Miracle-dz/UniFAR-FTUs huggingface dataset:
MB-MDR: Model-Based Multifactor Dimensionality Reduction for detecting interactions in high-dimensional genomic data

Analyzing the effects of genes and environmental factors on the development of complex diseases is a great challenge from both the statistical and computational perspectives. Several data mining methods have been proposed for interaction analysis, among them, the Multifactor Dimensionality Reduction method, MDR, (Ritchie et al. 2001) that has recently achieved a great popularity. MDR strategy is to reduce the multi-factor dimension to one by pooling multilocus genotypes into two groups of risk: high and low. Although MDR has proven its usefulness it suffers from some major drawbacks including that important interactions could be missed due to pooling too many cells together and that it cannot adjust for main effects and for confounding factors. In this paper we illustrate the limitations of MDR strategy and nonparametric approaches and demonstrate the value of using a model-based approach for analyzing interactions in case-control studies where adjustment for confounding variables and for main effects is required. We propose a new approach, a model based version of MDR, which we refer as Model-Based Multifactor Dimensionality Reduction (MBMDR). The proposed modelling approach is aimed to identify specific multi-locus genotypes that are associated with disease susceptibility and allows adjusting for marginal effects and confounders. The new methodology is illustrated with data from the Spanish Bladder Cancer Study.
Identification of Toxin A-Negative, Toxin B-Positive Clostridium difficile by PCR

ABSTRACT Toxigenic strains of Clostridium difficile have been reported to produce both toxins A and B nearly always, and nontoxigenic strains have been reported to produce neither of these toxins. Recent studies indicate that it is not always true. We established a PCR assay to differentiate toxin A-negative, toxin B-positive (toxin A−, toxin B+) strains from both toxin-positive (toxin A+, toxin B+) strains and both toxin-negative (toxin A−, toxin B−) strains as an alternative to cell culture assay and enzyme-linked immunosorbent assay (ELISA). By using the PCR primer set NK11 and NK9 derived from the repeating sequences of the toxin A gene, a shorter segment (ca. 700 bp) was amplified from toxin A−, toxin B+ strains compared to the size of the segment amplified from toxin A+, toxin B+ strains (ca. 1,200 bp), and no product was amplified from toxin A−, toxin B− strains. We examined a total of 421 C. difficile isolates by PCR. Of these, 48 strains showed a shorter segment by the PCR, were negative by ELISAs for the detection of toxin A, and were positive by cell culture assay. Although the cytotoxin produced by the toxin A−, toxin B+ strains was neutralized by anti-toxin B serum, the appearance of the cytotoxic effects on Vero cell monolayers was distinguishable from that of toxin A+, toxin B+ strains. By immunoblotting, the 44 toxin A−, toxin B+ strains were typed to serogroup F and the remaining four strains were serogroup X. Pulsed-field gel electrophoresis separated the 48 strains into 19 types. The PCR assay for the detection of the repeating sequences combined with PCR amplification of the nonrepeating sequences of either the toxin A or the toxin B gene is indicated to be useful for differentiating toxin A−, toxin B+ strains from toxin A+, toxin B+ and toxin A−, toxin B− strains and will contribute to elucidation of the precise role of toxin A−, toxin B+ strains in intestinal diseases.
Conceptual Confusion and Potential Advances in Athlete Burnout Research

More than 30 years of research on athlete burnout has yielded important insights and questions regarding the onset, nature, and consequences of this detrimental syndrome. Not surprisingly, burnout is considered an important matter, both from a research and practical standpoint. We comment on the work of Ryu, Ali, Kim, Choi, and Radlo, who examined the impact of burnout on cognitive performance among athletes.
Human papillomavirus detection by hybrid capture and its possible clinical use.

AIMS--To determine the sensitivity of the hybrid capture method for human papillomavirus (HPV) detection and potential clinical uses as a screening method for the identification of cervical intraepithelial neoplasia. METHODS--The presence of oncogenic types of HPV was tested for in samples taken from the cervix at colposcopy, and compared with detection by polymerase chain reaction (PCR) in 60 patients. Both sets of results were corrected with the pathology determined by biopsy and smear cytology. RESULTS--Hybrid capture detection showed 86% agreement with PCR. Eighty three percent of CIN 3 lesions, 62% of CIN 2, 59% of CIN 1 and 21% of normal controls were positive for oncogenic HPV types. CONCLUSION--The hybrid capture detection method is reliable, sensitive, and easy to use. The addition of HPV testing to cytological screening would detect a greater proportion of cervical dysplasia with a higher false positive rate.
Inkjet Printed Pressure Sensing Platform for Postural Imbalance Monitoring

In this paper, a low-cost printed pressure sensing platform is presented. The sensing platform consists of a flexible printed circuit board manufactured using conventional technology (defining the electrical connections and the capacitors dimensions) together with two flexible polymeric membranes made from a thermoplastic elastomer (TPU) printed with conductive ink Poly (3,4-ethylenedioxythiophene)-poly (styrenesulfonate) for definition of the electrodes. A capacitance-to-digital converter is used to measure the capacitance of the sensors, and a graphical interface in MATLAB allows real-time visualization of data. A prototype sensing platform was designed, fabricated, and tested. The capacitive sensors show a sensitivity of 50 fF/kPa in the region of operation, a noise of 1.2 fF/$\surd $ Hz, and a stability of better than 1.5% full scale. The proposed pressure sensor platform has the potential to integrate multiple sensing parameters for ubiquitous environment monitoring.
Cognitive impairment in relation to MRI metrics in patients with clinically isolated syndrome

Background: Cognitive deficits are frequent in multiple sclerosis (MS) and have been associated with morphologic brain changes. Less information exists on their extent and relation to MRI findings in clinically isolated syndrome (CIS). It is also unclear if structural changes as detected by magnetization transfer (MT) imaging may provide an additional explanation for cognitive dysfunction. Objective: To analyse the extent of cognitive deficits and their relation to MRI metrics including MT imaging in CIS compared to relapsing-remitting MS (RRMS). Methods: Forty-four CIS and 80 RRMS patients underwent the Brief Repeatable Battery of Neuropsychological Tests (BRB-N) and a 3 T MRI scan. Results: BRB-N subtests revealed similar results in CIS and RRMS. Impaired mental processing speed was most prevalent in both groups (CIS 13.6%; RRMS 16.3%) and thus served for correlation with MRI metrics. Using stepwise linear regression analyses, the strongest predictor for decreased mental processing speed was normalized cortex volume (p < 0.001) followed by T2-lesion load (p < 0.05) in RRMS, whereas cortical MT ratio was the only MRI parameter associated with decreased mental processing speed in CIS (p < 0.005). Conclusion: Cognitive dysfunction occurs in CIS in a pattern similar to RRMS, with impaired mental processing speed being most prevalent. Cortical MT-ratio changes may be an early sign for tissue changes related to impaired mental processing speed in CIS while this association shifts to increased signs of cortical atrophy and lesion load in RRMS.
Virtual surveillance of communicable diseases: a 20-year experience in France

Inserm has developed, since 1984, an information system based on a computer network of physicians in France. It allows for constitution of large databases on diseases, with individual description of cases, and to explore some aspects of the mathematical theory of communicable diseases. We developed user-friendly interfaces for remote data entry and GIS tools providing real-time atlas of the epidemiologic situation in any location. The continuous and ongoing surveillance network is constituted of about 1200 sentinel voluntary and unpaid investigators. We studied their motivation, reasons for either withdrawal or compliance using survival analyses. We implemented early warning systems for outbreak detection and for time-space forecasting. We conducted epidemiological surveys for investigating outbreaks. Large available time and space series allowed us to calibrate and explore synchronism of influenza epidemics, to test the assumption of panmixing in susceptibles-infectious-removed type models and to study the role of closing school in influenza morbidity and mortality in elderly. More than 250 000 cases of influenza, 150 000 cases of acute diarrheas, 35 000 patients for whom HIV tests have been prescribed by general practitioners and 25 000 cases of chickenpox have been collected. Detection of regional influenza or acute diarrhea outbreaks and forecasting of epidemic trends three weeks ahead are currently broadcasted to the French media and published on Sentiweb© on a weekly basis. Age-cohort-period models assessed field effectiveness of mass immunization strategies against measles and influenza in the country. Case-control studies with more than 1200 sets of cases of acute diarrheas and their matched controls showed the role of calicivirus and rotavirus as probable major causes of gastroenteritis during recurrent widespread outbreaks in winter in France. An age-specific model for chickenpox showed the probable role of children in disease transmission to their susceptible parents or grandparents. High level of synchronism between influenza epidemics has been demonstrated, either at a regional level (in France) or between France and the USA. The designation of our lab as a WHO collaborating center for electronic disease surveillance stimulates the development of global monitoring of diseases. We developed operational systems that are now available for the global monitoring of influenza (FluNet©), and human and animal rabies (RABNET©). Extension of electronic syndromic surveillance is needed in the world for improving surveillance capacities and real-time response against emerging diseases.
E-mail marketing in the context of cosmetics

This study investigates e-mail marketing using data from a survey of 839 Finnish customers of an international cosmetics brand. E-mail marketing involves the use of e-mail to send promotions and information to customers. In this context we address two research questions: (1) What e-mail advertising factors drive visits to a physical (i.e., bricks-and-mortar) company sales outlet? and, (2) Does e-mail advertising influence brand satisfaction? Our findings indicate that useful e-mails can influence customers to visit the store. Further, brand satisfaction is positively influenced if e-mails are interesting and also by the amount of e-mail received by customers.
CRFs-Based Named Entity Recognition Incorporated with Heuristic Entity List Searching

Chinese Named entity recognition is one of the most important tasks in NLP. Two kinds of Challenges we confront are how to improve the performance in one corpus and keep its performance in another different corpus. We use a combination of statistical models, i.e. a language model to recognize person names and two CRFs models to recognize Location names and Organization names respectively. We also incorporate an efficient heuristic named entity list searching process into the framework of statistical model in order to improve both the performance and the adaptability of the statistical NER system. We participate in the NER tests on open tracks of MSRA. The testing results show that our system can performs well.
Unsecured Debt, Consumer Bankruptcy, and Small Business

In this paper we develop a quantitative model of entrepreneurial activity (risk-taking) and consumer bankruptcy choices and use the model to study the effects of bankruptcy regulations on entrepreneurial activity, bankruptcy rate and welfare. We show that eliminating bankruptcy exemptions leads to a modest increase in the fraction of entrepreneurs, a large decrease in the overall bankruptcy rate and a significant welfare gain. In contrast, eliminating the whole consumer bankruptcy system leads to a large fall in the fraction of entrepreneurs and a substantial welfare loss. These two findings suggest that the consumer bankruptcy system is desirable but it must be well-designed with regard to bankruptcy asset exemptions. In particular, excessive bankruptcy exemptions can be counter-productive. Finally, we argue that entrepreneurial activity is important when studying different bankruptcy rules or regulations.
Evolution of penicillin resistance in Streptococcus pneumoniae; the role of Streptococcus mitis in the formation of a low affinity PBP2B in S. pneumoniae

Penicillin‐resistant strains of Streptococcus pneumoniae possess forms of penicillin‐binding proteins (PBPs) that have a low affinity for penicillin compared to those from penicillin‐sensitive strains. PBP genes from penicillin‐resistant isolates are very variable and have a mosaic structure composed of blocks of nucleotides that are similar to those found in PBP genes from penicillin‐sensitive isolates and blocks that differ by up to 21%. These chromosomally encoded mosaic genes have presumably arisen following transformation and homologous recombination with PBP genes from a number of closely related species. This study shows that PBP2B genes from many penicillin‐resistant isolates of S. pneumoniae contain blocks of nucleotides originating from Streptococcus mitis. In several instances it would appear that this material alone is sufficient to produce a low affinity PBP2B. In other examples PBP2B genes possess blocks of nucleotides from S. mitis and at least one additional unidentified species. Mosaic structure was aiso found in the PBP2B genes of penicillin‐sensitive isolates of S. mitis or S. pneumoniae. These mosaics did not confer penicillin resistance but nevertheless reveal something of the extent to which localized recombination occurs in these naturally transformable streptococci.
Economic satisfaction and relationship commitment in channels: The moderating role of environmental uncertainty, collaborative communication and coordination strategy

Purpose – The purpose of this paper is to focus on the linkage between economic satisfaction and relationship commitment in distribution channels. The moderating effects of three variables are considered: the use of behavior based coordination strategy; the perceived level of environmental uncertainty; and the use of collaborative communication strategy.Design/methodology/approach – The hypotheses are tested through a sample survey among 101 channel partners of mobile service providers in a state in India.Findings – The results indicate the moderating variables act as quasi moderators wherein they both directly and indirectly impact the dependent variable.Research limitations/implications – Limitations of the sampling methodology and sample size restricts the scope for generalizing the hypothesis. Further, data were collected from only one side of the dyad.Originality/value – The paper endorses and attempts to establish the view that channel satisfaction is a multidimensional concept and there are differe.
Glucose Signaling Pathway and Growth Conditions Regulate Gene Expression in Retrotransposon Ty2

Gene expression in the yeast retrotransposon Ty2 is regulated at transcriptional and translational levels. In this study, we have shown that the transcription of Ty2 is partially dependent on the membrane-bound glucose sensors Gpr1p and Mth1p in Saccharomyces cerevisiae. Transcription of Ty2 decreased approx. 3-fold in the gpr1, mth1 yeast mutant. Moreover, our results revealed that the transcription of Ty2 fluctuates during the growth stages of S. cerevisae. Both transcription and the frameshift rate of Ty2 rapidly dropped when the stationary stage yeast cells were inoculated into fresh medium. There was an instant activation of Ty2 transcription and a high level expression during the entire logarithmic stage of yeast growth. However, the transcription of Ty2 decreased 2-fold when the yeast cultures entered the stationary stage. The frameshift rate in Ty2 also varied depending on the growth conditions. The highest frameshift level was observed during the mid-logarithmic stage. It decreased up to 2-fold during the stationary stage. Furthermore, we have found that the frameshift rate of Ty2 diminished at least 5-fold in slowly growing yeasts. These results indicate that the transcription and the frameshift efficiency are coordinately regulated in the retrotransposon Ty2 depending on the growth conditions of S. cerevisiae.
A Probabilistic Model for Reconstruction of Torn Forensic Documents

In this paper we present a probabilistic approach to reconstruct a document from its torn pieces which is extremely helpful for the legal system. The method investigates several previously unexplored issues and proposes probabilistic dependencies of different (available) parts (or pieces) of a document. It iteratively calculates the probability of an arrangement subject to some constraints and attempts to produce the best possible configuration (or solution) using low level image statistics. The reconstruction method also ranks different (final) arrangements in order to help decision making process. Two types of data were used in the investigation. A set of documents where documents were torn naturally (as we do it in our daily life) and the second set consisting of documents that were torn to destroy particular evidences. Evaluation shows that the method is quite robust to tackle both the problems.
Functional Equivalence of an Evolutionarily Conserved RNA Binding Module*

Background: Diverse tristetraprolin family proteins exhibit sequence differences in their tandem zinc finger (TZF) RNA binding domains. Results: Replacement of the S. pombe Zfs1 TZF domain with those from distant species fully complements the Zfs1 deletion phenotype. Conclusion: Activities intrinsic to the TZF domain are interchangeable among distant eukaryotes. Significance: Accumulated sequence changes in TZF domains during evolution still permit high-affinity RNA binding. Members of the tristetraprolin (TTP) family of proteins participate in the regulation of mRNA turnover after initially binding to AU-rich elements in target mRNAs. Related proteins from most groups of eukaryotes contain a conserved tandem zinc finger (TZF) domain consisting of two closely spaced, similar CCCH zinc fingers that form the primary RNA binding domain. There is considerable sequence variation within the TZF domains from different family members within a single organism and from different organisms, raising questions about sequence-specific effects on RNA binding and decay promotion. We hypothesized that TZF domains from evolutionarily distant species are functionally interchangeable. The single family member expressed in the fission yeast Schizosaccharomyces pombe, Zfs1, promotes the turnover of several dozen transcripts, some of which are involved in cell-cell interactions. Using knockin techniques, we replaced the TZF domain of S. pombe Zfs1 with the equivalent domains from human TTP and the single family member proteins expressed in the silkworm Bombyx mori, the pathogenic yeast Candida guilliermondii, and the plant Chromolaena odorata. We found that the TZF domains from these widely disparate species could completely substitute for the native S. pombe TZF domain, as determined by measurement of target transcript levels and the flocculation phenotype characteristic of Zfs1 deletion. Recombinant TZF domain peptides from several of these species bound to an AU-rich RNA oligonucleotide with comparably high affinity. We conclude that the TZF domains from TTP family members in these evolutionarily widely divergent species are functionally interchangeable in mRNA binding and decay.
Treatment and prophylaxis of seborrheic dermatitis of the scalp with antipityrosporal 1% ciclopirox shampoo.

OBJECTIVE To demonstrate the efficacy, safety, and tolerance of ciclopirox shampoo for treatment and prophylaxis of seborrheic dermatitis of the scalp. DESIGN Multicenter, randomized, double-blind, vehicle-controlled study. After treatment with ciclopirox shampoo once or twice weekly or vehicle for 4 weeks (study segment A), responders were randomized to a 12-week prophylactic study arm (segment B). SETTING Forty-five medical centers in Germany (n = 19), France (n = 15), the United Kingdom (n = 8), and Austria (n = 3). Patients A total of 1000 patients with stable or exacerbating seborrheic dermatitis of the scalp. Interventions A total of 949 patients were randomized to receive ciclopirox treatment once or twice weekly or vehicle for 4 weeks. Thereafter, 428 responders received either ciclopirox prophylaxis once weekly or every 2 weeks or vehicle for 3 months. MAIN OUTCOME MEASURES Primary and secondary: response of "effectively treated" and "cured," with investigators and patients rating acceptability and tolerance. RESULTS Ciclopirox twice and once weekly produced response rates of 57.9% and 45.4%, respectively, compared with 31.6% for vehicle. Relapses occurred in 14.7% of patients using prophylactic ciclopirox once weekly, 22.1% of those in the prophylactic group shampooing once every 2 weeks, and 35.5% in the vehicle group. The few adverse events were evenly distributed among groups. Local tolerance and cosmetic acceptability were "good" in more than 85% of subjects. CONCLUSIONS Seborrheic dermatitis of the scalp responds well to 1% ciclopirox shampoo once or twice weekly for 4 weeks. A low relapse rate is maintained by once-weekly shampooing or shampooing once every 2 weeks. These treatments are safe and well-tolerated.
A LOW NOISE-LOW POWER-VARIABLE GAIN AMPLIFIER USING 0 . 13 ΜM CMOS TECHNOLOGY 1

A Low noise, Low power, variable gain amplifier is designed using TSMC 0. 13μM CMOS technology. In this design four stages of attenuators are used and the output of two stage amplifier is applied to it. Attenuators are used for obtaining variation in gain while amplifiers are used for high gain, high linearity and low noise figure. The design operates on frequency range of 40MHz to 950MHz. The power consumption achieved is less than 10mW and dynamic gain range is about 55dB. The variable gain obtained is -24 to 30 dB at 40MHz and -27 to 26 dB at 950 MHz. The noise figures of this design is 2 dB and the third order Intercept point (IIP3) is 6.2 dBm at maximum gain of 30dB.