gebhart/patrepeval huggingface dataset:
Software Defect Prediction for LSI Designs (2014)

While mining software repositories is a field which has greatly grown over the last ten years, Large Scale Integrated circuit (LSI) design repository mining has yet to reach the momentum of software's. We felt that it represents untouched potential especially for defect prediction. In an LSI, referred to as hardware later on, verification has a high cost compared to design. After studying existing software defect prediction techniques based on repository mining, we decided to adapt some for hardware design repositories in the hope of saving precious resources by focusing design and verification effort on the most defect prone parts of the design. By focusing our resources on the previously mentioned parts, we hope to improve our designs quality. We discuss how we applied these prediction techniques to hardware and show our results are promising for the future of hardware repository mining. Our results allowed us to estimate a possible total verification time reduction of 12%.
The National Science Foundation’s Investment in Sustainable Chemistry, Engineering, and Materials (2013)

In 2012, the National Science Foundation (NSF) created a new cross-directorate initiative—Sustainable Chemistry, Engineering, and Materials (SusChEM)—within its Science, Engineering and Education for Sustainability (SEES) portfolio. SusChEM aims to support the discovery of new science and engineering that will provide humanity with a safe, stable, and sustainable supply of chemicals and materials sufficient to meet future global demand. While NSF has historically supported research in this area, the SusChEM effort elevates this interest to a priority. In particular, NSF will support the discovery of new science and engineering that will (1) improve the harvesting and processing of natural resources, (2) develop replacement and substitute chemicals and materials for those that are scarce, toxic, and/or expensive, (3) extend the lifetime of materials through improved durability, (4) reduce energy consumption through improved catalysis, and (5) discover low-energy means of recycling, repurposing, recovering, and reusing chemicals and materials. This article provides an overview of the sustainability challenges that the mathematical, physical, and geological science and engineering communities are well poised to address and presents the National Science Foundation’s vision of the SusChEM initiative.
EXTH-70. CYP450 AND METABOLIC PROFILING OF ANTI-CANCER IMIPRIDONE ONC201 (2020)

Abstract Imipridone ONC201 is an investigational agent in phase II clinical trials for high grade gliomas as a single agent once weekly. Systemic and tumor exposure to ONC201 exceeds therapeutic thresholds consistently; however, exposure is variable despite fasted conditions and does not strongly covary with body weight or body surface area. Clinical trials with ONC201 have restricted the use of concomitant medication that induce or inhibit cytochrome P450 (CYP) enzymes; however, several supportive medications for glioma patients such as corticosteroids and anti-seizure medications can affect these enzymes. Studies in pooled human liver microsomes revealed that ONC201 is not an inducer of seven major drug-metabolizing human CYP enzymes: CYP 1A2, 2B6, 2C8, 2C9, 2C19, 2D6, and 3A4. However, ONC201 inhibits multiple CYPs IC50 values ranging from 34.9 to 428.6 μM and is substrate of CYP3A4 and, to lesser extent, other CYPs. Given potential metabolism of ONC201 by these enzymes, we conducted metabolic profiling in human hepatocytes that revealed at least 13 metabolites; however, only one was &amp;gt;10% abundance. The major metabolite, termed ONC207, that lacks a benzyl moiety of ONC201 was assayed by LC-MS-MS in plasma samples obtained from 16 ONC201-treated H3 K27M-mutant glioma patients. Peak plasma concentrations of ONC207 relative to ONC201 was 22% (range: 6%-48%) and its abundance was not correlated with ONC201, suggesting that variable exposure to ONC201 may not be associated with variable metabolism. ONC207 does not inhibit dopamine receptor D2 or cancer cell viability in contrast to the parent compound. In summary, ONC201 is an inhibitor and substrate, but not an inducer, of multiple CYP enzymes. The major metabolite of ONC207 appears to be biologically inactive and is unlikely to explain variable ONC201 exposure or its prolonged biological activity that outlives its systemic presence.
The iPod binocular home‐based treatment for amblyopia in adults: efficacy and compliance (2014)

The home-based dichoptic iPod approach represents a viable treatment for adults with amblyopia.
Insight into enhanced field-effect mobility of 4H-SiC MOSFET with Ba incorporation studied by Hall effect measurements (2018)

Improved performance in 4H-SiC metal-oxide-semiconductor field-effect transistors (MOSFETs) by incorporating Ba into insulator/SiC interfaces was investigated by using a combination of the Hall effect and split capacitance-voltage measurements. It was found that a moderate annealing temperature causes negligible metal-enhanced oxidation, which is rather beneficial for increments in field-effect mobility (μFE) of the FETs together with suppressed surface roughness of the gate oxides. The combined method revealed that, while severe μFE degradation in SiC-MOSFETs is caused by a reduction of effective mobile carriers due to carrier trapping at the SiO2/SiC interfaces, Ba incorporation into the interface significantly increases mobile carrier density with greater impact than the widely-used nitrided interfaces.
Highly Sensitive Detection and Removal of Lead Ions in Water Using Cysteine-Functionalized Graphene Oxide/Polypyrrole Nanocomposite Film Electrode (2015)

We synthesized cysteine-functionalized graphene oxide (sGO) using carbonyldiimidazole as a cross-linker via amide and carbamate linkages. The sGO/polypyrrole (PPy) nanocomposite film was grown on the working electrode surface of a screen-printed electrode (SPE) via controlled one-step electrochemical deposition. The sGO/PPy-SPE was used to detect lead ions (Pb(2+)) in water by first depositing Pb(2+) on the working electrode surface for 10 min at -1.2 V, and then anodic stripping by differential pulse voltammetry (DPV). The DPV signals were linear in the ranges of 1.4-28 ppb (R(2) = 0.994), 28-280 ppb (R(2) = 0.997), and 280-14 000 ppb (R(2) = 0.990) Pb(2+). The measurable detection limit of the sensor is 0.07 ppb (S/N = 3), which is more than 2 orders of magnitude below the 10 ppb threshold for drinking water set by the World Health Organization. The average removal efficiency of Pb(2+) deposited on the electrode was 99.2% (S/N = 3), with relative standard deviation (RSD) of 3.8%. Our results indicate good affinity of sGO/PPy nanocomposite to Pb(2+), which can be used to effectively adsorb and remove Pb(2+) in water samples. Therefore, sGO/PPy nanocomposite we synthesized is useful for highly sensitive on-site and real-time monitoring of heavy metal ions and water treatment.
Using a Statistical Machine Learning Tool for Diesel Engine Air Path Calibration (2014)

&lt;div class="section abstract"&gt;&lt;div class="htmlview paragraph"&gt;A full calibration exercise of a diesel engine air path can take months to complete (depending on the number of variables). Model-based calibration approach can speed up the calibration process significantly. This paper discusses the overall calibration process of the air-path of the Cat® C7.1 engine using statistical machine learning tool. The standard Cat® C7.1 engine's twin-stage turbocharger was replaced by a VTG (Variable Turbine Geometry) as part of an evaluation of a novel air system. The changes made to the air-path system required a recalculation of the air path's boost set point and desired EGR set point maps. Statistical learning processes provided a firm basis to model and optimize the air path set point maps and allowed a healthy balance to be struck between the resources required for the exercise and the resulting data quality.&lt;/div&gt;&lt;/div&gt;
Enhanced P-stereodependent stability of complexes formed by phosphorothioate oligonucleotides due to involvement of sulfur as strong hydrogen bond acceptor (2006)

Abstract The antisense or antigene properties are exerted not only by natural oligonucleotides, but also by their different analogs. Among them, phosphorothioate oligonucleotides (PS-DNA), in which the sugar-phosphate backbone is modified due to substitution of the sulfur atom for one of the nonbridging oxygens, are much more resistant toward nucleases and, simultaneously, maintain good hybridization properties. However, the substitution induces the P-chirality of dinucleoside phosphorothioate moiety and even short PS-DNA synthesized using standard chemical methods exist as a mixture of hundreds or thousands of diastereoisomers. Diastereomerically pure oligomers of [PS]-d(CG) 4 and [PS]-d(GC) 4 series, obtained using the oxathiaphospholane method, were investigated with respect to their ability to adopt the left-handed conformation at high sodium chloride concentration. Obtained data allow us to postulate the formation of a strong intramolecular hydrogen bond with anionic sulfur atom as an acceptor. Homopurine [All-R P -PS]-oligos, but not [All-S P -PS]-oligos, form with the RNA templates extremely stable triplex structures, so far not described in the literature. Most likely, the triplexes are stabilized by hydrogen bonds or water bridges with the participation of sulfur atoms of internucleotide linkage. Notably, target RNA molecules are "arrested" by properly designed [All-R P -PS]-DNA probes at submicromolar concentration, and as the result, they are not recognized by reverse transcriptase.
Evaluation of the degradation and metabolic effects of the gut peptide xenin on insulin secretion, glycaemic control and satiety (2010)

Recently, glucagon-like peptide 1 (GLP1) and glucose-dependent insulinotropic polypeptide (GIP) have received much attention regarding possible roles in aetiology and treatment of type 2 diabetes. However, peptides co-secreted from the same enteroendocrine cells are less well studied. The present investigation was designed to characterise the in vitro and in vivo effects of xenin, a peptide co-secreted with GIP from intestinal K-cells. We examined the enzymatic stability, insulin-releasing activity and associated cAMP production capability of xenin in vitro. In addition, the effects of xenin on satiety, glucose homoeostasis and insulin secretion were examined in vivo. Xenin was time dependently degraded (t(1/2)=162±6 min) in plasma in vitro. In clonal BRIN-BD11 cells, xenin stimulated insulin secretion at 5.6 mM (P<0.05) and 16.7 mM (P<0.05 to P<0.001) glucose levels compared to respective controls. Xenin also exerted an additive effect on GIP, GLP1 and neurotensin-mediated insulin secretion. In clonal β-cells, xenin did not stimulate cellular cAMP production, alter membrane potential or elevate intra-cellular Ca(2)(+). In normal mice, xenin exhibited a short-acting (P<0.01) satiety effect at high dosage (500 nmol/kg). In overnight fasted mice, acute injection of xenin enhanced glucose-lowering and elevated insulin secretion when injected concomitantly or 30 min before glucose. These effects were not observed when xenin was administered 60 min before the glucose challenge, reflecting the short half-life of the native peptide in vivo. Overall, these data demonstrate that xenin may have significant metabolic effects on glucose control, which merit further study.
Plasma interleukin-1 activity in humans undergoing hemodialysis with regenerated cellulosic membranes. (1987)

Because of the similarity between the acute phase response and the post-hemodialysis syndrome, it has been proposed that human blood monocytes adhering to the hemodialysis membrane are exposed to several inducers of interleukin-1 (IL-1). These include endotoxin from the dialysate fluid and C5a activated on the surface of regenerated cellulosic hemodialysis membranes. In order to test this hypothesis, we measured IL-1 plasma activity by employing gel filtration to remove IL-1 inhibitors and subsequent augmentation of lectin-induced murine thymocyte proliferation in each fraction. To evaluate the acute response of end stage renal disease patients during a single hemodialysis with a regenerated cellulosic membrane, plasmas were tested before and after hemodialysis. Control plasmas were obtained from healthy individuals. Plasma IL-1 activity eluted at a molecular weight of predominantly 15 kD. This material was neutralized by anti-human-IL-1 which does not recognize IL-2. IL-1 activity was detected in the pre-dialysis plasma of 6 out of 7 patients and rose in 6 patients following a 5 hour hemodialysis. This increase was associated with a significant rise in body temperature. This study supports the hypothesis that hemodialysis with regenerated cellulose might augment IL-1 production in endstage renal disease patients maintained on longterm hemodialysis. It demonstrates for the first time that dialysis patients have detectable plasma levels of IL-1 compared to normal individuals.
Crossover from weak localization to anti-weak localization in indium oxide systems with wide range of resistivity (2013)

We investigated the magnetoconductivity Δσ(H)≡1/ρ(H)−1/ρ(0) in a wide range of magnetic fields for three-dimensional indium oxide films doped with zinc, tin, or gallium in the range of resistivity ρ(300K) between 4.1×10−6 Ωm and 1.7×10−3 Ωm. The weak localization theory was fitted to data for Δσ(H) at various temperatures in the range 2.0 K≤T≤50 K by the use of suitable characteristics Dτin(T) and Dτso, where D, τin, and τso are the electron diffusion constant, inelastic scattering time, and spin-orbit (s-o) scattering time, respectively. It was found that (i) for films with a large value of ρ, the sign of Δσ(H) changes from positive to negative with decreasing temperature as a precursor to an anti-weak localization effect; (ii) the ratio τso/τin decreases from ≈4000 to≈4.0 with increasing ρ; (iii) the strong ρ dependence of Dτso cannot be explained by the model with a constant atomic number Z in a formula τso∝1/Z4 proposed by Abrikozov and Gorkov Zh. Eksp. Teor. Fiz. 42, 1088 (1962); [Sov. Phys. JETP 15, 752 (1962)]. As a reason for this ρ dependence, we suggest that the s-o scattering changes with increasing ρ from light oxygen atoms to heavy atoms, i.e., indium, zinc, and gallium, because of the decrease in the number of oxygen vacancies acting as s-o scattering centers.
A split-face, double-blind, randomized and placebo-controlled pilot evaluation of a novel oligopeptide for the treatment of recalcitrant melasma. (2009)

Melasma is a cutaneous disorder associated with an overproduction of melanin by the tyrosinase enzyme. A proprietary oligopeptide (Lumixyl) was previously shown to competitively inhibit mushroom and human tyrosinase without the associated toxicity of hydroquinone. The aim of this split-face, randomized, double-blind and placebo-controlled pilot study was to determine the effect of twice-daily topical application of this oligopeptide (0.01% w/w) on moderate, recalcitrant melasma over a 16-week course. Five female participants with Fitzpatrick phototype IV and moderate recalcitrant melasma enrolled and completed the study. Improvement in melasma and overall facial aesthetics as well as assessment of volunteer satisfaction was measured using 10- and five-point grading scales, respectively. Treatment was well tolerated with no visible signs of irritation or allergy. All five participants demonstrated statistically significant improvement in the appearance of melasma and overall facial aesthetics with high patient satisfaction. Results suggest that the oligopeptide may be useful in the treatment of melasma and warrants further evaluation.
Using micro-XRF to characterize chloride ingress through cold joints in 3D printed concrete (2023)

Digital fabrication methods with concrete have been rapidly developing, with many problems related to component production and material control being solved in recent years. These processes produce inherently layered cementitious components that are anisotropic, and in many cases, produces a weak interface between layers, which are generally referred to as cold joints. While material strength at these interfaces has been well studied in recent years, durability has received less attention, even though cold joints can function as channels for aggressive agents, such as chlorides. This work presents a method using micro-X-ray fluorescence (<i>μ</i>XRF) to image chloride ingress into layer interfaces of 3D printed fine-grained concrete specimens produced with varying layer deposition time intervals, and also compares it to neutron imaging of moisture uptake. The results show that cold joints formed after a 1 day time interval are highly susceptible to chloride ingress, and that curing conditions play a major role in how quickly interfacial transport can take place. The <i>μ</i>XRF method is also shown to be useful for study of transport of chlorides in cold joints, due to its spatial resolution and direct analysis of an aggressive species of interest.
Estrone, the major postmenopausal estrogen, binds ERa to induce SNAI2, epithelial-to-mesenchymal transition, and ER+ breast cancer metastasis (2022)

Recent work showed that the dominant post-menopausal estrogen, estrone, cooperates with nuclear factor κB (NF-κB) to stimulate inflammation, while pre-menopausal 17β-estradiol opposes NF-κB. Here, we show that post-menopausal estrone, but not 17β-estradiol, activates epithelial-to-mesenchymal transition (EMT) genes to stimulate breast cancer metastasis. HSD17B14, which converts 17β-estradiol to estrone, is higher in cancer than normal breast tissue and in metastatic than primary cancers and associates with earlier metastasis. Treatment with estrone, but not 17β-estradiol, and HSD17B14 overexpression both stimulate an EMT, matrigel invasion, and lung, bone, and liver metastasis in estrogen-receptor-positive (ER+) breast cancer models, while HSD17B14 knockdown reverses the EMT. Estrone:ERα recruits CBP/p300 to the SNAI2 promoter to induce SNAI2 and stimulate an EMT, while 17β-estradiol:ERα recruits co-repressors HDAC1 and NCOR1 to this site. Present work reveals novel differences in gene regulation by these estrogens and the importance of estrone to ER+ breast cancer progression. Upon loss of 17β-estradiol at menopause, estrone-liganded ERα would promote ER+ breast cancer invasion and metastasis.
An efficient tissue classifier for building patient-specific finite element models from X-ray CT images (1996)

We developed an efficient semiautomatic tissue classifier for X-ray computed tomography (CT) images which can be used to build patient- or animal-specific finite element (FE) models for bioelectric studies. The classifier uses a gray scale histogram for each tissue type and three-dimensional (3-D) neighborhood information. A total of 537 CT images from four animals (pigs) were classified with an average accuracy of 96.5% compared to manual classification by a radiologist. The use of 3-D, as opposed to 2-D, information reduced the error rate by 78%. Models generated using minimal or full manual editing yielded substantially identical voltage profiles. For the purpose of calculating voltage gradients or current densities in specific tissues, such as the myocardium, the appropriate slices need to be fully edited, however. Our classifier offers an approach to building FE models from image information with a level of manual effort that can be adjusted to the need of the application.
Author response: Convalescent plasma use in the USA was inversely correlated with COVID-19 mortality (2021)

A population-level analysis of convalescent plasma use and COVID-19 mortality in the USA revealed an inverse correlation and an estimate that recent declines in plasma use could have resulted in about 30,000 excess deaths.
Augmenting moving planar surfaces interactively with video projection and a color camera (2012)

Traditional applications of augmented reality superimpose generated images onto the real world through goggles or monitors held between objects of interest and the user. To render the augmented surfaces interactive, we may exploit directly existing computer vision techniques. However, when using video projection to alter directly the appearance of surfaces, most vision-based algorithms fail. Even Wear Ur World [5], a recent and otherwise well-received interactive projector-camera system, relies on colored thimbles as markers. As notable exception, Tele-Graffiti [6] was designed for normal visible-light cameras without markers, but still considers the light emitted from the projector as unwanted interference, limiting its application.
Unsupervised Clustering-Based Short-Term Solar Forecasting (2018)

Solar forecasting accuracy is highly affected by weather conditions, therefore, weather awareness forecasting models are expected to improve the forecasting performance. However, it may not be available or reliable to classify different forecasting tasks by only using predefined meteorological weather categorization. In this paper, an unsupervised clustering-based (UC-based) solar forecasting method is developed for short-term (1-h-ahead) global horizontal irradiance (GHI) forecasting. This UC-based method consists of three parts: GHI time series unsupervised clustering, pattern recognition, and UC-based forecasting. The daily GHI time series is first clustered by an Optimized Cross-validated ClUsteRing (OCCUR) method, which determines the optimal number of clusters and best clustering results. Then, support vector machine pattern recognition is adopted to recognize the category of a certain day using the first four hours' data in the forecasting stage. GHI forecasts are generated by the most suitable models in different clusters, which are built by a two-layer machine learning based multi-model (M3) forecasting framework. The developed UC-M3 method is validated by using 1-year of data with 13 solar features from three information sources. Numerical results show that 1) UC-based models outperform non-UC (all-in-one) models with the same M3 architecture by approximately 20%; and 2) M3-based models also outperform the single-algorithm machine learning models by approximately 20%.
Correction: Correcting the effect of hematocrit in whole blood coagulation analysis on paper-based lateral flow device (2018)

Correction for ‘Correcting the effect of hematocrit in whole blood coagulation analysis on paper-based lateral flow device’ by Hua Li <italic>et al.</italic>, <italic>Anal. Methods</italic>, 2018, DOI: 10.1039/c8ay00192h.
Complex Orthogonal Decomposition Applied to Nematode Posturing (2013)

The complex orthogonal decomposition (COD), a process of extracting complex modes from complex ensemble data, is summarized, as is the use of complex modal coordinates. A brief assessment is made on how small levels of noise affect the decomposition. The decomposition is applied to the posturing of Caenorhabditis elegans, an intensively studied nematode. The decomposition indicates that the worm has a multimodal posturing behavior, involving a dominant forward locomotion mode, a secondary, steering mode, and likely a mode for reverse motion. The locomotion mode is closer to a pure traveling waveform than the steering mode. The characteristic wavelength of the primary mode is estimated in the complex plane. The frequency is obtained from the complex modal coordinate's complex whirl rate of the complex modal coordinate, and from its fast Fourier transform. Short-time decompositions indicate the variation of the wavelength and frequency through the time record.