Miracle-dz/UniFAR-FTUs huggingface dataset:
Using peripheral smear review, age and absolute lymphocyte count as predictors of abnormal peripheral blood lymphocytoses diagnosed by flow cytometry

Absolute lymphocytosis in the elderly raises the possibility of malignancy and generally warrants further investigation. To better correlate clinical variables with the frequency of neoplastic lymphoid processes in this population, we retrospectively reviewed archived flow cytometric analyses from peripheral blood specimens on patients of 50 years of age and older that had been deemed suspicious for a lymphoproliferative process after peripheral smear review. Age, absolute lymphocyte count (ALC), white blood cell count and relative lymphocyte count were correlated with the results of flow cytometry. Of 71 total cases, 42 (59%) had an abnormal immunophenotype. Independent variables that showed significant differences between normal and abnormal immunophenotype were mean age (p = 0.001) and ALC (p = 0.0032). We combined age and absolute lymphocyte count variables to look for the best possible cutoff values to predict the likelihood of an abnormal immunophenotype. ALC cutoff values of ≥4 × 109 cells/L for patients over 67 years of age, and >6.7 × 109 cells/L for patients between 50 and 67 years of age, had a high sensitivity for detecting an abnormal immunophenotype.
Global microRNA Analysis of the NCI-60 Cancer Cell Panel

MicroRNAs (miRNA) are a group of short noncoding RNAs that regulate gene expression at the posttranscriptional level. They are involved in many biological processes, including development, differentiation, apoptosis, and carcinogenesis. Because miRNAs may play a role in the initiation and progression of cancer, they comprise a novel class of promising diagnostic and prognostic molecular markers and potential drug targets. By applying an LNA-enhanced microarray platform, we studied the expression profiles of 955 miRNAs in the NCI-60 cancer cell lines and identified tissue- and cell-type–specific miRNA patterns by unsupervised hierarchical clustering and statistical analysis. A comparison of our data to three previously published miRNA expression studies on the NCI-60 panel showed a remarkably high correlation between the different technical platforms. In addition, the current work contributes expression data for 369 miRNAs that have not previously been profiled. Finally, by matching drug sensitivity data for the NCI-60 cells to their miRNA expression profiles, we found numerous drug–miRNAs pairs, for which the miRNA expression and drug sensitivity profiles were highly correlated and thus represent potential candidates for further investigation of drug resistance and sensitivity mechanisms. Mol Cancer Ther; 10(3); 375–84. ©2011 AACR.
Using Explicit Strategy Instruction to Improve Reading Comprehension

For the purpose of this study, three students were explicitly taught three during reading comprehension strategies. Students were given a pre and post-assessment which were analyzed to determine the effectiveness and implications of explicit strategy instruction. Furthermore, a questionnaire, related to reading comprehension, was distributed to teachers at the school in which the study took place. Findings from the study suggest that although students’ comprehension scores did not improve, their attitudes toward reading improved and their ability to use a wide variety of strategies increased after receiving explicit strategy instruction. The primary implication of this study is teachers must be willing to invest time in explicit strategy instruction in order for their students to reap the full benefits of this instructional technique. Document Type Thesis Degree Name MS in Literacy Education Department Education Subject Categories Education This thesis is available at Fisher Digital Publications: http://fisherpub.sjfc. edu/education_ETD_masters/221 Using Explicit Strategy Instruction to Improve Reading Comprehension
Biochemical and Genetic Characterization of Carbapenem-Hydrolyzing β-Lactamase OXA-229 from Acinetobacter bereziniae

ABSTRACT Acinetobacter bereziniae (formerly Acinetobacter genomospecies 10) isolate Nec was recovered from a skin sample of a patient hospitalized in Paris, France. It was resistant to penicillins, penicillin-inhibitor combinations, and carbapenems. Cloning and expression in Escherichia coli identified the carbapenem-hydrolyzing class D β-lactamase OXA-229, which is weakly related to other oxacillinases (66% amino acid identity with the closest oxacillinase, OXA-58). It hydrolyzed penicillins, oxacillin, and imipenem but not expanded-spectrum cephalosporins. Sequencing of the genetic context of the blaOXA-229 gene did not identify an insertion sequence but did identify mutations in the promoter sequences in comparison to the fully susceptible A. bereziniae reference strain. The overexpression of blaOXA-229 in A. bereziniae Nec as a source of carbapenem resistance was identified by quantitative real-time PCR.
Exercise-induced suppression of acylated ghrelin in humans.

Ghrelin is an orexigenic hormone secreted from endocrine cells in the stomach and other tissues. Acylation of ghrelin is essential for appetite regulation. Vigorous exercise induces appetite suppression, but this does not appear to be related to suppressed concentrations of total ghrelin. This study examined the effect of exercise and feeding on plasma acylated ghrelin and appetite. Nine male subjects aged 19-25 yr participated in two, 9-h trials (exercise and control) in a random crossover design. Trials began at 0800 in the morning after an overnight fast. In the exercise trial, subjects ran for 60 min at 72% of maximum oxygen uptake between 0800 and 0900. After this, they rested for 8 h and consumed a test meal at 1100. In the control trial, subjects rested for 9 h and consumed a test meal at 1100. Area under the curve values for plasma acylated ghrelin concentration (assessed from venous blood samples) were lower over the first 3 h and the full 9 h of the exercise trial compared with the control trial: 317+/-135 vs. 510+/-186 pg.ml(-1). 3 h and 917+/-342 vs. 1,401+/-521 pg.ml(-1). 9 h (means+/-SE) respectively (P<0.05). Area under the curve values for hunger (assessed using a visual scale) were lower over the first 3 h of the exercise trial compared with the control trial (P=0.013). These findings demonstrate that plasma acylated ghrelin concentration and hunger are suppressed during running.
Trust and Rights in Multimedia Content Management Systems

Secure and trusted distribution of multimedia content is a key issue for content creators, content providers and distributors, as they want to fight piracy and receive the revenues derived from their creativity work. The provision of trust and protection has not been already solved by the existing multimedia distribution mechanisms. Such mechanisms lie on proprietary architectures and tools, and users have to cope with different viewers and players to consume multimedia contents. In order to provide enhanced multimedia capabilities to final users, several standards and initiatives have appeared. Our aim is to take profit of their effort to define an architecture flexible enough to provide the needed functionality to all the actors in the distribution value chain, protecting multimedia content from unauthorised usage.
Variomics Screen Identifies the Re-entrant Loop of the Calcium-activated Chloride Channel ANO1 That Facilitates Channel Activation*

Background: The calcium-activated chloride channel ANO1 regulates multiple physiological processes. Results: We identified residues that when mutated affected channel activity, intracellular trafficking, or localization and report the first structure-function map of ANO1. Conclusion: The re-entrant loop mediates calcium/voltage sensitivity and activation of ANO1. Significance: We provide new tools for studying ANO1 function in biological systems and its potential as a therapeutic target. The calcium-activated chloride channel ANO1 regulates multiple physiological processes. However, little is known about the mechanism of channel gating and regulation of ANO1 activity. Using a high-throughput, random mutagenesis-based variomics screen, we generated and functionally characterized ∼6000 ANO1 mutants and identified novel mutations that affected channel activity, intracellular trafficking, or localization of ANO1. Mutations such as S741T increased ANO1 calcium sensitivity and rendered ANO1 calcium gating voltage-independent, demonstrating a critical role of the re-entrant loop in coupling calcium and voltage sensitivity of ANO1 and hence in regulating ANO1 activation. Our data present the first unbiased and comprehensive study of the structure-function relationship of ANO1. The novel ANO1 mutants reported have diverse functional characteristics, providing new tools to study ANO1 function in biological systems, paving the path for a better understanding of the function of ANO1 and its role in health and diseases.
HIV‐1 Tat mutants in the cysteine‐rich region downregulate HLA class II expression in T lymphocytic and macrophage cell lines

Human macrophage and T cell lines were stably transfected with HIV‐1 wild‐type Tat or Tat mutants in the cysteine‐rich region displaying trans‐dominant negative effects on HIV‐1 life cycle. The expression of HLA class I and class II molecules was not affected by wild‐type Tat. Tat mutants, instead, profoundly down‐regulated in a dose‐dependent fashion the expression of class II, but not of class I, in both cell types by acting at the transcriptional level. Down‐regulation was manifested on constitutive and IFN‐γ‐induced class II gene expression and did not correlate with reduced transcription of the AIR‐1 gene product CIITA, the major transcriptional activator of class II genes, indicating that Tat mutants did not act by inhibiting AIR‐1 gene expression. Class II down‐modulation had important functional implications in macrophages, as both antigen processing and presenting capacity were inhibited. These results represent the first evidence that a modified HIV‐1 Tat product can act as a potent immunosuppressor by inhibiting the HLA class II expression necessary for triggering both cellular and humoral responses against pathogens. The use of these HIV‐1 Tat mutants also discloses new opportunities to investigate the molecular mechanisms underlying the coordinate HLA class II gene transcription.
Astroglial cradle in the life of the synapse

Astroglial perisynaptic sheath covers the majority of synapses in the central nervous system. This glial coverage evolved as a part of the synaptic structure in which elements directly responsible for neurotransmission (exocytotic machinery and appropriate receptors) concentrate in neuronal membranes, whereas multiple molecules imperative for homeostatic maintenance of the synapse (transporters for neurotransmitters, ions, amino acids, etc.) are shifted to glial membranes that have substantially larger surface area. The astrocytic perisynaptic processes act as an ‘astroglial cradle’ essential for synaptogenesis, maturation, isolation and maintenance of synapses, representing the fundamental mechanism contributing to synaptic connectivity, synaptic plasticity and information processing in the nervous system.
A Semantics for Probabilistic Quantifier-Free First-Order Languages, with Particular Application to Story Understanding

We present a semantics for interpreting probabilistic statements expressed in a first-order quantifier-free language. We show how this semantics places constraints on the probabilities which can be associated with such statements. We then consider its use in the area of story understanding. We show that for at least simple models of stories (equivalent to the script/plan models) there arc ways to specify reasonably good probabilities. Lastly, we show that while the semantics dictates seemingly implausibly low prior probabilities for equality statements, once they are conditioned by an assumption of spatio-temporal locality of observation the probabilities become "reasonable. "
A perspective on teaching software testing

This paper addresses the issue of how to approach the teaching of software testing. Relative to its importance in the software industry, software testing receives very little attention in the undergraduate curriculum. It is not practical to offer a separate course in software testing, so relevant test experiences need to be given throughout core courses. This paper presents a software testing framework identifying five essential principles that motivate the types of testing experiences a student should gain from the curriculum. The framework is illustrated using a simple test problem.
Brick tunnel randomization for unequal allocation to two or more treatment groups

Studies with unequal allocation to two or more treatment groups often require a large block size for permuted block allocation. This could present a problem in small studies, multi‐center studies, or adaptive design dose‐finding studies. In this paper, an allocation procedure, which generalizes the maximal procedure by Berger, Ivanova, and Knoll to the case of K⩾2 treatment groups and any allocation ratio, is offered. Brick tunnel (BT) randomization requires the allocation path drawn in the k‐dimensional space to stay close to the allocation ray that corresponds to the targeted allocation ratio. Specifically, it requires the allocation path to be confined to the set of the k‐dimensional unitary cubes that are pierced by the allocation ray (the ‘brick tunnel’). The important property of the BT randomization is that the transition probabilities at each node within the tunnel are defined in such a way that the unconditional allocation ratio is the same for every allocation step. This property is not necessarily met by other allocation procedures that implement unequal allocation. Copyright © 2011 John Wiley & Sons, Ltd.
The Influence of Victim and Perpetrator Intoxication on Juror Perceptions of Hostile Environment Sexual Harassment

Once unnoticed and unreported, sexual harassment claims have risen within the last two decades. Although guidelines published by the Equal Employment Opportunity Commission provide a definition of sexual harassment, researchers continue to examine variables affecting individual perceptions of sexual harassment. In addition to gender differences in perception, the present researcher examined the impact of perpetrator and victim intoxication on perceptions of sexual harassment. Results indicated that female participants were no more likely than male participants to label behaviors as sexual harassment when provided information on intoxication. However, when no information regarding the intoxication status of the perpetrator or victim was provided, females were more likely than males to perceive sexual harassment. There were no differences in perceptions of sexual harassment based on the perpetrator's intoxication status. Finally, participants were less likely to perceive sexual harassment when the victim was intoxicated than when the victim was sober.
Recombinational Repair Is Critical for Survival ofEscherichia coli Exposed to Nitric Oxide

ABSTRACT Nitric oxide (NO⋅) is critical to numerous biological processes, including signal transduction and macrophage-mediated immunity. In this study, we have explored the biological effects of NO⋅-induced DNA damage on Escherichia coli. The relative importance of base excision repair, nucleotide excision repair (NER), and recombinational repair in preventing NO⋅-induced toxicity was determined. E. coli strains lacking either NER or DNA glycosylases (including those that repair alkylation damage [alkA tag strain], oxidative damage [fpg nei nth strain], and deaminated cytosine [ung strain]) showed essentially wild-type levels of NO⋅ resistance. However, apyrimidinic/apurinic (AP) endonuclease-deficient cells (xth nfo strain) were very sensitive to killing by NO⋅, which indicates that normal processing of abasic sites is critical for defense against NO⋅. In addition, recA mutant cells were exquisitely sensitive to NO⋅-induced killing. Both SOS-deficient (lexA3) and Holliday junction resolvase-deficient (ruvC) cells were very sensitive to NO⋅, indicating that both SOS and recombinational repair play important roles in defense against NO⋅. Furthermore, strains specifically lacking double-strand end repair (recBCD strains) were very sensitive to NO⋅, which suggests that NO⋅ exposure leads to the formation of double-strand ends. One consequence of these double-strand ends is that NO⋅ induces homologous recombination at a genetically engineered substrate. Taken together, it is now clear that, in addition to the known point mutagenic effects of NO⋅, it is also important to consider recombination events among the spectrum of genetic changes that NO⋅ can induce. Furthermore, the importance of recombinational repair for cellular survival of NO⋅ exposure reveals a potential susceptibility factor for invading microbes.
Elevation of tear fluid plasmin in corneal disease

Abstract. Plasmin concentration was determined in tear fluid from 76 eyes showing corneal epithelial disorders, such as corneal ulcers and erosions due to trauma or contact lens wear. Nearly 70% of the eyes with corneal disease had plasmin in their tear fluid, whereas plasmin was present in only 20% of the eyes in a control group of 50 eyes. Re‐examination of the plasmin positive control eyes revealed conjunctival bacterial growth or mild subclinical viral infection in most cases. We conclude that plasmin is released into the tear fluid in the presence of corneal or conjunctival lesions or infections, suggesting a pathogenic role of plasmin in these disorders. The significance of the occurrence of plasmin in tear fluid during corneal wound healing is discussed.
On Problems of Knowledge in Fuzzy Control: Extended Abstract

The field of Fuzzy Control have enjoyed tremendous success in the last decade, with both theoretical and industrial developments being introduced at an increasing rateI. However, fuzzy control is just one application of Soft Computing methods in general, and Fuzzy Sets theory in particular. This principled approach to approximate reasoning is not limited only to control problems, but is useful also in closely related fields, such as Artificial Intelligence (AI) in its various forms and guises, Decision Sciences, Quantitative and Qualitative Decision Theory, theoretical studies of Uncertainty, Information and Knowledge, etc. As we seek to expand the success of fuzzy control to these fields, it is very tempting to attempt use of known methods in a familiar way to solve problems in these new domains. However, a principled analysis of the goals and assumptions underlying different fields may reveal important differences from the field of control which may make current methods insufficient. We take the position that as we look at real-world decision problems and domains, the familiar techniques of fuzzy control will be insufficient to provide adequate solutions, because these techniques are designed with the assumptions of the field of control in mind --assumptions which do not hold in such domains. The techniques are not incorrect, but simply insufficient, and can be augmented to provide the necessary theoretical and practical infrastructure for the new domains. This short abstract will attempt to point out our initial approach to such necessary augmentations of fuzzy control techniques. We will motivate the discussion with a very small scale decision problem, which despite its size, captures some of the underlying problems with current techniques and points the way at the necessary directions for development that will bridge the gap between fuzzy control techniques and the required technology.
Endogenous Carbamylation of Renal Medullary Proteins

Protein carbamylation is a post-translational modification that can occur in the presence of urea. In solution, urea is in equilibrium with ammonium cyanate, and carbamylation occurs when cyanate ions react with the amino groups of lysines, arginines, protein N-termini, as well as sulfhydryl groups of cysteines. The concentration of urea is elevated in the renal inner medulla compared with other tissues. Due to the high urea concentration, we hypothesized that carbamylation can occur endogenously within the rat inner medulla. Using immunoblotting of rat kidney cortical and medullary homogenates with a carbamyl-lysine specific antibody, we showed that carbamylation is present in a large number of inner medullary proteins. Using protein mass spectrometry (LC-MS/MS) of rat renal inner medulla, we identified 456 unique carbamylated sites in 403 proteins, including many that play important physiological roles in the renal medulla [Data can be accessed at https://helixweb.nih. gov/ESBL/Database/Carbamylation/Carbamylation_peptide_sorted. html]. We conclude that protein carbamylation occurs endogenously in the kidney, modifying many physiologically important proteins.
Journal of the International Aids Society Disability and Hiv/aids -a Systematic Review of Literature on Africa

This systematic review focuses on empirical work on disability and HIV/AIDS in Africa in the past decade and considers all the literature currently accessible. The review presents data from different surveys and summarizes the findings. In this way, it convincingly reveals that people with disabilities are very vulnerable to contracting HIV, and lack access to information, testing and treatment. The review further reveals gaps in the research and areas of concern. While vulnerability and accessibility have been investigated, there are few prevalence studies or evaluations available. A certain amount of work has focused on the deaf population, but little has been done for other disability groups. A growing area of concern is sexual abuse and exploitation of people with disabilities. Only a few studies or interventions focus on this crucial area.
Growth Hormone–Releasing Hormone Agonists Reduce Myocardial Infarct Scar in Swine With Subacute Ischemic Cardiomyopathy

Background Growth hormone–releasing hormone agonists (GHRH‐As) stimulate cardiac repair following myocardial infarction (MI) in rats through the activation of the GHRH signaling pathway within the heart. We tested the hypothesis that the administration of GHRH‐As prevents ventricular remodeling in a swine subacute MI model. Methods and Results Twelve female Yorkshire swine (25 to 30 kg) underwent transient occlusion of the left anterior descending coronary artery (MI). Two weeks post MI, swine were randomized to receive injections of either 30 μg/kg GHRH‐A (MR‐409) (GHRH‐A group; n=6) or vehicle (placebo group; n=6). Cardiac magnetic resonance imaging and pressure–volume loops were obtained at multiple time points. Infarct, border, and remote (noninfarcted) zones were assessed for GHRH receptor by immunohistochemistry. Four weeks of GHRH‐A treatment resulted in reduced scar mass (GHRH‐A: −21.9±6.42%; P=0.02; placebo: 10.9±5.88%; P=0.25; 2‐way ANOVA; P=0.003), and scar size (percentage of left ventricular mass) (GHRH‐A: −38.38±4.63; P=0.0002; placebo: −14.56±6.92; P=0.16; 2‐way ANOVA; P=0.02). This was accompanied by improved diastolic strain. Unlike in rats, this reduced infarct size in swine was not accompanied by improved cardiac function as measured by serial hemodynamic pressure–volume analysis. GHRH receptors were abundant in cardiac tissue, with a greater density in the border zone of the GHRH‐A group compared with the placebo group. Conclusions Daily subcutaneous administration of GHRH‐A is feasible and safe in a large animal model of subacute ischemic cardiomyopathy. Furthermore, GHRH‐A therapy significantly reduced infarct size and improved diastolic strain, suggesting a local activation of the GHRH pathway leading to the reparative process.