gebhart/patrepeval huggingface dataset:
Search Space Generation and Pruning System for Autotuners (2016)

This work tackles two simultaneous challenges faced by autotuners: the ease of describing a complex, multidimensional search space, and the speed of evaluating that space, while applying a multitude of pruning constraints. This article presents a declarative notation for describing a search space and a translation system for conversion to a standard C code for fast and multithreaded, as necessary, evaluation. The notation is Python-based and thus simple in syntax and easy to assimilate by the user interested in tuning rather than learning a new programming language. A large number of dimensions and a large number of pruning constraints may be expressed with little effort. The system is discussed in the context of autotuning the canonical matrix multiplication kernel for NVIDIA GPUs, where the search space has 15 dimensions and involves application of 10 complex pruning constrains. The speed of evaluation is compared against generators created using imperative programming style in various scripting and compiled languages.
Peripheral corticotropin-releasing factor mediates the elevation of plasma IL-6 by immobilization stress in rats (1998)

We previously reported the elevation of plasma interleukin (IL)-6 activity in response to immobilization stress in rats. To investigate the role of peripheral corticotropin-releasing factor (CRF) in this response, we examined the effects of CRF antagonists on immobilization-induced IL-6 response. Intravenous pretreatment with either [D-Phe12,Nle21,38,CalphaMeLeu37]-anti-human rat (h/r) CRF12-41 (1.5 mg/kg) or cyclo(30-33)[D-Phe12, Nle21,38,Glu30, Lys33]-h/rCRF12-41 (Astressin, 0.5 mg/kg) attenuated the IL-6 response to immobilization, which confirmed our previous finding that systemic administration of an antiserum against CRF blocked this response. In addition, an intraperitoneal injection of h/rCRF (100 micrograms/kg) or rat urocortin (10 and 100 micrograms/kg) increased the plasma IL-6 activity, mimicking the response to immobilization. An intravenous injection of h/rCRF (100 micrograms/kg) also elevated plasma IL-6 in adrenalectomized rats. These findings suggest that peripheral CRF mediates the plasma IL-6 elevation in response to immobilization.
Mining Association Rules of Simple Conjunctive Queries (2008)

We present an algorithm for mining association rules in arbitrary relational databases. We define association rules over a simple, but appealing subclass of conjunctive queries, and show that many interesting patterns can be found. We propose an efficient algorithm and a database-oriented implementation in SQL, together with several promising and convincing experimental results.
Quantification of uncertainties in thermoelectric properties of materials from a first-principles prediction method: An approach based on Gaussian process regression (2019)

We present the electron-phonon averaged via Gaussian process regression (EPA-GPR) method, in which the electron-phonon coupling matrix is represented as a function of two energies and is in turn modeled as a Gaussian process. The EPA-GPR method can be used as an efficient method to estimate thermoelectric properties of materials for fast-screening applications, comparable to the original electron-phonon averaged (EPA) method and the electron-phonon averaged via moving-least-squares (EPA-MLS) method. The EPA-GPR method does not require specification of any open parameter, unlike the other EPA-related methods, since all the hyperparameters in the model can be unambiguously estimated within the type II maximum likelihood (ML-II) approximation. Thus, the EPA-GPR method is a parameter-free estimation method. Additionally, the concept of Gaussian processes in the EPA-GPR method allows us to quantify the uncertainty in estimated properties of thermoelectric materials. One can randomly realize the electron-phonon coupling coefficients from the identified Gaussian process, and those realized samples can be further analyzed in the solution process of the semiclassical Boltzmann transport equation for charge carriers. The results of the semiclassical Boltzmann transport equation provide the statistical properties of the thermoelectric properties of interest. The means, standard deviations, histograms, and confidence intervals of the Seebeck coefficient, the electrical conductivity, and the power factor can be constructed and analyzed. The proposed EPA-GPR method is applied to a $p$-type half-Heusler compound, i.e., HfCoSb, as a case example, the results of which clearly present the advantages of the method.
ChemInform Abstract: DESIGN AND REACTIVITY OF ORGANIC FUNCTIONAL GROUPS: THE HIGHLY CRYSTALLINE 2-ALKOXY-N,N′-DIPHENYL-1,3,2-DIAZAPHOSPHOLANES AND THEIR FACILE CONVERSION INTO ALKYL HALIDES (1983)

Das Phosphorigsäuretriamid (I) reagiert mit den Alkoholen (II) zu den Estern (IV) ,.
AODR: A Novel Retransmission Scheme for WIA-FA Networks (2020)

In industrial wireless sensor networks (IWSNs), monitoring data generated by field devices are supposed to be delivered to the gateway with low latency and high reliability. However, most of industrial wireless standards are based on IEEE 802.15.4 and offer limited data rates, which prevents their adoption in critical scenarios. Based on IEEE 802.11, WIA-FA is proposed to address higher communication requirements in factory automation. In this paper, we first analyze the drawbacks of the default NACK-based retransmission scheme of WIA-FA, and then propose an automatic on-demand retransmission (AODR) scheme. Finally, we give a detailed reliability analysis of the proposed AODR scheme. Simulation results show that the proposed AODR scheme outperforms existing works in terms of reliability for different scenarios.
Pre-clinical assessment of rational design immuno-oncology biologics with improved therapeutic indices. (2018)

e15096 Background: The clinical anti-tumor immune responses demonstrated by immune checkpoint antagonists and cell-based therapies are unprecedented. However, the challenge with these therapeutic approaches is the systemic activation of the immune system leading to dose limiting immune related adverse events (irAEs). Focusing the activity of immuno-oncology agents to the tumor microenvironment is expected to overcome the limitations on dosing and efficacy posed by irAEs. We have developed and demonstrated a rational approach to efficiently design immuno-therapeutics that are locally activated by proteases in the tumor microenvironment and exhibit reduced systemic activities. Our approach, which we have termed Aklusion™, has the potential to improve the safety and efficacy of immuno-oncology therapeutics. Methods: We used anti-mouse CTLA4 antibody 9D9 and anti-mouse PD1 antibody J43 to demonstrate the benefits of localizing pharmacological activity to the tumor microenvironment. In vivo activity was characterized with syngeneic MC38 tumors in C57Bl/6 mice using tumor regression as a measure of efficacy. The potential for improved therapeutic index was evaluated using a Fluorescent Activated Cell (FAC) analysis of tumor and splenic T cell populations for anti-CTLA4. Induction of diabetes in NOD mice versus tumor eradication was used to evaluate expanded therapeutic index for the anti-PD1. Cleavage was assessed for anti-CTLA4 using mass spectrometry, whereas anti-PD1 cleavage was assessed by western blotting. Results: Akluded antibodies led to tumor reduction similar to the parental antibodies that was dependent on protease activity. Critically, the Akluded antibodies exhibit reduced levels of systemic activity compared to their parental antibody. In vivo cleavage indicates a fraction of the molecules in circulation have been cleaved. Conclusions: The data from these studies indicate the potential of Aklusion to improve the therapeutic index of immunomodulatory antibodies and biologics, enabling more efficacious dosing.
Map Validation and Self-location in a Graph-like World. (1993)

We present algorithms for the discovery and use of topological maps of an environmentby an ac-tive agent (such as a person or a mobile robot). We discuss several issues dealing with the use of pre-existing topological maps of graph-like worlds by an autonomous robot and present al-gorithms, worst cases complexity, and experi-mental results (for representative real-world ex-amples) for twokey problems. The rst of these problems is to verify that a given input map is a correct description of the world (the valida-tion problem). The second is to determine the robot&amp;apos;s physical position on an input map (the self-location problem). We present algorithms which require O(N 2) and O(N 3) steps to validate and locate the robot in a map (where N is the number of places in the map).
PRESSURIZED ELECTROOSMOTIC DEWATERING IN A FILTER CYCLE* (2001)

This paper describes the role of pressurized electroosmotic dewatering (EOD) in a filter cycle. A laboratory-scale filter-press was used to filter a highly conductive silica suspension under constant pressure, followed by washing and mechanical precompression of the filter cake and finally by pressurized EOD at constant electric current. The influence of filter cycle parameters (filtration and washing pressure and duration, mechanical pressure, and electric field intensity) on the final cake dryness and energy consumption was studied. Electrodes of different materials, forms, and surfaces were used. The optimal conditions of each filter cycle operation were found to minimize the energy consumption during EOD and maximize the cake dryness. With mechanical pressure and electric field intensity increasing, the total energy consumption increased, but the specific energy consumption (per kg of expressed water) decreased, and the final filter cake was dryer. The pressurized EOD also used less energy than thermal drying.
Origin of High-Resolution IETS-STM Images of Organic Molecules with Functionalized Tips (2014)

Recently, the family of high-resolution scanning probe imaging techniques using decorated tips has been complemented by a method based on inelastic electron tunneling spectroscopy (IETS). The new technique resolves the inner structure of organic molecules by mapping the vibrational energy of a single carbon monoxide (CO) molecule positioned at the apex of a scanning tunneling microscope (STM) tip. Here, we explain high-resolution IETS imaging by extending a model developed earlier for STM and atomic force microscopy (AFM) imaging with decorated tips. In particular, we show that the tip decorated with CO acts as a nanoscale sensor that changes the energy of its frustrated translation mode in response to changes of the local curvature of the surface potential. In addition, we show that high resolution AFM, STM, and IETS-STM images can deliver information about the charge distribution within molecules deposited on a surface. To demonstrate this, we extend our mechanical model by taking into account electrostatic forces acting on the decorated tip in the surface Hartree potential.
No smoke without fire: the impact of cigarette smoking on the immune control of tuberculosis (2022)

Cigarette smoke (CS) exposure is a key risk factor for both active and latent tuberculosis (TB). It is associated with delayed diagnosis, more severe disease progression, unfavourable treatment outcomes and relapse after treatment. Critically, CS exposure is common in heavily populated areas with a high burden of TB, such as China, India and the Russian Federation. It is therefore prudent to evaluate interventions for TB while taking into account the immunological impacts of CS exposure. This review is a mechanistic examination of how CS exposure impairs innate barrier defences, as well as alveolar macrophage, neutrophil, dendritic cell and T-cell functions, in the context of TB infection and disease.
Extracting Rules from Optimal Clusters of Self-Organizing Maps (2010)

Self-organizing map (SOM) neural networks have been successfully applied to solve classification and clustering problems. However, while most SOM models pursue their results as accurately as possible, they ignore the importance of understanding and explanation. This paper first finds the optimal solution for the number of SOM clusters by using the technique of particle swarm optimization (PSO) and then generates clustering rules by extracting implicit knowledge from a one-dimensional SOM neural architecture. The experimental results show that rules extracted by our method produce an improvement in performance compared with other rule extraction models. Our proposed approach is able to equip the self-organizing map with an explanatory capability through the use of rules.
Supplementary Figures S1-S12 from Genetic and Pharmacological Screens Converge in Identifying FLIP, BCL2, and IAP Proteins as Key Regulators of Sensitivity to the TRAIL-Inducing Anticancer Agent ONC201/TIC10 (2023)

&lt;p&gt;Supplementary Figures S1-S12. Validation of kinase regulators of ONC201 sensitivity (S1); KSR1 shifts the ONC201, but not lapatinib, dose-response curve downward (S2); KSR1 does not regulate ONC201-induced TRAIL or DR5 (S3); KSR1 does not affect ONC201-mediated inhibition of MAPK or Akt inhibition (S4); Distribution of ONC201 synergy instances by drug (S5); Validation of ONC201 combinatorial activity with approved anti-cancer small molecules (S6); ONC201 synergizes with sorafenib in HepG2 cells (S7); ONC201 and sorafenib cooperatively induce apoptosis, TRAIL, and DR5 in vivo (S8); ONC201 and sorafenib cooperatively induce apoptosis in HepG2 cells (S9); ONC201 and sorafenib combination therapy is well tolerated and effective in vivo (S10); FLIP, Mcl-1, and KSR-1 knockdown enhances ONC201 response in HCT116 cells (S11); Model of ONC201-induced TRAIL signaling and sensitivity factors (S12).&lt;/p&gt;
Dendritic cell–activated CD44hiCD8+ T cells are defective in mediating acute graft-versus-host disease but retain graft-versus-leukemia activity (2004)

Graft versus host disease (GVHD) is triggered by host antigen-presenting cells (APCs) that activate donor T cells to proliferate and differentiate, but which APC-activated donor T-cell subsets mediate GVHD versus beneficial antitumor effects is not known. Using a CD8(+) T cell-dependent mouse model of human GVHD, we found that host dendritic cell (DC)-induced CD44(hi)CD8(+) effector/memory T cells were functionally defective in inducing GVHD, whereas CD44(lo)CD8(+) naive phenotype T cells were extremely potent GVHD inducers. Depletion of CD44(lo)CD8(+) T cells from host DC-stimulated T cells before transplantation prevented GVHD without impairing their antitumor activity in vivo. Compared with CD44(lo)CD8(+) T cells, CD44(hi)CD8(+) T cells expressed high levels of Fas and were efficiently deleted in vivo following transplantation. These results suggest that ex vivo allogeneic DC stimulation of donor CD8(+) T cells may be useful for the prevention of GVHD and for optimizing antitumor therapies in vivo.
Custom-fit processors: letting applications define architectures (1996)

In this paper we report on a system which automatically designs realistic VLIW architectures highly optimized for one given application (the input for this system), while running all other code correctly. The system uses a product-quality compiler that generates very aggressive VLIW code. We retarget the compiler until we have found a VLIW architecture idealized for the application on the basis of performance, a cost function and a hardware budget. We show that we can automatically select architectures that achieve large speedups on color and image processing codes. Specialization is shown to be very valuable: The differences between architectural choices, even among reasonable-seeming architectures having similar costs, can be very great, often a factor of 5 (and sometimes much more). We show also that specialization is also very dangerous. A reasonable choice of architecture to fit one algorithm can be a very poor choice for another, even in the same domain. There is sometimes an architecture, near in cost and performance to the best, that does much better on a second algorithm.
Synthesis and characterization of a model saturated hydrocarbon diblock copolymer (1989)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis and characterization of a model saturated hydrocarbon diblock copolymerFrank S. Bates, Jeffrey H. Rosedale, Harvey E. Bair, and Thomas P. RussellCite this: Macromolecules 1989, 22, 6, 2557–2564Publication Date (Print):June 1, 1989Publication History Published online1 May 2002Published inissue 1 June 1989https://pubs.acs.org/doi/10.1021/ma00196a002https://doi.org/10.1021/ma00196a002research-articleACS PublicationsRequest reuse permissionsArticle Views498Altmetric-Citations77LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Mutual induced-fit mechanism drives binding between intrinsically disordered Bim and cryptic binding site of Bcl-xL (2023)

The intrinsically disordered region (IDR) of Bim binds to the flexible cryptic site of Bcl-xL, a pro-survival protein involved in cancer progression that plays an important role in initiating apoptosis. However, their binding mechanism has not yet been elucidated. We have applied our dynamic docking protocol, which correctly reproduced both the IDR properties of Bim and the native bound configuration, as well as suggesting other stable/meta-stable binding configurations and revealed the binding pathway. Although the cryptic site of Bcl-xL is predominantly in a closed conformation, initial binding of Bim in an encounter configuration leads to mutual induced-fit binding, where both molecules adapt to each other; Bcl-xL transitions to an open state as Bim folds from a disordered to an α-helical conformation while the two molecules bind each other. Finally, our data provides new avenues to develop novel drugs by targeting newly discovered stable conformations of Bcl-xL.
P1‐112: A brain computer interface to detect Alzheimer's disease (2011)

Non-invasive convenient biomarkers of brain function are essential for drug development and as diagnostic aids to primary care physicians and neurologists. Static imaging (MRI/PET/SPECT) and fluid based (blood and CSF) biomarkers don't typically capture inherent brain physiology and dynamic processes. The current study introduces a portable activated EEG medical device for the physiological assessment of brain health and responsiveness to therapy. Advanced wireless electroencephalography hardware has enabled BCI to develop a novel activated EEG system (MindScope™). This system conveniently assesses brain responsiveness to activation of sensory circuits by various stimuli as well as cognitive tasks. EEG is recorded at position Fp1 (10-20 electrode placement system) with a Bluetooth enabled telemetric headset. Proprietary BCI software (BCiLab™ Clinic) both (i) activates brain circuits (beyond resting state conditions) with auditory stimulation, photic stimulation and/or cognitive tasks from the CogState computer cognition battery or the Paced Arithmetic Serial Assessment Test (PASAT) while (ii) simultaneously recording the raw EEG data and subject responses for post-acquisition spectral analysis. Bench top assessment of the hardware/software system was conducted by BCI under a US Army Phase 1 SBIR contract. After IRB approval, preliminary assessment of MindScope™ was conducted in subjects (N = 10 in each of 20, 40, 60, 70, 80 years of age) and mild to moderate dementia patients, as assessed by Mini-mental State Exam. Analytical testing showed excellent signal to noise ratio of greater than 20 db as well as low intra subject variation. Preliminary studies with CNS active compounds have shown statistically significant differences pre versus post compound administration. Preliminary data in humans from the Palm Drive Hospital Aging study and the Alzheimer study will be presented. A physiologically focused battery of tasks to functionally activate EEG is able to probe elements of brain circuits not presently assessed with standard resting state quantitative EEG. The MindScope offers a convenient and novel alternative to rapidly, portably and non-invasively assess brain health and function with no requirement for technical EEG training. Further work is required to develop the necessary activated EEG signatures to map the brain for its physiological defects.
RF PERFORMANCE OF MULTIPLE-CHANNEL CARBON NANOTUBE TRANSISTORS (2006)

Carbon nanotube field effect transistors (CNTFETs) are high-mobility devices and expected to operate at very high-speed. Theoretical analyses suggest that the cutoff frequency (fT) of an ideal CNTFET is from 800 MHz to 1.3 THz when the gate length is 0.1 µm [1][2]. However, measuring the RF performance of CNTFETs, especially their cutoff frequencies, is generally difficult because their output impedances (∼10 5 Ω) are high enough compared with the impedance (50 Ω) of the measurement system using the network analyzer. This large mismatch hinders us from measuring accurate S-parameters and determining the cutoff frequencies of the devices. In this paper, we show the successful results of measuring the RF performance of CNTFETs. This was achieved by a newly developed multiple channel CNTFET structure whose output impedance is much lower than the usual single channel CNTFET, and a de-embedding scheme that removes existing errors in measured S-parameters. As shown in Fig.1, the evaluated CNTFET was fabricated on SiO2 insulator on the highresistive Si substrate. By the CVD method, approximately 200 CNT channels were grown from catalyst (Fe) islands that were patterned by electron-beam lithography. The gate oxide was SiO2 with the thickness of 40 nm. The top gate structure (L=0.2 µm) was used to reduce parasitic capacitances. The drain and source electrodes were formed by evaporation of Au, and made ohmic contacts with CNT channels. Using high-frequency probes, 2-port Sparameters of the device were measured by the network analyzer. Even using the multiple channel structure, the device impedance was still higher compared with usual RF transistors. Therefore, we applied the calibration method with which the parasitic error matrix can be effectively eliminated and the S-parameters of only the transistor part can be extracted using open-short-through standards on wafer (Fig.2). Resulting current gain (|h21|) and power gain (maximum stable gain) as a function of frequencies are shown in Fig.3. Determined cutoff frequency is 10.3 GHz, and the maximum stable gain is +3.8 dB at 10 GHz. These values are ones of the highest among the previously published papers[3][4][5]. To verify consistencies, we analyzed an equivalent small-signal circuit model of the CNTFET (Fig.4). From this model, the cutoff frequency was derived and approximately represented as;