gebhart/patrepeval huggingface dataset:
Assessing the Functional Bias of Commercial Microarrays Using the Onto-Compare Database (2003)

Microarrays are at the center of a revolution in biotechnology, allowing researchers to screen tens of thousands of genes simultaneously. Typically, they have been used in exploratory research to help formulate hypotheses. In most cases, this phase is followed by a more focused, hypothesis-driven stage in which certain specific biological processes and pathways are thought to be involved. Since a single biological process can still involve hundreds of genes, microarrays are still the preferred approach as proven by the availability of focused arrays from several manufacturers. Because focused arrays from different manufacturers use different sets of genes, each array will represent any given regulatory pathway to a different extent. We argue that a functional analysis of the arrays available should be the most important criterion used in the array selection. We developed Onto-Compare as a database that can provide this functionality, based on the Gene Ontology Consortium nomenclature. We used this tool to compare several arrays focused on apoptosis, oncogenes, and tumor suppressors. We considered arrays from BD Biosciences Clontech, PerkinElmer, Sigma-Genosys, and SuperArray. We showed that among the oncogene arrays, the PerkinElmer MICROMAX oncogene microarray has a better representation of oncogenesis, protein phosphorylation, and negative control of cell proliferation. The comparison of the apoptosis arrays showed that most apoptosis-related biological processes are equally well represented on the arrays considered. However, functional categories such as immune response, cell-cell signaling, cell-surface receptor linked signal transduction, and interleukins are better represented on the Sigma-Genoys Panorama human apoptosis array. At the same time, processes such as cell cycle control, oncogenesis, and negative control of cell proliferation are better represented on the BD Biosciences Clontech Atlas Select human apoptosis array.
Quantitative Comparison of Thermographic Data Sequences (2005)

Acceptance of thermography for nondestructive testing (NDT) has grown considerably in the past few years. In a typical implementation scenario, the inspector evaluates results visually in order to determine whether or not a repair is required or a part is acceptable. In online quality and process control applications, this approach is too slow, too subjective and not sensitive enough to be practical. In manufacturing, it is often necessary to automate the test process and compare a part to a discontinuity free gold standard sample, in order to make an instantaneous accept/ reject decision or adjust process parameters. In such cases, a part may be rejected because of structural, compositional or cosmetic irregularities. The issue is not whether a sample is good or bad, but whether or not it is identical to the master. Conventional thermographic analysis techniques can be difficult to apply in this situation, as direct comparison of entire image sequences is required. However, sequence comparison can be simplified, and even automated, by reducing an entire thermographic time sequence to a single fingerprint image, which is rotationally and translationally invariant and immune to shot to shot energy variations, ambient temperature variations and other common thermographic artifacts.
A Novel Generalized Metaheuristic Framework for Dynamic Capacitated Arc Routing Problems (2022)

The capacitated arc routing problem (CARP) is a challenging combinatorial optimization problem abstracted from many real-world applications, such as waste collection, road gritting, and mail delivery. However, few studies considered dynamic changes during the vehicles’ service, which can cause the original schedule infeasible or obsolete. The few existing studies are limited by the dynamic scenarios considered, and by overly complicated algorithms that are unable to benefit from the wealth of contributions provided by the existing CARP literature. In this article, we first provide a mathematical formulation of dynamic CARP (DCARP) and design a simulation system that is able to consider dynamic events while a routing solution is already partially executed. We then propose a novel framework which can benefit from the existing static CARP optimization algorithms so that they could be used to handle DCARP instances. The framework is very flexible. In response to a dynamic event, it can use either a simple restart strategy or a sequence transfer strategy that benefits from the past optimization experience. Empirical studies have been conducted on a wide range of DCARP instances to evaluate our proposed framework. The results show that the proposed framework significantly improves over state-of-the-art dynamic optimization algorithms.
Reliability of SiC Digital Telemetry Circuits on AlN Substrate (2013)

In this work, two silicon carbide based integrated circuits (frequency counter and timing generator) have been designed and fabricated as building blocks of a digital telemetry module for the purpose of sensing and transmitting pressure measurements from a geothermal well at temperatures up to 300°C. The frequency counter consists of one 4-bit counter, one 4-bit shift register, and one buffer. The timing generator contains an 8-bit counter, a D-flipflop, and some dedicated logic gates to generate timing pulses for the two channel frequency counter. These dies were flip-chip bonded to patterned gold thin-film aluminum nitride substrate circuit boards and tested for functionality in a lab oven at 300°C and prove to operate continuously for more than 1000 hours. Also the boards were subjected to random vibration at 20G RMS and also mechanical shock at 215G at 300°C and remained operational after 8 hours of vibration and 1000 shocks.
Component-based Synthesis Applied to Bitvector Programs (2010)

We define component-based synthesis to be the problem of synthesis of (straight-line) programs from appropriate composition of base components from a specified library of software components. The functional specification of the desired program and the library components is provided in the form of logical formulas that relate the respective input and output variables. This has applications in design of intricate circuits or algorithms, superoptimization, and API mining. Furthermore, automated synthesis provides the promise of correctness by construction, generation of efficient systems, and improvement in developer’s productivity. We solve the component-based synthesis problem using a constraint-based approach that involves first generating a synthesis constraint, and then solving the constraint. The synthesis constraint is a first-order logic formula whose size is quadratic in the number of components, but has quantifier alternation. We present a novel algorithm for solving such constraints. Our algorithm is based on counterexample guided iterative synthesis paradigm and uses off-the-shelf SMT solvers. We present experimental results on synthesizing a variety of bitvector algorithms that involve unintuitive composition of standard bitvector operations and are difficult to synthesize manually. We also compare our technique with existing synthesis approaches based on sketching and superoptimization. Our tool Brahma can efficiently synthesize highly nontrivial 10-20 line loop-free programs. These programs represent a state space of approximately 20 10 programs, and are beyond the reach of the other tools. 1.
Communication: The electronic structure of matter probed with a single femtosecond hard x-ray pulse (2014)

Physical, biological, and chemical transformations are initiated by changes in the electronic configuration of the species involved. These electronic changes occur on the timescales of attoseconds (10(-18) s) to femtoseconds (10(-15) s) and drive all subsequent electronic reorganization as the system moves to a new equilibrium or quasi-equilibrium state. The ability to detect the dynamics of these electronic changes is crucial for understanding the potential energy surfaces upon which chemical and biological reactions take place. Here, we report on the determination of the electronic structure of matter using a single self-seeded femtosecond x-ray pulse from the Linac Coherent Light Source hard x-ray free electron laser. By measuring the high energy resolution off-resonant spectrum (HEROS), we were able to obtain information about the electronic density of states with a single femtosecond x-ray pulse. We show that the unoccupied electronic states of the scattering atom may be determined on a shot-to-shot basis and that the measured spectral shape is independent of the large intensity fluctuations of the incoming x-ray beam. Moreover, we demonstrate the chemical sensitivity and single-shot capability and limitations of HEROS, which enables the technique to track the electronic structural dynamics in matter on femtosecond time scales, making it an ideal probe technique for time-resolved X-ray experiments.
Global health design: clinical immersion, opportunity identification and definition, and design experiences (2018)

We have developed an experiential learning global health design program that emphasizes direct interactions withstakeholders and first-hand exposure to the contexts in which solutions will be implemented. Students in the program gainpractical hands-on experience identifying and defining unmet global health needs in low-resource settings and applyhuman-centered and co-creative design approaches. Device designs that incorporate rigorously collected and analyzedfirst-hand data from diverse users and stakeholders rather than anecdotal or poorly represented information are moreeffective at meeting true needs. To date, more than 100 undergraduate student participants have identified hundreds ofneeds in collaboration with sub-Saharan and Asian healthcare providers. Approximately 400 students from the U.S.,Ghana, Ethiopia, and Uganda have contributed to the generation of technology concept solutions to address these needs.Program outcomes include approximately 100 student design projects completed at multiple institutions, student-leddesign-based conference publications and journal articles, device commercialization, and peer-to-peer mentoring withintraditional capstone design courses. In this paper we describe the curricular elements of the clinical immersion and designethnography experience. Additionally, we describe programmatic best practices that have emerged over the past 10 yearsand challenges students encounter when performing this front-end design work.
Implementation and optimization of software depth estimation for arm (2012)

3D imaging capable devices have been available on the market for a few years now and the availability of 3D contents is also picking up. However, 3D contents available for viewing is not growing fast enough to meet the demand. To compensate for such a problem, most 3D imaging devices are equipped with 2D to 3D conversion function. Also, common 3D contents available are mostly produced with 2 view points which poses a problem for autostereoscopic devices that is capable of displaying multiple view points. In the absence of multiview 3D contents, to produce natural viewing experience on such device, depth estimation is an essential technology in order to create more parallax images from source images. In this paper, we present the implementation of Toshiba's software depth estimation process on ARM processor which allows realtime processing on embedded devices such as TVs, mobile phones and tablet computers adopting stereoscopic or autostereoscopic 3D technology.
Temporal registration using 3D phase correlation and a maximum likelihood approach in the perceptual evaluation of video quality (2007)

The estimation of the video quality is often performed using a full reference approach. One of the most important steps in a video quality measurement algorithm is to find the corresponding frames between the reference and the distorted video sequence. In this paper an algorithm with three steps is proposed. First, an extended version of the phase correlation is used to find candidate images with an arbitrary temporal offset, spatial scaling or spatial shift. Based on the assumption that the spatial scaling and spatial shift does not change during the sequence a set of probable parameters is selected. Finally, a maximum likelihood estimation is applied to select those temporal offsets which support the smoothest playback. A set of video sequences degraded with several distortions which are typical for multimedia scenarios are used to compare the performance to other algorithms.
An Analysis of the Binding Efficiencies of Drugs and Their Leads in Successful Drug Discovery Programs (2010)

In order to investigate the evolution of binding efficiency in successful drug discovery programs, a data set of 60 lead/drug pairs with known binding affinities has been compiled and analyzed. Low-end thresholds for the binding efficiencies of viable leads and drugs have been derived. On average, the drugs in the set are significantly larger and more potent but have similar lipophilicity relative to their originating leads, suggesting that the ability to maintain low levels of lipophilicity while increasing molecular weight is one of the keys to a successful drug discovery program. A number of examples demonstrate that large increases in binding efficiency from leads to more elaborate drugs sharing the same scaffold can be achieved. The importance of dissecting a lead structure to identify the most efficient fragments and the option of sacrificing binding efficiency to optimize other properties are discussed, and relevant examples are highlighted.
Stimuli‐Responsive magnetic nanoparticles for monoclonal antibody purification (2013)

Monoclonal antibodies (mAbs) are important therapeutic proteins. One of the challenges facing large-scale production of monoclonal antibodies is the capacity bottleneck in downstream processing, which can be circumvented by using magnetic stimuli-responsive polymer nanoparticles. In this work, stimuli-responsive magnetic particles composed of a magnetic poly(methyl methacrylate) core with a poly(N-isopropylacrylamide-co-acrylic acid) (P(NIPAM-co-AA)) shell cross-linked with N, N'-methylenebisacrylamide were prepared by miniemulsion polymerization. The particles were shown to have an average hydrodynamic diameter of 317 nm at 18°C, which decreased to 277 nm at 41°C due to the collapse of the thermo-responsive shell. The particles were superparamagnetic in behavior and exhibited a saturation magnetization of 12.6 emu/g. Subsequently, we evaluated the potential of these negatively charged stimuli-responsive magnetic particles in the purification of a monoclonal antibody from a diafiltered CHO cell culture supernatant by cation exchange. The adsorption of antibodies onto P(NIPAM-co-AA)-coated nanoparticles was highly selective and allowed for the recovery of approximately 94% of the mAb. Different elution strategies were employed providing highly pure mAb fractions with host cell protein (HCP) removal greater than 98%. By exploring the stimuli-responsive properties of the particles, shorter magnetic separation times were possible without significant differences in product yield and purity.
Artificial Intelligence with Statistical Confidence Scores for Detection of Acute or Subacute Hemorrhage on Noncontrast CT Head Scans (2022)

AI that provided statistical confidence measures for ICH detection on NCCT scans reliably detected and subtyped hemorrhages, identified high-confidence predictions, and improved worklist prioritization in simulation.<b>Keywords:</b> CT, Head/Neck, Hemorrhage, Convolutional Neural Network (CNN) <i>Supplemental material is available for this article</i>. © RSNA, 2022.
Control-Oriented Model for Camless Intake Process—Part I1 (1998)

The improvement of internal combustion engine is largely accomplished though the introduction of innovative actuators that allow optimization and control of the flow, mixing, and combustion processes. The realization of such a novel system depends on the existence of an operational controller that will stabilize the engine and allow experimental testing which, consequently, leads to further development of the actuator and the engine controller. This iterative process requires a starting point which is the development of a control-oriented model. Although not fully validated, the control-oriented model reveals issues associated with uncertainties, nonlinearities, and limitation of different subsystems. Moreover, it aides in defining the controller structure and the necessary parameters for the calibration of the closed loop system. In this paper (Part I) we describe the development process of a control-oriented model for a camless intake process. We first model the multicylinder crankangle-based breathing dynamics and validate it against experimental data of a conventional engine with cam-driven valve profile during unthrottled operation. We then employ the assumption of uniform air pulses during the intake duration and derive a simple input-output representation of the cylinder air charge, pumping losses and associated uncertainties that can be used for designing an electronic valvetrain controller (Part II). [S0022-0434(00)02901-4]
Facile and Selective Aerobic Oxidation of Arylalkanes to Aryl Ketones Using Cesium Carbonate (2006)

Various arylalkanes such as fluorenes, xanthene, anthrone, 9,10-dihydroanthracene, and diphenylmethane are effectively transformed into the corresponding aryl ketones, while amino and aldehyde functionalities remain intact, under air in the presence of cesium carbonate.
Peroxisome Proliferator-Activated Receptor Ligands as Antiatherogenic Agents: Panacea or Another Pandora's Box? (2002)

Peroxisome proliferator activated receptors (PPARs) are members of the nuclear receptor super family that modulate gene expression upon ligand activation. They are 3 major subtypes of PPARs: alpha, delta (also called beta), and gamma. PPAR-gamma is widely expressed in the cardiovascular system and is involved in the regulation of tissue inflammation and smooth muscle cell growth pathways as well as in lipoprotein metabolism and coagulation cascades. PPAR-gamma ligands of (e.g., rosigitazone and pioglitazone) have been shown to exert antiatherogenic effects both in vitro and in vivo. PPAR-alpha ligands (e.g., clofibrate and benzofibrate) modulate lipoprotein metabolism, and affect inflammation and coagulation cascade. These effects may be helpful in resolving the dilemma arising from studies that showed significant mortality and morbidity benefits of fibrates in the face of minimal changes in HDL-cholesterol levels. The role of PPAR-delta in atherogenesis remains largely unknown, although it appears that PPAR-delta activation affects lipoprotein metabolism. PPAR ligands appear to be promising agents in limiting atherosclerosis; however, large-scale clinical trials are required to assess their safety and efficacy before they can be added to the clinicians' arsenal of antiatherosclerotic agents.
Pro-urokinase-type Plasminogen Activator Is a Substrate for Hepsin (2006)

Hepsin, a type II transmembrane serine protease, is strongly up-regulated in prostate cancer. Hepsin overexpression in a mouse prostate cancer model resulted in tumor progression and metastasis, associated with basement membrane disorganization. We investigated whether hepsin enzymatic activity was linked to the basement membrane defects by examining its ability to initiate the plasminogen/plasmin proteolytic pathway. Because plasminogen is not processed by hepsin, we investigated the upstream activators, urokinase-type plasminogen activator (uPA) and tissue-type plasminogen activator. Enzymatic assays with a recombinant soluble form of hepsin demonstrated that hepsin did not cleave pro-tissue-type plasminogen activator but efficiently converted pro-uPA into high molecular weight uPA by cleavage at the Lys158-Ile159 (P1-P1') peptide bond. uPA generated by hepsin displayed enzymatic activity toward small synthetic and macromolecular substrates indistinguishable from uPA produced by plasmin. The catalytic efficiency of pro-uPA activation by hepsin (kcat/Km 4.8 x 10(5) m(-1) s(-1)) was similar to that of plasmin, which is considered the most potent pro-uPA activator and was about 6-fold higher than that of matriptase. Conversion of pro-uPA was also demonstrated with cell surface-expressed full-length hepsin. A stable hepsinoverexpressing LnCaP cell line converted pro-uPA into high molecular weight uPA at a rate of 6.6 +/- 1.9 nm uPA h(-1), which was about 3-fold higher than LnCaP cells expressing lower hepsin levels on their surface. In conclusion, the ability of hepsin to efficiently activate pro-uPA suggests that it may initiate plasmin-mediated proteolytic pathways at the tumor/stroma interface that lead to basement membrane disruption and tumor progression.
Atmospheric pressure processed InGaZnO thin-film transistors (2013)

High-mobility indium-gallium-zinc oxide thin-film transistor (IGZO TFT) was demonstrated at 360 °C with the IGZO channel and aluminum oxide (AlOx) gate dielectric stack that was deposited ozone-assisted atmospheric pressure chemical vapour deposition used ultrasonic atomized solution mist as precursors. Field effect mobility of 7.7 cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> /Vs and subthreshold swing of 0.32 V/dec were achieved. These electrical properties are comparable to the vacuum-processed IGZO TFT.
Abstract 4649: Comprehensive isoform expression analysis reveals that EGFR and sEGFR are prognostic determinants of cancer (2010)

Abstract In July, 2009 the United States’ Food and Drug Agency (FDA) approved the use of a new biologically-targeted drug called ‘cetuximab’ (Erbitux) for the treatment of patients with advanced colorectal cancer (CRC). Cetuximab is a chimeric antibody directed against the extracellular domain of the epidermal growth factor receptor (EGFR). Paradoxically, EGFR expression, as it is currently measured by commercially available assays, has not been useful for predicting who will respond to cetuximab. We propose that one problem with these assays is their inability to measure EGFR and soluble EGFR (sEGFR) isoforms independently. We previously have documented the expression of an sEGFR isoform in human tissues (1), and have generated antibodies directed against a 31-mer peptide (residues 604-634) located within the unique 78 amino acid carboxy-terminal sequence of sEGFR (2). Interestingly, this anti-sEGFR antibody recognizes a second protein of ∼140-kDa (p140), which we have identified as human α5-integrin. Biochemical and mass spectrometry analyses show that a short region in the calf domain of α5-integrin shares sequence identity with the 31-mer sEGFR peptide. We have used this 31-mer antibody with an antibody directed against the intracellular domain of full-length EGFR to develop a novel EGFR vs. sEGFR/α5-integrin expression assay. This assay demonstrates that sEGFR/α5-integrin is co-expressed with EGFR in normal as well as malignant tissues, including in a number of carcinoma-derived cell lines. We also observe that high expression of EGFR and sEGFR/α5-integrin in a large cohort of ovarian cancer patients defines a strong adverse prognostic determinant of survival. These results implicate EGFR, sEGFR, and integrins as cancer biomarkers and demonstrate the critical importance of independently assessing both full-length and soluble EGFR isoforms in prognostic EGFR expression assays. *–JAW and ATB contributed equally to this study (1). Reiter et al. (2001) Genomics. 71(1):1-20 (2). Christensen et al. (2002) Hybrid Hybridomics. 21(3):183-9 Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 4649.