Miracle-dz/UniFAR-FTUs huggingface dataset:
Cancer Patients’ Trade-offs Among Efficacy, Toxicity, and Out-of-Pocket Cost in the Curative and Noncurative Setting

Background:When making treatment decisions, cancer patients must make trade-offs among efficacy, toxicity, and cost. However, little is known about what patient characteristics may influence these trade-offs. Methods:A total of 400 cancer patients reviewed 2 of 3 stylized curative and noncurative scenarios that asked them to choose between 2 treatments of varying levels of efficacy, toxicity, and cost. Each scenario included 9 choice sets. Demographics, cost concerns, numeracy, and optimism were assessed. Within each scenario, we used latent class methods to distinguish groups with discrete preferences. We then used regressions with group membership probabilities as covariates to identify associations. Results:The median age of the patients was 61 years (range, 27–90 y). Of the total number of patients included, 25% were enrolled at a community hospital, and 99% were insured. Three latent classes were identified that demonstrated (1) preference for survival, (2) aversion to high cost, and (3) aversion to toxicity. Across all scenarios, patients with higher income were more likely to be in the class that favored survival. Lower income patients were more likely to be in the class that was averse to high cost (P<0.05). Similar associations were found between education, employment status, numeracy, cost concerns, and latent class. Conclusions:Even in these stylized scenarios, socioeconomic status predicted the treatment choice. Higher income patients may be more likely to focus on survival, whereas those of lower socioeconomic status may be more likely to avoid expensive treatment, regardless of survival or toxicity. This raises the possibility that insurance plans with greater cost-sharing may have the unintended consequence of increasing disparities in cancer care.
Lead Hopping Using SVM and 3D Pharmacophore Fingerprints

The combination of 3D pharmacophore fingerprints and the support vector machine classification algorithm has been used to generate robust models that are able to classify compounds as active or inactive in a number of G-protein-coupled receptor assays. The models have been tested against progressively more challenging validation sets where steps are taken to ensure that compounds in the validation set are chemically and structurally distinct from the training set. In the most challenging example, we simulate a lead-hopping experiment by excluding an entire class of compounds (defined by a core substructure) from the training set. The left-out active compounds comprised approximately 40% of the actives. The model trained on the remaining compounds is able to recall 75% of the actives from the "new" lead series while correctly classifying >99% of the 5000 inactives included in the validation set.
All-Out Organizational Scrum as an Innovation Value Chain

When Scrum extends beyond software development into the organization, Agile techniques, notably Scrum, provide a built-in innovation process. There is more to innovation than coming up with good ideas. Innovating involves capitalizing on well implemented ideas. Implementing good ideas involves risk and consequently should be managed carefully.Scrum effectively implements Lean methods into organizations by providing simple yet effective tools and techniques. These tools and techniques extend beyond software. Unfortunately, because of Scrum's success and roots in software project management, the language of Scrum is software-centric. This paper describes the Scrum language from a business perspective so when Scrum extends into the organization, innovation in the form of value creation is a natural by-product.Two companies are in the process of implementing organizational Scrums, one a professional services organization and the other, an Internet-based product company. The description of all-out Scrum in this paper is based on these efforts.
Three different putative phosphate transport receptors are encoded by the Mycobacterium tuberculosis genome and are present at the surface of Mycobacterium bovis BCG

A gene encoding a protein homologous to the periplasmic ABC phosphate binding receptor PstS from Escherichia coli was cloned and sequenced from a lambda gt11 library of Mycobacterium tuberculosis by screening with monoclonal antibody 2A1-2. Its degree of similarity to the E. coli PstS is comparable to those of the previously described M. tuberculosis phosphate binding protein pab (Ag78, Ag5, or 38-kDa protein) and another M. tuberculosis protein which we identified recently. We suggest that the three M. tuberculosis proteins share a similar function and could be named PstS-1, PstS-2, and PstS-3, respectively. Molecular modeling of their three-dimensional structures using the structure of the E. coli PstS as a template and their inducibility by phosphate starvation support this view. Recombinant PstS-2 and PstS-3 were produced and purified by affinity chromatography. With PstS-1, these proteins were used to demonstrate the specificity of three groups of monoclonal antibodies. Using these antibodies in flow cytometry and immunoblotting analyses, we demonstrate that the three genes are expressed and their protein products are present and accessible at the mycobacterial surface as well as in its culture filtrate. Together with the M. tuberculosis genes encoding homologs of the PstA, PstB, and PstC components we cloned before, the present data suggest that at least one, and possibly several, related and functional ABC phosphate transporters exist in mycobacteria. It is hypothesized that the mycobacterial gene duplications presented here may be a subtle adaptation of intracellular pathogens to phosphate starvation in their alternating growth environments.
Analysis and design for discrete-time linear systems subject to actuator saturation

We present a method for estimating the domain of attraction for a discrete-time linear system under a saturated linear feedback. A simple condition is derived in terms of an auxiliary feedback matrix for determining if a given ellipsoid is contractively invariant. Moreover, the condition can be expressed as LMI in terms of all the varying parameters and hence can easily be used for controller synthesis. The following surprising result is revealed for systems with single input: suppose that an ellipsoid is made invariant with a linear feedback, then it is invariant under the saturated linear feedback if and only if it can be made invariant with any saturated (nonlinear) feedback.
Transforming co-NP Checks to Answer Set Computation by Meta-Interpretation

Many NP-complete problems can be encoded in the answer set semantics of logic programs in a very concise way, where the en- coding reflects the typical "guess and check" nature of NP problems: The property is encoded in a way such that polynomial size certificates for it correspond to stable models of a program. However, the problem- solving capacity of full disjunctive logic programs (DLPs) is beyond NP at the second level of the polynomial hierarchy. While problems there also have a "guess and check" structure, an encoding in a DLP is often non-obvious, in particular if the "check" itself is co-NP-complete; usually, such problems are solved by interleaving separate "guess" and "check" programs, where the check is expressed by inconsistency of the check pro- gram. We present general transformations of head-cycle free (extended) logic programs into stratified disjunctive logic programs which enable one to integrate such "guess" and "check" programs automatically into a single disjunctive logic program. Our results complement recent results on meta-interpretation in ASP, and extend methods and techniques for a declarative "guess and check" problem solving paradigm through ASP.
The Properties of Intergalactic C IV Absorption. II. Which Systems Are Associated with Galaxy Outflows?

Using the extremely high signal-to-noise ratio quasar absorption-line sample described in the first paper of this series, we investigate which intergalactic C IV absorption-line systems could be directly associated with galactic outflows at z = 2–3.5 from an analysis of the velocity widths of the C IV absorption-line systems. Only about half the systems with a peak τ(C IV) above 0.4 in the 1548 Å line (roughly a column density of C IV above about 2 × 1013 cm-2) have velocity widths large enough to originate in this way, and very few of the weaker systems do. The median velocity full width at one-tenth maximum is found to be 50 km s-1 for systems with peak τ(C IV) in the range 0.1–0.4 and 160 km s-1 for systems with a peak τ(C IV) in the range 0.4–3. We show that this critical value of τ(C IV) also separates systems that could be ionized by galaxy-like spectra from those in which the ionization is clearly active galactic nucleus–dominated. Together the results are consistent with a picture in which almost all the lower column density and at least half the higher column density systems lie in the more general intergalactic medium, whereas about half the higher column density systems could be produced directly by the outflows and possibly be ionized by their parent galaxies.
Inorganic Carbon Uptake during Photosynthesis : I. A Theoretical Analysis Using the Isotopic Disequilibrium Technique.

Equations have been developed which quantitatively predict the theoretical time-course of photosynthetic (14)C incorporation when CO(2) or HCO(3) (-) serves as the sole source of exogenous inorganic carbon taken up for fixation by cells during steady state photosynthesis. Comparison between the shape of theoretical (CO(2) or HCO(3) (-)) and experimentally derived time-courses of (14)C incorporation permits the identification of the major species of inorganic carbon which crosses the plasmalemma of photosynthetic cells and facilitates the detection of any combined contribution of CO(2) and HCO(3) (-) transport to the supply of intracellular inorganic carbon. The ability to discriminate between CO(2) or HCO(3) (-) uptake relies upon monitoring changes in the intracellular specific activity (by (14)C fixation) which occur when the inorganic carbon, present in the suspending medium, is in a state of isotopic disequilibrium (JT Lehman 1978 J Phycol 14: 33-42). The presence of intracellular carbonic anhydrase or some other catalyst of the CO(2)-HCO(3) (-) interconversion reaction is required for quantitatively accurate predictions. Analysis of equations describing the rate of (14)C incorporation provides two methods by which any contribution of HCO(3) (-) ions to net photosynthetic carbon uptake can be estimated.
Human Hepatic Progenitor Cells Express Hematopoietic Cell Markers CD45 and CD109

Objective: To clarify the precise characteristics of human hepatic progenitor cells (HPCs) for future cytotherapy in liver diseases. Methods: Hepatic progenitor-like cells were isolated and cultured from the livers of patients who had undergone partial hepatectomy for various pathologies but displayed no sign of hepatic dysfunction. These cells were characterized by transcriptomic profiling, quantitative real-time PCR and immunocyto/histochemistry. Results:Cultured HPCs contained polygonal, high nucleus/cytoplasm ratio and exhibited a global gene expression profile similar (67.8%) to that of primary hepatocytes. Among the genes with more than 20-fold higher expression in HPCs were a progenitor marker (CD90), a pentraxin-related gene (PTX3), collagen proteins (COL5A2, COL1A1 and COL4A2), cytokines (EGF and PDGFD), metabolic enzymes (CYBRD1, BCAT1, TIMP2 and PAM), a secreted protein (SPARC) and an endothelial protein C receptor (PROCR). Moreover, eight markers (ALB, AFP, CK8, CK18, CK19, CD90, CD117 and Oval-6) previously described as HPC markers were validated by qRT-PCR and/or immunocyto/histochemistry. Interestingly, human HPCs were also positive for the hematopoietic cell markers CD45 and CD109. Finally, we characterized the localization of HPCs in the canals of Hering and periportal areas with six previously described markers (Oval-6, CK8, CK18, CK19, CD90 and CD117) and two potential markers (CD45 and CD109). Conclusion: The human HPCs are highly similar to primary hepatocytes in their transcriptional profiles. The CD45 and CD109 markers could potentially be utilized to identify and isolate HPCs for further cytotherapy of liver diseases.
Binarization, Synchronous Binarization, and Target-side Binarization

Binarization is essential for achieving polynomial time complexities in parsing and syntax-based machine translation. This paper presents a new binarization scheme, target-side binarization, and compares it with source-side and synchronous binarizations on both string-based and tree-based systems using synchronous grammars. In particular, we demonstrate the effectiveness of targetside binarization on a large-scale tree-to-string translation system.
Preconcentration and preseparation procedure for platinum determination at trace levels by neutron activation analysis.

A procedure that simultaneously allows both preconcentration and preseparation of platinum for its determination by neutron activation analysis at trace levels (<0.1 microg x g(-1)) in environmental related matrixes is developed. The method is mainly based on a two-step chemical procedure: (i) a preirradiation concentration/separation based on a column chromatography separation where the platinum is previously retained and subsequently separated from Au, Ca, Na, Br, and P; (ii) a postirradiation separation/purification of the 199Au at 158.4 keV used for the platinum determination via [198Pt (n,gamma)-->199Pt (beta-)-->199Au]. The method eliminates the following radionuclides with the gamma lines in the region of 158 keV: 47Sc (daughter of Ca) at 159.3 keV; 199Au (produced by double neutron capture onto the natural 197Au) at 158.4 keV; 123m Te at 158.8 keV. In addition, the background activity deriving from 24Na, 32p, and 82Br is drastically reduced. The method was tested by the analysis of certified rock material and then applied for platinum determination in airborne particulate matter.
FIG: A Prototype Tool for Online Verification of Recovery Mechanisms

Network applications of the future will require advanced mechanisms for automatic failure recovery in order to provide an acceptable quality of service. Because of this requirement, there is a need for tools that can inject simulated faults to verify a system’s fault detection and recovery methods. We present a set of objectives that such a fault injection tool must meet, and describe a prototype we have developed that meets these criteria. This tool, FIG, is capable of selectively introducing and logging errors at the application/library boundary on a running system. Our expectation is that FIG will be used for software development and verification, as well as for on-site testing of production systems. We use a working version of this tool to test the behavior of several common UNIX applications under simulated failures and offer suggestions from these tests on how to develop software with a higher degree of failure recoverability.
The Tolerogenic Peptide, hCDR1, Down-Regulates the Expression of Interferon-α in Murine and Human Systemic Lupus Erythematosus

Background The tolerogenic peptide, hCDR1, ameliorated manifestations of systemic lupus erythematosus (SLE) via the immunomodulation of pro-inflammatory and immunosuppressive cytokines and the induction of regulatory T cells. Because type I interferon (IFN-α) has been implicated to play a role in SLE pathogenesis, we investigated the effects of hCDR1 on IFN-α in a murine model of SLE and in human lupus. Methodology/Principal Findings (NZBxNZW)F1 mice with established SLE were treated with hCDR1 (10 weekly injections). Splenocytes were obtained for gene expression studies by real-time RT-PCR. hCDR1 down-regulated significantly IFN-α gene expression (73% inhibition compared to vehicle treated mice, p = 0.002) in association with diminished clinical manifestations. Further, hCDR1 reduced, in vitro, IFN-α gene expression in peripheral blood mononuclear cells (PBMC) of 10 lupus patients (74% inhibition compared to medium, p = 0.002) but had no significant effects on the expression levels of IFN-α in PBMC of primary anti-phospholipid syndrome patients or of healthy controls. Lupus patients were treated for 24 weeks with hCDR1 (5) or placebo (4) by weekly subcutaneous injections. Blood samples collected, before and after treatment, were frozen until mRNA isolation. A significant reduction in IFN-α was determined in hCDR1 treated patients (64.4% inhibition compared to pretreatment expression levels, p = 0.015). No inhibition was observed in the placebo treated patients. In agreement, treatment with hCDR1 resulted in a significant decrease of disease activity. IFN-α appears to play a role in the mechanism of action of hCDR1 since recombinant IFN-α diminished the immunomodulating effects of hCDR1 on IL-1β, TGFβ and FoxP3 gene expression. Conclusions/Significance We reported previously that hCDR1 affected various cell types and immune pathways in correlation to disease amelioration. The present studies demonstrate that hCDR1 is also capable of down-regulating significantly (and specifically to lupus) IFN-α gene expression. Thus, hCDR1 has a potential role as a novel, disease specific treatment for lupus.
Bounds on the Rate of 2-D Bit-Stuffing Encoders

A method for bounding the rate of bit-stuffing encoders for 2-D constraints is presented. Instead of considering the original encoder, we consider a related one which is quasi-stationary. We use the quasi-stationary property in order to formulate linear requirements that must hold on the probabilities of the constrained arrays that are generated by the encoder. These requirements are used as part of a linear program. The minimum and maximum of the linear program bound the rate of the encoder from below and from above, respectively. A lower bound on the rate of an encoder is also a lower bound on the capacity of the corresponding constraint. For some constraints, our results lead to tighter lower bounds than what was previously known.
Effectiveness of Grassland Vegetation on a Temporary Capped Landfill Site

We studied the effectiveness of grassland vegetation of a temporary capping system consisting of differently compacted boulder marl and its impact on the water balance components. This study presents the modelled water balances for the period between 2008 and 2015, performed with HELP 3.95 D (German edition). The model requires landfill design and weather data as well as soil physical and evapotranspiration parame- ters including the leaf area indices and evaporative zone depth with regard to the grassland vegetation. The modelled average annual actual evapotranspiration rates ranged between 277 and 390 mm year-1 or rather 33 and 66% of the annual precipitation (10-year average of 728 mm). The actual evapotranspiration rates are strongly influenced by the maximum leaf area indices that increased between 2008 and 2015 from 1.0 to 3.5 as well as the evaporative zone depth that also increased from 20 cm in 2008 to 50 cm in 2015. The empirical-mathematical – based HELP model is a useful option to successfully determine the water balance components of a landfill capping system under the given weather and site conditions including the development of the grassland vegetation.
Unorganized Malicious Attacks Detection

Recommender system has attracted much attention during the past decade. Many attack detection algorithms have been developed for better recommendations, mostly focusing on shilling attacks, where an attack organizer produces a large number of user profiles by the same strategy to promote or demote an item. This work considers a different attack style: unorganized malicious attacks, where attackers individually utilize a small number of user profiles to attack different items without any organizer. This attack style occurs in many real applications, yet relevant study remains open. We first formulate the unorganized malicious attacks detection as a matrix completion problem, and propose the Unorganized Malicious Attacks detection (UMA) approach, a proximal alternating splitting augmented Lagrangian method. We verify, both theoretically and empirically, the effectiveness of our proposed approach.
Self-Aware Adaptation in FPGA-based Systems

Self-Aware Adaptive computing systems are capable of adapting their behavior and resources thousands of times based on changing environmental conditions and demands. This allows them to automatically find the best way to accomplish a given goal with the resources at hand. This capability would benefit the full range of computer systems, from embedded devices to servers to supercomputers. Although such a system may seem rather far fetched, we believe that basic semiconductor technology, computer architecture and software systems have advanced to the point that the time is ripe to realize such a system. In this paper we present an implementation of an FPGA-based Self-Aware Adaptive computing system which blends techniques developed in different research fields, i.e, monitoring, decision making, and self-adaptation. The result is a system built on top of a set of enabling technology that proves the effectiveness of using Self-Aware Adaptive computing systems. We used the Application Heartbeats to assess performance goals and to inspect application progress and the Implementation Switch Service to switch between different implementations of the same algorithm (both in software and in hardware) at runtime. Preliminary results show the effectiveness and the usability of the proposed approach.
Predicting the Execution Time of Workflow Blocks Based on Their Input Features

The ability to accurately estimate the execution time of computationally expensive e-science algorithms enables better scheduling of workflows that incorporate those algorithms as their building blocks, and may give users an insight into the expected cost of workflow execution on cloud resources. When a large history of past runs can be observed, crude estimates such as the average execution time can easily be provided. We make the hypothesis that, for some algorithms, better estimates can be obtained by using the histories to learn regression models that predict execution time based on selected features of their inputs. We refer to this property as input predictability of algorithms. We are motivated by e-science workflows that involve repetitive training of multiple learning models. Thus, we verify our hypothesis on the specific case of the C4.5 decision tree builder, a well-known learning method whose training execution time is indeed sensitive to the specific input dataset, but in nonobvious ways. We use the case study to demonstrate a method for assessing input predictability. While this yields promising results, we also find that its more general applicability involves a trade off between the black-box nature of the algorithms under analysis, and the need for expert insight into relevant features of their inputs.