gebhart/patrepeval huggingface dataset:
The Berkeley Out-of-Order Machine (BOOM): An Industry-Competitive, Synthesizable, Parameterized RISC-V Processor (2015)

Abstract : BOOM is a synthesizable, parameterized, superscalar out-of-order RISC-V core designed to serve as the prototypical baseline processor for future micro-architectural studies of out-of-order processors. Our goal is to provide a readable, open-source implementation for use in education, research, and industry. BOOM is written in roughly 9,000 lines of the hardware construction language Chisel. We leveraged Berkeleys open-source Rocket-chip SoC generator, allowing us to quickly bring up an entire multi-core processor system (including caches and uncore) by replacing the in-order Rocket core with an out-of-order BOOM core. BOOM supports atomics, IEEE754-2008 floating-point, and page-based virtual memory. We have demonstrated BOOM running Linux, SPEC CINT2006, and CoreMark.
Flutamide, Testolactone, and Reduced Hydrocortisone Dose Maintain Normal Growth Velocity and Bone Maturation Despite Elevated Androgen Levels in Children with Congenital Adrenal Hyperplasia (2000)

Treatment outcome in congenital adrenal hyperplasia is often sub-optimal due to hyperandrogenism, treatment-induced hypercortisolism, or both. We previously reported better control of linear growth, weight gain, and bone maturation in a short term cross-over study of a new four-drug treatment regimen containing an antiandrogen (flutamide), an inhibitor of androgen to estrogen conversion (testolactone), reduced hydrocortisone dose, and fludrocortisone, compared to the effects of a control regimen of hydrocortisone and fludrocortisone. Twenty-eight children have completed 2 yr of follow-up in a subsequent long term randomized parallel study comparing these two treatment regimens. During 2 yr of therapy, compared to children receiving hydrocortisone, and fludrocortisone treatment, children receiving flutamide, testolactone, reduced hydrocortisone dose (average of 8.7 +/- 0.6 mg/m2 x day), and fludrocortisone had significantly (P < or = 0.05) higher plasma 17-hydroxyprogesterone, androstenedione, dehydroepiandrosterone, dehydroepiandrosterone sulfate, and testosterone levels. Despite elevated androgen levels, children receiving the new treatment regimen had normal linear growth rate (at 2 yr, 0.1 +/- 0.5 SD units), and bone maturation (at 2 yr, 0.7 +/- 0.3 yr bone age/yr chronological age). No significant adverse effects were observed after 2 yr. We conclude that the regimen of flutamide, testolactone, reduced hydrocortisone dose, and fludrocortisone provides effective control of congenital adrenal hyperplasia with reduced risk of glucocorticoid excess. A long term study of this new regimen is ongoing.
Windows 2000 Disk IO Performance (2000)

This paper is an empirical study of the random and sequential I/O performance of Windows 2000 using the NT File System. It continues the work done by Riedel, et. al. in their 1997 paper exploring sequential IO performance under Windows NT 4.0. This paper explores the performance and overhead of today&amp;apos;s Intel Pentium III based memory and IO subsystems, including the processor bus, the PCI bus, the disk controllers, the SCSI and IDE buses, and the disk media. It also examines the performance available from IDE RAID, a relatively new technology built from inexpensive IDE disks. Network IO performance is briefly covered. We describe how to achieve good throughput, and discuss the major bottlenecks. While Riedel&amp;apos;s model of software performance remains largely unchanged, increases in hardware performance have made the 32bit, 33MHz PCI bus the dominant bottleneck reaching saturation with three disks.
Advances in Neuroendoscopy (1994)

Department of Neurosurgery, University of Cincinnati College of Medicine, 231 Bethesda Avenue, P.O. Box 670515, Cincinnati, OH 45267–0515
The simian T-lymphotropic/leukemia virus from Pan paniscus belongs to the type 2 family and infects Asian macaques (1997)

The proviral DNA of the simian T-leukemia/lymphotropic virus (STLV) isolate, originally obtained from a captive colony of pygmy chimpanzees (Pan paniscus) (STLV(pan-p)), was cloned from the DNA of the chronically infected human T-cell line L93-79B. The entire proviral DNA sequence was obtained and compared with sequences of the known genotypes of STLV and human T-leukemia/lymphotropic virus types 1 and 2 (HTLV-1 and -2). Phylogenetic analysis indicates that STLV-2(pan-p) is an early divergence within the type 2 lineage and should be referred to as STLV-2(pan-p). Since STLV-2(pan-p) has been found in African nonhuman primates, we investigated its infectiousness and pathogenicity in Asian monkeys. Pigtailed macaques were inoculated with human cells harboring STLV(pan-p), and infection was assessed by virus isolation, PCR analysis of peripheral blood mononuclear cells, and seroconversion against viral antigens in HTLV-1/HTLV-2 and Western blot assay. Pigtailed macaques became persistently infected by STLV-2(pan-p), and the virus could be transferred by blood transfusion from an infected pigtailed macaque to a rhesus macaque. In addition, like HTLV-1 and HTLV-2, STLV-2(pan-p) was infectious in rabbits. In summary, STLV-2(pan-p) is a novel retrovirus distantly related to HTLV-2 and displays a host range similar to that demonstrated for other HTLV and STLV strains.
PCR-Based Method for the Introduction of Mutations in Genes Cloned and Expressed in Vaccinia Virus (1998)

Vaccinia virus expression systems allow efficient expression of genes and facilitate functional studies of expressed proteins in cultured mammalian cells. We designed and tested a rapid method to introduce defined mutations in genes inserted and expressed in vaccinia virus. PCR mutagenesis is used to construct a recombination cassette that contains: (i) the mutated exogenous gene, (ii) recombination flanks to direct insertion into the virus genome and (iii) a selectable gene to allow easy isolation of recombinant viruses. To generate recombinant viruses, the recombination cassette is transfected into vaccinia virus-infected cells. The procedure does not require cloning, and the mutated gene versions are inserted directly into the vaccinia virus genome downstream of a vaccinia virus strong promoter. The method was tested by introducing a point mutation into Aequorea victoria green fluorescent protein (GFP), known to alter the fluorescence absorption and emission spectra of the protein. This system should facilitate and speed the isolation of virus recombinants expressing mutated versions of any given gene and can be adapted to random mutagenesis procedures, exon shuffling or other PCR-based mutagenesis protocols.
Rhodium-Catalyzed Heck-Type Coupling of Boronic Acids with Activated Alkenes in an Aqueous Emulsion (2004)

Intermolecular couplings between arylboronic acids and activated alkenes catalyzed by a water-soluble tert-butyl amphos-rhodium complex were found to progress at room temperature and generated Heck-type products with high yields and excellent selectivity. Substitution on the alkene component encouraged the formation of products arising from a conjugate addition-protonation process. In the case of Heck product formation, it was necessary to add two equivalents of the alkene component whereby one equivalent is believed to act as a sacrificial hydride acceptor.
The in-context slider (2008)

As information environments grow in complexity, we yearn for simple interfaces that streamline human cognition and effort. Users need to perform complex operations on thousands of objects. Human attention and available screen real estate are constrained. We develop a new fluid interface component for the visualization and adjustment of values while authoring, the In-Context Slider, which reduces physical effort and demand on attention by using fluid mouse gestures and in-context interaction. We hypothesize that such an interface will make adjusting values easier for the user. We evaluated the In-Context Slider as an affordance for adjusting values of interest in text and images, compared with a more typical interface. Participants performed faster with the In-Context Slider. They found the new interface easier to use and more natural for expressing interest. We then integrated the In-Context Slider in the information composition platform, combinFormation. Participants experienced the In-Context Slider as easier to use while developing collections to answer open-ended information discovery questions. This research is relevant for many applications in which users provide ratings, such as recommender systems, as well as for others in which users' adjustment of values on concurrently displayed objects is integrated with extensive interactive functionality.
Mitogen-Activated Protein Kinase Inhibitors and T-Cell-Dependent Immunotherapy in Cancer (2020)

Mitogen-activated protein kinase (MAPK) signaling networks serve to regulate a wide range of physiologic and cancer-associated cell processes. For instance, a variety of oncogenic mutations often lead to hyperactivation of MAPK signaling, thereby enhancing tumor cell proliferation and disease progression. As such, several components of the MAPK signaling network have been proposed as viable targets for cancer therapy. However, the contributions of MAPK signaling extend well beyond the tumor cells, and several MAPK effectors have been identified as key mediators of the tumor microenvironment (TME), particularly with respect to the local immune infiltrate. In fact, a blockade of various MAPK signals has been suggested to fundamentally alter the interaction between tumor cells and T lymphocytes and have been suggested a potential adjuvant to immune checkpoint inhibition in the clinic. Therefore, in this review article, we discuss the various mechanisms through which MAPK family members contribute to T-cell biology, as well as circumstances in which MAPK inhibition may potentiate or limit cancer immunotherapy.
Aleurain: a barley thiol protease closely related to mammalian cathepsin H. (1985)

We have isolated and sequenced a 1400-base-pair cDNA derived from gibberellic acid-treated aleurone cell mRNA. This sequence contains an open reading frame that would code for a protein of 361 amino acids. The carboxyl-terminal two-thirds of the predicted amino acid sequence is closely related to that of the rat lysosomal thiol protease cathepsin H; the initial 143 amino acids may code for a secretory peptide plus a prosegment. The expression of this aleurone thiol protease mRNA is unusual in that, in aleurone cells, its abundance is regulated by the plant hormones gibberellic acid and abscisic acid, but it is also expressed at high levels in leaf and root tissue. This protease may represent the equivalent of a plant lysosomal thiol protease.
Lymphocyte Reactivity to Clostridium perfringens Antigens and Toxoid in Patients with Arthritis (1995)

Journal Article Lymphocyte Reactivity to Clostridium perfringens Antigens and Toxoid in Patients with Arthritis Get access H. STROöM, H. STROöM *Division of Rheumatology, Department of Medicine, Danderyd Hospital, Karolinska HospitalStockholm, Sweden Search for other works by this author on: Oxford Academic PubMed Google Scholar A. JOHANSSON BORG, A. JOHANSSON BORG †Department of Clinical Immunology, Karolinska HospitalStockholm, Sweden Search for other works by this author on: Oxford Academic PubMed Google Scholar C.-E. NORD, C.-E. NORD ‡Department of Oral Microbiology, Huddinge Hospital, Karolinska HospitalStockholm, Sweden Search for other works by this author on: Oxford Academic PubMed Google Scholar B. OLHAGEN, B. OLHAGEN §Department of Rheumatology, Karolinska HospitalStockholm, Sweden Search for other works by this author on: Oxford Academic PubMed Google Scholar E. MÖLLER E. MÖLLER †Department of Clinical Immunology, Karolinska HospitalStockholm, Sweden Search for other works by this author on: Oxford Academic PubMed Google Scholar Rheumatology, Volume 34, Issue 11, November 1995, Pages 1095–1096, https://doi.org/10.1093/rheumatology/34.11.1095 Published: 01 November 1995 Article history Accepted: 29 June 1995 Published: 01 November 1995
Identification of selectivity‐determining residues in cytochrome P450 monooxygenases: A systematic analysis of the substrate recognition site 5 (2008)

The large and diverse family of cytochrome P450 monooxygenases (CYPs) was systematically analyzed to identify selectivity- and specificity-determining residues in the substrate recognition site 5, which is located in close vicinity to the heme center. A positively charged heme-interacting residue was identified in the structures of 29 monooxygenases and in 97.7% of the 6379 CYP sequences investigated here. This heme-interacting residue restricts the conformation of the substrate recognition site 5 and is preferentially located at position 10 or 11 after the conserved ExxR motif (in 94.4% of the sequences), in 3.3% of the sequences at position 9 or 12. As a result, a classification by the position of the heme-interacting residue allows to predict residues that are closest to the heme center and restrict its accessibility. In 98.4% of all CYP sequences a preferentially hydrophobic residue is located at position 5 after the ExxR motif that is predicted to point close to the heme center. Replacing this residue by hydrophobic residues of different size has been shown to change substrate specificity and regioselectivity for CYPs of different superfamilies. Twenty-seven percent of all CYPs are predicted to contain a second selectivity-determining residue at position 9 after the ExxR motif that can be identified by the pattern EXXR-X(7)-{P}-x-P-[HKR].
Design, Synthesis, and Evaluation of Novel Boronic-Chalcone Derivatives as Antitumor Agents (2003)

A series of boronic-chalcone derivatives were synthesized and tested for antitumor activity against human breast cancer cell lines. The results show the boronic-chalcones are more toxic to breast cancer cells compared to normal breast cells than other known chalcones.
The total antioxidant content of more than 3100 foods, beverages, spices, herbs and supplements used worldwide (2010)

This database is to our best knowledge the most comprehensive Antioxidant Food Database published and it shows that plant-based foods introduce significantly more antioxidants into human diet than non-plant foods. Because of the large variations observed between otherwise comparable food samples the study emphasizes the importance of using a comprehensive database combined with a detailed system for food registration in clinical and epidemiological studies. The present antioxidant database is therefore an essential research tool to further elucidate the potential health effects of phytochemical antioxidants in diet.
The role of fibrinolysis in adhesion formation. (1997)

Postsurgical abdominal adhesions and their sequelae continue to present major clinical and medicoeconomic problems. A complex network of mediators and responses affecting at least five interrelated biological systems, including the fibrinolytic system, are involved in the pathogenesis of postsurgical adhesions. The fibrinolytic system degrades fibrin through the action of the enzyme plasmin, which is stored as the inactive substrate plasminogen. Fibrinolysis, by mediating fibrin degradation, appears to play a pivotal role in adhesiogenesis. Tissue-type plasminogen activator (tPA) is the chief plasminogen activator in the blood, but its activity is restricted by plasminogen activating inhibitors type 1 (PAI-1) and type 2 (PAI-2). Inadequate peritoneal fibrinolysis may result from decreased tPA, increased PAI-1 and PAI-2, or both. The causal relationship between a reduction in fibrinolytic capacity and the formation of adhesions has been demonstrated in animals. In human studies, plasminogen activator activity (PAA) was significantly reduced in peritoneal biopsies from patients with peritonitis compared with those from normal patients. During surgery, PAA declined significantly in both normal and inflamed peritoneum. tPA was responsible for about 95% of PAA. Reduced fibrinolysis in human peritoneum associated with peritonitis and abdominal surgery correlates with increased adhesion formation and may thus be an important early biochemical event leading to adhesion formation. The regulation of plasmin-mediated fibrin degradation in the peritoneal cavity is poorly understood. However, new insights in the cellular distribution of fibrinolytic components in peritoneal tissue suggest that the mesothelium appears to have a principal role in fibrin regulation in the peritoneal cavity and in the early formation of adhesions.
Adaptive Learning Portal Architecture for E-Learner (2013)

Teachers usually have a personal understanding of what ”good teaching” means from their experience and domain knowledge background in education, lots of them create learning resources(LR) and put on the web for learners or students to study. In fact, most of student can not find the suitable LR (e.g. learning materials, or learning assets, or learning packages) from webs, In this paper, we based on ontology and fuzzy technology to propose an architecture for adaptive and re-usability in personalized web-based E-Education Portal, help learners fetch the LR from ontology LR repositories according by the learner characteristics/attribute (e.g. domain knowledge background and Kolb's [11] ”Learning Style”), and we also interested in exploiting the semantic relationships that characterize theses LRs, so we redefine two ”relation” attributes from Dublin Core [10] metadata schema call ”Pre_Relation” and ”Succ_Relation” for enhance LR relations in order to recommend the relative LRs for learner further reference.
Fusion of Positron Emission Tomography (PET) and Gene Array Data: A New Approach for the Correlative Analysis of Molecular Biological and Clinical Data (2007)

The combined assessment of data obtained by positron emission tomography (PET) and gene array techniques provide new capabilities for the interpretation of kinetic tracer studies. The correlative analysis of the data helps to detect dependencies of the kinetics of radiotracer on gene expression. Furthermore, gene expression may be predicted using regression functions if a significant correlation exists, which raises new aspects regarding the interpretation of dynamic PET examinations. The development of new radiopharmaceuticals requires the knowledge of the enhanced expression of genes, especially genes controlling receptors and cell surface proteins. The GenePET program facilitates an interactive approach together with the use of key words to identify possible targets for new radiopharmaceuticals.
Character-Aware Neural Language Models (2015)

We describe a simple neural language model that relies only on character-level inputs. Predictions are still made at the word-level. Our model employs a convolutional neural network (CNN) and a highway network over characters, whose output is given to a long short-term memory (LSTM) recurrent neural network language model (RNN-LM). On the English Penn Treebank the model is on par with the existing state-of-the-art despite having 60% fewer parameters. On languages with rich morphology (Arabic, Czech, French, German, Spanish, Russian), the model outperforms word-level/morpheme-level LSTM baselines, again with fewer parameters. The results suggest that on many languages, character inputs are sufficient for language modeling. Analysis of word representations obtained from the character composition part of the model reveals that the model is able to encode, from characters only, both semantic and orthographic information.
Convection-enhanced delivery of AAV-2 combined with heparin increases TK gene transfer in the rat brain (2001)

Adeno-associated virus type2 (AAV-2) binds to heparan-sulfate proteoglycans on the cell surface. In vivo, attachment of viral particles to cells adjacent to the injection tract limits the distribution of AAV-2 when infused into the CNS parenchyma and heparin co-infusion might decrease the binding of AAV-2 particles to cells in the vicinity of the infusion tract. We have previously shown that heparin co-infusion combined with convection enhanced delivery enhances distribution of the GDNF family trophic factors (heparin-binding proteins) in the rat brain. In this work we show that heparin co-infusion significantly increases the volume of distribution of AAV-2 as demonstrated by immunoreactivity to the transgene product 6 days after infusion into the rat striatum.
An Improved Definition of Synergistic and Antagonistic Effects (1975)

Presently accepted methods for calculating the expected response for combinations of agents such as herbicides or other growth regulators from the responses of individual agents can lead to unacceptable results. This may be true even if responses within the linear region of the individual response curves are used in such calculations. A solution to this problem is to assign parameters to response curves of individual agents and to define the expected response function for combinations of agents by the weighted algebraic means of these parameters.
The JAK2 V617F Mutation Is Uncommon in Patients with Juvenile Myelomonocytic Leukemia. (2005)

Abstract Juvenile myelomonocytic leukemia (JMML) is a rare, clonal myeloproliferative disorder afflicting young children and is characterized by specific hypersensitivity of JMML cells to GM-CSF in vitro. The pathogenesis of JMML seems to arise from dysregulation of GM-CSF signal transduction. Approximately, 75% of patients with JMML exhibit dysregulation due to mutations in RAS, NF1 or PTPN11, all of which are positioned in the GM-CSF pathway. Potential causative mutations in remaining patients are anticipated to be in signaling components downstream of the GM-CSF receptor. Recently, a somatic point mutation (JAK2 V617F) in the JAK2 gene, which plays a major role in the development of hematopoietic cells by transducing signals from growth factor receptors including GM-CSF receptor, was found commonly in polycythemia vera, essential thrombocythemia and idiopathic myelofibrosis. All these myeloproliferative disorders are also characterized by hypersensitivity of hematopoietic progenitor cells to several growth factors and cytokines. Because the frequency of JAK2 V617F mutation in JMML remains unknown, we performed mutational analysis of JAK2 in 39 Japanese children (aged 1 to 69 months) with JMML to assess the pathogenetic relevance of this mutation in JMML, in addition to mutational analysis of PTPN11 and N-RAS. Genomic DNA were prepared from bone marrow or peripheral blood samples taken at initial diagnosis. Mutations of JAK2 (exon 12), PTPN11 (exon 3 and 13) and N-RAS (exon 1 and 2) were screened by direct sequencing. PTPN11 or N-RAS mutations were found in 19 (49%) or 3 (8%) patients respectively, and this is compatible with previous reports. In this study, no JAK2 V617F mutations were detected in any of the 39 JMML patients. In conclusion, we confirmed the presence of PTPN11 and N-RAS mutations in JMML. However, the JAK2 V617F mutation appears to be uncommon in patients with JMML, while it is extraordinarily common in classic MPD. Future investigation should focus on other signaling components in the same signaling pathway as JAK2, or on other parallel signal transduction cascades of the GM-CSF receptor.