Miracle-dz/UniFAR-FTUs huggingface dataset:
Validation of Methods for Oropharyngeal Cancer HPV Status Determination in US Cooperative Group Trials

Tumor human papillomavirus (HPV) status is a prognostic factor for oropharyngeal cancer, but classification methods are not standardized. Here we validate the HPV classification methods used in US cooperative group trials. Tumor DNA and RNA purified from 240 paraffin-embedded oropharyngeal cancers diagnosed from 2000 to 2009 were scored as evaluable if positive for DNA and mRNA controls by quantitative polymerase chain reaction (PCR). Eighteen high-risk (HR) HPV types were detected in tumors by consensus PCR, followed by HR-HPV E6/7 oncogene expression analysis by quantitative reverse transcriptase PCR. The sensitivity (S), specificity (SP), and positive (PPV) and negative predictive values (NPV) of p16 expression detected by immunohistochemistry (IHC) and HPV16 detected by in situ hybridization (ISH) were evaluated in comparison with HR-HPV E6/7 oncogene expression. Interrater agreement among 3 pathologists was evaluated by &kgr; statistics. Of 235 evaluable tumors, 158 (67%; 95% confidence interval, 61.2-73.3) were positive for HR-HPV E6/7 oncogene expression [HPV type 16 (92%), 18 (3%), 33 (3%), 35 (1%), or 58 (1%)]. p16 IHC had high sensitivity (S 96.8%, SP 83.8%, PPV 92.7%, and NPV 92.5%), whereas HPV16 ISH had high specificity (S 88.0%, SP 94.7%, PPV 97.2%, and NPV 78.9%) for HR-HPV oncogene expression. Interrater agreement was excellent for p16 (&kgr;=0.95 to 0.98) and HPV16 ISH (&kgr;=0.83 to 0.91). Receiver operating curve analysis determined the cross-product of p16 intensity score and percentage of tumor staining to optimally discriminate HR-HPV E6/7-positive and HR-HPV E6/7-negative tumors. p16 IHC and HPV16 ISH assays show excellent performance, with high sensitivity and specificity, respectively. A new validated H-score for p16 IHC assessment is proposed. Appropriate assay choice depends on clinical implications of a false-positive or false-negative test.
Development of 6 U CubeSat’s Deployable Solar Panel with Burn Wire Triggering Holding and Release Mechanism

In the present work, a deployable solar panel based on a burn wire triggering holding and release mechanism was developed for use of 6 U CubeSat. The holding and release mechanism was designed based on a nichrome burn wire cutting method widely used for CubeSat applications. However, it provides a high loading capability, reliable wire cutting, multiplane constraints, and handling simplicity during the tightening process of wire. A demonstration model of a printed circuit board-based solar panel stiffened by a high-pressure fiberglass-laminated G10 material was fabricated and tested to validate the effectiveness of the design and functionality of the mechanism under various test conditions. The structural safety of the solar panel combined with the mechanism in a launch vibration environment was verified through sine and random vibration tests at qualification level.
Soil Fungi: Their Potential use as a Forensic Tool

As a grave is an anomalous environment and differs from its surroundings, criminal investigators employ different techniques for locating, recovering, and analyzing clandestine graves. In this study were identified the fungi found in the soil under corpses in decomposition with an aim at relating the copresence of human remains and different fungal species. Were isolated the fungi in three ways: soil washing, serial dilutions, and moist chamber growth. Dichotomomyces cejpii, Talaromyces trachyspermus, Talaromyces flavus, and Talaromyces sp. were the representative species found—with those belonging to the ammonia group, whose fungi are the first in the succession of cadaver decomposition directly in the ground. The mycobiota found at the present study area clearly differs to mycobiota identified in control sample and from previously described species for other areas of Buenos Aires Province, Argentina. Further forensic examples of this type are needed to develop fully the detailed use of mycology as a forensic tool.
A novel resolution independent gradient edge predictor for lossless compression of medical image sequences

ABSTRACT Digital visualization of human body in terms of medical images with high resolution and bit depth generates tremendous amount of data. In the field of medical diagnosis, lossless compression technique is preferred that facilitates efficient archiving and transmission of medical images avoiding false diagnosis. Among various approaches to lossless compression of medical images, predictive coding techniques have high coding efficiency and low complexity. Gradient Edge Detector (GED) used in predictive coding is based on threshold value for prediction and choice of threshold is very important for efficient prediction. However, no specific method is adopted in the literature for threshold value selection. This paper presents an efficient prediction solution targeted at lossless compression of 8 bits and higher bit depth volumetric medical images up to 16 bits. Novelty of the proposed technique is developing Resolution Independent Gradient Edge Predictor (RIGED) algorithm to support 8- and 16-bit depth medical images. Percentage improvement of the proposed model is 30.39% over state-of-the-art Median Edge Detector (MED) and 0.92% over Gradient Adaptive Predictor (GAP) in terms of entropy for medical image dataset of different modalities having different resolutions and bit depths.
Effects of parametric perturbations on the onset of chaos in the Josephson-junction model: Theory and analog experiments.

We propose an analog apparatus simulating a standard Josephson junction, which allows easy experimental manipulations and measurements. We center our attention on the onset of chaotic responses, in particular on its dependence on the different physical parameters, and we obtain quite good agreement with other existing data. Great attention is also paid to compare the results with the theoretical threshold of chaos we deduce from Melnikov's method: The agreement is globally as good as possible, taking into account the approximations and the validity of the method; in particular, we obtain a description of the behavior of the threshold for small frequencies, and of the important role played by the dc bias term. We also discuss, both theoretically and experimentally, the case of a Josephson junction to which a periodic modulating term has been added.
How a Realistic Mathematics Education Approach and Microcomputer-Based Laboratory Worked in Lessons on Graphing at an Indonesian Juniour High School

This study focuses on the applicability of ICT-supported lessons based on a Realistic Mathematics Education (RME) approach in an Indonesian classroom context. The topic chosen for the research experiment was pupils’ graphing skills with emphasis on graph interpretation and with application especially to kinematics. One class was involved in this study and 13 – 14 years old pupils used the specially designed materials and activities. This included the use of motion detectors in pupils’ experimental work. The authors investigated the expectations, performances, and opinions of the pupils and the teacher with respect to the activities and analyzed pupils’ thinking and understanding in the reformed setting. The results of the classroom experiment indicated that the pupils made remarkable progress in their performances that can be attributed to the chosen approach. The pupils’ and the teacher’s opinions on the teaching and learning activities in general also tended to be positive.
Physical Activity in Multiple Sclerosis: A Comparative Study of Vitamin D, Brain-Derived Neurotrophic Factor and Regulatory T Cell Populations

Background: Previous studies suggest beneficial effects of exercise in multiple sclerosis (MS). However, knowledge on the effects of physical activity on the immune system is limited. Objective: To assess potential relationships between cardiorespiratory fitness, cognitive function, and immune parameters in physically active and inactive MS patients. Methods: We identified 83 patients with relapsing-remitting disease, an unrestricted walking range, and stable interferon-β treatment from our data base. Based on the subjective report of physical activity, the lower/inactive (n = 21) and upper/active quartiles (n = 21) of patients were selected. We assessed the frequency of T cells, B cells, NK cells, monocytes and regulatory T cell populations by flow cytometry, measured brain-derived neurotrophic factor and vitamin D serum levels by ELISA, and conducted spiroergometry and transcranial sonography. Results: Physical activity and cardiorespiratory fitness were not associated with brain-derived neurotrophic factor, frequency of T regulatory cells or any other immune cell subpopulation. However, we found a positive correlation of vitamin D serum levels with cardiorespiratory fitness. Conclusion: Overall, we found no negative effect of physical activity on the immune system. The association between vitamin D and cardiorespiratory fitness most likely reflects longer hours of sunlight exposure in active patients, suggesting a desirable ‘side- effect’ of physical activity.
Early parasite containment is decisive for resistance to Leishmania major infection

We investigated the early spread of Leishmania major in various mouse strains. In BALB/c mice, which are extremely vulnerable to L. major infection, the parasites disseminated within 10‐24 h from the site of subcutaneous footpad infection in to the popliteal lymph node, spleen, lung, liver and bone marrow. Application of recombinant (r)IL‐12 prior to infection prevented the early dissemination of parasites into visceral organs and the animals healed the infection. In three mouse strains tested, C57BL/6, CBA/J and C3H/HeJ, which are all resistant to L. major infection, the parasites remained localized in the footpad and in the draining LN for 3 days without evidence of dissemination. In C57BL/6 mice, depletion of NK1.1+ cells or neutralization of interferon (IFN)‐γ prior to infection led to rapid parasite spreading with kinetics similar to those seen in susceptible animals. Depletion of either CD4+ or CD8+ T cells in vivo prior to infection did not alter the kinetics of dissemination in any mouse strain tested. Experiments with severe‐combined immunodeficient mice provided further evidence that parasite containment depends on natural killer cells and IFN‐γ, but is independent of T cells. The finding that all resistant mouse strains restrict the spread of the parasites within the first 24 h after infection strongly suggests that early parasite containment is closely associated with a resistant phenotype. The data show that local restriction of parasites in the pre‐T cell phase of the infection is mediated by the innate immune system and suggest that this function plays an important role in the development of a protective T cell response.
Down syndrome and consanguinity

Background: Among the genetics disorders, Down syndrome (DS) is the major cause of mental retardation, congenital heart and intestinal disease. So far, no certain therapeutic method has been suggested for the treatment of this syndrome. The aim of the current survey was to investigate the frequency of parental consanguinity, maternal age in the patients with DS. Materials and Methods: This study was conducted on 38 consecutive patients with clinically and laboratory confirmed DS who referred to the genetic lab of a referral University Hospital. The G-banding method for karyotyping was employed. Results: The patients were 21 males and 17 females within the age of 16 days to 28 years old. Free trisomy (92.1%, n = 35) was the most common chromosomal abnormality. The frequency of DS was higher among the non-consanguine marriages (71.1%) in comparison with the consanguine marriages (28.9%). Mean age of the mothers in the consanguine marriages (mean = 27.1 ± 6.3) was lower than in the non-consanguine marriages (mean = 31.1 ± 7.7). Conclusion: Higher frequency of DS among the non-consanguine marriages in comparison with the consanguine marriages, may suggest that DS diagnostic tests might be done on all embryos regardless of the parents’ familial relationship.
Change in MS-related disability in a population-based cohort

Objectives: To study the change in disability over 10 years in individual patients constituting the 1991 Olmsted County, MN, multiple sclerosis (MS) prevalence cohort. Methods: The authors reassessed this 1991 cohort in 2001. The authors determined the Expanded Disability Status Scale scores (EDSS) for each patient still alive, and within the year prior to death for those who died. The authors analyzed determinants of potential prognostic significance on change in disability. Results: Follow-up information was available for 161 of 162 patients in the 1991 cohort. Only 15% had received immunomodulatory therapy. The mean change in EDSS for the entire cohort over 10 years was 1 point and 20% worsened by ≥2 points. For patients with EDSS <3 in 1991 (n = 66), 83% were ambulatory without a cane 10 years later. For patients with EDSS of 3 through 5 in 1991 (n = 33), 51% required a cane to ambulate (48%) or worse (3%). For patients with EDSS 6 to 7 in 1991 (n = 39), 51% required a wheelchair or worse in 2001. Gait impairment at onset, progressive disease, or longer duration of disease were associated with more worsening of disability (p < 0.002). The 10-year survival was decreased compared with the Minnesota white population for both men and women. Conclusions: Although survival was reduced and 30% of patients progressed to needing a cane or wheelchair or worse over the 10-year follow-up period, most remained stable or minimally progressed. Patients within the EDSS 3.0 through 5.0 range are at moderate risk of developing important gait limitations over the 10-year period. The authors did not identify factors strongly predictive of worsening disability in this study.
Regulation by transforming growth factor-beta 1 of G1 cyclin-dependent kinases in human retinal epithelial cells.

Transforming growth factor beta (TGFbeta) is a potent inhibitor of epithelial cell proliferation, delaying or arresting cell cycle progression in mid-late G1. In long-term life span cells this growth inhibitory action has been attributed to regulatory events on both the levels and activities of G1 cyclin-dependent kinases (CDKs). CDK inhibitors have been shown to play important role in the TGFbeta-induced inhibition of G1 CDKs. In this work, we have investigated the effect of TGFbeta1 on both cell proliferation and G1 CDK activities in primary cultures of human retinal pigment epithelial (RPE) cells. We show that TGFbeta1 exerts a partial inhibitory effect on RPE cell proliferation by causing a significant increase of the RPE cell number in G1. TGFbeta1 induces an up-regulation of the CDK inhibitor p15(INK4B)with its subsequent association to CDK4, and a decline in CDK4 protein level. In parallel, we have observed a decline of p27(KIP1)associated to CDK4 and a significant increase of the inhibitor associated to CDK2. Finally, we show that TGFbeta1 reduces both CDK4 and CDK2 enzymatic activities. The fact that TGFbeta exerts only partial inhibitions on G1 CDKs and cell cycle progression in RPE cells suggests a propensity of these cells to escape from the anti-proliferative action of the cytokine, a phenomenon which could be reinforced during the development of proliferative vitreoretinopathy.
Sublethal effects of diflovidazin on demographic parameters of the predatory mite, Neoseiulus californicus (Acari: Phytoseiidae)

ABSTRACT The present study ﬁrst evaluated the sublethal eﬀects of diﬂovidazin (Flumite®) with three concentrations (LC5, LC10, and LC20) on life table parameters of Neoseiulus californicus (McGregor) (Acari: Phytoseiidae), as an eﬀective predator of Tetranychus urticae (Koch) (Acari: Tetranychidae). Experimental results indicated that exposure to the sublethal concentrations of diﬂovidazin, has no signiﬁcant eﬀect on the development time of the treated mite oﬀspring. Diﬂovidazin treatments gradually reduced the longevity and total life span of both sexes. The highest fecundity was observed in the control treatment (35.31 oﬀspring/female), while the lowest was related to the LC20 concentration. However, the eﬀects of diﬀerent treatments on intrinsic (r), as well as ﬁnite rate of increase (λ) of this predator were insigniﬁcant. The r value, ranged from 0.2112 to 0.1989 day−1 for the mites treated with distilled water and the LC20 concentration, respectively. Furthermore, λ was not aﬀected by enhancing the concentration, as the values were 1.2401 and 1.2205 day−1 for the mites treated with control and LC20, respectively. Those treated with LC20 had a signiﬁcantly reduced R0, compared to those treated with control only. Thereby, the sublethal eﬀects of diﬂovidazin in combination with N. californicus were emphasized for designing management programs of T. urticae.
Characterization of adrenal lesions with 1.5-T MRI: preliminary observations on comparison of three in-phase and out-of-phase gradient-echo techniques.

OBJECTIVE The purpose of this study was to use previously described quantitative evaluation methods to compare the performance of 3D gradient-recalled echo (GRE) and magnetization-prepared (MP) GRE in-phase and out-of phase sequences with standard 2D GRE technique in the characterization of adrenal lesions. MATERIALS AND METHODS The study sample consisted of 44 consecutively registered patients (22 men, 22 women; mean age, 59.1 ± 11.6 years) with 50 adrenal lesions who underwent standard abdominal MRI that included in-phase and out-of-phase 2D GRE (n = 41), 3D GRE (n = 35), MP GRE (n = 36), or a combination of these techniques. The adrenal signal intensity (SI) index and adrenal-to-spleen, adrenal-to-liver, and adrenal-to-muscle SI ratios of each lesion were calculated and compared for the three techniques by independent samples Student t test. The area under the receiver operating characteristic (ROC) curve (AUC) for each evaluation method was determined, and comparisons of independent ROC curves were performed for all sequences. RESULTS For all sequences, the mean adrenal SI index and SI ratios of adenomas and nonadenomas differed significantly (p < 0.001). For the 3D GRE and MP GRE techniques, adrenal SI index and modified adrenal-to-spleen ratio, respectively, had the larger AUCs, but the difference was not statistically significant. Different thresholds for the three techniques were recommended for discriminating adenoma from nonadenoma. CONCLUSION The results of characterization of adrenal lesions with MP GRE and 3D GRE in-phase and out-of-phase MRI techniques are comparable to those obtained with the reference standard 2D GRE technique. Different thresholds should be selected according to the in-phase and out-of-phase techniques used and for the various evaluation methods.
Association between tuberculosis and atopy: role of the CD14-159C/T polymorphism.

BACKGROUND The development of allergic hypersensitivity depends on both genetic and environmental factors. Different amounts of microbial products could affect patients with atopy and different genotypes. OBJECTIVE We aimed to evaluate the role of varying degrees of exposure to infection by Mycobacterium tuberculosis (tuberculosis) in atopic patients and analyze the association with genetic factors. METHODS We performed CD14-159C/T genotyping in atopic patients (n=118) and healthy individuals (n=62) and recorded the following variables: rural lifestyle, exposure to persons with tuberculosis, bacille Calmette-Guerin (BCG) vaccination, tuberculin skin test (TST), skin prick test, and phenotypes of atopy. Blood samples were analyzed for soluble-CD14 (sCD14), interferon (IFN) y, total immunoglobulin (Ig) E, and eosinophil levels. A score was used to identify the likelihood of exposure to tuberculosis. RESULTS Almost all the study participants had had a BCG vaccination, and half had a positive TST result. No differences were observed between atopic patients with high/low tuberculosis scores and CD14 genotypes in terms of atopic phenotypes, allergen sensitization, and levels of total IgE, sCD14, and IFN-y. However, the frequency of asthma was higher in atopic patients with a high tuberculosis score and was not associated with CD14 genotypes. Eosinophil counts in blood were higher in atopic patients with a high tuberculosis score and CC+CT genotypes. CONCLUSIONS These results suggest that the C allele of the CD14-159C/T polymorphism has a marked effect on eosinophil levels in atopic patients with increased exposure to tuberculosis. In addition, the degree of exposure to tuberculosis in atopic patients may modify the development of asthma.
Ethanol production from paper sludge by simultaneous saccharification and co‐fermentation using recombinant xylose‐fermenting microorganisms

Simultaneous saccharification and co‐fermentation (SSCF) of waste paper sludge to ethanol was investigated using two recombinant xylose‐fermenting microbes: Zymomonas mobilis 8b and Saccharomyces cerevisiae RWB222. S. cerevisiae RWB222 produced over 40 g/L ethanol with a yield of 0.39 g ethanol/g carbohydrate on paper sludge at 37°C, while similar titers and yields were achieved by Z. mobilis 8b at 30°C. Both S. cerevisiae RWB222 and Z. mobilis 8b exhibited decreasing cell viability at 37°C when producing over 40 g/L ethanol. A high ethanol concentration can account for S. cerevisiae RWB222 viability loss, but ethanol concentration was not the only factor influencing Z. mobilis 8b viability loss at 37°C. Over 3 g/L residual glucose was observed at the end of paper sludge SSCF by Z. mobilis 8b, and a statistical analysis revealed that a high calcium concentration originating from paper sludge, a high ethanol concentration, and a high temperature were the key interactive factors resulting in glucose accumulation. The highest ethanol yields were achieved by SSCF of paper sludge with S. cerevisiae RWB222 at 37°C and Z. mobilis 8b at 30°C. With good sugar consumption at 37°C, S. cerevisiae RWB222 was able to gain an improvement in the polysaccharide to sugar yield compared to that at 30°C, whereas Z. mobilis 8b at 30°C had a lower polysaccharide to sugar yield, but a higher sugar to ethanol yield than S. cerevisiae. Both organisms under optimal conditions achieved a 19% higher overall conversion of paper sludge to ethanol than the non‐xylose utilizing S. cerevisiae D5A at its optimal process temperature of 37°C. Biotechnol. Bioeng. 2010;107: 235–244. © 2010 Wiley Periodicals, Inc.