gebhart/patrepeval huggingface dataset:
A little knowledge can go a long way towards program understanding (2002)

Large, complex software systems are hard to learn and navigate. In an ideal environment, documentation can help in this process. However the latter is usually out of date and hard to use. Others have proposed using large knowledge bases to model software systems, however these are very, extensive to build and may be as unmaintainable as the code. We propose instead to use a highly circumscribed, small, conceptual knowledge base, whose purpose is to help the apprentice navigate a software system, and facilitate search within the code. We present our vision, and some initial experiments which involve building such a knowledge base in a semiautomated way.
The T cell receptor (TRA) locus in the rabbit ( <i>Oryctolagus cuniculus</i> ): Genomic features and consequences for invariant T cells (2019)

The rabbit has been widely used in immunology and infectiology. Rabbit immunoglobulins have been extensively studied, leading to the discovery of their idiotypes, allotypic diversity, and of the diversification of the primary repertoire by hyperconversion. Much less is known about rabbit T cell receptors (TR), especially TRA. This isotype is particularly important for innate-like T cells, which typically express invariant TRA (iTRA). The presence of such cells in the rabbit remains an enigma. Rabbit NKT cells seem to be very rare, and lagomorphs lack MAIT cells. TRAV1, the variable gene expressed in the iTRA of these cells across most mammals, and MR1, the MH1-like receptor that present riboflavin derivatives to MAIT cells, are missing in rabbit. An alternative iTRA has been identified, that may be expressed by new innate-like T cells. To facilitate TRA repertoire analyses in rabbit, we report here a full description of TRA and TRD loci and a subgroup definition based on IMGT® classification. Rabbit TRA rearrangements follow the same temporal pattern that is observed in mouse and human. Rare transcripts expressing TRDV/TRDD/TRDJ rearrangements spliced to TRAC were detected. TRA and TRD genes have been made available in IMGT and IMGT/HighV-QUEST, allowing easy analysis of TRA/TRD RepSeq.
Preparation of <i>C</i><sub>2</sub>-Symmetric Bicyclo[2.2.2]octa-2,5-diene Ligands and Their Use for Rhodium-Catalyzed Asymmetric 1,4-Addition of Arylboronic Acids (2005)

[reaction: see text] C2-symmetric bicyclo[2.2.2]octa-2,5-dienes containing benzyl, phenyl, and substituted phenyl groups at 2 and 5 positions were prepared enantiomerically pure by way of bicyclo[2.2.2]octane-2,5-dione as a key intermediate. These chiral diene ligands were successfully applied to rhodium-catalyzed asymmetric 1,4-addition of arylboronic acids to alpha,beta-unsaturated ketones. High enantioselectivity (up to 99% ee) as well as high catalytic activity was observed in the addition to both cyclic and linear substrates.
Synthesis and Characterization of Ionic Block Copolymer Templated Calcium Phosphate Nanocomposites (2008)

Self-assembling thermo-reversibly gelling anionic and zwitterionic pentablock copolymers were used as templates for precipitation of calcium phosphate nanostructures, controlling their size and ordered structural arrangement. Calcium and phosphate ions were dissolved in a block-copolymer micellar dispersion at low temperatures. Aging at ambient temperature produced inorganic nanoparticles, presumably nucleated by ionic interactions. The self-assembled nanocomposites were characterized by small-angle X-ray and neutron scattering (SAXS/SANS), nuclear magnetic resonance (NMR), thermogravimetric analysis (TGA), and transmission electron microscopy (TEM). 1H−31P NMR with 1H spin diffusion from polymer to phosphate proved the formation of nanocomposites, with inorganic particle sizes from ∼2 nm, characterized by 1H−31P dipolar couplings, to >100 nm. TEM analysis showed polymer micelles surrounded by calcium phosphate. SAXS attested that a significant fraction of the calcium phosphate was templated by the polymer micelles. SANS data indicated that the order of the polymer was enhanced by the inorganic phase. The nanocomposite gels exhibited higher moduli than the neat polymer gels. The calcium phosphate was characterized by TGA, X-ray diffraction, high-resolution TEM, and various NMR techniques. An unusual crystalline phase with ≥2 chemically and ≥3 magnetically inequivalent HPO42− ions was observed with the zwitterionic copolymer, highlighting the influence of the polymer on the calcium phosphate crystallization. The inorganic fraction of the nanocomposite was around 30 wt % of the dried hydrogel. Thus, a significant fraction of calcium phosphate has been templated by the tailored self-assembling ionic block copolymers, providing a bottom-up approach to nanocomposite synthesis.
Mobilization of the galactomannan-containing cell walls of tomato seeds: where does β-mannosidase fit into the picture? (2003)

This chapter discusses β-mannosidase activity and synthesis during germination, and compares the activities of the other major enzymes involved in tomato endosperm cell wall galactomannan metabolism.
Process modeling for carbon-phenolic nozzle materials (1989)

A thermochemical model based on the SINDA heat transfer program is developed for carbon-phenolic nozzle material processes. The model can be used to optimize cure cycles and to predict material properties based on the types of materials and the process by which these materials are used to make nozzle components. Chemical kinetic constants for Fiberite MX4926 were determined so that optimization of cure cycles for the current Space Shuttle Solid Rocket Motor nozzle rings can be determined.
Fabrication and characterization of a clover type position sensitive detector (2003)

A new type of lateral-effect position-sensitive photodetector (PSD) has been fabricated on silicon using standard IC technology. The new geometry is called a clover PSD. The experimental performance of tetralateral, pin-cushion, and clover PSDs is compared in terms of measurement linearity and sensitivity. The distortion in linearity is more severe than the simulated values in every case, since the diffused layers in the devices were not uniform. It is observed that the clover PSD has better linearity than both pin-cushion and tetralateral PSDs. The sensitivity of the clover PSD is found to be twice as high as that of the pin-cushion PSD, whereas theory predicts a five times improvement. The discrepancy is explained in terms of the much higher sensitivity of the clover PSD to contact and external parasitic resistances.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Murine Model for Non-invasive Imaging to Detect and Monitor Ovarian Cancer Recurrence (2014)

Epithelial ovarian cancer is the most lethal gynecologic malignancy in the United States. Although patients initially respond to the current standard of care consisting of surgical debulking and combination chemotherapy consisting of platinum and taxane compounds, almost 90% of patients recur within a few years. In these patients the development of chemoresistant disease limits the efficacy of currently available chemotherapy agents and therefore contributes to the high mortality. To discover novel therapy options that can target recurrent disease, appropriate animal models that closely mimic the clinical profile of patients with recurrent ovarian cancer are required. The challenge in monitoring intra-peritoneal (i.p.) disease limits the use of i.p. models and thus most xenografts are established subcutaneously. We have developed a sensitive optical imaging platform that allows the detection and anatomical location of i.p. tumor mass. The platform includes the use of optical reporters that extend from the visible light range to near infrared, which in combination with 2-dimensional X-ray co-registration can provide anatomical location of molecular signals. Detection is significantly improved by the use of a rotation system that drives the animal to multiple angular positions for 360 degree imaging, allowing the identification of tumors that are not visible in single orientation. This platform provides a unique model to non-invasively monitor tumor growth and evaluate the efficacy of new therapies for the prevention or treatment of recurrent ovarian cancer.
<i>Mycobacterium tuberculosis</i>Lipomannan Induces Apoptosis and Interleukin-12 Production in Macrophages (2004)

The mycobacterial cell wall component lipoarabinomannan (LAM) has been described as a virulence factor of Mycobacterium tuberculosis, and modification of the terminal arabinan residues of this compound with mannose caps (producing mannosyl-capped LAM [ManLAM]) in M. tuberculosis or with phosphoinositol caps (producing phosphoinositol-capped LAM [PILAM]) in Mycobacterium smegmatis has been implicated in various functions associated with these lipoglycans. A structure-function analysis was performed by using LAMs and their biosynthetic precursor lipomannans (LMs) isolated from different mycobacterial species on the basis of their capacity to induce the production of interleukin-12 (IL-12) and/or apoptosis of macrophage cell lines. Independent of the mycobacterial species, ManLAMs did not induce IL-12 gene expression or apoptosis of macrophages, whereas PILAMs induced IL-12 secretion and apoptosis. Interestingly, uncapped LAM purified from Mycobacterium chelonae did not induce IL-12 secretion or apoptosis. Furthermore, LMs, independent of their mycobacterial origins, were potent inducers of IL-12 and apoptosis. The precursor of LM, phosphatidyl-myo-inositol dimannoside, had no activity, suggesting that the mannan core of LM was required for the activity of LM. The specific interaction of LM with Toll-like receptor 2 (TLR-2) but not with TLR-4 suggested that these responses were mediated via the TLR-2 signaling pathway. Our experiments revealed an important immunostimulatory activity of the biosynthetic LAM precursor LM. The ratio of LAM to LM in the cell wall of mycobacteria may be an important determinant of virulence, and enzymes that modify LM could provide targets for development of antituberculosis drugs and for derivation of attenuated strains of M. tuberculosis.
The Relationship between the Structural Geometry of a Textile Fabric and Its Physical Properties (1956)

A simplified nomograph has been designed to permit rapid solution of Peirce's geo metric relationships for plain weaves. To illustrate use of the nomograph, several practical problems in cloth structure are presented and worked out in some detail. Advantages and limitations of the nomograph are discussed.
Ischemic Preconditioning of Skeletal Muscle Improves Tissue Oxygenation During Reperfusion (1999)

Ischemic preconditioning (IPC) renders tissue resistant to the deleterious effects of prolonged ischemia and reperfusion by prior exposure to brief, repeated periods of vascular occlusion. Although the mechanism by which IPC exerts its effect is unclear, it likely mediates an attenuation in capillary no-reflow. Tissue oximetry provides a potential technique to assess microvascular flow during ischemia/reperfusion and to measure the effect of IPC on muscle tissue oxygenation. The authors aimed to (a) establish that tissue oximetry is a sensitive method to assess the "no-reflow" phenomenon in skeletal muscle; and (b) to test the hypothesis that IPC would increase tissue oxygenation during reperfusion. In Group 1 (n = 5), the rabbit rectus femoris muscle was subjected to 2-hr ischemia. In Group 2 (n = 5), the muscle was subjected to 3.5-hr ischemia. In Group 3 (n = 6) the muscle was subjected to 3.5-hr ischemia preceded by three cycles of 10 min of pedicle occlusion and 10 min of reperfusion. Muscle oxygen tension was continuously monitored during the ischemic interval and for 6 hr of reperfusion. It was found that muscle oxygen tension in the flap at 5, 10, 30, 60, and 360 min after reperfusion was significantly decreased after 3.5-hr ischemia, compared with 2-hr ischemia (p < 0.05). Muscle oxygen tension at 30 and 60 min after reperfusion was significantly improved in the preconditioned group (p < 0.05). The results suggest that tissue oximetry is a sensitive method to assess tissue perfusion in reperfused skeletal muscle. Ischemic preconditioning improves tissue oxygenation during reperfusion following prolonged ischemia, which likely reflects an attenuation in capillary no-reflow.
Modal study of the role of excess noise in x-ray lasers (1991)

Current x-ray laser designs rely on amplifying spontaneous emission in a high-temperature plasma. A central problem in the study of x-ray lasers is determining and optimizing the degree of transverse spatial coherence for holographic applications. The inherent non-power-orthogonal character of the normal modes in a general amplifying medium necessarily results in excess noise and cross-correlation effects that can significantly affect the predicted coherence and intensity profiles of an x-ray laser. In particular, loosely bound discrete transverse eigenstates of the paraxial wave equation have previously been found to dominate the intensity and coherence in the low-amplification regime if the continuum eigenstates are omitted from the spectrum [London, Strauss, and Rosen, Phys. Rev. Lett. 65, 563 (1990)]. A detailed analysis of the role of excess noise on steady-state laser intensity and coherence is presented for the simple case of a transverse square gain and density profile in a finite geometry. The inclusion of the continuum portion of the spectrum is found to substantially reduce the level of excess noise and to alter the coherence predictions for low and intermediate gain-length products.
Prognosis after surgical treatment for pancreatic cancer in patients aged 80 years or older: a multicenter study (2016)

This study demonstrates that the postoperative prognosis in octogenarian patients was not good as that in younger patients possibly due to less frequent completion of adjuvant chemotherapy.
Water flattens graphene wrinkles: laser shock wrapping of graphene onto substrate-supported crystalline plasmonic nanoparticle arrays (2015)

Hot electron injection into an exceptionally high mobility material can be realized in graphene-plasmonic nanoantenna hybrid nanosystems, which can be exploited for several front-edge applications including photovoltaics, plasmonic waveguiding and molecular sensing at trace levels. Wrinkling instabilities of graphene on these plasmonic nanostructures, however, would cause reactive oxygen or sulfur species to diffuse and react with the materials, decrease charge transfer rates and block intense hot-spots. No ex situ graphene wrapping technique has been explored so far to control these wrinkles. Here, we present a method to generate seamless integration by using water as a flyer to transfer the laser shock pressure to wrap graphene onto plasmonic nanocrystals. This technique decreases the interfacial gap between graphene and the covered substrate-supported plasmonic nanoparticle arrays by exploiting a shock pressure generated by the laser ablation of graphite and the water impermeable nature of graphene. Graphene wrapping of chemically synthesized crystalline gold nanospheres, nanorods and bipyramids with different field confinement capabilities is investigated. A combined experimental and computational method, including SEM and AFM morphological investigation, molecular dynamics simulation, and Raman spectroscopy characterization, is used to demonstrate the effectiveness of this technique. Graphene covered gold bipyramid exhibits the best result among the hybrid nanosystems studied. We have shown that the hybrid system fabricated by laser shock can be used for enhanced molecular sensing. The technique developed has the characteristics of tight integration, and chemical/thermal stability, is instantaneous in nature, possesses a large scale and room temperature processing capability, and can be further extended to integrate other 2D materials with various 0-3D nanomaterials.
Modification de la structure chimique du bois par des alcoxysilanes diversement substitués (2006)

Une étude fondamentale des phénomènes au niveau moléculaire lors de la modification chimique du pin maritime (Pinus pinaster) par des trialcoxysilanes modèles diversement substitués a été entreprise au cours de ce travail de thèse. Dans un premier chapitre, la modification chimique du bois à partir du 3- isocyanatopropyltriéthoxysilane (IPTES) et son couplage ultérieur avec le méthyltriméthoxysilane (MTMS) ont été étudiés. La réaction avec IPTES a été réalisée en présence de dilaurate de dibutylétain (DBTDL) et a conduit au greffage de fonctions triethoxysilanes réactives à l’intérieur des parois cellulaires. Des polymères de MTMS ont ensuite été fixés durablement à l’intérieur du bois, par l’intermédiaire de ces fonctions . Dans un deuxième chapitre, les interactions entre les polymères lignocellulosiques et la fonction trialcoxysilane ont été plus particulièrement étudiées, grâce à des méthodes d’investigation moléculaires comme l’IRTF ou la RMN du solide. La condensation de la fonction triméthoxysilane avec les groupements hydroxyles du bois a été confirmée en milieu anhydre (en présence d’éthylamine) mais les liaisons formées se sont avérées hydrolysables. En présence d’eau (et de DBTDL), la fonction triméthoxysilane a été hydrolysée et condensée à l’intérieur du bois, sous forme de polysiloxanes stables. Un greffage durable et significatif a alors été obtenu pour une teneur en eau contrôlée de 8% à l’intérieur du bois.
Scaling of non-linear viscoelastic transitions in soft colloidal glasses (2006)

We have employed a biological chemistry approach to dissect the mechanisms underpinning cellular responses to oxidant stress and to develop biologically relevant anti-oxidants. We have used telomere biology to define cellular stress responses and have observed telomere independent, p21- and p16-dependent stasis following oxidative insult in human fibroblasts. This was accompanied by a [corrected] reduction in XRCC5 expression and a reduction in [corrected] SIRT 1 expression. Using these markers in conjunction with senescence-associated beta-galactosidase expression, we have developed and screened novel nitrone based anti-oxidant compounds. We have identified functional compounds that are unsuitable for use in primary human cells. This has allowed subsequent identification of suitably structured compounds that act as superior biological anti-oxidants, which have potential for use in clinical interventions.
Regression of the lesions of epidermodysplasia verruciformis (1982)

Journal Article Regression of the lesions of epidermodysplasia verruciformis Get access S. JABLONSKA, S. JABLONSKA Department of Dermatology, Warsaw School of Medicine, Warsaw, Poland Dr S. Jablonska, Department of Dermatology, Koszykowa 82 A, 02–008 Warszawa, Poland. Search for other works by this author on: Oxford Academic Google Scholar S. OBALEK, S. OBALEK Department of Dermatology, Warsaw School of Medicine, Warsaw, Poland Search for other works by this author on: Oxford Academic Google Scholar G. ORTH, G. ORTH Unité de Papillomavirus, Department de Virologie, Institut Pasteur, Paris, France Search for other works by this author on: Oxford Academic Google Scholar M. HAFTEK, M. HAFTEK Department of Dermatology, Warsaw School of Medicine, Warsaw, Poland Search for other works by this author on: Oxford Academic Google Scholar MJARZABEK CHORZELSKA MJARZABEK CHORZELSKA Department of Dermatology, Warsaw School of Medicine, Warsaw, Poland Search for other works by this author on: Oxford Academic Google Scholar British Journal of Dermatology, Volume 107, Issue 1, 1 July 1982, Pages 109–116, https://doi.org/10.1111/j.1365-2133.1982.tb00298.x Published: 01 July 1982 Article history Accepted: 14 October 1981 Published: 01 July 1982
Training Dependency Parser Using Light Feedback (2012)

We introduce lightly supervised learning for dependency parsing. In this paradigm, the algorithm is initiated with a parser, such as one that was built based on a very limited amount of fully annotated training data. Then, the algorithm iterates over unlabeled sentences and asks only for a single bit of feedback, rather than a full parse tree. Specifically, given an example the algorithm outputs two possible parse trees and receives only a single bit indicating which of the two alternatives has more correct edges. There is no direct information about the correctness of any edge. We show on dependency parsing tasks in 14 languages that with only 1 % of fully labeled data, and light-feedback on the remaining 99 % of the training data, our algorithm achieves, on average, only 5 % lower performance than when training with fully annotated training set. We also evaluate the algorithm in different feedback settings and show its robustness to noise. 1
Crystal structure of an enhancer of rudimentary homolog (ERH) at 2.1 Å resolution (2005)

The enhancer of rudimentary gene, e(r), of Drosophila melanogaster encodes an enhancer of rudimentary (ER) protein with functions implicated in pyrimidine biosynthesis and the cell cycle. The ER homolog (ERH) is highly conserved among vertebrates, invertebrates, and plants. Xenopus laevis ERH was reported to be a transcriptional repressor. Here we report the 2.1 Angstroms crystal structure of murine ERH (Protein Data Bank ID 1WZ7), determined by the multiwavelength anomalous dispersion (MAD) method. The monomeric structure of ERH comprises a single domain consisting of three alpha-helices and four beta-strands, which is a novel fold. In the crystal structure, ERH assumes a dimeric structure, through interactions between the beta-sheet regions. The formation of an ERH dimer is consistent with the results of analytical ultracentrifugation. The residues at the core region and at the dimer interface are highly conserved, suggesting the conservation of the dimer formation as well as the monomer fold. The long flexible loop (44 approximately 53) is also significantly conserved, suggesting that this loop region may be important for the functions of ERH. In addition, the putative phosphorylation sites are located at the start of the beta2-strand (Thr18) and at the start of the alpha1-helix (Ser24), implying that the phosphorylation might cause some structural changes.