gebhart/patrepeval huggingface dataset:
ThreadScan (2015)

The concurrent memory reclamation problem is that of devising a way for a deallocating thread to verify that no other concurrent threads hold references to a memory block being deallocated. To date, in the absence of automatic garbage collection, there is no satisfactory solution to this problem. Existing tracking methods like hazard pointers, reference counters, or epoch-based techniques like RCU, are either prohibitively expensive or require significant programming expertise, to the extent that implementing them efficiently can be worthy of a publication. None of the existing techniques are automatic or even semi-automated. In this paper, we take a new approach to concurrent memory reclamation: instead of manually tracking access to memory locations as done in techniques like hazard pointers, or restricting shared accesses to specific epoch boundaries as in RCU, our algorithm, called ThreadScan, leverages operating system signaling to automatically detect which memory locations are being accessed by concurrent threads. Initial empirical evidence shows that ThreadScan scales surprisingly well and requires negligible programming effort beyond the standard use of Malloc and Free.
A genetic algorithm for bin packing and line balancing (2003)

The authors present an efficient genetic algorithm for two NP-hard problems, the bin packing and the line balancing problems. They define the two problems precisely and specify a cost function suitable for the bin packing problem. It is shown that the classic genetic algorithm performs poorly on grouping problems and an encoding of solutions of fitting these problems is presented. Efficient crossover and mutation operators are introduced for bin packing. The modification necessary to fit these operators for line balancing is given. Results of performance tests on randomly generated data are included. The line balancing tests cover real-world problem sizes. The results and areas of further research are discussed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
The Rational Design of Selective Benzoxazepin Inhibitors of the α-Isoform of Phosphoinositide 3-Kinase Culminating in the Identification of ( S )-2-((2-(1-Isopropyl-1 H -1,2,4-triazol-5-yl)-5,6-dihydrobenzo[ f ]imidazo[1,2- d ][1,4]oxazepin-9-yl)oxy)propanamide (GDC-0326) (2016)

Inhibitors of the class I phosphoinositide 3-kinase (PI3K) isoform PI3Kα have received substantial attention for their potential use in cancer therapy. Despite the particular attraction of targeting PI3Kα, achieving selectivity for the inhibition of this isoform has proved challenging. Herein we report the discovery of inhibitors of PI3Kα that have selectivity over the other class I isoforms and all other kinases tested. In GDC-0032 (3, taselisib), we previously minimized inhibition of PI3Kβ relative to the other class I insoforms. Subsequently, we extended our efforts to identify PI3Kα-specific inhibitors using PI3Kα crystal structures to inform the design of benzoxazepin inhibitors with selectivity for PI3Kα through interactions with a nonconserved residue. Several molecules selective for PI3Kα relative to the other class I isoforms, as well as other kinases, were identified. Optimization of properties related to drug metabolism then culminated in the identification of the clinical candidate GDC-0326 (4).
Search for a Structure in the Bs0π± Invariant Mass Spectrum with the ATLAS Experiment (2018)

A search for the narrow structure, X(5568), reported by the D0 Collaboration in the decay sequence X→B_{s}^{0}π^{±}, B_{s}^{0}→J/ψϕ, is presented. The analysis is based on a data sample recorded with the ATLAS detector at the LHC corresponding to 4.9 fb^{-1} of pp collisions at 7 TeV and 19.5 fb^{-1} at 8 TeV. No significant signal was found. Upper limits on the number of signal events, with properties corresponding to those reported by D0, and on the X production rate relative to B_{s}^{0} mesons, ρ_{X}, were determined at 95% confidence level. The results are N(X)<382 and ρ_{X}<0.015 for B_{s}^{0} mesons with transverse momenta above 10 GeV, and N(X)<356 and ρ_{X}<0.016 for transverse momenta above 15 GeV. Limits are also set for potential B_{s}^{0}π^{±} resonances in the mass range 5550 to 5700 MeV.
HIV Protease Inhibitors Enhance the Efficacy of Irradiation (2007)

Tumor vascular endothelium is rather resistant to the cytotoxic effects of radiation. The HIV protease inhibitors (HPI) amprenavir, nelfinavir, and saquinavir have previously been shown to sensitize tumor cells to the cytotoxic effects of radiation. Additionally, this class of drug has been shown to inhibit angiogenesis and tumor cell migration. Therefore, in the current study, we wanted to determine whether HPIs could enhance the effect of radiation on endothelial function. Our study shows that HPIs, particularly nelfinavir, significantly enhance radiations effect on human umbilical vein endothelial cells (HUVEC) and tumor vascular endothelium. We show that pretreatment of HUVEC with nelfinavir results in enhanced cytotoxicity, including increased apoptosis, when combined with radiation. Moreover, using several functional assays, we show that combination treatment effectively blocks endothelial cell migration and organization. These findings were accompanied by attenuation of Akt phosphorylation, a known pathway for radioresistance. Last, in vivo analysis of tumor microvasculature destruction showed a more than additive effect for nelfinavir and radiation. This study shows that HPIs can enhance the effect of ionizing radiation on vascular endothelium. Therefore, the Food and Drug Administration-approved drug, nelfinavir, may be an effective radiosensitizer in the clinic.
Filtered OFDM Based URLLC in 5G New Radio: Principles and Performance (2019)

In this paper, the principles and performance of 5G new radio (NR) based ultra-reliable low-latency communications (URLLC) building on subband filtered cyclic-prefix orthogonal-frequency- division-multiplexing (CP-OFDM) are provided and analyzed. We will demonstrate that subband filtered URLLC allows to achieve highly reliable link performance, which is not affected by interference induced by a mobile broadband service using a different numerology. In addition, we analyze and demonstrate asynchronous URLLC uplink performance with relaxed power control requirements to show that significant receiving power differences in the 5G NR base station (gNB) receiver can be tolerated, especially if highly selective subband filtering is applied in both the URLLC devices transmitters and the gNB’s receiver. We also demonstrate how the mobile broadband users may be interfered by the URLLC users in mixed numerology scenario, unless sufficient guard bands and sophisticated waveform signal processing solutions improving spectral localization in transmitter and receiver side are applied. Overall, the results show that by using subband filtering on top of basic CP-OFDM processing, frequency multiplexing URLLC and enhanced mobile broadband (eMBB) services within one 5G NR carrier is feasible.
Supplementary Figure 3 from Functional Identification of Cancer-Specific Methylation of <i>CDO1</i>, <i>HOXA9</i>, and <i>TAC1</i> for the Diagnosis of Lung Cancer (2023)

&lt;p&gt;PDF file - 287KB, DNA Methylation of CDO1, HOXA9, and TAC1 is Highly Sensitive for Stage I NSCLC in the Cancer Genome Atlas.&lt;/p&gt;
On routing for custom integrated circuits (1982)

This paper presents a novel and effective strategy for routing custom integrated circuits as well as solutions to subproblems associated with this strategy. Given an initial placement of rectangular blocks, the routing strategy includes the following major steps: construction of a channel graph, estimation of channel widths (based on a statistical model for signal nets and topological routing of power and ground nets), placement modification to include the estimated channel widths, topological routing for signal nets, and finally track assignment.
A lower bound on the estimator variance for the sparse linear model (2010)

We study the performance of estimators of a sparse nonrandom vector based on an observation which is linearly transformed and corrupted by white Gaussian noise. Using the framework of reproducing kernel Hilbert spaces, we derive a new lower bound on the estimator variance for a given differentiable bias function (including the unbiased case) and an almost arbitrary transformation matrix (including the underdetermined case considered in compressed sensing theory). For the special case of a sparse vector corrupted by white Gaussian noise-i.e., without a linear transformation-and unbiased estimation, our lower bound improves on a previously proposed bound.
Constitutive modeling and FE implementation for anisotropic hardening under proportional loading conditions (2018)

Anisotropic hardening response (or evolution of yield surface) is an important issue for numerical modeling of sheet metal forming and springback. Lee et al. (2017) recently introduced an improved constitutive model based on the Stoughton and Yoon (2009)'s equation, called the S-Y2009 model in this paper, in order to capture the anisotropic hardening in proportional loading conditions. The Lee et al. (2017)'s model was built by coupling the S-Y2009 model and a non-quadratic model to control the curvature of the yield fitting for more accurate prediction of the yield surface. The Lee et al. (2017)'s model (called the coupled model in this paper) showed good agreements with the measured data. However, in the aforementioned paper, a simulation study for sheet metal forming process with the coupled model was not reported. This paper presents the coupled model in two points of view. The first is the ability of the coupled model to capture the evolution of the yield surface. The other is the performance of the coupled model to describe the anisotropic hardening in a bulge test simulation. Predicting the anisotropic hardening including the biaxial stress state is important to follow the measured data. For the simulation, the coupled model was implemented into Vectorized User MATerial interface (VUMAT) of ABAQUS. The Yld2000-2d model was also incorporated in the comparison because the Yld2000-2d model has been showing good agreements with the initial anisotropy. The results of this study show that capturing the anisotropic hardening is important and the presented approach can be a good model in the sheet metal forming simulation under the proportional loading conditions.
Photochemistry (2008)

Abstract Photochemistry involves chemical reactions caused by the absorption of light and photochemists study the interaction of light with matter. Light in this context is defined as radiation from uv (ultraviolet) and visible (vis) sources including the sun. Mostly photoscientists work with lamps made from gas vapors (mercury or xenon) or from lasers. The interests of photoscientists in natural systems range from understanding the processes of vision of humans, animals, insects, invertebrates and even birds to developing new methods to study photosynthesis—the conversion of sunlight and carbon dioxide to carbohydrates and oxygen. Studies in solar energy conversion—the use of sunlight to produce electrical energy, heat, or even hydrogen from water—are, also, topic of substantial current interest. Commercial applications of photochemical reactions include xerography, photography, imaging, photolithography, stereolithography, rapid prototyping and photopolymerization. These likely amount to $100 billion or more in sales annually. Nearly 15% of all the publications in American Chemical Society journals involve the photosciences in one form or other, and more than 1000 photosciences papers were published in the top 24 journals in chemistry alone in 2007. The photosciences represent a huge, burgeoning academic, industrial and environmental area of basic and applied research.
TRANSFECTION OF NF ƒÛB DECOY OLIGODEOXYNUCLEOTIDES USING “EFFICIENT ULTRASOUND - GENE TRANSFER” INTO DONOR KIDNEYS PROLONGED SURVIVAL OF RAT RENAL ALLOGRAFTS (2008)

Azuma, H1; Nomi, H1; Ibuki, N1; Tomita, N2; Morishita, R2; Horie, S3; Takahara, S4; Katsuoka, Y1 Author Information
Interplay of Failure Rate, Performance, and Test Cost in TCAM under Process Variations (2013)

As process variations grow with technology scaling, failure rates increase and are predicted to be so high as to render devices unusable for computing domain. In order to continue to benefit from scaling, three dimensions can be explored: increasing operational margins, testing, and the resilience of applications. The solutions in each dimension bring out different trade-offs in yield, failure rate, test cost, and performance. We use a ternary content-addressable memory (TCAM) as a case study to better understand these trade-offs. We develop two new delay tests for TCAMs, and a new method to estimate yield, failure rate, test cost, and performance of TCAM under process variations when various tests are used. Our results show that with little test overhead and negligible yield loss, our new tests can significantly decrease the failure rates of TCAMs shipped to customers.
Data from A Synthetic Lethal Screen Reveals Enhanced Sensitivity to ATR Inhibitor Treatment in Mantle Cell Lymphoma with ATM Loss-of-Function (2023)

&lt;div&gt;Abstract&lt;p&gt;Mechanisms to maintain genomic integrity are essential for cells to remain viable. Not surprisingly, disruption of key DNA damage response pathway factors, such as ataxia telangiectasia-mutated (ATM)/ataxia telangiectasia and RAD3-related (ATR) results in loss of genomic integrity. Here, a synthetic lethal siRNA-screening approach not only confirmed ATM but identified additional replication checkpoint proteins, when ablated, enhanced ATR inhibitor (ATRi) response in a high-content γ-H2AX assay. Cancers with inactivating &lt;i&gt;ATM&lt;/i&gt; mutations exhibit impaired DNA double-stranded break (DSB) repair and rely on compensatory repair pathways for survival. Therefore, impairing ATR activity may selectively sensitize cancer cells to killing. ATR inhibition in an &lt;i&gt;ATM&lt;/i&gt;-deficient context results in phosphorylation of DNA-dependent protein kinase catalytic subunits (DNA-PKcs) and leads to induction of γ-H2AX. Using both &lt;i&gt;in vitro&lt;/i&gt; and &lt;i&gt;in vivo&lt;/i&gt; models, ATR inhibition enhanced efficacy in ATM loss-of-function mantle cell lymphoma (MCL) compared with ATM wild-type cancer cells. In summary, single-agent ATR inhibitors have therapeutic utility in the treatment of cancers, like MCL, in which ATM function has been lost.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Implications:&lt;/b&gt; These data suggest that single-agent ATR inhibitors have therapeutic utility and that ATR uses a complex and coordinated set of proteins to maintain genomic stability that could be further exploited. &lt;i&gt;Mol Cancer Res; 13(1); 120–9. ©2014 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
Hierarchical mixed-level simulation of VHDL descriptions (2002)

We present a hierarchical multilevel VHDL simulator for large systems described at the transistor, gate and higher levels. We exploit the hierarchy and regularity in VHDL descriptions to reduce the memory requirements drastically. The simulation algorithm handles MOS digital designs with bidirectional signal flow. We have augmented VHDL descriptions with signal strengths and timing; and also proposed a method to extend VHDL to accept transistor-level descriptions. Simulation results are provided for sample VHDL circuits.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Supplementary Table 1 from Identification of <i>SULF2</i> as a Novel Transcriptional Target of p53 by Use of Integrated Genomic Analyses (2023)

Supplementary Table 1 from Identification of &lt;i&gt;SULF2&lt;/i&gt; as a Novel Transcriptional Target of p53 by Use of Integrated Genomic Analyses
A continuous non-linear shadowing model of columnar growth (2007)

We propose the first continuous model with long range screening (shadowing) that described columnar growth in one space dimension, as observed in plasma sputter deposition. It is based on a new continuous partial derivative equation with non-linear diffusion and where the shadowing effects apply on all the different processes.
IgE antibodies to animal‐derived lipocalin, kallikrein and secretoglobin are markers of bronchial inflammation in severe childhood asthma (2012)

Multi-sensitization towards lipocalin, kallikrein and secretoglobin components is associated with increased bronchial inflammation in severe asthmatics. In addition, crossreactive patterns were observed between different lipocalin components.
Rapid production of the major birch pollen allergen Bet v 1 in Nicotiana benthamiana plants and its immunological in vitro and in vivo characterization (2000)

Type I allergies are immunological disorders that afflict a quarter of the world's population. Improved diagnosis of allergic diseases and the formulation of new therapeutic approaches are based on the use of recombinant allergens. We describe here for the first time the application of a rapid plant‐based expression system for a plant‐derived allergen and its immunological characterization. We expressed our model allergen Bet v 1, the major birch pollen allergen, in the tobacco‐related species Nicotiana benthamiana using a tobacco mosaic virus vector. Two weeks postinoculation, plants infected with recombinant viral RNA containing the Bet v 1 coding sequence accumulated the allergen to levels of 200 u‐g/g leaf material. Total nonpurified protein extracts from plants were used for immunological characterizations. IgE immunoblots and ELISA (enzyme‐linked immunoassay) inhibition assays showed comparable IgE binding properties for tobacco recombinant (r) Bet v 1 and natural (n) Bet v 1, suggesting that the B cell epitopes were preserved when the allergen was expressed in N. benthamiana plants. Using a murine model of type I allergy, mice immunized with crude leaf extracts containing Bet v 1 with purified rBet v 1 produced in E. coli or with birch pollen extract generated comparable allergen‐specific IgE and IgG1 antibody responses and positive type I skin test reactions. These results demonstrate that nonpurified Bet v 1 overexpressed in N. benthamina has the same immunogenicity as purified Bet v 1 produced in E. coli or nBet v 1. We therefore conclude that this plant expression system offers a viable alternative to fermentation‐based production of allergens in bacteria or yeasts. In addition, there may be a broad utility of this system for the development of new and low‐cost vaccination strategies against allergy.—Krebitz, M., Wiedermann, U., Essl, D., Steinkellner, H., Wagner, B., Turpen, T. H., Ebner, C., Scheiner, O., Breiteneder, H. Rapid production of the major birch pollen allergen Bet v 1 in Nicotiana benthamiana plants and its immunological in vitro and in vivo characterization. FASEB J . 14, 1279–1288 (2000)
HIV-1 Vpu restricts Fc-mediated effector functions in vivo (2022)

Non-neutralizing antibodies (nnAbs) can eliminate HIV-1-infected cells via antibody-dependent cellular cytotoxicity (ADCC) and were identified as a correlate of protection in the RV144 vaccine trial. Fc-mediated effector functions of nnAbs were recently shown to alter the course of HIV-1 infection in vivo using a vpu-defective virus. Since Vpu is known to downregulate cell-surface CD4, which triggers conformational changes in the viral envelope glycoprotein (Env), we ask whether the lack of Vpu expression was linked to the observed nnAbs activity. We find that restoring Vpu expression greatly reduces nnAb recognition of infected cells, rendering them resistant to ADCC. Moreover, administration of nnAbs in humanized mice reduces viral loads only in animals infected with a vpu-defective but not with a wild-type virus. CD4-mimetics administration, known to "open" Env and expose nnAb epitopes, renders wild-type viruses sensitive to nnAbs Fc-effector functions. This work highlights the importance of Vpu-mediated evasion of humoral responses.
Dystrophin Expression in Muscles of Duchenne Muscular Dystrophy Patients After High-Density Injections of Normal Myogenic Cells (2006)

A clinical trial was conducted to test a new protocol of normal muscle precursor cell (MPC) allotransplantation in skeletal muscles of patients with Duchenne muscular dystrophy (DMD). Cultured MPCs obtained from one of the patient's parents were implanted in 0.25 or 1 cm of a Tibialis anterior in 9 patients with DMD. MPC injections were placed 1 to 2 mm from each other, and a similar pattern of saline injections was done in the contralateral muscle. The patients were immunosuppressed with tacrolimus. Muscle biopsies were performed at the injected sites 4 weeks later. In the biopsies of the cell-grafted sites, there were myofibers expressing donor's dystrophin in 8 patients. The percentage of myofibers expressing donor's dystrophin varied from 3.5% to 26%. Evidence of small myofiber neoformation was observed in some patients. Donor-derived dystrophin transcripts were detected by reverse transcriptase-polymerase chain reaction in the cell-grafted sites in all patients. The protocol of immunosuppression was sufficient to obtain these results, although it is not certain whether acute rejection was efficiently controlled in all the cases. In conclusion, intramuscular allotransplantation of normal MPCs can induce the expression of donor-derived dystrophin in skeletal muscles of patients with DMD, although this expression is restricted to the sites of MPC injection.
Parallel Eyes (2016)

Our research explores how humans can understand and develop viewing behaviors with mutual paralleled first person view sharing in which a person can see others' first person video perspectives as well as their own perspective in realtime. We developed a paralleled first person view sharing system which consists of multiple video see-through head mounted displays and an embedded eye tracking system. With this system, four persons can see four shared first person videos of each other. We then conducted workshop based research with two activities, drawing pictures and playing a simple chasing game with our view sharing system. Our results show that 1) people can complement each other's memory and decisions and 2) people can develop their viewing behaviors to understand their own physical embodiment and spatial relationship with others in complex situations. Our findings about patterns of viewing behavior and design implications will contribute to building design experience in paralleled view sharing applications.
Potential‐Resolved Electrogenerated Chemiluminescence for the Selective Detection of Multiple Luminophores (2015)

Abstract Electrogenerated chemiluminescence (ECL) is fundamentally dependent on the applied electrode potential, and measuring ECL intensity over a range of different potentials is commonly used to examine the underlying chemical reaction pathways responsible for the emission of light. Several research groups have now demonstrated that the applied potential can be exploited to selectively elicit ECL from: 1) multiple excited states within a single chemical species; 2) multiple emitters sharing a common co‐reactant; or 3) distinct ECL systems. This new generation of multiplexed ECL processes has been facilitated by the extensive development of novel electrochemiluminophores and instrumental approaches such as the near‐continuous collection of ECL spectra with CCD detectors during voltammetry or chronoamperometry experiments.