Miracle-dz/UniFAR-FTUs huggingface dataset:
The Problem of Induction

The problem of induction is sometimes motivated via a comparison between rules of induction and rules of deduction. Valid deductive rules are necessarily truth preserving, while inductive rules are not. So, for example, one valid deductive rule might be this: (D) From premises of the form “All F are G” and “a is F ,” the corresponding conclusion of the form “a is G” follows. The rule (D) is illustrated in the following depressing argument: (DA) All people are mortal. I am a person. So, I am mortal. The rule here is “valid” in the sense that there is no possible way in which premises satisfying the rule can be true without the corresponding conclusion also being true. A possible inductive rule might be this: (I) From premises of the form “Many many F s are known to be G,” “There are no known cases of F s that are not G,” and “a is F ,” the corresponding conclusion can be inferred of the form “a is G. ” The rule (I) might be illustrated in the following “inductive argument. ” (IA) Many many people are known to have been moral. There are no known cases of people who are not mortal. I am a person. So, I am mortal.
EXTENDING INFERENCE IN CONTINUOUS TIME BAYESIAN NETWORKS by Liessman

The continuous time Bayesian network (CTBN) has been defined to enable reasoning about complex systems in continuous time by representing the system as a factored, finite-state, continuous-time Markov process. The dynamics of the CTBN are described by each node’s conditional intensity matrices, determined by the states of the parents in the network. As the CTBN is a relatively new model, many extensions that have been defined and researched with respect to Bayesian networks (BNs) have not yet been extended to CTBNs. The proposed research intends to address some of these. First, we intend to formally prove several complexity results with respect to CTBNs. Specifically, it is known that exact inference in CTBN is NP-hard due to the use of a Bayesian network to set the initial states of the nodes. However, we propose to prove that exact inference in CTBNs is still NP-hard even when the initial states are fully observed. Furthermore, we suspect and intend to prove that approximate inference in CTBNs, as with Bayesian networks, is also NP-hard. Second, we propose to formalize both uncertain and negative evidence in the context of CTBNs and extend existing inference algorithms to be able to support these new types of evidence. Third, we show how methods for sensitivity analysis of Markov processes can be applied to the CTBN while exploiting the conditional independence structure of the network. This is done through what we call “node isolation,” which approximates a nodes’ unconditional intensity matrix, analogous to marginalization in a Bayesian network. Lastly, we intend to investigate how and when the node isolation process might be used in approximate inference to increase efficiency without significantly decreasing accuracy. This prospectus reviews preliminary progress on these goals and outlines the direction of future research for the completion of this doctoral research.
Sex Differences in Quality of Life in Stroke Survivors: Data From the Tinzaparin in Acute Ischaemic Stroke Trial (TAIST)

Background and Purpose— Female sex is predictive of poor functional outcome in stroke, even after correction for prognostic factors. Poor quality of life (QoL) is observed in stroke survivors with lower scores seen in the most disabled patients. We used data from the Tinzaparin in Acute Ischaemic Stroke Trial (TAIST) to assess the relationship between sex and QoL after ischemic stroke. Methods— TAIST was a randomized, controlled trial assessing the safety and efficacy of tinzaparin versus aspirin in 1484 patients with acute ischemic stroke. QoL was measured at 180 days postrandomization using the Short Form-36 health survey, which assesses QoL across 8 domains. The relationship between sex and each domain was assessed using ordinal regression, both unadjusted and adjusted for key prognostic factors. Results— Of the 1484 patients randomized into TAIST, 216 had died at 180 days postrandomization. A total of 1268 survivors were included in this analysis, 694 males (55%) and 574 females (45%). Females tended to score lower than males across all QoL domains (apart from general health); statistically significant lower scores were seen for physical functioning (OR: 0.58, 95% CI: 0.47 to 0.72), vitality (OR: 0.79, 95% CI: 0.64 to 0.98), and mental health (OR: 0.75, 95% CI: 0.61 to 0.93). The results for physical functioning and mental health remained significant after adjustment for prognostic variables (OR: 0.73, 95% CI: 0.58 to 0.92; OR: 0.76, 95% CI: 0.60 to 0.95, respectively). Conclusions— QoL, in particular physical function and mental health domains, is lower in female patients after stroke. This difference persists even after correction for known prognostic factors such as age and stroke severity.
Developmental roles and molecular characterization of a Drosophila homologue of Arabidopsis Argonaute1, the founder of a novel gene superfamily

Arabidopsis Argonaute1 (AGO1) is the founder of a novel gene superfamily that is conserved from fission yeasts to humans. AGO1, and several other members of this superfamily are necessary for stem cell renewal or RNA interference. However, little has been reported about their roles in animal development or about the molecular activities of any of the members.
Perseveration by NK1R-/- (‘knockout’) mice is blunted by doses of methylphenidate that affect neither other aspects of their cognitive performance nor the behaviour of wild-type mice in the 5-Choice Continuous Performance Test

The underlying cause(s) of abnormalities expressed by patients with attention deficit hyperactivity disorder (ADHD) have yet to be delineated. One factor that has been associated with increased vulnerability to ADHD is polymorphism(s) of TACR1, which is the human equivalent of the rodent NK1 (substance P-preferring) receptor gene (Nk1r). We have reported previously that genetically altered mice, lacking functional NK1R (NK1R–/–), express locomotor hyperactivity, which was blunted by the first-line treatment for ADHD, methylphenidate. Here, we compared the effects of this psychostimulant (3, 10 and 30 mg/kg, intraperitoneally) on the behaviour of NK1R-/- mice and their wild types in the 5-Choice Continuous Performance Test, which emulates procedures used to study attention and response control in ADHD patients. Methylphenidate increased total trials (a measure of ‘productivity’) completed by wild types, but not by NK1R-/- mice. Conversely, this drug reduced perseveration by NK1R-/- mice, but not by wild types. Other drug-induced changes in key behaviours were not genotype dependent, especially at the highest dose: for example, % omissions (an index of inattentiveness) was increased, whereas % false alarms and % premature responses (measures of impulsivity) declined in both genotypes, indicating reduced overall response. These findings are discussed in the context of the efficacy of methylphenidate in the treatment of ADHD. Moreover, they lead to several testable proposals. First, methylphenidate does not improve attention in a subgroup of ADHD patients with a functional deficit of TACR1. Second, these patients do not express excessive false alarms when compared with other groups of subjects, but they do express excessive perseveration, which would be ameliorated by methylphenidate.
Chemical stability of tramadol hydrochloride injection admixed with selected pain drugs

Background: Tramadol hydrochloride (HCl) and ketorolac tromethamine are analgesic drugs, which are commonly used in combination in postoperative pain management. According to some studies, metoclopramide and magnesium sulfate (MgSO4) as adjuvant agents can improve analgesia and decrease the need for other pain drugs. Materials and Methods: The chemical stability of tramadol HCl combined with ketorolac tromethamine and metoclopramide HCl has been studied using a stability-indicating high-performance liquid chromatographic assay method. Calibration curves were produced using linear regression of the peak area against concentration of each drug, with an r2 value ≥ 0.96. Our aim was to investigate the stability of admixture solution of tramadol HCl combined with ketorolac tromethamine and metoclopramide HCl for 48 h (25°C) and 5 days (5°C), with MgSO4, which has never been assessed. Results: Data obtained for admixtures prepared and stored at temperatures of 25°C and 5°C, show that all drugs have reached at least 98% of the initial concentration. Conclusions: For the purpose of pre-preparing drug admixtures to use with confidence, tramadol HCl infusions may be prepared in advance and then thawed before use in clinical units. On the basis of our results, the intravenous mixture of tramadol (7.69 mg/mL), metoclopramide (0.19 mg/mL), ketorolac (1.15 mg/mL), and magnesium sulfate (77 mg/mL) may be considered for a possible commercial formulation.
An Optimal Graph Theoretic Approach to Data Clustering: Theory and Its Application to Image Segmentation

A novel graph theoretic approach for data clustering is presented and its application to the image segmentation problem is demonstrated. The data to be clustered are represented by an undirected adjacency graph G with arc capacities assigned to reflect the similarity between the linked vertices. Clustering is achieved by removing arcs of G to form mutually exclusive subgraphs such that the largest inter-subgraph maximum flow is minimized. For graphs of moderate size ( approximately 2000 vertices), the optimal solution is obtained through partitioning a flow and cut equivalent tree of G, which can be efficiently constructed using the Gomory-Hu algorithm (1961). However for larger graphs this approach is impractical. New theorems for subgraph condensation are derived and are then used to develop a fast algorithm which hierarchically constructs and partitions a partially equivalent tree of much reduced size. This algorithm results in an optimal solution equivalent to that obtained by partitioning the complete equivalent tree and is able to handle very large graphs with several hundred thousand vertices. The new clustering algorithm is applied to the image segmentation problem. The segmentation is achieved by effectively searching for closed contours of edge elements (equivalent to minimum cuts in G), which consist mostly of strong edges, while rejecting contours containing isolated strong edges. This method is able to accurately locate region boundaries and at the same time guarantees the formation of closed edge contours. >
Determination of Cellular Processing Rates for a Trastuzumab-Maytansinoid Antibody-Drug Conjugate (ADC) Highlights Key Parameters for ADC Design

Antibody-drug conjugates (ADCs) are a promising class of cancer therapeutics that combine the specificity of antibodies with the cytotoxic effects of payload drugs. A quantitative understanding of how ADCs are processed intracellularly can illustrate which processing steps most influence payload delivery, thus aiding the design of more effective ADCs. In this work, we develop a kinetic model for ADC cellular processing as well as generalizable methods based on flow cytometry and fluorescence imaging to parameterize this model. A number of key processing steps are included in the model: ADC binding to its target antigen, internalization via receptor-mediated endocytosis, proteolytic degradation of the ADC, efflux of the payload out of the cell, and payload binding to its intracellular target. The model was developed with a trastuzumab-maytansinoid ADC (TM-ADC) similar to trastuzumab-emtansine (T-DM1), which is used in the clinical treatment of HER2+ breast cancer. In three high-HER2-expressing cell lines (BT-474, NCI-N87, and SK-BR-3), we report for TM-ADC half-lives for internalization of 6–14 h, degradation of 18–25 h, and efflux rate of 44–73 h. Sensitivity analysis indicates that the internalization rate and efflux rate are key parameters for determining how much payload is delivered to a cell with TM-ADC. In addition, this model describing the cellular processing of ADCs can be incorporated into larger pharmacokinetics/pharmacodynamics models, as demonstrated in the associated companion paper.
In situ silica reinforcement of vinyltriethoxysilane‐grafted styrene–butadiene rubber by sol–gel process

Grafting polymerization of vinyltriethoxysilane (VTES) onto styrene–butadiene rubber (SBR) was firstly carried out in latex, using potassium persulfate (KPS) as initiator. The grafted SBR was further reinforced with silica produced by sol–gel reaction of tetraethoxysilane (TEOS). The grafted of VTES onto SBR was characterized and confirmed by ATR-FTIR and 1H-NMR. Results revealed that the addition of VTES could considerably improve the content of silica, bound rubber in SBR and utilized efficiency of TEOS. Meanwhile, the curing characteristics and mechanical properties of the vulcanized in situ reinforced SBR-g-VTES were also investigated and compared with that of the silica-reinforced SBR prepared by mechanical mixing. The delta torque, tensile, and tear strength of in situ reinforced SBR-g-VTES were higher than that of silica-reinforced SBR. Dynamic mechanical analysis showed that the interaction between silica and SBR of in situ reinforced SBR-g-VTES was also better than that of the silica-reinforced SBR. © 2012 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2013
FORECASTING DAILY VOLATILITY USING RANGE-BASED DATA

Users of agricultural markets frequently need to establish accurate representations of expected future volatility. The fact that range-based volatility estimators are highly efficient has been acknowledged in the literature. However, it is not clear whether using range-based data leads to better risk management decisions. This paper compares the performance of GARCH models, range-based GARCH models, and log-range based ARMA models in terms of their forecasting abilities. The realized volatility will be used as the forecasting evaluation criteria. The conclusion helps establish an efficient forecasting framework for volatility models.
Grasping Kinematics from the Perspective of the Individual Digits: A Modelling Study

Grasping is a prototype of human motor coordination. Nevertheless, it is not known what determines the typical movement patterns of grasping. One way to approach this issue is by building models. We developed a model based on the movements of the individual digits. In our model the following objectives were taken into account for each digit: move smoothly to the preselected goal position on the object without hitting other surfaces, arrive at about the same time as the other digit and never move too far from the other digit. These objectives were implemented by regarding the tips of the digits as point masses with a spring between them, each attracted to its goal position and repelled from objects' surfaces. Their movements were damped. Using a single set of parameters, our model can reproduce a wider variety of experimental findings than any previous model of grasping. Apart from reproducing known effects (even the angles under which digits approach trapezoidal objects' surfaces, which no other model can explain), our model predicted that the increase in maximum grip aperture with object size should be greater for blocks than for cylinders. A survey of the literature shows that this is indeed how humans behave. The model can also adequately predict how single digit pointing movements are made. This supports the idea that grasping kinematics follow from the movements of the individual digits.
Automatic Selection of Context Configurations for Improved Class-Specific Word Representations

This paper is concerned with identifying contexts useful for training word representation models for different word classes such as adjectives (A), verbs (V), and nouns (N). We introduce a simple yet effective framework for an automatic selection of class-specific context configurations. We construct a context configuration space based on universal dependency relations between words, and efficiently search this space with an adapted beam search algorithm. In word similarity tasks for each word class, we show that our framework is both effective and efficient. Particularly, it improves the Spearman’s rho correlation with human scores on SimLex-999 over the best previously proposed class-specific contexts by 6 (A), 6 (V) and 5 (N) rho points. With our selected context configurations, we train on only 14% (A), 26.2% (V), and 33.6% (N) of all dependency-based contexts, resulting in a reduced training time. Our results generalise: we show that the configurations our algorithm learns for one English training setup outperform previously proposed context types in another training setup for English. Moreover, basing the configuration space on universal dependencies, it is possible to transfer the learned configurations to German and Italian. We also demonstrate improved per-class results over other context types in these two languages.
Structural basis for control by phosphorylation.

The talk will review our current understanding of the structural consequences of post translational modification by phosphorylation. Studies on active and inactive protein kinases have taught us much about the role of the activation segment in control of kinase activity. We have recently solved the structure of the active phosphorylase kinase catalytic domain in complex with a peptide substrate. The peptide sequence was derived from sequences obtained from the peptide library search for kinase specilicities by Cantley and colleagues. The results demonstrate a key role for the activation segment in substrate recognition that is likely to be common for many protein kinases. Studies with the cyclin dependent protein kinase, CDK2, and its phosphorylation by Civl (CAK in vivo), the kinase activating enzyme from S. cerevisiae, have shown that phosphorylalion of CDK2 proceeds more rapidly with CDK2 alone than in the presence of cyclin A. The activity of the phosphorylated CDK2 is (). 39f of the fully active CDK2(phosphorylated)-cyclin A complex. The crystal structure of the phosphorylated CDK2 shows an inactive conformation in which the activation segment not localised. The structural results provide an explanation for the low activity, Staurosporine is a potent inhibitor for most but not all protein kinases. Recent structural studies with CDK2-staurosporine complex have shown the structural basis for the potent inhibition of CDK2 and provide possible explanations for lower potency against certain protein kinases such asCDK4 and CKl.
Human Heart Cytosolic Reductases and Anthracycline Cardiotoxicity

Anthracyclines are a class of antitumor drugs widely used for the treatment of a variety of malignancy, including leukemias, lymphomas, sarcomas, and carcinomas. Different mechanisms have been proposed for anthracycline antitumor effects including freeradical generation, DNA intercalation/binding, activation of signaling pathways, inhibition of topoisomerase II and apoptosis. A life‐threatening form of cardiomyopathy hampers the clinical use of anthracyclines. According to the prevailing hypothesis, anthracyclines injure the heart by generating damaging free radicals through iron‐catalyzed redox cycling. Although the “iron and freeradical hypothesis” can explain some aspects of anthracycline acute toxicity, it is nonetheless disappointing when referred to chronic cardiomyopathy. An alternative hypothesis implicates C‐13 alcohol metabolites of anthracyclines as mediators of myocardial contractile dysfunction (“metabolite hypothesis”). Hydroxy metabolites are formed upon two‐electron reduction of the C‐13 carbonyl group in the side chain of anthracyclines by cytosolic NADPH‐dependent reductases. Anthracycline alcohol metabolites can affect myocardial energy metabolism, ionic gradients, and Ca 2+ movements, ultimately impairing cardiac contraction and relaxation. In addition, alcohol metabolites can impair cardiac intracellular iron handling and homeostasis, by delocalizing iron from the [4Fe‐4S] cluster of cytoplasmic aconitase. Chronic cardiotoxicity induced by C‐13 alcohol metabolite might be primed by oxidative stress generated by anthracycline redox cycling (“unifying hypothesis”). Putative cardioprotective strategies should be aimed at decreasing C‐13 alcohol metabolite production by means of efficient inhibitors of anthracycline reductases, as short‐chain coenzyme Q analogs and chalcones that compete with anthracyclines for the enzyme active site, or by developing novel anthracyclines less susceptible to reductive metabolism.
The Prediction Of BRDFs From Surface Profile Measurements

This paper discusses methods of predicting the BRDF of smooth surfaces from profile measurements of their surface finish. The conversion of optical profile data to the BRDF at the same wavelength is essentially independent of scattering models, while the conversion of mechanical measurements, and wavelength scaling in general, are model dependent. Procedures are illustrated for several surfaces, including two from the recent HeNe BRDF round robin, and results are compared with measured data. Reasonable agreement is found except for surfaces which involve significant scattering from isolated surface defects which are poorly sampled in the profile data.
Controlled Clinical Laboratory Comparison of Two Supplemented Aerobic and Anaerobic Media Used in Automated Blood Culture Systems To Detect Bloodstream Infections

ABSTRACT A 20-ml blood sample was collected from adult patients with suspected bloodstream infections and distributed equally into the four volume-controlled bottles of a blood culture set consisting of aerobic and anaerobic BACTEC Plus/F bottles and aerobic and anaerobic BacT/Alert FAN bottles. All bottles were incubated in their respective instruments for a standard 5-day protocol or until the instruments signalled positivity. Samples in all bottles with negative results by these instruments were terminally subcultured. A total of 8,390 blood culture sets were obtained during the study period, of which 4,402 (52.5%) met the study criteria. Of these, 946 (21.5%) were positive either by instrument signal or by additional terminal subculture of all negative bottles and yielded growth of microorganisms. Five hundred eighty-nine (13.4%) blood culture sets were considered to have recovered 663 clinically significant organisms. When both the BACTEC and the BacT/Alert systems were used, 465 positive sets were detected; BACTEC alone detected 52 positive sets and BacT/Alert alone detected 72 (P = 0.09). No differences were found between the two systems in microbial recovery rate from blood cultures obtained from patients on antibiotic therapy. Significantly more members of the family Enterobacteriaceae (P < 0.01) were detected from patients without antimicrobial therapy by BacT/Alert than by BACTEC. The false-negative rates were 0.20% for BACTEC and 0.32% for BacT/Alert. A significantly higher false-positive rate was found for BACTEC (P < 0.0001). Both systems were comparable for the time to detection of microorganisms. However, gram-positive bacteria were detected faster by BACTEC andEnterobacteriaceae were detected faster on average by BacT/Alert. We concluded that both systems are comparable in their abilities to recover aerobic and anaerobic organisms from blood cultures and a terminal subculture might not be necessary for either of the two systems. The increased positivity rate when using an anaerobic bottle in a two-bottle blood culture set is due to the additional blood volume rather than to the use of an anaerobic medium.