Miracle-dz/UniFAR-FTUs huggingface dataset:
NADP-dependent Mannitol Dehydrogenase, a Major Allergen of Cladosporium herbarum*

Cladosporium herbarum is an important allergenic fungal species that has been reported to cause allergic diseases in nearly all climatic zones. 5–30% of the allergic population displays IgE antibodies against molds. Sensitization to Cladosporium has often been associated with severe asthma and less frequently with chronic urticaria and atopic eczema. However, no dominant major allergen of this species has been found so far. We present cloning, production, and characterization of NADP-dependent mannitol dehydrogenase of C. herbarum (Cla h 8) and show that this protein is a major allergen that is recognized by IgE antibodies of ∼57% of all Cladosporium allergic patients. This is the highest percentage of patients reacting with any Cladosporium allergen characterized so far. Cla h 8 was purified to homogeneity by standard chromatographic methods, and both N-terminal and internal amino acid sequences of protein fragments were determined. Enzymatic analysis of the purified natural protein revealed that this allergen represents a NADP-dependent mannitol dehydrogenase that interconverts mannitol and d-fructose. It is a soluble, non-glycosylated cytoplasmic protein. Two-dimensional protein analysis indicated that mannitol dehydrogenase is present as a single isoform. The cDNA encoding Cla h 8 was cloned from a λ-ZAP library constructed from hyphae and spores. The recombinant non-fusion protein was expressed in Escherichia coli and purified to homogeneity. Its immunological and biochemical identity with the natural protein was shown by enzyme activity tests, CD spectroscopy, IgE immunoblots with sera of patients, and by skin prick testing of Cladosporium allergic patients. This protein therefore is a new major allergen of C. herbarum.
Lifestyle, Environmental, and Genetic Predictors of Bulky DNA Adducts in a Study Population Nested within a Prospective Danish Cohort

Bulky DNA adducts are considered a potential biomarker of cancer risk. In this study, the association between various lifestyle, environmental, and genetic factors and the levels of bulky DNA adducts in peripheral leukocytes was examined in a study group nested within a population-based prospective Danish cohort. At enrollment, blood samples were collected and information on lifestyle, including dietary and smoking habits, obtained. Previously, bulky DNA adducts were measured in 245 individuals who developed lung cancer and 255 control members of the cohort. Of these 500 individuals, data on 375 individuals were included in this study, excluding 125 cases, which developed lung cancer within the first 3 yr after blood sampling. Bulky DNA adduct levels were measured by 32 P-postlabeling technique and polymorphisms in carcinogen metabolism and DNA repair genes were determined. Potential predictors of bulky DNA adduct levels were analyzed by univariate and multivariate regression analyses. Women tended to have higher adduct levels than men. Living in central Copenhagen and surface darkness of fried meat and fish were associated with quantitative higher adduct levels. No significant associations were found between dietary factors or smoking and DNA adduct levels. Further, the results showed no prominent associations between any of 12 genetic polymorphisms and adduct levels. Overall, our study showed only few associations between dietary, environmental, and genetic factors and levels of bulky DNA adducts measured in peripheral leukocytes in a general Danish population.
Understanding the Energy and Precision Requirements for Online Learning

It is well-known that the precision of data, hyperparameters, and internal representations employed in learning systems directly impacts its energy, throughput, and latency. The precision requirements for the training algorithm are also important for systems that learn on-the-fly. Prior work has shown that the data and hyperparameters can be quantized heavily without incurring much penalty in classification accuracy when compared to floating point implementations. These works suffer from two key limitations. First, they assume uniform precision for the classifier and for the training algorithm and thus miss out on the opportunity to further reduce precision. Second, prior works are empirical studies. In this article, we overcome both these limitations by deriving analytical lower bounds on the precision requirements of the commonly employed stochastic gradient descent (SGD) on-line learning algorithm in the specific context of a support vector machine (SVM). Lower bounds on the data precision are derived in terms of the the desired classification accuracy and precision of the hyperparameters used in the classifier. Additionally, lower bounds on the hyperparameter precision in the SGD training algorithm are obtained. These bounds are validated using both synthetic and the UCI breast cancer dataset. Additionally, the impact of these precisions on the energy consumption of a fixed-point SVM with on-line training is studied.
The use of ice for pain associated with chest tube removal.

Every year more than 300,000 patients undergo cardiothoracic surgery, requiring placement of at least one chest tube. Removal of these chest tubes has been described as one of the worst intensive care unit experiences for these patients. Pain associated with chest tube removal (CTR) has been poorly controlled in many surgical patients. The purpose of this experimental study was to ascertain if the application of ice would decrease pain before, during, and after chest tube removal. Fifty postcardiac surgery patients were randomly assigned to two groups. The experimental group received ice therapy before CTR, whereas control subjects received a placebo. Pain intensity and pain distress were measured on a 0-10 numeric rating scale, and pain quality was measured using the McGill Pain Questionnaire-Short Form (MPQ-SF). Differences in pain intensity and pain distress between the experimental and control groups were not significant. A significant change in pain over time was noted in both groups, with pain intensity and distress being most severe during actual chest tube removal. Additionally, patients who received preprocedural pain medication did not differ in their levels of pain intensity or distress. Both groups used all the quality descriptors on the MPQ-SF for the sensory and affective components of pain, with cramping and gnawing as the most frequently chosen words. Continued research with larger samples is encouraged to further evaluate ice and other interventions that can be used to manage pain associated with CTR.
Environmental influences on the phenology of pine

Phenology has been defined as the study of the timing of recurring biological events, the causes of their timing with regard to abiotic and biotic forces and the interrela tion among phases of the same or different event (Reichle 1973, Leith 1974). The role of phenology in forest eco systems has been discussed for several decades. Today, understanding how tree phenology is quantitatively re lated to environment is even more important because of anticipated global environmental change. One of the first steps in modeling tree growth is to define climatic conditions under which growth initiates and ceases. Increased ambient temperatures can be ex pected to change growth patterns through effects on plant processes such as dormancy deepening, cold hardiness and dormancy release. Modeling the phenology of pines under current and altered climates may not be easy be cause of their wide geographic and climatic range and the diversity of genotypes that have evolved. We have selected to review the phenology of six con trasting species of pine: Pinus radiata D. Don (Monterey pine), P. taeda L. (loblolly pine), P. strobus L. (eastern white pine), P. elliottii Engelm. (slash pine), P. contorta Doug. ex. Loud, (lodgepole pine), and P. sylvestris L. (Scots pine). The specific emphasis is on interactions between environment and tree morphology, anatomy and physiology and how these interactions affect patterns of tree growth and stand productivity. The phenophases to be considered are: shoot growth, stem diameter growth, foliage and branch production and root growth. Com ments on other phenophases will be made where they appear to have major, short duration impacts on the growth activities being considered.
Blood pressure and carotid artery intima-media thickness in children and adolescents: the role of obesity.

INTRODUCTION The measurement of carotid artery intima-media thickness in children and adolescents has attracted a great deal of research and clinical interest in recent years, because it can provide evidence that early arterial lesions are already present in asymptomatic subjects who have risk factors for cardiovascular disease. The aim of the present study was to investigate possible correlations between parameters of 24-hour ambulatory blood pressure monitoring (ABPM) and carotid artery intima-media thickness in obese and nonobese children and adolescents. METHODS We studied 128 children and adolescents who were referred for investigation for possible hypertension. All participants in the study underwent ABPM and ultrasound measurement of the intima-media thickness of the common and internal carotid arteries. Obesity was defined as a body mass index (BMI) the 95th percentile for age and sex. RESULTS Carotid artery intima-media thickness was significantly greater in obese than in non-obese children and adolescents. Linear correlations were observed between common and internal carotid artery intima-media thickness and the BMI percentile, the BMI z score, and parameters from ABPM. Multifactorial analysis of covariance showed that obesity and age were correlated with mean carotid artery intima-media thickness, independently of sex and values of clinic blood pressure and ABPM. CONCLUSIONS Obese children and adolescents have greater carotid artery intima-media thickness than nonobese subjects, independently of blood pressure. These findings suggest a possible role for childhood obesity in the early onset of carotid artery atherosclerosis.
Stromal Cell–Derived Factor-1 (SDF-1)/CXCL12 Attenuates Diabetes in Mice and Promotes Pancreatic β-Cell Survival by Activation of the Prosurvival Kinase Akt

OBJECTIVE—Diabetes is caused by a deficiency of pancreatic β-cells that produce insulin. Approaches to enhance β-cell mass by increasing proliferation and survival are desirable. We determined whether stromal cell–derived factor (SDF)-1/CXCL12 and its receptor, CX chemokine receptor (CXCR)4, are important for the survival of β-cells. RESEARCH DESIGN AND METHODS—Mouse pancreata and clonal β-cells were examined for expression of SDF-1 and CXCR4, activation of AKT and downstream signaling pathways by SDF-1, and protection against apoptosis and diabetes induced by streptozotocin (STZ). RESULTS—CXCR4 is expressed in β-cells, and SDF-1 is expressed in microvascular endothelial cells within the islets and in surrounding interstitial stromal tissue. Transgenic mice overexpressing SDF-1 within their β-cells (RIP-SDF-1 mice) are resistant to STZ-induced β-cell apoptosis and diabetes. In MIN6 β-cells, a CXCR4 antagonist (AMD3100) induces apoptosis, increases reactive oxygen species, decreases expression levels of the anti-apoptotic protein Bcl-2, and reduces phosphorylation of the proapoptotic protein Bad. Active phosphorylated prosurvival kinase Akt is increased both in the β-cells of RIP-SDF-1 mice and in INS-1 cells treated with SDF-1 and sensitive to AMD3100. Inhibition of AKT expression by small interfering RNA attenuates the ameliorative effects of SDF-1 on caspase-dependent apoptosis induced by thapsigargin or glucose deprivation in INS-1 β-cells. Specific inhibition of Akt activation by a soluble inhibitor (SH-5) reverses the anti-apoptotic effects of SDF-1 in INS-1 cells and mouse islets. CONCLUSIONS—SDF-1 promotes pancreatic β-cell survival via activation of Akt, suggesting that SDF-1 agonists may prove beneficial for treatment of diabetes.
The Role of School-Based Colleagues in Shaping the Commitment of Novice Special and General Education Teachers

We compare beginning special and general education teachers’ access to school-based colleagues. Our findings demonstrate that colleague relationships are critical for the experiences of beginning teachers, as are the school organizational norms that these beginning teachers experience. For special education teachers in particular, perception of colleague support was a strong predictor of retention plans. Similar results were seen with respect to their perception of the level of collective responsibility among the faculty. Taken together, these results suggest that schools and districts should make efforts to facilitate productive relationships between general and special education faculty, as well as to differentiate induction support for beginning special educators.
MODELING THE INTERACTION OF EMOTION AND COGNITION

Research on the interaction between emotion and cognition has become particularly active along the last years, so that lots of computational models of emotion have been developed. However, to the date, none of them address fully the integration of emotion generation and its effects in the context of cognitive processes. This work tries to unify several models of computational emotions for embodied agents with the work done in cognitive architectures, based on psychological theories and applications.
Deciphering key features in protein structures with the new ENDscript server

ENDscript 2 is a friendly Web server for extracting and rendering a comprehensive analysis of primary to quaternary protein structure information in an automated way. This major upgrade has been fully re-engineered to enhance speed, accuracy and usability with interactive 3D visualization. It takes advantage of the new version 3 of ESPript, our well-known sequence alignment renderer, improved to handle a large number of data with reduced computation time. From a single PDB entry or file, ENDscript produces high quality figures displaying multiple sequence alignment of proteins homologous to the query, colored according to residue conservation. Furthermore, the experimental secondary structure elements and a detailed set of relevant biophysical and structural data are depicted. All this information and more are now mapped on interactive 3D PyMOL representations. Thanks to its adaptive and rigorous algorithm, beginner to expert users can modify settings to fine-tune ENDscript to their needs. ENDscript has also been upgraded as an open platform for the visualization of multiple biochemical and structural data coming from external biotool Web servers, with both 2D and 3D representations. ENDscript 2 and ESPript 3 are freely available at http://endscript.ibcp. fr and http://espript.ibcp. fr, respectively.
A basic study on attribute name extraction from the web

A large number of semistructured documents exist on the Web. We can find pages that contain keywords by using a search engine. But when we want to obtain information about an object like a notebook computer with 1 GB memory, a method is needed that automatically extracts attribute name (in this example, ldquomemoryrdquo) and attribute value (in this example, ldquo1 GBrdquo). In the past, many researchers examined extracting attribute values corresponding to each attribute name. This paper discribes a method that extracts schemas (sets of attribute names) using bootstrapping algorithm.
Ventral frontal satiation-mediated responses to food aromas in obese and normal-weight women.

BACKGROUND Sensory properties of foods promote and guide consumption in hunger states, whereas satiation should dampen the sensory activation of ingestive behaviors. Such activation may be disordered in obese individuals. OBJECTIVE Using functional magnetic resonance imaging (fMRI), we studied regional brain responses to food odor stimulation in the sated state in obese and normal-weight individuals targeting ventral frontal regions known to be involved in coding for stimulus reward value. DESIGN Forty-eight women (25 normal weight; 23 obese) participated in a 2-day (fed compared with fasting) fMRI study while smelling odors of 2 foods and an inedible, nonfood object. Analyses were conducted to permit an examination of both general and sensory-specific satiation (satiation effects specific to a given food). RESULTS Normal-weight subjects showed significant blood oxygen level-dependent responses in the ventromedial prefrontal cortex (vmPFC) to food aromas compared with responses induced by the odor of an inedible object. Normal-weight subjects also showed general (but not sensory-specific) satiation effects in both the vmPFC and orbitofrontal cortex. Obese subjects showed no differential response to the aromas of food and the inedible object when fasting. Within- and between-group differences in satiation were driven largely by changes in the response to the odor of the inedible stimulus. Responses to food aromas in the obese correlated with trait negative urgency, the tendency toward negative affect-provoked impulsivity. CONCLUSIONS Ventral frontal signaling of reward value may be disordered in obesity, with negative urgency heightening responses to food aromas. The observed nature of responses to food and nonfood stimuli suggests that future research should independently quantify each to fully understand brain reward signaling in obesity.
From the Community of Andean Nations (CAN) to the Common Market of the South (Mercosur): A New Integration Strategy for Venezuela

The year 2006 marked a milestone in the history of the regional integration of Venezuela. After 33 years as a member of CAN, the country withdrew from the integration agreement and joined Mercosur, marking a significant change in regional integration strategy. In this paper, the causes of this change, as well as its economic and political effects, have been analyzed through desk research. One of the main conclusions is that Chavez decided to use regional integration as a tool to address the liberal policies of the United States, regardless of the economic consequences. Another is that, due to the economic and institutional deterioration of Venezuela, the non-oil productive sector is not ready to compete with other members of Mercosur.
Dynamical Robustness against Multiple Mutations in Signaling Networks

It has been known that the robust behavior of a cellular signaling network is strongly related to the structural characteristics of the network, such as connectivity, the number of feedback loops, and the number of feed-forward loops. Previous studies proved such relationships through dynamical simulations of various random network models. Most of them, however, focused on robustness against a single node mutation. Considering that complex diseases such as cancer are mostly caused by simultaneous dysfunction of multiple genes, it is needed to investigate the robustness of a network against multiple node mutations. In this paper, we investigated the robustness of a network against multiple node mutations through extensive simulations on the basis of Boolean network models. We found that the robustness against multiple mutations is, in most cases, weaker than the robustness against a single node mutation on average. Moreover, we found that the robustness against multiple mutations is strongly positively correlated with the robustness against single mutation. The difference between the multiple- and single-mutation robustness became larger as the number of mutated nodes increased or the number of nodes that are robust to single-mutation decreased. We further found that a node of relatively large connectivity or being involved with many feedback loops tends to be non-robust against multiple mutations. This finding is supported by the observation that poly-genic disease genes have high connectivity and are involved with a large number of feedback loops than mono-genic disease genes in a human signaling network. Together, our study shows that previous studies for a single node mutation can be extended to understand the network dynamics for multiple node mutations.
Re-planning for a successful project schedule

Time-to-market or project duration has increasing significance for commercial software development. We report on a longitudinal study of a project at IBM Hursley Park. The focus of this study was schedule behaviour; however, we explored a range of related factors, including planned versus actual progress, resource allocation and functionality delivered. In the course of the 12-month study, evidence was collected from eight interviews, 49 project meetings, a number of project documents and a feedback workshop. The project leader considered the project to be a success, not only in terms of satisfying resource and schedule objectives, but also in the marketplace. Whilst many of the originally planned external commitments were met, it is clear that the project did not adhere to its original (detailed) plan and indeed there were no less than seven re-plans. These re-plans were mainly in response to mis-estimates in the original plan, rather than in response to the introduction of additional requirements (of which there were several) or problems with external dependencies. Furthermore, these re-plans suggest a distinction between the nature of the initial planning process and the nature of the re-planning process during the project. Attention is also directed at the implications these re-plans have for software metrics and cost estimation research.
Using Communicative Approach in Arabic Language Classroom to Develop Arabic Speaking Ability

Studies have shown that most Malay learners of Arabic language exhibit weak performance in speaking Arabic despite spending years of learning the language. Among the causes of the problem are traditional methods like reading, translation, and memorization that are popularly used in the teaching and learning of Arabic language. Since Arabic language is not widely used in Malaysian society, the only chance the students have to speak Arabic is in the classroom. Therefore the researcher designed a series of classroom activities using communicative approach for a period of 14 weeks on 45 students of Islamic Education minoring in the Teaching of Arabic as Second Language at the Institute of Education at the International Islamic University Malaysia. Surveys were administered to the students before and after the communicative activities took place. In addition the researcher also performed classroom observation and collected self reports from the students after each activity. The results from paired sample t-test showed that students’ perception on Arabic speaking and ability to speak Arabic improved after 14 weeks. In addition level of difficulty faced to speak Arabic decreased gradually. Results from the Pearson Product Moment correlation coefficient suggested that the improved perceptions of speaking Arabic lessened the difficulties faced by students in speaking Arabic. The results also suggested that the improved perceptions towards speaking Arabic increased students’ ability to speak Arabic.