gebhart/patrepeval huggingface dataset:
Heap cloning: Enabling dynamic symbolic execution of java programs (2011)

The dynamic symbolic-execution technique can automatically perform symbolic execution of programs that use problematic features of Java, such as native methods. However, to compute precise symbolic execution, the technique requires manual effort to specify models for problematic code. Furthermore, existing approaches to perform symbolic execution either cannot be extended to perform dynamic symbolic execution or incur significant imprecision. In this paper, we present a novel program-transformation technique called heap cloning. Heap cloning transforms a program in such a way that dynamic symbolic execution of the transformed program results in the same path constraints as dynamic symbolic execution of the original program. However, symbolic execution of the transformed program produces feedback on where imprecision is introduced, and that feedback can reduce the manual effort required to build models. Furthermore, such transformation can enable existing approaches to perform symbolic execution systems to overcome their limitations. In this paper, we also present a system, called Cinger, that leverages heap cloning, and that we used to perform an empirical evaluation. The empirical evaluation shows that Cinger can compute precise path constraints, and requires little (if any) manual effort for a set of large real-world programs.
Database Sharding (2015)

In this paper, the authors present an architecture and implementation of a distributed database system using sharding to provide high availability, fault-tolerance, and scalability of large databases in the cloud. Sharding, or horizontal partitioning, is used to disperse the data among the data nodes located on commodity servers for effective management of big data on the cloud.
Digital Beamforming on Receive in Elevation for Multidimensional Waveform Encoding SAR Sensing (2014)

This letter investigates the performance of a waveform-separation approach employing a posteriori digital beamforming (DBF) in elevation for multidimensional waveform encoding SAR sensing. The signal-to-noise ratio scaling factor in elevation and full-Doppler-band range ambiguity-to-signal ratio are defined to give global assessment of the DBF approach. Constraints for the selection of elevation subaperture number and their relevant influence on image quality are investigated. By theoretical analysis and simulation, the subaperture number can be appropriately selected by a tradeoff between the data volume and imaging performance. Further strategies for data reduction and performance optimization are briefly discussed.
Phase Transitions of the Polariton Condensate in 2D Dirac Materials (2018)

For the quantum well in an optical microcavity, the interplay of the Coulomb interaction and the electron-photon (e-ph) coupling can lead to the hybridizations of the exciton and the cavity photon known as polaritons, which can form the Bose-Einstein condensate above a threshold density. Additional physics due to the nontrivial Berry phase comes into play when the quantum well consists of the gapped two-dimensional Dirac material such as the transition metal dichalcogenide MoS_{2} or WSe_{2}. Specifically, in forming the polariton, the e-ph coupling from the optical selection rule due to the Berry phase can compete against the Coulomb electron-electron (e-e) interaction. We find that this competition gives rise to a rich phase diagram for the polariton condensate involving both topological and symmetry breaking phase transitions, with the former giving rise to the quantum anomalous Hall and the quantum spin Hall phases.
Protein subcellular localization profiling of breast cancer cells by dissociable antibody microarray staining (2010)

We have developed dissociable antibody microarray (DAMA) staining technology that provides a new approach to the global analysis of protein subcellular localization (SCL) in fixed cells. We have developed and optimized this technology for protein SCL profiling, generated ChipView, a program for management and analysis of molecular image database, and utilized the technique to identify proteins with unique SCL in breast cancer cell lines. We compared the SCL profiles of 325 proteins among nine different breast cell lines, and have identified one protein, Cyclin B1, with distinctively different SCLs between normal and cancer cell lines. With classic individual immunostaining, Cyclin B1 was confirmed to localize to the cytoplasm of seven breast cancer cell lines and in both cytoplasm and nuclei of two normal breast cell lines, and to have higher expression levels in the cancer cell lines tested.
A role for eukaryotic initiation factor 4B overexpression in the pathogenesis of diffuse large B-cell lymphoma (2013)

Dysregulated expression of factors that control protein synthesis is associated with poor prognosis of many cancers, but the underlying mechanisms are not well defined. Analysis of the diffuse large B-cell lymphoma (DLBCL) translatome revealed selective upregulation of mRNAs encoding anti-apoptotic and DNA repair proteins. We show that enhanced synthesis of these proteins in DLBCL is mediated by the relief of repression that is normally imposed by structure in the 5'-untranslated regions of their corresponding mRNAs. This process is driven by signaling through mammalian target of rapamycin, resulting in increased synthesis of eukaryotic initiation factor (eIF) 4B complex (eIF4B), a known activator of the RNA helicase eIF4A. Reducing eIF4B expression alone is sufficient to decrease synthesis of proteins associated with enhanced tumor cell survival, namely DAXX, BCL2 and ERCC5. Importantly, eIF4B-driven expression of these key survival proteins is directly correlated with patient outcome, and eIF4B, DAXX and ERCC5 are identified as novel prognostic markers for poor survival in DLBCL. Our work provides new insights into the mechanisms by which the cancer-promoting translational machinery drives lymphomagenesis.
Precision Agriculture Technology for Crop Farming (2015)

Explores the Sustainable Development of Agriculture in Technology Precision agriculture technology, when properly integrated into the crop production process, can greatly improve overall production and sustainability. Precision Agriculture Technology for Crop Farming focuses on the technology of site-specific crop management; detailing applications for sensing, data handling, modeling, and control. Written by experts who have contributed significantly to the development of precision agriculture technology, this book reviews its history—establishing background on the various processes and applications—describes the current status, and offers insight into the future technology of precision agriculture. Introducing processes and applications based on a global scale, the book reveals how precision agriculture can be used in large-scale agriculture, community agriculture, and diversified farming. It includes site-specific information from a variety of information sources for planning, planting, growing, and harvesting agricultural crops. It also presents a new concept based on the control system theory that can be used to formulate systematic methods for more effective precision crop production. In addition, this author: Describes yield monitors and guidance systems, GPS-based soil sampling, real-time crop and soil sensors, and remote sensing Evaluates a Japanese model of community-based precision agriculture aimed at high profitability and reliability under regional and environmental constraints Highlights autonomous vehicles, field robots, and other intelligent machinery, emerging developments, and future technology in the field of production agriculture Precision Agriculture Technology for Crop Farming provides an overview of precision agriculture technology development, discusses current and future considerations, and aims to facilitate the successful integration of precision agriculture technology.
Results with a 32-element dual mode imager (2010)

We present advances with a 32 element scalable, segmented dual mode imager. Scaling up the number of cells results in a 1.4 increase in efficiency over a system we deployed last year. Variable plane separation has been incorporated which further improves the efficiency of the detector. By using 20 cm diameter cells we demonstrate that we could increase sensitivity by a factor of 6. We further demonstrate gamma ray imaging in from Compton scattering. This feature allows for powerful dual mode imaging. Selected results are presented that demonstrate these new capabilities.
Predictor Model of Root Caries in Older Adults: Reporting of Evidence to the Translational Evidence Mechanism (2010)

The model demonstrated a high probability that a sound surface will remain caries free. However, one and multiple-surface lesions aggressively infect adjoining surfaces. Maturing of the carious lesion occurs with the 4-surface lesion, decreasing the probability of tooth loss. Thus, maintaining a sound root surface and early treatment intervention reduces the risk of tooth dysfunction (morphological destruction) and loss. DATABASE FILTERS: P: Tooth/Subject characteristics-Older adults, 65 years of age or more, male and female participants, regional rural Iowa residents, race unspecified, functional status-non-institutionalized level unspecified, risk level unspecified I: Root caries P (C-not applicable): Probability/Statistical significance for decision data only/Clinical significance-dataset over 20 years old/Utility data not included/Cost data not included/Meaning in practice undetermined. O: Each year through a three year cycle, caries progression from a sound root surface A: Data attached: ■ Published manuscript □ Unpublished manuscript □ Raw data R: Primary author contact information present.
Heterologous viral expression systems in fosmid vectors increase the functional analysis potential of metagenomic libraries (2013)

The extraordinary potential of metagenomic functional analyses to identify activities of interest present in uncultured microorganisms has been limited by reduced gene expression in surrogate hosts. We have developed vectors and specialized E. coli strains as improved metagenomic DNA heterologous expression systems, taking advantage of viral components that prevent transcription termination at metagenomic terminators. One of the systems uses the phage T7 RNA-polymerase to drive metagenomic gene expression, while the other approach uses the lambda phage transcription anti-termination protein N to limit transcription termination. A metagenomic library was constructed and functionally screened to identify genes conferring carbenicillin resistance to E. coli. The use of these enhanced expression systems resulted in a 6-fold increase in the frequency of carbenicillin resistant clones. Subcloning and sequence analysis showed that, besides β-lactamases, efflux pumps are not only able contribute to carbenicillin resistance but may in fact be sufficient by themselves to convey carbenicillin resistance.
Clinical implications of multiple drug resistance efflux pumps of pathogenic bacteria (2007)

Resistance of microorganisms to many classes of antibiotics and other drugs is a major problem throughout the world. This antimicrobial resistance can be mediated by various mechanisms such as enzymatic inactivation of the drug, alteration of the target and decreased intracellular concentration of the antimicrobial. The latter mechanism is mediated by either decreased influx or increased efflux or a combination of both. Recently, efflux has become increasingly recognized as a major component of resistance. Some efflux pumps selectively extrude specific antibiotics such as macrolides, lincosamides and/or streptogramins and tetracyclines, whereas others, referred to as multiple drug resistance pumps, expel a variety of structurally diverse anti-infectives with different modes of action. This phenomenon, whereby a single transporter is able to recognize and transport multiple antimicrobials with no common structural homology, was first described in the late 1980s in higher eukaryotes where P-glycoprotein was found to play a role in resistance to anti-cancer chemotherapeutic agents. Later, it became apparent that efflux systems were also present in microorganisms. Efflux pump inhibitors offer considerable promise as therapeutic agents, as they should restore the activity of standard antibiotics.
A radio frequency device for measurement of minute dielectric property changes in microfluidic channels (2009)

We demonstrate a sensitive radio frequency (rf) device to detect small dielectric property changes in microfluidic channel. The device consists of an on-chip Wilkinson power divider and a rat-race hybrid, which are built with planar microstrip lines and thin film chip resistors. Interference is used to cancel parasitic background signals. As a result, the measurement sensitivity is improved by more than 20 dB compared with conventional transmission lines. Compared with an ultrasensitive slot antenna/cuvette assembly [K. M. Taylor and D. W. van der Weide, IEEE Trans. Microwave Theory Tech. 53, 1576 (2005)], the proposed rf device is two times more sensitive.
Aromatic H/D Exchange Reaction Catalyzed by Groups 5 and 6 Metal Chlorides (2005)

Groups 5 and 6 metal chlorides such as MoCl5, WCl6, NbCl5 and TaCl5 were found to be simple and very efficient catalysts for the aromatic H/D exchange reactions. Compared with other metal chlorides such as ZnCl2, SnCl4 and TiCl4, groups 5 and 6 metal chlorides showed better catalytic activity in the H/D exchange reaction of naphthalene with C6D6. Deuteration of anthracene using MoCl5 as a catalyst proceeded within 24 h at room temperature. Other aromatic compounds such as toluene, diphenylmethane and 1,1,2-triphenylethane were also deuterated smoothly in C6D6 within 24 h at room temperature.
The Use of Allele-Specific Recombinant Fcγ Receptor IIIb Antigens for the Detection of Granulocyte Antibodies (1999)

The Fcgamma receptor IIIb (FcgammaRIIIb) for the Fc domain of IgG is expressed exclusively on neutrophils. The FcgammaRIIIb bears allotypic polymorphisms referred to as NA1, NA2, and SH, which are known for their frequent involvement in alloimmune and autoimmune neutropenias as well as in transfusion reactions. The bactericidal capacity of isolated neutrophils is easily activatable, and activation results in self-desintegration, thus preventing storage of neutrophils. As a result, only freshly isolated granulocytes can be used for antibody screening, often making it impossible to use typed panel cells. To provide a readily available source of typed panel cells, we therefore established stable mammalian cells expressing recombinant NA1, NA2, and SH antigens. We isolated mRNA from typed neutrophils and then transcribed it in cDNA. The cDNA that codes for the different forms of the FcgammaRIIIb was amplified by polymerase chain reaction and was subsequently subcloned into the mammalian expression vector pcDNA3. Chinese hamster ovary (CHO) cells were transfected with allele-specific constructs, and stable cell lines expressing FcgammaRIIIb were selected by flow cytometry. Because human sera show high background fluorescence with transfectants in flow cytometry, the monoclonal antibody-specific isolation of granulocyte antigens (MAIGA) assay was performed. By MAIGA assay, we tested 14 well-characterized human alloantibodies directed against the antigens NA1, NA2, and SH; 5 FcgammaRIIIb-specific isoantibodies; and 12 FcgammaRIIIb-reactive autoantibodies. Except one NA1- and one SH-specific alloantibody, all other antibodies could be identified by the use of CHO transfectants. In contrast to neutrophils, fixed CHO cells can be stored at 4 degrees C for at least 4 weeks or stored frozen for a longer period. This longer shelf life of the transfected CHO cells compared with isolated neutrophils will simplify the detection of the clinically most important FcgammaRIIIb-reactive alloantibodies and autoantibodies.
Factory-In-a-Box – Mobile Production Capacity on Demand (2007)

Change and uncertainty dominate today’s business environment. Meeting customer demands require a high degree of flexibility, low-cost/low volume- manufacturing skills, and short delivery times. In this highly competitive environment there is a great need to identify and develop unique manufacturing capabilities within industry. This paper will present an ongoing research project in Sweden called Factory-in-a-Box with the objective to develop mobile production capacity on demand. The Factory-in-a-Box concept consists of standardized production modules that are installed in e.g. a container and transported by e.g. a truck or by train. The modules may rapidly be combined into production systems that can be reconfigured for a new product and/or scaled to handle new volumes. The key features of this futuristic production system concept are flexibility, mobility, and speed. In the research project five fully operative demonstrators have been developed and implemented in close cooperation between different academic and industrial partners in Sweden.
Disease management mitigates risk of pathogen transmission from maricultured salmonids (2014)

Open marine net pens facilitate virus and sea lice transfer, occasionally leading to infections and outbreaks of disease in farmed salmon. A review of 3 salmon pathogens (infectious salmon anaemia virus [ISAV], salmon alphavirus [SAV] and the salmon louse Lepeophtheirus salmonis) shows that increased risk of exposure to neighbouring farms is inversely related to distance from and directly related to biomass at the source of infection. Epidemiological techniques integrating data from oceanography, diagnostics and pathogen shedding rates and viability contribute to improved understanding of pathogen transmission pathways among farms and permit the designation of areas of risk associated with sources of infection. Occupation of an area of risk may increase the likelihood of exposure, infection and disease among susceptible fish. Disease mitigation in mariculture occurs at 2 scales: area-based (coordinated stocking, harvesting and fallowing) and farm-based (vaccination, early pathogen detection, veterinary prescribed treatments and depopulation or early harvest in the event of viral disease). Collectively, implementation of mitigation measures results in virus disease outbreaks of shorter duration with lower mortality and therefore reduces the likelihood of pathogen transmission. In contrast, the mitigation of sea lice transmission is less likely to be effective in some areas due to the loss of parasite sensitivity to therapeutants and to dissemination of larval lice when parasites occur below management thresholds. For wild populations, risk of pathogen spillback is estimated from farm-based epidemiological data; however, validation, particularly for ISAV and SAV, is required using direct surveillance.
CD150 Association with Either the SH2-Containing Inositol Phosphatase or the SH2-Containing Protein Tyrosine Phosphatase Is Regulated by the Adaptor Protein SH2D1A (2001)

CD150 (SLAM/IPO-3) is a cell surface receptor that, like the B cell receptor, CD40, and CD95, can transmit positive or negative signals. CD150 can associate with the SH2-containing inositol phosphatase (SHIP), the SH2-containing protein tyrosine phosphatase (SHP-2), and the adaptor protein SH2 domain protein 1A (SH2D1A/DSHP/SAP, also called Duncan's disease SH2-protein (DSHP) or SLAM-associated protein (SAP)). Mutations in SH2D1A are found in X-linked lymphoproliferative syndrome and non-Hodgkin's lymphomas. Here we report that SH2D1A is expressed in tonsillar B cells and in some B lymphoblastoid cell lines, where CD150 coprecipitates with SH2D1A and SHIP. However, in SH2D1A-negative B cell lines, including B cell lines from X-linked lymphoproliferative syndrome patients, CD150 associates only with SHP-2. SH2D1A protein levels are up-regulated by CD40 cross-linking and down-regulated by B cell receptor ligation. Using GST-fusion proteins with single replacements of tyrosine at Y269F, Y281F, Y307F, or Y327F in the CD150 cytoplasmic tail, we found that the same phosphorylated Y281 and Y327 are essential for both SHP-2 and SHIP binding. The presence of SH2D1A facilitates binding of SHIP to CD150. Apparently, SH2D1A may function as a regulator of alternative interactions of CD150 with SHP-2 or SHIP via a novel TxYxxV/I motif (immunoreceptor tyrosine-based switch motif (ITSM)). Multiple sequence alignments revealed the presence of this TxYxxV/I motif not only in CD2 subfamily members but also in the cytoplasmic domains of the members of the SHP-2 substrate 1, sialic acid-binding Ig-like lectin, carcinoembryonic Ag, and leukocyte-inhibitory receptor families.
IgA-Mediated Killing of Tumor Cells by Neutrophils Is Enhanced by CD47–SIRPα Checkpoint Inhibition (2019)

Therapeutic monoclonal antibodies (mAb), directed toward either tumor antigens or inhibitory checkpoints on immune cells, are effective in cancer therapy. Increasing evidence suggests that the therapeutic efficacy of these tumor antigen-targeting mAbs is mediated-at least partially-by myeloid effector cells, which are controlled by the innate immune-checkpoint interaction between CD47 and SIRPα. We and others have previously demonstrated that inhibiting CD47-SIRPα interactions can substantially potentiate antibody-dependent cellular phagocytosis and cytotoxicity of tumor cells by IgG antibodies both <i>in vivo</i> and <i>in vitro</i> IgA antibodies are superior in killing cancer cells by neutrophils compared with IgG antibodies with the same variable regions, but the impact of CD47-SIRPα on IgA-mediated killing has not been investigated. Here, we show that checkpoint inhibition of CD47-SIRPα interactions further enhances destruction of IgA antibody-opsonized cancer cells by human neutrophils. This was shown for multiple tumor types and IgA antibodies against different antigens, i.e., HER2/neu and EGFR. Consequently, combining IgA antibodies against HER2/neu or EGFR with SIRPα inhibition proved to be effective in eradicating cancer cells <i>in vivo</i> In a syngeneic <i>in vivo</i> model, the eradication of cancer cells was predominantly mediated by granulocytes, which were actively recruited to the tumor site by SIRPα blockade. We conclude that IgA-mediated tumor cell destruction can be further enhanced by CD47-SIRPα checkpoint inhibition. These findings provide a basis for targeting CD47-SIRPα interactions in combination with IgA therapeutic antibodies to improve their potential clinical efficacy in tumor patients.
Edge-Based Adaptation for a 1 IIR + 1 Discrete-Time Tap DFE Converging in $5~\mu$ s (2016)

A 16 Gb/s 1-tap Infinite impulse response (IIR) + 1-tap discrete-time (DT) decision feedback equalizer (DFE) with integrated clock recovery and adaptation is demonstrated in 28 nm FD-SOI CMOS. Using a CMOS phase rotator, 0.7 unit interval (UI) high-frequency jitter tolerance is achieved when operating mesochronously, and over 0.4 UI operating plesiochronously. The half-rate architecture includes a novel 2:1 multiplexer to reduce delay in the IIR feedback path. With a 28 dB loss channel, a BER below 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-12</sup> is measured over a 0.32 UI timing window with a TX swing of 0.8 Vpp-diff. Using a 2 Vpp-diff TX swing, a 30 dB loss channel has a measured BER below 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-12</sup> over a 0.3 UI timing window. A novel edge-based algorithm adapts both IIR and DT equalizer coefficients using the same high-speed circuitry and signals required for clock recovery. The algorithm utilizes all transitions to inform the adaptation of all equalizer coefficients, thereby providing faster convergence than previously-reported algorithms which await specific patterns. Moreover, the adaptation freezes automatically unless a diverse set of data patterns is received, thereby making the algorithm robust in the presence of poorly-conditioned data. The adaptive DFE converges within 5 μs.