Miracle-dz/UniFAR-FTUs huggingface dataset:
Influenza genome analysis using pyrosequencing method: current applications for a moving target

Pyrosequencing is a high-throughput non-gel-based DNA sequencing method that was introduced in the late 1990s. It employs a DNA sequencing-by-synthesis approach based on real-time measurement of pyrophosphate released from incorporation of dNTPs. A cascade of enzymatic reactions proportionally converts the pyrophosphate to a light signal recorded in a form of peaks, known as pyrograms. Routinely, a 45–60-nucleotide sequence is obtained per reaction. Recent improvements introduced in the assay chemistry have extended the read to approximately 100 nucleotides. Since its advent, pyrosequencing has been applied in the fields of microbiology, molecular biology and pharmacogenomics. The pyrosequencing approach was first applied to analysis of influenza genome in 2005, when it played a critical role in the timely detection of an unprecedented rise in resistance to the adamantane class of anti-influenza drugs. More recently, pyrosequencing was successfully applied for monitoring the emergence and spread of influenza A (H1N1) virus resistance to oseltamivir, a newer anti-influenza drug. The present report summarizes known applications of the pyrosequencing approach for influenza genome analysis with an emphasis on drug-resistance detection.
Testing the FMR1 Promoter for Mosaicism in DNA Methylation among CpG Sites, Strands, and Cells in FMR1-Expressing Males with Fragile X Syndrome

Variability among individuals in the severity of fragile X syndrome (FXS) is influenced by epigenetic methylation mosaicism, which may also be common in other complex disorders. The epigenetic signal of dense promoter DNA methylation is usually associated with gene silencing, as was initially reported for FMR1 alleles in individuals with FXS. A paradox arose when significant levels of FMR1 mRNA were reported for some males with FXS who had been reported to have predominately methylated alleles. We have used hairpin-bisufite PCR, validated with molecular batch-stamps and barcodes, to collect and assess double-stranded DNA methylation patterns from these previously studied males. These patterns enable us to distinguish among three possible forms of methylation mosaicism, any one of which could explain FMR1 expression in these males. Our data indicate that cryptic inter-cell mosaicism in DNA methylation can account for the presence of FMR1 mRNA in some individuals with FXS.
Comparison of refractive errors and factors associated with spectacle use in a rural and urban South Indian population

Purpose: To compare the prevalence of refractive errors and factors associated with spectacle use in a rural and urban south Indian population. Materials and Methods: Four thousand eight hundred subjects (age >39 years) each from rural and urban Tamil Nadu were enumerated for a population-based study. All participants underwent a complete ophthalmic evaluation including best-corrected visual acuity (BCVA), objective and subjective refraction. Out of 3924 rural responders 63.91% and out of 3850 urban responders 81.64% were phakic in the right eye with BCVA of 20/40 or better and were included in the study. Association of spectacle use and refractive errors with different parameters were analysed using logistic regression. Statistical Analysis: Chi square, t test, Chi square for trend and Pearson′s correlation coefficient were used for analysis. Results: Spectacle use was significantly higher and positively associated with literacy and employment in the urban population. The age and gender-adjusted prevalence of emmetropia, myopia of spherical equivalent (SE) ≤-0.50 diopter sphere (DS), high myopia (SE ≤-5.00DS), hyperopia (SE >0.50DS) and astigmatism ≤ 0.50 diopter cylinder (DC) were 46.8%, 31.0%, 4.3%, 17.9% and 60.4% respectively in the rural population and 29.0%, 17.6%, 1.5%, 51.9%, 59.1% respectively in the urban population. The prevalence of emmetropia decreased with age (p < 0.001); prevalence of myopia and high myopia increased with age (p = 0.001) and were associated with nuclear sclerosis (p = 0.001) in both populations. Hyperopia was commoner among women than men (p = 0.001); was positively associated with diabetes mellitus (p = 0.008) in the rural population and negatively with nuclear sclerosis (p = 0.001) in both populations. Conclusion: Spectacle use was found to be significantly lower in the rural population. The pattern of refractive errors was significantly different between both populations.
Metacognitive theory and assessment in dementia: Do we recognize our areas of weakness?

Anosognosia, disordered awareness of cognitive and behavioral deficits, is a striking and common symptom of Alzheimer's disease (AD), yet its etiology, clinical correlates, and prognostic value are unclear. Historically, disordered awareness has been a conceptually challenging phenomenon, evidenced by the numerous and diverse theories that aim to explain the manner in which this syndrome arises. We review many of these theories, focusing on the neuroanatomic substrates of awareness, and highlighting the potential roles of critical regions such as the right prefrontal and parietal cortices in enabling self-awareness. We then address methodological limitations such as use of subjective measurement tools that likely contribute to the conceptual ambiguity surrounding anosognosia. We argue that metacognitive techniques used in healthy adults, such as the Feeling of Knowing task, offer models for dissecting awareness into clear and identifiable cognitive components in patients with AD. We critique several studies that have pioneered such tasks in AD, and offer guidelines for future implementation of such methods. A final goal of this review is to advocate for a multidimensional approach to studying metacognitive skills that will facilitate the objective investigation of deficit awareness as it relates to a variety of disease variables such as prognosis, neuropsychological profile, neuropathological distribution, psychiatric symptoms, and clinical course. (JINS, 2005, 11, 910–919.)
Drawing boundaries: using individual evolved class boundaries for binary classification problems

This paper describes a technique which can be used with Genetic Programming (GP) to reduce implicit bias in binary classification tasks. Arbitrarily chosen class boundaries can introduce bias, but if individuals can choose their own boundaries, tailored to their function set, then their outputs are automatically scaled into a suitable range. These boundaries evolve over time as the individuals adapt to the data. Our system calculates the Evolved Class Boundary(ECB) for each individual in every generation, with the twin aims of reducing training times and improving test fitness. The method is tested on three benchmark binary classification data sets from the medical domain. The results obtained suggest that the strategy can improve training, validation and test fitness, and can also result in smaller individuals as well as reduced training times. Our approach is compared with a standard benchmark GP system, as well as with over twenty other systems from the literature, many of which use highly tuned, non-EC methods, and is shown to yield superior results in many cases.
On temperature dependence of deformation mechanism and the brittle–ductile transition in semiconductors

Recent deformation experiments on semiconductors have shown the occurrence of a break in the variation of the critical resolved shear stress of the crystal as a function of temperature. These and many other examples in the literature evidence a critical temperature at which a transition occurs in the deformation mechanism of the crystal. In this paper, the occurrence of a similar transition in two polytypes of SiC is reported and correlated to the microstructure of the deformed crystals investigated by transmission electron microscopy, which shows evidence for partial dislocations carrying the deformation at high stresses and low temperatures. Based on these results and data in the literature, the explanation is generalized to other semiconductors and a possible relationship to their brittle–ductile transition is proposed.
Quasi-Static Models Based on Artificial Neural Neworks for Calculating the Characteristic Parameters of Multilayer Cylindrical Coplanar Waveguide and Strip Line

In this paper, two different neural models are proposed for calculating the quasi-static parameters of multilayer cylindrical coplanar waveguides and strip lines. These models were basically developed by training the artificial neural networks with the numerical results of quasi-static analysis. Neural models were trained with four different learning algorithms to obtain better performance and faster convergence with simpler structure. When the performances of neural models are compared with each other, the best test results are obtained from the multilayered perceptrons trained by the Levenberg- Marquardt algorithm. The results obtained from the neural models are in very good agreements with the theoretical results available in the literature.
Exploring differences in response to treatment with peginterferon alpha 2a (40kD) and ribavirin in chronic hepatitis C between genotypes 2 and 3

Summary. Chronic hepatitis C virus (HCV) infections with genotype 2 or 3 are associated with favourable sustained virologic response (SVR) rates. However, genotype 3 may respond less well. We reassessed all treatment‐naive patients with genotype 2 and 3 participating in a large expanded‐access, non‐randomized, open‐label trial, evaluating 180μg pegylated interferon (peg‐IFN) alpha‐2a (40kD) once weekly and 800 mg/day ribavirin for 24–48 weeks. Factors measured prior to initiation of antiviral therapy were considered in the multiple logistic regression model for predicting SVR. In total, 180 patients were analysed of which 72 (40%) were infected by genotype 2 and 108 (60%) genotype 3. The baseline characteristics between patients infected by genotype 2 or 3 were no different including the distribution of hepatic fibrosis stages by METAVIR score. Overall SVR was lower in those patients infected with genotype 3. The significant multivariate predictors of lack of SVR were hepatic fibrosis (P = 0.014) and genotype 3 (P = 0.030). The negative impact of cirrhosis (METAVIR score F4) on treatment response was more evident among subjects with genotype 3 than those with genotype 2 (P = 0.027). There is significant interaction between cirrhosis and genotype 3 leading to a poor antiviral response in such patients requiring an alternate management strategy. This finding should be confirmed in a larger population.
A Fast Re-scoring Strategy to Capture Long-Distance Dependencies

A re-scoring strategy is proposed that makes it feasible to capture more long-distance dependencies in the natural language. Two pass strategies have become popular in a number of recognition tasks such as ASR (automatic speech recognition), MT (machine translation) and OCR (optical character recognition). The first pass typically applies a weak language model (n-grams) to a lattice and the second pass applies a stronger language model to N best lists. The stronger language model is intended to capture more long-distance dependencies. The proposed method uses RNN-LM (recurrent neural network language model), which is a long span LM, to re-score word lattices in the second pass. A hill climbing method (iterative decoding) is proposed to search over islands of confusability in the word lattice. An evaluation based on Broadcast News shows speedups of 20 over basic N best re-scoring, and word error rate reduction of 8% (relative) on a highly competitive setup.
Mitochondrial Dna Depletion in HIV-Infected Patients is More Pronounced with Chronic Hepatitis C and Enhanced following Treatment with Pegylated Interferon plus Ribavirin

Background Mitochondrial DNA (mtDNA) damage seems to be responsible for many of the toxicities associated with the long-term use of nucleoside analogues in HIV-infected patients. These adverse effects, mainly lipoatrophy, seem to be even more pronounced in subjects with hepatitis C virus (HCV) co-infection. However, there is no information about a possible additive effect of HCV on mtDNA depletion nor about the impact of ribavirin use in HIV/HCV-coinfected individuals. Patients and methods mtDNA was measured in peripheral blood mononuclear cells (PBMC) collected from 192 individuals classified into 4 groups: HIV-neg/HCV-neg (control group, n=11), HIV-pos/HCV-neg (56), HIV-neg/HCV-pos (18) and HIV-pos/HCV-pos (107). A duplex real-time NASBA assay was used to quantify mtDNA on maximal platelet-depleted specimens and all experiments were run in duplicate. The mtDNA copy number per cell was estimated taking as reference the nuclear DNA copy number. Results The mean mtDNA values in the control group was 757 copies/cell, while it was 428, 349 and 296 for HIV-pos, HCV-pos and HIV/HCV-coinfected individuals, respectively (P<0.001 for all groups relative to the control group). No significant differences were observed when comparing patients with HIV or HCV infections alone, but coinfected individuals showed a lower mtDNA copy number than patients infected with HIV (P<0.001) or with HCV (P=0.089). In a subset of 18 patients with HIV/HCV-coinfection, treatment with pegylated interferon plus ribavirin produced a further reduction in mtDNA (mean value, 189 copies/cell; P=0.009). Conclusions HIV and HCV may independently cause mtDNA depletion in PBMC. Coinfection may result in more pronounced mtDNA depletion. The administration of interferon plus ribavirin may further enhance mtDNA depletion. These findings may explain the greater risk of lipoatrophy of antiretroviral therapy in HIV-infected patients with HCV coinfection and why anti-HCV therapy may aggravate this effect.
Conservative surgical approach for thyroid and lymph‐node involvement in papillary thyroid carcinoma of childhood and adolescence

Prior to 1990s, papillary thyroid carcinomas (PTCs) in childhood/adolescence underwent a standard therapeutic approach (total thyroidectomy plus elective neck dissection, followed by radioactive iodine (RAI) ablation), with an overall survival of about 100%. The aim of this study is to outline the possibility of a conservative approach (hemithyroidectomy plus selective neck dissection of clinically involved nodes, followed by TSH‐suppressive therapy) in a selected group of patients.
Minimizing the Effect of sinusoidal Trends in Detrended Fluctuation Analysis

The detrended fluctuation analysis (DFA) [Peng et al., 1994] and its extensions (MF-DFA) [Kantelhardt et al., 2002] have been used extensively to determine possible long-range correlations in self-affine signals. While the DFA has been claimed to be a superior technique, recent reports have indicated its susceptibility to trends in the data. In this report, a smoothing filter is proposed to minimize the effect of sinusoidal trends and distortion in the log–log plots obtained by DFA and MF-DFA techniques.
MUSE: a scripting language for the development of interactive speech analysis and recognition tools

Speech research is a complex endeavor, as reflected in the numerous tools and specialized languages the modern researcher needs to learn. These tools, while adequate for what they have been designed for, are difficult to customize or extend in new directions, even though this is often required. We feel this situation can be improved and propose a new scripting language, MUSE, designed explicitly for speech research, in order to facilitate exploration of new ideas. MUSE is designed to support many modes of research from interactive speech analysis through compute-intensive speech understanding systems, and has facilities for automating some of the more difficult requirements of speech tools: user interactivity, distributed computation, and caching. In this paper we describe the design of the MUSE language and our current prototype MUSE interpreter.
Evaluation of Iranian microbiology laboratories for identification of etiologic agents of bacterial meningitidis. Survey results of an external quality assessment scheme (EQAS) programme.

OBJECTIVE To determine the ability of Iranian microbiology laboratories for identification and susceptibility testing of Streptococcus pneumoniae and Haemophilus influenzae as causative agents of bacterial meningitides. METHODS Two strains of bacteria including Haemophilus influenzae and Streptococcus pneumoniae as a common causative agents of meningitides were chosen and coded as strain number 1 and number 2. The strains were distributed among 679 microbiology laboratories. All laboratories were requested for identification of each unknown microorganism and susceptibility testing of S. pneumoniae against five commonly used antibiotics. RESULTS Of 679 microbiology laboratories 310 (46%) laboratories participated in the survey and among these, 258 laboratories completely identified S. pneumoniae. About 85% laboratories produced correct susceptibility testing against oxacillin, erythromycin, tetracycline, and vancomycin. Of 310 received responses only 50 laboratories identified H. influenza correctly. The majority of the laboratories did not have the capacity to identification H. influenza. CONCLUSION Microbiology laboratories in our country are qualified for identification and susceptibility testing of S. pneumoniae. However, majority of laboratories are not qualified for identification of H. influenzae.
Patient Decision Making: Use of and Adherence to Telephone-Based Nurse Triage Recommendations

Objective . Health plans, employer groups, and medical providers offer telephone-based nurse triage services to provide ready access to medical advice and information to assist patients in making decisions about their medical needs. The purpose of this study is to assess patient adherence to nurse triage recommendations. Patients and Methods . The study includes data for members of an HMO located in a large metropolitan area who used the triage service during 1997 (n = 22,998). The nurse triage call data are linked with medical claims and encounter data to assess patient medical service utilization following a call to the triage service to assess triage adherence. The authors consider no use of medical services following a triage call with the recommendation to use self-care advice at home an indicator of adherence to this recommendation. Results . The percentage of callers who adhered to triage recommendations to use hospital emergency services, physician office services, or self-care advice was 79.2%, 57.4%, and 65.8%, respectively. Adherence varies somewhat by age. Conclusion . The reported adherence levels are lower than those obtained from self-reported data reported elsewhere. Given the inherent limitations of both types of data, actual telephone-based nurse triage adherence may lie between the 2 levels.
A single molecule visualization of DNA diffusion and partitioning in model porous materials

A SINGLE MOLECULE VISUALIZATION OF DNA DIFFUSION AND PARTITIONING IN MODEL POROUS MATERIALS FEBRUARY 2005 DMYTRO NYKYPANCHUK, DIPLOMA, IVAN FRANKO UNIVERSITY M.S., UNIVERSITY OF MASSACHUSETTS AMHERST Ph.D., UNIVERSITY OF MASSACHUSETTS AMHERST Directed by: Professor David A. Hoagland and Professor Helmut H. Strey We developed an experimental approach that enables molecule visualizations of macromolecular diffusion and partitioning within well-defined pores. By colloidal templating, two-dimensional arrays of open, submicron cavities interconnected by small holes were created in dense polyacrylamide gels. Cavity size of the arrays varied from 600 to 1400 nm, with the corresponding holes about 4-5 times smaller. DNA molecules of sizes from 2.69 to 48.5 kbp were inserted into the cavity arrays and monitored by fluorescent microscopy. In video sequences, individual chain positions identified as the chains diffused under Brownian motion over a period of seconds to tens of minutes. For larger chains, dynamic configurations were resolved during the motion. Over full range of molecular and pore sizes, we found that chain dynamics could be understood through the entropic barriers transport mechanism. At high confinement (large molecules in small cavities), this mechanism produces unexpected trends, for example, independence of diffusion coefficient on molecular size or faster diffusion of molecules in smaller pores. These trends reflect segmental excluded volume. Complicated dynamics akin to motion of an inchworm characterized the largest DNA chains, those with radius of gyration larger than the cavity radius. Diffusion of linear and circular DNA molecules was compared for different molecular sizes, and the resulting differences in diffusion coefficient explained by differences in diffusion mechanism; linear molecules translocate through holes by forming loops, while linear chains predominantly translocate by threading one chain end. A similar colloidal templating approach was also employed to create isolated cavity pair interconnected by a small hole. When templated by bidisperse colloid, the two cavities have unequal diameters. A DNA chain trapped inside such pair partitions unevenly, preferring the larger cavity, which afford greater configurational freedom. This sort of partitioning underlies many separation technologies but had not been visualized previously. The partition coefficient between cavities was measured visually for many combinations of cavity and molecular sizes, trends in this coefficient were then compared to existing theories for polymer partitioning. Good agreement over a two orders-of-magnitude variation of partition coefficient was obtained when effect of excluded volume on confinement free energy was introduced in a mean-field manner.
The Effects of Dwell on the LCF Behavior of IN617

Much has been studied on the individual effects of creep and fatigue on alloy life. However, not much is known of the combined effects of these two mechanisms. Therefore, a study was put into place to determine the effects of dwell on fatigue life and deformation mechanisms, for IN617, a solid-solution strengthened Ni-base alloy used widely in the power generation and aerospace industries. Low cycle fatigue (LCF) tests were conducted from 649–982°C with either tensile or compressive dwell. Fracture surfaces of the test specimens as well as longitudinal and transverse sections were examined via scanning electron microscopy to determine the damage and failure mechanisms. Test results confirmed tensile dwell lives that were significantly lower than those seen in compressive dwell. The mechanics for the reduction in cyclic life for tensile dwell was attributed to creep damage accumulation at grain boundaries that led to widespread intergranular cracking and failure. Tensile dwell life reductions were largest in tests at moderate (649–760°C) temperatures. The failed specimens for this temperature range showed the most evidence of grain boundary cavitation and intergranular cracking. At higher test temperatures, the tensile dwell sensitivity for IN617 was significantly reduced or almost entirely eliminated at high temperatures (871–982°C). This was attributed to the lower stresses that developed at these temperatures for a given strain range. The LCF testing and subsequent analysis indicated that a substantial tensile stress during dwell time coupled with moderate temperatures, to allow for diffusion creep, lead to grain boundary damage that can reduce cyclic life.