Miracle-dz/UniFAR-FTUs huggingface dataset:
Application of a Newly Developed ARB Software-Integrated Tool for In Silico Terminal Restriction Fragment Length Polymorphism Analysis Reveals the Dominance of a Novel pmoA Cluster in a Forest Soil

ABSTRACT TRF-CUT, an ARB-implemented tool, was developed to predict in silico the terminal restriction fragments of aligned small-subunit rRNA gene or functional gene sequences. Application of this new tool to perform directed terminal restriction fragment length polymorphism analysis of pmoA products obtained from a forest soil revealed that novel cluster I methanotrophic bacteria were dominant.
E-Business Transformation through Effective Enterprise Resource Management

This paper reports on research carried out in 1999-2001 on the use of e-Business applications in ERP-based organisations. Multiple structured interviews were used to collect data on ten established organisations from a diverse range of industries. The findings are analysed according to the level of sophistication of e-Business models and their transformational impact on the organisation. Early adopters of e-Business show a trend towards cost reductions and administrative efficiencies from procurement and self-service applications used by customers and employees. More mature users focus on strategic advantage and generate this through an evolutionary model of organisational change. A complex case study of e-Business integration with a global supplier and their corporate customers is analysed to identify specific stages of benefits accrual through the e-Business transformation process. Collectively the set of case studies is used to demonstrate the increased benefits derived from an e-Business architecture based on a network of ERP enabled organisations.
Suspicious timing error prediction with in-cycle clock gating

Conventionally, circuits are designed to add pessimistic timing margin to solve delay variation problems, which guarantees “always correct” operations. However, due to the fact that such a worst-case condition occurs rarely, the traditional pessimistic design method is therefore becoming one of the main obstacles for designers to achieve higher performance and/or ultra-low power consumption. By monitoring timing error occurrence during circuit operation, adaptive timing error detection and recovery methods have gained wide interests recently as a promising solution. As an extension of existing research, in this paper, we propose a suspicious timing error prediction method for performance or energy efficiency improvement in pipeline designs. Experimental results show that with when compared with typical margin designs, the proposed method can 1) achieve up to 1.41X throughput improvement with in-situ timing error prediction ability; and 2) allow the design to be overclocked by up to 1.88X with “always correct” outputs.
The extracytoplasmic function sigma factors: role and regulation

Alternative sigma factors provide a means of regulating gene expression in response to various extracellular changes. One such class of sigma factors appears to control a variety of functions, including expression of heat‐shock genes in Escherichia coli, biosynthesis of alginates and carotenoids in Pseudomonas aeruginosa and Myxococcus xanthus, respectively, iron uptake in E. coli and Pseudomonas spp. , nickel and cobalt efflux in Alcaligenes europhus, plant pathogenicity in Pseudomonas syringae and synthesis of outer membrane proteins in Photobacterium sp. strain SS9. Most of these activities deal with extracytoplasmic functions, and such sigmas have been designated as ECF sigma factors. They have also been characterized in Mycobacteria as well as Gram‐positive bacteria such as Streptomyces coelicolor and Bacillus subtilus and the archaea Sulpholobus acidocaldarius. ECF factors belong to a subfamily of the sigma 70 class, based on their sequence conservation and function across bacterial species. The promoter consensus sequences recognized by the ECF factors are also highly conserved. In most of the cases, the activity of these factors is modulated by a cognate inner membrane protein that has been shown, both in E. coli and in P. aeruginosa, to act as an anti‐sigma activity. This inner membrane protein is presumed to serve as a sensor and signalling molecule, allowing an adaptive response to specific environmental change. Presumably, an on‐and‐off switch of the anti‐sigma activity leads to the release of the sigma factor and thereby to the co‐ordinate transcription of the specific regulon it governs.
Chronic pain in older adults: prevalence, incidence, and risk factors

Objectives: Chronic pain is common in older adults, yet little is known of its development and the factors that predict its persistence and onset at old age. The aims of this longitudinal cohort study were to examine the prevalence and incidence of chronic pain and to explore possible risk factors for its persistence and onset in a representative sample of older Swedish adults. Method: Data were collected through questionnaires and followed up after 12 and 24 months. Chronic pain was defined as pain symptoms that lasted more than 3 months, regardless of the specific cause or site. Logistic regression analyses were used to identify odds ratios (ORs) with 95% confidence intervals (CIs) for potential predictors. Results: Out of 2000 older adults approached (aged 65–103 years), 1141 were included in the study. Chronic pain was reported among 38.5% of the participants, and was more common among females and among adults over 85 years of age. The incidence was estimated to be 5.4% annually. Being female (OR 3.19, 95% CI 1.04–9.59), having a lower body mass index (BMI; OR 0.89, 95% CI 0.79–0.99), more than one pain location (OR 4.02, 95% CI 1.56–10.35), higher severity (OR 1.79, 95% CI 1.13–2.83), and longer duration (OR 1.08, 95% CI 1.01–1.15) were associated with the persistence of chronic pain, but this association did not remain significant for men when divided by gender. Younger age (OR 0.89, 95% CI 0.89–0.99) was associated with new onset of chronic pain. Conclusions: Even though pain was often highly prevalent and persistent, our results show that both recovery and onset of pain occurred. Pain characteristics, rather than age-related symptoms and psychosocial variables, predicted pain persistence among older women but not among older men. These findings highlight the importance of early pain management in the prevention of future pain.
Changes in Gene and Protein Expression in Magnetic Field–Treated Human Glioma Cells

Because few cancer studies have examined protein profiles and genetic regulation from a single carcinogen exposure, the objective of this study was to determine genetic change via microarray and to evaluate whether that change was a precursor to cellular protein changes. In separate but experimentally identical studies, human glioma SF767 cells were exposed for 3 h to 60-Hz magnetic fields (sham or 1.2 μT). Microarray results suggested that magnetic field treatment resulted in the up-regulation of 5 genes, whereas 25 genes were down-regulated. The mean abundance of 10 identified proteins was altered following 1.2 μT exposure relative to sham (3 increase, 7 decrease). These studies suggest a limited but complicated response in the glioma cells to the magnetic field treatment.
Blind separation of mixture of independent sources through a quasi-maximum likelihood approach

We propose two methods for separating mixture of independent sources without any precise knowledge of their probability distribution. They are obtained by considering a maximum likelihood (ML) solution corresponding to some given distributions of the sources and relaxing this assumption afterward. The first method is specially adapted to temporally independent non-Gaussian sources and is based on the use of nonlinear separating functions. The second method is specially adapted to correlated sources with distinct spectra and is based on the use of linear separating filters. A theoretical analysis of the performance of the methods has been made. A simple procedure for optimally choosing the separating functions is proposed. Further, in the second method, a simple implementation based on the simultaneous diagonalization of two symmetric matrices is provided. Finally, some numerical and simulation results are given, illustrating the performance of the method and the good agreement between the experiments and the theory.
Coreference for NLP Applications

This paper presents several techniques for performing automatic coreference annotation and performance results for each of them. To demonstrate that they can be applied to real-world data, we have built a simple question-answering system which uses the techniques. A system using coreference is compared to a baseline system with the result that the addition of the coreference annotation improves performance.
Understanding patient satisfaction with received healthcare services: A natural language processing approach

Important information is encoded in free-text patient comments. We determine the most common topics in patient comments, design automatic topic classifiers, identify comments ' sentiment, and find new topics in negative comments. Our annotation scheme consisted of 28 topics, with positive and negative sentiment. Within those 28 topics, the seven most frequent accounted for 63% of annotations. For automated topic classification, we developed vocabulary-based and Naive Bayes ' classifiers. For sentiment analysis, another Naive Bayes ' classifier was used. Finally, we used topic modeling to search for unexpected topics within negative comments. The seven most common topics were appointment access, appointment wait, empathy, explanation, friendliness, practice environment, and overall experience. The best F-measures from our classifier were 0.52(NB), 0.57(NB), 0.36(Vocab), 0.74(NB), 0.40(NB), and 0.44(Vocab), respectively. F- scores ranged from 0.16 to 0.74. The sentiment classification F-score was 0.84. Negative comment topic modeling revealed complaints about appointment access, appointment wait, and time spent with physician.
Health Psychology 2000:The Development of Professional Health Psychology

This Final Report of the European Federation of Professional Psychologists' Associations (EFPPA) Task Force on Health Psychology defines the nature and scope of health psychology and its possible future development to the year 2000 and beyond. Training needs and objectives are specified for professional health psychologists working in Europe. Practical and policy implications of medical progress and societal changes are discussed. The future development of health psychology as a profession depends on putting theory and policy into practice through the implementation of high quality training. Currently there are relatively few European countries where this has yet happened. Training programmes need to be introduced in all European countries within the framework of each member- country's national laws, regulations and practices.
Evolution of Cannabinoid Receptors in Vertebrates: Identification of a CB2 Gene in the Puffer Fish Fugu rubripes

9 -tetrahydrocannabinol, the psychoactive ingredient of cannabis, exerts effects in humans by binding to the Gprotein-coupled cannabinoid receptors CB 1 and CB2, which are expressed in the nervous and immune systems, respectively. Genes encoding CB 1 receptors have also been discovered in non-mammalian vertebrates, including the puffer fish Fugu rubripes. Here the identification of aFugu gene that encodes an ortholog of mammalian CB 2 receptors is reported. This is the first CB 2 gene to be identified in a non-mammalian vertebrate, and it indicates that the gene duplication event that gave rise to CB 1 and CB2 receptors occurred before the divergence of teleosts and tetrapods. Moreover, non-mammalian vertebrate species can now be considered as potential model systems in which the physi
Exploring the Role of Part of Speech in the Lexicon

The Problem: Words in natural language sentences exhibit regularities in where they can appear in a sentence. These regularities are captured as parts of speech: nouns name things in the world; verbs represent actions and events; adjectives and adverbs describe properties of nouns and manners of verbs. Natural language has tremendous freedom in sharing meaning between these parts of speech (consider the noun and verb “document”), but most modern dictionaries [8, 9] separate these with little to link closely related words of different parts of speech. Human experiments may give some insight into good ways of creating those links in machine-readable dictionaries.
Market Makers versus the General Public: A First Look at S&P500 Futures Trade Data

This paper considers 15 minute records of trading volume and traded prices coinciding with the reporting intervals required by the Commodity Futures Trading Commission. Records are extracted from trade records for market trade and also two way trade between market makers (CT1) and the general public (CT4) from January 1994 to June 2004. Futures price records are matched with S&P500 cash index price records. Simultaneous volatility models are specified and estimated to test trading volume to futures volatility lead/lag effects and also futures volatility to cash index volatility lead/lag effects. As we disaggregate from the market records to CT1 and CT4 records and further into year to year samples volume to futures volatility leading effects and also futures volatility to cash volatility leading effects dominate. The results raise important issues for risk management and dynamic hedging models employing intra-day trader data. A number of important issues for further analysis are also raised in this paper.
Loss of P-type ATPase ATP13A2/PARK9 function induces general lysosomal deficiency and leads to Parkinson disease neurodegeneration

Parkinson disease (PD) is a progressive neurodegenerative disorder pathologically characterized by the loss of dopaminergic neurons from the substantia nigra pars compacta and the presence, in affected brain regions, of protein inclusions named Lewy bodies (LBs). The ATP13A2 gene (locus PARK9) encodes the protein ATP13A2, a lysosomal type 5 P-type ATPase that is linked to autosomal recessive familial parkinsonism. The physiological function of ATP13A2, and hence its role in PD, remains to be elucidated. Here, we show that PD-linked mutations in ATP13A2 lead to several lysosomal alterations in ATP13A2 PD patient-derived fibroblasts, including impaired lysosomal acidification, decreased proteolytic processing of lysosomal enzymes, reduced degradation of lysosomal substrates, and diminished lysosomal-mediated clearance of autophagosomes. Similar alterations are observed in stable ATP13A2-knockdown dopaminergic cell lines, which are associated with cell death. Restoration of ATP13A2 levels in ATP13A2-mutant/depleted cells restores lysosomal function and attenuates cell death. Relevant to PD, ATP13A2 levels are decreased in dopaminergic nigral neurons from patients with PD, in which ATP13A2 mostly accumulates within Lewy bodies. Our results unravel an instrumental role of ATP13A2 deficiency on lysosomal function and cell viability and demonstrate the feasibility and therapeutic potential of modulating ATP13A2 levels in the context of PD.
Mutations in gag proteins P12 and P15 of Moloney murine leukemia virus block early stages of infection

A collection of mutants of Moloney murine leukemia virus with deletions in the gag gene was generated by restriction enzyme site-directed mutagenesis of a cloned proviral DNA. The mutants all contained deletions of the NarI site in the P12 region, and some contained deletions extending into the adjacent P15 region. The deletions did not significantly affect the assembly or release of viral particles. Examination of endogenous reverse transcription products demonstrated normal synthesis of minus- and plus-strand strong-stop DNAs, indicating that the RNA genome was packaged and that reverse transcription in detergent-permeabilized virions was not impaired. The virion particles contained high levels of an abnormal protein which corresponded to a P15-P12 fusion protein; proteolytic processing of this abnormal protein was completely blocked by all the mutations. The infectivity of the particles was dramatically reduced. Analysis of the low-molecular-weight DNA in infected NIH/3T3 cells indicated that the mutant virions could not carry out viral DNA synthesis. These data suggest that the P12 and P15 proteins may not be critical for virion assembly but do play an important role in early steps of viral infection.
Voluntary Assurance on Interim Financial Statements and Earnings Quality

Under current Canadian securities regulatory requirements, public companies are able to choose whether to have their interim financial statements reviewed by external auditors on a quarter by quarter basis, but they must disclose when there has been no review performed. This differs from US practice where the Securities and Exchange Commission (SEC) requires a timely review of interim financial statements by the company’s auditor. Thus, the Canadian regulatory environment provides a natural laboratory to study the association between the determinants of voluntary reviews and earnings quality. Our study provides evidence that large and highly levered firms with independent board of directors tend to have their interim statements reviewed voluntarily. Moreover, quarterly discretionary accruals of reviewed firms are generally smaller than those of non-reviewed firms, reflecting better earnings quality. We control for possible self-selection bias in our empirical tests.
An Exocrine Pancreatic Stress Test with 11C-Acetate PET and Secretin Stimulation

The purpose of this study was to develop a noninvasive imaging test of pancreatic exocrine function. Methods: In this pilot study, 5 healthy volunteers underwent two 60-min dynamic 11C-acetate PET studies, one before and one after intravenous secretin administration. Kinetic analysis of the pancreas was performed using a 1-compartment model and an image-derived input function. From summed images, standardized uptake values were measured from the pancreas and the liver, and the pancreas-to-liver ratio was computed. Results: The baseline k1 and k2 data for all 5 volunteers were consistent. After secretin stimulation, the k1 and k2 significantly increased (paired t test P = 0.046 and P = 0.023, respectively). In the summed PET images, the pancreas-to-liver ratio decreased (P = 0.037). Increased 11C-acetate activity was observed in the duodenum after secretin stimulation consistent with secretin-induced secretion. Conclusion: 11C-acetate PET studies with secretin stimulation show potential as a noninvasive method for assessing pancreatic exocrine function.
FPGA-based embedded visual servoing platform for quick response visual servoing

The response speed of visual servoing depends on the computation platform's data transfer and computation capability. In this work, we proposed an embedded FPGA-based visual servoing platform (VSP) to meet the requirements on data transfer and computation capability for quick response visual servoing tasks. To address the data transfer capability issue, we adopted coprocessor-like system architecture, which provided direct connections between vision processing IPs and peripheral modules. To address the computation capability issue, we exploit as much parallelism within vision processing algorithms as possible to ensure high visual information update frequency. Two visual servoing tasks that required quick response, a ball catching and a high speed target shooting tasks, were chosen to verify the applicability and effectiveness of the VSP. In the ball catching case, we achieved 85% catch success rate and 58Hz visual update frequency. In the high speed target shooting case, we achieved 91% average hit rate and 402 Hz visual update frequency.
Generation of Janus kinase 1 (JAK1) conditional knockout mice

The biological functions of the Janus kinase 1 (JAK1) are suggested to be pleiotropic since this signal transducer is ubiquitously expressed and coupled to a variety of cytokine receptors. Consequently, mice that are deficient in this tyrosine kinase were reported to die shortly after birth. To facilitate studies that address the biological and molecular functions of JAK1 during postnatal development, we performed gene targeting in embryonic stem cells and generated a Cre/lox‐based conditional knockout mouse model. Expression of Cre recombinase in the germline converted the Jak1 conditional knockout allele (Jak1fl) into a null allele (Jak1‐) that when subsequently crossed into homozygosity led to a complete absence of the JAK1 protein in developing embryos. JAK1 deficient embryos were visibly smaller starting at E15.5. Newborn pups exhibited signs of apnea and died within hours after birth. The examination of fibroblasts from conditional knockout embryos and their littermate wildtype controls expressing JAK1 showed that lack of this Janus kinase resulted in an impaired tyrosine phosphorylation and activation of the downstream Signal Transducers and Activators of Transcription (STATs) 1, 3, and 6. JAK1 conditional knockout mice will be an invaluable tool to study cytokine signaling during normal development and disease progression in adult animals.
Searching Experience Sharing Based on Ant Colony Model

Search engine is an important tool to all the Internet users. It helps users finding useful contents in the cyberspace. However, searching experiences among different users are difficult to be shared and accumulated. In this paper, a concept called search-trail is proposed. Based on ant colony model, search-trails are created from the searching steps to the target contents. The search-trails built from various users are very similar to the trails generated in an ant colony. The simulations of the proposed solution demonstrate that even in the case of few searching experienced users, the generated search-trails still possess 96.29% similarity to the expected ones in 60 days. It shows that the concept of search-trails can really help users accumulating, sharing and reusing their search experiences.
Which Free Cash Flow Is Value Relevant? The Case of the Healthcare Industry

The definition of free cash flow (FCF) varies widely in accounting theory and practice. The objective of this study is to empirically identify which definition is the most value relevant for the healthcare industry. Using a sample of 14,866 observations from 1988 to 2010, the author shows that the FCF defined as cash flow from operations less capital expenditures is the one most associated with stock prices. The author recommends that the FASB require healthcare companies to disclose that FCF, or at least require companies voluntarily disclosing FCF to use that definition. This should help retail investors make better decisions.
Fungal small nuclear ribonucleoproteins share properties with plant and vertebrate U‐snRNPs.

snRNAs with properties closely related to those of the major vertebrate U‐snRNAs are present in the fungi Aspergillus nidulans, Neurospora crassa and Schizosaccharomyces pombe. These RNAs possess a tri‐methyl guanosine cap structure and a subset cross‐hybridizes with human U1 and U2 clones. In the form of snRNPs, snRNAs from these fungi as well as from Saccharomyces cerevisiae and pea plants are immunoprecipitated by human and anti‐Sm or anti‐(U1)RNP autoimmune antibodies. On micro‐injection into the cytoplasm of Xenopus oocytes, the snRNAs are packaged into ribonucleoprotein particles and migrate into the nucleus. The results demonstrate a hitherto unsuspected degree of evolutionary conservation in snRNA structure, snRNP protein structure, and sites of RNA‐protein interaction within snRNPs.