Miracle-dz/UniFAR-FTUs huggingface dataset:
DNA-binding requirements of the yeast protein Rap1p as selected in silico from ribosomal protein gene promoter sequences

MOTIVATION High-level transcriptional activation of most ribosomal protein (rp) genes in Saccharomyces cerevisiae is promoted by the global DNA-binding factor Rap1p. The creation of the complete database of yeast rp gene promoter sequences enabled us to develop a computational selection strategy aimed at acquiring detailed information concerning the DNA-binding specificity of Rap1p. RESULTS Rap1p sites in rp gene promoters are often found in duplicate, exhibiting strong preferences in both spacing and orientation. Using these preferences, a weight matrix was selected that represents the in vivo binding requirements of Rap1p. The resulting matrix renders the identification of functional Rap1p binding sites more accurate and allowed us to re-evaluate previous in vitro data. Tandemly arranged Rap1p binding sites appear to be typical for rp gene promoters and differ in preferred spacing from sites occurring in (sub)telomeric repeats. The preferred spacing that is found in duplicate Rap1p binding sites of rp gene promoters is restricted to a small window between 15 and 26 bp. This is proposed to reflect the borders within which binding co-operativity operates. The data presented clearly illustrate that computational selection strategies provide information that reaches beyond experimental data. AVAILABILITY The rp database is available at the url: http://www. chem.vu. nl/BMB/Database.html.
A digitally controlled transient suppression method for integrated DC-DC converters

In this paper a transient suppression method applicable to integrated DC-DC converter is introduced. This method is designed for point-of-load applications where load current frequently varies. An auxiliary buck stage is added to a traditional buck stage that turns on only during transient to assist sinking or injecting load current. This helps swiftly to restore the output voltage to steady state and reduce transient variation. Simulation shows that for a 3W, 12V to 1V buck converter, this method effectively suppress the overshoot to be less than 3% when subjected to a 3A to 0A transient. This represents a 30% reduction in output voltage variations during transient comparing to control methods that only focus on fast recovery.
The Prognostic Value of the CT Scan in Conservatively Treated Patients With Intracerebral Hematoma

Prognostic factors for survival and neurological recovery were assessed in 42 patients with non trauma tic intracerebral hematoma (ICH) diagnosed by CT scan. None underwent surgical evacuation of hematoma. CT scans were used to determine location and volume of ICH and presence or absence of intraventricular hemorrhage (IVH). Only 11 patients (26%) died and 17 patients (40.5%) recovered fully. Mortality was associated with: 1) loss of consciousness as a presenting symptom (63.5% mortality rate versus 13% when there was no loss of consciousness at the onset; (p < 0.01). 2) extension of the bleeding into the ventricular system (45% mortality rate versus 9% when hemorrhages were confined to brain parenchy- ma; (p < 0.01). 3) location of hematoma in the posterior fossa (mortality rate of 43% versus 23% for Intrahemispherlc hematomas). Mortality was unaffected by age of patients and size of ICH. Full neurologi- cal and functional recovery occurred mainly when estimated volume of hematomas was less than 15 cc and with lobar hematomas regardless of size. In survivors there is CT evidence of complete resolution of ICH. Our data indicates a favourable outcome in a relatively large percentage of patients with ICH treated conservatively and therefore questions the need for surgical evacuation of hematoma. Stroke Vol 15, No 1, 1984
The Interplay of Personal Traits and Autobiographical Memory

This study investigated the effects of social setting and perceived audience on autobiographical memories shared with a stranger in written formats. The influence ofexperimenter presence individual differences in biological sex and gender identity (feminine, masculine, undifferentiated, androgynous) on narrative length, content, structure; and theme were explored. Sex differences included men expressing more overall and negative emotionality in an individual rather than in a group setting, and women wrote lengthier narratives than men. Gender differences included feminine individuals using more emotion words in a groups rather than individual setting, and using more negative emotions in the presence of a group with the experimenter absent as compared to other conditions; Masculine and Androgynous individuals used more negative emotion words in the individual setting when the experimenter was present; Undifferentiated individuals using more negative emotions words in the individual setting when the experimenter was absent; Androgynous individuals wrote more socially-themed narratives in a group setting; and Masculine individuals wrote more socially·themed narratives in an individual setting. Overall, participants wrote more detailed narratives in the individual setting than when writing in a group. Findings are somewhat consistent with previous research regarding such areas as narrative length and theme, with areas ofdiscrepancies and implications for future research discussed.
Abundance ratios of volatile vs. refractory elements in planet-harbouring stars: hints of pollution?

We present the [ X /H] trends as a function of the elemental condensation temperature T C in 88 planet host stars and in a volume-limited comparison sample of 33 dwarfs without detected planetary companions. We gathered homogeneous abundance results for many volatile and refractory elements spanning a wide range of T C , from a few dozen to several hundred kelvin. We investigate possible anomalous trends of planet hosts with respect to comparison sample stars to detect evidence of possible pollution events. No significant differences are found in the behaviour of stars with and without planets. This is consistent with a “primordial” origin of the metal excess in planet host stars. However, a subgroup of 5 planet host and 1 comparison sample stars stands out as having particularly high [ X /H] vs. T C slopes.
New Circulating-Water Devices Warm More Quickly than Forced-Air in Volunteers

BACKGROUND:Newer circulating-water systems supply more heat than forced-air, mainly because the heat capacity of water is much greater than for that of dry warm air and, in part, because they provide posterior as well as anterior heating. Several heating systems are available, but three major ones have yet to be compared directly. We therefore compared two circulating-water systems with a forced-air system during simulation of upper abdominal or chest surgery in volunteers. METHODS:Seven healthy volunteers participated on three separate study days. Each day, they were anesthetized and cooled to a core temperature near 34°C, which was maintained for 45–60 min. They were then rewarmed with one of three warming systems until distal esophageal core temperature reached 36°C or anesthesia had lasted 8 h. The warming systems were 1) energy transfer pads (two split torso pads and two universal pads; Kimberly Clark, Roswell, GA); 2) circulating-water garment (Allon MTRE 3365 for cardiac surgery, Akiva, Israel); and 3) lower body forced-air warming (Bair Hugger #525, #750 blower, Eden Prairie, MN). Data are presented as mean ± sd; P < 0.05 was statistically significant. RESULTS:The rate of increase of core temperature from 34°C to 36°C was 1.2°C ± 0.2°C/h with the Kimberly Clark system, 0.9°C ± 0.2°C/h with the Allon system, and 0.6°C ± 0.1°C/h with the Bair Hugger (P = 0.002). CONCLUSIONS:The warming rate with the Kimberly Clark system was 25% faster than with the Allon system and twice as fast as with the Bair Hugger. Both circulating-water systems thus warmed hypothermic volunteers in significantly less time than the forced-air system.
Drowning in data: digital library architecture to support scientific use of embedded sensor networks

New technologies for scientific research are producing a deluge of data that is overwhelming traditional tools for data capture, analysis, storage, and access. We report on a study of scientific practices associated with dynamic deployments of embedded sensor networks to identify requirements for data digital libraries. As part of continuing research on scientific data management, we interviewed 22 participants in 5 environmental science projects to identify data types and uses, stages in their data life cycle, and requirements for digital library architecture. We found that scientists need continuous access to their data from the time that field experiments are designed through final analysis and publication, thus reflecting a broader notion of "digital library. " Six categories of requirements are discussed: the ability to obtain and maintain data in the field, verify data in the field, document data context for subsequent interpretation, integrate data from multiple sources, analyze data, and preserve data. Three digital library efforts currently underway within the Center for Embedded Networked Sensing are addressing these requirements, with the goal of a tightly coupled interoperable framework that, in turn, will be a component of cyberinfrastructure for science.
Exploring the effects of gender and learning styles on computer programming performance: implications for programming pedagogy

Computer programming has been taught in secondary schools for more than two decades. However, little is known about how students learn to program. From the curriculum implementation perspectives, learning style helps address the issue of learner differences, resulting in a shift from a teacher-centred approach to a learner-focused approach. This study aims to investigate the effects of gender and learning styles on computer programming performance. The Gregorc Style Delineator (GSD) was employed to measure learning styles. A test was administered to assess students’ programming performance. Two hundred and seventeen secondary school students of age from 14 to 19 participated in this study. Results indicated that no gender differences in programming performance were found after controlling for the effect of student ability. Academic ability had a differential effect on programming knowledge. Sequential learners in general performed better than random learners. These results suggest the importance of the ordering dimension of the GSD in influencing programming performance. Implications of the findings in relation to programming pedagogy are discussed in this paper. [ABSTRACT FROM AUTHOR]
Interleukin-10 Prevents Diet-Induced Insulin Resistance by Attenuating Macrophage and Cytokine Response in Skeletal Muscle

OBJECTIVE Insulin resistance is a major characteristic of type 2 diabetes and is causally associated with obesity. Inflammation plays an important role in obesity-associated insulin resistance, but the underlying mechanism remains unclear. Interleukin (IL)-10 is an anti-inflammatory cytokine with lower circulating levels in obese subjects, and acute treatment with IL-10 prevents lipid-induced insulin resistance. We examined the role of IL-10 in glucose homeostasis using transgenic mice with muscle-specific overexpression of IL-10 (MCK-IL10). RESEARCH DESIGN AND METHODS MCK-IL10 and wild-type mice were fed a high-fat diet (HFD) for 3 weeks, and insulin sensitivity was determined using hyperinsulinemic-euglycemic clamps in conscious mice. Biochemical and molecular analyses were performed in muscle to assess glucose metabolism, insulin signaling, and inflammatory responses. RESULTS MCK-IL10 mice developed with no obvious anomaly and showed increased whole-body insulin sensitivity. After 3 weeks of HFD, MCK-IL10 mice developed comparable obesity to wild-type littermates but remained insulin sensitive in skeletal muscle. This was mostly due to significant increases in glucose metabolism, insulin receptor substrate-1, and Akt activity in muscle. HFD increased macrophage-specific CD68 and F4/80 levels in wild-type muscle that was associated with marked increases in tumor necrosis factor-α, IL-6, and C-C motif chemokine receptor-2 levels. In contrast, MCK-IL10 mice were protected from diet-induced inflammatory response in muscle. CONCLUSIONS These results demonstrate that IL-10 increases insulin sensitivity and protects skeletal muscle from obesity-associated macrophage infiltration, increases in inflammatory cytokines, and their deleterious effects on insulin signaling and glucose metabolism. Our findings provide novel insights into the role of anti-inflammatory cytokine in the treatment of type 2 diabetes.
Quality of care for acute myocardial infarction in 58 U.S. emergency departments.

OBJECTIVES The objectives of this study were to determine concordance of emergency department (ED) management of acute myocardial infarction (AMI) with guideline recommendations and to identify ED and patient characteristics predictive of higher guideline concordance. METHODS The authors conducted a chart review study of ED AMI care as part of the National Emergency Department Safety Study (NEDSS). Using a primary hospital discharge diagnosis of AMI (International Classification of Diseases, Ninth Revision, Clinical Modification [ICD-9-CM], codes 410.XX), a random sample of ED visits for AMI in 58 urban EDs across 20 U.S. states between 2003 and 2006 were identified. Concordance with American College of Cardiology/American Heart Association (ACC/AHA) guideline recommendations was evaluated using five individual quality measures and a composite concordance score. Concordance scores were calculated as the percentage of eligible patients who received guidelines-recommended care. These percentage scores were rescaled from 0 to 100, with 100 indicating perfect concordance. RESULTS The cohort consisted of 3,819 subjects; their median age was 65 years, and 62% were men. The mean (± standard deviation [SD]) ED composite concordance score was 61 ± 8), with a broad range of values (42 to 84). Except for aspirin use (mean concordance, 82), ED concordance scores were low (beta-blocker use, 56; timely electrocardiogram [ECG], 41; timely fibrinolytic therapy, 26; timely ED disposition for primary percutaneous coronary intervention [PCI] candidates, 43). In multivariable analyses, older age (beta-coefficient per 10-year increase, -1.5; 95% confidence interval [CI] = -2.4 to -0.5) and southern EDs (beta-coefficient, -5.2; 95% CI = -9.6 to -0.9) were associated with lower guideline concordance, whereas ST-segment elevation on initial ED ECG was associated with higher guideline concordance (beta-coefficient, 3.6; 95% CI = 1.5 to 5.7). CONCLUSIONS Overall ED concordance with guideline-recommended processes of care was low to moderate. Emergency physicians should continue to work with other stakeholders in AMI care, such as emergency medical services (EMS) and cardiologists, to develop strategies to improve care processes.
E. coli K-12 and EHEC Genes Regulated by SdiA

Background Escherichia and Salmonella encode SdiA, a transcription factor of the LuxR family that regulates genes in response to N-acyl homoserine lactones (AHLs) produced by other species of bacteria. E. coli genes that change expression in the presence of plasmid-encoded sdiA have been identified by several labs. However, many of these genes were identified by overexpressing sdiA on a plasmid and have not been tested for a response to sdiA produced from its natural position in the chromosome or for a response to AHL. Methodology/Principal Findings We determined that two important loci reported to respond to plasmid-based sdiA, ftsQAZ and acrAB, do not respond to sdiA expressed from its natural position in the chromosome or to AHLs. To identify genes that are regulated by chromosomal sdiA and/or AHLs, we screened 10,000 random transposon-based luciferase fusions in E. coli K-12 and a further 10,000 in E. coli O157:H7 for a response to AHL and then tested these genes for sdiA-dependence. We found that genes encoding the glutamate-dependent acid resistance system are up-regulated, and fliE is down-regulated, by sdiA. Gene regulation by sdiA of E. coli is only partially dependent upon AHL. Conclusions/Significance The genes of E. coli that respond to plasmid-based expression of sdiA are largely different than those that respond to chromosomal sdiA and/or AHL. This has significant implications for determining the true function of AHL detection by E. coli.
Fundamental superstrings as holograms

The worldsheet of a macroscopic fundamental superstring in the Green-Schwarz light-cone gauge is viewed as a possible boundary hologram of the near horizon region of a small black string. For toroidally compactified strings, the hologram has global symmetries of AdS3 × Sd−1 × T8−d (d = 3, ., 8), only some of which extend to local conformal symmetries. We construct the bulk string theory in detail for the particular case of d = 3. The symmetries of the hologram are correctly reproduced from this exact worldsheet description in the bulk. Moreover, the central charge of the boundary Virasoro algebra obtained from the bulk agrees with the Wald entropy of the associated small black holes. This construction provides an exact CFT description of the near horizon region of small black holes both in Type-II and heterotic string theory arising from multiply wound fundamental superstrings.
Analysis of Bias in Measurements of Potassium, Sodium and Hemoglobin by an Emergency Department-Based Blood Gas Analyzer Relative to Hospital Laboratory Autoanalyzer Results

Objective The emergency departments (EDs) of Chinese hospitals are gradually being equipped with blood gas machines. These machines, along with the measurement of biochemical markers by the hospital laboratory, facilitate the care of patients with severe conditions who present to the ED. However, discrepancies have been noted between the Arterial Blood Gas (ABG) analyzers in the ED and the hospital laboratory autoanalyzer in relation to electrolyte and hemoglobin measurements. The present study was performed to determine whether the ABG and laboratory measurements of potassium, sodium, and hemoglobin levels are equivalent, and whether ABG analyzer results can be used to guide clinical care before the laboratory results become available. Materials and Methods Study power analyses revealed that 200 consecutive patients who presented to our ED would allow this prospective single-center cohort study to detect significant differences between ABG- and laboratory-measured potassium, sodium, and hemoglobin levels. Paired arterial and venous blood samples were collected within 30 minutes. Arterial blood samples were measured in the ED by an ABL 90 FLEX blood gas analyzer. The biochemistry and blood cell counts of the venous samples were measured in the hospital laboratory. The potassium, sodium, and hemoglobin concentrations obtained by both methods were compared by using paired Student’s t-test, Spearman’s correlation, Bland-Altman plots, and Deming regression. Results The mean ABG and laboratory potassium values were 3.77±0.44 and 4.2±0.55, respectively (P<0.0001). The mean ABG and laboratory sodium values were 137.89±5.44 and 140.93±5.50, respectively (P<0.0001). The mean ABG and laboratory Hemoglobin values were 12.28±2.62 and 12.35±2.60, respectively (P = 0.24). Conclusion Although there are the statistical difference and acceptable biases between ABG- and laboratory-measured potassium and sodium, the biases do not exceed USCLIA-determined limits. In parallel, there are no statistical differences and biases beyond USCLIA-determined limits between ABG- and laboratory-measured hemoglobin. Therefore, all three variables measured by ABG were reliable.
Principal regression analysis

A new paradigm for multivariate regression is proposed; principal regression analysis (PRA). It entails learning a low dimensional subspace over sample-specific regressors. For a given input, the model predicts a subspace thought to contain the corresponding response. Using this subspace as a prior, the search space is considerably more constrained. An efficient local optimisation strategy is proposed for learning and a practical choice for its initialisation suggested. The utility of PRA is demonstrated on the task of non-rigid face and car alignment using challenging "in the wild" datasets, where substantial performance improvements are observed over alignment with a conventional prior.
Templates and Turns in Qualitative Studies of Strategy and Management

Purpose – This chapter presents four different approaches to doing and writing qualitative research in strategy and management based on different epistemological foundations. It describes two well-established “templates” for doing such work, and introduces two more recent “turns” that merit greater attention. Design/Methodology/Approach – The chapter draws on methodological texts and a detailed analysis of successful empirical exemplars from the strategy and organization literature to show how qualitative research on strategy processes can be effectively carried out and written up. Findings – The two “templates” are based on different logics and modes of writing. The first is based on a positivist epistemology and aims to develop nomothetic theoretical propositions, while the second is interpretive and more concerned to capture and gain insight from the meanings given to organizational phenomena. The two “turns” (the practice turn and the discursive turn) are not as well defined but are generating innovative contributions based on new ways of considering the social world. Originality/Value – The chapter should be helpful to researchers considering qualitative methods for the study of strategy processes. It contributes by comparing different approaches and by recognizing that part of the challenge of doing qualitative research lies in writing it up to communicate its insights in a credible way. Thus while describing the different methods, the chapter also draws attention to effective forms of writing. In addition, it introduces and assesses two more recent “turns” that offer promising routes to novel insight as well as having particular ontological and epistemological affinities with qualitative research methods.
Anticoagulation Strategies in Venovenous Hemodialysis in Critically Ill Patients: A Five-Year Evaluation in a Surgical Intensive Care Unit

Renal failure is a common complication among critically ill patients. Timing, dosage, and mode of renal replacement (RRT) are under debate, but also anticoagulation strategies and vascular access interfere with dialysis success. We present a retrospective, five-year evaluation of patients requiring RRT on a multidisciplinary 50-bed surgical intensive care unit of a university hospital with special regard to anticoagulation strategies and vascular access. Anticoagulation was preferably performed with unfractionated heparin or regional citrate application (RAC). Bleeding and suspected HIT-II were most common causes for RAC. In CVVHD mode filter life span was significantly longer under RAC compared to heparin or other anticoagulation strategies (P = 0.001). Femoral vascular access was associated with reduced filter life span (P = 0.012), especially under heparin anticoagulation (P = 0.015). Patients on RAC had higher rates of metabolic alkalosis (P = 0.001), required more transfusions (P = 0.045), and showed higher illness severity measured by SOFA scores (P = 0.001). RRT with unfractionated heparin represented the most common anticoagulation strategy in this study population. However, patients with bleeding risk and severe organ dysfunction were more likely placed on RAC. Citrate provided longer filter life spans regardless of vascular access site. Attention has to be paid to metabolic disturbances.