Miracle-dz/UniFAR-FTUs huggingface dataset:
Solution structure of a reverse transcriptase recognition site of a LINE RNA from zebrafish

Long interspersed nuclear element (LINE) is known to be transposed by reverse transcription using its RNA transcript. Recognition of the 3' stem-loop of LINE RNA by its reverse transcriptase (RT) is an important step of the retrotransposition. Our previous study revealed that the second G residue (G8) in the GGAUA loop of a 17mer LINE RNA from eel, UnaL2-17, is recognized by its RT and the U residue (U10) in the same loop is required to maintain the loop structure (Baba S, Kajikawa M, Okada N, Kawai G. Solution structure of an RNA stem-loop derived from the 3' conserved region of eel LINE UnaL2. RNA 2004;10:1380-1387). ZfL2-2, a LINE from zebrafish, has the same 3' stem-loop with UnaL2 and ZfL2-1 has similar but distinct 3' stem-loop with an insertion which can form an additional stem-loop. Here, we determined the solution structure of the 34mer RT recognition site of the LINE RNA (ZfL2-1-34). It was found that ZfL2-1-34 forms a hairpin with an internal loop, the tertiary structure of which is superimposed with that of ZfL2-2. It is noted that A10 and the inserted stem-loop, starting with A12, in ZfL2-1-34 located at the positions corresponding to those of G8 and U10, respectively, in UnaL2-17. These results strongly suggest that the two LINEs share the similar recognition mechanism and the A10 in ZfL2-1-34 is the determinant recognized by its RT.
Ribosomal DNA Sequence Analysis of Mucosa-Associated Bacteria in Crohn’s Disease

Background:Enteric bacteria are implicated in the pathogenesis of Crohn’s disease (CD); however, no specific causative organisms have been identified. Aims:This study was undertaken to correlate disease activity with changes in intestinal biota in patients with CD. Subjects:Ribosomal DNA analysis was used to explore the composition of the intestinal biota in patients with (1) CD undergoing colonoscopy, (2) CD undergoing surgical resection, and (3) no inflammatory bowel disease. Methods:Primers targeting bacterial 16S ribosomal DNA (rDNA) were used to amplify bacterial DNA associated with active CD lesions, comparable normal tissue from patients with CD, and normal control tissue. Each amplicon was cloned. Seven hundred thirty-nine rDNA clones were sequenced from 16 biopsies from CD patients, 15 surgical samples, and 10 biopsies from normal control patients. Results:Known extracellular or intracellular pathogens were not found. No rDNA sequence, phylogenetic group, or subgroup was consistently associated with CD lesions compared with normal tissues from the same patients. Colonic biopsies from CD-afflicted patients compared with biopsies from normal control subjects had an increase in facultative bacteria; in small bowel, CD patients had an increase in the Ruminococcus gnavus subgroup with a decrease in the Clostridium leptum and Prevotella nigrescens subgroups. However, differences in small bowel may have reflected individual variation rather than disease association. Surgical samples showed differences when compared with biopsy-derived samples. Conclusions:These findings suggest that CD is not caused by invasive pathogens associated specifically with the sites of lesions but that dysbiosis exists in this condition.
A Comparison of Logistic Regression to Decision Tree Induction in the Diagnosis of Carpal Tunnel Syndrome

This paper aims to compare and contrast two types of model (logistic regression and decision tree induction) for the diagnosis of carpal tunnel syndrome using four ordered classification categories. Initially, we present the classification performance results based on more than two covariates (multivariate case). Our results suggest that there is no significant difference between the two methods. Further to this investigation, we present a detailed comparison of the structure of bivariate versions of the models. The first surprising result of this analysis is that the classification accuracy of the bivariate models is slightly higher than that of the multivariate ones. In addition, the bivariate models lend themselves to graphical analysis, where the corresponding decision regions can easily be represented in the two-dimensional covariate space. This analysis reveals important structural differences between the two models.
Strapped for Time or Stressed Out? Predictors of Work Interruption and Unmet Need for Workplace Support Among Informal Elder Caregivers

Objective: We evaluate whether strong associations between unmet need and work interruption observed among informal elder caregivers are explained by caregiver personal characteristics, caregiving situations, or diminished caregiver well-being. Method: We analyze a proprietary survey of informal elder caregivers conducted by a single large U.S. employer (N = 642 caregivers). Results: Unmet need was about twice as common among those experiencing mild (29.79%) or severe interruption (35.00%) relative to those who did not interrupt work (16.87%). Although caregiver characteristics and aspects of caregiving situation show links to either unmet need or work interruption specifically, the association between unmet need and work interruption was not explained by these factors, or by caregiver well-being. Discussion: Needs-related work interruptions may arise by other workplace processes, such as organizational culture, that should be measured and tested explicitly by future research.
Cost-effectiveness implications of the timing of antiretroviral therapy in HIV-infected adults.

BACKGROUND The appropriate time to initiate antiretroviral therapy is controversial for human immunodeficiency virus (HIV)-infected patients with CD4 cell counts between 200/microL and 350/microL and low levels of HIV RNA, potentially leading to barriers to treatment access. OBJECTIVE To examine the effect of cholesterol changes and fat redistribution symptoms on the clinical benefits and cost-effectiveness of early antiretroviral therapy in these patients. METHODS We used a state-transition model to compare initiating antiretroviral therapy at CD4 cell counts of 350/microL (early therapy) with initiating therapy at CD4 cell counts of 200/microL (deferred therapy) in patients with HIV RNA levels of 10,000 to 30,000 copies/mL. Data were from randomized clinical trials, cohort studies, and other published literature. RESULTS If cholesterol changes associated with antiretroviral therapy resulted in a permanent increase in coronary heart disease risk, life expectancy with early therapy was 16.54 years (vs 16.66 years without this risk) and with deferred therapy was 13.73 years (vs 13.80 years without this risk). Early therapy was a more efficient use of resources (ie, dominated) compared with deferred therapy. Early therapy cost $13,000 per quality-adjusted life-year compared with no therapy with or without increased coronary heart disease risk, and $17,000 to $24,000 per quality-adjusted life-year taking into account the quality-of-life reduction in patients with fat distribution symptoms. Early therapy had a higher quality-adjusted life expectancy than deferred therapy as long as this quality-of-life reduction was 70% or less. CONCLUSIONS Changes in cholesterol or quality of life associated with antiretroviral therapy do not justify limiting access to early HIV treatment. The effect of fat redistribution symptoms on quality of life will determine the optimal choice of early vs deferred therapy for an individual patient.
ABILITY OF ADULT PATIENTS TO PREDICT ABSENCE OR PRESENCE OF FEVER IN AN EMERGENCY DEPARTMENT TRIAGE CLINIC

Introduction: Fever is the most appreciated manifestation of disease which usually raises high therapeutic expectations. Patients seek medical advice because they think they are sick and feverish. If they feel that they are sick but not feverish, they may not seek medical advice. Subjective fever may also be an important clue to further evaluation of the patient. Objective: The aim of this study was to assess the reliability of adult patients to predict absence or presence of fever in Emergency Department triage clinic. Methods: A prospective study of 1241 ambulatory adult patients (above 12 years of age) was carried out over a three-week period. All patients were asked whether or not they had fever or felt they had fever or were running a temperature before oral temperature was taken with an IVAC digital machine. Two sets of temperature readings were taken to define fever as 37.8°C or greater, and 38.0°C or greater. Results: The sensitivity and specificity of detecting fever by subjective means was 89.6% and 94.5% for male and 90.0% and 94.8% for female. The accuracy rates were 93.9% and 94.6% respectively. The prevalence of objective fever was 8.7% yielding general positive and negative predictive values of 80.9% and 98.9% with an accuracy rate of 94.2%. Conclusion: The reliability of adult patients attending triage clinic in assessing subjective fever was found to be good. Four out of five of our patients who believed they had a fever were actually found to have an objective temperature increase (38.0°C or greater). This means that medical staff should take a complaint of subjective fever in our population more seriously.
Ultrasound-guided vacuum-assisted core biopsy in the diagnosis and treatment of focal lesions of the breast – own experience

INTRODUCTION Vacuum-assisted core biopsy (VACB) guided by ultrasound is a minimally invasive method used in diagnosis and treatment of breast focal lesions. Vacuum-assisted core biopsy is an interesting minimally invasive alternative to open surgical biopsy. AIM To assess the value of ultrasound-guided vacuum-assisted core biopsy in the diagnosis and treatment of breast focal lesions. MATERIAL AND METHODS In the period 2009-2010, 397 ultrasound-guided vacuum-assisted core biopsies were performed. Mean age of the patients was 41.7 years (18-92 years), and size of the lesions ranged from 3 mm to 65 mm, mean size being 12 mm. All women with diagnosed atypical ductal hyperplasia or cancer were qualified for surgery. The patients with histopathologically benign lesions were under follow-up. RESULTS Samples sufficient for histopathological examination were obtained from 394 cases (99.2%). Of all 397 lesions, 293 (73.7%) were diagnosed as benign, there were 6 (1.6%) cases of atypical ductal hyperplasia and 98 (24.7%) malignant lesions. Three hundred and sixty-nine lesions were below 15 mm in diameter, of which 339 (91.9%) were totally removed during the VACB. CONCLUSIONS The results obtained confirm high efficiency of ultrasound-guided VACB in the differential diagnosis of breast focal lesions, including impalpable ones. It is a safe method with a low complication rate. In the case of benign lesions with a diameter not exceeding 15 mm, it allows one to excise the whole lesion and is a very good alternative to an open surgical biopsy. Vacuum-assisted core biopsy should be a standard and the method of choice in diagnosing breast lesions.
Identification of Cysteine Ubiquitylation Sites on the Sec23A Protein of the COPII Complex Required for Vesicle Formation from the ER

Background: COPII is a multiprotein complex that surrounds carrier vesicles budding from the Endoplasmic Reticulum and allows the recruitment of secretory proteins. The Sec23a protein plays a crucial role in the regulation of the dynamics of COPII formation ensuring the proper function of the secretory pathway. Objective: Since few evidences suggest that ubiquitylation could have a role in the COPII regulation, the present study was aimed to establish whether the Sec23a component of the vesicular envelope COPII could be ubiquitylated Method: Sec23a ubiquitylation was revealed by co-immunoprecipitation experiments. Recombinant Sec23a was gel-purified and analyzed by mass spectrometry subjected to trypsin proteolysis. Signature peptides were identified by the presence of Gly–Gly remnants from the C-terminus of the ubiquitin attached to the amino acid residues of the substrate. Recombinant Sec23a proteins bearing mutations in the ubiquitylation sites were used to evaluate the effect of ubiquitylation in the formation of COPII Results: We identified two cysteine ubiquitylation sites showed at position 432 and 449 of the Sec23a protein sequence. Interestingly, we revealed that the amino acid residues of Sec23a joined to ubiquitin were cysteine instead of the conventional lysine residues. This unconventional ubiquitylation consists of the addition of one single ubiquitin moiety that is not required for Sec23a degradation. Immunofluorescence results showed that Sec23a ubiquitylation might influence COPII formation by modulating Sec23a interaction with the ER membrane. Presumably, this regulation could occur throughout continual ubiquitylation/de-ubiquityliation cycles. Conclusion: Our results suggest a novel regulatory mechanism for the Sec23a function that could be crucial in several pathophysiological events known to alter COPII recycling
Methyl (2Z)-((2Z)-2-{(2E)-[1-(4-methylphenyl)ethylidene]hydrazinylidene}-4-oxo-3-phenyl-1,3-thiazolidin-5-ylidene)ethanoate

The asymmetric unit of the title compound, C21H19N3O3S, contains two independent molecules. In one molecule, the 1,3-thiazolidine ring forms dihedral angles of 86.19 (8) and 8.37 (8)° with the phenyl and benzene rings, respectively. The corresponding dihedral angles in the other molecule are 69.60 (7) and 14.08 (7)°. The dihedral angle between the phenyl and benzene rings is 84.70 (8)° in one molecule and 69.62 (8)° in the other. In the crystal, molecules pack in layers approximately parallel to (10-2). There are weak C—H⋯O hydrogen bonds within these layers. Further weak C—H⋯O hydrogen bonding occurs between the layers to form a three-dimensional network. A weak C—H⋯π interaction is also observed.
Magnetic Field and Fluid Flow Computation of Plural Kinds of Magnetic Particles for Magnetic Separation

Magnetic chromatography is an effective system for fine magnetic particle separation because of its strong magnetic field gradients. We have been developing the magnetic chromatography system to separate two or more kinds of fine magnetic particle with different sizes. To evaluate the performances of our developed system, we have also developed a simulation code with taking into account the fluid dynamics and magnetics. It is, however, difficult to consider two or more kinds of fine magnetic particles with different sizes in the simulation, because magnetic interferences between two or more kinds of magnetic particles need to be considered. Therefore, we have newly developed a simulation code to deal with magnetic interferences between two or more kinds of fine magnetic particles.
Scalable classification-based word prediction and confusible correction

We present a classification-based word prediction model bas ed on IGTREE, a decision-tree induction algorithm with favorable scalingabilities. Through a first series of experiments we demonstrate that the system exhibits log-li near increases in prediction accu- racy and decreases in discrete perplexity, a new evaluation metric, with increasing numbers of training examples. The induced trees grow linearly with t he amount of training examples. Trained on 30 million words of newswire text, prediction acc uracies reach 42.2% on the same type of text. In a second series of experiments we show that th is generic approach to word pre- diction can be specialized to confusible prediction, yield ing high accuracies on nine example confusible sets in all genres of text. The confusible-speci fic approach outperforms the generic word-prediction approach, but with more data the differenc e decreases. RESUME. Cet article presente un modele pour la tâche de prediction demots, consideree ici comme une tâche de classification. Ce modele repose sur l'uti lisation de IGTREE, un algo- rithme d'inference d'arbre de decision capable de traiter ala fois un grand nombre de classes et d'exemples d'apprentissage. A travers une premiere serie d'experimentations nous montrons que la capacite de prediction du modele augmente log-lineai rement avec le nombre d'exemples d'entrainement. Le meme comportement est obtenu avec laperplexite discrete, une nouvelle metrique introduite pour la tâche de prediction de mots ; la t aille des arbres inferes croit, elle, lineairement. Lorsque notre modele est entraine sur un corp us journalistique de 30 millions de mots, le nombre de mots correctement predits est de 42.2 % sur des textes journalistiques. Une seconde serie d'experimentations demontre que ce predicte ur generique peut etre specialise pour traiter des configurations dans lesquelles l'ensembledes mots a predire se restreint a un petit ensemble. Le modele specialise atteint des meilleursresultats que le classifieur generique.
The acquisition of Egyptian Arabic as a native language

Foreword Preface AcknowledgementsList of Symbols 1. INTRODUCTION Scope of the Study Goals of the StudyNeed for the StudyDuration and Location of the Study DurationLocationMethodology Followed Recordings and Transcriptions Types of Speech Observed Children in the Study Families in the Village and in the Study Approach Used with Village Residents Assistance Received in Conducting the StudyStructural Sketch of the Language The Root and Pattern SystemPhonologyMorphologySyntax 2. BASIC CHARACTERISTICS OF THE PHYSICAL AND FAMILY ENVIRONMENT The Physical Environment The Village SurroundingsFamily HomesThe Government Cooperative UnitPhysical Characteristics of the Children in the StudyThe Social Structure The Extended FamilyRoles of Family MembersTraining of ChildrenChildren's Daily Routines, Work and GamesFormal EducationEffects of the Social Structure on ChildrenSpecial Uses of Language 3. THE DEVELOPMENT OF PHONOLOGY The Phonological System in Adult Language ConsonantsVowelsFunctional Load of PhonemesSyllable TypesThe Babbling Stage Theoretical ConsiderationsData Obtained in This StudyEarly ImitationClassification of DataStages of Acquisition of the Phonological System Theoretical ConsiderationsStage IStage IITwo Intermediate Case StudiesStage IIIOrder of Acquisition of Phonemes Individual PhonemesPhoneme CombinationsSummaryComparison with Phonemic Development in Other LanguagesImitation Theoretical ConsiderationsData Obtained in This StudyThe Imitation TestsFinal Observations 4. EARLY COMMUNICATION AND INITIAL VOCABULARY Comprehension Theoretical ConsiderationsThe Comprehension TestConclusionsEffects of Other Factors on PerformanceEarly Speech and Vocabulary Theoretical ConsiderationsData Obtained in This StudyBaby Talk Theoretical ConsiderationsData Obtained in This StudyLinguistic FeaturesSocial ContextBelief System 5. THE DEVELOPMENT OF SYNTAX Early Stages of Syntactic Development Theoretical ConsiderationsThe One-Word StageThe Multi-Word StagesThe Acquisition of the Negative Rules for Negation in Adult LanguageThe Negation TestChild Syntactical Rules and Stages for NegationThe Acquisition of the Interrogative Rules for Interrogation in Adult LanguageThe Interrogation TestChild Syntactical Rules and Stages for InterrogationSummary 6. THE DEVELOPMENT OF MORPHOLOGY Early Stages of Morphological Development Theoretical ConsiderationsSome Characteristics of Early Morphological DevelopmentThe Acquisition of Inflectional Affixes for Noun Plurals Rules for Pluralizing Nouns in Adult LanguageThe Noun Plural TestChild Rules and Stages for Noun PluralizationsThe Acquisition of the Inflectional Affixes and Agreement for Adjectives Rules for Adjective Inflection and Agreement in Adult LanguageThe Adjective TestChild Rules and Stages for Adjective Inflection and AgreementSummary 7. CONCLUSION Review of Findings in This StudyImplications for Theories Regarding Language and Primary Language AcquisitionSuggestions for Further ResearchBibliography
Are ultrasound, laser and exercise superior to each other in the treatment of subacromial impingement syndrome? A randomized clinical trial.

BACKGROUND Subacromial impingement syndrome (SIS) is the most common reason for shoulder pain. Ultrasound and laser are the physical therapy modalities, in conservative treatment of SIS. AIM The aim of this study was to define and compare the efficacy of ultrasound, laser and exercise in the treatment of SIS. DESIGN This was a randomized controlled trial with-pre and post-treatment evaluations SETTING Out-patients referred to physical medicine and rehabilitation unit. POPULATION This study was performed on 52 patients with SIS. The patients were randomly allocated into three groups METHODS The patients were treated five days a week for three weeks with hotpack+ultrasound+exercise (the first group); hotpack+laser+exercise (the second group), or hotpack+exercise (the third group). The pre and post treatment ranges of motion were measured in the patients. The visual analogue scale (VAS) was used to evaluate the severity of pain. Constant scoring was used to evaluate the shoulder functions and the results were compared after the treatment. RESULTS When the post-treatment results of the groups were compared with the pretreatment results, there was a statistically significant improvement in each of the three groups, in the pain, the range of motion and the functional improvement at the shoulder (P<0.05). However, the inter-group comparison did not reveal any statistically significant difference in the parameters indicating improvement (P>0.05). CONCLUSION The results of this study demonstrated that ultrasound and laser treatments were not superior to each other in the treatment of SIS. CLINICAL REHABILITATION IMPACT . Exercise treatment forms the base for the conservative treatment.
Communicating the Right Emotion to Generate Help for Connected Versus Unconnected Others

This study investigated the effectiveness of positive versus negative and of other-focused versus mixed- (ego- and other-) focused feelings evoked in advertisements promoting help for connected versus unconnected needy people. Results showed that when help is asked for people to whom respondents feel connected, positive (vs. negative) and mixed-focused (vs. other-focused) feelings led to more positive ad evaluations and increased respondents’ helping intentions. When help was needed for unconnected people, the negative ads were most effective. Furthermore, it was investigated whether the effect of other-focused versus mixed-focused feelings on ad evaluations and helping intentions was mediated by people’s motivation to help.
Identification of Dynamic Bearing Parameters: A Review

In this paper, we present a review of the experimental identification of dynamic parameters of bearings in a rotating machine. Major emphasis is given to vibration-based identification methods and the review encompasses descriptions of experimental measurement techniques, mathematical modeling, parameter extraction algorithms and uncertainty in the estimates applied to a variety of bearings. The parameter extraction algorithms include the descriptions of governing equations of the rotor-bearing system and identification methods in both time and frequency domains. The identification techniques have been classified based on methods used to excite the system. The review includes a variety of bearings and similar components, which play an active link between the rotating and stationary parts of a machine. Based on the state of the art in bearing identification, conclusions are made and future directions are suggested.