gebhart/patrepeval huggingface dataset:
Leptospira interrogans Lsa23 protein recruits plasminogen, factor H and C4BP from normal human serum and mediates C3b and C4b degradation (2015)

It has been reported that pathogenic Leptospira are resistant to normal human serum (NHS) due to their ability to evade the complement immune system by interacting with factor H (FH) and C4b-binding protein (C4BP) regulators. Moreover, plasmin generation on the leptospiral surface diminishes C3b and IgG deposition, decreasing opsonophagocytosis by immune competent cells. We have previously reported that Lsa23 (LIC11360) is a multipurpose protein capable of binding purified extracellular matrix molecules, FH, C4BP and plasminogen (PLG)/plasmin in the presence of PLG activators. In this work, we provide further evidence that Lsa23 is located at the bacterial surface by using immunofluorescence microscopy. We show that Lsa23 has the ability to acquire FH, C4BP and PLG from NHS, and use these interactions to evade innate immunity. The binding with the complement regulators FH and C4BP preserves factor I (FI) activity, leading to C3b and C4b degradation products, respectively. C3b and C4b alpha-chain cleavage was also observed when Lsa23 bound to PLG generating plasmin, an effect blocked by the protease inhibitor aprotinin. Lsa23 also inhibited lytic activity by NHS mediated by both classical and alternative complement pathways. Thus, Lsa23 has the ability to block both pathways of the complement system, and may help pathogenic Leptospira to escape complement-mediated clearance in human hosts. Indeed, NHS treated with Lsa23 confers a partial serum resistance phenotype to Leptospira biflexa, whereas blocking this protein with anti-Lsa23 renders pathogenic L. interrogans more susceptible to complement-mediated killing. Thus, Lsa23 is a multifunctional protein involved in many pathways, featuring C4b cleavage by plasmin, knowledge that may help in the development of preventive approaches to intervene with human complement escape by this versatile pathogen.
Prutor: A System for Tutoring CS1 and Collecting Student Programs for\n Analysis (2016)

An introductory programming course (CS1) is an integral part of any\nundergraduate curriculum. Due to large number and diverse programming\nbackground of students, providing timely and personalised feedback to\nindividual students is a challenging task for any CS1 instructor. The help\nprovided by teaching assistants (typically senior students) is not sufficient\nas it suffers from unintentional bias and, most of the time, not quick enough.\n In this paper, we present Prutor, a tutoring system platform to conduct\nintroductory programming courses. Prutor is a cloud-based web application that\nprovides instant and useful feedback to students while solving programming\nproblems. Prutor stores, at regular intervals, the snapshots of students'\nattempts to solve programming problems. These intermediate versions of the\nstudent programs provide the instructors (and data analysts) a view of the\nstudents' approach to solving programming problems. Since Prutor is accessible\nthrough any standard web browser, students do not need to worry about\ndependencies external to the programming course, viz. Operating Systems,\nEditors, Compilers, Compiler Options, etc.. This enables the students to focus\non solving only the programming problems. Apart from the code snapshots at\nregular intervals, Prutor also collects other valuable data such as the time\ntaken by the students to solve the problems, the number of compile and\nexecution events, and the errors made. We have used this data in developing\nintelligent tools for giving feedback to students, some of which are described\nbriefly in this paper. This system thus serves as a platform for tutoring as\nwell as data collection for researchers.\n
Stress polarity dependence of the activation energy in time-dependent dielectric breakdown of thin gate oxides (1998)

Stress polarity dependence of the activation energies in the two time dependent dielectric breakdown measurements, the constant-current injection (Q/sub bd/ testing) and the constant-voltage stressing (t/sub bd/ testing) are investigated for gate oxides with the thickness ranging from 10 to 4 nm. A remarkable polarity dependence of the activation energies appears in the t/sub bd/ testing when the oxide thickness decreases. This phenomenon is found to be due to a characteristic temperature dependence of the gate current density during the whole t/sub bd/ testing period for thinner oxides, which is considered as a result from the temperature dependence of the electron trapping process during the stressing.
Circulating exosomal microRNA-203 is associated with metastasis possibly via inducing tumor-associated macrophages in colorectal cancer (2017)

A primary tumor can create a premetastatic niche in distant organs to facilitate the development of metastasis. The mechanism by which tumor cells communicate with host cells to develop premetastatic niches is unclear. We focused on the role of microRNA (miR) signaling in promoting metastasis. Here, we identified <i>miR-203</i> as a signaling molecule between tumors and monocytes in metastatic colorectal cancer (CRC) patients. Notably, high expression of serum exosomal <i>miR-203</i>, a major form in circulation, was associated with distant metastasis and an independent poor prognostic factor, whereas low expression in tumor tissues was a poor prognostic factor in CRC patients. We also found that exosomes carrying <i>miR-203</i> from CRC cells were incorporated into monocytes and <i>miR-203</i> could promote the expression of M2 markers <i>in vitro</i>, suggesting <i>miR-203</i> promoted the differentiation of monocytes to M2-tumor-associated macrophages (TAMs). In a xenograft mouse model, <i>miR-203</i>-transfected CRC cells developed more liver metastasis compared to control cells. In conclusion, serum exosomal <i>miR-203</i> expression is a novel biomarker for predicting metastasis, possibly via promoting the differentiation of monocytes to M2-TAMs in CRC. Furthermore, we propose the concept of site-dependent functions for <i>miR-203</i> in tumor progression.
Cost-effectiveness of MR Imaging–guided Strategies for Detection of Prostate Cancer in Biopsy-Naive Men (2017)

Purpose To evaluate the cost-effectiveness of multiparametric diagnostic magnetic resonance (MR) imaging examination followed by MR imaging-guided biopsy strategies in the detection of prostate cancer in biopsy-naive men presenting with clinical suspicion of cancer for the first time. Materials and Methods A decision-analysis model was created for biopsy-naive men who had been recommended for prostate biopsy on the basis of abnormal digital rectal examination results or elevated prostate-specific antigen levels (age groups: 41-50 years, 51-60 years, and 61-70 years). The following three major strategies were evaluated: (a) standard transrectal ultrasonography (US)-guided biopsy; (b) diagnostic MR imaging followed by MR imaging-targeted biopsy, with no biopsy performed if MR imaging findings were negative; and (c) diagnostic MR imaging followed by MR imaging-targeted biopsy, with a standard biopsy performed when MR imaging findings were negative. The following three MR imaging-guided biopsy strategies were further evaluated in each MR imaging category: (a) biopsy with cognitive guidance, (b) biopsy with MR imaging/US fusion guidance, and (c) in-gantry MR imaging-guided biopsy. Model parameters were derived from the literature. The primary outcome measure was net health benefit (NHB), which was measured as quality-adjusted life-years (QALYs) gained or lost by investing resources in a new strategy compared with a standard strategy at a willingness-to-pay (WTP) threshold of $50 000 per QALY gained. Probabilistic sensitivity analysis was performed by using Monte Carlo simulations. Results Noncontrast MR imaging followed by cognitively guided MR biopsy (no standard biopsy if MR imaging findings were negative) was the most cost-effective approach, yielding an additional NHB of 0.198 QALY compared with the standard biopsy approach. Noncontrast MR imaging followed by in-gantry MR imaging-guided biopsy (no standard biopsy if MR imaging findings were negative) led to the highest NHB gain of 0.251 additional QALY compared with the standard biopsy strategy. All MR imaging strategies were cost-effective in 94.05% of Monte Carlo simulations. Analysis by age groups yielded similar results. Conclusion MR imaging-guided strategies for the detection of prostate cancer were cost-effective compared with the standard biopsy strategy in a decision-analysis model. <sup>©</sup> RSNA, 2017 Online supplemental material is available for this article.
Gaussian-3 theory using density functional geometries and zero-point energies (1999)

A variation of Gaussian-3 (G3) theory is presented in which the geometries and zero-point energies are obtained from B3LYP density functional theory [B3LYP/6-31G(d)] instead of geometries from second-order perturbation theory [MP2(FU)/6-31G(d)] and zero-point energies from Hartree–Fock theory [HF/6-31G(d)]. This variation, referred to as G3//B3LYP, is assessed on 299 energies (enthalpies of formation, ionization potentials, electron affinities, proton affinities) from the G2/97 test set [J. Chem. Phys. 109, 42 (1998)]. The G3//B3LYP average absolute deviation from experiment for the 299 energies is 0.99 kcal/mol compared to 1.01 kcal/mol for G3 theory. Generally, the results from the two methods are similar, with some exceptions. G3//B3LYP theory gives significantly improved results for several cases for which MP2 theory is deficient for optimized geometries, such as CN and O2+. However, G3//B3LYP does poorly for ionization potentials that involve a Jahn–Teller distortion in the cation (CH4+, BF3+, BCl3+) because of the B3LYP/6-31G(d) geometries. The G3(MP2) method is also modified to use B3LYP/6-31G(d) geometries and zero-point energies. This variation, referred to as G3(MP2)//B3LYP, has an average absolute deviation of 1.25 kcal/mol compared to 1.30 kcal/mol for G3(MP2) theory. Thus, use of density functional geometries and zero-point energies in G3 and G3(MP2) theories is a useful alternative to MP2 geometries and HF zero-point energies.
Imaging impact of multilayer tuning in EUV masks, experimental validation (2014)

This paper reports on the experimental validation of adapting the multilayer periodicity of an EUV mask to mitigate pattern shifts at wafer level. This EUV specific pattern shift will eventually contribute to overlay budgets which continue to tighten with decreasing technology node. A good understanding of its manipulators, i.e., mask 3D effects, is paramount. By means of mask diffractometry and scanner exposures at numerical aperture of 0.33 the mask-induced pattern shift at wafer level is verified. These measurements are then correlated to rigorous simulations using a calibrated EUV mask stack model to accurately predict the imaging impact of multilayer tuning in EUV masks. A comprehensive interpretation of the mask 3D impact on pattern shift at wafer level will be presented based on simulated diffraction pupils supported by experimental verification at both mask and wafer level.
Catalytic Carbon Oxidation Over Ruthenium‐Based Catalysts (2006)

Exceptional activity in carbon oxidation is displayed by a zeolite-supported ruthenium catalyst (see diagram; Y=carbon weight loss) that unlike platinum catalysts does not require the presence of NOx in the gas stream. This catalyst opens up a new route for catalytic soot oxidation in diesel engine exhaust filters.
Printed dose-recording tag based on organic complementary circuits and ferroelectric nonvolatile memories (2015)

We have demonstrated a printed electronic tag that monitors time-integrated sensor signals and writes to nonvolatile memories for later readout. The tag is additively fabricated on flexible plastic foil and comprises a thermistor divider, complementary organic circuits, and two nonvolatile memory cells. With a supply voltage below 30 V, the threshold temperatures can be tuned between 0 °C and 80 °C. The time-temperature dose measurement is calibrated for minute-scale integration. The two memory bits are sequentially written in a thermometer code to provide an accumulated dose record.
ChemInform Abstract: Synthesis, Structure, and Reactivity of Trimethylphosphine‐Zirconocene Thioaldehyde Complexes. (1987)

Abstract The zirconocene thioaldehyde complexes (IV), which are stabilized by coordination of a trimethylphosphine ligand, are prepared simply by treatment of (I) with a thiol (II) and heating the resulting compounds (III) in the presence of trimethylphosphine.
Carbon-13 NMR spectroscopy as a probe for the exclusively steric effects of ligand superstructure on the binding constants of lacunar macrobicyclic complexes with dioxygen (1985)

ADVERTISEMENT RETURN TO ISSUEPREVArticleCarbon-13 NMR spectroscopy as a probe for the exclusively steric effects of ligand superstructure on the binding constants of lacunar macrobicyclic complexes with dioxygenKenneth A. Goldsby, Thomas J. Meade, Maasaki Kojima, and Daryle H. BuschCite this: Inorg. Chem. 1985, 24, 16, 2588–2590Publication Date (Print):July 1, 1985Publication History Published online1 May 2002Published inissue 1 July 1985https://pubs.acs.org/doi/10.1021/ic00210a027https://doi.org/10.1021/ic00210a027research-articleACS PublicationsRequest reuse permissionsArticle Views41Altmetric-Citations4LEARN 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
Effect of Enrichment Procedure upon Auxotroph Recovery in Escherichia coli K-12 (1975)

Proline-requiring auxotrophs are recovered preferentially after mutant enrichment procedures (e.g., penicillin) which perturb the cell envelope, but not after procedures (e.g., thymineless death) which affect other cellular targets. This probably stems from effects of penicillin and similar antibiotics upon proline metabolic and transport enzymes associated with the cell envelope.
Denoising Electromagnatic Surveys Using LSTMs (2022)

Resistivity readings obtained from electromagnetic crosswell surveys provide insight for reservoir water saturation prediction. Although high resistivity values should map to low water saturation and vice versa, in many cases the readings may not be consistent with this correlation. This is due to factors that add noise to the resistivity reading, such as the borehole effect and the salinity of the injected water. Here, we attempt to treat the resistivity reading to negatively correlate with water saturation, enhancing the accuracy and interperability of water saturation prediction models. We utilize the resistivity readings from locations further from sources of noise to correct the inconsistencies in the resistivity readings using a Long-Short Term Memory (LSTM) Neural Network approach. Our results demonstrate that by addressing noisy inconsistencies in the data, the performance of the water saturation model increases in terms of R2 from 0.62 to 0.70. Moreover, upon deploying model interpretation method, namely, SHAP TreeExplainer, we show that the resistivity-based features in the water saturation prediction model posses higher importance values than before the enhancement, in comparison with porosity features.
PiRA: IC authentication utilizing intrinsic variations in pin resistance (2015)

The rapidly rising incidences of counterfeit Integrated Circuits (ICs) including cloning attacks pose a significant threat to the semiconductor industry. Conventional functional/structural testing are mostly ineffective to identify different forms of cloned ICs. On the other hand, existing design for security (DfS) measures are often not attractive due to additional design effort, hardware overhead and test cost. In this paper, we propose a novel robust IC authentication approach, referred to as PiRA, to validate the integrity of ICs in presence of cloning attacks. It exploits intrinsic random variations in pin resistances across ICs to create unique chip-specific signatures for authentication. Pin resistance is defined as the resistance looking into or out the pin according to set parameters and biasing conditions, measured by standard tests for IC defect/performance analysis such as input leakage, protection diode and output load current tests. A major advantage of PiRA over existing methodologies is that it incurs virtually zero design effort and overhead. Furthermore, unlike most authentication approaches, it works for all chip types including analog/mixed-signal ICs and can be applied to legacy designs. Theoretical analysis as well as experimental measurements with common digital and analog ICs verify the effectiveness of PiRA.
ChemInform Abstract: Cubic ↔ Orthorhombic Transition in the Stoichiometric Spinel LiMn2O4. (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.
An effective π-extended squaraine for solution-processed organic solar cells with high efficiency (2016)

A π-extension strategy is an effective way for squaraines for achieving high-performance photovoltaic materials capable of showing much enhanced hole mobility.
Serving large-scale batch computed data with project Voldemort (2012)

Current serving systems lack the ability to bulk load massive immutable data sets without affecting serving performance. The performance degradation is largely due to index creation and modification as CPU and memory resources are shared with request serving. We have extended Project Voldemort, a general-purpose distributed storage and serving system inspired by Amazon's Dynamo, to support bulk loading terabytes of read-only data. This extension constructs the index offline, by leveraging the fault tolerance and parallelism of Hadoop. Compared to MySQL, our compact storage format and data deployment pipeline scales to twice the request throughput while maintaining sub 5 ms median latency. At LinkedIn, the largest professional social network, this system has been running in production for more than 2 years and serves many of the data-intensive social features on the site.
ChemInform Abstract: BUILDING BLOCKS OF OLIGOSACCHARIDES. PART XLIV. SYNTHESIS OF 3‐DEOXY‐D‐MANNO‐2‐OCTULOSONIC ACID (KDO) OLIGOSACCHARIDES (1983)

Abstract Das Glycosylbromid (Ib), das aus (Ia) durch Behandeln mit Titantetrabromid gewonnen wird, reagiert mit dem Galactose‐Derivat (II) zum (,S‐verknüpften Disaccharid (III).
Analysis of tiling array expression studies with flexible designs in Bioconductor (waveTiling) (2012)

The waveTiling package provides the user with a convenient tool for the analysis of tiling array trancriptome data for a multitude of experimental set-ups. Regardless of the study design, the probe-wise analysis allows for the detection of transcriptional effects in both exonic, intronic and intergenic regions, without prior consultation of existing annotation.
Characterization of the biosynthetic gene cluster for the ribosomally synthesized cyclic peptide ustiloxin B in Aspergillus flavus (2014)

Ustiloxin B is a secondary metabolite known to be produced by Ustilaginoidea virens. In our previous paper, we observed the production of this compound by Aspergillus flavus, and identified two A. flavus genes responsible for ustiloxin B biosynthesis (Umemura et al., 2013). The compound is a cyclic tetrapeptide of Tyr-Ala-Ile-Gly, whose tyrosine is modified with a non-protein coding amino acid, norvaline. Although its chemical structure strongly suggested that ustiloxin B is biosynthesized by a non-ribosomal peptide synthetase, in the present study, we observed its synthesis through a ribosomal peptide synthetic (RiPS) pathway by precise sequence analyses after experimental validation of the cluster. The cluster possessed a gene (AFLA_094980), termed ustA, whose translated product, UstA, contains a 16-fold repeated peptide embedding a tetrapeptide, Tyr-Ala-Ile-Gly, that is converted into the cyclic moiety of ustiloxin B. This result strongly suggests that ustiloxin B is biosynthesized through a RiPS pathway and that UstA provides the precursor peptide of the compound. The present work is the first characterization of RiPS in Ascomycetes and the entire RiPS gene cluster in fungi. Based on the sequence analyses, we also proposed a biosynthetic mechanism involving the entire gene cluster. Our finding indicates the possibility that a number of unidentified RiPSs exist in Ascomycetes as the biosynthetic genes of secondary metabolites, and that the feature of a highly repeated peptide sequence in UstA will greatly contribute to the discovery of additional RiPS.
Ultrafast exciton dynamics in ZnO: Excitonic versus electron-hole plasma lasing (2011)

The use of ZnO bulk and especially nanolayer and nanowire structures for novel device applications has led to a renewal of interest in high-electron-density processes in ZnO, such as those occurring during lasing in ZnO. Using a pump-probe reflectometry technique, we investigate the ultrafast exciton dynamics of bulk ZnO under femtosecond laser excitation close to lasing conditions. Under intense excitation by 266-nm femtosecond (fs) pump pulses, the exciton resonance becomes highly damped and does not recover for several picoseconds. This slow recovery indicates a significant screening of the Coulomb interaction. Even below the lasing thresholds typically found for ZnO nanolayers and nanowires, we observe damping of the exciton resonance for several picoseconds, which indicates that the primary mechanism for lasing in ZnO induced by femtosecond laser pumping is electron-hole plasma recombination.
Broadband 10 Gb/s operation of graphene electro‐absorption modulator on silicon (2016)

Abstract High performance integrated optical modulators are highly desired for future optical interconnects. The ultra‐high bandwidth and broadband operation potentially offered by graphene based electro‐absorption modulators has attracted a lot of attention in the photonics community recently. In this work, we theoretically evaluate the true potential of such modulators and illustrate this with experimental results for a silicon integrated graphene optical electro‐absorption modulator capable of broadband 10 Gb/s modulation speed. The measured results agree very well with theoretical predictions. A low insertion loss of 3.8 dB at 1580 nm and a low drive voltage of 2.5 V combined with broadband and athermal operation were obtained for a 50 μm‐length hybrid graphene‐Si device. The peak modulation efficiency of the device is 1.5 dB/V. This robust device is challenging best‐in‐class Si (Ge) modulators for future chip‐level optical interconnects.