gebhart/patrepeval huggingface dataset:
Learning from examples to improve code completion systems (2009)

The suggestions made by current IDE's code completion features are based exclusively on static type system of the programming language. As a result, often proposals are made which are irrelevant for a particular working context. Also, these suggestions are ordered alphabetically rather than by their relevance in a particular context. In this paper, we present intelligent code completion systems that learn from existing code repositories. We have implemented three such systems, each using the information contained in repositories in a different way. We perform a large-scale quantitative evaluation of these systems, integrate the best performing one into Eclipse, and evaluate the latter also by a user study. Our experiments give evidence that intelligent code completion systems which learn from examples significantly outperform mainstream code completion systems in terms of the relevance of their suggestions and thus have the potential to enhance developers' productivity.
Systemic Toxicity From Topically Applied Lidocaine in Conjunction With Fractional Photothermolysis (2006)

Application of a 30% topical lidocaine gel to a limited area in conjunction with fractional photothermolysis may generate serum lidocaine levels high enough to elicit systemic toxicity. Laser surgeons should be alert to this phenomenon, particularly in patients with underlying hepatic, endocrine, cardiac, or central nervous system/psychiatric dysfunction; in patients with a low body mass index; and in patients who are taking medications that may interfere with hepatic lidocaine metabolism.
A Novel Histone H4 Mutant Defective in Nuclear Division and Mitotic Chromosome Transmission (1996)

The histone proteins are essential for the assembly and function of th e eukaryotic chromosome. Here we report the first isolation of a temperature-sensitive lethal histone H4 mutant defective in mitotic chromosome transmission Saccharomyces cerevisiae. The mutant requires two amino acid substitutions in histone H4: a lethal Thr-to-Ile change at position 82, which lies within one of the DNA-binding surfaces of the protein, and a substitution of Ala to Val at position 89 that is an intragenic suppressor. Genetic and biochemical evidence shows that the mutant histone H4 is temperature sensitive for function but not for synthesis, deposition, or stability. The chromatin structure of 2 micrometer circle minichromosomes is temperature sensitive in vivo, consistent with a defect in H4-DNA interactions. The mutant also has defects in transcription, displaying weak Spt- phenotypes. At the restrictive temperature, mutant cells arrest in the cell cycle at nuclear division, with a large bud, a single nucleus with 2C DNA content, and a short bipolar spindle. At semipermissive temperatures, the frequency of chromosome loss is elevated 60-fold in the mutant while DNA recombination frequencies are unaffected. High-copy CSE4, encoding an H3 variant related to the mammalian CENP-A kinetochore antigen, was found to suppress the temperature sensitivity of the mutant without suppressing the Spt- transcription defect. These genetic, biochemical, and phenotypic results indicate that this novel histone H4 mutant defines one or more chromatin-dependent steps in chromosome segregation.
Evaluation of binning strategies for tissue classification in computed tomography images (2006)

Binning strategies have been used in much research work for image compression, feature extraction, classification, segmentation and other tasks, but rarely is there any rigorous investigation into which binning strategy is the best. Binning becomes a "hidden parameter" of the research method. This work rigorously investigates the results of three different binning strategies, linear binning, clipped binning, and nonlinear binning, for co-occurrence texture-based classification of the backbone, liver, heart, renal, and splenic parenchyma in high-resolution DICOM Computed Tomography (CT) images of the human chest and abdomen. Linear binning divides the gray-level range of [0..4095] into <i>k1</i> equally sized bins, while clipped binning allocates one large bin for low intensity gray-levels [0..855] (air), one for higher intensities [1368..4095] (bone), and <i>k2</i> equally sized bins for the soft tissues between [856..1368]. Nonlinear binning divides the gray-level range of [0..4095] into <i>k3</i> bins of different sizes. These bins are further used to calculate the co-occurrence statistical model and its ten Haralick descriptors for texture quantification of gray-level images. The results of the texture quantification using each one of the three strategies and for different values of <i>k1</i>, <i>k2</i> and <i>k3</i> are evaluated with respect to their discrimination power using a decision tree classification algorithm and four classification performance metrics (sensitivity, specificity, precision and accuracy). Our preliminary results obtained on 1368 segmented DICOM images show that the optimal number of gray-levels is equal to 128 for linear binning, 512 for clipped binning, , and 256 for non-linear binning. Furthermore, when comparing the results of the three approaches, the nonlinear binning approach shows significant improvement for heart and spleen.
Influence of interleukin-15 on CD8+ natural killer cells in human immunodeficiency virus type 1-infected chimpanzees (2007)

Chimpanzees are susceptible to human immunodeficiency virus type-1 (HIV-1) and develop persistent infection but generally do not progress to full-blown AIDS. Several host and immunological factors have been implicated in mediating resistance to disease progression. Chimpanzees have a higher prevalence of circulating natural killer (NK) cells than humans; however, their role in mediating resistance to disease progression is not well understood. Furthermore, NK cell survival and activity have been shown to be dependent on interleukin-15 (IL-15). Accordingly, the influence of IL-15 on NK cell activity and gamma interferon (IFN-gamma) production was evaluated in naive and HIV-1-infected chimpanzees. In vitro stimulation of whole-blood cultures with recombinant gp120 (rgp120) resulted in enhanced IFN-gamma production predominantly by the CD3(-) CD8(+) subset of NK cells, and addition of anti-IL-15 to the system decreased IFN-gamma production. Moreover, in vitro stimulation with recombinant IL-15 (rIL-15) augmented IFN-gamma production from this subset of NK cells and increased NK cell cytotoxic activity. Stimulation with rgp120 also resulted in a 2- to 7-fold increase in IL-15 production. These findings suggest that chimpanzee CD3(-) CD8(+) NK cells play a vital role in controlling HIV-1 infection by producing high levels of IFN-gamma, and that IL-15 elicits IFN-gamma production in this subpopulation of NK cells in HIV-1-infected chimpanzees.
Distribution and Characterization of Autoantibodies to Interleukin 1α in Normal Human Sera (1990)

Antibodies against IL-1 alpha were detected in sera of apparently healthy individuals. The immunoglobulins belonged to the IgG class, particularly IgG1, IgG2, and IgG4. [125I]rIL-1 alpha bound to Fab fragments of IgG, and IgG immune complexes of molecular weights from 160 to 700 kDa were formed in the sera by [125I]rIL-1 alpha. The occurrence of detectable anti-IL-1 alpha IgG in sera of 32 male and 32 female donors was 25 and 22% respectively. As judged by Scatchard analysis of the binding data, the capacity and avidity of binding were greater in the male than in the female sera (mean capacity to bind [125I]rIL-1 alpha: 10 [0.7-27] versus 3.3 [0.5-7.3] ng/ml; and mean Kd: 5.5 [5-7] versus 11 [4-16] pM). The antibodies did not cross-bind human recombinant IL-1 beta, IL-2, IL-6, or tumour necrosis factor alpha (TNF-alpha). It is concluded that native IL-1 alpha seems to trigger production of specific, high-avidity IgG antibodies in a relatively large number of normal individuals. These autoantibodies may regulate immunoinflammatory processes involving IL-1 alpha.
Very low resistance multilayer Ohmic contact to n-GaN (1996)

A new metallization scheme has been developed for obtaining very low Ohmic contact to n-GaN. The metallization technique involves the deposition of a composite metal layer Ti/Al/Ni/Au (150 Å/2200 Å/400 Å/500 Å) on n-GaN preceded by a reactive ion etching (RIE) process which most likely renders the surface highly n type. Of the several attempts and with annealing at 900 °C for 30 s, contacts with specific resistivity values of ρs=8.9×10−8 Ω cm2 or lower for a doping level of 4×1017 cm−3 were obtained. The physical mechanism underlying the realization of such a low resistivity is elucidated.
Anti-TNF therapies in rheumatoid arthritis, Crohn's disease, sepsis, and myelodysplastic syndromes (2000)

An attempt has been made in this article to summarize the state-of-the-art clinical experience with the use of anti-TNF therapies in four diseased states with special emphasis on myelodysplastic syndromes. Given the central role of TNF-alpha in initiating and perpetuating the chronic damage produced in the diseased organs by controlling a cascade of pro-inflammatory cytokines, as well as its acute role in sepsis, theoretically speaking, neutralization of this peptide was a natural therapeutic choice. Results of the initial clinical trials appear encouraging and sometimes dramatic in their efficacy. The mechanism of response however, is interesting in that even when TNF-alpha is directly targeted by a monoclonal antibody, the resulting benefits can frequently not be attributed to TNF suppression alone. Rather, it appears that a more general effect on the T-lymphocytes is also contributing to the responses being seen. This raises the new possibility of combining anti-cytokine and anti-T-cell strategies to treat at least the more chronic diseases such as Crohn's disease and myelodysplastic syndromes. Continued clinical trials testing these strategies are clearly warranted.
The Tumor Suppressor Kinase LKB1 Activates the Downstream Kinases SIK2 and SIK3 to Stimulate Nuclear Export of Class IIa Histone Deacetylases (2013)

Histone deacetylases 4 (HDAC4), -5, -7, and -9 form class IIa within the HDAC superfamily and regulate diverse physiological and pathological cellular programs. With conserved motifs for phosphorylation-dependent 14-3-3 binding, these deacetylases serve as novel signal transducers that are able to modulate histone acetylation and gene expression in response to extracellular cues. Here, we report that in a PKA-sensitive manner the tumor suppressor kinase LKB1 acts through salt-inducible kinase 2 (SIK2) and SIK3 to promote nucleocytoplasmic trafficking of class IIa HDACs. Both SIK2 and SIK3 phosphorylate the deacetylases at the conserved motifs and stimulate 14-3-3 binding. SIK2 activates MEF2-dependent transcription and relieves repression of myogenesis by the deacetylases. Distinct from SIK2, SIK3 induces nuclear export of the deacetylases independent of kinase activity and 14-3-3 binding. These findings highlight the difference among members of the SIK family and indicate that LKB1-dependent SIK activation constitutes an important signaling module upstream from class IIa deacetylases for regulating cellular programs controlled by MEF2 and other transcription factors.
Polyphosphate enhances fibrin clot structure (2008)

Polyphosphate, a linear polymer of inorganic phosphate, is present in platelet dense granules and is secreted on platelet activation. We recently reported that polyphosphate is a potent hemostatic regulator, serving to activate the contact pathway of blood clotting and accelerate factor V activation. Because polyphosphate did not alter thrombin clotting times, it appeared to exert all its procoagulant actions upstream of thrombin. We now report that polyphosphate enhances fibrin clot structure in a calcium-dependent manner. Fibrin clots formed in the presence of polyphosphate had up to 3-fold higher turbidity, had higher mass-length ratios, and exhibited thicker fibers in scanning electron micrographs. The ability of polyphosphate to enhance fibrin clot turbidity was independent of factor XIIIa activity. When plasmin or a combination of plasminogen and tissue plasminogen activators were included in clotting reactions, fibrin clots formed in the presence of polyphosphate exhibited prolonged clot lysis times. Release of polyphosphate from activated platelets or infectious microorganisms may play an important role in modulating fibrin clot structure and increasing its resistance to fibrinolysis. Polyphosphate may also be useful in enhancing the structure of surgical fibrin sealants.
Brain Abnormalities in Neuromyelitis Optica (2006)

Asymptomatic brain lesions are common in NMO, and symptomatic brain lesions do not exclude the diagnosis of NMO. These observations justify revision of diagnostic criteria for NMO to allow for brain involvement.
Inhibition of Urinary Kallikrein Excretion by Semi-Purified Renin in the Rat (1979)

1. Rat kidney extracts obtained at successive stages of a purification procedure, which allows the separation of renin and kallikrein, were used in order to investigate their effect upon urinary excretion of kallikrein, sodium, potassium and water in hyperhydrated rats. 2. Only the purified fraction containing renin reduced kallikrein excretion. The decrease of kallikrein coincided with a considerable increase in sodium, potassium and water excretion. 3. The natriuretic effect of renin extract did not depend on the presence of kallikrein. The injection of a mixture of renin and kallikrein attenuated the effect of renin alone, indicating that both enzymes exert antagonistic actions on the excretion of electrolytes and water by the kidneys. 4. A purified fraction of kidney extract containing no kallikrein and only traces of renin activity, had a stimulatory effect on kallikrein, water and electrolyte excretion.
Novel aspects of Sjögren’s syndrome in 2012 (2013)

Sjögren's syndrome (SS) is a systemic progressive autoimmune disease characterized by a complex pathogenesis requiring a predisposing genetic background and involving immune cell activation and autoantibody production. The immune response is directed to the exocrine glands, causing the typical 'sicca syndrome', but major organ involvement is also often seen. The etiology of the disease is unknown. Infections could play a pivotal role: compared to normal subjects, patients with SS displayed higher titers of anti-Epstein-Barr virus (EBV) early antigens, but lower titers of other infectious agent antibodies such as rubella and cytomegalovirus (CMV) suggest that some infections may have a protective role against the development of autoimmune disease. Recent findings seem to show that low vitamin D levels in patients with SS could be associated with severe complications such as lymphoma and peripheral neuropathy. This could open new insights into the disease etiology. The current treatments for SS range from symptomatic therapies to systemic immunosuppressive drugs, especially B cell-targeted drugs in cases of organ involvement. Vitamin D supplementation may be an additional tool for optimization of SS treatment.
High-Frequency Graphene Voltage Amplifier (2011)

While graphene transistors have proven capable of delivering gigahertz-range cutoff frequencies, applying the devices to RF circuits has been largely hindered by the lack of current saturation in the zero band gap graphene. Herein, the first high-frequency voltage amplifier is demonstrated using large-area chemical vapor deposition grown graphene. The graphene field-effect transistor (GFET) has a 6-finger gate design with gate length of 500 nm. The graphene common-source amplifier exhibits ∼5 dB low frequency gain with the 3 dB bandwidth greater than 6 GHz. This first AC voltage gain demonstration of a GFET is attributed to the clear current saturation in the device, which is enabled by an ultrathin gate dielectric (4 nm HfO(2)) of the embedded gate structures. The device also shows extrinsic transconductance of 1.2 mS/μm at 1 V drain bias, the highest for graphene FETs using large-scale graphene reported to date.
Insulin resistance is an important determinant of left ventricular mass in the obese. (1993)

LV mass in the normotensive nondiabetic obese population is strongly associated with, and may be mediated by, the degree of insulin resistance and its associated hyperinsulinemia, independent of BMI and blood pressure.
Overcoming STI571 resistance with the farnesyl transferase inhibitor SCH66336 (2002)

The development of chronic myeloid leukemia (CML) is dependent on the deregulated tyrosine kinase of the oncoprotein BCR-ABL. STI571 (imatinib mesylate), an abl tyrosine kinase inhibitor, has proven remarkably effective for the treatment of CML. However, resistance to STI571 because of enhanced expression or mutation of the BCR-ABL gene has been detected in patients. In the current study we show that the farnesyl transferase inhibitor (FTI) SCH66336 (lonafarnib) inhibits the proliferation of STI571-resistant BCR-ABL-positive cell lines and hematopoietic colony formation from peripheral blood samples of STI571-resistant patients with CML. Moreover, SCH66336 enhances STI571-induced apoptosis in STI571-sensitive cells and, in patients with STI571 resistance from gene amplification, cooperates with STI571 to induce apoptosis. Our data provide a rationale for combination clinical trials of STI571 and SCH66336 in CML patients and suggest that combination therapy may be effective in patients with STI571 resistance.
Progesterone metabolite allopregnanolone in women with premenstrual syndrome (1997)

Subjects with PMS manifested lower levels of the anxiolytic metabolite allopregnanolone in the luteal phase when compared with controls. Diminished concentrations of allopregnanolone in women with PMS may lead to an inability to enhance gamma aminobutyric acid-mediated inhibition during states of altered central nervous system excitability, such as ovulation or physiologic or psychological stress. The lowered metabolite levels could contribute to the genesis of various mood symptoms of the disorder, such as anxiety, tension, and depression.
Susceptibility of Predaceous Hemipteran Species to Selected Insecticides on Soybean in Louisiana (1998)

Journal Article Susceptibility of Predaceous Hemipteran Species to Selected Insecticides on Soybean in Louisiana Get access Michael L. Boyd, Michael L. Boyd 1 Department of Entomology, Louisiana Agricultural Experiment Station, Louisiana State University Agriculhlral Center, Baton Rouge, LA 70803 1Current address: Department of Entomology, University of Missouri Delta Research Center, Portageville. MO 63873. Search for other works by this author on: Oxford Academic PubMed Google Scholar David J. Boethel David J. Boethel Department of Entomology, Louisiana Agricultural Experiment Station, Louisiana State University Agriculhlral Center, Baton Rouge, LA 70803 Search for other works by this author on: Oxford Academic PubMed Google Scholar Journal of Economic Entomology, Volume 91, Issue 2, 1 April 1998, Pages 401–409, https://doi.org/10.1093/jee/91.2.401 Published: 01 April 1998
Aptamer-Functionalized Au Nanoparticles for the Amplified Optical Detection of Thrombin (2004)

The catalytic enlargement of aptamer-functionalized Au nanoparticles amplifies the optical detection of aptamer-thrombin complexes in solution and on surfaces.
Safety and Clinical Activity of the Programmed Death-Ligand 1 Inhibitor Durvalumab in Combination With Poly (ADP-Ribose) Polymerase Inhibitor Olaparib or Vascular Endothelial Growth Factor Receptor 1-3 Inhibitor Cediranib in Women's Cancers: A Dose-Escalation, Phase I Study (2017)

Purpose Data suggest that DNA damage by poly (ADP-ribose) polymerase inhibition and/or reduced vascular endothelial growth factor signaling by vascular endothelial growth factor receptor inhibition may complement antitumor activity of immune checkpoint blockade. We hypothesize the programmed death-ligand 1 (PD-L1) inhibitor, durvalumab, olaparib, or cediranib combinations are tolerable and active in recurrent women's cancers. Patients and Methods This phase I study tested durvalumab doublets in parallel 3 + 3 dose escalations. Durvalumab was administered at 10 mg/kg every 2 weeks or 1,500 mg every 4 weeks with either olaparib tablets twice daily or cediranib on two schedules. The primary end point was the recommended phase II dose (RP2D). Response rate and pharmacokinetic analysis were secondary end points. Results Between June 2015 and May 2016, 26 women were enrolled. The RP2D was durvalumab 1,500 mg every 4 weeks with olaparib 300 mg twice a day, or cediranib 20 mg, 5 days on/2 days off. No dose-limiting toxicity was recorded with durvalumab plus olaparib. The cediranib intermittent schedule (n = 6) was examined because of recurrent grade 2 and non-dose-limiting toxicity grade 3 and 4 adverse events (AEs) on the daily schedule (n = 8). Treatment-emergent AEs included hypertension (two of eight), diarrhea (two of eight), pulmonary embolism (two of eight), pulmonary hypertension (one of eight), and lymphopenia (one of eight). Durvalumab plus intermittent cediranib grade 3 and 4 AEs were hypertension (one of six) and fatigue (one of six). Exposure to durvalumab increased cediranib area under the curve and maximum plasma concentration on the daily, but not intermittent, schedules. Two partial responses (≥15 months and ≥ 11 months) and eight stable diseases ≥ 4 months (median, 8 months [4 to 14.5 months]) were seen in patients who received durvalumab plus olaparib, yielding an 83% disease control rate. Six partial responses (≥ 5 to ≥ 8 months) and three stable diseases ≥ 4 months (4 to ≥ 8 months) were seen in 12 evaluable patients who received durvalumab plus cediranib, for a 50% response rate and a 75% disease control rate. Response to therapy was independent of PD-L1 expression. Conclusion To our knowledge, this is the first reported anti-PD-L1 plus olaparib or cediranib combination therapy. The RP2Ds of durvalumab plus olaparib and durvalumab plus intermittent cediranib are tolerable and active. Phase II studies with biomarker evaluation are ongoing.
Low power video object motion-tracking architecture for very low bit rate online video applications (2002)

This paper presents a low power VLSI architecture for video object motion-tracking that can be used in very low bit rate online video applications. Power has been reduced at both algorithmic and arithmetic levels. The video object motion-tracking architecture consists of two main parts, a mesh-based motion estimation unit and a mesh-based motion compensation unit. The mesh-based motion estimation unit implements parallel block matching motion estimation units to optimize the latency. The mesh-based motion compensation unit uses parallel multiplication-free affine core. The architecture has been prototyped and its performance measures have been evaluated. This processor can be used in online object-based video applications.
Detailed deletion mapping on chromosome arm 12q in human pancreatic adenocarcinoma: Identification of a 1‐cM region of common allelic loss (1996)

As a first step toward understanding molecular mechanisms in human pancreatic carcinogenesis, we searched for the location of tumor suppressor genes by examining loss of heterozygosity (LOH) in 44 pancreatic cancer specimens. We used 46 microsatellite markers that spanned all of the autosomes. Frequent LOH was observed in six chromosomal regions: in chromosome arms 1p (32%), 6q (37%), 9p (50%), 12q (30%), 17p (59%), and 18q (35%). Because chromosome arm 12q is a reported target for allelic loss in some other cancers, we focused on this region with 66 primary specimens and identified the minimal common region of allelic loss within a 1-cM interval in 12q22-q23.1. Microsatellite instability (MI) was also examined in this study, and the incidence of MI(+) cases, in which MI of two or more microsatellite loci was detected, was 61% (27 of 44 informative cases). In pancreatic tumors with MI(+), mutations of the transforming growth factor β receptor II (RII) gene were not detected. Genes Chromosom Cancer 17:88–93 (1996). © 1996 Wiley-Liss, Inc.