gebhart/patrepeval huggingface dataset:
The Malta CMOS pixel detector prototype for the ATLAS Pixel ITK (2019)

The ATLAS experiment is planning a major upgrade of its tracking detectors, both strip and pixel, to take full advantage of the High Luminosity LHC. A novel Monolithic Active Pixel Sensor based on 180 nm TowerJazz CMOS imaging technology, dubbed MALTA, has been designed to meet the radiation hardness requirements (1.5x10$^{15}$ 1 MeV $n_{eq}$/cm$^{2}$) of the outer barrel layers of the ITk Pixel detector. MALTA combines low noise (ENC<20 e$^{-}$) and low power operation (1 $\mu$W/pixel) with a fast signal response (25 ns bunch crossing) in small pixel size (36.4x36.4 $\mu$m$^{2}$), with a novel high-speed asynchronous readout architecture to cope with the high hit-rates expected at HL-LHC. Extensive lab testing and characterisation in particle beam tests have been conducted on this design and compared with previous prototypes of the same technology. An overview of the sensor technology and readout architecture are presented along with the preliminary results from laboratory tests, radioactive source tests and beam tests.
Selecting Elliptic Curves for Cryptography: An Efficiency and Security Analysis. (2014)

We select a set of elliptic curves for cryptography and analyze our selection from a performance and security perspective. This analysis complements recent curve proposals that suggest (twisted) Edwards curves by also considering the Weierstrass model. Working with both Montgomery-friendly and pseudo-Mersenne primes allows us to consider more possibilities which help to improve the overall efficiency of base field arithmetic. Our Weierstrass curves are backwards compatible with current implementations of prime order NIST curves, while providing improved efficiency and stronger security properties. We choose algorithms and explicit formulas to demonstrate that our curves support constant-time, exception-free scalar multiplications, thereby offering high practical security in cryptographic applications. Our implementation shows that variable-base scalar multiplication on the new Weierstrass curves at the 128-bit security level is about 1.4 times faster than the recent implementation record on the corresponding NIST curve. For practitioners who are willing to use a different curve model and sacrifice a few bits of security, we present a collection of twisted Edwards curves with particularly efficient arithmetic that are up to 1.42, 1.26 and 1.24 times faster than the new Weierstrass curves at the 128-, 192- and 256-bit security levels, respectively. Finally, we discuss how these curves behave in a real-world protocol by considering different scalar multiplication scenarios in the transport layer security protocol. The proposed curves and the results of the analysis are intended to contribute to the recent efforts towards recommending new elliptic curves for Internet standards.
Grain refinement and superplasticity of pipes processed by high-pressure sliding (2020)

The high-pressure sliding (HPS) process was applied for grain refinement of a pipe form of an Al-3wt%Mg-0.2wt%Sc alloy by developing two types of straining techniques (called in this study anvil sliding and mandrel sliding). To achieve a homogeneous microstructure throughout the cross-section of the pipe, the sample is rotated around the longitudinal axis every after sliding operation by introducing multi-pass technique, named multi-pass HPS (MP-HPS) as developed earlier for rods. The MP-HPS-processed sample shows ultrafine-grained structures with an average grain size of ∼260 and ∼300 nm after the HPS processing using anvil sliding and mandrel sliding. The samples also exhibit superplasticity with total elongations well more than 400%, respectively. A finite-element method is used to simulate the evolution of strain in the HPS processing and demonstrates that the simulation well represents the experimental results.
Supplementary Table S6 from Cyst Fluid Telomerase Activity Predicts the Histologic Grade of Cystic Neoplasms of the Pancreas (2023)

&lt;p&gt;Supplementary Table S6; Description of cases that provided endoscopically aspirated cyst fluid samples during their preoperative EUS examination.&lt;/p&gt;
Human ORFeome Version 1.1: A Platform for Reverse Proteomics (2004)

The advent of systems biology necessitates the cloning of nearly entire sets of protein-encoding open reading frames (ORFs), or ORFeomes, to allow functional studies of the corresponding proteomes. Here, we describe the generation of a first version of the human ORFeome using a newly improved Gateway recombinational cloning approach. Using the Mammalian Gene Collection (MGC) resource as a starting point, we report the successful cloning of 8076 human ORFs, representing at least 7263 human genes, as mini-pools of PCR-amplified products. These were assembled into the human ORFeome version 1.1 (hORFeome v1.1) collection. After assessing the overall quality of this version, we describe the use of hORFeome v1.1 for heterologous protein expression in two different expression systems at proteome scale. The hORFeome v1.1 represents a central resource for the cloning of large sets of human ORFs in various settings for functional proteomics of many types, and will serve as the foundation for subsequent improved versions of the human ORFeome.
Abstract B35: The strength of drug selection determines the maximum fitness cost of resistance mutations in culture and xenografts (2015)

Abstract This abstract is being presented as a short talk. A full abstract is printed in the Proffered Abstracts section (PR07) of the Conference Proceedings. Citation Format: Lee A. Albacker, Rainer Kohler, Ralph Weissleder, Peter K. Sorger. The strength of drug selection determines the maximum fitness cost of resistance mutations in culture and xenografts. [abstract]. In: Proceedings of the AACR Precision Medicine Series: Drug Sensitivity and Resistance: Improving Cancer Therapy; Jun 18-21, 2014; Orlando, FL. Philadelphia (PA): AACR; Clin Cancer Res 2015;21(4 Suppl): Abstract nr B35.
Sodium First Approach, to Reset Our Mind for Improving Management of Sodium, Water, Volume and Pressure in Hemodialysis Patients, and to Reduce Cardiovascular Burden and Improve Outcomes (2022)

New physiologic findings related to sodium homeostasis and pathophysiologic associations require a new vision for sodium, fluid and blood pressure management in dialysis-dependent chronic kidney disease patients. The traditional dry weight probing approach that has prevailed for many years must be reviewed in light of these findings and enriched by availability of new tools for monitoring and handling sodium and water imbalances. A comprehensive and integrated approach is needed to improve further cardiac health in hemodialysis (HD) patients. Adequate management of sodium, water, volume and hemodynamic control of HD patients relies on a stepwise approach: the first entails assessment and monitoring of fluid status and relies on clinical judgement supported by specific tools that are online embedded in the HD machine or devices used offline; the second consists of acting on correcting fluid imbalance mainly through dialysis prescription (treatment time, active tools embedded on HD machine) but also on guidance related to diet and thirst management; the third consist of fine tuning treatment prescription to patient responses and tolerance with the support of innovative tools such as artificial intelligence and remote pervasive health trackers. It is time to come back to sodium and water imbalance as the root cause of the problem and not to act primarily on their consequences (fluid overload, hypertension) or organ damage (heart; atherosclerosis, brain). We know the problem and have the tools to assess and manage in a more precise way sodium and fluid in HD patients. We strongly call for a sodium first approach to reduce disease burden and improve cardiac health in dialysis-dependent chronic kidney disease patients.
Predicting Low Toxicity and Scalable Solvent Systems for High‐Speed Roll‐to‐Roll Perovskite Manufacturing (2022)

Safer Ink Systems In article number 2100567, Richard Swartwout and co-workers demonstrated the coating performance of their new, safer solvent ink mixture with an effective permissible exposure limit 10x higher than traditional DMF/DMSO ink systems. Regulatory requirements limit exposure to solvent vapors generated from ink-based coating processes. For perovskite photovoltaics, this requires new ink formulations that exclude traditionally hazardous solvents while simultaneously coating uniformly at scale.
Dual protection of hydroponic tomatoes from rhizosphere pathogens Ralstonia solanacearum and Fusarium oxysporum f.sp. radicis‐lycopersici and airborne conidia of Oidium neolycopersici with an ozone‐generative electrostatic spore precipitator (2007)

An ozone‐generative electrostatic spore precipitator was developed to protect nursery‐stage seedlings of tomato from both airborne conidia of powdery mildew ( Oidium neolycopersici ) and root‐infecting pathogen propagules of bacterial wilt ( Ralstonia solanacearum ) and fusarium crown and root rot ( Fusarium oxysporum f.sp. radicis‐lycopersici ). The device was a cylindrical electrostatic spore precipitator (S2 cylinder) in which a positively charged straight conductor wire insulated with a transparent acrylic cylinder originated from a spore‐precipitation cylinder (S1 cylinder) designed to physically control airborne conidia of tomato powdery mildew in greenhouses. The S2 cylinder consisted of two sites for conidial attraction and ozone production. The site for ozone production was located at the end of the cylinder, where an earthed copper conductor ring (as a cathode) was attached to the edge of the cylinder, responding to the anodal tip of a positively charged central conductor wire. Distinct types of discharge (corona, corona‐streamer, streamer and arc discharge) occurred between the two electrodes and were dependant on the voltages applied to the wire and the distances between the electrodes. The highest ozone production was observed through streamer discharge. The remaining portion of the S2 cylinder, which was dielectrically polarized by a positively charged wire, created a non‐uniform electric field outside the cylinder to attract conidia that came into the generated field. Hydroponic culture troughs to raise tomato seedlings in a nursery greenhouse were paralleled with S2 cylinders. The aim was to control rhizosphere pathogens R. solanacearum and F. oxysporum f.sp. radicis‐lycopersici and to prevent them entering the hydroponic system during cultivation, while at the same time trapping O. neolycopersici conidia in the spaces between the cylinders. The results indicated that susceptible tomato plants in culture troughs attached to the S2 cylinders remained uninfected by both rhizosphere and aerial pathogens throughout the experimental period (2 and 3 weeks, respectively). This suggests that the present system will enable the dual control of both these pathogens in hydroponic systems in greenhouses.
Examination of the ambient effects on the stability of amorphous indium-gallium-zinc oxide thin film transistors using a laser-glass-sealing technology (2014)

The effect of an ambient atmosphere with a positive bias constant current stress (CCS) and a negative bias illumination stress (NBIS) on the stability of amorphous In-Ga-Zn-O thin film transistors (TFTs) is examined by utilizing a glass-hermetic-sealant with a moisture permeability of less than 10−6 g/m2 · day. In the CCS test, the threshold voltage shift (ΔVth) was remarkably suppressed in the glass-sealed TFTs. The unsealed and resin-sealed TFTs exhibited large ΔVth values. During the NBIS tests, the glass-sealed TFTs had almost the same negative ΔVth as the unsealed and resin sealed TFTs. Among the different TFTs, no significant differences were observed in the threshold voltage, the subthreshold swing and the saturation mobility as a function of the photon energy. It is concluded that ambient molecules were the primary origin of the instability of the ΔVth, induced by a CCS, but they were not related to the NBIS instability. The major role of the effective passivation layers in the NBIS test was not to simply block out the ambient effects, but to reduce the extra density of states at/near the surface of the back channel.
Search for resonant production of strongly coupled dark matter in proton-proton collisions at 13 TeV (2022)

A bstract The first collider search for dark matter arising from a strongly coupled hidden sector is presented and uses a data sample corresponding to 138 fb −1 , collected with the CMS detector at the CERN LHC, at $$ \sqrt{s} $$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:msqrt> <mml:mi>s</mml:mi> </mml:msqrt> </mml:math> = 13 TeV. The hidden sector is hypothesized to couple to the standard model (SM) via a heavy leptophobic Z′ mediator produced as a resonance in proton-proton collisions. The mediator decay results in two “semivisible” jets, containing both visible matter and invisible dark matter. The final state therefore includes moderate missing energy aligned with one of the jets, a signature ignored by most dark matter searches. No structure in the dijet transverse mass spectra compatible with the signal is observed. Assuming the Z′ boson has a universal coupling of 0.25 to the SM quarks, an inclusive search, relevant to any model that exhibits this kinematic behavior, excludes mediator masses of 1.5–4.0 TeV at 95% confidence level, depending on the other signal model parameters. To enhance the sensitivity of the search for this particular class of hidden sector models, a boosted decision tree (BDT) is trained using jet substructure variables to distinguish between semivisible jets and SM jets from background processes. When the BDT is employed to identify each jet in the dijet system as semivisible, the mediator mass exclusion increases to 5.1 TeV, for wider ranges of the other signal model parameters. These limits exclude a wide range of strongly coupled hidden sector models for the first time.
Relics Modeling and Application to Virtual Museum. (1998)

The authors have been concentrating on developing a real-time ortho imaging, drawing and modeling system for a recording system of relics using a CCD camera and line lasers. There are still, however, some issues which need to be resolved before this system may become operational. These problems include imaging for shadow areas occurring in hollow areas on complicated relics or faint areas at the top of columnar relics and lack of an exquisiteness for an edged image for a drawing.This paper describes an imaging approach for these shadow and faint areas synthesizing an ortho and a central projection image which are taken using a color CCD camera. The most remarkable points of this approach are its ability to obtain a color ortho projection image and a color 3D model. As for further additional results of this system, visualization of relics from several view points can be achieved on the computer using an animation technique. Some virtual archeological examples are demonstrated in this paper.
A novel SHAPE reagent enables the analysis of RNA structure in living cells with unprecedented accuracy (2020)

Due to the mounting evidence that RNA structure plays a critical role in regulating almost any physiological as well as pathological process, being able to accurately define the folding of RNA molecules within living cells has become a crucial need. We introduce here 2-aminopyridine-3-carboxylic acid imidazolide (2A3), as a general probe for the interrogation of RNA structures in vivo. 2A3 shows moderate improvements with respect to the state-of-the-art selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) reagent NAI on naked RNA under in vitro conditions, but it significantly outperforms NAI when probing RNA structure in vivo, particularly in bacteria, underlining its increased ability to permeate biological membranes. When used as a restraint to drive RNA structure prediction, data derived by SHAPE-MaP with 2A3 yields more accurate predictions than NAI-derived data. Due to its extreme efficiency and accuracy, we can anticipate that 2A3 will rapidly take over conventional SHAPE reagents for probing RNA structures both in vitro and in vivo.
Multiple timescales of learning within a single task: Continuous-time changes in evidence-accumulation processes during perceptual decision-making (2022)

Abstract Drift Diffusion Models have enabled strong advances in our understanding of decision-making, yet their application to examining learning has not been common. Using data from participants completing a dynamic random dot-motion direction discrimination task across four days, we characterized alterations in two components of perceptual decision-making (drift rate and response boundary). Continuous-time learning DDMs were applied to characterize trajectories of performance change, with different models allowing for varying dynamics. The best-fitting model included drift rate changing as a continuous, exponential function of cumulative trial number. In contrast, response boundary changed within each daily session, but in an independent manner across daily sessions. Our results highlight two different processes underlying the pattern of behavior observed across the entire learning trajectory, one involving a continuous tuning of perceptual sensitivity, and another more variable process describing participants’ threshold of when enough evidence is present to act.
Oxygen Reduction Reaction Electrocatalysts Derived from Iron Salt and Benzimidazole and Aminobenzimidazole Precursors and Their Application in Microbial Fuel Cell Cathodes (2018)

In this work, benzimidazole (BZIM) and aminobenzimidazole (ABZIM) were used as organic-rich in nitrogen precursors during the synthesis of iron-nitrogen-carbon (Fe-N-C) based catalysts by sacrificial support method (SSM) technique. The catalysts obtained, denoted Fe-ABZIM and Fe-BZIM, were characterized morphologically and chemically through SEM, TEM, and XPS. Moreover, these catalysts were initially tested in rotating ring disk electrode (RRDE) configuration, resulting in similar high electrocatalytic activity toward oxygen reduction reaction (ORR) having low hydrogen peroxide generated (<3%). The ORR performance was significantly higher compared to activated carbon (AC) that was the control. The catalysts were then integrated into air-breathing (AB) and gas diffusion layer (GDL) cathode electrode and tested in operating microbial fuel cells (MFCs). The presence of Fe-N-C catalysts boosted the power output compared to AC cathode MFC. The AB-type cathode outperformed the GDL type cathode probably because of reduced catalyst layer flooding. The highest performance obtained in this work was 162 ± 3 μWcm<sup>-2</sup>. Fe-ABZIM and Fe-BZIM had similar performance when incorporated to the same type of cathode configuration. Long-term operations show a decrease up to 50% of the performance in two months operations. Despite the power output decrease, the Fe-BZIM/Fe-ABZIM catalysts gave a significant advantage in fuel cell performance compared to the bare AC.
Tyrosine kinase triggering in thymocytes undergoing positive selection (1992)

Developing T cells undergo distinct selection processes that determine the T cell receptor (TcR) repertoire. One of these processes is positive selection. Positive selection involves the differentiation to mature T cells of thymocytes bearing TcR capable of recognizing antigens in the context of self-major histocompatibility complex (MHC) molecules. To study the potential involvement of tyrosine phosphorylation in the mechanism of positive selection, we have analyzed the activities of the tyrosine kinases pp56lck and pp59fyn in thymocytes expressing a unique TcR specific for HY antigen+ H-2 Db. Thymocytes undergoing positive selection displayed higher kinase specific activities of pp56lck and pp59fyn than nonselecting thymocytes. Furthermore, these increases in kinase activities were found only in the CD4+CD8+ subpopulation of thymocytes, where the selection process is believed to occur. These data suggest that tyrosine phosphorylation is part of the intracellular signals involved in MHC class I-driven positive selection from CD4+CD8+ immature thymocytes to CD4-CD8+ mature cells.
Transcriptome Analysis Reveals the Different Response to Toxic Stress in Rootstock Grafted and Non-Grafted Cucumber Seedlings (2020)

Autotoxicity of root exudates is one of the main reasons for consecutive monoculture problem (CMP) in cucumber under greenhouse cultivation. Rootstock grafting may improve the tolerance of cucumber plants to autotoxic stress. To verify the enhanced tolerance to autotoxic stress and illuminate relevant molecular mechanism, a transcriptomic comparative analysis was performed between rootstock grafted (RG) and non-grafted (NG) cucumber plants by a simulation of exogenous cinnamic acid (CA). The present study confirmed that relatively stable plant growth, biomass accumulation, chlorophyll content, and photosynthesis was observed in RG than NG under CA stress. We identified 3647 and 2691 differentially expressed genes (DEGs) in NG and RG cucumber plants when compared to respective control, and gene expression patterns of RNA-seq was confirmed by qRT-PCR. Functional annotations revealed that DEGs response to CA stress were enriched in pathways of plant hormone signal transduction, MAPK signaling pathway, phenylalanine metabolism, and plant-pathogen interaction. Interestingly, the significantly enriched pathway of photosynthesis-related, carbon and nitrogen metabolism only identified in NG, and most of DEGs were down-regulated. However, most of photosynthesis, Calvin cycle, glycolysis, TCA cycle, and nitrogen metabolism-related DEGs exhibited not or slightly down-regulated in RG. In addition, several stress-related transcription factor families of AP2/ERF, bHLH, bZIP, MYB. and NAC were uniquely triggered in the grafted cucumbers. Overall, the results of this study suggest that rootstock grafting improve the tolerance of cucumber plants to autotoxic stress by mediating down-regulation of photosynthesis, carbon, and nitrogen metabolism-related DEGs and activating the function of stress-related transcription factor. The transcriptome dataset provides an extensive sequence resource for further studies of autotoxic mechanism at molecular level.
Development of precipiting antibodies in rabbits inoculated with Streptococcus pneumoniae by crossed immunoelectrophoresis. (1987)

The antibody response of rabbits immunized with a strain of Streptococcus pneumoniae serotype 1 was studied by crossed immunoelectrophoresis. Sera taken every 4 weeks up to eight months post inoculation were tested in order to observe the development of precipiting antibodies, a complete response being encountered on week ten.
An organic ferroelectric field effect transistor with poly(vinylidene fluoride-co-trifluoroethylene) nanostripes as gate dielectric (2014)

We demonstrate the fabrication of an organic Ferroelectric Field Effect Transistor (FeFET) incorporating a ferroelectric gate dielectric made of nanostripes obtained by nanoimprinting poly(vinylidene fluoride-co-trifluoroethylene) over a layer of semiconducting poly(triarylamine). The imprinting process results in a decreased switching voltage for the ferroelectric, by a factor of ca. 1.5, resulting in a decreased operating voltage compared to a reference FeFET with a continuous ferroelectric layer. The transistor consists of a large number of nanostripe-gated transistors placed in parallel, which also offers interesting possibilities for a strong size reduction of organic FeFETs.
3303 The Application Model On Field Overlay Architecture (2008)

生産現場の情報の活用範囲が生産業務に直接関係のない業務へも広がっている.これらの業務には、現場情報を業務の目的に合うよう活用するために、生産現場と情報系システムを有機的に結合したシステム化が望まれる.我々は、このようなシステム化への対応に、業務を熟知している業務担当者自身によるアプリケーション構築が有効であると考えている.本論文では、機能ブロック型アプリケーションモデルを元にした、業務担当者によるアプリケーション構築のコンセプトを提案する.