
Biologic monitoring of dental office sterilizers in Mexico.

BACKGROUND Biologic indicators (BIs) are the quality control applicable to sterilization cycles, but their use was not previously taught in Mexican dental schools or recommended by professional associations. A Mexican official standard, the Mexican Official Norm, published by health authorities in 1999 makes it compulsory for dentists to biologically verify sterilization cycles. However, only a few dentists comply because the use of BIs is largely unknown and the standard is not being enforced. OBJECTIVE To evaluate the incidence of sterilization failures in a convenience sample of dental offices in Mexico. METHODS Spore strips were distributed to dentists interested in using this service. The dentists mailed the processed BIs to the laboratory for culture. RESULTS In 6 years, 3277 tests were submitted from 82 dental offices. Thirty-four offices (41%) submitted 1 to 12 tests, 22 (27%) sent 14 to 48 tests, 18 (22%) mailed 49 to 96 tests, and 8 (10%) sent >97 tests. The sterilization methods were steam (74.4%), dry heat (20%), and chemical vapor (5.6%). A total of 242 sterilization failures (7.4% of all cycles) were detected. Convection dry heat failed with a greater frequency with chi(2) analysis (chi(2) = 13.71, P =. 0175). CONCLUSIONS Sterilization failures occurred in instrument loads used in patient treatment. Steam and chemical vapor under pressure failed less often than convection dry heat. When corrective action is taken, routine use of BIs increases patient safety.
Improving the speed of convergence of a maximum-likelihood motion estimation algorithm of a human face

For human face motion estimation the shape of a human face is considered to be rigid and described by a triangular mesh. The motion is described by six parameters: one three-dimensional translation vector and three rotation angles. The motion parameters are estimated by maximizing the conditional probability of the frame to frame intensity differences at observation points. The speed of convergence is improved by detecting outliers in the observation points and excluding them from motion estimation. For outlier detection an algorithm based on random sample consensus (RANSAC) has been developed. Experimental results reveal that the average processing time for motion estimation per frame is reduced by 67.49%.
Power Yield Analysis Under Process and Temperature Variations

In this paper, a method is proposed to accurately estimate the power yield, considering process-induced temperature and supply voltage variations. Process variations impose statistical behavior on the temperature and leakage current. This, in turn, impacts the IR drops due to the variations in the current, drawn off the power grid. By considering the process-induced statistical profile of the temperature and Vdd, the power yield is estimated for a chip. This helps check the robustness of the circuits early in the design process. The experimental results on the ISCAS89 benchmarks indicate a significant yield loss, if the statistical measures of the temperature and voltage drop are ignored. Monte Carlo simulations verify the accuracy of the developed methodology.
ANTI-WINDUP SCHEMES FOR NONLINEAR ACTIVE DISTURBANCE REJECTION CONTROL IN MARINE STEAM TURBINE

Nonlinear characteristics are very common in marine steam turbine, such as control input constraints and external disturbances. Based on the active disturbance rejection control (ADRC), an anti-windup scheme is proposed to eliminate the undesired effects of nonlinear characteristics in the control system. In this scheme, firstly, a method of setting parameter is designed for nonlinear active disturbance rejection control (NLADRC). Then, two kinds of anti-windup schemes are proposed in this paper for NLADRC in the presence of control input constraints and external disturbances. Finally, simulation study is carried out for a first order delay object with actuator constraints, simulation results show that both schemes can achieve good anti-windup performance. The method is further extended to marine steam turbine control, with simulation results demonstrating that both methods have their own advantages.
Diagnosis of primary human herpesvirus 6 and 7 infections in febrile infants by polymerase chain reaction

Primary human herpesvirus 6 (HHV-6) and 7 (HHV-7) infections were identified in febrile children by qualitative and quantitative polymerase chain reaction (PCR) assays. Diagnosis was based on the differential detection of viral DNA in peripheral blood mononuclear cells (PBMC), but not in saliva. Six of 41 febrile infants, but none of seven non-febrile controls, were identified with primary infections (three HHV-6, three HHV-7). These children had significantly higher viral loads in PBMC (HHV-6, median 24 213 genomes/106PBMC; HHV-7, median 6 040 000 genomes/106 PBMC) than DNA-aemic, saliva PCR positive children (HHV-6, median 1606 genomes/106 PBMC, p < 0.01; HHV-7, median 7089 genomes/106 PBMC, p < 0.05). Viral DNA was detected in serum by PCR in only 50% of primary infections. All three children with primary HHV-7 infection had febrile convulsions. Thus PCR, including quantitative assays, may identify primary HHV-6 and HHV-7 infections when an appropriate combination of clinical specimens is used.
Towards parallel educational worlds

Augmented Reality, 3D virtual worlds, etc.: the technology has evolved tremendously and so has its application to the field of education. Digital technologies have advanced to the point, where we are reproducing digitally more and more aspects of our life. We have parallel worlds: on the one hand the real world, and on the other virtual worlds, that can in fact be linked to the real one. They have different properties, but they can enrich and complement each other. In this paper, we explore the possibilities and challenges of these parallel worlds for educational uses.
Influence of the Interests of Children with Autism on Everyday Learning Opportunities

Findings from a pilot study investigating the influence of the interests of young children with autism on parents' provision of everyday informal child learning opportunities are described. 17 children (13 boys, 4 girls) were divided into two groups that received everyday learning opportunities of Low interest and High interest, based on parents' bi-weekly ratings of the interestingness of the opportunities to the children, using an investigator-developed measure. A brief intervention of 12 to 14 weeks showed that the children in the High interest-based group were provided more learning opportunities than were the Low interest-based group, and that the parents indicated that their children benefited more from the learning opportunities. Implications for future research are described.
Mechanism Of Cell Surface Activation Of 72-kDa Type IV Collagenase

Matrix metalloproteases are secreted by mammalian cells as zymogens and, upon activation, initiate tissue remodeling by proteolytic degradation of collagens and proteoglycans. Activation of the secreted proenzymes and interaction with their specific inhibitors determine the net enzymatic activity in the extracellular space. We have previously demonstrated that 72T4Cl can be activated by a plasma membrane-dependent mechanism specific for this enzyme. Here, we report purification of the membrane activator of 72T4Cl, which is a new metalloprotease identical to a recently cloned membrane-type matrix metalloprotease (MT-MMP). We demonstrate that activated MT-MMP acts as a cell surface tissue inhibitor of metalloprotease 2 (TIMP-2) receptor with Kd = 2.54 × 10−9M. The activator•TlMP-2 complex in turn acts as a receptor for 72T4Cl (Kd = 0.56 × 10−9M), binding to the carboxyl-end domain of the enzyme. Activation of 72T4Cl on the cell membrane provides a basic mechanism for spatially regulated extracellular proteolysis and presents a new target for prognosis and treatment of metastatic disease. The activator, purified as a tri-molecular complex of MT-MMP•TIMP2•carboxyl-end domain of 72T4Cl, is itself an activated form of MT-MMP, posing the following question: what is the mechanism of the activator's activation?
Comparative Analysis of Glycogene Expression in Different Mouse Tissues Using RNA-Seq Data

Glycogenes regulate a wide array of biological processes in the development of organisms as well as different diseases such as cancer, primary open-angle glaucoma, and renal dysfunction. The objective of this study was to explore the role of differentially expressed glycogenes (DEGGs) in three major tissues such as brain, muscle, and liver using mouse RNA-seq data, and we identified 579, 501, and 442 DEGGs for brain versus liver (BvL579), brain versus muscle (BvM501), and liver versus muscle (LvM442) groups. DAVID functional analysis suggested inflammatory response, glycosaminoglycan metabolic process, and protein maturation as the enriched biological processes in BvL579, BvM501, and LvM442, respectively. These DEGGs were then used to construct three interaction networks by using GeneMANIA, from which we detected potential hub genes such as PEMT and HPXN (BvL579), IGF2 and NID2 (BvM501), and STAT6 and FLT1 (LvM442), having the highest degree. Additionally, our community analysis results suggest that the significance of immune system related processes in liver, glycosphingolipid metabolic processes in the development of brain, and the processes such as cell proliferation, adhesion, and growth are important for muscle development. Further studies are required to confirm the role of predicted hub genes as well as the significance of biological processes.
A Flexible Paper-Based Microdischarge Array Device: A Novel Route to Cost-Effective and Simple Setup Microplasma Generation Devices

A low-cost and simple-arranged paper-based microplasma array device made by tape and Xerox paper was presented. Uniform array of discharge can be sustained in Ar, He, and ambient air atmosphere. Stable discharge can be sustained for at least 55 min when plasma is ignited in Ar ambient, based on the examination of time-resolved optical emission spectra. Throughout the conditions investigated, the power consumed by the device was well below 0.3 W. We also demonstrated that stable and uniform discharge can be generated when the device was bent to a radius of curvature of 2.5 mm.
Preoperative and postoperative mapping of cerebrovascular reactivity in moyamoya disease by using blood oxygen level-dependent magnetic resonance imaging.

OBJECT The ability to map cerebrovascular reactivity (CVR) at the tissue level in patients with moyamoya disease could have considerable impact on patient management, especially in guiding surgical intervention and assessing the effectiveness of surgical revascularization. This paper introduces a new noninvasive magnetic resonance (MR) imaging-based method to map CVR. Preoperative and postoperative results are reported in three cases to demonstrate the efficacy of this technique in assessing vascular reserve at the microvascular level. METHODS Three patients with angiographically confirmed moyamoya disease were evaluated before and after surgical revascularization. Measurements of CVR were obtained by rapidly manipulating end-tidal PCO2 between hypercapnic and hypocapnic states during MR imaging. The CVR maps were then calculated by comparing the percentage of changes in MR signal with changes in end-tidal PCO2. Presurgical CVR maps showed distinct regions of positive and negative reactivity that correlated precisely with the vascular territories supplied by severely narrowed vessels. Postsurgical reactivity maps demonstrated improvement in the two patients with positive clinical outcome and no change in the patient in whom a failed superficial temporal artery-middle cerebral artery bypass was performed. CONCLUSIONS Magnetic imaging-based CVR mapping during rapid manipulation of end-tidal PCO2 is an exciting new method for determining the location and extent of abnormal vascular reactivity secondary to proximal large-vessel stenoses in moyamoya disease. Although the study group is small, there seems to be considerable potential for guiding preoperative decisions and monitoring efficacy of surgical revascularization.
Transcultural Adaptation and Validation of the Korean Version of the Brief Illness Perception Questionnaire for Patients with Pulmonary Tuberculosis

Background and Aim: The brief illness perception questionnaire (BIPQ) has been used in many populations for both adults and children, and it provides a rapid assessment of illness perception. This study was performed to create a translated version of the BIPQ to fit the Korean society and to test its validity through pulmonary tuberculosis (TB) patients. Methods: Translation and transcultural adaptation of BIPQ, applicable to the Korean society, was performed in accordance with the international guidelines. Internal consistency, test-retest reliability, concurrent validity, and discrimination validity were evaluated. To assess the discrimination validity, the BIPQ scores were compared between pulmonary TB and chronic obstructive pulmonary disease (COPD). Results: Sixty-eight patients with pulmonary TB participated in this study. Cronbach's α coefficient was 0.753, which indicated satisfactory internal consistency. The concurrent validity showed significant correlations (Pearson's correlation of 0.753). The test-retest reliability was confirmed with an intraclass correlation coefficient of 0.892. The total score of BIPQ in patients with COPD was significantly higher than that in those with pulmonary TB (37.67 vs. 30.85; P= 0.005), which supported the discrimination validity. Conclusions: The Korean version of BIPQ was found to be a reliable and valid questionnaire for patients with pulmonary TB.