gebhart/patrepeval huggingface dataset:
Stencil codes on a vector length agnostic architecture (2018)

Data-level parallelism is frequently ignored or underutilized. Achieved through vector/SIMD capabilities, it can provide substantial performance improvements on top of widely used techniques such as thread-level parallelism. However, manual vectorization is a tedious and costly process that needs to be repeated for each specific instruction set or register size. In addition, automatic compiler vectorization is susceptible to code complexity, and usually limited due to data and control dependencies. To address some these issues, Arm recently released a new vector ISA, the Scalable Vector Extension (SVE), which is Vector-Length Agnostic (VLA). VLA enables the generation of binary files that run regardless of the physical vector register length.
A Novel Weighted Mismatched Filter for Reducing Range Sidelobes (2018)

Pulse compression, usually achieved using a matched filter, is extensively applied in radar/sonar systems. This process improves the signal-to-noise ratio (SNR) of the received signal without increasing the peak transmitted power. However, it is often desirable to accept a slight penalty in the target SNR in order to suppress the range sidelobes. In this paper, a novel weighted mismatched filter (WMMF) that can reduce range sidelobes to the designed level over specified regions is proposed. Two algorithms are provided to calculate the WMMF in different situations. A novel performance metric, the mean sidelobe level over a specified region, is also proposed to demonstrate the performance of the proposed method. Then, the SNR loss is deduced and analyzed based on several experiments. Finally, simulations and experiments based on real measured data are conducted to illustrate the effectiveness of this method. The theoretical evaluation and experiments show that the proposed WMMF can be used for all types of waveforms based on pulse compression processing and can flexibly and effectively suppress range sidelobes. Moreover, the mainlobe and the SNR loss can also be controlled by the proposed algorithms. In addition, this method can be easily applied to existing radar systems without modifying the radar transmitter or receiver.
Biochemical characterization of VLA-1 and VLA-2. Cell surface heterodimers on activated T cells. (1985)

The very late antigen complexes VLA-1 and VLA-2 which appear on long-term activated human T cells have been characterized with respect to 1) subunit arrangement, 2) location of monoclonal antibody (MAb) binding sites, 3) carbohydrate content, and 4) protein homology. Cross-linking experiments showed that the VLA-1 complex is a heterodimer composed of an Mr 210,000 subunit (alpha 1) in acid-labile association with an Mr 130,000 subunit (beta). The VLA-2 complex is a heterodimer with an Mr 165,000 subunit (alpha 2) in base-labile association with the Mr 130,000 beta subunit. The subunits of VLA-1 (alpha 1 beta) and VLA-2 (alpha 2 beta) each appear to be arranged with 1:1 stoichiometry. The MAb A-1A5 has been shown to bind to an epitope on the common beta subunit, consistent with its recognition of both the VLA-1 and VLA-2 heterodimers. On the other hand, MAb TS2/7 bound to an epitope of the alpha 1 subunit, thus explaining the specific recognition of the VLA-1 heterodimer by TS2/7. Digestion of the alpha 1, alpha 2, and beta subunits with neuraminidase and with endoglycosidase F revealed that each subunit contains substantial sialic acid and N-linked carbohydrate. By one-dimensional peptide mapping, the alpha 1, alpha 2, and beta subunits were shown to be highly nonhomologous with respect to each other, although each subunit from different T cell sources appeared highly homologous if not identical.
Tautomer Enumeration and Stability Prediction for Virtual Screening on Large Chemical Databases (2009)

Tautomeric rearrangements affect the results of cheminformatics applications that depend on the knowledge of the 2D or 3D structure of a compound, such as tools for database searches, fingerprint generation, virtual screening, and physical-chemical properties prediction. In this paper we present TauThor, a tool to enumerate tautomers and predict tautomer stability in the aqueous medium. The enumeration is based on a recursive process that generates tautomers according to the general scheme HX-Y=Z left harpoon over right harpoon X=Y-ZH. The stability of a tautomer is calculated by using a library of 145 fragments associated with experimental tautomeric percentages in water and a pK(a) based-method that utilizes pK(a) values predicted by MoKa. Predicted tautomeric ratios based on pK(a) calculations were benchmarked against literature data for a set of eleven compounds. The FDA approved drugs database, the NCI database and two vendor databases - Specs Screening Library and Asinex Gold Collection - were used to illustrate the impact of tautomerism on chemical libraries and to evaluate the relative occurrences of alternative tautomeric forms.
Supplementary Data from Nudix Hydrolase NUDT16 Regulates 53BP1 Protein by Reversing 53BP1 ADP-Ribosylation (2023)

Supplementary Data from Nudix Hydrolase NUDT16 Regulates 53BP1 Protein by Reversing 53BP1 ADP-Ribosylation
Low-noise phase imaging by hybrid uniform and structured illumination transport of intensity equation (2014)

We demonstrate a new approach to the transport of intensity equation (TIE) phase retrieval method which uses structured illumination to improve low-frequency noise performance. In the hybrid scheme, two phase images are acquired: one with uniform and one with sinusoidal grating illumination intensity. The former preserves the high spatial frequency features of the phase best, whereas the latter dramatically increase the response at low spatial frequencies (where traditional TIE notoriously suffers). We then theoretically prove the design of a spectral filter that optimally combines the two phase results while suppressing noise. The combination of uniformly and structured illuminated TIE (hybrid TIE) phase imaging is experimentally demonstrated optically with a calibrated pure phase object.
Nanoscale “Quantum” Islands on Metal Substrates: Microscopy Studies and Electronic Structure Analyses (2010)

Confinement of electrons can occur in metal islands or in continuous films grown heteroepitaxially upon a substrate of a different metal or on a metallic alloy. Associated quantum size effects (QSE) can produce a significant height-dependence of the surface free energy for nanoscale thicknesses of up to 10-20 layers. This may suffice to induce height selection during film growth. Scanning STM analysis has revealed remarkable flat-topped or mesa-like island and film morphologies in various systems. We discuss in detail observations of QSE and associated film growth behavior for Pb/Cu(111), Ag/Fe(100), and Cu/fcc-Fe/Cu(100) [A/B or A/B/A], and for Ag/NiAl(110) with brief comments offered for Fe/Cu₃Au(001) [A/BC binary alloys]. We also describe these issues for Ag/5-fold i-Al-Pd-Mn and Bi/5-fold i-Al-Cu-Fe [A/BCD ternary icosohedral quasicrystals]. Electronic structure theory analysis, either at the level of simple free electron gas models or more sophisticated Density Functional Theory calculations, can provide insight into the QSE-mediated thermodynamic driving force underlying height selection.
Micro- and Cryo-Techniques Prevent the Loss of Structural Information. EM-Studies on High-Pressure Frozen Tissues, Suspensions and Cell Monolayer. (1999)

Abstract Cells are information driven systems. Cellular information is stored in certain molecules, at certain places, in a certain concentration, at a particular time and under given physiological conditions. The goal of biological electron microscopy is to provide this information network, to correlate the cellular ultrastructure and its function. In this sense, it is essential to combine the high resolution of our electron optical instruments with a high information density of the biological system. Most of the structural information is lost in the course of the different preparation steps prior to electron microscopy. For this reason it is necessary that all preparation steps such as: 1. sampling: e.g. excision of tissues, 2. cryoimmobilisation, 3. follow-up procedures: e.g. freeze-fracturing, freeze-substitution and embedding, should have identical high quality levels preventing or minimizing the loss of structural information. To this aim our methodological activities focus on the development of special micro-techniques for the sampling of: a) native tissues, with an automatic fine-needle biopsy technique (1), of b) suspensions, with a special cellulose capillary technique (2), of c) cell monolayer, with a thin film cultivation technique (3) and the application/perfection of cryotechniques (high-pressure freezing (HPF) and freeze-substitution). In particular, the high-pressure freezer (HPM 010, Bal-Tec) has proven to be a highly useful tool for successful cryoimmobilization of almost any kinds of cells and tissues, bulk specimens (&amp;lt; 200 μm in thickness) being included. This freezing technique does not require any cryoprotection, and if combined with our micro-techniques the risk of inducing artefacts as a result of specimen preparation prior to freezing is minimized.
Design Research of Nanopositioner Based on SPM and Its Simulation of FEM (2007)

A novel nanopositioning stage was designed according to the scanning property of SPM with flexure hinge as kinematic structure and piezoelectric ceramic as actuator. Kinetic precision and X directional area of nanopositioner are 1.55nm and 26.4 micron, respectively, which is demonstrated by kinetic analysis and finite element method FEM simulation. Designed nanopositioner based on SPM moves at 3 dimensions with nanometer scale and its motion of X, Y, and Z directions is decoupled and isotropic. Furthermore, frame of nanopositioner is simple and manufacturing is convenient, which will have broad prospect in the field of nanopositioning and nanotracing.
Associations between Plasma Lipid Mediators and Chronic Daily Headache Outcomes in Patients Randomized to a Low Linoleic Acid Diet with or without Added Omega-3 Fatty Acids (2023)

A previous report showed that 12-week lowering of dietary omega-6 linoleic acid (LA) coupled with increased omega-3 polyunsaturated fatty acid (PUFA) intake (H3-L6 diet) reduced headache frequency and improved quality of life in patients with chronic daily headaches (CDHs) compared to dietary LA reduction alone (L6 diet). The trial also showed that targeted dietary manipulation alters PUFA-derived lipid mediators and endocannabinoids. However, several additional classes of lipid mediators associated with pain in preclinical models were not measured. The current secondary analysis investigated whether the clinical benefits of the H3-L6 diet were related to changes in plasma unesterified PUFA-derived lipid mediators known to be involved in nociception, including prostanoids. Lipid mediators were measured by ultra-high-pressure liquid chromatography coupled with tandem mass-spectrometry. Compared to baseline, dietary LA lowering with or without added omega-3 fatty acids did not alter unesterified n-6 PUFA-derived lipid mediators, although several species derived from LA, di-homo-gamma-linolenic acid, and arachidonic acid were positively associated with headache frequency and intensity, as well as mental health burden. Alpha-linolenic acid (ALA)-derived metabolites were also associated with increased headache frequency and intensity, although they did not change from the baseline in either dietary group. Compared to baseline, docosahexaenoic acid (DHA)-derived epoxides were more elevated in the H3-L6 group compared to the L6 group. Diet-induced elevations in plasma DHA-epoxides were associated with reduced headache frequency, better physical and mental health, and improved quality of life (p < 0.05). Prostanoids were not detected, except for PGF2-alpha, which was not associated with any outcomes. This study demonstrates that diet-induced changes in DHA-epoxides were associated with pain reduction in patients with chronic headaches, whereas n-6 PUFA and ALA metabolites were associated with nociception. Lipid mediator associations with mental health and quality of life paralleled pain management outcomes in this population. The findings point to a network of multiple diet-modifiable lipid mediator targets for pain management in individuals with CDHs.
Analysis and design of microwave devices based on ridge gap waveguide technology (2016)

The usage of high frequency microwave devices is rapidly increasing with the advances achieved in the communication systems. However, the standard guiding structures have high losses such as microstrip technology, or difficulty in manufacturing such as in the case of waveguides. The newly developed ridge gap waveguide (RGW) technology resolves the problems above as it has low losses and does not require electrical contacts as required in the waveguides. The concept of RGW is simple as it allows the wave propagations in the guiding part and eliminates the leakage in all other directions. The region that surrounds the ridge consists of two parallel surfaces; one is a perfect electric conductor (PEC) and the second is a perfect magnetic conductor (PMC). The gap between the two surfaces should be less than a quarter wavelength. Periodic conducting nails realize the PMC that practically has a possible bandwidth 2.5:1 and in some cases exceeds 3:1. Usually, the design of these surfaces relies on the unit cell analysis that is based on determining its band gap, the estimation of the band gap is performed numerically. The band gap of the cell is the operating bandwidth of the complete structure. For the first time, we presented a method to measure the band gap from s-parameter measurements. Utilization of the broadband characteristics strongly depends on the proper design of the transition between the RGW and the standard guiding structures and connectors. Most of the available transitions make use of around one-third of the possible bandwidth. Therefore, we present new transitions that utilize the whole possible bandwidth of the RGW. The presented work can be divided into four major parts. Several microwave components are designed based on the RGW such as power divider, hybrid couplers, and a circulator. New methods are presented for efficient and accurate design of these components. One of the main contributions is related to the RGW circulator design; it's an accurate design procedure that can be used with other technologies as well. In addition, a new setup to measure the low relative permittivity of thin materials such as fabrics is presented. An example of a leaky wave antenna using split slot arrays is presented. These studies highlight the RGW advantages and can be considered as a step towards the standardization of this technology.
The Role of Individual Differences in the Accuracy of Confidence Judgments (2002)

Generally, self-assessment of accuracy in the cognitive domain produces overconfidence, whereas self-assessment of visual perceptual judgments results in underconfidence. Despite contrary empirical evidence, in models attempting to explain those phenomena, individual differences have often been disregarded. The authors report on 2 studies in which that shortcoming was addressed. In Experiment 1, participants (N= 520) completed a large number of cognitive-ability tests. Results indicated that individual differences provide a meaningful source of overconfidence and that a metacognitive trait might mediate that effect. In further analysis, there was only a relatively small correlation between test accuracy and confidence bias. In Experiment 2 (N = 107 participants), both perceptual and cognitive ability tests were included, along with measures of personality. Results again indicated the presence of a confidence factor that transcended the nature of the testing vehicle. Furthermore, a small relationship was found between that factor and some self-reported personality measures. Thus, personality traits and cognitive ability appeared to play only a small role in determining the accuracy of self-assessment. Collectively, the present results suggest that there are multiple causes of miscalibration, which current models of over- and underconfidence fail to encompass.
Clinical Significance of Proteinuria at Posttransplant 1 Year in Kidney Transplantation (2012)

Purpose: Proteinuria in the nontransplant population is understood a progressive renal disease. We analyzed the prevalence and clinical influence of proteinuria at posttransplant 1 year in kidney transplant recipients and investigated the related factors that affect the degree of proteinuria. Methods: At 1 year after transplantation, we measured the amount of eliminated protein in 24-hour urine among 644 recipients, who were performed living or deceased donor KT from January 1996 to December 2010. Results: Total 372 male and 272 female recipients were included. The mean amount of urinary protein was 424.4 ± 1010 mg/day (range, 13.88 ˜ 8691 mg/day). 388 (60.2%) recipient had micro-proteinuria and the rest 256 (39.8%) had overt proteinuria. Of those, Nephrotic range proteinuria was found in 17 (2.6%) recipients. Non-nephrotic range proteinuria was in 239 (37.1%) recipients. The latter was categorized into low grade proteinuria of 224 (34.8%) and high grade proteinuria of 15 (2.3%). The proteinuria at posttransplant 1 year was a high correlation with serum creatinine at posttransplant 1 and 2 year and estimated GFR at postoperative 2 year. But not with creatinine clearance. The more graft loss was observed in recipients with more severe proteinuria. Male patient, recipient with anti-HCV Ab, unrelated donor, anti-thymocyte immunoglobulin at the time of reperfusion, maintenance immunosuppression with cyclosporine or without mycophenolate mofetil were strongly associated with the amount of proteinuria. Conclusion: This study demonstrated that the prevalence of proteinuria in kidney transplant recipient was considerably high. In addition, the presence as well as quantified level of proteinuria are worthy as predictive marker for inferior allograft function.
Wood flour‐high density polyethylene composites: Influence of silanization and esterification on mechanical properties (2020)

Abstract Silanization and esterification are strategies used to treat wood flour (WF) to produce surface functionalized hydrophobic WF leading to an improvement in dispersion and compatibility between wood phase and polymer phase. Silanization involves functionalization of alkyl groups by coupling trimethoxy (propyl) silane (MPS), and esterification functionalizes WF with ester groups, using acetic anhydride (Ac). Modified WF was incorporated into recycled high‐density polyethylene (HDPE) to form reHDPE/mod‐WF composite system. Both modifications produced highly hydrophobic WF surfaces which improved the dispersion in the reHDPE matrix; resulting in a significant difference in impact strength, specifically at 20 wt% filler, from 74.5 Jm −1 to 146.3 Jm −1 and 113.5 Jm −1 , that is, up to 96% and 52% for MPS‐WF and Ac‐WF, respectively. However, filler agglomeration higher than 20 wt% reduces the composite impact strength. The results herein demonstrate that alkyl‐functionalized WF show excellent dispersion in the reHDPE system and is the preferred technique to improve system mechanical resilience as compared to esterification.
Noninvasive Molecular Imaging of Tuberculosis-Associated Inflammation With Radioiodinated DPA-713 (2013)

[(125)I]Iodo-DPA-713 accumulates specifically in tuberculosis-associated inflammatory lesions by selective retention within macrophages and phagocytic cells. [(125)I]Iodo-DPA-713 SPECT provides higher lesion-specific signal-to-noise ratios than [(18)F]FDG PET and may prove to be a more specific biomarker to monitor tuberculosis in situ.
Detecting emerging concepts in textual data mining (2001)

This article summarizes our research to date in the automatic identification of emerging trends in textual data. Applications are numerous: the detection of trends in warranty repair claims, for example, is of genuine interest to NCSA industrial partners Caterpillar and Boeing. Technology forecasting is another example with numerous applications of both academic and practical interest. In general, trending analysis of textual data can be performed in any domain that involves written records of human endeavors whether scientific or artistic in nature
Endogenous Versus Tumor-Specific Host Response to Breast Carcinoma: A Study of Stromal Response in Synchronous Breast Primaries and Biopsy Site Changes (2010)

The results suggest that the DTF fibroblast response is host-specific, whereas the CSF1 response may be tumor-elicited. Our findings provide further insight into stromal response and may facilitate the development of therapeutic strategies to target particular stromal subtypes.
Tunable liquid crystal filters including variable FWHM control (2010)

Meadowlark Optics has successfully built and demonstrated a liquid crystal based tunable filter with novel FWHM tunability. This allows separate control over both the location of a narrow spectral bandpass and the width of the bandpass function. This non-mechanical, imaging filter thus enables random access of the visible to near IR spectrum and also controlling the specificity of the transmitted light. We will discuss both the relative trade-offs in this filter design space and present data from functional units.
Strategies for drug‐eluting stent treatment of bifurcation coronary artery disease in the United States: Insights from the e‐Cypher S.T.L.L.R.Trial (2008)

Main branch stenting without SB protection is the most common approach utilized in the STLLR study, which may reflect contemporary DES bifurcation strategies in the Unite States. This strategy was associated with an acceptable low incidence of adverse outcomes at 1-year.
Exploiting Offload Enabled Network Interfaces (2015)

Network interface cards are one of the key components to achieve efficient parallel performance. In the past, they have gained new functionalities such as lossless transmissionand remote direct memory access that are now ubiquitous in high-performance systems. Prototypes of next generation network cards now offer new features that facilitate device programming. In this work, various possible uses of network offload features are explored. We use the Portals 4 interface specification as an example to demonstrate various techniques such as fully asynchronous, multi-schedule asynchronous, and solo collective communications. MPI collectives are used as a proof of concept for how to leverage our proposed semantics. In a solo collective, one or more processes can participate in a collective communication without being aware of it. This semantic enables fully asynchronous algorithms. We discuss how the application of the solo collectives can improve the performance of iterative methods, such as multigrid solvers. The results obtained show how this work may be used to accelerate existing MPI applications, but they also display how these techniques could ease the programming of algorithms outside of the Bulk Synchronous Parallel (BSP) model.