gebhart/patrepeval huggingface dataset:
Speeding up slicing (1994)

Program slicing is a fundamental operation for many software engineering tools. Currently, the most efficient algorithm for interprocedural slicing is one that uses a program representation called the system dependence graph. This paper defines a new algorithm for slicing with system dependence graphs that is asymptotically faster than the previous one. A preliminary experimental study indicates that the new algorithm is also significantly faster in practice, providing roughly a 6-fold speedup on examples of 348 to 757 lines.
Steady-state absorption and fluorescence study : Dipole moments of coumarins (2006)

The absorption and fluorescence spectra of 7-dimethylamino cyclopenta [c] coumarin (C138) and 4-methyl-piperidino [g] coumarin (C339) dyes were measured in neutral, aprotic and protic solvents. Solvatochromic shifts of absorption and fluorescence as a function of different solvent polarity parameters (bulk as well as microscopic) were analyzed for these dyes and the ground state dipole moment (μ g ) and the first excited singlet state dipole moment (μ e ) were estimated to be μ g = 2.2 and 3.42 D and μ e = 4.58 and 5.2 D, respectively, for C138 and C339. The dipole moment values of μ g = 3.4 D and μ g = 3.8 D were also obtained for C138 and C339 respectively from ab- initio calculations. The results are compared and discussed.
Gene Prediction with Conditional Random Fields (2005)

Given a sequence of DNA nucleotide bases, the task of gene prediction is to find subsequences of bases that encode proteins. Reasonable performance on this task has been achieved using generatively trained sequence models, such as hidden Markov models. We propose instead the use of a discriminitively trained sequence model, the conditional random field (CRF). CRFs can naturally incorporate arbitrary, non-independent features of the input without making conditional independence assumptions among the features. This can be particularly important for gene finding, where including evidence from protein databases, EST data, or tiling arrays may improve accuracy. We evaluate our model on human genomic data, and show that CRFs perform better than HMM-based models at incorporating homology evidence from protein databases, achieving a 10 % reduction in base-level errors. 1
The Effect of Triazolam on Arousal and Respiration in Central Sleep Apnea Patients (1990)

It was hypothesized that triazolam might decrease central apneas associated with arousal periods in patients with central sleep apnea by hastening the onset of consolidated sleep. Five male patients, diagnosed as having central sleep apnea on a screening night, participated in a double-blind randomized crossover study of the effect of placebo, 0.125 mg triazolam, and 0.25 mg triazolam on sleep, respiration, and daytime function. Results indicated that the medication increased total sleep and decreased central apnea index and number of brief arousals. Improved sleep quality was reflected in improved daytime psychomotor performance and alertness. These data, if replicated, imply that benzodiazepine use may be beneficial in patients with central sleep apnea.
<title>Probabilistic approach to fractal-based texture discrimination</title> (1993)

This paper studies the distribution of power law signatures for various texture types within a grayscale texture quilt. The fractal based features are extracted for the quilt using the covering method. Three features for the power law regression line are extracted. They are slope, y- intercept, and an F test statistic. The underlying distributions of these features are modeled using a nonparametric probability density estimation technique known as adaptive mixtures. These distribution models are then used to distinguish between the sixteen textures in the quilt.
Osteopontin as an Adjunct to CA125 in Detecting Recurrent Ovarian Cancer (2004)

OPN may be a clinically useful adjunct to CA125 in detecting recurrent ovarian cancer.
Troglitazone, a Peroxisome Proliferator-activated Receptor γ (PPARγ) Ligand, Selectively Induces the Early Growth Response-1 Gene Independently of PPARγ (2003)

Troglitazone (TGZ) is a peroxisome proliferator-activated receptor gamma (PPAR gamma) ligand that has pro-apoptotic activity in human colon cancer. Although TGZ binds to PPAR gamma transcription factors as an agonist, emerging evidence suggests that TGZ acts independently of PPAR gamma in many functions, including apoptosis. Early growth response-1 (Egr-1) transcription factor has been linked to apoptosis and shown to be activated by extracellular signal-regulated kinase (ERK). We investigated whether TGZ-induced apoptosis may be related to Egr-1 induction, because TGZ has been known to induce ERK activity. Our results show that Egr-1 is induced dramatically by TGZ but not by other PPAR gamma ligands. TGZ affects Egr-1 induction at least by two mechanisms; TGZ increases Egr-1 promoter activity by 2-fold and prolongs Egr-1 mRNA stability by 3-fold. Inhibition of ERK phosphorylation in HCT-116 cells abolishes the Egr-1 induction by TGZ, suggesting its ERK-dependent manner. Further, the TGZ-induced Egr-1 expression results in increased promoter activity using a reporter system containing four copies of Egr-1 binding sites, and TGZ induces Egr-1 binding activity to Egr-1 consensus sites as assessed by gel shift assay. In addition, TGZ induces ERK-dependent phosphorylation of PPAR gamma, resulting in the down-regulation of PPAR gamma activity. The fact that TGZ-induced apoptosis is accompanied by the biosynthesis of Egr-1 suggests that Egr-1 plays a pivotal role in TGZ-induced apoptosis in HCT-116 cells. Our results suggest that Egr-1 induction is a unique property of TGZ compared with other PPAR gamma ligands and is independent of PPAR gamma activation. Thus, the up-regulation of Egr-1 may provide an explanation for the anti-tumorigenic properties of TGZ.
Targeting the lipids LPA and S1P and their signalling pathways to inhibit tumour progression (2007)

The bioactive lipids lysophosphatidic acid (LPA) and sphingosine 1-phosphate (S1P), the enzymes that generate and degrade them, and the receptors that receive their signals are all potential therapeutic targets in cancer. LPA and S1P signalling pathways can modulate a range of cellular processes that contribute to tumourigenesis, such as proliferation and motility, and components of the signalling pathways often show aberrant expression and altered activity upon malignant transformation. This article reviews LPA- and S1P-mediated activities that might contribute to the aetiology of cancer, and examines the potential of the many antagonists that have been developed to inhibit LPA and S1P signalling pathways. In addition, the outcomes of various clinical trials using LPA- and S1P-associated targets in cancer and other diseases are described, and future directions are discussed.
Large-area wide-angle spectrally selective plasmonic absorber (2011)

A simple metamaterial-based wide-angle plasmonic absorber is introduced, fabricated, and experimentally characterized using angle-resolved infrared spectroscopy. The metamaterials are prepared by nano-imprint lithography, an attractive low-cost technology for making large-area samples. The matching of the metamaterial's impedance to that of vacuum is responsible for the observed spectrally selective ``perfect'' absorption of infrared light. The impedance is theoretically calculated in the single-resonance approximation, and the responsible resonance is identified as a short-range surface plasmon. The spectral position of the absorption peak (which is as high as $95%$) is experimentally shown to be controlled by the metamaterial's dimensions. The persistence of ``perfect'' absorption with variable metamaterial parameters is theoretically explained. The wide-angle nature of the absorber can be utilized for subdiffraction-scale infrared pixels exhibiting spectrally selective absorption/emissivity.
K<sub>ATP</sub> Channel Mutations and Neonatal Diabetes (2017)

Since the discovery of the K<sub>ATP</sub> channel in 1983, numerous studies have revealed its physiological functions. The K<sub>ATP</sub> channel is expressed in various organs, including the pancreas, brain and skeletal muscles. It functions as a "metabolic sensor" that converts the metabolic status to electrical activity. In pancreatic beta-cells, the K<sub>ATP</sub> channel regulates the secretion of insulin by sensing a change in the blood glucose level and thus maintains glucose homeostasis. In 2004, heterozygous gain-of-function mutations in the KCNJ11 gene, which encodes the Kir6.2 subunit of the K<sub>ATP</sub> channel, were found to cause neonatal diabetes. In some mutations, diabetes is accompanied by severe neurological symptoms [developmental delay, epilepsy, neonatal diabetes (DEND) syndrome]. This review focuses on mutations of Kir6.2, the pore-forming subunit and sulfonylurea receptor (SUR) 1, the regulatory subunit of the K<sub>ATP</sub> channel, which cause neonatal diabetes/DEND syndrome and also discusses the findings of the pathological mechanisms that are associated with neonatal diabetes, and its neurological features.
Single-layer TiO_2 and multilayer TiO_2–SiO_2 optical coatings prepared from colloidal suspensions (1987)

Single-layer coatings on fused silica substrates have been prepared from aqueous colloidal suspensions of titania at room temperature. These coatings were porous and had a refractive index of 1.9. Multilayer high reflectivity dielectric coatings were also prepared by laying down quarterwave thick alternating coats at room temperature of this titania with silica, prepared from a colloidal suspension of silica. Single-shot laser damage threshold measurements at 1064-nm wavelength with a pulse length of 1 ns were carried out for both the titania and titania-silica systems. These averaged 7.5 and 6.2 J/cm(2), respectively.
Sequential development of angiotensin receptors and angiotensin I converting enzyme during angiogenesis in the rat subcutaneous sponge granuloma (1997)

1. The vasoconstrictor peptide antiotensin II (AII) can stimulate angiogenesis, an important process in wound healing, tumour growth and chronic inflammation. To elucidate mechanisms underlying AII-enhanced angiogenesis, we have studied a subcutaneous sponge granuloma model in the rat by use of 133Xe clearance, morphometry and quantitative in vitro autoradiography. 2. When injected directly into the sponge, AII (1 nmol day-1) increased 133Xe clearance from, and fibrovascular growth in sponge granulomas, indicating enhanced angiogenesis 6 to 12 days after implantation. This AII-enhanced angiogenesis was inhibited by daily doses (100 nmol/sponge) of the specific but subtype non-selective AII receptor antagonist (Sar1, Ile8)AII, and by the selective non-peptide AT1 receptor antagonists losartan and DuP 532. In contrast, AII-enhanced neovascularization was not inhibited by the AT2 receptor antagonist PD123319, nor was it mimicked by the AT2 receptor agonist CGP42112A (each at 100 nmol/sponge day-1). 3. AI (1 nmol/sponge day-1), the angiotensin converting enzyme (ACE) inhibitors captopril (up to 100 micrograms/sponge day-1) and lisinopril (40 micrograms/sponge day-1), or AII receptor antagonists did not affect angiogenesis in the absence of exogenous AII. 4. [125I]-(Sar1, Ile8)AII binding sites with characteristics of AT1 receptors were localized to microvessels and to non-vascular cells within the sponge stroma from 4 days after implantation, and were at higher density than in skin throughout the study. 5. [125I]-(Sar1, Ile8)AII binding sites with characteristics of AT2 receptors were localized to non-vascular stromal cells, were of lower density and appeared later than did AT1 sites. 6. The ACE inhibitor [125I]-351A bound to sites with characteristics of ACE, 14 days after sponge implantation. [125I]-351A bound less densely to sponge stroma than to skin. 7. We propose that AII can stimulate angiogenesis, acting via AT1 receptors within the sponge granuloma. AT1 and AT2 receptors and ACE develop sequentially during microvascular maturation, and the role of the endogenous angiotensin system in angiogenesis will depend on the balanced local expression of its various components. Pharmacological modulation of this balance may provide novel therapeutic approaches in angiogenesis-dependent diseases.
Konsultationsprocessen i almen praksis (1994)

Almen medicin, konsultationsproces, læge-patient forhold, compliance, kvalitet
Shadow matting and compositing (2003)

In this paper, we describe a method for extracting shadows from one natural scene and inserting them into another. We develop physically-based shadow matting and compositing equations and use these to pull a shadow matte from a source scene in which the shadow is cast onto an arbitrary planar background. We then acquire the photometric and geometric properties of the target scene by sweeping oriented linear shadows (cast by a straight object) across it. From these shadow scans, we can construct a shadow displacement map without requiring camera or light source calibration. This map can then be used to deform the original shadow matte. We demonstrate our approach for both indoor scenes with controlled lighting and for outdoor scenes using natural lighting.
Percutaneous transluminal angioplasty of the carotid artery. (1986)

Percutaneous transluminal angioplasty (PTA) is being extensively applied to treat arteriosclerotic lesions. However, this application has not been widely accepted for the treatment of carotid artery stenosis. Successful attempts to relieve cerebral ischemia from extracranial carotid arterial stenosis by PTA are reported. Twenty-seven patients with arteriosclerotic stenosis, fibromuscular disease, and Takayasu carotid arterial stenosis were treated by PTA. All anatomic carotid stenotic lesions were corrected without any neurologic complication. Follow-ups ranged from 3 months to 4 years without recurrent symptoms in any patient. These results may suggest that some patients with cerebral ischemia secondary to extracranial carotid artery stenosis may be treated safely and effectively by PTA.
Effect of gradient and section orientation on quantitative analysis of knee joint cartilage (2000)

The object of this study was to determine the influence of the gradient and section orientation on cartilage thickness and volume measurements in the knee joint. Eight specimens were imaged with a fat-suppressed gradient-echo sequence, applying sagittal, transverse, and coronal section orientations. Images were additionally acquired with exchanged gradient directions, and with computed tomography (CT) arthrography. After segmentation and three-dimensional (3D) reconstruction, the volume, the mean, and the maximal 3D cartilage thickness were computed. No effect of changes in the gradient orientation was found, suggesting that susceptibility-induced geometric distortion is not a relevant problem in quantitative cartilage imaging. Sagittal images produced similar data to that obtained with transverse (patella) or coronal (tibia) sections, demonstrating that all knee joint cartilages can be accurately quantified from a single sagittal data set. Whereas no significant systematic deviation between magnetic resonance imaging (MRI) and CT arthrography was recorded in the patella, there was a 10%-15% underestimation of tibial cartilage thickness in MRI.
Antitumor activity exhibited by orally administered extract from fruit body of Grifola frondosa (Maitake). (1988)

The acid-insoluble, alkali-soluble, hot-water-extractable polymer (a polysaccharide containing approximately 30% of protein; D-fraction) obtained from the fruit bodies of Grifola frondosa (maitake) exhibited antitumor activities against allogenic and syngeneic tumors on oral administration to mice. Winn assay conducted to examine the tumor growth-suppressing effect revealed a complete inhibition of the tumor by the oral administration of D-fraction. This fact indicates that stimulation of the immune response system triggered by the tumor-bearing state is activated by D-fraction. Consequently, the activity of D-fraction on cells associated with immune response was examined. The cytolytic activity and interleukin-1 productivity of macrophages or T cells which exhibit antigen-specific cytotoxicity were enhanced. D-fraction was found to potentiate the delayed-type hypersensitivity response which is associated with tumor growth suppression.
A high throughput DNA extraction method with high yield and quality (2012)

A high throughput system for DNA extraction from sorghum leaves and seeds was developed and validated. The main advantages of the method are low cost, high yield, high quality, and high throughput. One person can process two 96-well plates in a working day at a cost of $0.10 per sample of magnetic beads plus other consumables that other methods will also need.
Properties of voltage‐gated chloride channels of the ClC gene family. (1995)

We review the properties of ClC chloride channels, members of an expanding gene family originally discovered by the cloning of the ClC-0 chloride channel from Torpedo electric organ. There are at least nine different ClC genes in mammals, several of which seem to be expressed ubiquitously, while others are expressed in a highly specific manner (e.g. the muscle-specific ClC-1 channel and the kidney-specific ClC-K channels). The newly cloned rat ClC-4 is strongly expressed in liver and brain, but also in heart, muscle, kidney and spleen. ClC chloride channels are structurally unrelated to other channel proteins and have twelve putative transmembrane domains. They function as multimers with probably four subunits. Functional characterization is most advanced with ClC-0, ClC-1 (mutations which cause myotonia) and ClC-2, a swelling-activated chloride channel. Many of the new ClC family members cannot yet be expressed functionally.
Gene integration in the Escherichia coli chromosome mediated by Tn21 integrase (Int21) (1996)

A replication-thermosensitive, pSC101-derived plasmid containing the int gene and RHS-2 from the integron in Tn21 and a kanamycin resistance marker has been constructed and used to obtain Tn21 integrase (Int21)-mediated plasmid integration in the Escherichia coli chromosome. Colonies carrying an integrated plasmid were obtained after growth at 42 degrees C. Southern hybridization and PCR experiments indicated that they contained the plasmid specifically integrated through the RHS into different positions in the E. coli chromosome. Nucleotide sequence determination of the plasmid-chromosome junctions showed that integration sites in the chromosome were pentanucleotides with the sequence described for Int21 secondary sites.
The chemistry of plant-growth regulators. Part I. 2 : 4-Dichloro-6-hydroxyphenoxyacetic acid and related compounds (1954)

G. W. K. Cavill and D. L. Ford, J. Chem. Soc., 1954, 565 DOI: 10.1039/JR9540000565
Synthetic Approaches to Rapamycin: Synthesis of a C10-C26 Fragment via a One-Pot Julia Olefination Reaction (1996)

Key steps in a synthesis of the C10-C26 fragment of the immunosuppressant Rapamycin include (a) the use of a metallated benzothiazolyl sulfone in a one-pot Julia olefination to create the C21-C22 alkene stereoselectively and (b) a diastereoselective acid-catalysed cyclisation of a hydroxyl function onto a ketenedithioacetal (1,4-asymmetric induction) in order to create the oxane ring and fix the stereochemistry at C11.
Tacrolimus (FK 506)--a new therapeutic agent for severe recalcitrant psoriasis (1992)

Background-Psoriasis, a disease of unknown etiology, is in some patients severe, extremely debilitating, and unresponsive to conventional therapies, including UV-B, oral psoralen with longwave UV radiation in the A range (PUVA), oral retinoids, and methotrexate.We report the results from our study of seven patients with refractory psoriasis who were treated with the new immunosuppressive drug, tacrolimus (FK 506).Observations-All seven patients showed a dramatic resolution of psoriasis that remained in remission as long as they received full-dose therapy.Serial skin biopsy specimens demonstrated a rapid disappearance of the inflammatory infiltrate and a slower resolution of the epidermal changes.Tacrolimus was well tolerated during the 5.5 to 14 months of observation.Side effects, including nephrotoxicity and hypertension, were controlled by appropriate modification of drug dosage.Conclusions-Tacrolimus, a new immunosuppressive agent, is effective in treating patients with severe recalcitrant psoriasis.The mechanism of its action in psoriasis is unknown, but it may be related to its ability to modulate immune function.Further studies will establish criteria for patient selection and drug dosage, to maximize efficacy of this agent in psoriasis, while minimizing its toxicity.Psoriasis, a common heritable disease that affects the skin, the joints, or both, has many characteristics of an immunologically mediated disease.Included, among these characteristics are a variable HLA association, lymphocytic infiltration of skin lesions, and evidence of cytokine activity or increased expression of new antigens during exacerbations. 1,2Circumstantial evidence for an immune etiology is the striking remission of psoriatic lesions that can be achieved with cyclosporine, 3-6 an immunosuppressive drug whose use for this purpose has been limited its by nephrotoxicity, hypertension, and other dose-related side effects.We report our experience with tacrolimus (FK 506), another immunosuppressive drug that is unrelated chemically to cyclosporine but also inhibits helper T-lymphocyte activation and the synthesis and expression of cytokines. 6,7Encouraging results with tacrolimus have been reported in trials of whole organ transplantation. 8-10 PATIENTS AND METHODSClinical features are summarized in Table 1.Amelioration of psoriasis in four patients was incidental to the primary objective, preventing organ rejection of heart (one patient) or liver transplantation (three patients).The liver disease in one of the latter patients was caused by
Radioimmunotherapy of experimental pancreatic cancer with 131I‐labeled monoclonal antibody PAM4 (1997)

We examined the therapeutic efficacy of 131I-labeled murine monoclonal antibody (MAb) PAM4 against human pancreatic cancers carried as xenografts in athymic nude mice. Animals bearing the CaPanI tumor (0.2 cm3) were either untreated or were given, 131I-labeled nonspecific Ag8 antibody. By week 7 mean tumor size had grown 16.5 ± 8.4-fold and 4.2 ± 2.5-fold for the untreated and 131I-Ag8-treated animals, respectively. In contrast, animals administered 131I-PAM4 exhibited marked regression of tumors to an average of 15% of initial tumor volume. Since most pancreatic cancer patients present with large tumor burdens, the limitation of 131I-PAM4 treatment with respect to initial tumor size was investigated in animals bearing tumors of approximately 0.5 cm3, 1.0 cm3 and 2.0 cm3. Significant extension of survival time (>3-fold increase) was noted for both the 0.5 cm3 and 1.0 cm3 131I-PAM4-treated groups, compared to their respective untreated controls. Even in the group bearing large 2.0-cm3 tumors, survival was increased 2-fold over the control group. To further improve anti-tumor effects in large tumors, 2 injections of 131I-PAM4 were administered at a 4-week interval to animals bearing tumors of approximately 1.0 cm3. Significant extended survival was noted for the group receiving 2 doses when compared to the group receiving only 1 dose. Int. J. Cancer 71:660-667, 1997. © 1997 Wiley-Liss, Inc.
Mucosal Healing and Fibrosis after Acute or Chronic Inflammation in Wild Type FVB-N Mice and C57BL6 Procollagen α1(I)-Promoter-GFP Reporter Mice (2012)

One DSS cycle in FVB-N mice provides a model to study mucosal injury and subsequent mucosal healing. The procollagen α1(I)-GFP transgenic provides a useful model to study activation of a gene encoding a major extracellular matrix protein during acute or chronic experimental intestinal inflammation and fibrosis.