Miracle-dz/UniFAR-FTUs huggingface dataset:
NRC Publications Archive (NPArC) Archives des publications du CNRC (NPArC) Data Integration and Knowledge Discovery in Life Sciences

Recent advances in various forms of omics technologies have generated huge amount of data. To fully exploit these data sets that in many cases are publicly available, robust computational methodologies need to be developed to deal with the storage, integration, analysis, visualization, and dissemination of these data. In this paper, we describe some of our research activities in data integration leading to novel knowledge discovery in life sciences. Our multi-strategy approach with integration of prior knowledge facilitates a novel means to identify informative genes that could have been missed by the commonly used methods. Our transcriptomics-proteomics integrative framework serves as a means to enhance the confidence of and also to complement transcriptomics discovery. Our new research direction in integrative data analysis of omics data is targeted to identify molecular associations to disease and therapeutic response signatures. The ultimate goal of this research is to facilitate the development of clinical test-kits for early detection, accurate diagnosis/prognosis of disease, and better personalized therapeutic management.
An Operational Framework to Reason about Policies Behavior in Trust Management System

In this paper we show that the logical framework proposed by Becker et al. to reason about security policy behavior in a trust management context can be captured by an operational framework that is based on the language proposed by Miller to deal with scoping and/or modules in logic programming in 1989. The framework of Becker et al. uses propositional Horn clauses to represent both policies and credentials, implications in clauses are interpreted in counterfactual logic, a Hilbert-style proof is defined and a system based on SAT is used to proof whether properties about credentials, permissions and policies are valid in trust management systems, i.e. formulas that are true for all possible policies. Our contribution is to show that instead of using a SAT system, this kind of validation can rely on the operational semantics (derivability relation) of Miller’s language, which is very close to derivability in logic programs, opening up the possibility to extend Becker et al.’s framework to the more practical first order case since Miller’s language is first order.
Polychlorinated biphenyls in Mexican cereals and their packings.

The content of polychlorinated biphenyls in Mexican cereals and in their packaging materials was determined. All the samples had polychlorinated biphenyls. In all the food samples and in 73% of the packings, the concentrations of polychlorinated biphenyls exceeded the tolerance limits established by the U.S. Food and Drug Administration. A correlation was found between the values for polychlorinated biphenyls in the cereals and those in their packings, therefore, it is concluded that the main source of polychlorinated biphenyls in Mexican cereals is the transference of those present in the recycled paperboard used for the packings.
Amygdalo-Hypothalamic Circuit Allows Learned Cues to Override Satiety and Promote Eating

Organisms eat not only in a response to signals related to energy balance. Eating also occurs in response to “extrinsic,” or environmental, signals, including learned cues. Such cues can modify feeding based on motivational value acquired through association with either rewarding or aversive events. We provide evidence that a specific brain system, involving connections between basolateral amygdala and the lateral hypothalamus, is crucial for allowing learned cues (signals that were paired with food delivery when the animal was hungry) to override satiety and promote eating in sated rats. In an assessment of second-order conditioning, we also found that disconnection of this circuitry had no effect on the ability of a conditioned cue to support new learning. Knowledge about neural systems through which food-associated cues specifically control feeding behavior provides a defined model for the study of learning that may be informative for understanding mechanisms that contribute to eating disorders and more moderate forms of overeating.
An incremental update strategy in Deep Web

An effective incremental web crawler maintains a local repository of web pages up to date. In this paper, we will introduce an approach to update pages in Deep Web. Unlike traditional studies which mainly concentrate on “important pages” or “refresh”, We classify pages with different ways of calculating the measure of their respective priorities, obtain the coefficient ratio between the derived categories through experimental statistics, and automatically adjust parameters to achieve the incremental update.
Evidence and Quantification of the Vasopressin Arterial Pressure Control System in the Dog

We determined quantitatively the importance of vasopressin (AVP) release in the regulation of arterial pressure during hemorrhagic hypotension in dogs. The recovery of arterial pressure after rapid hemorrhage was studied in 10 dogs with spinal cord destruction below the level of C-l to remove efferent sympathetic nerve activity. Bilateral nephrectomy was used to remove the reninangiotensin system. Results for this group were compared to those for another group of dogs in which the entire central nervous system, including the pituitary gland, were removed surgically. In all groups, arterial pressure was lowered rapidly from an average control value of 106 ± 2 (mean ± SE) to 51 ± 1 mm Hg by hemorrhage. In dogs with spinal cord destruction and bilateral nephrectomy, arterial pressure rose from 51 mm Hg to 89 ± 3 mm Hg in 3 minutes and stabilized at that level over the next 30 minutes, representing a 71% compensation of arterial pressure. Left atrial pressure fell from 3.3 to 0.8 mm Hg during hemorrhage and subsequently rose only 12% during the hemorrhage. Plasma AVP rose during hemorrhage from 19 ± 2 to 75 ± 10 μU/ml. Injection of the competitive AVP inhibitors, [1-deaminopenicillamine, 4-valine]-8-D-arginine-vasopressin (dPVDAVP), completely reversed the effects and returned the compensated pressure to 50 mm Hg. In the complete absence of the central nervous system, arterial pressure compensation averaged only 10 ± 3%. Plasma osmolality, sodium and potassium concentrations, hematocrit, and heart rate were unchanged in all experimental groups. The relationships involved in the AVP-arterial pressure control system were determined quantitatively and analyzed. A systems analysis using experimentally determined values for AVP secretion and metabolism, plasma AVP, and changes in arterial pressure closely predicted the changes observed during hemorrhage. It appears from this study that AVP has potent systemic vasoconstrictor actions enabling it to make a significant contribution in the restoration of arterial pressure during hemorrhage. Circ Res 46: 58-67, 1980
The 5' region of the human transferrin gene: structure and potential regulatory sites.

Transferrin (Tf) is the iron transport protein in vertebrate serum. The complete organization of the human Tf gene is now determined (Park,I., Schaeffer,E., Sidoli,A., Baralle,F.E., Cohen,G.N. and Zakin,M.M., 1985, Proc. Natl. Acad. Sci. USA 82:3149- 3153, and unpublished results). The human Tf gene is about 33.5 Kb long and is organized in 17 exons and 16 introns. The transcription start point was determined and the total length of Tf mRNA is 2315 bp. The DNA sequence of 620 bp of the 5' region of the human Tf gene is presented here. The 5' region was isolated from a genomic library prepared from the leucocyte DNA of one individual. The sequence of the 5'-promoter region was compared to conserved sequences considered to be cis-acting regulatory regions and several of these sequences have been detected in the human Tf 5'-region. These include multiple metal binding regulatory elements (MBS in the figure) (Stuart,G.W., Searle,P.F. and Palmiter,R.D., 1985, Nature 317:828-831), two transcription factor Spi binding sequences (Spi) (Dynan,W.S. and Tjian,R., 1985, Nature 316:774-778), a progesterone receptor element (PR) (Mulvihill,E.R., Le Pennec,J.P. and Chambon,P., 1982, Cell 28:621-632), a glucocorticoid regulatory sequence (GC) (Buetti,E. and Diggelmann,H. , 1983, EMBO The identification of these putative regulatory regions constitutes an interesting start point for the study of the regulation of human Tf gene expression.
Budgeted Cell Planning for Cellular Networks With Small Cells

Heterogeneous networks (HetNets), where small cells are deployed within the coverage of macrocells, can increase capacity and enhance coverage of a cellular system. Compared with macrocells, small cells have superiority in terms of low installation and operation cost because of their small physical size and low transmission power. Hence, HetNets are deemed as a cost-effective way to address the everlasting radio spectrum crisis. On the other hand, HetNets also unfold a new paradigm from the viewpoint of cellular network planning. In this paper, we study the budgeted cell planning problem in HetNets, where our aim is to maximize the number of traffic demand nodes whose required rates are fully satisfied with a given budget. Our optimization task is challenging, and the formulated problem is hard to solve because of constraints in practical cellular systems, including power limitation, available bandwidth, and traffic requirements. We develop an approximation algorithm that yields an (e - 1)/2e fraction of the optimum, which not only provides quality-guaranteed solutions to the budgeted cel planning problem but sheds useful lights on how to plan a HetNet with limited capital expenditure as well. Preliminary numerical results show that small cells can improve the capacity of a cellular system significantly if they are properly planned.
Giving Users the Steering Wheel for Guiding Resource-Adaptive Systems

Abstract : Addressing resource variation plays an increasingly important role in engineering today's software systems. Research in resource-adaptive applications takes an important step towards addressing this problem. However, existing solutions stop short of addressing the fact that different user tasks often have specific goals of quality of service, and that such goals often entail multiple aspects of quality of service. This paper presents a framework for engineering software systems capable of adapting to resource variations in ways that are specific to the quality goals of each user task. For that, users are empowered to specify their task-specific preferences with respect to multiple aspects of quality of service. Such preferences are then exploited to both coordinate resource usage across the applications supporting the task, and to dynamically control the resource adaptation polices of those applications. A user study validates that non-expert users can use this framework to successfully control the behavior of such adaptive systems.
Bone marrow stromal cells use TGF-β to suppress allergic responses in a mouse model of ragweed-induced asthma

Bone marrow stromal cells [BMSCs; also known as mesenchymal stem cells (MSCs)] effectively suppress inflammatory responses in acute graft-versus-host disease in humans and in a number of disease models in mice. Many of the studies concluded that BMSC-driven immunomodulation is mediated by the suppression of proinflammatory Th1 responses while rebalancing the Th1/Th2 ratio toward Th2. In this study, using a ragweed induced mouse asthma model, we studied if BMSCs could be beneficial in an allergic, Th2-dominant environment. When BMSCs were injected i.v. at the time of the antigen challenge, they protected the animals from the majority of asthma-specific pathological changes, including inhibition of eosinophil infiltration and excess mucus production in the lung, decreased levels of Th2 cytokines (IL-4, IL-5, and IL-13) in bronchial lavage, and lowered serum levels of Th2 immunoglobulins (IgG1 and IgE). To explore the mechanism of the effect we used BMSCs isolated from a variety of knockout mice, performed in vivo blocking of cytokines and studied the effect of asthmatic serum and bronchoalveolar lavage from ragweed challenged animals on the BMSCs in vitro. Our results suggest that IL-4 and/or IL-13 activate the STAT6 pathway in the BMSCs resulting in an increase of their TGF-β production, which seems to mediate the beneficial effect, either alone, or together with regulatory T cells, some of which might be recruited by the BMSCs. These data suggest that, in addition to focusing on graft-versus-host disease and autoimmune diseases, allergic conditions—specifically therapy resistant asthma—might also be a likely target of the recently discovered cellular therapy approach using BMSCs.
Effects of Cigarette Smoking Intensity on the Mucociliary Clearance of Active Smokers

Background: Smoking impairs mucociliary clearance and increases respiratory infection frequency and severity in subjects with and without smoking-related chronic lung diseases. Objective: This study evaluated the effects of smoking intensity on mucociliary clearance in active smokers. Methods: Seventy-five active smokers were grouped into light (1-10 cigarettes/day; n = 14), moderate (11-20 cigarettes/day; n = 34) and heavy smokers (≥21 cigarettes/day; n = 27) before starting a smoking cessation programme. Smoking behaviour, nicotine dependence, pulmonary function, carbon monoxide in exhaled air (exCO), carboxyhaemoglobin (COHb) and mucociliary clearance measured by the saccharin transit time (STT) test were all evaluated. An age-matched non-smoker group (n = 24) was assessed using the same tests. Results: Moderate (49 ± 7 years) and heavy smokers (46 ± 8 years) had higher STT (p = 0.0001), exCO (p < 0.0001) and COHb (p < 0.0001) levels compared with light smokers (51 ± 15 years) and non-smokers (50 ± 11 years). A positive correlation was observed between STT and exCO (r = 0.4; p < 0.0001), STT and cigarettes/day (r = 0.3, p = 0.02) and exCO and cigarettes/day (r = 0.3, p < 0.01). Conclusion: Smoking impairs mucociliary clearance and is associated with cigarette smoking intensity.
Structure and function of the MRP2 (ABCC2) protein and its role in drug disposition

The multi-drug resistance protein 2 (MRP2; ABCC2) is an ATP-binding cassette transporter playing an important role in detoxification and chemoprotection by transporting a wide range of compounds, especially conjugates of lipophilic substances with glutathione, glucuronate and sulfate, which are collectively known as phase II products of biotransformation. In addition, MRP2 can also transport uncharged compounds in cotransport with glutathione, and thus can modulate the pharmacokinetics of many drugs. The other way around, its expression and activity are also altered by certain drugs and disease states. Unlike other members of the MRP/ABCC family, MRP2 is specifically expressed on the apical membrane domain of polarised cells as hepatocytes, renal proximal tubular cells, enterocytes and syncytiotrophoblasts of the placenta. Several naturally ocurring mutations leading to the absence of functional MRP2 protein from the apical membrane have been described causing the human DubinJohnson syndrome associated with conjugated hyperbilirubinaemia. Experimental mutation studies have revealed critical amino acids for substrate binding in the MRP2 molecule. This review is, therefore, focused on the structure and function of MRP2, the substrates transported and the clinical relevance of MRP2.
An Exploratory Assessment of a College Substance Abuse Recovery Program: Augsburg College's StepUP Program

ABSTRACT Objective: To describe the academic, life functioning, and drug use outcomes of students who participated in the StepUP recovery program, a college program designed to support sobriety for students recovering from substance abuse. Method: Eighty-three StepUP program students (46 current students and 37 alumni) participated in a survey using a slightly modified version of the Global Appraisal for Individual Needs (Dennis, 1998), which assesses drug involvement, mental health, and other life-functioning domains. In addition, a subset of 20 current students completed a second assessment approximately 6 months after the first. Results: The large majority of both current students and alumni reported that they abstained from alcohol and drug use, and that they regularly attended self-help groups. Perceived personal assets and social support were endorsed at high levels by the respondents, as were screens for mental health problems. Conclusions: Students involved in the StepUP program either currently or in the past were largely able to maintain sobriety, as well as a favorable GPA. StepUP students also endorsed a sizeable amount of assets and social support, which espouse the maintenance of sobriety.
Salvia macrosiphon seeds and seed oil: pharmacognostic, anti-inflammatory and analgesic properties

Background and objectives: Wild Sage (Salvia macrosiphon Boiss.) known as " Marvak" in Persian is one of the polymorphic and abundant plants of Lamiaceae. The plants whole seeds usually soaked or boiled in hot water are widely used for inflammatory ailments in folk medicine. Documents have shown that there is scant information on the chemical constituents of this plant seeds. The current study was carried out to assess the phytochemical constituents of Salvia macrosiphon seeds as well as anti-inflammatory activities. Methods: The seed oil extracted via a Soxhlet extractor was subjected to pharmacognostic assays using High Performance Thin Layer Chromatography (HPTLC), Gas chromatography/mass spectrometry (GC/MS) analysis of fatty acids and sterols as well as evaluation of the possible anti-inflammatory activities in rats. Results: Total ash, acid insoluble and water soluble ash values were determined as 51.67±7.53, 10.00±0.02 and 30.01±5.01 mg/g, respectively. HPTLC assessment revealed the presence of different steroids, triterpenes and fatty acids. Amount of sterols in oil was found 2.44, 24.92 and 4.60 mg/g for esterified β -sitosterol, free β -sitosterol and free stigmasterol, respectively. The αlinolenic acid (77.69±6.10%) was the principal fatty acid. Regarding the anti-inflammatory activity, the seed oil showed low activity in the early phase of formalin test; however, could not significantly inhibit the neutrophil-induced damage by reducing MPO activity in the paws of the rat. Conclusion: The seed oil did not exhibit satisfactory effects on acute inflammation in this study but considering the rich phytosterols content, the seed and its oil can be introduced as useful dietary supplements.
Influence of Additional Acylation Site(s) of Influenza B Virus Hemagglutinin on Syncytium Formation

We studied the effects of an increase in the hydrophobicity of the transmembrane domain (TM) and cytoplasmic tail (CT) of influenza B virus hemagglutinin (BHA) on fusion activities. For this purpose, we created mutant HAs with novel acylation site(s) in the TM and/or CT. All mutants were able to induce hemifusion and to form fusion pores as well as could wild type (wt) BHA. However, the ability of these mutants to form syncytia was impaired, indicating that the increase in the hydrophobicity of these domains (especially the CT) affected fusion pore dilation.
Fostering local knowledge and human development in globalization of education

Since there are increasing international concerns with both the positive and negative impacts of globalization on indigenous and national development, how to manage the realities and practices of globalization and localization in education for maximizing the benefits and minimizing the disadvantages for the development of individuals and their local community inevitably becomes a key issue in educational development particularly in the developing countries. Proposes a typology of multiple theories of fostering local knowledge and human development to address this key concern. These theories have varied emphasis on global dependence and local orientation and therefore they have their own characteristics, strengths, and limitations. The typology can provide a wide spectrum of alternatives for policy‐makers and educators to conceptualize and formulate their strategies and practices in developing local education. Also presents how to facilitate individual learning and organizational learning in fast‐changing local and global environments and how to foster both individual knowledge and institutional knowledge in schools as the major contribution to the growth of local knowledge and local development. It is hoped that the theories and ideas raised in this paper can benefit the ongoing international efforts for globalization and localization in education for the future of our next generations in the new millennium.
Eigenshape kernel based mean shift for human tracking

An eigenshape kernel based mean shift tracker is proposed in this paper. In contrast with the symmetric constant kernel used in the traditional mean shift tracker, this tracker employs eigenshape to construct an arbitrarily shaped kernel that is adaptive to object shape. Therefore, background information is adaptively excluded from the target. Furthermore, the eigenshape kernels are integrated with color and gradient features, which enhance tracking robustness. Experiments demonstrate that this tracker outperforms the traditional mean shift tracker significantly especially when target shape deformation, target occlusion and background clutter occur.
Cancer incidence among male Massachusetts firefighters, 1987-2003.

BACKGROUND Firefighters are known to be exposed to recognized or probable carcinogens. Previous studies have found elevated risks of several types of cancers in firefighters. METHODS Standardized morbidity odds ratio (SMORs) were used to evaluate the cancer risk in white, male firefighters compared to police and all other occupations in the Massachusetts Cancer Registry from 1986 to 2003. Firefighters and police were identified by text search of the usual occupation field. All other occupations included cases with identifiable usual occupations not police or firefighter. Control cancers were those not associated with firefighters in previous studies. RESULTS Risks were moderately elevated among firefighters for colon cancer (SMOR = 1.36, 95% CI: 1.04-1.79), and brain cancer (SMOR = 1.90, 95% CI: 1.10-3.26). Weaker evidence of increased risk was observed for bladder cancer (SMOR = 1.22, 95% CI: 0.89-1.69), kidney cancer (SMOR = 1.34, 95% CI: 0.90-2.01), and Hodgkin's lymphoma (SMOR = 1.81, 95% CI: 0.72-4.53). CONCLUSIONS These findings are compatible with previous reports, adding to the evidence that firefighters are at increased risk of a number of types of cancer.