gebhart/patrepeval huggingface dataset:
The design of a data flow analyzer (1982)

This paper presents an efficient inter-procedural data flow analysis algorithm for precisely determining aliases in programs that employ a rich set of parameter passing mechanisms and pointer data types. This approach handles the use of pointers bounded to a data type as in Pascal, as well as unbounded pointers that can point to the same locations to which variables map. In the last step of this approach, the alias information is used to compute data flow information that is required for optimization.
Decision-feedback equalization for digital communication over dispersive channels. (1967)

In this report, a decision-theory approach to the problem of digital communication over known dispersive channels is adopted to arrive at the structures of the optimal and two sub-optimal receivers: the &amp;quot;conventional &amp;quot; and &amp;quot;decision-feedback &amp;quot; equal-izers, both employing matched and transversal filters. The conventional equalizer is similar to some equalization modems finding current application, while the new decision-feedback equalizer (as its name implies) utilizes its previous decisions in making a decision on the present baud. The parameters of these two equalizers are optimized under a criterion which min-imizes the sum of the intersymbol interference and additive noise distortions appear-ing at their outputs. Algorithms for evaluating the performances of the conventional and decision-feedback equalizers are developed, proving especially useful at high SNR where simulation techniques become ineffective. To determine the dependence of their performance and sidelobe-suppression properties upon SNR and transversal filter length, the new algorithms were used to study the
Neurologic symptoms after great saphenous vein harvesting for coronary artery bypass grafting. (2003)

This study demonstrates that saphenous neuralgia after harvesting the GSV for CABG is a rare consequence. The main symptom is anaesthesia but its duration is generally no longer than 2 months. Hyperaesthesia and pain, for the early onset and the early disappearance, are considered as a normal consequence of surgical procedure.
Arginyl and histidyl groups are essential for organic anion exchange in renal brush-border membrane vesicles. (1988)

The effect of side chain modification on the organic anion exchanger in the renal brush-border membrane was examined to identify what amino acid residues constitute the substrate binding site. One histidyl-specific reagent, diethyl pyrocarbonate (DEPC), and 2 arginyl-specific reagents, phenylglyoxal and 2,3-butanedione, were tested for their effect on the specifically mediated transport of p-amino[3H]hippurate (PAH), a prototypic organic anion. The specifically mediated transport refers to the difference in the uptake of [3H]PAH in the absence and presence of a known competitive inhibitor, probenecid, and was examined in brush-border membrane vesicles isolated from the outer cortex of canine kidneys. The experiments were performed utilizing a rapid filtration assay. DEPC, phenylglyoxal, and 2,3-butanedione inactivated the specifically mediated PAH transport, i.e. probenecid inhibitable transport with IC50 values of 160, 710, and 1780 microM, respectively. The rates of PAH inactivation by DEPC and phenylglyoxal were suggestive of multiple pseudo first-order reaction kinetics and were consistent with a reaction mechanism whereby more than 1 arginyl or histidyl residue is inactivated. Furthermore, PAH (5 mM) did not affect the rate of phenylglyoxal inactivation. In contrast, PAH (5 mM) affected the rate of DEPC inactivation. The modification by DEPC was specific for histidyl residues since transport could be restored by treatment with hydroxylamine. The results demonstrate that histidyl and arginyl residues are essential for organic anion transport in brush-border membrane vesicles. We conclude that the histidyl residue constitutes the cationic binding site for the anionic substrate, whereas the arginyl residue(s) serves to guide the substrate to or away from the histidyl site.
Adoptive Cell Therapy for Metastatic Melanoma (2017)

Adoptive cell therapy (ACT) of tumor-infiltrating lymphocytes (TILs) is a powerful form of immunotherapy by inducing durable complete responses that significantly extend the survival of melanoma patients. Mutation-derived neoantigens were recently identified as key factors for tumor recognition and rejection by TILs. The isolation of T-cell receptor (TCR) genes directed against neoantigens and their retransduction into peripheral T cells may provide a new form of ACT.Genetic modifications of T cells with chimeric antigen receptors (CARs) have demonstrated remarkable clinical results in hematologic malignancies, but are so far less effective in solid tumors. Only very limited reports exist in melanoma. Progress in CAR T-cell engineering, including neutralization of inhibitory signals or additional safety switches, may open opportunities also in melanoma.We review clinical results and latest developments of adoptive therapies with TILs, T-cell receptor, and CAR-modified T cells and discuss future directions for the treatment of melanoma.
Novel Splice Variants of ING4 and Their Possible Roles in the Regulation of Cell Growth and Motility (2006)

The ING4 gene is a candidate tumor suppressor gene that functions in cell proliferation, contact inhibition, and angiogenesis. We identified three novel splice variants of ING4 with differing activities in controlling cell proliferation, cell spreading, and cell migration. ING4_v1 (the longest splice variant), originally identified as ING4, encodes an intact nuclear localization signal (NLS), whereas the other three splice variants (ING4_v2, ING4_v3, and ING4_v4) lack the full NLS, resulting in increased cytoplasmic localization of these proteins. We found that one of the three ING4 variants, ING4_v2, is expressed at the same level as the original ING4 (ING4_v1), suggesting that ING4 variants may have significant biological functions. Growth suppressive effects of the variants that have a partial NLS (ING4_v2 and ING4_v4) were attenuated by a weaker effect of the variants on p21(WAF1) promoter activation. ING4_v4 lost cell spreading and migration suppressive effects; on the other hand, ING4_v2 retained a cell migration suppressive effect but lost a cell spreading suppressive effect. Therefore, ING4_v2, which localized primarily into cytoplasm, might have an important role in the regulation of cell migration. We also found that ING4_v4 played dominant-negative roles in the induction of p21(WAF1) promoter activation and in the suppression of cell motility by ING4_v1. In addition, ING4 variants had different binding affinities to two cytoplasmic proteins, protein-tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha1, and G3BP2a. Understanding the functions of the four splice variants may aid in defining their roles in human carcinogenesis.
High-quality MOSFETs with ultrathin LPCVD gate SiO/sub 2/ (1992)

MOSFETs and MOS capacitors with ultrathin (65 AA) low-pressure chemical vapor deposition (LPCVD) gate SiO/sub 2/ have been fabricated and compared to those with thermal SiO/sub 2/ of identical thickness. Results show that the devices with LPCVD SiO/sub 2/ have higher transconductance and current drivability, better channel hot-carrier immunity, lower defect density, and better time-dependent dielectric breakdown (TDDB) characteristics than devices with conventional thermal SiO/sub 2/.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Metabotropic Glutamate Receptor II in the Brains of Parkinsonian Patients (2009)

Modulation of basal ganglia group II metabotropic glutamate receptors (mGluR2/3) is a potential therapeutic alternative to levodopa in Parkinson disease (PD). We used receptor-binding autoradiography of the mGluR2/3-selective radioligand [H]LY341495 in postmortem brain specimens from PD patients (n = 14) and controls (n=11) to investigate possible contributions of changes in ligand binding of this receptor to levodopa-associated motor complications experienced premortem in PD patients. The PD patients included those with and without histories of dyskinesias and those with and without "wearing off," which is defined as a reduced period of benefit from levodopa. Specific binding of [H]LY341495 to mGluR2/3 in the basal ganglia was higher in the caudate nucleus than the putamen and lower by approximately half in the external and internal globus pallidus (GPi) in controls. [H]LY341495-specific binding was reduced in the caudate and GPi in patients without wearing-off (-22% caudate, -30% GPi), compared with controls and with patients who had experienced wearing-off; there were no differences among PD patients with or without dyskinesias. These data suggest that an adaptive downregulation of mGluR2/3 in PD patients without wearing-off may compensate for increased glutamate. They indicate a key role for mGluR2/3 in control of movement and the potential for mGluR2/3-targeted drugs in the management of wearing-off fluctuations in PD.
The ompA signal peptide directed secretion of Staphylococcal nuclease A by Escherichia coli. (1985)

The hybrid pre-enzyme formed by fusion of the signal peptide of the OmpA protein, a major outer membrane protein of Escherichia coli, to Staphylococcal nuclease A, a protein secreted by Staphylococcus aureus, is translocated across the cytoplasmic membrane of E. coli with concomitant cleavage of the signal peptide. A DNA fragment containing the coding sequence for the ompA signal peptide was initially ligated to a DNA fragment containing the coding sequence for nuclease A, with a linker sequence of 33 nucleotides separating the coding sequences. When this fused gene was induced, an enzymatically active nuclease was secreted into the periplasmic space; sequential Edman degradation of this protein revealed that the ompA signal peptide was removed at its normal cleavage site resulting in a modified version of the nuclease having 11 extra amino acid residues attached to the amino terminus of nuclease A. The 33 nucleotides between the coding sequences for the ompA signal peptide and the structural gene for nuclease A were subsequently deleted by synthetic oligonucleotide-directed site-specific mutagenesis. The nuclease produced by this hybrid gene was secreted into the periplasmic space and by sequential Edman degradation was identical to nuclease A. Thus, the ompA signal peptide is able to direct the secretion of fused staphylococcal nuclease A, and signal peptide processing occurs at the normal cleavage site. When the hybrid gene is expressed under the control of the lpp promoter, nuclease A is produced to the extent of 10% of the total cellular protein.
Cutaneous presentation of ALK-positive anaplastic large cell lymphoma following insect bites: evidence for an association in five cases (2009)

In these cases the sequence of events between the insect bites and the occurrence of both skin lesions and satellite lymphadenopathy suggest a direct relationship between the bite and the presentation with anaplastic large cell lymphoma. We postulate that insect bite-associated antigens could result in an influx of T lymphocytes, some bearing the t(2;5). The subsequent release of cytokines at the site of the bite could act as a 'second hit', eliciting activation of the latter cells, which would then express the oncogenic NPM-ALK protein and undergo uncontrolled proliferation.
COMMENTARY: Myotonic dystrophy reviewed: back to the future? (1994)

Journal Article COMMENTARY: Myotonic dystrophy reviewed: back to the future? Get access Bé Wieringa Bé Wieringa Department of Cell Biology and Histology, Faculty of Medical Sciences University of NijmegenThe Netherlands * To whom correspondence should be addressed Search for other works by this author on: Oxford Academic PubMed Google Scholar Human Molecular Genetics, Volume 3, Issue 1, January 1994, Pages 1–7, https://doi.org/10.1093/hmg/3.1.1-a Published: 01 January 1994 Article history Received: 01 November 1993 Accepted: 11 November 1993 Published: 01 January 1994
A 24-to-72GS/s 8b time-interleaved SAR ADC with 2.0-to-3.3pJ/conversion and >30dB SNDR at nyquist in 14nm CMOS FinFET (2018)

Optical communication standards, such as ITU OTU-4, OIF 112G and 100/400Gb/s Ethernet, require ADCs with more than 50GS/s and at least 5 ENOB to enable complex digital equalization, and a growing number of appropriate designs have been presented [1-4], mostly time-interleaved SAR ADCs. Most of these ADCs were not intended for input frequencies up to Nyquist and report an input range up to approximately 20GHz, often equivalent to the analog 3dB bandwidth. Ultimately, the analog bandwidth is less relevant than SNDR at high frequencies because an FIR filter can equalize amplitude degradation, but not increase SNDR. The design presented in this paper does not focus on the 3dB bandwidth, but it is optimized for best SNDR at the Nyquist frequency of up to 36GHz. Low power and area are critical for many applications and are achieved by an optimized SAR that allows low supply voltages while still maintaining high speed and accuracy. At 72GS/s, the ADC achieves 39.3dB at low input frequencies and 30.4dB at Nyquist. It consumes 235mW at 72GS/s and 97mW at 48GS/s, which results in 3.3pJ and 2.0pJ per conversion, respectively. The ADC is implemented in an area of 0.15mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> in 14nm CMOS FinFET technology.
Identification of phosphates involved in catalysis by the ribozyme RNase P RNA. (1995)

The RNA subunit of ribonuclease P (RNase P RNA) is a catalytic RNA that cleaves precursor tRNAs to generate mature tRNA 5' ends. Little is known concerning the identity and arrangement of functional groups that constitute the active site of this ribozyme. We have used an RNase P RNA-substrate conjugate that undergoes rapid, accurate, and efficient self-cleavage in vitro to probe, by phosphorothioate modification-interference, functional groups required for catalysis. We identify four phosphate oxygens where substitution by sulfur significantly reduces the catalytic rate (50-200-fold). Interference at one site was partially rescued in the presence of manganese, suggesting a direct involvement in binding divalent metal ion cofactors required for catalysis. All sites are located in conserved sequence and secondary structure, and positioned adjacent to the substrate phosphate in a tertiary structure model of the ribozyme-substrate complex. The spatial arrangement of phosphorothioate-sensitive sites in RNase P RNA was found to resemble the distribution of analogous positions in the secondary and potential tertiary structures of other large catalytic RNAs.
Anthrax Toxin: Causative Agent in the Death of Rhesus Monkeys (1962)

Anthrax toxin was present in the blood obtained from rhesus monkeys at the terminal stage of anthrax and was also present in increasing amounts in the lymph as death approached. When sterile toxin produced in vitro was injected in sufficient amounts, monkeys died unless they were injected with specific antiserum. Death with symptoms of toxemia occurred within 2 hours after injection of 10(11) spores, whereas 10(10) spores or less required 20 or more hours of growth in vivo to cause death.
Cadherin‐catenin complex: Protein interactions and their implications for cadherin function (1996)

Cadherins comprise a family of calcium-dependent glycoproteins that function in mediating cell-cell adhesion in virtually all solid tissues of multicellular organisms. In epithelial cells, E-cadherin represents a key molecule in the establishment and stabilization of cellular junctions. On the cellular level, E-cadherin is concentrated at the adherens junction and interacts homophilically with E-cadherin molecules of adjacent cells. Significant progress has been made in understanding the extra- and intracellular interactions of E-cadherin. Recent success in solving the three-dimensional structure of an extracellular cadherin domain provides a structural basis for understanding the homophilic interaction mechanism and the calcium requirement of cadherins. According to the crystal structure, individual cadherin molecules cooperate to form a linear cell adhesion zipper. The intracellular anchorage of cadherins is regulated by the dynamic association with cytoplasmic proteins, termed catenins. The cytoplasmic domain of E-cadherin is complexed with either β-catenin or plakoglobin (γ-catenin). β-catenin and plakoglobin bind directly to α-catenin, giving rise to two distinct cadherin-catenin complexes (CCC). α-catenin is thought to link both CCC's to actin filaments. The anchorage of cadherins to the cytoskeleton appears to be regulated by tyrosine phosphorylation. Phosphorylation-induced junctional disassembly targets the catenins, indicating that catenins are components of signal transduction pathways. The unexpected association of catenins with the product of the tumor suppressor gene APC has led to the discovery of a second, cadherin-independent catenin complex. Two separate catenin complexes are therefore involved in the cross-talk between cell adhesion and signal transduction. In this review we focus on protein interactions regulating the molecular architecture and function of the CCC. In the light of a fundamental role of the CCC during mammalian development and tissue morphogenesis, we also discuss the phenotypes of embryos lacking E-cadherin or β-catenin. © 1996 Wiley-Liss, Inc.
End-to-End Weakly-Supervised Semantic Alignment (2018)

We tackle the task of semantic alignment where the goal is to compute dense semantic correspondence aligning two images depicting objects of the same category. This is a challenging task due to large intra-class variation, changes in viewpoint and background clutter. We present the following three principal contributions. First, we develop a convolutional neural network architecture for semantic alignment that is trainable in an end-to-end manner from weak image-level supervision in the form of matching image pairs. The outcome is that parameters are learnt from rich appearance variation present in different but semantically related images without the need for tedious manual annotation of correspondences at training time. Second, the main component of this architecture is a differentiable soft inlier scoring module, inspired by the RANSAC inlier scoring procedure, that computes the quality of the alignment based on only geometrically consistent correspondences thereby reducing the effect of background clutter. Third, we demonstrate that the proposed approach achieves state-of-the-art performance on multiple standard benchmarks for semantic alignment.
Transgenic animals in biomedical research (1991)

The advent of transgenic technology, in which foreign genetic information is stably introduced into the mammalian germ line, has dramatically enhanced our basic knowledge of physiologic and pathologic processes. Transgenic animals created by these genetic manipulations are being used to provide insights into gene regulation, development, pathogenesis, and the treatment of disease. Furthermore, transgenic biotechnology holds great promise for the creation of genetically superior livestock and the industrial production of precious pharmaceuticals. It is evident now that the study and use of transgenic animals will significantly improve the human condition.
Molecular Heterogeneity Has a Major Impact on the Measurement of Circulating N-Terminal Fragments of A- and B-Type Natriuretic Peptides (2004)

Molecular heterogeneity of the circulating forms causes a serious risk of preanalytical errors in assays for NT-proBNP and, to a lesser extent, NT-proANP. The development of a sandwich assay for NT-proBNP would be especially challenging. The most robust and reliable assays use antibodies directed at the central portions of NT-proANP or NT-proBNP.
Copper interconnection deposition techniques and integration (2002)

Copper has been deposited into prepatterned high-aspect-ratio (3:1) trenches using electroplating (EP), CVD and sputter reflow. Filling capability, electrical properties, electromigration lifetimes and mechanical stress are examined. Also, barriers against Cu diffusion are studied using electrical bias at elevated temperatures. CVD Cu can fill high aspect ratio features that electroplating cannot. Sputter-reflowed Cu can also fill high aspect ratio features, but has a high thermal budget for features >0.4 /spl mu/m. Preliminary results show that CVD Cu may be limited by electromigration lifetime.
Sequence analysis of a functional polymerase (L) gene of bovine respiratory syncytial virus: determination of minimal trans-acting requirements for RNA replication. (1998)

The complete nucleotide sequence of a functional clone of the large polymerase (L) gene of bovine respiratory syncytial virus (BRSV) strain A51908 was determined by analysis of cloned cDNAs obtained from genomic and mRNAs. The BRSV L gene is 6573 nt in length and the derived polypeptide has 2162 aa. Alignment of the sequences of the BRSV L gene, and its encoded protein, with sequences of the L gene and protein of human respiratory syncytial virus strain A2 showed 77% identity at the nucleotide level and 84% identity at the amino acid level. By comparison, the L gene and protein of avian pneumovirus showed only 50% identity at the nucleotide level and 64% identity at the amino acid level. A minigenome was constructed to encode a BRSV vRNA analogue containing the gene for chloramphenicol acetyltransferase (CAT) under the control of putative BRSV transcription motifs and flanked by the BRSV genomic termini. Transfection of plasmids encoding the BRSV minigenome, nucleocapsid protein (N), phosphoprotein (P) and L protein, each under the control of T7 promoter, into cells infected with a vaccinia virus recombinant expressing the T7 RNA polymerase gave rise to CAT activity and progeny with the minigenome. This result indicates that the N, P and L proteins are necessary and sufficient for transcription and replication of the BRSV minigenome and are functional. Further, inclusion of small amounts of the M2 protein along with the N, P and L proteins greatly augmented minigenome transcription.
De novo maintenance therapy with denileukin diftitox (Ontak®) in a patient with peripheral T‐cell lymphoma is associated with prolonged remission (2008)

Peripheral T-cell lymphoma (PTCL) is an aggressive form of non-Hodgkin's lymphoma (NHL), associated with poor prognosis and without standard approach to treatment. Denileukin diftitox (Ontak) is a synthetic fusion protein combining the receptor-binding domain of interleukin-2 to the enzymatically active portion of diphtheria toxin. While approved for the treatment of cutaneous T-cell lymphoma, it has demonstrated activity in non-Hodgkin's lymphomas of both T-cell and B-cell origin. This report documents the first case of de novo maintenance therapy with denileukin diftitox sustaining an ongoing complete response at the molecular level for 2 years in a patient with PTCL.
Abundant calcitonin receptors in isolated rat osteoclasts. Biochemical and autoradiographic characterization. (1986)

Calcitonin receptors have been characterized for the first time in isolated osteoclasts. These receptors have been demonstrated by autoradiographic and biochemical methods, and the cells have also been shown to respond to calcitonin with a dose-dependent increase in cyclic AMP. The receptors in rat osteoclasts are specific and of high affinity (dissociation constant, Kd, 1 to 6 X 10(-10) M), and are present in greater numbers than in any cell previously studied (greater than 10(6) per cell). Chemical cross-linking of 125I-labeled salmon calcitonin to osteoclasts using disuccinimidyl suberate resulted in identification of a receptor component with a relative molecular weight of 80,000-90,000. By counting grains in autoradiographic experiments, we found that greater than 80% of specifically bound radioactivity was associated with multinucleate osteoclasts and the remainder was associated with mononuclear cells that are not osteoblasts, but that may be osteoclast precursors.