gebhart/patrepeval huggingface dataset:
High-Speed MEMS-Based Gas Chromatography (2006)

This paper reports microfabricated silicon-glass separation columns for high-speed micro gas chromatography (muGC) systems. The microfabricated columns are integrated with resistive heaters and temperatures sensors and capacitive pressure sensors to allow temperature and pressure programming and flow control and to achieve reproducible separations in a muGC system. These 25-cm-long, 150-mum-wide, and 250-mum-deep columns are fabricated on a 1.2-cm square die using a silicon-on-glass dissolved wafer process. Programmed with temperature ramps of 10 degC/s, the low-mass columns separate eleven-component gaseous mixtures in less than 10 s, including alkanes from C <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">5</sub> to C <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">16</sub> and simulants for C-4, TNT, sarin, and mustard gas. When used in arrayed architectures, these MEMS columns should allow high-speed analysis without sacrificing separation efficiency
NRAS and BRAF mutations arise early during melanoma pathogenesis and are preserved throughout tumor progression. (2003)

The Ras-Raf-mitogen-activated protein kinase/extracellular signal-regulated kinase-extracellular signal-regulated kinase signaling pathway is activated in the vast majority of melanomas. Activation occurs through either NRAS or BRAF mutations, both of which arise early during melanoma pathogenesis and are preserved throughout tumor progression.
Comparison of a Direct and Indirect Method for Measuring Flavins-Assessing Flavin Status in Patients Receiving Total Parenteral Nutrition (2009)

Background: Riboflavin, flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD) are cofactors in oxidation-reduction reactions. The aim of this study was to compare a direct high performance liquid chromatography (HPLC) method with an indirect enzymatic method to assess flavin status and establish reference intervals. The HPLC method was used to assess prevalence of flavin deficiency in total parenteral nutrition (TPN) patients.
Initiation of Apoptosis by Granzyme B Requires Direct Cleavage of Bid, but Not Direct Granzyme B–Mediated Caspase Activation (2000)

The essential upstream steps in granzyme B-mediated apoptosis remain undefined. Herein, we show that granzyme B triggers the mitochondrial apoptotic pathway through direct cleavage of Bid; however, cleavage of procaspases was stalled when mitochondrial disruption was blocked by Bcl-2. The sensitivity of granzyme B-resistant Bcl-2-overexpressing FDC-P1 cells was restored by coexpression of wild-type Bid, or Bid with a mutation of its caspase-8 cleavage site, and both types of Bid were cleaved. However, Bid with a mutated granzyme B cleavage site remained intact and did not restore apoptosis. Bid with a mutation preventing its interaction with Bcl-2 was cleaved but also failed to restore apoptosis. Rapid Bid cleavage by granzyme B (<2 min) was not delayed by Bcl-2 overexpression. These results clearly placed Bid cleavage upstream of mitochondrial Bcl-2. In granzyme B-treated Jurkat cells, endogenous Bid cleavage and loss of mitochondrial membrane depolarization occurred despite caspase inactivation with z-Val-Ala-Asp-fluoromethylketone or Asp-Glu-Val-Asp-fluoromethylketone. Initial partial processing of procaspase-3 and -8 was observed irrespective of Bcl-2 overexpression; however, later processing was completely abolished by Bcl-2. Overall, our results indicate that mitochondrial perturbation by Bid is necessary to achieve a lethal threshold of caspase activity and cell death due to granzyme B.
Deep Learning with Sets and Point Clouds (2016)

We introduce a simple permutation equivariant layer for deep learning with set structure.This type of layer, obtained by parameter-sharing, has a simple implementation and linear-time complexity in the size of each set. We use deep permutation-invariant networks to perform point-could classification and MNIST-digit summation, where in both cases the output is invariant to permutations of the input. In a semi-supervised setting, where the goal is make predictions for each instance within a set, we demonstrate the usefulness of this type of layer in set-outlier detection as well as semi-supervised learning with clustering side-information.
Regression of Hypertensive Left Ventricular Hypertrophy by Losartan Compared With Atenolol (2004)

Antihypertensive treatment with losartan, plus hydrochlorothiazide and other medications when needed for pressure control, resulted in greater LVH regression in patients with ECG LVH than conventional atenolol-based treatment. Thus, angiotensin receptor antagonism by losartan has superior efficacy for reversing LVH, a cardinal manifestation of hypertensive target organ damage.
A New Superoxide-generating Oxidase in Murine Osteoclasts (2001)

Superoxide production contributes to osteoclastic bone resorption. Evidence strongly indicates that NADPH oxidase is an enzyme system responsible for superoxide generation in osteoclasts. A membrane-bound subunit, p91, is the catalytic domain of NADPH oxidase. However, osteoclasts from p91 knockout mice still produce superoxide at a rate similar to that observed in wild type mice. This unexpected phenomenon prompted us to examine the osteoclasts for an alternative to the p91-containing oxidase. In this study, the cloning of a NADPH oxidase subunit (Nox 4) with 578 amino acids is reported. Nox 4 has 58% similarity in amino acids with the known p91 subunit of NADPH oxidase. Nox 4 is present and active in osteoclasts. Antisense oligonucleotides of Nox 4 reduced osteoclastic superoxide generation as well as resorption pit formation by osteoclasts. This new oxidase complex was present and functional in osteoclasts from p91 knockout mice, explaining the normal resorptive activity seen in the osteoclasts where no p91 is present.
Spectral Reflectance Imaging for a Multiplexed, High-Throughput, Label-Free, and Dynamic Biosensing Platform (2010)

There are a number of emerging optical biosensing techniques utilizing interferometric and resonant characteristics of light. We have recently demonstrated an interferometric technique, the spectral reflectance imaging biosensor (SRIB) that uses optical wave interference to detect changes in the optical path length as a result of capture of biological material on the microarray surface without the need for labels and secondary reagents. In this paper, we review the principles and performance of the SRIB technique in the context of label-free biosensors and demonstrate its high-throughput, quantitative and calibrated, versatile, and dynamic (kinetic) capabilities. A unique aspect of the SRIB system is that the measurement technique is independent of surface conformation and allows for utilization of novel polymeric coatings for surface binding, thus providing a versatile and high-density platform. We present experimental results on multiplexed antibody/antigen arrays and DNA hybridization in real time, as well as specific binding of whole virus particles. The simplicity of the overall system, its high sensitivity and compatibility with glass surface chemistries, and a linear dynamic range of nearly four orders of magnitude makes SRIB a promising platform for multiplexed detection of different biological analytes in a complex sample, with potential impact in research and clinical applications.
Structure of the Promoter Region and Tissue Specificity of the Human Glycophorin C Gene (1989)

Glycophorin C (GPC) is an integral membrane protein of human erythrocytes which plays an important role in regulating the deformability and mechanical stability of red cells. Recently, the structural gene for this glycoprotein has been cloned (Colin, Y., Le Van Kim, C., Tsapis, A., Clerget, M., d'Auriol, L., London, J., Galibert, F., and Cartron, J. P. (1989) J. Biol. Chem. 264, 3773-3780), and we have now determined the sequence of the 1050 base pairs of DNA preceding the transcription initiation site mapped in erythroid cells. This region contains different potential regulatory cis-acting elements found in a variety of eukaryotic promoters (TATA box, CAAT box, Sp1-binding site) as well as sequences present in the promoter and enhancer regions of genes specific for the erythroid lineage (CACCC box and NF-E1-binding site). Northern blot analysis and immunological studies indicate that the GPC gene is expressed in a large number of cells and tissues. However, the level of transcription as well as the glycosylation of the mature GPC differ in erythroid and nonerythroid cells. Primer extension analysis and mapping of the 5' end GPC mRNA by the polymerase chain reaction indicate that different transcription sites are utilized for the expression of the GPC gene in erythroid and nonerythroid tissues and cell lines.
Virus Isolation and Production (1990)

HIV-1 was first isolated from a primary culture of cells recovered from a lymph node biopsy taken from a young homosexual man [1]. The culture conditions used were those classic for the long-term culture of T lymphocytes, namely, three-day stimulation with phytohemagglutinin and maintenance in Interleukin 2 (IL-2). No virus was recovered from comparable cultures of this patient’s peripheral blood lymphocytes. Subsequently, the frequent isolation of HIV-1 from primary cultures and cocultures of peripheral blood lymphocytes from patients with AIDS and pre-AIDS was reported [2,3]. Today, two systems, one based on the helper T lymphocyte and one based on the mononuclear phagocyte, are commonly used for HIV-1 isolation. Because cells of the mononuclear phagocyte series and helper T lymphocytes bear the CD4 molecule, an essential component of the virus receptor [4,5], they are major natural host cells for HIV-1 infection and replication. Although other kinds of cells such as fibroblasts [6], endothelial cells [7], glial cells [8], and enterochromaffin cells [9] have been suggested as potential HIV-1 host cells, the evidence that these kinds of cells represent major sites of virus replication and expression in vivo is limited. With respect to this discussion, these kinds of cells are not commonly considered sources of isolable HIV-1 and they are certainly suboptimal for HIV-1 propagation for most purposes because the magnitude of virus expression is considerably lower than that from the natural host cells. T lymphocytes and mononuclear phagocytes, then, usually serve as the source of virus from clinical specimens. They also often serve as target cells for HIV-1 infection when cocultured with patient material.
Analytic Formulation for Kinematics, Statics, and Shape Restoration of Multibackbone Continuum Robots Via Elliptic Integrals (2009)

This paper presents a novel and unified analytic formulation for kinematics, statics, and shape restoration of multiple-backbone continuum robots. These robots achieve actuation redundancy by independently pulling and pushing three backbones to carry out a bending motion of two-degrees-of-freedom (DoF). A solution framework based on constraints of geometric compatibility and static equilibrium is derived using elliptic integrals. This framework allows the investigation of the effects of different external loads and actuation redundancy resolutions on the shape variations in these continuum robots. The simulation and experimental validation results show that these continuum robots bend into an exact circular shape for one particular actuation resolution. This provides a proof to the ubiquitously accepted circular-shape assumption in deriving kinematics for continuum robots. The shape variations due to various actuation redundancy resolutions are also investigated. The simulation results show that these continuum robots have the ability to redistribute loads among their backbones without introducing significant shape variations. A strategy for partially restoring the shape of the externally loaded continuum robots is proposed. The simulation results show that either the tip orientation or the tip position can be successfully restored.
Chronic staphylococcal osteomyelitis: a new experimental rat model (1993)

A rat model of chronic staphylococcal osteomyelitis was developed. Fibrin glue (5 microliters) and Staphylococcus aureus (2 x 10(6) CFU/5 microliters) were inoculated into the proximal metaphysis of the tibia. The rats were killed at intervals of between 1 and 6 months, and the tibias were removed. Induced lesions were evaluated by radiographic, macroscopic, and histological examinations and bacterial counts. Roentgenograms revealed osteomyelitis in more than 90% of the tibias. Gross bone pathology revealed skeletal deformation, new bone formation, abscesses, and draining skin fistulas in more than 80% of cases. Histological examination revealed osteomyelitis in more than 90% of cases, and bacterial counts were positive in 86% of cases. Only fibrin glue (5 microliters) was inoculated into controls. Controls showed no osteomyelitic lesions, and counts were negative in seven of eight control tibias. The main feature of this model is the use of fibrin glue instead of the sclerosing agents and foreign bodies used in other models. The model reproduces lesions similar to those of human posttraumatic osteomyelitis and can be reliably used in pathophysiological and therapeutic studies.
Growth modification of the rabbit mandible using therapeutic ultrasound: is it possible to enhance functional appliance results? (2003)

Previous studies have shown that functional appliances can enhance mandibular growth when applied during the active growth period. However, besides patient compliance problems with bulky appliances and prolonged treatment demands, there is contradictory evidence that functional appliances have a significant long-term effect. Is there a method to enhance the growth response and improve the long-term success of functional appliances? Previous studies have also found that therapeutic ultrasound (US) can stimulate cartilage and bone growth. The objective of this study was to evaluate the effect of therapeutic US on condylar and mandibular growth in the rabbit model. Eight growing New Zealand male rabbits were chosen for this study. They received therapeutic US on one side of the mandible for 20 minutes/day for four weeks. Anthropometrical and histological evaluations revealed that US enhances mandibular growth by condylar endochondreal bone growth and consequently mandibular ramus growth. The significant results of this study support conducting a long-term study to evaluate the ultimate stability of the results obtained. Also, they suggest an extended research with a larger sample size and investigating the molecular basis of this stimulatory effect, together with forward posturing splints for optimal macroscopic and microscopic responses.
FastTrack: Leveraging Heterogeneous FPGA Wires to Design Low-Cost High-Performance Soft NoCs (2018)

Networks-on-Chip (NoCs) implemented on FPGAs have to be designed differently from ASICs to fully exploit the unique architectural features and properties of the FPGA fabric. The FPGA-friendly bufferless, deflection routed Hoplite NoC is almost an order of magnitude smaller and runs at a faster operating frequency than competing classic buffered FPGA NoCs. It is able achieve this by sacrificing NoC link utilization that suffers due to the cost of packet deflections and associated high latency traversals. In this paper, we address these shortcomings by developing FastTrack, which is an FPGA-optimized, high-radix NoC that exploits the segmented interconnect structure of modern FPGAs. We adapt the NoC organization to use express bypass links in the NoC to skip multiple router stages in a single cycle. Our FastTrack design can be tuned to use different express link lengths for performance, and supports depopulation strategies for controlling the balance between FPGA LUT and wiring cost. For the Xilinx Virtex-7 485T FPGA, an 8×8 FastTrack NoC is 1.7- 2.5× larger than a base Hoplite NoC, but operates at almost the same clock frequency. FastTrack delivers throughput and latency improvements across a range of statistical workloads (2.5×), and traces extracted from FPGA accelerator case studies such as Sparse Matrix-Vector Multiplication (2.5×), Graph Analytics (2.8×), Token LU Factorization Dataflow (1.4×) and Multi-processor overlay applications (2×). FastTrack also shows energy efficiency improvements by factors of up to 2.2× over baseline Hoplite due to higher sustained rates and high speed operation of express links made possible by fast FPGA interconnect.
Highly Emissive Self‐assembled Organic Nanoparticles having Dual Color Capacity for Targeted Immunofluorescence Labeling (2008)

A new benzoxazole molecule has been synthesized and self-assembled with functionalized diacetylene molecules to obtain well-defined nanoparticles of 80 nm diameter. The nanoparticles show enhanced fluorescence emission of 38% quantum yield compared to 3% in THF solution. Selective targeting and dual color visualization of patterned avidin arrays were achieved by using these nanoparticles to demonstrate their promising application for immunofluorescence labeling. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2089/2008/adma200701601_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Free electron laser induces specific immobilization of heparin on polysulfone films (2001)

Covalent immobilization of heparin has been developed to reduce the amount of heparin administered systematically during long-term dialysis. Recently, it was doubted partially because of the complexion during immobilization process. In this study, we investigated a novel method for specific immobilization of heparin on polysulfone (PSF) via free electron laser (FEL) irradiation. Laser wavelengths of 6.18 or 6.31 microm, the typical absorption bands of carboxyl groups of heparin and aromatic rings in PSF, respectively, were chosen to irradiate the thin heparin membrane formed on PSF surfaces. The amount of heparin immobilized on PSF was measured by the toluidine blue method. The binding of heparin on PSF was analyzed by X-ray photoelectron spectroscopy (XPS). The immobilization of heparin resulted in a hydrophilic surface on which decreased platelet adhesion was observed. The efficiency differences, depending on laser wavelengths, were discussed from the point of view of structural and environmental differences of light-absorbing groups.
Inter- and Intramolecular Reductive Coupling Reactions:  An Approach to the Phorbol Skeleton (2000)

[reaction: see text] An expeditious convergent route to the ABC-tricyclic core of the phorbol esters is described. The chemistry capitalizes upon both inter- and intramolecular reductive coupling processes promoted electrochemically and via the use of samarium diiodide.
Dual-energy contrast-enhanced digital breast tomosynthesis – a feasibility study (2010)

Contrast-enhanced digital breast tomosynthesis (CE-DBT) is a novel modality for imaging breast lesion morphology and vascularity. The purpose of this study is to assess the feasibility of dual-energy subtraction as a technique for CE-DBT (a temporal subtraction CE-DBT technique has been described previously). As CE-DBT evolves, exploration of alternative image acquisition techniques will contribute to its optimisation. Evaluation of dual-energy CE-DBT was conducted with Institutional Review Board (IRB) approval from our institution and in compliance with federal Health Insurance Portability and Accountability Act (HIPAA) guidelines. A 55-year old patient with a known malignancy in the right breast underwent imaging with MRI and CE-DBT. CE-DBT was performed in the medial lateral oblique view with a DBT system, which was modified under IRB approval to allow high-energy image acquisition with a 0.25 mm Cu filter. Image acquisition occurred via both temporal and dual-energy subtraction CE-DBT. Between the pre- and post-contrast DBT image sets, a single bolus of iodinated contrast agent (1.0 ml kg(-1)) was administered, followed by a 60 ml saline flush. The contrast agent and saline were administrated manually at a rate of approximately 2 ml s(-1). Images were reconstructed using filtered-back projection and transmitted to a clinical PACS workstation. Dual-energy CE-DBT was shown to be clinically feasible. In our index case, the dual-energy technique was able to provide morphology and kinetic information about the known malignancy. This information was qualitatively concordant with that of CE-MRI. Compared with the temporal subtraction CE-DBT technique, dual-energy CE-DBT appears less susceptible to motion artefacts.
A 9-b charge-to-digital converter for integrated image sensors (1996)

Charge-to-digital conversion offers advantages over conventional charge readout techniques because it performs digitization directly in the charge domain. The approach consolidates hardware, reduces power and weight, and eliminates many sources of noise and nonlinearity. This paper introduces an architecture for a charge-to-digital converter (CDC) that is tailored toward a charge-coupled device (CCD) implementation. New methods of generating charge, sensing charge, and comparing charge packets are described that improve conversion accuracy. Factors limiting device performance are discussed. Measured results are presented for two prototype CDCs. The first, using buried channel CCDs, is optimized for resolution. It achieves 56 dB spurious free dynamic range (SFDR) at a 2 MHz sampling rate and operates from 5 V. The second, using surface channel CCDs, is optimized for power and speed. It achieves 49 dB SFDR at a 15 MHz sampling rate and consumes 13 mW power at its maximum sampling rate of 22 MHz.
Chemiluminescent and bioluminescent techniques (1991)

Light-emitting chemical reactions (chemiluminescence, CL) and biological reactions (bioluminescence, BL) have a diverse range of analytical applications but relatively few have been adopted by routine clinical laboratories. Advantages of CL and BL assays include sensitivity (attomole and sub-attomole detection limits), speed (signal generated in a few seconds and in some cases stable for several hours), nonhazardous reagents, and simple procedures. The most promising clinical applications are in immunoassay, protein blotting, and DNA probe assays. Chemiluminescent molecules exploited as labels include luminol, isoluminol, acridinium esters, thioesters and sulfonamides, and phenanthridinium esters. Separation and nonseparation assays have been devised, based on isoluminol and acridinium ester labels. The combination of the amplification properties of an enzyme and a CL or BL detection reaction provides a highly sensitive analytical system. Since 1983, CL and BL methods have been developed for many enzyme labels, e.g., alkaline phosphatase, glucose-6-phosphate dehydrogenase, horseradish peroxidase, Renilla luciferase, and xanthine oxidase. Currently, the most successful enzyme assays are the enhanced CL method for a peroxidase label involving a mixture of luminol, hydrogen peroxide, and an enhancer (e.g., p-iodophenol) and the direct CL method for alkaline phosphatase, with an adamantyl 1,2-dioxetane phenyl phosphate as substrate. Both systems are very sensitive (the detection limit for alkaline phosphatase when using the dioxetane reagent is 0.001 amol) and produce long-lived light emission (greater than 30 min), which is ideal for membrane applications in which light emission is detected with photographic film or a charge-coupled device camera.