Miracle-dz/UniFAR-FTUs huggingface dataset:
Analysis of the nucleic acid annealing activities of nucleocapsid protein from HIV-1

Retroviral nucleocapsid (NC) protein is an integral part of the virion nucleocapsid where it is in tight association with genomic RNA and the tRNA primer. NC protein is necessary for the dimerization and encapsidation of genomic RNA, the annealing of the tRNA primer to the primer binding site (PBS) and the initial strand transfer event. Due to the general nature of NC protein-promoted annealing, its use to improve nucleic acid interactions in various reactions can be envisioned. Parameters affecting NC-promoted nucleic acid annealing of NCp7 from HIV-1 have been analyzed. The promotion of RNA:RNA and RNA:DNA annealing by NCp7 is more sensitive to the concentration of MgCl2 than the promotion of DNA:DNA hybridization. Stimulation of complex formation for all three complexes was efficient at 0-90 mM NaCl, between 23 and 55 degrees C and at pH values between 6.5 and 9.5, inclusive. Parameters affecting NCp7-promoted hybridization of tRNA(Lys,3) to the PBS, which appears to be specific for NC protein, will be discussed. Results implicate the basic regions of NCp7, but not the zinc fingers, in promoting the annealing of complementary nucleic acid sequences. Finally, NCp7 strand transfer activity aids the formation of the most stable nucleic acid complex.
Evidence for the late origin of introns in chloroplast genes from an evolutionary analysis of the genus Euglena.

The origin of present day introns is a subject of spirited debate. Any intron evolution theory must account for not only nuclear spliceosomal introns but also their antecedents. The evolution of group II introns is fundamental to this debate, since group II introns are the proposed progenitors of nuclear spliceosomal introns and are found in ancient genes from modern organisms. We have studied the evolution of chloroplast introns and twintrons (introns within introns) in the genus Euglena. Our hypothesis is that Euglena chloroplast introns arose late in the evolution of this lineage and that twintrons were formed by the insertion of one or more introns into existing introns. In the present study we find that 22 out of 26 introns surveyed in six different photosynthesis-related genes from the plastid DNA of Euglena gracilis are not present in one or more basally branching Euglena spp. These results are supportive of a late origin for Euglena chloroplast group II introns. The psbT gene in Euglena viridis, a basally branching Euglena species, contains a single intron in the identical position to a psbT twintron from E.gracilis, a derived species. The E.viridis intron, when compared with 99 other Euglena group II introns, is most similar to the external intron of the E.gracilis psbT twintron. Based on these data, the addition of introns to the ancestral psbT intron in the common ancester of E.viridis and E.gracilis gave rise to the psbT twintron in E.gracilis.
Divalent metal ion binding to a conserved wobble pair defining the upstream site of cleavage of group I self-splicing introns.

The upstream site of cleavage of all group I self-splicing introns is identified by an absolutely conserved U.G base pair. Although a wobble C.A pair can substitute the U.G pair, all other combinations of nucleotides at this position abolish splicing, suggesting that it is an unusual RNA structure, rather than sequence, that is recognized by the catalytic intron core. RNA enzymes are metalloenzymes, and divalent metal ion binding may be an important requirement for splice site recognition and catalysis. The paramagnetic broadening of NMR resonances upon manganese binding at specific sites was used to probe the interaction between divalent metal ions and an oligonucleotide model of a group I intron ribozyme substrate. Unlike previous studies in which only imino proton resonances were monitored, we have used isotopically labelled RNA and a set of complete spectral assignments to identify the location of the divalent metal binding site with much greater detail than previously possible. Two independent metal binding sites were identified for this oligonucleotide. A first metal binding site is located in the major groove of the three consecutive G.C base pairs at the end of double helical stem. A second site is found in the major groove of the RNA double helix in the vicinity of the U.G base pair. These results suggest that metal ion coordination (or a metal bridge) and tertiary interactions identified biochemically, may be used by group I intron ribozymes for substrate recognition.
Using Surgical Appropriateness Criteria to Examine Outcomes of Total Knee Arthroplasty in a United States Sample

We determined outcomes for patients classified as appropriate, inconclusive, or inappropriate for total knee arthroplasty (TKA) using a modified version of a validated appropriateness algorithm. Outcome measurement was conceptualized as short‐term postoperative change attributable primarily to surgery and rehabilitation (2 months) and as longer‐term postoperative change and recovery (1 and 2 years).
Major Depression Diagnoses Among Patients With Systemic Sclerosis: Baseline and One‐Month Followup

Depression is common in many rheumatic diseases and is associated with poor prognosis. No studies of patients with any rheumatic diseases, however, have assessed the stability of major depressive disorder (MDD) diagnoses over time. The objective of the present study was to assess the stability of MDD diagnoses among patients with systemic sclerosis (SSc; scleroderma), a rare autoimmune rheumatic disease, across 2 assessments approximately 1 month apart.
The RDP (Ribosomal Database Project)

The Ribosomal Database Project (RDP) is a curated database that offers ribosome-related data, analysis services and associated computer programs. The offerings include phylogenetically ordered alignments of ribosomal RNA (rRNA) sequences, derived phylogenetic trees, rRNA secondary structure diagrams, and various software for handling, analyzing and displaying alignments and trees. The data are available via anonymous FTP (rdp.life.uiuc.edu), electronic mail (server@rdp.life.uiuc.edu), gopher (rdpgopher.life.uiuc.edu) and WWW (http://rdpwww.life.uiuc.edu/ ). The electronic mail and WWW servers provide ribosomal probe checking, approximate phylogenetic placement of user-submitted sequences, screening for possible chimeric rRNA sequences, automated alignment, and a suggested placement of an unknown sequence on an existing phylogenetic tree.
Knee Extensor Muscle Strength in Middle‐Aged and Older Individuals Undergoing Arthroscopic Partial Meniscectomy: A Systematic Review and Meta‐Analysis

People with meniscal tears are at high risk to develop or progress to knee osteoarthritis. Knee extensor weakness is considered a risk factor for osteoarthritis and is often reported in these individuals. The purpose of this systematic review and meta‐analysis was to investigate knee extensor strength in people undergoing an arthroscopic partial meniscectomy (APM).
Herpes Zoster Reactivation in Patients With Rheumatoid Arthritis: Analysis of Disease Characteristics and Disease‐Modifying Antirheumatic Drugs

To identify the rheumatoid arthritis (RA) characteristics associated with increased herpes zoster (HZ) risk in the Corrona registry RA patients, and to evaluate the risk in initiators of tumor necrosis factor inhibitors (TNFi) or non‐TNFi biologic agents or (among those who were currently on or had been previously treated with methotrexate [MTX]) conventional synthetic disease‐modifying antirheumatic drugs (csDMARDs) other than MTX.
Concepts of Fitness And Wellness: A Comprehensive Lifestyle Approach

Section 1: Lifestyles for Health, Wellness, and Fitness 1: Health, Wellness, Fitness, and Healthy Lifestyles: An Introduction 2: Self-Management and Self-Planning Skills for Health Behavior Change Section II: An Introduction to Physical Activity 3: Preparing for Physical Activity 4: The Health Benefits of Physical Activity 5: How Much Physical Activity Is Enough? Section III: The Physical Activity Pyramid 6: Moderate Physical Activity: Being Active in Diverse Environments 7: Cardiovascular Fitness 8: Active Aerobics, Sports, and Recreational Activities 9: Flexibility 10: Muscle Fitness and Resistance Exercises Section IV: Physical Activity: Special Considerations 11: Body Mechanics: Posture, Questionable Exercises, and Care of the Back and Neck 12: Performance Benefits of Physical Activity Section V: Nutrition and Body Composition 13: Body Composition 14: Nutrition 15: Managing Diet and Activity for Healthy Body Fatness Section VI: Stress Management 16: Stress and Health 17: Stress Management, Relaxation, and Time Management Section VII: Avoiding Destructive Behaviors 18: The Use and Abuse of Tobacco 19: The Use and Abuse of Alcohol 20: The Use and Abuse of Other Drugs 21: Preventing Sexually Transmitted Infections Section VIII: Making Informed Choices 22: Cancer, Diabetes, and Other Health Threats 23: Evaluating Fitness and Wellness Products: Becoming an Informed Consumer 24: Toward Optimal Health and Wellness: Planning for Healthy Lifestyle Change Appendix A: Metric Conversion Chart Appendix B: Canada's Food Guide to Healthy Eating Appendix C: Calorie, Fat, Saturated Fat, Cholesterol, and Sodium Content of Selected Fast-Food Items Appendix D: Calorie Guide to Common Foods Appendix E: Calories of Protein, Carbohydrates, and Fats in Foods
Characterization of the effects of Escherichia coli replication terminator protein (Tus) on transcription reveals dynamic nature of the tus block to transcription complex progression

We have characterized the blocks to progression of T7 and T3 RNA polymerase transcription complexes created when a Tus protein is bound to the template. The encounter with Tus impedes the progress of the transcription complexes of either enzyme. The duration of the block depends on which polymerase is used and the orientation of Tus on the DNA. Both genuine termination (dissociation of the transcription complex) and halting followed by continued progression after the block is abrogated are observed. The fraction of complexes that terminates depends on which polymerase is used and on the orientation of the Tus molecule. The efficiency of the block to transcription increases as the Tus concentration is increased, even if the concentration of Tus is already many times in excess of what is required to saturate its binding sites on the template in the absence of transcription. The block to transcription is rapidly abrogated if an excess of a DNA containing a binding site for Tus is added to a transcription reaction in which Tus and template have been preincubated. Finally, we find that transcription will rapidly displace Tus from a template under conditions that generate persistent blocks to transcription. These observations reveal that during the encounter with the transcription complex Tus rapidly dissociates from the template but that at sufficiently high concentrations Tus usually rebinds before the transcription complex can move forward. The advantage of a mechanism which can create a persistent block to transcription or replication complex progression, which can nevertheless be rapidly abrogated in response to down regulation of the blocking protein, is suggested.
THE EDUCATIONAL EFFECTS FOR PEDIATRIC RESIDENTS OF A COMPUTER- BASED TRAINING ABOUT THE PART C EARLY INTERVENTION PROGRAM

Title of Thesis: THE EDUCATIONAL EFFECTS FOR PEDIATRIC RESIDENTS OF A COMPUTER-BASED TRAINING ABOUT THE PART C EARLY INTERVENTION PROGRAM Regina Anne Pettko, Master of Arts, 2011 Thesis directed by: Professor Joan Lieber Department of Special Education This study examined knowledge gains about early intervention programs using a computer-based training with pediatric residents. Fourteen pediatric re sidents at the University of Maryland School of Medicine were pre-tested, provided with traini ng, and post-tested. Given in a computer lab, the training was part of the residency educa tion program. Results showed a statistically significant increase in test sc ores postintervention. The training was more effective in teaching about early interve ion law, philosophy, and recommendations for physician screenings than it was in teaching bes t practices for making referrals to the early intervention program. Finding s were consistent with past studies on computer trainings in other medical topics. Limitations inc luded small sample size and lack of a control group or follow-up assessment to measure maintenance and generalization of knowledge gained. Further investigation should look into the kinds of learning for which a computer is suitable versus the kinds that require more personal teacher-student relationships. THE EDUCATIONAL EFFECTS FOR PEDIATRIC RESIDENTS OF A COMPUT ERBASED TRAINING ABOUT THE PART C EARLY INTERVENTION PROGRAM By Regina Anne Pettko Thesis submitted to the Faculty of the Graduate School of the University of Maryland, College Park in partial fulfillment of the requirements for the degree of Master of Arts 2011
Comparative Risk of Harm Associated With the Use of Targeted Immunomodulators: A Systematic Review

To systematically compare the risk of adverse events (AEs) for 13 targeted immunomodulators (TIMs) indicated for ankylosing spondylitis (AS), inflammatory bowel diseases, juvenile idiopathic arthritis, plaque psoriasis, psoriatic arthritis (PsA), or rheumatoid arthritis (RA).
Seroprevalence of HIV in acute orthopaedic trauma at the Charlotte Maxeke Johannesburg Academic Hospital

Methods All patients admitted at the Orthopaedic Trauma Unit of the academic hospital during a six-month period from 1 July 2008 to 31 December 2008 were counselled and an informed consent for HIV testing was obtained. Only acute orthopaedic trauma patients aged 18 years and above, with a Glasgow Coma Scale of 15/15 and competent to give consent were recruited for the study. Where the consent was given blood samples were analysed by way of a rapid HIV test followed by a confirmatory ELISA when the rapid HIV tested positive. Those patients who tested positive for the virus were then counselled and offered referral to an HIV centre for follow-up.
Association of Anticentromere Antibodies With More Severe Exocrine Glandular Dysfunction in Sjögren's Syndrome: Analysis of the Sjögren's International Collaborative Clinical Alliance Cohort

Anticentromere antibodies (ACAs) define a subset of primary Sjögren's syndrome (SS) with a unique phenotype, including features of limited cutaneous systemic sclerosis and a lower frequency of anti‐SSA/SSB antibodies. We sought to determine whether ACAs are associated with more severe exocrine glandular dysfunction in a large cohort of primary SS subjects.
ACTIVITY: a database on DNA/RNA sites activity adapted to apply sequence-activity relationships from one system to another

ACTIVITY is a database on DNA/RNA site sequences with known activity magnitudes, measurement systems, sequence-activity relationships under fixed experimental conditions and procedures to adapt these relationships from one measurement system to another. This database deposits information on DNA/RNA affinities to proteins and cell nuclear extracts, cutting efficiencies, gene transcription activity, mRNA translation efficiencies, mutability and other biological activities of natural sites occurring within promoters, mRNA leaders, and other regulatory regions in pro- and eukaryotic genomes, their mutant forms and synthetic analogues. Since activity magnitudes are heavily system-dependent, the current version of ACTIVITY is supplemented by three novel sub-databases: (i) SYSTEM, measurement systems; (ii) KNOWLEDGE, sequence-activity relationships under fixed experimental conditions; and (iii) CROSS_TEST, procedures adapting a relationship from one measurement system to another. These databases are useful in molecular biology, pharmacogenetics, metabolic engineering, drug design and biotechnology. The databases can be queried using SRS and are available through the Web, http://wwwmgs. bionet.nsc. ru/systems/Activity/.
Cost‐Effectiveness of Triple Therapy Versus Etanercept Plus Methotrexate in Early Aggressive Rheumatoid Arthritis

To evaluate the cost‐effectiveness of all 4 interventions in the Treatment of Early Aggressive Rheumatoid Arthritis (TEAR) clinical trial: immediate triple (IT), immediate etanercept (IE), step‐up triple (ST), and step‐up etanercept (SE). Step‐up interventions started with methotrexate and added either etanercept or sulfasalazine plus hydroxychloroquine to patients with persistent disease activity.
Internal audit independence and objectivity: a review of current literature and opportunities for future research

This paper reviews the recent European and international literature on internal audit independence and objectivity. We focus on s tudies involving internal auditors that have been undertaken since the Institute of Internal Auditors’ revised definition of internal audit in 1999. The topics we examine are the internal auditor’s dual role as a provider of both assurance and consulting activities, the organizational status of internal audit, internal audit’s involvement in risk management, outsourcing and cosourcing of internal audit activities and the use of internal audit as a training ground for managers. Following our review of each of these topics, we discuss opportunities for further research.
Mutagenesis of the peptidyltransferase center of 23S rRNA: the invariant U2449 is dispensable.

U2449 is one of many invariant residues in the central loop of domain V of 23S rRNA, a region that constitutes part of the peptidyltransferase center of the ribosome. In Escherichia coli, this U is post-transcriptionally modified to dihydrouridine (D) and is the only D modification found in E.coli rRNAs. To analyze the role of this base and its modification in ribosomal function, all three base substitutions were constructed on a plasmid copy of the rrnB operon and assayed for their ability to support cell growth in a strain of E.coli lacking chromosomal rrn operons. Both purine substitution mutations were not viable. However, growth and antibiotic sensitivity of cells expressing only the mutant D2449C rRNA was indistinguishable from wild type. We conclude that while a pyrimidine is required at position 2449 for proper ribosomal function, the D modification is dispensable.
A Comparison between Maprotiline (Ludiomil) and Amitriptyline in the Treatment of Depressive Reaction in General Practice

In this trial in depressive reaction in general practice, maprotiline and amitriptyline, in a fixed dosage regime of 50 mg three times daily for three weeks, were equally effective therapeutic agents; all but two of the patients improving during the trial. Thirteen patients (16% of the group) withdrew from the study due to the severity of side-effects, predominantly because of drowsiness. In those patients who completed the trial both compounds were relatively well tolerated. The general pattern of side-effects ('mild’ drowsiness and dry mouth) was similar for both treatments, although maprotiline appeared to cause more dizziness than amitriptyline.
Temporomandibular Joint Involvement in Association With Quality of Life, Disability, and High Disease Activity in Juvenile Idiopathic Arthritis

To evaluate the demographic, disease activity, disability, and health‐related quality of life (HRQOL) differences between children with juvenile idiopathic arthritis (JIA) and their healthy peers, and between children with JIA with and without clinical temporomandibular joint (TMJ) involvement and its determinants.
Disease Activity During Pregnancy and the First Year Postpartum in Women With Systemic Lupus Erythematosus

Disease activity measured by validated methods has been sparsely examined during and after pregnancy in women with systemic lupus erythematosus (SLE). The aim of this study was to describe the longitudinal course of disease activity during pregnancy and the first year postpartum using the Lupus Activity Index in Pregnancy (LAI‐P).
Prevalence of Underweight, Stunting and Wasting Among Children in Qazvin, Iran

Background and Aim: Malnutrition and growth impairment are among the most common problems in children of developing countries. The aim of present study was to determine underweight, stunting, and wasting status in children less than 2 years in Qazvin (Iran) in 2007. Materials and Methods: In this study, 804 children aged between 0-24 months were evaluated. Data were collected through both family and child's health records. Results: According to World Health Organization (WHO) standard underweight, stunting, and wasting were observed in 11.7%, 11.5%, and 0.7% of the children, respectively. There was a significant correlation between underweight and the family size and birth order and also between stunting and family size, birth order, and parent education (p<0.05). Conclusion: This study revealed that the most common types of growth impairment in children under two years of age are underweight and stunting. Interventional measures are recommended.
Thermal denaturation of nucleosomal core particles

Thermal denaturation of very homogeneous preparations of core particles from chicken erythrocyte chromatin is studied by several techniques. The change in absorbance, which is very closely paralleled by changes in heat capacity, which is very closely paralleled by changes in heat capacity, is a biphasic process with inflexions at 60 degrees C and 74 degrees C. In contrast, isolated DNA of the same length denatures in a single transition around 44 degrees C. Monitoring the circular dichroism of the cores during thermal denaturation reveals biphasic changes in the secondary structure of the DNA, preceding the base unstacking by 10 degrees C in the first and 3 degrees C in the second phase. However, measurable alterations in the secondary structure of the histones are confined to the second phase with a melting temperature at 71 degrees C. Increase in the ionic strength of the buffer from 1 mM to 10 mM leads to almost monophasic melting curves as measured by absorbance and CD, while not causing any measurable conformational changes at room temperature. The melting of core particles is interpreted as a denaturation of about 40 base pairs in the first phase, followed by a massive breakdown of the native structure of a tight histone-DNA complex, which frees the remaining 100 base pairs for unstacking.