gebhart/patrepeval huggingface dataset:
Selective code transformation for dual instruction set processors (2007)

Embedded systems are often constrained in terms of both code size and execution time, because of a limited amount of available memory and real-time nature of applications. A dual instruction set processor, which supports a reduced instruction set (16 bits/instruction), in addition to a full instruction set (32 bits/instruction), allows an opportunity for a tradeoff between these two design criteria. Specifically, while the reduced instruction set can be used to reduce code size by providing smaller instructions, a program compiled into the reduced instruction set typically runs slower than the same program compiled into the full instruction set. Motivated by this observation, we propose a code generation technique that exploits this tradeoff relationship by selectively using the two instruction sets for different sections in the program. The proposed technique, called selective code transformation, not only provides a mechanism to enable a flexible tradeoff between a program's code size and its execution time, but also facilitates program optimization toward enhancing its worst case performance. The results from our experiments show that our proposed technique can be effectively used to fine-tune an application program on a spectrum of code size and execution performance, which, in turn, enables a system-wide optimization on memory space and execution speed involving multiple applications.
T-cell Immunometabolism: Therapeutic Implications in Organ Transplantation (2021)

Although solid-organ transplantation has evolved steadily with many breakthroughs in the past 110 y, many problems remain to be addressed, and advanced therapeutic strategies need to be considered. T-cell immunometabolism is a rapidly advancing field that has gathered much attention recently, providing ample mechanistic insight from which many novel therapeutic approaches have been developed. Applications from the field include antitumor and antimicrobial therapies, as well as for reversing graft-versus-host disease and autoimmune diseases. However, the immunometabolism of T cells remains underexplored in solid-organ transplantation. In this review, we will highlight key findings from hallmark studies centered around various metabolic modes preferred by different T-cell subtypes (categorized into naive, effector, regulatory, and memory T cells), including glycolysis, glutaminolysis, oxidative phosphorylation, fatty acid synthesis, and oxidation. This review will discuss the underlying cellular signaling components that affect these processes, including the transcription factors myelocytomatosis oncogene, hypoxia-inducible factor 1-alpha, estrogen-related receptor alpha, and sterol regulatory element-binding proteins, along with the mechanistic target of rapamycin and adenosine monophosphate-activated protein kinase signaling. We will also explore potential therapeutic strategies targeting these pathways, as applied to the potential for tolerance induction in solid-organ transplantation.
Cloning of a gamma-aminobutyric acid type C receptor subunit in rat retina with a methionine residue critical for picrotoxinin channel block. (1995)

Ionotropic receptors for gamma-aminobutyric acid (GABA) are important to inhibitory neurotransmission in the mammalian retina, mediating GABAA and GABAC responses. In many species, these responses are blocked by the convulsant picrotoxinin (PTX), although the mechanism of block is not fully understood. In contrast, GABAC responses in the rat retina are extremely resistant to PTX. We hypothesized that this difference could be explained by molecular characterization of the receptors underlying the GABAC response. Here we report the cloning of two rat GABA receptor subunits, designated r rho 1 and r rho 2 after their previously identified human homologues. When coexpressed in Xenopus oocytes, r rho 1/r rho 2 heteromeric receptors mimicked PTX-resistant GABAC responses of the rat retina. PTX resistance is apparently conferred in native heteromeric receptors by r rho 2 subunits since homomeric r rho 1 receptors were sensitive to PTX; r rho 2 subunits alone were unable to form functional homomeric receptors. Site-directed mutagenesis confirmed that a single amino acid residue in the second membrane-spanning region (a methionine in r rho 2 in place of a threonine in r rho 1) is the predominant determinant of PTX resistance in the rat receptor. This study reveals not only the molecular mechanism underlying PTX blockade of GABA receptors but also the heteromeric nature of native receptors in the rat retina that underlie the PTX-resistant GABAC response.
Multi-agent control system for a municipal water system (2006)

Abstract. The control system for a municipal water system needs to meet the criteria of maintaining continuity and reliability in the water supply for satisfying the consumer demand while saving the energy costs and maintaining the quality of water. In this paper, we propose an intelligent agent system for a municipal water system. This work shows the benefits of using the agent-based approach in handling different scenarios including the uncertain behavior of the system. A distributed control strategy is implemented and promising results are evaluated in a simulation of a water distribution system.
Performance evaluation of four-layer DOI detectors using multi-pixel photon counter arrays (2010)

Multi-pixel photon counters (MPPC) have many advantages for PET detectors, such as high internal gain, high photon detection efficiency, lower power supply and insensitivity to magnetic fields. However, the saturation effect is unavoidable phenomenon for PET detectors using MPPCs which need to collect large number of scintillation photons to achieve high energy and timing resolutions. In a lot of cases, pulse height of PET detectors using MPPCs are saturated in high energy region. On the other hand, since our DOI encoding method previously presented is sharing scintillation photons to multiple pixels, the saturation effect can be suppressed. We constructed prototype four-layer detectors using two MPPC arrays and evaluated their detector performances. We constructed the prototype detector consisting of four layers of a 6 × 6 array of Lu <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2(1-x)</sub> Y <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2x</sub> SiO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">5</sub> (LYSO) (Lu: 98%, Y: 2%) crystals (Proteus Inc., U. S. A.), and a MPPC array of 4 × 4 pixels (S11064 series, Hamamatsu Photonics K.K.). The size of each crystal element was 1.46 mm × 1.46 mm × 4.5 mm and all surfaces of crystal elements were chemically etched. For comparison, the two types of MPPC, S11064-050P (3600 cells) and S11064-025P (14400 cells), were used in the experiment. As a result, the all of the crystals of the detector using 050P were clearly identified while the crystal identification performance of the detector using 025P was degraded due to lower photon detection efficiency. The energy resolution of 11.0-13.6% (050P) and 12.7-15.2% (025P) were achieved. No saturations were observed for both detectors under the 511keV energy region.
Water‐Based Single‐Walled‐Nanotube‐Filled Polymer Composite with an Exceptionally Low Percolation Threshold (2004)

An emulsion polymer (i.e., latex) has been used as the polymer matrix starting material in order to lower the percolation threshold of single‐walled‐carbon‐nanotube (SWNT)‐filled polymer composites (e.g., see Figure). A percolation threshold below 0.04 wt.‐% SWNT is achieved. This composite system offers the potential for conductive polymers that are relatively inexpensive, mechanically robust, environmentally stable, and easy to process.
GWAS Meets TCGA to Illuminate Mechanisms of Cancer Predisposition (2013)

Genome-wide association studies (GWASs) have unraveled a large number of cancer risk alleles. Understanding how these allelic variants predispose to disease is a major bottleneck confronting translational application. In this issue, Li and colleagues combine GWASs with The Cancer Genome Atlas (TCGA) to disambiguate the contributions of germline and somatic variants to tumorigenic gene expression programs. They find that close to half of the known risk alleles for estrogen receptor (ER)-positive breast cancer are expression quantitative trait loci (eQTLs) acting upon major determinants of gene expression in tumors.
Salvaging the endothelium in acute respiratory distress syndrome: a druggable intersection between TLR4 and NAD+signalling (2021)

The acute respiratory distress syndrome (ARDS) remains an intractable problem for intensivists, even with advancements in critical care and mechanical ventilation. Mortality rates in ARDS patients are around 35–45% [1]. However, these mortality numbers represent a conservative estimate of the ARDS healthcare impact, because survivors exhibit staggering rates of morbidity and mortality in the aftermath of their intensive care unit (ICU) stay, including neurocognitive dysfunction that can prohibit the return to activities of daily living [2, 3]. Development of medical therapies that improve both the short- and long-term outcomes of these critically ill patients remain an urgent unmet need. eNAMPT neutralisation may be effective treatment in acute respiratory distress syndrome <https://bit.ly/3oaES9c> We thank Raymond Langley for his helpful discussions regarding the circulating metabolome in sepsis.
Highly Linear 60-GHz SiGe Downconversion/Upconversion Mixers (2017)

A linear RF to IF downconversion and IF to RF upconversion mixers for 60-GHz transceivers were implemented in 0.13-μm SiGe technology. The mixers were implemented using a mixing core only topology for enhanced linearity, with no local oscillator (LO) buffers and a transformer-based matching network for IF frequencies. The downconversion mixer at full attenuation shows a minimum of 10-dBm IIP3 and maximum measured loss of 6.5 dB within the entire 57-66 GHz frequency band. Without attenuation, the conversion gain is above 4 dB, with better than 2-dBm IIP3 and a noise figure maximum value of 14 dB within the band. The transmit mixer exhibits less than 2.5-dB conversion loss, better than 7.5-dBm OIP3 with minimal temperature variations. For improved LO to RF isolation, separated dc bias control is used in the mixing devices providing over 46-dBc LO suppression within the band. The mixers occupy only 0.47 and 0.22 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> consuming 56 mW for downconversion mixer with IF amplifier and 27 mW for upconversion mixer.
Novel S1P1 Receptor Agonists − Part 3: From Thiophenes to Pyridines (2013)

In preceding communications we summarized our medicinal chemistry efforts leading to the identification of potent, selective, and orally active S1P1 agonists such as the thiophene derivative 1. As a continuation of these efforts, we replaced the thiophene in 1 by a 2-, 3-, or 4-pyridine and obtained less lipophilic, potent, and selective S1P1 agonists (e.g., 2) efficiently reducing blood lymphocyte count in the rat. Structural features influencing the compounds’ receptor affinity profile and pharmacokinetics are discussed. In addition, the ability to penetrate brain tissue has been studied for several compounds. As a typical example for these pyridine based S1P1 agonists, compound 53 showed EC50 values of 0.6 and 352 nM for the S1P1 and S1P3 receptor, respectively, displayed favorable PK properties, and penetrated well into brain tissue. In the rat, compound 53 maximally reduced the blood lymphocyte count for at least 24 h after oral dosing of 3 mg/kg.
Modelling and practical iterative mitigation of phase noise in SC-FDMA (2012)

This paper addresses the modelling, and practical estimation and mitigation of phase noise in single-carrier frequency division multiple access (SC-FDMA) systems. Special emphasis is kept on 3GPP Long Term Evolution signals. First, new way to model the phase noise effect in SC-FDMA is given and the phase noise effect is analysed based on it. Then, practical (based on practical signals and signalling environment) phase-noise estimation algorithm and a way to mitigate the effects are proposed. The performance of the algorithm is studied in practical extended ITU-R Vehicular A multipath channel and with both free-running oscillator and phase-locked-loop oscillator models.
<title>Novel video-processing schemes integrating image compression and pattern recognition</title> (1997)

In comparison to present security applications, pattern recognition techniques can be categorized as 'hard' automatic target recognition (ATR) and 'soft' ATR. The first category has been established for years and deals with specific object recognition. On the other hand, the second, less established category operates on very fast object class-level recognition only. The second category usually employs very fast processing and an image database. In this paper, we introduce a novel method to integrate a compression technique based on logic data representation with soft ATR. This new compression method applies Arnold's Differential Mapping Singularities Theory in the context of 3D object projection into the 2D image plane, and takes advantage of the fact that object edges can be interpreted in terms of singularities, which can be described isomorphically by simple polynomials. Therefore, compared to state- of-the-art still image compression, such as JPEG, there is no information los in high contrast, high-dynamic range image areas; as a result, the global peak signal noise ratio can be very high By using linked edges to represent an object, it is possible to use a simple set of parameters for real-time 'soft' ATR. This publication discuses various security applications of this new scheme, which is integrated with ATR compression.
A processed human immunoglobulin epsilon gene has moved to chromosome 9. (1982)

Processed genes--genes that resemble processed RNA transcripts rather than interrupted genomic sequences--have been identified as dispersed members of several gene families. Here we describe a processed gene that is one of the three human IgE-like sequences present in the human genome. The processed IgE gene has precisely lost its three intervening sequences, thereby fusing its four coding domains. The homology of the gene to its functional counterpart ends in an adenine-rich tail followed by an 11-base-pair sequence that is directly repeated 150 base pairs 5' to its first coding domain. In addition, the processed gene is located on human chromosome 9 rather than on chromosome 14, the site of the active immunoglobulin locus. The structure and evident mobility of this sequence support the concept that sequences can move about in the genome via RNA intermediates and that processed genes are a prominent feature of genomic structure.
A review of clinicopathologic characteristics, therapy, and outcomes of 22 patients with aggressive B-cell lymphoma. (2012)

e21123 Background: B cell lymphoma, unclassifiable, with features intermediate between diffuse large B cell lymphoma (DLBCL) and Burkitt lymphoma (BL) or Burkitt like lymphoma is a high grade lymphoma that is associated with a high proliferation index and a complex karyotype mostly involving MYC and BCL-2 genes, so called “double hit” as well as BCL-6 or CYCLIND1 genes, so called “triple hit”. This high grade lymphoma shows an aggressive behavior for which the most appropriate therapeutic approach is yet to be established. Methods: This was a single center retrospective review of pts with a confirmed diagnosis of B cell lymphoma, unclassifiable, with features intermediate between DLBCL and BL from 2006 to 2011. The definitive diagnosis in all cases was based on morphological and phenotypic features, and genetic abnormalities involving MYC, BCL-2, BCL-6, and or CYCLIND1. Clinicopathological data was extracted including age, gender, primary disease location, phenotypic subtype, genetic abnormalities by FISH, IPI scores, treatment regimens and survival data . Descriptive statistical analyses were utilized. Kaplan-Meier method was used to estimate OS and log rank test was used to compare the groups. All data were analyzed using SPSS version 20.0 statistical software. Results: 22 pts with &amp;quot;Double or Triple Hit&amp;quot; lymphomas were identified between 2006 and 2011. The age range at diagnosis was 33-87 years with median age of 66. 16 of 22 pts (73%) were ≥ 60 years old. Male to female ratio was 1.75 :1 (14:8). The median ECOG PS was 1. No pts had HIV. A majority of pts presented with extranodal disease 17 with only 5 pts presenting with nodal disease. The median survival of the entire cohort was 9 months with ranges 32 to 2 months. 16 of 22 pts (73%) are currently alive. In the cohort of pts that are currently alive, 10 was treated with RCHOP and 6 with RHyperCVAD. Pts who presented with CNS disease had a worse prognosis when compared to the entire cohort with a median overall survival of 6.5 months (p=0.016). Conclusions: RCHOP was the most utilized treatment regimen in the cohort of alive patients. CNS disease is associated with worse prognosis in patients with &amp;quot;Double or Triple Hit&amp;quot; lymphomas.
High dynamic range, cascaded-focus nanosecond optical limiter (2000)

Optical limiters are devices used to protect sensitive detection components from damage against intense light
Inhibition of human natural killing by heterologous and monoclonal antibodies. (1982)

Abstract Heterologous rat antiserum (as well as the IgG and Fab2 fragments) made against NalO4-treated alloimmune human cytotoxic lymphocytes (termed RH2) is a potent inhibitor of NK cytolysis using Molt-4 or K562 target cells. Inhibition was not due to trivial mechanisms such as serum toxicity, lymphocyte or target cell agglutination, or precipitation of chromium-labeled proteins released from dead targets. Inhibition was demonstrated initially at the level of the effector NK cells because 1) Molt-4 target cells could not absorb out blocking activity; 2) Percoll-fractionated large granular lymphocytes (LGL) enriched in NK cytolytic activity removed the blocking activity of RH2 antibody more effectively than Percoll fractions depleted of cytolytic NK activity; 3) RH2 blocked cytolysis in a single cell assay in which NK target conjugates are formed before the addition of the antibody; and 4) RH2 inhibited NK cytolysis when added at the CA++-dependent "programming" step without dissociating the bound targets. Finally, the addition of RH2 to "programmed" targets during the killer cell-independent step of NK lysis (KCIL) inhibited 51Cr release. Thus, while initial blocking was at the level of the effector NK cell, inhibition during KCIL was at the level of the target, suggesting transfer of the moieties was important for cytolysis. Monoclonal antibodies that were also capable of inhibiting NK cytolysis were prepared by fusion of immune rat spleen cells and SP 2/0 myeloma cells. Two antibodies (termed RH 7.2 and 17.2) inhibited 51Cr release when added at the Ca++ pulse. Furthermore, 7.2 but not 17.2 inhibited binding of NK cells to Molt-4 or K562 targets sugesting binding and cytolysis may occur through related or closely associated structures present on the NK cell surface. The relationship of these finidings to the overall cytolytic reaction mechanism of the NK cell is discussed.
Interactive illustrations for visualizing complex three-dimensional objects (2008)

Illustrations are essential for conveying the internal structure of complex 3D objects. This dissertation describes techniques for creating and viewing interactive digital illustrations that use dynamic cutaway and exploded views to expose important internal parts, while retaining enough context from surrounding structures to help the viewer mentally reconstruct the object. I incorporate these techniques in three prototype illustration systems: the 3D cutaway views system generates dynamic, browsable cutaway illustrations from 3D input models; the image-based exploded views system converts static 2D exploded views into interactive 2.5D illustrations; and the 3D exploded views system generates interactive exploded views from 3D models. 
The contributions of my work include a formal survey of illustration conventions for creating effective cutaways and exploded views, as well as new algorithmic encodings of these conventions that enable interactive tools for cutting and exploding 3D objects. I also describe techniques for authoring and viewing interactive illustrations. Overall, my work demonstrates that with the right set of tools, it is possible and practical to create interactive cutaway and exploded view illustrations that offer a compelling and dynamic viewing experience.
Mutations in Two Short Noncoding Mononucleotide Repeats in Most Microsatellite-Unstable Colorectal Cancers (2005)

DNA mismatch repair (MMR)-deficient cells typically accumulate mutations in short repetitive DNA tracts. This microsatellite instability (MSI) facilitates malignant transformation when affecting genes with growth-related and caretaker functions. To date, several putative MSI target genes have been proposed mainly based on high mutation frequency within their coding regions. However, some intronic repeat mutations have also been suggested to associate with MSI tumorigenesis, indicating the need for additional analyses on noncoding repeats. Here we have analyzed an intronic T9 repeat of semenogelin I (SEMG1) and report mutation frequencies of 51% (75 of 146) and 62% (8 of 13) in MMR-deficient primary colorectal cancers and cell lines, respectively. The putative effect of the SEMG1 mutations was assessed by RNA and protein level analyses, but no differences were detected between colorectal cancer cell lines with different SEMG1 status. Subsequently, the general background mutation frequency of MSI colorectal cancers was assessed by screening for intergenic T9 repeat alterations. One of 10 examined repeats was mutated in 70% (102 of 145) of the colorectal cancers evaluated. The frequencies observed here are notably higher than previously published in noncoding repeats shorter than 10 bp in MMR-deficient primary tumors. Our results indicate that high mutation frequencies, similar or higher than those observed in proposed and approved target genes, can be detected in repeat tracts of MSI tumors without any apparent selection pressure. These data call for urgent and thorough large-scale evaluation of mutation frequencies in neutral short repetitive sequences in MMR-deficient tumors.
Occurrence of Free d -Amino Acids and Aspartate Racemases in Hyperthermophilic Archaea (1999)

The occurrence of free D-amino acids and aspartate racemases in several hyperthermophilic archaea was investigated. Aspartic acid in all the hyperthermophilic archaea was highly racemized. The ratio of D-aspartic acid to total aspartic acid was in the range of 43.0 to 49.1%. The crude extracts of the hyperthermophiles exhibited aspartate racemase activity at 70 degrees C, and aspartate racemase homologous genes in them were identified by PCR. D-Enantiomers of other amino acids (alanine, leucine, phenylalanine, and lysine) in Thermococcus strains were also detected. Some of them might be by-products of aspartate racemase. It is proven that D-amino acids are produced in some hyperthermophilic archaea, although their function is unknown.