Miracle-dz/UniFAR-FTUs huggingface dataset:
Characterization of Ancestral Mycobacterium tuberculosis by Multiple Genetic Markers and Proposal of Genotyping Strategy

ABSTRACT Sixty-eight ancestral Mycobacterium tuberculosis isolates were previously identified by using the tuberculosis-specific deletion 1 (TbD1) PCR and mycobacterial interspersed-repetitive-unit-variable-number tandem repeat (MIRU-VNTR) typing (Y. J. Sun, R. Bellamy, A. S. G. Lee, S. T. Ng, S. Ravindran, S.-Y. Wong, C. Locht, P. Supply, and N. I. Paton, J. Clin. Microbiol. 42:1986-1993, 2004). These TbD1+ ancestral isolates were further characterized and typed in this study by IS6110 restriction fragment length polymorphism (RFLP) typing, VNTR typing using exact tandem repeats (VNTR-ETR), and spoligotyping of the direct-repeat region. To our knowledge, this is the first characterization of this genogroup by multiple genetic markers based on a fairly large sample size. In this genogroup, all spoligotypes were characterized by the absence of spacers 29 to 32 and 34. In addition, VNTR-ETR typing could add further resolution to the clustered isolates identified by MIRU-VNTR, and the combination of MIRU-VNTR and VNTR-ETR, called MIRU-ETR, showed the highest discriminatory power for these strains compared to IS6110 RFLP typing and spoligotyping alone. However, MIRU-ETR appeared to still cluster some probably epidemiologically unrelated strains, as judged by IS6110 RFLP divergence. Therefore, a typing strategy based on stepwise combination of MIRU-ETR and IS6110 RFLP is proposed to achieve maximal discrimination for unrelated TbD1+ strains. This typing strategy may be useful in areas where TbD1+ ancestral strains are prevalent.
Pathogenic activity of circulating anti-desmoglein-3 autoantibodies isolated from pemphigus vulgaris patients

Introduction There are scarce data on immunochemical properties of pemphigus antibodies detected in clinical remission in pemphigus vulgaris (PV) patients. The aim of the study was to compare biological activity of anti-Dsg3 autoantibodies purified from the sera of PV patients in active stage and in clinical remission. Material and methods The effect of purified antibodies on expression of procaspase-3, Bax, Bcl-2, uPAR, IL-1β, IL-6, and TNF-α mRNAs in the HaCaT keratinocytes was evaluated by Western blot and RT-PCR method. Results Incubation of HaCaT cells with anti-Dsg-3 autoantibodies caused their binding to cell membranes surfaces. Anti-Dsg3 autoantibodies isolated from the patients in active stage and clinical remission showed proapoptotic effect, caused enhanced expression of analyzed proinflammatory cytokines’ mRNAs and uPAR mRNA. Conclusions Our data revealed similar pathogenic activity of anti Dsg-3 autoantibodies isolated from active and clinical remission PV patients.
Cyclosporine A and pentosan polysulfate sodium for the treatment of interstitial cystitis: a randomized comparative study.

PURPOSE In a previous retrospective analysis, cyclosporine A (CyA) was highly efficient in treating patients with interstitial cystitis. A prospective randomized study with this immunosuppressive agent was warranted. We compared CyA to pentosan polysulfate sodium (PPS) in patients with interstitial cystitis. MATERIALS AND METHODS A total of 64 patients with interstitial cystitis meeting the National Institute of Diabetes and Digestive and Kidney Diseases criteria were enrolled in a randomized prospective study. Patients were randomized in a 1:1 ratio to 1.5 mg/kg CyA twice daily (27 women, 5 men) or 100 mg PPS 3 times daily (26 women, 6 men) for a period of 6 months. The primary end point was daily micturition frequency, and secondary end points were mean and maximal voided volume, number of nocturia episodes, O'Leary-Sant symptom and problem indexes, visual analogue scale for pain, and subjective global response assessment. RESULTS CyA was superior to PPS in all clinical outcome parameters measured at 6 months. Micturition frequency in 24 hours was significantly reduced in the CyA arm compared to the PPS arm (-6.7 +/- 4.7 vs -2.0 +/- 5.1 times). The clinical response rate (according to global response assessment) was 75% for CyA compared to 19% for PPS (p <0.001). Although there were more adverse events in the CyA arm than in the PPS arm, 29 patients completed the 6-month followup in both groups. CONCLUSIONS CyA is more effective than PPS in interstitial cystitis.
Russian Error-Annotated Learner English Corpus: a Tool for Computer-Assisted Language Learning

The paper describes the learner corpus composed of English essays written by native Russian speakers. REALEC (Russian Error-Annotated Learner English Corpus) is an error-annotated, available online corpus, now containing more than 200 thousand word tokens in almost 800 essays. It is one of the first Russian ESL corpora, dynamically developing and striving to improve both in size and in features offered to users. We describe our perspective on the corpus, data sources and tools used in compiling it. Elaborate self-made classification of learners’ errors types is thoroughly described. The paper also presents a pilot experiment on creating test sets for particular learners’ problems using corpus data.
Adaptations in endocannabinoid signaling in response to repeated homotypic stress: a novel mechanism for stress habituation

Daily life stressors are a major environmental factor contributing to precipitation and exacerbation of mental illness. Animal models using repeated homotypic stress induce anxious and depressive phenotypes and are used to study the pathophysiology of affective disorders. Here we discuss data demonstrating that repeated homotypic stress produces temporally and anatomically distinct changes in endocannabinoid signaling components within stress‐responsive brain regions. We also present evidence describing the neural and behavioral correlates of these adaptations in endocannabinoid signaling. These data support a role for endocannabinoid signaling in the central nervous system response to chronic, homotypic stress, and specifically in the process of stress–response habituation. The clinical implications of these findings for the pathophysiology and treatment of affective disorders are discussed.
Average Frobenius distributions for elliptic curves with nontrivial rational torsion

In this paper we consider the Lang-Trotter conjecture (Conjecture 1 below) for various families of elliptic curves with prescribed torsion structure. We prove that the Lang-Trotter conjecture holds in an average sense for these families of curves (see Theorem 3). Let E/Q denote an elliptic curve and let ∆E denote its discriminant. As usual, let ap(E) = p + 1 − #E(Fp). Then we have the following conjecture of Lang and Trotter [10].
Converting context to indoor position using built-in smartphone sensors

This paper describes the work in progress of converting context to indoor position using built-in smartphone sensors. This research will ultimately contribute towards a self-sufficient indoor positioning system that works without any interaction with a pre-deployed communication infrastructure. Such selfsufficiency is desired from several points of view. It makes the system more scalable, privacy-preserving (no communication means less chances of privacy leakage), and energy-efficient (radio interfaces consume orders of magnitude more energy than MEMS sensors, such as accelerometers).
Rolling Rod Electrostatic Microgenerator

The difficulty of maximizing the proof mass, and lack of broadband operation, are key issues for miniaturized energy-harvesting devices. Here, a novel electrostatic energy harvester is presented, employing an external free-rolling proof mass to address these issues. A description of the operating principle is given, and the kinetic dynamics of the cylinder are analyzed. The electrostatics of the system are simulated, identifying the device performance for different dielectric dimensions and surface specifications. The fabrication of a prototype device is presented, and physical characterization results demonstrate a successful fabrication technique for dielectric sizes down to 100 nm. Capacitance measurements reveal a capacitance ratio of 4 and are in agreement with simulation results. A voltage gain of 2.4 is demonstrated. The device is suitable for energy harvesting from low-frequency high-amplitude ambient motion sources such as the human body.
Discovery learning in computer science

INTRODUCTION Teaching things to oneself, in order to solve one’s own problems, is an incredibly effective way of learning. Discovery learning is any process in which instructors create oruse situationsin which students will learn some body of knowledge through such self-teaching. A simple example of discovery learning could be a project in which students are given some goal to reach, but not a cut-anddried means of reaching the goal – instead, they are left to find their own way to the goal, through library research, forming and asking pertinent questions of an expert, independent invention, et cetera.
Underrecognized Arthropod-Borne and Zoonotic Pathogens in Northern and Northwestern Thailand: Serological Evidence and Opportunities for Awareness

Abstract Although scrub typhus and murine typhus are well-described tropical rickettsial illnesses, especially in Southeast Asia, only limited evidence is available for rickettsia-like pathogens contributing to the burden of undifferentiated febrile illness. Using commercially available kits, this study measured immunoglobulin G (IgG) antibody seroprevalence for Coxiella burnetii, Ehrlichia chaffeensis, Bartonella henselae, Anaplasma phagocytophilum, and spotted fever group rickettsiae (SFGR) in 375 patients enrolled in undifferentiated febrile illness studies at Chiangrai (northern Thailand) and Mae Sot (Thai–Myanmar border). Ehrlichia and SFGR were the most common causes of IgG seropositivity. A distinct relationship between age and seropositivity was found in Chiangrai with acquisition of IgG titers against Ehrlichia, Bartonella, Anaplasma, and SFGR in young adulthood, suggesting cumulative exposure to these pathogens. At Mae Sot, high early IgG titers against Ehrlichia and SFGR were common, whereas Anaplasma and Bartonella IgG titers increased at 50–60 years. Q fever associated with low IgG positivity at both study sites, with significantly higher prevalence at 30 years of age in Chiangrai. These data suggest that other rickettsial illnesses could contribute to the burden of febrile illness in Thailand and possibly adjacent regions. Improved diagnostics and better understanding of antibody longevity and cross-reactivity will improve identification and management of these easily treatable infectious diseases.
BID is a Critical Factor Controlling Cell Viability Regulated by IFN-&agr;

Clinical applications of human interferon (IFN)-&agr; have met with varying degrees of success. Nevertheless, key molecules in cell viability regulated by IFN-&agr; have not been clearly identified. Our previous study indicated that IFN (&agr;, &bgr;, and &ohgr;) receptor (IFNAR) 1/2- and IFN regulatory factor 9-RNA interference (RNAi) completely restored cell viability after IFN-&agr; treatment in human ovarian adenocarcinoma OVCAR3 cells sensitive to IFN-&agr;. In this study, IFNAR1/2- and IFN regulatory factor 9-RNAi inhibited the gene expression of tumor necrosis factor-related apoptosis-inducing ligand (TRAIL), but not of Fas ligand, after IFN-&agr; treatment. In fact, TRAIL but not Fas ligand inhibited the viability of OVCAR3 cells. IFN-&agr; notably upregulated the levels of TRAIL protein in the supernatant and on the membrane of OVCAR3 cells. After TRAIL signaling, caspase 8 inhibitor and BH3 interacting domain death agonist (BID)-RNAi significantly restored cell viability in response to IFN-&agr; and TRAIL in OVCAR3 cells. Furthermore, BID-RNAi prevented both IFN-&agr; and TRAIL from collapsing the mitochondrial membrane potential (&Dgr;&PSgr;m). Finally, we provided important evidence that BID overexpression led to significant inhibition of cell viability after IFN-&agr; or TRAIL treatments in human lung carcinoma A549 cells resistant to IFN-&agr;. Thus, this study suggests that BID is crucial for cell viability regulated by IFN-&agr; which can induce mitochondria-mediated apoptosis, indicating a notable potential to be a targeted therapy for IFN-&agr; resistant tumors.
Ventricular Fibrosis Suggested by Cardiovascular Magnetic Resonance in Adults With Repaired Tetralogy of Fallot and Its Relationship to Adverse Markers of Clinical Outcome

Background— Late morbidity and mortality remain problematic after repair of tetralogy of Fallot (TOF). We hypothesized that fibrosis detected by late gadolinium enhancement (LGE) cardiovascular magnetic resonance (CMR) would be present in adults with repaired TOF and would be related to adverse markers of outcome. Method and Results— LGE was scored in the right and left ventricles (RV and LV) of 92 adult patients who had undergone TOF repair. RV LGE was seen in all patients at surgical sites located in the outflow tract (99%) or the site of ventricular septal defect patching (98%) and in the inferior RV insertion point (79%) and trabeculated myocardium (24%). LV LGE (53%) was located at the apex consistent with apical vent insertion (49%), in the inferior or lateral wall consistent with infarction (5%), or in other areas (8%). Patients with supramedian RV LGE score were older (38 versus 27 years, P<0.001) and more symptomatic (38% versus 8% in New York Heart Association class II or greater, P=0.001), had increased levels of atrial natriuretic peptide (7.3 versus 4.9 pmol/L, P=0.041), and had a trend to higher brain natriuretic peptide (12.3 versus 7.2 pmol/L, P=0.086), exercise intolerance (maximum &OV0312;o2 24 versus 28 mL · min−1 · kg−1, P=0.021), RV dysfunction (RV end-systolic volume 61 versus 55 mL/m2, P=0.018; RV ejection fraction 50% versus 56%, P=0.007), and clinical arrhythmia (26% versus 10%, P=0.039). Non–apical vent LV LGE also correlated with markers of adverse outcome. In a multivariate model, RV LGE remained a predictor of arrhythmia. Conclusions— RV and LV LGE were common after TOF repair and were related to adverse clinical markers, including ventricular dysfunction, exercise intolerance, and neurohormonal activation. Furthermore, RV LGE was significantly associated with clinical arrhythmia.
Pen computing for air traffic control

Modernizing workstations for air traffic controllers is a challenge: designers must increase efficiency without affecting safety in any way. Air traffic control is a time-intensive and safety-critical activity, and thus interaction efficiency and low error rates are crucial. Classical interaction techniques have been used in prototype workstations, but the resulting efficiency is not always satisfactory. This leads designers to consider more advanced interaction techniques. This paper reports on the design and a preliminary evaluation of the first prototype of project IMAGINE, which represents the second generation of graphical interfaces for air traffic control. This prototype, GRIGRI, uses a high resolution touch screen and provides mark based input through the screen. The use of gestures, as well as the use of multi-modal techniques, make interaction faster, and closer to the controllers’ habits.
Estimating Fetal and Maternal Genetic Contributions to Premature Birth From Multiparous Pregnancy Histories of Twins Using MCMC and Maximum-Likelihood Approaches

Abstract The analysis of genetic and environmental contributions to preterm birth is not straightforward in family studies, as etiology could involve both maternal and fetal genes. Markov Chain Monte Carlo (MCMC) methods are presented as a flexible approach for defining user-specified covariance structures to handle multiple random effects and hierarchical dependencies inherent in children of twin (COT) studies of pregnancy outcomes. The proposed method is easily modified to allow for the study of gestational age as a continuous trait and as a binary outcome reflecting the presence or absence of preterm birth. Estimation of fetal and maternal genetic factors and the effect of the environment are demonstrated using MCMC methods implemented in WinBUGS and maximum likelihood methods in a Virginia COT sample comprising 7,061 births. In summary, although the contribution of maternal and fetal genetic factors was supported using both outcomes, additional births and/or extended relationships are required to precisely estimate both genetic effects simultaneously. We anticipate the flexibility of MCMC methods to handle increasingly complex models to be of particular relevance for the study of birth outcomes.
Jumps in Financial Markets: A New Nonparametric Test and Jump Dynamics

This article introduces a new nonparametric test to detect jump arrival times and realized jump sizes in asset prices up to the intra-day level. We demonstrate that the likelihood of misclassification of jumps becomes negligible when we use high-frequency returns. Using our test, we examine jump dynamics and their distributions in the U.S. equity markets. The results show that individual stock jumps are associated with prescheduled earnings announcements and other company-specific news events. Additionally, S&P 500 Index jumps are associated with general market news announcements. This suggests different pricing models for individual equity options versus index options. The Author 2007. Published by Oxford University Press on behalf of The Society for Financial Studies. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org. , Oxford University Press.
Did You Notice It?—How Can We Predict the Subjective Detection of Video Quality Changes From Eye Movements?

In the case of videos, the measurement of subjective detection of quality degradation usually needs observers to report the detection. However, if this detection could be automatically deduced by nonintrusive means, viewing would not be disturbed. This study examined how the subjective detection of quality degradation can be seen from eye movements, both in terms of group averages as well as from cases of single viewing times. In the experiment, the subjects were given the task of detecting local quality degradation in a video and reporting its significance to the quality of a video. The results of group averages showed that detection of the degraded area changed the viewing strategy from a search with short fixation to an evaluation with long fixations; most importantly, once the evaluation phase had begun, fixations concentrated on a smaller area than in the search phase. The change in eye movements was due to detection and not the quality level. The change in task was also seen in the eye movement measurements from single viewings, the spatial entropy of fixations being the best predictor of subjective detection, with a prediction accuracy rate of 78%. The combination of a temporal change in saccade amplitude and fixation duration averages also predicted detection in single viewing cases, with an accuracy of 68% The study discusses the use of eye movement measurements in video quality estimation and demonstrates that it is possible to predict subjective perception based on the stage of the task.
Reading optimally builds on spoken language: implications for deaf readers.

Reading is not merely "language by eye. " Rather, it builds fundamentally on primary language processes. For hearing readers, this means that spoken language processes, including phonological processes, are critical to high achievement in reading. We examine the implications of this fact for deaf readers by considering the relationship between language and reading and by reviewing the research on the use of phonology by deaf readers. The research, although mixed in its results, suggests that the use of phonology is associated with higher levels of reading skill among deaf readers. We examine related questions, including the additional semantic and visual strategies available to deaf readers, how some deaf readers gain access to the spoken structure of language, and implications for how to improve reading achievement.
Effect of Beta-Blockers on Number of Osteoblasts and Osteoclasts in Alveolar Socket Following Tooth Extraction in Wistar Rats

Statement of the Problem: Various researchers have suggested the use of β2-adrenergic receptor antagonists in prevention or treatment of bone resorption. Purpose: This study aimed to evaluate the effect of β2-adrenergic receptor antagonists on number of osteoclasts and osteoblasts involved in the healing of extraction socket of maxillary first molar in rats. Materials and Method: Maxillary first molars of 40 rats were extracted and divided into two groups. The test group received 0.1 mg/kg propranolol intraperitoneally daily. The controls received normal saline. At days 7, 14, 21 and 28 post-extraction, 5 rats were euthanized from each group. Maxillary bone was resected and the mean number of osteoblasts and osteoclasts in tooth socket was measured. Results: After 1 week, the number of osteoclasts in the controls was significantly higher than the test group. A significant increase in the number of osteoclasts in both groups at week 1 was observed compared to the following weeks (p< 0.05). The number of osteoblasts in the controls at second week reached its maximum rate but stayed constant in the 3rd and 4th weeks. Osteoblasts in the test group increased similar to the controls but reached its maximum at 3rd week and showed a significant increase compared to the controls (p< 0.05). Conclusion: β2 adrenergic receptor antagonists decrease the number of osteoclasts and increase the number of osteoblasts during extraction socket healing.
Demodulation-Oriented Automatic Modulation Identification Algorithm

This paper presents a novel automatic modulation identification (AMI) algorithm, named demodulation-oriented automatic modulation identification (DAMI) algorithm, in software radios. DAMI algorithm may identify each modulated signal with a subset rather than one-to-one scheme because any scheme of a subset can employ the same demodulation algorithm. Aiming at AM, SSB, DSB, FM, OOK, PSK, QPSK, FSK, MSK and GMSK, the developed algorithm was simulated in the AWGN, Rician and Rummler channel, respectively. Simulation results showed that on condition of SNR of 15 dB DAMI algorithm's average running time decreased by 34.6% and its average correct identification rate increased by 7.0% at least in comparison with those of the ordinary automatic modulation identification (OAMI) algorithm. The DAMI algorithm takes on the main remarkable features of tolerable errors, and improved correct identification rate, and decreased identification time. Because of the software Radios' specialties, DAMI algorithm is perfectly suitable for software radios.