gebhart/patrepeval huggingface dataset:
Specializing generic Java data structures (2021)

The Collections framework is an essential utility in virtually every Java application. It offers a set of fundamental data structures that exploit Java Generics and the Object type in order to enable a high degree of reusability. Upon instantiation, Collections are parametrized by the type they are meant to store. However, at compile-time, due to type erasure, this type gets replaced by Object, forcing the data structures to manipulate references of type Object (the root of the Java type system). In the bytecode, the compiler transparently adds type checking instructions to ensure type safety, and generates bridge methods to enable the polymorphic behavior of parametrized classes. This approach can introduce non-trivial runtime overheads when applications extensively manipulate Collections.
ChemInform Abstract: A Novel Class of Ruthenium Catalysts for Olefin Metathesis. (1999)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Laser System for Livermore's Mono Energetic Gamma-Ray Source (2011)

A Mono-energetic Gamma-ray (MEGa-ray) source, based on Compton scattering of a high-intensity laser beam off a highly relativistic electron beam, requires highly specialized laser systems. To minimize the bandwidth of the {gamma}-ray beam, the scattering laser must have minimal bandwidth, but also match the electron beam depth of focus in length. This requires a {approx}1 J, 10 ps, fourier-transform-limited laser system. Also required is a high-brightness electron beam, best provided by a photoinjector. This electron source requires a second laser system with stringent requirements on the beam including flat transverse and longitudinal profiles and fast rise times. Furthermore, these systems must be synchronized to each other with ps-scale accuracy. Using a novel hyper-dispersion compressor configuration and advanced fiber amplifiers and diode-pumped Nd:YAG amplifiers, we have designed laser systems that meet these challenges for the X-band photoinjector and Compton-scattering source being built at Lawrence Livermore National Laboratory.
ChemInform Abstract: Rapid Access to 3‐Aminoindazoles from Tertiary Amides. (2015)

Abstract Benzamides [e.g. (I)] react with nucleophilic hydrazides (e.g. [II]) to give aminohydrazones [e.g. (III)], which undergo Pd‐catalyzed C—H amination to afford aminoindazoles [e.g. (IV)].
The Relationship between Ligand Aggregation and G-Quadruplex DNA Selectivity in a Series of 3,4,9,10-Perylenetetracarboxylic Acid Diimides (2002)

Human telomeres are comprised of d(TTAGGG) repeats that are capable of forming\nG-quadruplex DNA structures. Ligands that bind to and stabilize these G-quadruplex DNA structures are\npotential inhibitors of the cancer cell-associated enzyme telomerase. Other potential biological uses of\nG-quadruplex targeting ligands have been proposed. One particularly challenging aspect of the contemplated\nuses of G-quadruplex targeting ligands is their selectivity for G-quadruplex DNA versus double-stranded\nDNA structures. We have previously reported the observation that two structurally related 3,4,9,10-perylenetetracarboxylic acid diimide-based G-quadruplex DNA ligands, PIPER [&lt;i&gt;N&lt;/i&gt;,&lt;i&gt;N&lt;/i&gt;‘-bis(2-(1-piperidino)ethyl)-3,4,9,10-perylenetetracarboxylic acid diimide] and Tel01 [&lt;i&gt;N&lt;/i&gt;,&lt;i&gt;N&lt;/i&gt;‘-bis(3-(4-morpholino)propyl)-3,4,9,10-perylenetetracarboxylic acid diimide], have different levels of G-quadruplex DNA binding selectivity at\npH 7 as determined by absorbance changes in the presence of different DNA structures [Kerwin, S. M.,\nChen, G., Kern, J. T., and Thomas, P. W. (2002) &lt;i&gt;Bioorg. Med. Chem. Lett.&lt;/i&gt; &lt;i&gt;12&lt;/i&gt;, 447−450]. Here we report\nthat the less G-quadruplex DNA selective ligand PIPER can unwind double-stranded, closed circular\nplasmid DNA, as determined by a topoisomerase I assay. A model for the interaction of Tel01 with the\nG-quadruplex DNA structure formed by d(TAGGGTTA) was determined from NMR experiments. This\nmodel is similar to the previously published model for PIPER bound to the same G-quadruplex DNA and\nfailed to provide a structural basis for the observed increased selectivity of Tel01 interaction with\nG-quadruplex DNA. In contrast, investigation into the aggregation state of Tel01 and PIPER as well as\nother 3,4,9,10-perylenetetracarboxylic acid diimide analogues bearing basic side chains demonstrates that\nligand aggregation is correlated with G-quadruplex DNA binding selectivity. For all six analogues examined,\nthose ligands that were aggregated at pH 7 in 70 mM potassium phosphate, 100 mM KCl, 1 mM EDTA\nbuffer also demonstrated G-quadruplex DNA binding selectivity under these buffer conditions. Ligands\nthat were not aggregated under these conditions display much lower levels of G-quadruplex DNA selectivity.\nThe aggregation state of these ligands is extremely sensitive to the buffer pH. Tel01, which is aggregated\nat pH 7, is not aggregated at pH 6.4, where it demonstrates only modest G-quadruplex DNA binding\nselectivity, and PIPER in pH 8.5 buffer is both aggregated and highly G-quadruplex DNA-selective. To\nour knowledge, these studies demonstrate the first DNA structure selectivity as achieved through pH-mediated ligand aggregation. The potential impact of these findings on the selectivity of other classes of\nG-quadruplex DNA ligands is discussed.
Improving vertical handovers using IEEE 802.21 services and multicast addressing (2012)

The use of multi-interface devices has grown at the same time as the demands for efficient mobility services in heterogeneous networks. In this scenario, service continuity has become a crucial requirement. In order to achieve these demands, efficient handover schemes should be deployed, aiming the Seamless Handover. However, handover delay and packet loss are still issues to be solved. The main purpose of this paper is to present an improvement for Vertical Handovers using IP mobility, aiming Seamless Handover. In this work, the framework provided by IEEE 802.21 is used to enable handover in heterogeneous networks. Besides, a FMIPv6 extension called FaHMA is proposed in order to efficiently manage mobility in these networks. Simulation results have shown that FaHMA achieves better results than FMIPv6 in the evaluated scenarios.
A randomized trial of radical surgery (S) versus thoracic radiotherapy (TRT) in patients (pts) with stage IIIA-N2 non-small cell lung cancer (NSCLC) after response to induction chemotherapy (ICT) (EORTC 08941) (2005)

LBA7015 Background: The optimal locoregional treatment -TRT or S- following systemic ICT of pts with stage IIIA-N2 NSCLC is unclear. 5-year survival rate in uncontrolled series of either modality varies between 5–25%. Methods: Selected pts with histological or cytological proven stage IIIA-N2 NSCLC were given 3 cycles of platinum-based ICT. Responding pts were then randomized between S: radical resection with lymph node dissection and optional postoperative radiotherapy (PORT), or TRT: at least 40 Gy in 2 Gy daily fractions on the mediastinum with a boost to at least 60 Gy on the involved field (IF). In order to observe an increase of 5-year overall survival (OS) from 15 (TRT) to 25% (S), 292 events out of 358 randomized pts had to be observed (log rank test, power 80%, type I error 5%). Secondary endpoints were progression free survival (PFS) and toxicity. Results: ICT achieved an average response rate of 61.5% (95%CI: 57.6–65.5) among the 572 registered pts who started protocol treatment. Of these, 333 were randomized (167 to S and 166 to TRT), having the following characteristics: median age 62 years; male 74%; squamous/non-squamous: 39/61%; T1/2/3: 12/72/15%. In 151 operated pts, the following rates were observed: exploratory thoracotomy: 14%; radical resection: 50%; pathological downstaging: 40%; operative mortality: 4%; PORT 27% up to now. Among 153 irradiated TRT pts, median total treatment time was 43 days (15–60). CT- scan planning was used in 92%. The median total dose delivered to the normal mediastinum/IF was 40/60 Gy, respectively. Currently, 278 events have occurred after a median duration of follow-up of 58 months. Final analysis of OS and PFS will be submitted by March 25. Conclusions: Study partially supported by NCI Grants 5U10CA11488–24 through 5U10CA11488–34. No significant financial relationships to disclose.
Quaternary salts of 2-[(hydroxyimino)methyl]imidazole. 4. Effect of various side-chain substituents on therapeutic activity against anticholinesterase intoxication (1991)

A series of quaternary salt derivatives of 2-[(hydroxyimino)methyl]-1-methylimidazole incorporating various side chains bearing ether, silyl, nitrile, ester, halogen, nitro, sulfone, amino, or aminosulfonyl substituents was prepared and evaluated in vivo for the treatment of anticholinesterase intoxication. Test results in the mouse revealed that the type and location of the side-chain substituent both have a significant influence on the toxicity and antidotal effectiveness of the compounds. Some of the more active examples represent the most potent therapeutics to date against intoxication by the powerful cholinesterase inhibitors soman and tabun. Significantly, the antidotal effectiveness of the compounds was not dependent on the inhibiting agent nor was there any correlation between in vivo efficacy and in vitro reactivation of ethyl (4-nitrophenyl)methylphosphonate inhibited human acetylcholinesterase. These observation suggested that the main mode of antidotal protection by the compounds is something other than enzyme reactivation.
EPR investigation of pure and Co-doped ZnO oriented nanocrystals (2016)

Pure and cobalt-doped zinc oxide aligned nanorods have been grown by the low-temperature (90 °C) aqueous chemical method on amorphous ZnO seed layer, deposited on a sapphire substrate. High crystallinity of these objects is demonstrated by the electron paramagnetic resonance investigation at liquid helium temperature. The successful incorporation of Co<sup>2+</sup> ions in substitution of Zn<sup>2+</sup> ones in the ZnO matrix has also been confirmed. A drastic reduction of intrinsic ZnO nanorods core defects is observed in the Co-doped samples, which enhances the structural quality of the NRs. The quantification of substitutional Co<sup>2+</sup> ions in the ZnO matrix is achieved by comparison with a reference sample. The findings in this study indicate the potential of using the low-temperature aqueous chemical approach for synthesizing material for spintronics applications.
Like Partying? Your Face Says It All. Predicting the Ambiance of Places\n with Profile Pictures (2015)

To choose restaurants and coffee shops, people are increasingly relying on\nsocial-networking sites. In a popular site such as Foursquare or Yelp, a place\ncomes with descriptions and reviews, and with profile pictures of people who\nfrequent them. Descriptions and reviews have been widely explored in the\nresearch area of data mining. By contrast, profile pictures have received\nlittle attention. Previous work showed that people are able to partly guess a\nplace's ambiance, clientele, and activities not only by observing the place\nitself but also by observing the profile pictures of its visitors. Here we\nfurther that work by determining which visual cues people may have relied upon\nto make their guesses; showing that a state-of-the-art algorithm could make\npredictions more accurately than humans at times; and demonstrating that the\nvisual cues people relied upon partly differ from those of the algorithm.\n
Preparation of highly chemoselective N-phthaloyl chitosan in aqueous media (2011)

Highly chemoselective N-phthaloylations of chitosan were achieved by reaction in aqueous acetic acid media in concentrations from 0 to 10.0%. The degree of substitution (DS) values of phthaloyl groups determined by elemental analysis and 1H NMR were approximately 1. The 1H and 13C NMR spectra strongly support the structural uniformity of N-phthaloyl chitosan.
Computation of supersonic and low subsonic cascade flows using an explicit Navier-Stokes technique and the kappa-epsilon turbulence model (1991)

A fully explicit two-dimensional flow solver, based on a four-stage Runge-Kutta scheme, was developed and utilized to predict two-dimensional viscous flow through turbomachinery cascades for which experimental data is available. The formulation is applied to the density averaged Navier-Stokes equations. Several features of the technique improve the ability of the code to predict high Reynolds number flows on highly stretched grids. These include a low Reynolds number compressible form of the k-epsilon turbulence model, anisotropic scaling of artificial dissipation terms and locally varying timestep evaluation based on hyperbolic and parabolic stability considerations. Comparisons between computation and experiment are presented for both a supersonic and a low-subsonic compressor cascade. These results indicate that the code is capable of predicting steady two-dimensional viscous cascade flows over a wide range of Mach numbers in reasonable computational times.
Supplementary Figure Legends from Genomic Copy Number Dictates a Gene-Independent Cell Response to CRISPR/Cas9 Targeting (2023)

&lt;p&gt;Supplementary Figure Legends&lt;/p&gt;
76. RESULTS OF ARTHROSCOPIC LATERAL MENISCECTOMY ON STABLE KNEE: MORE THAN 20 YEARS FOLLOW-UP IN 89 KNEES (2011)

Purpose of the study: The purpose of this retrospective multicentric analysis was to study the functional and radiological outcomes at more than 20 years of 89 arthroscopic lateral menisectomy procedures performed on stable knees. Materialandmethod: The series included 89 arthroscopic lateral meniscectomies performed on knee with intact anterior cruciate ligaments (ACL). Mean follow-up was 22±3 years; 56 male, mean BMI 25±4, mean age at meniscectomy 35 years, mean age at last follow-up 57 years. Most of the injuries were vertical (41%), complex (22%) and radial (20%) lesions. The middle segment was involved in 79%. The meniscectomy removed more than one-third of the meniscus in 67%. All patients were reviewed by an independent operator for subjective assessment KOOS (100% normal) and IKDC, and for objective clinical and radiological measurements (IKDC). P Results: Revisions were performed for 16% of the knees. Intense or moderate activity was maintained by all patients. The subjective IKDC score was 71.1±23, comparable with an age and gender matched population. The mean KOOS score was 82% for pain, 80% for symptoms, 85% for daily activities, 64% for sports, and 69% for quality of life. The rate of of osteoarthritis was 56%, and 44% of patients had a difference between the two knees for osteoarthritis. The incidence of osteoarthritis was 53% and shift to valgus on the arthritic side was significantly associated with osteoarthritis, while the opposite side was well aligned. The knee was pain free in 27% of patients. Significant factors for good prognosis were age less than 38 years at first operation, moderate BMI, and minimal cartilage damage (grade 0 or 1). Conclusion: After the first postoperative year after arthroscopic lateral meniscectomy on a stable knee, the results remain stable and satisfactory for more than 22 years. Nevertheless, patients aged over 40 with a high BMI and cartilage damage at the time of the first operation have a less encouraging prognosis.
La biologie des cibles PD-1 et CTLA-4 et la question des biomarqueurs (2019)

The identification in the 1990's of the role of CTLA-4 and PD-1, two inhibitory receptors of T lymphocytes, in the control of the anti-tumor immune responses, led to the awarding of the Nobel Prize in Physiology or Medicine in 2018 to Dr. James Allison and Dr. Tasuku Honjo. These inhibitory receptors called immune checkpoints are essential to prevent any deleterious impact of on-going immune responses against pathogens or cancer cells on healthy tissues and, hence, guarantee the integrity of the host. These major discoveries have led James Allison and Tasuku Honjo to develop anti-CTLA-4 and anti-PD1/L-1 antibodies, respectively, in order to switch off these immune "brakes", making it possible to efficiently attack tumor cells. CTLA-4 regulates the amplitude of the early T-cell activation and inhibits the activity of CD28, a major activating co-receptor expressed by T cells. PD-1 is expressed by memory and effector T lymphocytes and is involved in the regulation of chronically activated cells, as observed during inflammatory processes. Immunotherapeutic treatments resulting from these discoveries have now a major place in the arsenal of anti-cancer therapies. This review presents firstly a synthesis of knowledge on CTLA-4, PD-1 and their ligands, their mechanisms of action and regulation and, secondly, an overview of biomarkers that have been associated with clinical response to anti-PD-1/PD-L1 and anti-CTLA-4 antibody therapies.
A receptor-like protein mediates the response to pectin modification by activating brassinosteroid signaling (2014)

The brassinosteroid (BR) signaling module is a central regulator of plant morphogenesis, as indicated by the large number of BR-responsive cell wall-related genes and the severe growth defects of BR mutants. Despite a detailed knowledge of the signaling components, the logic of this auto-/paracrine signaling module in growth control remains poorly understood. Recently, extensive cross-talk with other signaling pathways has been shown, suggesting that the outputs of BR signaling, such as gene-expression changes, are subject to complex control mechanisms. We previously provided evidence for a role of BR signaling in a feedback loop controlling the integrity of the cell wall. Here, we identify the first dedicated component of this feedback loop: a receptor-like protein (RLP44), which is essential for the compensatory triggering of BR signaling upon inhibition of pectin de-methylesterification in the cell wall. RLP44 is required for normal growth and stress responses and connects with the BR signaling pathway, presumably through a direct interaction with the regulatory receptor-like kinase BAK1. These findings corroborate a role for BR in controlling the sensitivity of a feedback signaling module involved in maintaining the physico-chemical homeostasis of the cell wall during cell expansion.
Active learning of intuitive control knobs for synthesizers using gaussian processes (2014)

Typical synthesizers only provide controls to the low-level parameters of sound-synthesis, such as wave-shapes or filter envelopes. In contrast, composers often want to adjust and express higher-level qualities, such as how "scary" or "steady" sounds are perceived to be. We develop a system which allows users to directly control abstract, high-level qualities of sounds. To do this, our system learns functions that map from synthesizer control settings to perceived levels of high-level qualities. Given these functions, our system can generate high-level knobs that directly adjust sounds to have more or less of those qualities. We model the functions mapping from control-parameters to the degree of each high-level quality using Gaussian processes, a nonparametric Bayesian model. These models can adjust to the complexity of the function being learned, account for nonlinear interaction between control-parameters, and allow us to characterize the uncertainty about the functions being learned. By tracking uncertainty about the functions being learned, we can use active learning to quickly calibrate the tool, by querying the user about the sounds the system expects to most improve its performance. We show through simulations that this model-based active learning approach learns high-level knobs on certain classes of target concepts faster than several baselines, and give examples of the resulting automatically- constructed knobs which adjust levels of non-linear, high- level concepts.
Supplemental Information from Targeting of HPV-16<sup>+</sup> Epithelial Cancer Cells by TCR Gene Engineered T Cells Directed against E6 (2023)

&lt;p&gt;Table S1 lists human peptide sequences with homology to E6 29-38. Figure S1 shows testing of TCRs raised in HLA-A2 transgenic mice. Figure S2 depicts testing of HPV+ cell lines for HLA-A*02:01-restricted recognition by T cells.&lt;/p&gt;
Interaction of optical solitons with a forward Raman pump wave (1989)

The interaction between optical solitons and a forward Raman pump wave in fibers is investigated. It is found that when their relative velocity is small and the soliton pulse width is short, the soliton frequency is shifted by the interaction. Near zero relative velocity the pulse shape is distorted, in addition to having a frequency shift.
80 nm gate-length Si/Si 0.7 Ge 0.3 n -MODFET with 194 GHz f max (2003)

DC and RF performance of scaled n-channel Si/SiGe modulation-doped field effect transistors (n-MODFETs) grown by ultra-high vacuum chemical vapour deposition is reported. Devices with source-to-drain spacing of 300 nm, and gate length of 80 nm (70 nm) displayed fmax=194 GHz (175 GHz) and fT=70 GHz (79 GHz).
Electrical and Optical Properties of Layered Oxysulfides with CuS Layers: Sr−Cu−M−O−S System (M = Zn, Ga, In) (2001)

The electrical and optical properties of layered oxysulfides (Sr−Cu−M−O−S system (M = Zn, Ga, In)), which have common CuS layers, were studied to examine their potential as wide-gap p-type semiconductors. The attempts of electrical conductivity control by Na doping demonstrated that the conductivities of the Sr2-xNaxCu2ZnO2S2 (σ = 2.2 × 10-8 S cm-1 for x = 0.0) and Sr2-xNaxCuGaO3S (σ = 2.2 × 10-4 S cm-1 for x = 0.0) at room temperature increased up to 1.2 × 10-1 and 2.4 × 10-2 S cm-1 for x = 0.1, respectively, with an increase in Na concentration. In addition, both Hall and Seebeck measurements proved that these conductive oxysulfides were p-type semiconductors. The diffuse reflectance spectra of the materials revealed that the optical absorption edges were approximately 450 nm for Sr2Cu2ZnO2S2, 480 nm for Sr2CuGaO3S, and 540 nm for Sr2CuInO3S. It became evident from these results that the layered oxysulfides (Sr−Cu−M−O−S system (M = Zn, Ga, In)) were wide-gap p-type semiconductors utilizing the CuS layers as electrical conduction paths.
A Derivate of the Antibiotic Doxorubicin Is a Selective Inhibitor of Dengue and Yellow Fever Virus Replication In Vitro (2010)

A doxorubicin derivate, SA-17, that carries a squaric acid amide ester moiety at the carbohydrate (α-l-daunosaminyl) group was identified as a selective inhibitor of in vitro dengue virus (DENV) serotype 2 replication (50% effective concentration [EC(50)] = 0.34 ± 0.20 μg/ml [0.52 ± 0.31 μM]). SA-17 is markedly less cytostatic than the parent compound, resulting in a selectivity index value of ∼100. SA-17 also inhibits yellow fever virus 17D (YFV-17D) replication (EC(50) = 3.1 ± 1.0 μg/ml [4.8 ± 1.5 μM]), although less efficiently than DENV replication, but proved inactive against a variety of enveloped and nonenveloped viruses. SA-17 inhibits in vitro flavivirus replication in a dose-dependent manner, as was assessed by virus yield reduction assays and quantification of viral RNA by means of real-time quantitative reverse transcriptase PCR (RT-qPCR) (∼2 to 3 log reduction). The anti-DENV activity was confirmed using a Renilla luciferase-expressing dengue reporter virus. Time-of-drug-addition studies revealed that SA-17 acts at the very early stages of the viral replication cycle (i.e., virus attachment and/or virus entry). This observation was corroborated by the observation that SA-17, unlike the nucleoside analogue ribavirin, does not inhibit the replication of DENV subgenomic replicons. Preincubation of high-titer stocks of DENV or YFV-17D with ≥5 μg/ml SA-17 resulted in 100% inhibition of viral infectivity (≥3 log reduction). SA-17, however, did not prove virucidal.