gebhart/patrepeval huggingface dataset:
An Energy-Efficient Processor Architecture for Embedded Systems (2008)

We present an efficient programmable architecture for compute-intensive embedded applications. The processor architecture uses instruction registers to reduce the cost of delivering instructions, and a hierarchical and distributed data register organization to deliver data. Instruction registers capture instruction reuse and locality in inexpensive storage structures that arc located near to the functional units. The data register organization captures reuse and locality in different levels of the hierarchy to reduce the cost of delivering data. Exposed communication resources eliminate pipeline registers and control logic, and allow the compiler to schedule efficient instruction and data movement. The architecture keeps a significant fraction of instruction and data bandwidth local to the functional units, which reduces the cost of supplying instructions and data to large numbers of functional units. This architecture achieves an energy efficiency that is 23x greater than an embedded RISC processor.
Characterization of mesendoderm: a diverging point of the definitive endoderm and mesoderm in embryonic stem cell differentiation culture (2005)

Bipotent mesendoderm that can give rise to both endoderm and mesoderm is an established entity from C. elegans to zebrafish. Although previous studies in mouse embryo indicated the presence of bi-potent mesendoderm cells in the organizer region, characterization of mesendoderm and its differentiation processes are still unclear. As bi-potent mesendoderm is implicated as the major precursor of definitive endoderm, its identification is also essential for exploring the differentiation of definitive endoderm. In this study, we have established embryonic stem (ES) cell lines that carry GFP gene in the goosecoid (Gsc) gene locus and have investigated the differentiation course of mesendodermal cells using Gsc expression as a marker. Our results show that mesendoderm is represented as a Gsc-GFP+ E-cadherin(ECD)+ PDGFRalpha(alphaR)+ population and is selectively induced from ES cells under defined conditions containing either activin or nodal. Subsequently, it diverges to Gsc+ ECD+ alphaR- and Gsc+ ECD- alphaR+ intermediates that eventually differentiate into definitive endoderm and mesodermal lineages, respectively. The presence of mesendodermal cells in nascent Gsc+ ECD+ alphaR+ population was also confirmed by single cell analysis. Finally, we show that the defined culture condition and surface markers developed in this study are applicable for obtaining pure mesendodermal cells and their immediate progenies from genetically unmanipulated ES cells.
In vivo multispectral photoacoustic and photothermal flow cytometry with multicolor dyes: A potential for real‐time assessment of circulation, dye‐cell interaction, and blood volume (2011)

Recently, photoacoustic (PA) flow cytometry (PAFC) has been developed for in vivo detection of circulating tumor cells and bacteria targeted by nanoparticles. Here, we propose multispectral PAFC with multiple dyes having distinctive absorption spectra as multicolor PA contrast agents. As a first step of our proof-of-concept, we characterized high-speed PAFC capability to monitor the clearance of three dyes (Indocyanine Green [ICG], Methylene Blue [MB], and Trypan Blue [TB]) in an animal model in vivo and in real time. We observed strong dynamic PA signal fluctuations, which can be associated with interactions of dyes with circulating blood cells and plasma proteins. PAFC demonstrated enumeration of circulating red and white blood cells labeled with ICG and MB, respectively, and detection of rare dead cells uptaking TB directly in bloodstream. The possibility for accurate measurements of various dye concentrations including Crystal Violet and Brilliant Green were verified in vitro using complementary to PAFC photothermal (PT) technique and spectrophotometry under batch and flow conditions. We further analyze the potential of integrated PAFC/PT spectroscopy with multiple dyes for rapid and accurate measurements of circulating blood volume without a priori information on hemoglobin content, which is impossible with existing optical techniques. This is important in many medical conditions including surgery and trauma with extensive blood loss, rapid fluid administration, and transfusion of red blood cells. The potential for developing a robust clinical PAFC prototype that is safe for human, and its applications for studying the liver function are further highlighted.
On transition from laminar to turbulent flow in the boundary layer (1941)

Abstract Information on transition from laminar to turbulent flow in boundary layers on stream line bodies of revolution in a water stream is obtained from visual an d photographic observation of the movements of small particles and filament bands. The cases considered are transition caused by isotropic turbulence in the free stream , by a falling velocity in a stream substantially free from turbulence, and by flow disturbances from surface wires. A non-dimensional number, specified in terms of the intensity and scale of turbulence, the boundary-layer thickness, and the mean velocity just outside the layer, is found to be representative of the conditions of flow in the boundary layer of a body in a turbulent stream: and values of this number at transition obtained from observations made for a body of revolution have the same order of magnitude as those calculated for a flat plate from measurements taken by Hall and Hislop. Transition in a region of falling velocity in a steady stream arises from a separation of the laminar boundary layer from the surface; and after separation, the flow in the layer becomes turbulent and then rejoins the surface. The observed position of transition is near the position of separation given by a solution of the momentum equation for laminar flow and for the observed distribution of velocity just outside the layer. Flow disturbances from a surface wire placed in a laminar boundary layer cause fully developed turbulent flow to be established at the wire when u2d/v&amp;gt; 400, where d is the wire diameter, u2 is the velocity in the laminar layer at a distance d from the surface, and v is the kinematic viscosity. The measured maximum value of the downstream component of turbulent velocity in the stream behind a grid is about 3.3 times the root-mean-square value.
Mechanism of inactivation of human leukocyte elastase by a chloromethyl ketone: kinetic and solvent isotope effect studies (1986)

The mechanism of inactivation of human leukocyte elastase (HLE) by the chloromethyl ketone MeOSuc-Ala-Ala-Pro-Val-CH2Cl was investigated. The dependence of the first-order rate constant for inactivation on concentration of chloromethyl ketone is hyperbolic and suggests formation of a reversible "Michaelis complex" prior to covalent interaction between the enzyme and inhibitor. However, the observed Ki value is 10 microM, at least 10-fold lower than dissociation constants for complexes formed from interaction of HLE with structurally related substrates or reversible inhibitors, and suggests that Ki is a complex kinetic constant, reflecting the formation and accumulation of both the Michaelis complex and a second complex. It is proposed that this second complex is a hemiketal formed from attack of the active site serine on the carbonyl carbon of the inhibitor. The accumulation of this intermediate may be a general feature of reactions of serine proteases and chloromethyl ketones derived from specific peptides and accounts for the very low Ki values observed for these reactions. The solvent deuterium isotope effect (SIE) on the inactivation step (ki) is 1.58 +/- 0.07 and is consistent with rate-limiting, general-catalyzed attack of the active site His on the methylene carbon of the inhibitor with displacement of chloride anion. The general catalyst is thought to be the active site Asp. In contrast, the SIE on the second-order rate constant for HLE inactivation, ki/Ki, is inverse and equals 0.64 +/- 0.05.(ABSTRACT TRUNCATED AT 250 WORDS)
Chip-Based Nanostructured Sensors Enable Accurate Identification and Classification of Circulating Tumor Cells in Prostate Cancer Patient Blood Samples (2012)

The identification and analysis of circulating tumor cells (CTCs) is an important goal for the development of noninvasive cancer diagnosis. Here we describe a chip-based method using nanostructured microelectrodes and electrochemical readout that confirms the identity of isolated CTCs and successfully interrogates them for specific biomarkers. We successfully analyze and classify prostate tumor cells, first in cultured cells, and ultimately in a pilot study involving blood samples from 16 prostate cancer patients as well as additional healthy controls. In all cases, and for all biomarkers investigated, the novel chip-based assay produced results that agreed with polymerase chain reaction (PCR). The approach developed has a simple workflow and scalable multiplexing, which makes it ideal for further studies of CTC biomarkers.
Circulating free DNA in the management of breast cancer. (2014)

Circulating cell-free DNA (cfDNA) is now under investigation as a "liquid biopsy" in the real time management of cancer. In The New England Journal of Medicine Dawson et al. reported a proof of concept investigation of tumour specific alterations in cfDNA and demonstrate that this fraction termed "circulating tumour DNA" (ctDNA) shows greater correlation with changes in tumour burden than two other circulating biomarkers (CA 15-3 and circulating tumor cell counts) in individuals with metastatic breast cancer receiving therapy.
Ectopic Fat in Insulin Resistance, Dyslipidemia, and Cardiometabolic Disease (2014)

The relationship between insulin resistance and visceral and muscle fat is complex. Recent research findings are unraveling some of the mysteries and suggesting therapeutic approaches to restoring insulin sensitivity.
Engineered herpes simplex virus 1 is dependent on IL13Rα2 receptor for cell entry and independent of glycoprotein D receptor interaction (2002)

In the first stage of engineering a herpes simplex virus (HSV)-1 that specifically targets human malignant glioma cells, we constructed a recombinant virus designated R5111 in which we have ablated the binding sites for sulfated proteoglycans in glycoproteins B and C, replaced the amino-terminal 148 aa in glycoprotein C by IL-13 flanked at its amino terminus with a signal peptide, and inserted a second copy of IL-13 after the amino acid 24 of glycoprotein D. In the process, the binding site for HveA, a viral entry receptor, was disrupted. We have also transformed a cell line (J1.1) lacking HSV-1 receptors to express IL13Ralpha2 receptor (J13R cells). We report the following: the R5111 recombinant virus replicates as well as wild-type virus in a variety of cell lines including cell lines derived from brain tumors. R5111 failed to replicate in the parent J1.1 cell line but multiplied to titers similar to those obtained in other cell lines in the J13R cell line. On the basis of the evidence that R5111 can use the IL13Ralpha2 receptor for entry, we conclude that HSV-1 can use receptors other than HveA or nectins, provided it can bind to them. The domains of gD that interact with HveA and nectin receptors are independent of each other. Lastly, the fusogenic activities of the glycoproteins in the viral envelope are not dependent on a set of unique interactions between glycoprotein D and its receptor. The construction of R5111 opens the way for construction of viruses totally dependent on selected receptors for entry or imaging of targeted cells.
Arterial Gene Transfer Using Pure DNA Applied Directly to a Hydrogel-Coated Angioplasty Balloon (1993)

Direct arterial gene transfer has been previously achieved using double-balloon catheters and perforated balloons, in most cases facilitated by the use of cationic liposomes or viral vectors. These gene delivery systems, however, have been compromised by issues relating to efficacy and/or safety, and furthermore require that angioplasty be performed independent of gene transfer. We investigated the possibility that arterial gene transfer might be performed during balloon angioplasty by delivery of naked genetic material from a thin coat of hydrogel polymer applied to a standard angioplasty balloon. Transfections with luciferase DNA applied to a hydrogel balloon were performed in rabbit arteries. Luciferase expression 3 days after transfection was tested in three different models: (i) an organ culture model (n = 10); (ii) surgically exposed carotid arteries (n = 14); and (iii) external iliac arteries using a percutaneous approach (n = 13). Supplementary transfections (n = 3), intended to identify the site of arterial transfection, were performed using the gene encoding for nuclear-specific beta-galactosidase (beta-gal). All rabbit arteries transfected with the luciferase gene (37/37; 100%) expressed luciferase activity. Gene expression achieved in vivo, either in the surgically exposed carotid arteries or in the external iliac arteries transfected percutaneously, was quantitatively similar to that achieved in the organ culture model. Reduction in the duration of inflation from 30 min to 1 min had no statistically significant impact on transfection efficiency. Gene expression was documented to persist up to 14 days post percutaneous transfection. Analysis of arteries transfected with nuclear-specific beta-gal showed the presence of the transgene in intimal and subintimal sites. These results demonstrate that vascular gene transfer can be performed successfully without liposomes or viral vectors using DNA applied to a standard angioplasty catheter balloon coated with hydrogel. Percutaneous transfection with a hydrogel-coated balloon permits gene transfer coincident with the angioplasty procedure itself, even with inflations as short as 1 min.
‘Interfacial buffer effect’ of self-assembled monolayers of a carboxylic acid terminated alkanethiol on a gold electrode (1994)

Assembled monolyers of a carboxylic acid terminated alkanethiol on a gold electrode have been found to show an ‘interfacial buffer effect’ on the redox reaction of a pH-dependent electroactive compound embedded in the monolayers.
Computational methods for detecting copy number variations in cancer genome using next generation sequencing: principles and challenges (2013)

Accurate detection of somatic copy number variations (CNVs) is an essential part of cancer genome analysis, and plays an important role in oncotarget identifications. Next generation sequencing (NGS) holds the promise to revolutionize somatic CNV detection. In this review, we provide an overview of current analytic tools used for CNV detection in NGS-based cancer studies. We summarize the NGS data types used for CNV detection, decipher the principles for data preprocessing, segmentation, and interpretation, and discuss the challenges in somatic CNV detection. This review aims to provide a guide to the analytic tools used in NGS-based cancer CNV studies, and to discuss the important factors that researchers need to consider when analyzing NGS data for somatic CNV detections.
Identification of a Novel Growth Factor-like Lipid, 1-O-cis-Alk-1′-enyl-2-lyso-sn-glycero-3-phosphate (Alkenyl-GP) That Is Present in Commercial Sphingolipid Preparations (1998)

Lysophosphatidic acid, a member of the acidic phospholipid autacoid (APA) family of lipid mediators, elicits diverse cellular effects that range from mitogenesis to the prevention of programmed cell death. Sphingosine 1-phosphate and sphingosylphosphorylcholine have also been proposed to be ligands of the APA receptors. However, key observations that provide the foundation of this hypothesis have not been universally reproducible, leading to a controversy in the field. We provide evidence that 1-O-cis-alk-1'-enyl-2-lyso-sn-glycero-3-phosphate (alkenyl-GP) is present in some commercial sphingolipid preparations and is responsible for many of their APA-like effects, which were previously attributed to sphingosylphosphorylcholine. Alkenyl-GP was generated by acidic and basic methanolysis from ethanolamine lysoplasmalogen, which was present in the sphingomyelin fraction that is used to manufacture sphingosylphosphorylcholine. We present the structural identification of alkenyl-GP, using 1H and 13C NMR, Fourier transform infrared spectrometry, and mass spectrometry. Alkenyl-GP was a potent activator of the mitogen-activated protein kinases ERK1/2 and elicited a mitogenic response in Swiss 3T3 fibroblasts. In contrast, sphingosylphosphorylcholine at a concentration of 10 microM was only a weak mitogen and only weakly activated the extracellular signal-regulated protein kinases. Alkenyl-GP has recently been detected as an injury-induced component in the anterior chamber of the eye (Liliom, K., Guan, Z., Tseng, H., Desiderio, D. M., Tigyi, G., and Watsky, M. (1998) Am. J. Physiol. 274, C1065-C1074), indicating that this lipid is a naturally occurring member of the APA mediator family.
Nanoporous Silicon Produced by Metal-Assisted Etching: A Detailed Investigation of Optical and Contact Properties for Solar Cells (2015)

We present a detailed investigation of the optical and contact quality of silicon wafers textured using metal-assisted etching (MAE) to produce a nanoporous silicon (nSi) surface. We show that the solar weighted reflectance (R <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">w</sub> ) of the bare optimized MAE nSi structure is only ~8%, and this is further reduced to 3% with the addition of an Al <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> O <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> /TiO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> stack. We also show that the optical path length enhancement can be >20 near the band edge of Si. The contact resistivity measurements of phosphorus-doped MAE nSi samples show that good contact can be made even on lightly doped samples, and we find no significant difference in contact quality between surfaces with different surface area enlargements (between ~2.2 and 2.7). This loosens constraints on finger width, helping to achieve reduced shading losses.
A 20 mA-receive 55 mA-transmit GSM transceiver in 0.25 μm CMOS (2003)

In a typical GSM handset, the battery takes as much as 20% of the cost, as well as volume and weight. Power consumption, which dictates the required battery size, is one of the most important considerations in design of transceiver ICs. Typical current consumption of BJT transceiver ICs reported in previous ISSCCs is 50 mA for 900 MHz GSM. This CMOS transceiver consumes less than 20 mA in the receive mode, despite the lower g/sub m//I ratio inherent to MOS transistors. Although external components are used where performance is critical, elimination of unnecessary passives makes their count low by present commercial standards. The receiver architecture is a single-IF (71MHz) superheterodyne, with interstage filter between the LNA and mixer for image reject and blocking performance. RF filter insertion losses make it necessary to have a LNA NF no more than 2dB and mixer NF no more than 15dB, to maintain 9dB overall receiver NF.
Adaptive Opto-Electronic Compensator for Excessive Filtering, Chromatic and Polarization Mode Dispersion (2005)

We propose an opto-electronic equalizer combining optical and electronic equalizers optimized jointly by the novel opto-electronic least mean squares algorithm. Through simulation, we demonstrate that it can efficiently compensate GVD, PMD and excessive optical filtering.
Patterning of Submicron Metal Features and Pillars in Multilevel Metallization (1988)

A novel multilevel interconnect scheme has been developed as part of an advanced submicron CMOS process technology. A salient feature of this interconnect scheme is the use of metal pillars for vertical connections between the devices on the substrate and the first level of metallization, as well as between successive levels of metallization, in place of the conventional etched contacts and vias. The pillar and conductor levels, with feature dimensions below 1 μm, were defined using contrast enhancement lithography and reactive ion etching. The application of these techniques to the definition of small and sparse photoresist features on an uneven metallic substrate and to the subsequent pattern transfer to the underlying metal films is described. The issues of surface topography and reflectivity, small‐area photoresist coverage, and dimension and profile control in the patterning of submicron features are addressed.
Potent, Selective and Orally Bioavailable Dihydropyrimidine Inhibitors of Rho Kinase (ROCK1) as Potential Therapeutic Agents for Cardiovascular Diseases (2008)

Recent studies using known Rho-associated kinase isoform 1 (ROCK1) inhibitors along with cellular and molecular biology data have revealed a pivotal role of this enzyme in many aspects of cardiovascular function. Here we report a series of ROCK1 inhibitors which were originally derived from a dihydropyrimidinone core 1. Our efforts focused on the optimization of dihydropyrimidine 2, which resulted in the identification of a series of dihydropyrimidines with improved pharmacokinetics and P450 properties.
Cloning and Expression of Two Human Lysophosphatidic Acid Acyltransferase cDNAs That Enhance Cytokine-Induced Signaling Responses in Cells (1997)

Lysophosphatidic acid (LPA) and phosphatidic acid (PA) are two phospholipids involved in signal transduction and in lipid biosynthesis in cells. LPA acyltransferase (LPAAT), also known as 1-acyl sn-glycerol-3-phosphate acetyltransferase (EC 2.3.1.51), catalyzes the conversion of LPA to PA. In this study, we describe the isolation and characterization of two human cDNAs that encode proteins possessing LPAAT activities. These two proteins, designated here as LPAAT-α and LPAAT-β, contain extensive sequence sequence similarities to microbial or plant LPAAT sequences. LPAAT-α mRNA was detected in all tissues with highest expression in skeletal muscle whereas LPAAT-β was expressed predominantly in heart and liver tissues. Expression of these two cDNAs in an Escherichia coli strain with a mutated LPAAT gene (plsC) complements its growth defect and shifts the equilibrium of cellular lipid content from LPA to PA and other lipids. Overexpression of these two cDNAs in mammalian cells leads to increased LPAAT activity in cell-free extracts using an in vitro assay that measures the conversion of fluorescently labeled LPA to PA. This increase in LPAAT activity correlates with enhancement of transcription and synthesis of tumor necrosis factor-α and interleukin-6 from cells upon stimulation with interleukin-1β, suggesting LPAAT overexpression may amplify cellular signaling responses from cytokines.
A Prospective Study of Omeprazole Suspension to Prevent Clinically Significant Gastrointestinal Bleeding from Stress Ulcers in Mechanically Ventilated Trauma Patients (1998)

In a prospective, evaluative study of 60 trauma patients who required mechanical ventilation and had at least one additional risk factor for stress ulcer development, omeprazole suspension prevented clinically significant gastrointestinal bleeding, maintained excellent control of gastric pH, produced no toxicity, and was the least costly medication alternative.
On deriving rules for nativised pronunciation in navigation queries (1999)

Navigation queries are typical examples of contexts in which a recognizer may have to deal with non-native names.In order to build a pronunciation lexicon with these names, special GtoP rules may be derived.The paper addresses this problem in the context of navigation queries in French including German names and viceversa.The special GtoP rules were mostly based on statistics derived from cross-lingual spoken corpora.