Miracle-dz/UniFAR-FTUs huggingface dataset:
Interaction of DNA‐dependent protein kinase with DNA and with Ku: biochemical and atomic‐force microscopy studies

DNA‐dependent protein kinase (DNA‐PK or the scid factor) and Ku are critical for DNA end‐joining in V(D)J recombination and in general non‐homologous double‐strand break repair. One model for the function of DNA‐PK is that it forms a complex with Ku70/86, and this complex then binds to DNA ends, with Ku serving as the DNA‐binding subunit. We find that DNA‐PK can itself bind to linear DNA fragments ranging in size from 18 to 841 bp double‐stranded (ds) DNA, as indicated by: (i) mobility shifts; (ii) crosslinking between the DNA and DNA‐PK; and (iii) atomic‐force microscopy. Binding of the 18 bp ds DNA to DNA‐PK activates it for phosphorylation of protein targets, and this level of activation is not increased by addition of purified Ku70/86. Ku can stimulate DNA‐PK activity beyond this level only when the DNA fragments are long enough for the independent binding to the DNA of both DNA‐PK and Ku. Atomic‐force microscopy indicates that under such conditions, the DNA‐PK binds at the DNA termini, and Ku70/86 assumes a position along the ds DNA that is adjacent to the DNA‐PK.
A Genome-Wide Screen for β-Catenin Binding Sites Identifies a Downstream Enhancer Element That Controls c-Myc Gene Expression

ABSTRACT Mutations in components of the Wnt signaling pathway initiate colorectal carcinogenesis by deregulating the β-catenin transcriptional coactivator. β-Catenin activation of one target in particular, the c-Myc proto-oncogene, is required for colon cancer pathogenesis. β-Catenin is known to regulate c-Myc expression via sequences upstream of the transcription start site. Here, we report that a more robust β-catenin binding region localizes 1.4 kb downstream from the c-Myc transcriptional stop site. This site was discovered using a genome-wide method for identifying transcription factor binding sites termed serial analysis of chromatin occupancy. Chromatin immunoprecipitation-scanning assays demonstrate that the 5′ enhancer and the 3′ binding element are the only β-catenin and TCF4 binding regions across the c-Myc locus. When placed downstream of a simian virus 40-driven promoter-luciferase construct, the 3′ element activated luciferase transcription when introduced into HCT116 cells. c-Myc transcription is negligible in quiescent HCT116 cells but is induced when cells reenter the cell cycle after the addition of mitogens. Using these cells, we found that β-catenin and TCF4 occupancy at the 3′ enhancer precede occupancy at the 5′ enhancer. Association of c-Jun, β-catenin, and TCF4 specifically with the downstream enhancer underlies mitogen stimulation of c-Myc transcription. Our findings indicate that a downstream enhancer element provides the principal regulation of c-Myc expression.
Towards ultraprotective mechanical ventilation

Purpose of review To survey the causes of ventilator-induced lung injury focusing on its mechanical determinants, lung stress and strain. Recent findings Tidal volume per ideal body weight (tidal volume/IBW) and airway pressure (PAW) are poor surrogates of strain and stress, which are respectively defined as the ratio of volume variation to lung resting volume and transpulmonary pressure. In healthy lungs, ventilation becomes lethal with strain reaching total lung capacity (tidal volume/IBW around 30–40 ml/kg) and with its related stress (roughly 24 cmH2O). The striking discrepancy between experimental data and clinical scenarios (harm at tidal volume/IBW of 12 ml/kg) may be explained by lung dishomogeneity, locally generating ‘stress risers’ or ‘pressure multipliers’. When mechanical ventilation becomes unsafe, as inferred from computed tomography-scan evaluation of dishomogeneity and stress/strain values, lung protective strategies can be maximized by further reducing tidal volume and increasing PAW (e.g. high frequency oscillatory ventilation). In alternative, artificial lungs may provide adequate gas exchange while reducing the load of mechanical ventilation. Recently, outcome benefit was shown with the use of this technique in H1N1 patients. Summary When lung protective strategy is considered unsafe, various techniques of extracorporeal respiratory support may be applied, which by decreasing the load of mechanical ventilation, allow partial to total lung rest.
Isolation and Antimicrobial Susceptibilities of Chlamydial Isolates from Western Barred Bandicoots

ABSTRACT A range of species of Chlamydiales have previously been detected in a variety of Australian marsupials, including koalas and western barred bandicoots. Thirty-seven ocular, urogenital, or nasal swabs were obtained from 21 wild western barred bandicoots. Chlamydia culture and antibiotic susceptibility testing were performed for cycloheximide-treated HEp-2 cells in 96-well microtiter plates. Chlamydia spp. were isolated from 11 specimens from 9 (42.8%) bandicoots. All isolates were identified as Chlamydiales by conventional PCR with 16S and 23S rRNA gene primers specific to Chlamydiales and were confirmed to be Chlamydia pneumoniae by a C. pneumoniae-specific ompA-based real-time PCR assay and 16S rRNA and 23S rRNA gene signature sequence analyses. The MICs of azithromycin, doxycycline, ciprofloxacin, and enrofloxacin for 10 C. pneumoniae isolates from these bandicoots ranged from 0.015 to 1 μg/ml, 0.25 to 1 μg/ml, 0.25 to 2 μg/ml, and 0.25 to 0.5 μg/ml, respectively. The MICs at which 90% of isolates were inhibited and the minimal bactericidal concentrations were within the ranges reported previously for human isolates of C. pneumoniae.
FASON: First and Second Order Information Fusion Network for Texture Recognition

Deep networks have shown impressive performance on many computer vision tasks. Recently, deep convolutional neural networks (CNNs) have been used to learn discriminative texture representations. One of the most successful approaches is Bilinear CNN model that explicitly captures the second order statistics within deep features. However, these networks cut off the first order information flow in the deep network and make gradient back-propagation difficult. We propose an effective fusion architecture - FASON that combines second order information flow and first order information flow. Our method allows gradients to back-propagate through both flows freely and can be trained effectively. We then build a multi-level deep architecture to exploit the first and second order information within different convolutional layers. Experiments show that our method achieves improvements over state-of-the-art methods on several benchmark datasets.
Prior knowledge involved in inferencing information from warnings for younger and older adults

Abstract Warning comprehension is critical to safely use medications and products with health-related consequences, especially for older adults who often use multiple medications. The ability to infer from short texts influences the warning comprehension process and in turn is influenced by prior knowledge. Mixed evidence suggests that age may moderate inferencing ability. This study combined quantitative and qualitative measures to explore the role of prior knowledge in inferencing and age-related differences in the nature of the information used. Twenty younger (18–28) and 20 older (65–75) adults evaluated whether 16 one-sentence statements were true (consistent) or false (inconsistent) in relation to two-sentence text passages that were real (i.e. taken from products such as cleaners and OTC medications) or their reverse. Statements contained information explicitly stated or implied in the text passage. Accuracy was generally high, higher for real text passages (than reversed) and explicit statements (than implicit). Older adults did less well than younger adults for reversed text passages. Qualitative analyses suggest that given contradictory information, older adults rely on prior knowledge more than younger adults, which may account for age-related differences in their conclusions. Thus, older adults may be more likely to misinterpret health-related communications if the information conflicts with their prior knowledge.
Preservation of urine for flow cytometric and visual microscopic testing.

BACKGROUND Preservatives that could prevent destruction of cells, casts, and bacteria in urine are of great practical importance because they allow centralization and improvement of accuracy of urine particle counting. We compared two in-house mixtures and one commercial solution, as well as refrigeration, for their ability to preserve urine for both automated analysis (flow cytometry) and visual microscopy. METHODS Urine specimens were preserved by refrigeration at 4 degrees C without preservatives (procedure 1); in a lyophilized solution intended to preserve specimens for bacterial culture (Urine C&S tubes; BD Preanalytical Solutions; procedure 2); in 10 mL/L formalin-0.15 mol/L NaCl (procedure 3); in 80 mL/L ethanol-20 g/L polyethylene glycol (procedure 4); and by storage at 20 degrees C without preservatives (procedure 5). Test strip measurements were used to select specimens positive for leukocyte esterase, hemoglobin, albumin, or nitrite. For 106 consecutive strip-positive specimens, urinalysis was performed by UF-100 (Sysmex) and by phase-contrast microscopy after Sternheimer supravital staining. Automated analysis was performed at arrival in the morning, on the same day in the afternoon, and after 1 and 3 days. Visual microscopy was performed at arrival and 3 days later. RESULTS Urine bacterial counts were well preserved with procedures 1-3, with a false-positive rate of 0.0-3.4% at day 3 vs 28% without preservation (procedure 5). Erythrocytes were poorly preserved for 3 days (kappa coefficients, 0.24-0.61); after 1 day, fair preservation was seen with procedure 2 (kappa = 0.78), compared with less favorable preservation with procedure 1 (kappa = 0.61) or procedure 5 (kappa = 0.66). Leukocytes were well preserved by all five procedures in the acidic adult urines investigated. Counts of casts and large epithelial cells were artifactually increased by procedure 3. Procedure 2 performed at least as well as refrigeration for specimens analyzed with visual microscopy. CONCLUSIONS Urine specimens from adults can be stabilized at room temperature for both automated particle analysis and visual microscopy.
The Particulars on Universals: A Comparison of the Acquisition of Tense-Aspect Morphology among Japanese- and French-Speaking Learners of English

<p> This study investigated the relationship between L1 and the developmental sequences for the acquisition of temporal morphology that are predicted by the aspect hypothesis. The use of tense-aspect markers in 7,784 past contexts by 139 Japanese- and French-speaking ESL learners was analyzed. A repeated measures ANOVA supported the predictions of the aspect hypothesis. For both L1 groups, the marking of past spread from achievements and accomplishments (telics) through activities to statives, and the preferred non-past responses for statives and activities were present and progressive, respectively. The magnitude, rather than the direction, of the lexical aspect effect with achievements was the only significant L1 difference. The results lend support to the hypothesis that the influence of lexical aspect on the acquisition of grammatical morphology is a language learning universal. They are also consistent with research on other linguistic features in which selective influence of L1 on developmental sequences has been observed. </p> <p> La présente étude avait pour but d'examiner le rapport entre la langue première (L1) et les séquences de développement de l'acquisition de la morphologie temporelle telles que prévues par l'hypothèse aspectuelle. Les analyses portent sur l'emploi du temps et de l'aspect en anglais de 139 apprenants francophones et japonais dans 7 784 contextes au passé. Les résultats d'une analyse de variance sur des mesures répétées confirment les prévisions de l'hypothèse aspectuelle. Dans les deux groupes d'apprenants, pour marquer le passé, l'emploi de la forme du prétérit simple s'étend des achèvements et des accomplissements (verbes téliques) aux activités et aux états (verbes atéliques). Pour le non-passé, il y avait une préférence pour l'emploi du présent avec les états et du progressif avec les activités. La seule différence significative selon la L1 se trouvait dans la grandeur de l'effet de l'aspect lexical pour les achèvements. Ces résultats appuient l'hypothèse selon laquelle l'influence de l'aspect lexical sur l'acquisition de la morphologie grammaticale constitue un universel de l'acquisition des langues. Ils sont aussi compatibles avec des recherches sur d'autres traits linguistiques où l'on a observé l'influence sélective de la L1 sur les séquences de développement. </p>
Primary RET-mutated lung neuroendocrine carcinoma in MEN2B: response to RET-targeted therapy.

Multiple endocrine neoplasias (MENs) are genetic syndromes distinguished by speciﬁc patterns of benign and malignant tumors of endocrine glands. MEN2 is caused by autosomal dominant inheritance of a gain-of-function mutation in the RET proto-oncogene on chromosome 10 (Mulligan & Ponder 1995, Santoro et al . 1995) and is further subclassiﬁed into three syndromes based on clinical phenotype: MEN2A (medullary thyroid cancer (MTC), pheochromocytoma, primary parathyroid hyper-plasia); MEN2B (MTC and pheochromocytoma), and familial medullary thyroid cancer (MTC only). MEN is ﬁrst suspected when an index patient presents with one or more tumors speciﬁc to that syndrome. Of all MEN2B cases, 95% are represented by a germline point mutation affecting codon 918 (exon 16) resulting in a methionine to threonine alteration (M918T), inducing constitutive activation of the intracellular tyrosine kinase domain of the encoded RET receptor tyrosine kinase (RTK) (Alberti et al . 2003). Tumor formation occurs in the neuroendocrine organs where constitutively activated RET is expressed. the described
Are Test Accommodations for English Language Learners Fair?

Test accommodations have been proposed to help overcome the unfair challenges faced by English Language Learners (ELLs) due to their relatively low English proficiency. A test accommodation is regarded as effective when it improves the test performance of ELLs. However, this improvement raises the question of whether such accommodations give ELLs an unfair advantage. One criterion used in determining a test accommodation's fairness is that it should only remove the disadvantage that ELLs face in regard to their low language proficiency, without giving ELLs any additional advantages. This criterion is met when the test accommodation does not improve the test performance of the non-ELLs when the same accommodation is applied to them. To determine the fairness and, thus, the validity of test accommodations for ELLs, a meta-analysis using hierarchical linear modeling was conducted to compare the effects of test accommodations on the test performance of ELLs and on that of non-ELLs. The results indicated that test accommodations improved ELLs' test performance by about 0.156 standard deviation units but did not discernibly influence the test performance of non-ELLs. This meta-analysis, therefore, constitutes evidence to support the fairness and validity of providing test accommodations for ELLs.
Rates and predictors of anxiety and depressive disorders in adolescents of parents with HIV

Abstract Children with a parent with HIV (PWH) are expected to be at increased risk for anxiety and depressive disorders because of the potential impact of parental HIV illness and death. PWH and their adolescent children were initially recruited in the context of a randomized intervention trial, with more than 60% of adolescents experiencing death of a parent prior to assessment. Using the Composite International Diagnostic Interview, lifetime and recent anxiety and depressive disorders were measured 4 years following enrollment. Adolescents of PWH had high rates of any lifetime and recent anxiety disorders. In particular, both lifetime and recent rates of post-traumatic stress disorder were high. Lifetime anxiety disorders were significantly associated with older age, baseline emotional distress and prior traumatic exposure, while lifetime depressive disorders were associated with female gender, parental bereavement and prior traumatic exposure. These findings demonstrate the need for appropriate screening and treatment of adolescents of PWH.
Relations With Faculty as Social Capital for College Students: Evidence From Puerto Rico

In this study, a social capital framework was adopted to investigate the extent to which academically focused interactions with faculty and other institutional agents serve as social capital for college students, using National Survey of Student Engagement data from a large, science, technology, engineering and math-focused institution in Puerto Rico. As expected, previous achievement variables were the strongest factors in explaining college grade point average. Perceived quality of relations with faculty members was more important than frequency of interactions in explaining performance. Further research utilizing more specific measures of student-faculty interaction is necessary. Institutional interventions can help increase student-faculty interaction and cultivate broadened access to this form of social capital.
Diagnosis of Bovine Paratuberculosis by a Novel Enzyme-Linked Immunosorbent Assay Based on Early Secreted Antigens of Mycobacterium avium subsp. paratuberculosis

ABSTRACT We previously reported that protein antigens of serodiagnostic potential were more abundant in culture filtrates than cellular extracts from liquid cultures of Mycobacterium avium subsp. paratuberculosis (D. Cho and M. T. Collins, Clin. Vaccine Immunol. 13:1155-1161, 2006). Based on this observation, a novel enzyme-linked immunosorbent assay (ELISA) using antigens secreted by young (early- to mid-log-phase) cultures of M. avium subsp. paratuberculosis JTC303 (a low-passage isolate originating from the ileum of a Holstein bull) in mycobactin-supplemented Watson-Reid medium (pH 6.0) was developed and evaluated using a previously described panel of bovine sera (M. T. Collins et al., Clin. Diagn. Lab. Immunol. 12:685-692, 2005) that included 444 paratuberculosis cases and 412 controls. The new assay, called JTC-ELISA, had a significantly higher diagnostic sensitivity and an equivalent specificity compared to those of five commercial paratuberculosis ELISA kits. By receiver-operating characteristic analysis, the JTC-ELISA had the highest area under the curve of the six assays evaluated. The JTC-ELISA was particularly sensitive at detecting low-level fecal shedders of Mavium subsp. paratuberculosis (40%; the sensitivity of the commercial kits was 20%). The JTC-ELISA works effectively on both serum and milk samples for the detection of cattle with subclinical M. avium subsp. paratuberculosis infections, providing a cost-effective diagnostic tool to support paratuberculosis control programs in cattle herds.
The Experience of Anxiety in Young Adults With Autism Spectrum Disorders

Anxiety is known to be common among young adults with autism spectrum disorders (ASD), yet little is known about the nature of their experiences or the strategies they use to live and cope with their reported anxiety. In this qualitative study, we began to address this issue through two focus groups involving 11 young adults with ASD, and 10 parents and professionals. Participants in each group were asked to discuss the triggers for anxiety, the consequences of anxiety, and strategies they have used, would like to use, or have seen individuals with ASD use to manage their anxiety. The participants identified multiple personal and environmental sources of anxiety, noting the substantial impact they have on their everyday lives at home, work, university, and in the community. Their individual experiences and strategies for living and coping with anxiety are presented.
Important Variables in Reasoning about Social Rules

In everyday life people produce and accept behaviours that deviate to some extent from a rule, but are nevertheless recognised as examples of the rule. This study analyses the effects of three variables, i.e. type of substitution, centrality of the element involved in the transgression, and linguistic formulation of rules, on judgements of acceptability and seriousness of such deviations. Three groups of 60 subjects each (4-year-olds, 9-year-olds, and adults) were randomly assigned to receive one of three linguistic formulations of a prudential rule. In the first, the rule was stated without justification; in the second, the goal of the rule was stated; in the third, a description of the actions and the items necessary to obey the rule was given. All subjects had to judge a variety of rule transgressions based on elimination, unsuitable substitution or suitable substitution of a central or a peripheral element of the rule. Linguistic formulation had, at best, a modest effect on judgements. However, there were strong effects of type of substitution and centrality. Moreover, the effects of these variables differed with age and the subjects showed an increasing capacity to take into account all the elements involved.
An Introduction to the Sport Commitment Model

This article introduces a sport-specific theoretical model of commitment. Sport commitment is defined as a psychological state representing the desire or resolve to continue sport participation. The Sport Commitment Model proposes that sport commitment is determined by sport enjoyment, involvement alternatives, personal investments, social constraints, and involvement opportunities. Greater sport enjoyment, personal investments, social constraints, involvement opportunities, and less attractive involvement alternatives are predicted to lead to higher levels of sport commitment. Constitutive definitions were established for each of the model's components, and questionnaire items were developed. Results from the first empirical test of the model conducted with girls (n = 95) and boys (n = 83) participating in a Little League program showed that the questionnaire items formed reliable scales. Correlational analyses demonstrated that several predictors were related to sport commitment as hypothesized. Stepwis.
Regret in economic and psychological theories of choice

Numerous studies have shown that choice can be influenced by expectations of regret or disappointment (or, for positive outcomes, of rejoicing or elation). Psychological researchers measure these expectations with self-report instruments, economists infer them from observed choice behavior. The present study examines whether the emotion postulates embodied in economic choice models correspond to expected and experienced emotions as measured by self-report. In a laboratory study (n = 50) of student participants playing real-money lotteries, we included questionnaire measures of expected emotions for each possible lottery outcome. These emotion measures are reliable and well behaved, and modestly predictive of actual choices. They did not, however, conform well to the specific postulates of economic choice models, though they did show some of the juxtaposition effects proposed in such models. Emotional reactions to decision outcomes may be better characterized by broad measures of positive and negative affect than as nuanced mixtures of distinct emotions.