gebhart/patrepeval huggingface dataset:
Implementing real-time collaboration in TouchDevelop using AST merges (2015)

Collaborating on a piece of code is notoriously difficult when the number of people involved goes above 1. In particular, every computer programmer dreads the "merge conflict", a brutal, unforgiving experience, where they must reconcile their changes with someone else's. If offline collaboration is already so painful, real-time collaboration seems even less of an option. It turns out, though, that by reasoning on changes at the level of the program AST, rather than the program text, we can devise a new conflict-free merge algorithm. The algorithm is particularly well-suited to real-time collaboration: we implemented it in the TouchDevelop web programming environment and dub the algorithm diffTree.
A physics-based investigation of Pt-salt doped carbon nanotubes for local interconnects (2017)

We investigate, by combining physical and electrical measurements together with an atomistic-to-circuit modeling approach, the conductance of doped carbon nanotubes (CNTs) and their eligibility as possible candidate for next generation back-end-of-line (BEOL) interconnects. Ab-initio simulations predict a doping-related shift of the Fermi level, which reduces shell chirality variability and improves electrical conductance up to 90% by converting semiconducting shells to metallic. Circuit-level simulations predict up to 88% signal delay improvement with doped vs. pristine CNT. Electrical measurements of Pt-salt doped CNTs provide up to 50% of resistance reduction which is a milestone result for future CNT interconnect technology.
Further studies of the electronic spectra of octachlorodirhenate(2-) and octabromodirhenate(2-). Assignment of the weak bands in the 600-350-nm region. Estimation of the dissociation energies of metal-metal quadruple bonds (1977)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTFurther studies of the electronic spectra of octachlorodirhenate(2-) and octabromodirhenate(2-). Assignment of the weak bands in the 600-350-nm region. Estimation of the dissociation energies of metal-metal quadruple bondsWilliam C. Trogler, Charles D. Cowman, Harry B. Gray, and F. Albert CottonCite this: J. Am. Chem. Soc. 1977, 99, 9, 2993–2996Publication Date (Print):April 1, 1977Publication History Published online1 May 2002Published inissue 1 April 1977https://pubs.acs.org/doi/10.1021/ja00451a023https://doi.org/10.1021/ja00451a023research-articleACS PublicationsRequest reuse permissionsArticle Views185Altmetric-Citations34LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Genetic analysis of a pigment producing mutant of Vibrio cholerae (2008)

Only two out of more than 200 V. cholerae serogroups, classified on the basis of LPS structure, are associated with epidemic or pandemic cholera. These toxigenic serogroups carry phage-derived pathogenicity islands coding for the main virulence factors for establishment of cholera disease – cholera toxin (CTX) and toxin-coregulated pilus (TCP). The latter also serves as a bacterial surface receptor for the CTXΦ – the filamentous phage which carries the cholera toxin genes into otherwise harmless to human, environmental bacterium V. cholerae. In its natural aquatic habitat V. cholerae is subject to predator grazing, bacteriophage killing, temperature and pH changes, seasonality of plankton blooms and other environmental factors. Therefore understanding V. cholerae pathogenic and virulence potential requires the knowledge of its interaction not only with human host but also members of aquatic environment and environmental factors. V. cholerae is capable of killing the nematode Caenorhabditis elegans. Using a reverse genetics approach, we demonstrated that the quorum sensing regulated protease PrtV is essential for this killing. Other proteases did not seem to contribute to virulence in this model. The data from this study suggest that the PrtV could be important to V. cholerae in its natural niche for its resistance to the grazing predators. The PrtV protease belongs to an M6 family of metallopeptidases which is represented by an Immune Inhibitor A protease from the insect killing bacterium Bacillus thuringiensis. To characterize the protease in more detail, the PrtV was cloned, overexpressed in V. cholerae and purified from the culture supernatant. The enzyme was calcium stabilized and inhibited by metal ion chelators. In tests with in vitro cultured cells of the human intestinal cell line HCT8, the PrtV protein showed a cytotoxic effect leading to cell detachment and death. Using human blood plasma as a source of potential substrates, and by tests with purified candidate substrate proteins, we have identified fibrinogen (all α, β and γ chains), fibronectin and plasminogen to be degraded by the protease. Additionally, PrtV was found to alter the stability of V. cholerae cytolysin implicating its role in modulation of the reactogenicity of V. cholerae secreted factors. Pigmentation has been considered to be important in microbial pathogenesis because it has been associated with virulence in many microorganisms. Using transposon mutagenesis we identified the mutated locus of a pigment producing V. cholerae strain to encode a gene of a tyrosine catabolic pathway. The mutation in a putative homogentisate 1,2-dioxigenase gene lead to accumulation of homogentisic acid, its spontaneous oxidation and formation of a dark pigment. The pigment producing strain was altered in its ability to survive UV exposure and H2O2 stress, and was more efficient in colonizing the suckling mouse intestine compared to the wild type strain. Under the in vitro growth conditions the major virulence factor TcpA and CT expression was found to be somewhat enhanced too.
Tumour auto-antibody screening: performance of protein microarrays using SEREX derived antigens (2010)

Protein microarray is an efficient means for auto-antibody-based detection when using SEREX-derived clones expressing antigenic proteins. Protein microarrays are preferred to macroarrays due to the easier handling and the high reproducibility of auto-antibody testing. Especially when using only a few microliters of patient samples protein microarrays are ideally suited for validation of auto-antibody signatures for diagnostic purposes.
ChemInform Abstract: Synthesis and Evaluation of Potential Radioligands for the Progesterone Receptor. (1986)

Abstract Gemäß Formelschema werden Iod‐ und Amid‐Steroide (IV), (VI), Und (VIII) dargestellt, die auf Progesteronrezeptor‐Affinität getestet werden.
Nanoscale Indentation of Polymer Systems Using the Atomic Force Microscope (1997)

Abstract The use of the atomic force microscope (AFM) to measure surface forces has been developed to optimize its operation as a surface imaging tool. This capability can potentially be extended to evaluate nanoscale material response to indentation and would be ideal for the evaluation of multi-component polymer systems, such as adhesives and composites. In this paper, previous work related to the development of the AFM as a nanoindentation device is reviewed, and a technique is proposed which allows the AFM to be used to probe local stiffness changes in polymer systems. Cantilever probes with spring constants ranging from 0.4–150 N m were used to investigate a number of polymer systems, including an elastomer, several polyurethane systems, thermally cured epoxies, a thermoplastic polymer-thermosetting polymer adhesive system, and a thermoplastic matrix composite. Key Words: Atomic force microscopeforce curvesindentationelastic moduluspolymerselastomerpolyurethaneepoxyfiber-reinforced polymer compositeinterphase regions
Ultra-CEP-stable single-cycle pulses at 2.2  µm (2023)

Single-cycle optical pulses with controllable carrier-envelope phase (CEP) form the basis to manipulate the nonlinear polarization of matter on a sub-femtosecond time scale. Moreover, nonlinear light–matter energy exchange and frequency conversion processes benefit from longer, infrared wavelengths. We report a highly stable source of 6.9-fs, single-cycle pulses at 2.2 µm, based on a directly diode-pumped Cr:ZnS oscillator with 22.9-MHz repetition rate. Extreme spectral broadening of the oscillator output to a super-octave bandwidth (1.1–3.1 µm) is achieved in a single rutile (TiO 2 ) plate. Excellent agreement with simulations provides a precise understanding of the underlying nonlinear pulse propagation. A comprehensive investigation of alternative broadening materials and additional simulations single out the exceptional broadening in TiO 2 due to the favorable interplay of self-focusing, and plasma formation accompanied by self-phase modulation and self-compression. Unprecedented reproducibility of the single-cycle waveforms is ensured by a unique combination of active CEP stabilization with a residual CEP jitter of only 5.9 mrad (0.1 Hz to 11.45 MHz) and a relative intensity noise of 0.036% (0.1 Hz to 1 MHz). The new single-cycle source permits efficient downconversion to the mid-infrared by cascaded intra-pulse difference frequency generation, giving access to sub-femtosecond manipulation of electric currents in low-bandgap materials with an unprecedented degree of control.
Brain Magnetic Resonance Imaging at 3 Tesla Using BLADE Compared With Standard Rectilinear Data Sampling (2006)

PROPELLER (BLADE) brain magnetic resonance imaging is also applicable at 3 T. In addition to minimizing motion artifacts, the PROPELLER acquisition scheme reduces other magnetic resonance artifacts that would otherwise degrade scan quality.
2-D Phosphopeptide Mapping (2003)

A major mechanism that cells use to regulate protein function is by phosphorylation and/or dephosphorylation of serine, threonine, and tyrosine residues. Phosphopeptide mapping of these phosphorylated residues allows investigation into the positive and negative regulatory roles these sites may play in vivo. In addition, phosphopeptide mapping can uncover the specific phosphorylated residue and, hence, kinase recognition sites, thus helping in the identification of the relevant kinase(s) and/or phosphatase(s).
Model based direct binary search halftone optimization with a dual interpretation (2002)

The direct binary search (DBS) algorithm is an iterative method designed to minimize one metric of error between the grayscale original and halftone image. This metric incorporates a model for the human visual system. To achieve the optimization, an initial halftone is adjusted until a local minimum of the metric is achieved at each pixel. However this local minimum can be shown to simultaneously minimize another metric of error using another visual model; this alternative metric and visual model combination are referred to as the dual interpretation of DBS. An analysis of this dual reveals the origin of tone reproduction bias in DBS. Many model based halftoning algorithms are effected by this problem. The dual can also be used to quantify the perceived tone reproduction capabilities of DBS and provides insight on why DBS yield very high quality halftones. Despite the complexity of the DBS algorithm it can be implemented with surprising efficiency. We demonstrate how the algorithm simultaneously exploits two different visual models and error metrics to efficiently yield very high quality halftones.
Neural correlates of visual spatial selective attention are altered at early and late processing stages in human amblyopia (2020)

Amblyopia is a neurodevelopmental visual disorder which results in reduced visual acuity in one eye and impaired binocular interactions. Previous studies suggest attentional deficits in amblyopic individuals. However, spatial cues which orient attention to a visual field improved performance. Here, we investigate the neural correlates of auditory-visual spatial selective attention in amblyopia during EEG recording. An auditory cue, that was followed by the presentation of two Gabor patches presented in the lower left and right visual fields, indicated the most likely location of an upcoming target Gabor. The target Gabor differed in orientation from the more frequently presented non-target Gabor patches. Adults with amblyopia and neurotypical observers were asked to detect the target Gabor monocularly at the cued location, while withholding their response to targets presented at the uncued location and to all non-target Gabor patches. Higher response rates were observed for cued compared to uncued targets in both groups. However, amblyopic individuals detected targets less efficiently with their amblyopic eye as compared to their fellow eye. Correspondingly, event-related potentials (ERPs) recorded to the onset of the non-target Gabor patches were delayed at early processing stages (150-300 ms: posterior N100) and reduced in amplitude at later time windows (150-350 ms: P200, 300-500 ms: sustained activity) in the amblyopic eye compared to the fellow eye. Such interocular differences were not observed in neurotypical observers. These findings suggest that neural resources allocated to the early formation of visual discrimination as well as later stimulus recognition processes are altered in the amblyopic eye.
Synthesis of a D3-symmetric “trefoil” knotted cyclophane (2011)

A D(3)-symmetric knotted cyclophane, with a subgraph of trefoil topology, was synthesized by cyclization of a D(3)-symmetric scaffold. Control of configuration at the three metal-based stereocenters arises from a bascule/pivot mechanism.
ControlFlag: A Self-Supervised Idiosyncratic Pattern Detection System\n for Software Control Structures (2020)

Software debugging has been shown to utilize upwards of half of developers'\ntime. Yet, machine programming (MP), the field concerned with the automation of\nsoftware (and hardware) development, has recently made strides in both research\nand production-quality automated debugging systems. In this paper we present\nControlFlag, a self-supervised MP system that aims to improve debugging by\nattempting to detect idiosyncratic pattern violations in software control\nstructures. ControlFlag also suggests possible corrections in the event an\nanomalous pattern is detected. We present ControlFlag's design and provide an\nexperimental evaluation and analysis of its efficacy in identifying potential\nprogramming errors in production-quality software. As a first concrete evidence\ntowards improving software quality, ControlFlag has already found an anomaly in\nCURL that has been acknowledged and fixed by its developers. We also discuss\nfuture extensions of ControlFlag.\n
Modeling simulation and visualization of conformal 3D lung tumor dosimetry (2009)

Lung tumors move during breathing depending on the patient's patho-physiological condition and orientation, thereby compromising the accurate deposition of the radiation dose during radiotherapy. In this paper, we present and validate a computer-based simulation framework to calculate the delivered dose to a 3D moving tumor and its surrounding normal tissues. The computer-based simulation framework models a 3D volumetric lung tumor and its surrounding tissues, simulates the tumor motion during a simulated dose delivery both as a self-reproducible motion and a random motion using the dose extracted from a treatment plan, and predicts the amount and location of radiation doses deposited. A radiation treatment plan of a small lung tumor (1-3 cm diameter) was developed in a commercial planning system (iPlan software, BrainLab, Munich, Germany) to simulate the radiation dose delivered. The dose for each radiation field was extracted from the software. The tumor motion was simulated for varying values of its rate, amplitude and direction within a single breath as well as from one breath to another. Such variations represent the variations in tumor motion induced by breathing variations. During the simulation of dose delivery, the dose on the target was summed to generate the real-time dose to the tumor for each beam independently. The simulation results show that the dose accumulated on the tumor varies significantly with both the tumor size and the tumor's motion rate, amplitude and direction. For a given tumor motion rate, amplitude and direction, the smaller the tumor size the smaller is the percentage of the radiation dose accumulated. The simulation results are validated by comparing the center plane of the 3D tumor with 2D film dosimetry measurements using a programmable 4D motion phantom moving in a self-reproducible pattern. The results also show the real-time capability of the framework at 40 discrete tumor motion steps per breath, which is higher than the number of four-dimensional computed tomography (CT) steps (approximately 20) during a single breath. The real-time capability enables the framework to be coupled with real-time tumor monitoring systems such as implanted fiducials for computing the dose delivered in real time during the treatment.
Accumulation of Exogenous Ouabain in Plasma and Organs and Systolic Blood Pressure Elevation in Spontaneously Hypertensive Rats (1995)

Much evidence support the concept that endgenous digitalis-like factor (EDLF), a Na+-K+-ATPase inhibitor, may exist and play important roles in the pathophysiology of salt-sensitive and volume-dependent hypertension. Ouabain has been isolated as a candidate EDLF. However, we demonstrated that the adrenals highly accumulate exogenous ouabain in Wistar rats and release it into plasma at volume expansion in reduced renal mass hypertensive rats. In this study, accumulation of exgenous ouabain in plasma and organs was compared between spontaneously hypertensive rats (SHR) and Wistar-Kyoto rats (WKY) to determine its
Extracting clues from human interpreter speech for spoken language translation (2008)

In previous work, we reported dramatic improvements in automatic speech recognition (ASR) and spoken language translation (SLT) gained by applying information extracted from spoken human interpretations. These interpretations were artificially created by collecting read sentences from a clean parallel text corpus. Real human interpretations are significantly different. They suffer from frequent synopses, omissions and self-corrections. Expressing these differences in BLEU score by evaluating human interpretations with carefully created human translations, we found that human interpretations perform two to three times worse than state-of-the art SLT. Facing these stark differences, we address the question if and how ASR and SLT can profit from human interpretations. In the following we describe initial experiments that apply knowledge derived from real human interpretations for improving English and Spanish ASR and SLT. Our experiments are conducted on a small European Parliamentary Plenary Sessions development set.
Crystal structure of the substrate-recognition domain of theShigellaE3 ligase IpaH9.8 (2016)

Infectious diseases caused by bacteria have significant impacts on global public health. During infection, pathogenic bacteria deliver a variety of virulence factors, called effectors, into host cells. The Shigella effector IpaH9.8 functions as an ubiquitin ligase, ubiquitinating the NF-κB essential modulator (NEMO)/IKK-γ to inhibit host inflammatory responses. IpaH9.8 contains leucine-rich repeats (LRRs) involved in substrate recognition and an E3 ligase domain. To elucidate the structural basis of the function of IpaH9.8, the crystal structure of the LRR domain of Shigella IpaH9.8 was determined and this structure was compared with the known structures of other IpaH family members. This model provides insights into the structural features involved in substrate specificity.
Nanopatterning of Functional Solid Structures by Dip Pen Nanolithography (2003)

Journal Article Nanopatterning of Functional Solid Structures by Dip Pen Nanolithography Get access Ming Su, Ming Su Northwestern University, Materials Sciences and Engineering Dept., Evanston, IL, 60208 Search for other works by this author on: Oxford Academic Google Scholar Vinayak P Dravid Vinayak P Dravid Northwestern University, Materials Sciences and Engineering Dept., Evanston, IL, 60208 Search for other works by this author on: Oxford Academic Google Scholar Microscopy and Microanalysis, Volume 9, Issue S02, 1 August 2003, Pages 1238–1239, https://doi.org/10.1017/S1431927603446199 Published: 24 July 2003
New perspective on passively quenched single photon avalanche diodes: effect of feedback on impact ionization (2012)

Single-photon avalanche diodes (SPADs) are primary devices in photon counting systems used in quantum cryptography, time resolved spectroscopy and photon counting optical communication. SPADs convert each photo-generated electron hole pair to a measurable current via an avalanche of impact ionizations. In this paper, a stochastically self-regulating avalanche model for passively quenched SPADs is presented. The model predicts, in qualitative agreement with experiments, three important phenomena that traditional models are unable to predict. These are: (1) an oscillatory behavior of the persistent avalanche current; (2) an exponential (memoryless) decay of the probability density function of the stochastic quenching time of the persistent avalanche current; and (3) a fast collapse of the avalanche current, under strong feedback conditions, preventing the development of a persistent avalanche current. The model specifically captures the effect of the load's feedback on the stochastic avalanche multiplication, an effect believed to be key in breaking today's counting rate barrier in the 1.55-μm detection window.
Coagulation factors promote brown adipose tissue dysfunction and abnormal systemic metabolism in obesity (2022)

Brown adipose tissue (BAT) has a role in maintaining systemic metabolic health in rodents and humans. Here, we show that metabolic stress induces BAT to produce coagulation factors, which then-together with molecules derived from the circulation-promote BAT dysfunction and systemic glucose intolerance. When mice were fed a high-fat diet (HFD), the levels of tissue factor, coagulation Factor VII (FVII), activated coagulation Factor X (FXa), and protease-activated receptor 1 (PAR1) expression increased significantly in BAT. Genetic or pharmacological suppression of coagulation factor-PAR1 signaling in BAT ameliorated its whitening and improved thermogenic response and systemic glucose intolerance in mice with dietary obesity. Conversely, the activation of coagulation factor-PAR1 signaling in BAT caused mitochondrial dysfunction in brown adipocytes and systemic glucose intolerance in mice fed normal chow. These results indicate that BAT produces endogenous coagulation factors that mediate pleiotropic effects via PAR1 signaling under metabolic stress.