gebhart/patrepeval huggingface dataset:
Learned garbage collection (2020)

Several programming languages use garbage collectors (GCs) to automatically manage memory for the programmer. Such collectors must decide when to look for unreachable objects to free, which can have a large performance impact on some applications. In this preliminary work, we propose a design for a learned garbage collector that autonomously learns over time when to perform collections. By using reinforcement learning, our design can incorporate user-defined reward functions, allowing an autonomous garbage collector to learn to optimize the exact metric the user desires (e.g., request latency or queries per second). We conduct an initial experimental study on a prototype, demonstrating that an approach based on tabular Q learning may be promising.
Molecular analysis of human anti-factor VIII antibodies by V gene phage display identifies a new epitope in the acidic region following the A2 domain (2000)

Abstract One of the major binding sites for factor VIII inhibitors is located within the A2 domain. In this study, phage display technology was used to isolate 2 human monoclonal antibodies, termed VK34 and VK41, directed toward the heavy chain of factor VIII. The VHdomain of a single-chain variable domain antibody fragment (scFv) VK34 is encoded by germline gene segment DP-10. Epitope-mapping studies revealed that scFv VK34 is directed against amino acid residues Arg484–Ile508 , a previously identified binding site for factor VIII inhibitors in the A2 domain. ScFv VK34 inhibited factor VIII activity with a titer of 280 BU/mg. The VH domain of VK41 was encoded by germline gene segment DP-47. A phage corresponding to VK41 competed with a monoclonal antibody for binding to amino acid residues Asp712–Ala736 in the acidic region adjacent to the A2 domain. Reactivity of VK41 with a factor VIII variant in which we replaced amino acid residues Asp712–Ala736for the corresponding region of heparin cofactor II was strongly reduced. In addition, substitution of Tyr718719723 for Phe abrogated binding of VK41 to factor VIII. ScFv VK41 did not inhibit factor VIII activity. This study not only defines the primary structure of human anti-factor VIII antibodies reactive with the A2 domain, it also describes an antibody with an epitope not previously identified in the antibody repertoire of hemophilia patients with an inhibitor.
Bioequivalent pharmacokinetics for generic and originator hepatitis C direct-acting antivirals (2018)

Mass production of low-cost, generic direct-acting antivirals (DAAs) will be required to achieve targets of eliminating hepatitis C (HCV) by 2030. The pharmaceutical companies Gilead and Bristol-Myers Squibb have granted voluntary licences (VLs) to generic companies to mass produce the DAAs sofosbuvir and daclatasvir at low cost. However, generic manufacturers need to demonstrate bioequivalent pharmacokinetics for their DAAs, compared to the originator versions, to fulfil World Health Organization standards for prequalification. The aim of this study was to determine whether generic forms of sofosbuvir and daclatasvir had bioequivalent pharmacokinetics to the originator versions. Generic companies were contacted for results of bioequivalence studies with sofosbuvir and daclatasvir, two of the most widely used DAAs in the developing world. Data on maximum concentration (C<sub>max</sub>) and area under the curve (AUC) were compiled from five generic companies. Pre-specified limits for the 90% confidence intervals were 80-125% of the originator pharmacokinetic concentrations for AUC, and 69-145% for C<sub>max</sub>. The pharmacokinetics of generic sofosbuvir and daclatasvir were shown to be bioequivalent to the originator versions for all five generic companies. This is a crucial step towards securing prequalification of the manufacture of these drugs from these companies. WHO prequalification of bioequivalent generic DAAs could then permit their export to eligible countries for mass-treatment programmes. Mass-treatment with low-cost generic HCV DAAs is the most promising method to achieve the ambitious World Health Organization targets for HCV elimination by 2030.
Basic parameter measurement and channel broadening effect in the submicrometer MOSFET (1984)

An improved measurement technique of the basic MOSFET parameters is presented. This method is based on the measured data of two identical devices with different channel lengths. The effect of series resistance and channel length can be separated from the mobility measurement. This is the only method in which it has been proved that mobility can be measured on a short channel device. A new technique of channel length and series resistance is done by the measurement of newly defined quantity, R <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">T</inf> K, which is the equivalent channel length that includes the effect of series resistance. Because of the success of this measurement method, a new phenomena, which we call channel broadening effect, was investigated. Its effects on the submicrometer device characteristics were investigated.
Regulation of the transition from research to clinical practice in human assisted conception (2001)

This review discusses the place of regulation in the transition from research to clinical practice in human assisted conception, with particular emphasis on the United Kingdom and the role of the Human Fertilisation and Embryology Authority (HFEA). A contrast is drawn between advances in other areas of medical practice, in which the evidence base is considerable, and in assisted conception, in which it is often weak. This comparison leads to the central issue: how to balance the needs of patients with the need to ensure safety and efficacy in the introduction of new techniques. Comfort is derived from biological considerations that indicate that early human embryos are remarkably resilient and adaptable to challenges to their physiology. Regulatory practice in other countries is considered briefly. The review concludes that there are no easy rules or answers in managing the transition from research into the clinic, but that bodies such as the HFEA have a responsibility to: (i) encourage research to widen the evidence base and (ii) err on the side of caution when faced with decisions on licensing new techniques.
A Control IC for an Optocoupler-less DC-DC Converter with a Current Mirror Detection Circuit (2001)

A control IC has been developed that can provide a small flyback DC-DC converter without an optocoupler. This IC has new detection and control circuits using current mirrors and level-shift circuit technology. It reduces the mounting area of the DC-DC converter by 30%, and the DC-DC converter exhibits constant-voltage characteristics and conversion efficiency comparable to those of conventional converters.
Luminescence and afterglow due to defects in β -SiAlON crystal powder (2020)

Abstract Si 6− z Al z O z N 8− z ( β -SiAlON):Eu 2+ is among the most suitable green phosphors for white LEDs. To further improve the performance of this phosphor, it is important to investigate the properties of the nitride host crystal, β -SiAlON, which is considered to contain nitrogen vacancy defects (V N ) to some extent. From time-resolved fluorescence (TR-F) measurements of β -SiAlON without luminescent activators, we observed blue, yellow, and ultraviolet emissions. We focused on the blue emission typically centered at 460 nm, which was quenched at room temperature, but showed a continued afterglow for several milliseconds. The electron spin resonance signal of Si dangling bonds due to V N in β -SiAlON was observed to have a high concentration of 5.8 × 10 16 g −1 . We have previously reported the blue emission in nitride phosphor CaAlSiN 3 :Eu 2+ , for which the origin has been identified as V N . Therefore, we predicted that the blue afterglow might cause the green emission of the Eu 2+ ions to continue for several milliseconds in β -SiAlON:Eu 2+ . In this study, we proved that spectra decay characteristics measured by TR-F are useful for clarifying the phosphor characteristics interacting with the defects of β -SiAlON, such as V N .
Intelligent AC Drives: The Technology and the Market (1991)

A modem AC inverter drive system which combines new variable-flux motor control algorithms with compact and sophisticated power-electronics circuitry and components is described. The drive was essentially developed in two locations with microprocessor based motor controls being studied at the University of Auckland before being integrated into new inverter circuits at PDL Electronics, Napier. This paper gives a brief overview of AC drive concepts leading to the new 'intelligent' inverters and compares the performance of these inverters with competitors. It discusses 'University/Industry' cooperation and then traces the marketing of these devices in the International industrial market place before highlighting some of the applications that the drive has been used in.
Highlights from Two Decades of Synthetic Radical Chemistry (2001)

Abstract For Abstract see ChemInform Abstract in Full Text.
An n →π* Interaction in the Bound Substrate of Aspartic Proteases Replicates the Oxyanion Hole (2019)

Aspartic proteases regulate many biological processes and are prominent targets for therapeutic intervention. Structural studies have captured intermediates along the reaction pathway, including the Michaelis complex and tetrahedral intermediate. Using a Ramachandran analysis of these structures, we discovered that residues occupying the P1 and P1′ positions (which flank the scissile peptide bond) adopt the dihedral angle of an inverse γ-turn and polyproline type-II helix, respectively. Computational analyses reveal that the polyproline type-II helix engenders an n→π∗ interaction in which the oxygen of the scissile peptide bond is the donor. This interaction stabilizes the negative charge that develops in the tetrahedral intermediate, much like the oxyanion hole of serine proteases. The inverse γ-turn serves to twist the scissile peptide bond, vacating the carbonyl π∗ orbital and facilitating its hydration. These previously unappreciated interactions entail a form of substrate-assisted catalysis and offer opportunities for drug design.
Dynamics of excited-state absorbers: an analytical approach (2000)

An overview is given on the demonstration of consistent analytical approach for ESA applicable for nano- and picosecond pulses of arbitrary shape. Results are presented, that can be used to optimize the performance of tandem limiting devices and to significantly simplify numerial codes for ESA modeling.
Developments of two 4 × 10 Gb/s VCSEL array drivers in 65 nm CMOS for HEP experiments (2017)

This paper presents the designs and test results of two radiation tolerant 4 × 10 Gb/s vertical cavity surface emitting laser (VCSEL) array drivers VLAD and lpVLAD, both fabricated in a 1.2 V 65 nm CMOS technology. VLAD adopts a power efficient bandwidth-boost technology, and lpVLAD employs a novel high-efficiency output structure to achieve an ultra-low power consumption of 2.2 mW/Gb/ch with 2 mA bias current and 6 mA modulation current. Both drivers are optically tested passing 10 Gb/s eye mask with all channels active under the radiation of a total dose up to 350 Mrad(SiO(2)).
Chromatin and histones from Giardia lamblia: A new puzzle in primitive eukaryotes (2001)

The three deepest eukaryote lineages in small subunit ribosomal RNA phylogenies are the amitochondriate Microsporidia, Metamonada, and Parabasalia. They are followed by either the Euglenozoa (e.g., Euglena and Trypanosoma) or the Percolozoa as the first mitochondria-containing eukaryotes. Considering the great divergence of histone proteins in protozoa we have extended our studies of histones from Trypanosomes (Trypanosoma cruzi, Crithidia fasciculata and Leishmania mexicana) to the Metamonada Giardia lamblia, since Giardia is thought to be one of the most primitive eukaryotes. In the present work, the structure of G. lamblia chromatin and the histone content of the soluble chromatin were investigated and compared with that of higher eukaryotes, represented by calf thymus. The chromatin is present as nucleosome filaments which resemble the calf thymus array in that they show a more regular arrangement than those described for Trypanosoma. SDS-polyacrylamide gel electrophoresis and protein characterization revealed that the four core histones described in Giardia are in the same range of divergence with the histones from other lower eukaryotes. In addition, G. lamblia presented an H1 histone with electrophoretic mobility resembling the H1 of higher eukaryotes, in spite of the fact that H1 has a different molecular mass in calf thymus. Giardia also presents a basic protein which was identified as an HU-like DNA-binding protein usually present in eubacteria, indicating a chimaeric composition for the DNA-binding protein set in this species. Finally, the phylogenetic analysis of selected core histone protein sequences place Giardia divergence before Trypanosoma, despite the fact that Trypanosoma branch shows an acceleration in the evolutionary rate pointing to an unusual evolutionary behavior in this lineage.
The effects of kallidinogenase on choroidal blood flow in a hypertensive rabbit model (1999)

Kallidinogenase was shown to improve ophthalmic circulation by increasing chorioretinal blood flow in renal hypertensive rabbits.
Zirconia‐Based Potentiometric Sensor Using a Pair of Oxide Electrodes for Selective Detection of Carbon Monoxide (1997)

By using a pair of oxide electrodes, a stabilized‐zirconia‐based sensor was developed for selective detection of CO at high temperature. Among the oxide pair examined, the combination of CdO and was best suited for the electrode couple, giving quick and selective response to CO in air at 600°C. The 90% response and the 90% recovery times of the sensor to 200 ppm CO was as short as ca. 8 and 10 s, respectively, at 600°C. The EMF value was linearly related with the logarithm of CO concentration in the range of 20 to 4000 ppm. Moreover, the cross‐sensitivities to other gases, such as , NO, , and , were small or insignificant.
Extreme Ultraviolet Transient Grating Spectroscopy of Vanadium Dioxide (2014)

Nonlinear spectroscopy in the extreme ultraviolet (EUV) and soft x-ray spectral range offers the opportunity for element selective probing of ultrafast dynamics using core-valence transitions (Mukamel et al., Acc. Chem. Res. 42, 553 (2009)). We demonstrate a step on this path showing core-valence sensitivity in transient grating spectroscopy with EUV probing. We study the optically induced insulator-to-metal transition (IMT) of a VO2 film with EUV diffraction from the optically excited sample. The VO2 exhibits a change in the 3p-3d resonance of V accompanied by an acoustic response. Due to the broadband probing we are able to separate the two features.
Sensing and splicing applications of small core Ge-doped photonic crystal fibers (2008)

Sensor related properties of a small core (4.1&mu;m) Ge-doped photonic crystal fiber (PCF) are being reported. Fiber Bragg gratings with 35% and almost 100 % reflectivity were written in the Ge-doped PCF before and after hydrogen loading, respectively, by use of a UV laser. A 5.6pm/&deg;C temperature sensitivity of the FBG was observed. Additionally, a novel method is demonstrated to splice such PCF by use of a commercial fusion splicer with default splice parameters for standard single mode fibers (SMF). No parameter adjustments are required to splice the PCF to various SMFs and a low splice loss of 1.0 ~ 1.4dB can be achieved. No splice interface emerges at the splice joint, which is of advantage for the sensing applications of such a PCF.
T-cell Responses to TP53 “Hotspot” Mutations and Unique Neoantigens Expressed by Human Ovarian Cancers (2018)

<b>Purpose:</b> This was a study prospectively evaluating intratumoral T-cell responses to autologous somatic mutated neoepitopes expressed by human metastatic ovarian cancers.<b>Patients and Methods:</b> Tumor-infiltrating lymphocytes (TIL) were expanded from resected ovarian cancer metastases, which were analyzed by whole-exome and transcriptome sequencing to identify autologous somatic mutations. All mutated neoepitopes, independent of prediction algorithms, were expressed in autologous antigen-presenting cells and then cocultured with TIL fragment cultures. Secretion of IFNγ or upregulation of 41BB indicated a T-cell response.<b>Results:</b> Seven women with metastatic ovarian cancer were evaluated, and 5 patients had clear, dominant T-cell responses to mutated neoantigens, which were corroborated by comparison with the wild-type sequence, identification of the minimal epitope, human leukocyte antigen (HLA) restriction element(s), and neoantigen-specific T-cell receptor(s). Mutated neoantigens were restricted by HLA-B, -C, -DP, -DQ, and/or -DR alleles and appeared to principally arise from random, somatic mutations unique to each patient. We established that <i>TP53</i> "hotspot" mutations (c.659A>G; p.Y220C and c.733G>A; p.G245S) expressed by two different patients' tumors were both immunogenic in the context of HLA-DRB3*02:02.<b>Conclusions:</b> Mutation-reactive T cells infiltrated ovarian cancer metastases at sufficient frequencies to warrant their investigation as adoptive cell therapy. In addition, transfer of <i>TP53</i> "hotspot" mutation-reactive T-cell receptors into peripheral blood T cells could be evaluated as a gene therapy for a diverse range of tumor histologies. <i>Clin Cancer Res; 24(22); 5562-73. ©2018 AACR</i> <i>See related commentary by McNeish, p. 5493</i>.
Temporal and spatial expression of osteoactivin during fracture repair (2010)

We previously identified osteoactivin (OA) as a novel secreted osteogenic factor with high expression in developing long bones and calvaria, and that stimulates osteoblast differentiation and matrix mineralization in vitro. In this study, we report on OA mRNA and protein expression in intact long bone and growth plate, and in fracture calluses collected at several time points up to 21 days post-fracture (PF). OA mRNA and protein were highly expressed in osteoblasts localized in the metaphysis of intact tibia, and in hypertrophic chondrocytes localized in growth plate, findings assessed by in situ hybridization and immunohistochemistry, respectively. Using a rat fracture model, Northern blot analysis showed that expression of OA mRNA was significantly higher in day-3 and day-10 PF calluses than in intact rat femurs. Using in situ hybridization, we examined OA mRNA expression during fracture healing and found that OA was temporally regulated, with positive signals seen as early as day-3 PF, reaching a maximal intensity at day-10 PF, and finally declining at day-21 PF. At day-5 PF, which correlates with chondrogenesis, OA mRNA levels were significantly higher in the soft callus than in intact femurs. Similarly, we detected high OA protein immunoexpression throughout the reparative phase of the hard callus compared to intact femurs. Interestingly, the secreted OA protein was also detected within the newly made cartilage matrix and osteoid tissue. Taken together, these results suggest the possibility that OA plays an important role in bone formation and serves as a positive regulator of fracture healing.
WATCHMAN: An Overlay Distributed AAA Architecture for Mobile Ad hoc Networks (2008)

Access control concerns in MANETs are very serious and considered as a crucial challenge for operators who prospects to employ unrivaled capabilities of such networks for different applications. We propose a novel hierarchical distributed AAA architecture for proactive link state routing protocols notably OLSR. This proposal contains a lightweight and secure design of an overlay authentication and authorization paradigm for mobile nodes as well as a reliable accounting system to enable operators to charge nodes based on their connection duration time. We also suggest a hierarchical distributed AAA (Authentication, Authorization, and Accounting) server architecture with resource and location aware election mechanism. Moreover, this proposal mitigates the OLSR security issues noticeably and eventually defines a node priority-based quality of service.
ADIPEC 2013 Technical Conference Manuscript (2013)

by the named author(s). Abstract: The increasing demand of oil and gas has led to exploit oil fields and gas reservoirs with an increased content of contaminants. Reserves of natural gas are abundant, but about 40% of the fields contain high concentration of hydrogen sulfide, carbon dioxide and chlorides. This makes such fields difficult to exploit and need a complex system for refining with a significant associated cost. Such fields are referred as Sour and are found in many areas of the world but the Middle East and Central Asia hold the largest volumes. Design of equipment for such harsh environments, especially high pressure centrifugal compressor needs a deep knowledge of equation of state of gas mixture, material science and manufacturing technologies. Material selection is performed taking into account several parameters like minimum design temperature, wet and dry conditions of different compressor stages, partial pressure of hydrogen sulfide, carbon dioxide and the amount of other contaminants like halides, elemental sulphur, mercury, etc… This paper describes the design approach and the material selection for centrifugal compressors operating in extreme sour service. Particular attention will be dedicated to the influence of chlorides on material stress corrosion cracking resistance. Secondly a description of GE Oil&Gas manufacturing technologies experience is provided by reporting standard special processes and new trends in manufacturing technologies.
<title>Optical phase plates as a creative medium for special effects in images</title> (2001)

A new paradigm and methods for special effects in images were recently proposed by artist and movie producer Steven Hylen. Based on these methods, images resembling painting may be formed using optical phase plates. The role of the mathematical and optical properties of the phase plates is studied in the development of these new art forms. Results of custom software as well as ASAP simulations are presented.
Delay analysis using FDTD for source synchronous interfaces (2006)

This paper investigates delay and current return effects utilizing a parallel conformal finite difference time domain (PFDTD) method [Wenhua Yu, 2003]. Methodology, modeling, and integration to system level simulation for several interconnect structures are presented.