Miracle-dz/UniFAR-FTUs huggingface dataset:
Knowledge Representation for Commonsense Reasoning with Text

The reader of a text actively constructs a rich picture of the objects, events, and situation described. The text is a vague, insufficient, and ambiguous indicator of the world that the writer intends to depict. The reader draws upon world knowledge to disambiguate and clarify the text, selecting the most plausible interpretation from among the (infinitely) many possible ones. In principle, any world knowledge whatsoever in the reader's mind can affect the choice of an interpretation. Is there a level of knowledge that is general and common to many speakers of a natural language? Can this level be the basis of an explanation of text interpretation? Can it be identified in a principled, projectable way? Can this level be represented for use in computational text understanding? We claim that there is such a level, called naive semantics (NS), which is commonsense knowledge associated with words. Naive semantics identifies words with concepts, which vary in type. Nominal concepts are categorizations of objects based upon naive theories concerning the nature and typical description of conceptualized objects. Verbal concepts are naive theories of the implications of conceptualized events and states. 2 Concepts are considered naive because they are not always objectively true, and bear only a distant relation to scientific theories. An informal example of a naive nominal concept is the following description of the typical lawyer.
Radiation-Induced Error Criticality in Modern HPC Parallel Accelerators

In this paper, we evaluate the error criticality of radiation-induced errors on modern High-Performance Computing~(HPC) accelerators (Intel Xeon Phi and NVIDIA K40) through a dedicated set of metrics. We show that, as long as imprecise computing is concerned, the simple mismatch detection is not sufficient to evaluate and compare the radiation sensitivity of HPC devices and algorithms. Our analysis quantifies and qualifies radiation effects on applications' output correlating the number of corrupted elements with their spatial locality. Also, we provide the mean relative error (dataset-wise) to evaluate radiation-induced error magnitude. We apply the selected metrics to experimental results obtained in various radiation test campaigns for a total of more than 400 hours of beam time per device. The amount of data we gathered allows us to evaluate the error criticality of a representative set of algorithms from HPC suites. Additionally, based on the characteristics of the tested algorithms, we draw generic reliability conclusions for broader classes of codes. We show that arithmetic operations are less critical for the K40, while Xeon Phi is more reliable when executing particles interactions solved through Finite Difference Methods. Finally, iterative stencil operations seem the most reliable on both architectures.
A machine‐learning approach to coding book reviews as quality indicators: Toward a theory of megacitation

A theory of “megacitation” is introduced and used in an experiment to demonstrate how a qualitative scholarly book review can be converted into a weighted bibliometric indicator. We employ a manual human‐coding approach to classify book reviews in the field of history based on reviewers' assessments of a book author's scholarly credibility (SC) and writing style (WS). In total, 100 book reviews were selected from the American Historical Review and coded for their positive/negative valence on these two dimensions. Most were coded as positive (68% for SC and 47% for WS), and there was also a small positive correlation between SC and WS (r = 0.2). We then constructed a classifier, combining both manual design and machine learning, to categorize sentiment‐based sentences in history book reviews. The machine classifier produced a matched accuracy (matched to the human coding) of approximately 75% for SC and 64% for WS. WS was found to be more difficult to classify by machine than SC because of the reviewers' use of more subtle language. With further training data, a machine‐learning approach could be useful for automatically classifying a large number of history book reviews at once. Weighted megacitations can be especially valuable if they are used in conjunction with regular book/journal citations, and “libcitations” (i.e., library holding counts) for a comprehensive assessment of a book/monograph's scholarly impact.
CHEMICAL CHARACTERIZATION OF THE ISOLATED CELL SURFACE OF AMOEBA

The cell surface has been isolated from uninucleate, freshwater, phagocytic amoebae by a new procedure. Several criteria were employed to demonstrate purity of the cell surface fraction. All morphological components of the tripartite surface were present in the isolated surface and the weight of the isolated surface was quantitatively accounted for by the components analyzed. Chemical analyses showed the presence of lipid, protein, and carbohydrate. Mannose was the predominant neutral sugar. Analyses for three different strains of Amoeba were similar. Phosphate was found to be the major anionic group in the cell surface material. Sulfate, uronic acid, sialic acid, muramic acid, and nonamidated glutamic acid and aspartic acid were absent. Evidence is presented suggesting that the phosphate is associated with an unidentified nonreducing polyol.
Vitamins and minerals: issues associated with too low and too high population intakes

There is an ongoing increase in the availability of foods fortified with micronutrients and dietary supplements. This may result in differing intakes of micronutrients within the population and perhaps larger differences in intakes. Insight into population micronutrient intakes and evaluation of too low or too high intakes is required to see whether there are potential problems regarding inadequacy or excessive intakes. Too low population intakes are evaluated against an estimated average requirement; potential too high population intakes are evaluated against a tolerable upper intake level (UL). Additional health effects, seriousness, and incidence of these health effects are not considered but these can be taken into account in a benefit-risk assessment. Furthermore, authorities would like to regulate food fortification and supplementation in such a way that most of the population is not at risk of potentially high intakes. Several models are available for estimating maximum levels of micronutrients for food fortification and dietary supplements. Policy makers and risk managers need to decide how to divide the ‘free space’ between food fortification and/or dietary supplements, while protecting populations from adverse health effects.
Bayesian Models for Combining Data Across Domains and Domain Types in Predictive fMRI Data Analysis ( Thesis Proposal )

In the context of predictive fMRI data analysis, in particular classification-based analysis, the analysis is usually done separately for a particular subject in a specific study, or by combining data across subjects and studies after normalization to a common template by assuming that there are no inter-subject and inter-study variations. These approaches are suboptimal for a number of reasons. Based on findings in the cognitive neuroscience field, there is a reason to believe that data from other subjects and from different but similar studies exhibit similar patterns of activations, implying that there is some potential for leveraging data from other subjects. However, each subject’s brain might still exhibit some variations in the activations compared to other subjects’ brains, based on factors such as differences in anatomy, experience, or environment. Furthermore, current normalization techniques might blur and distort the data, causing some loss of information. I propose to investigate and develop principled Bayesian methods to tackle these problems, and by doing so, enable combining data across domains and domain types, of which subjects and studies are instances. One goal is to improve predictive performance when compared with predictive analysis of each domain and domain type separately, especially in cases where there is a lot of commonality of activations across different domains and domain types. Another goal is to figure out the extent of commonality of various cognitive phenomena across domains and domain types.
Healthcare providers' intentions to engage in an interprofessional approach to shared decision-making in home care programs: A mixed methods study

In an interprofessional approach to shared decision-making (IP-SDM), an interprofessional team collaborates in identifying best options and helps patients determine their preferences, enabling them to take more control over the treatment plan. However, little is known about fostering IP-SDM in Canada's healthcare system. Therefore, we sought to evaluate health professionals' intentions to engage in IP-SDM in home care and explore the factors associated with this intention. A total of 272 eligible home care providers completed a questionnaire based on the theory of planned behavior. Eight managers and one healthcare team caring for the frail elderly were interviewed about possible barriers and facilitators. Analysis involved descriptive statistics and multivariate analysis of quantitative data and content analysis of qualitative data. On a scale of − 3 (strongly disagree) to +3 (strongly agree), the mean intention to engage in IP-SDM was positive (1.42 ± 1.39). The intention was influenced by the following theory-based determinants (R 2 = 57%; p ≤ 0.002), i.e. cognitive attitude (p < 0.001) subjective norm (p < 0.0001) and perceived behavioral control (p < 0.0001), with variations depending on the type of provider. Barriers included lack of time, poor team cohesion and high staff turnover. Facilitators included team cohesion and shared tools. Future programs implementing IP-SDM could address these barriers and facilitators.
The 21-Nucleotide, but Not 22-Nucleotide, Viral Secondary Small Interfering RNAs Direct Potent Antiviral Defense by Two Cooperative Argonautes in Arabidopsis thaliana[W][OA]

This work identifies cooperative action of ARGONAUTE1 and ARGONAUTE2 in virus resistance conferred by 21-nucleotide virus-derived small interfering RNAs (siRNAs). It also reveals that 22-nucleotide viral siRNAs do not guide efficient antiviral defense, demonstrating a qualitative difference between 21- and 22-nucleotide classes of siRNAs in RNA silencing. Arabidopsis thaliana defense against distinct positive-strand RNA viruses requires production of virus-derived secondary small interfering RNAs (siRNAs) by multiple RNA-dependent RNA polymerases. However, little is known about the biogenesis pathway and effector mechanism of viral secondary siRNAs. Here, we describe a mutant of Cucumber mosaic virus (CMV-Δ2b) that is silenced predominantly by the RNA-DEPENDENT RNA POLYMERASE6 (RDR6)-dependent viral secondary siRNA pathway. We show that production of the viral secondary siRNAs targeting CMV-Δ2b requires SUPPRESSOR OF GENE SILENCING3 and DICER-LIKE4 (DCL4) in addition to RDR6. Examination of 25 single, double, and triple mutants impaired in nine ARGONAUTE (AGO) genes combined with coimmunoprecipitation and deep sequencing identifies an essential function for AGO1 and AGO2 in defense against CMV-Δ2b, which act downstream the biogenesis of viral secondary siRNAs in a nonredundant and cooperative manner. Our findings also illustrate that dicing of the viral RNA precursors of primary and secondary siRNA is insufficient to confer virus resistance. Notably, although DCL2 is able to produce abundant viral secondary siRNAs in the absence of DCL4, the resultant 22-nucleotide viral siRNAs alone do not guide efficient silencing of CMV-Δ2b. Possible mechanisms for the observed qualitative difference in RNA silencing between 21- and 22-nucleotide secondary siRNAs are discussed.
BindingDB: a web-accessible molecular recognition database.

This paper presents an initial description of the BindingDB, a public web-accessible database of measured binding affinities for various molecular types (http://www.bindingdb.org). The BindingDB allows queries based upon a range of criteria, including chemical similarity or substructure, sequence homology, numerical criteria (e.g. delta G(o) < 5 kcal/mol) and reactant names (e.g. "lysozyme"). Principles of Human-Computer Interactions are being employed in creating the query interface and user-feedback is being solicited. The data specification includes significant experimental detail. A full dictionary has been created for isothermal titration calorimetry data in consultation with experimentalists and data dictionaries for enzyme-inhibition and other measurement techniques are being developed. Currently, the BindingDB contains several data sets of broad interest, such as antigen-antibody binding and cyclodextrin/small molecule binding. However, it is anticipated that online deposition by experimentalists will ultimately contribute to a larger flow of data. We are actively developing software and file specifications to facilitate such deposition.
Automatic Detection of Point of View Differences in Wikipedia

We investigate differences in point of view (POV) between two objective documents, where one is describing the subject matter in a more positive/negative way than the other, and present an automatic method for detecting such POV differences. We use Amazon Mechanical Turk (AMT) to annotate sentences as positive, negative or neutral based on their POV towards a given target. A statistical classifier is trained to predict the POV score of a document, which reflects how positive/negative the document’s POV towards its target is. The results of our experiments on a set of articles in the Arabic and English Wikipedias from the people category show that our method successfully detects POV differences.
Co-option of Liver Vessels and Not Sprouting Angiogenesis Drives Acquired Sorafenib Resistance in Hepatocellular Carcinoma

Background: The anti-angiogenic Sorafenib is the only approved systemic therapy for advanced hepatocellular carcinoma (HCC). However, acquired resistance limits its efficacy. An emerging theory to explain intrinsic resistance to other anti-angiogenic drugs is ‘vessel co-option,’ ie, the ability of tumors to hijack the existing vasculature in organs such as the lungs or liver, thus limiting the need for sprouting angiogenesis. Vessel co-option has not been evaluated as a potential mechanism for acquired resistance to anti-angiogenic agents. Methods: To study sorafenib resistance mechanisms, we used an orthotopic human HCC model (n = 4-11 per group), where tumor cells are tagged with a secreted protein biomarker to monitor disease burden and response to therapy. Histopathology, vessel perfusion assessed by contrast-enhanced ultrasound, and miRNA sequencing and quantitative real-time polymerase chain reaction were used to monitor changes in tumor biology. Results: While sorafenib initially inhibited angiogenesis and stabilized tumor growth, no angiogenic ‘rebound’ effect was observed during development of resistance unless therapy was stopped. Instead, resistant tumors became more locally infiltrative, which facilitated extensive incorporation of liver parenchyma and the co-option of liver-associated vessels. Up to 75% (±10.9%) of total vessels were provided by vessel co-option in resistant tumors relative to 23.3% (±10.3%) in untreated controls. miRNA sequencing implicated pro-invasive signaling and epithelial-to-mesenchymal-like transition during resistance development while functional imaging further supported a shift from angiogenesis to vessel co-option. Conclusions: This is the first documentation of vessel co-option as a mechanism of acquired resistance to anti-angiogenic therapy and could have important implications including the potential therapeutic benefits of targeting vessel co-option in conjunction with vascular endothelial growth factor receptor signaling.
Diversification of glial lineages: A novel method to clone brain cells in vitro on nitrocellulose substratum

We have developed a novel in vitro method to analyze the diversification of glial cells during development. The primary advantage of the approach is that glial lineages are formed in discrete clones on a nitrocellulose substratum where the relationship of the progeny is strictly defined. This method facilitates the comparison of a large complement of astrocyte and oligodendrocyte lineages under controlled conditions. Clones were formed by plating a brain dissociate on nitrocellulose at very low density (5,000–40,000 cells/154 mm2). However, growth depended on diffusible factors produced by brain cells growing under the nitrocellulose support at high density (feeder layer). The cloning efficiency of cells from mouse forebrain (P0) was 1–3%. This means we can detect 100,000 to 300,000 clonal progenitors in the dissociate (107 cells per forebrain) using the clonal culture technique. Cell phenotypes were determined by immunocytochemical staining with anti‐glial fibrillary acidic protein (GFAP) to label astrocytes and anti‐galactocerebroside (GC) and anti‐myelin basic protein (MBP) to label oligodendrocytes. There was a remarkable diversity of glia represented in different lineages. The number of astrocyte clones was greater than the number of oligodendrocyte clones but combined their total was 90%. Clone sizes were distributed over a wide range, which indicated that growth rates varied. Clones appeared compact or dispersed but astrocyte clones exhibited three different morphologies—fibroblast‐like, stellate, and elongated. Oligodendrocytes had different morphologies distinct from astrocytes. Although there were different glial lineages the cells in most clones were homogeneous, indicating the progeny had the same fate. However, a small number of the clones, approximately 2%, were heterogeneous and contained both astrocytes and oligodendrocytes. The application of this technique to glial lineages demonstrates that intrinsic factors have a role in determining cell fate since different clones formed under the same external conditions. Finally, these results are consistent with the existence of multiple glial progenitors or the continued presence of multipotential progenitors at the time of birth.
Prevalence and costs of acute and chronic potentially avoidable pediatric hospitalizations in Tennessee.

BACKGROUND Potentially avoidable pediatric hospitalizations (PAPH) can now be identified using an analytical tool developed by the federal Agency for Healthcare Research and Quality (AHRQ). We apply this new tool to Tennessee inpatient discharge records for 2005 to determine the prevalence of PAPH and analyze the variation patterns of PAPH across racial, gender, and insurance status lines. METHODS Retrospective analysis of administrative data based on the UB-92 claims forms submitted by all short-term acute-care hospitals in Tennessee for 2005. RESULTS Tennessee had higher prevalence rates of PAPH than seen in the nation overall for four of the five Ambulatory-Care Sensitive Conditions (ACSC), identified by AHRQ as those hospitalizations which can potentially be avoided. Variations of the rates of PAPH across racial, gender and insurance subgroups were found to mirror those found for pediatric hospitalizations for all conditions. However, when PAPH were grouped according to whether they were chronic or acute in terms of their primary admitting condition, Black children were over-represented in PAPH for chronic conditions such as asthma and diabetes. In addition, Black children's average costs are significantly higher than those for White children irrespective of whether the admitting condition was chronic or acute. CONCLUSIONS The high rates of PAPH reported in this study imply a weakness in Tennessee's primary care for children. These high rates also point out opportunities for reducing expensive hospitalizations associated with poorly controlled diabetes, asthma exacerbations, and dehydration due to gastroenteritis.
Risk assessment of GM stacked events obtained from crosses between GM events

A. De Schrijver*, Y. Devos, M. Van den Bulcke, P. Cadot, M. De Loose, D. Reheul and M. Sneyers Division of Biosafety and Biotechnology, Scientific Institute of Public Health, Juliette Wytsmanstraat 14, 1050 Brussels, Belgium (Tel.: D32 2 642 5293; fax: D32 2 642 5292; e-mail: ads@sbb.ihe.be) Department of Plant Production, Faculty of Bioscience Engineering, University of Ghent, Coupure Links 653, 9000 Ghent, Belgium Department of Clinical Immunology, Catholic University of Leuven, 3000 Leuven, Belgium Department of Technology and Food, Institute for Agricultural and Fisheries Research, 9820 Merelbeke, Belgium
Analyzing civic complaints for proactive maintenance in smart city

To transform a city into a smart city it is important to focus on civic issues faced by the inhabitants. Civic complaints incorporate problems related to street condition, traffic, noise, water etc. Their analysis can contribute to proactive decisions to be taken by the city authority. Urban Computing is applied in many areas like transportation, environment, and security etc. but there is a need to explore more on urban planning from the perspective to analyze root cause of civic issues and reducing their concentration. In the present work, segregation of different urban areas is done and issues critical in a region are determined. Primarily, two phase clustering has been performed. In first phase, a dynamic grid based clustering is done on the basis of spatial attribute to analyze complaints that may have strong inter-dependency. In second phase, the location based clusters are further clustered based on complaint category which helps in determining regions of city imitating similar complaint behavior. The analysis is done on real world data acquired for two cities New York (USA) and Bangalore (India). Experimental results are visualized to show better interpretation. The results will help in planning strategies to improve inhabitant's satisfaction rate and consequently improving their quality of life.
Balance between MKK6 and MKK3 Mediates p38 MAPK Associated Resistance to Cisplatin in NSCLC

The p38 MAPK signaling pathway has been proposed as a critical mediator of the therapeutic effect of several antitumor agents, including cisplatin. Here, we found that sensitivity to cisplatin, in a system of 7 non-small cell lung carcinoma derived cell lines, correlated with high levels of MKK6 and marked activation of p38 MAPK. However, knockdown of MKK6 modified neither the response to cisplatin nor the activation of p38 MAPK. Deeper studies showed that resistant cell lines also displayed higher basal levels of MKK3. Interestingly, MKK3 knockdown significantly decreased p38 phosphorylation upon cisplatin exposure and consequently reduced the response to the drug. Indeed, cisplatin poorly activated MKK3 in resistant cells, while in sensitive cell lines MKK3 showed the opposite pattern in response to the drug. Our data also demonstrate that the low levels of MKK6 expressed in resistant cell lines are the consequence of high basal activity of p38 MAPK mediated by the elevated levels of MKK3. This finding supports the existence of a regulatory mechanism between both MAPK kinases through their MAPK. Furthermore, our results were also mirrored in head and neck carcinoma derived cell lines, suggesting our observations boast a potential universal characteristic in cancer resistance of cisplatin. Altogether, our work provides evidence that MKK3 is the major determinant of p38 MAPK activation in response to cisplatin and, hence, the resistance associated with this MAPK. Therefore, these data suggest that the balance between both MKK3 and MKK6 could be a novel mechanism which explains the cellular response to cisplatin.