gebhart/patrepeval huggingface dataset:
Polymerization of Single-Wall Carbon Nanotubes under High Pressures and High Temperatures (2002)

Survey studies of pressure−temperature-induced transformations of single-wall carbon nanotubes (SWNT) at 1.5, 8.0, and 9.5 GPa and temperatures ranging from 200 to 1500 °C in a piston-cylinder or “Toroid” type high pressure devices have been carried out. It was found that the combined effects of high pressures and high temperatures produce irreversible changes in the SWNT structure, in contrast with the reversible effect of high pressure alone, previously studied by several research groups. The Raman, electron microscopy, and X-ray diffraction data obtained in the present work provide evidence for covalent interlinking of SWNT by sp3 C−C bonds which escalates with the increasing treatment temperature and pressure. The formation of new carbon structures such as nano- and microcrystalline diamond-like (cubic and hexagonal) and nanographite phases under higher pressures (8.0 and 9.5 GPa) has been observed.
Data from Characterization of Genetically Modified T-Cell Receptors that Recognize the CEA:691-699 Peptide in the Context of HLA-A2.1 on Human Colorectal Cancer Cells (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; Carcinoembryonic antigen (CEA) is a tumor-associated protein expressed on a variety of adenocarcinomas. To develop an immunotherapy for patients with cancers that overexpress CEA, we isolated and genetically modified a T-cell receptors (TCRs) that specifically bound a CEA peptide on human cancer cells.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental Design:&lt;/b&gt; HLA-A2.1 transgenic mice were immunized with CEA:691-699. A CEA-reactive TCR was isolated from splenocytes of these mice and was genetically introduced into human peripheral blood lymphocytes via RNA electroporation or retroviral transduction. Amino acid substitutions were introduced throughout the complementarity determining regions (CDR1, CDR2, and CDR3) of both TCR α and β chains to improve recognition of CEA.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; Murine lymphocytes bearing the CEA-reactive TCR specifically recognized peptide-loaded T2 cells and HLA-A2.1&lt;sup&gt;+&lt;/sup&gt; CEA&lt;sup&gt;+&lt;/sup&gt; human colon cancer cells. Both CD8&lt;sup&gt;+&lt;/sup&gt; and CD4&lt;sup&gt;+&lt;/sup&gt; human lymphocytes expressing the murine TCR specifically recognized peptide-loaded T2 cells. However, only gene-modified CD8&lt;sup&gt;+&lt;/sup&gt; lymphocytes specifically recognized HLA-A2.1&lt;sup&gt;+&lt;/sup&gt; CEA&lt;sup&gt;+&lt;/sup&gt; colon cancer cell lines, and tumor cell recognition was weak and variable. We identified two substitutions in the CDR3 of the α chain that significantly influenced tumor cell recognition by human peripheral blood lymphocytes. One substitution, T for S at position 112 (S112T), enhanced tumor cell recognition by CD8&lt;sup&gt;+&lt;/sup&gt; lymphocytes, and a second dually substituted receptor (S112T L110F) enhanced tumor cell recognition by CD4&lt;sup&gt;+&lt;/sup&gt; T cells.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusions:&lt;/b&gt; The modified CEA-reactive TCRs are good candidates for future gene therapy clinical trials and show the power of selected amino acid substitutions in the antigen-binding regions of the TCR to enhance desired reactivities.&lt;/p&gt;&lt;/div&gt;
Label-free detection of cytokines using optical microcavities (2008)

Ultra-high-Q microresonators have demonstrated sensitive and specific chemical and biological detection. The sensitivity is derived from the long photon lifetime inside the cavity and specificity is achieved through surface functionalization. Here, ultra-high-Q microcavities demonstrate label-free, single molecule detection of Interleukin-2 (IL-2) in fetal bovine serum (FBS). IL-2 is a cytokine released in response to immune system activation. The surface of the microtoroids was sensitized using anti-IL-2. The detection mechanism relies upon a thermo-optic mechanism to enhance resonant wavelength shifts induced through binding of a molecule.
The “Voice” Has It: Screen Reader Adoption and Switching Behavior Among Vision Impaired Persons in India (2013)

We present results from a mixed methods study of screen reader use and switching behavior among people with vision impairments in India. We examine loyalty and experimentation with screen readers and find that the main drivers of adoption for early users differ significantly from the factors that drive continued use by advanced users. We discuss the factor that emerges as one of the strongest stated drivers of early adoption, text-to-speech "voice" quality, particularly a "human-sounding voice" as one of the key features differentiating free/open source products from more expensive proprietary products. While the initial preferences are driven by voice quality, application support becomes more important over time as users speed up their sound settings and become more comfortable with the resultant non-human-sounding speech. We discuss these findings from two theoretical perspectives--first, through the application of the economics of behavior switching, and second, vis-à-vis novice and expert approaches toward new product adoption. We argue that these findings further our understanding of initial user comfort related to assistive technology adoption, and the impact of early technology choices on long-term technology switching behavior.
ChemInform Abstract: GENERAL APPROACH FOR THE SYNTHESIS OF POLYQUINANES. FACILE GENERATION OF MOLECULAR COMPLEXITY VIA REACTION OF 1,2‐DICARBONYL COMPOUNDS WITH DIMETHYL 3‐OXOGLUTARATE (1982)

Abstract Die Umsetzung des Glutarats (II) mit 1,2‐Diketonen (I) eröffnet den Weg zu verschiedenen Polychinan‐Derivaten wie (IV), (Vc), (VII) bzw. (X) über die jeweils angegebenen Stufen [die Darstellung von (Ia) bzw. (Ic) ist beschrieben; die Wolff‐ Kishner‐Reduktion von (Vb) zu (Vc) ist bekannt].
Geometry sensing by dendritic cells dictates spatial organization and PGE 2 -induced dissolution of podosomes Koen van den DriesSuzanne F. G. van HeldenJoost te RietRuth Diez-Ahedo • Carlo ManzoMachteld M. OudFrank N. van LeeuwenRoland Brock • Maria F. Garcia-ParajoAlessandra CambiCarl G. Figdor (2012)

Assembly and disassembly of adhesion struc- tures such as focal adhesions (FAs) and podosomes regulate cell adhesion and differentiation. On antigen-pre- senting dendritic cells (DCs), acquisition of a migratory and immunostimulatory phenotype depends on podosome dissolution by prostaglandin E2 (PGE2). Whereas the effects of physico-chemical and topographical cues have been extensively studied on FAs, little is known about how podosomes respond to these signals. Here, we show that, unlike for FAs, podosome formation is not controlled by substrate physico-chemical properties. We demonstrate that cell adhesion is the only prerequisite for podosome formation and that substrate availability dictates podosome density. Interestingly, we show that DCs sense 3-dimen- sional (3-D) geometry by aligning podosomes along the edges of 3-D micropatterned surfaces. Finally, whereas on a 2-dimensional (2-D) surface PGE2 causes a rapid increase in activated RhoA levels leading to fast podosome disso- lution, 3-D geometric cues prevent PGE2-mediated RhoA activation resulting in impaired podosome dissolution even after prolonged stimulation. Our findings indicate that 2-D Koen van den Dries and Suzanne F.G. van Helden contributed equally to this work.
Optical apparatus for forming correlation spectrometers and optical processors (2023)

Optical apparatus for forming correlation spectrometers and optical processors. The optical apparatus comprises one or more diffractive optical elements formed on a substrate for receiving light from a source and processing the incident light. The optical apparatus includes an addressing element for alternately addressing each diffractive optical element thereof to produce for one unit of time a first correlation with the incident light, and to produce for a different unit of time a second correlation with the incident light that is different from the first correlation. In preferred embodiments of the invention, the optical apparatus is in the form of a correlation spectrometer; and in other embodiments, the apparatus is in the form of an optical processor. In some embodiments, the optical apparatus comprises a plurality of diffractive optical elements on a common substrate for forming first and second gratings that alternately intercept the incident light for different units of time. In other embodiments, the optical apparatus includes an electrically-programmable diffraction grating that may be alternately switched between a plurality of grating states thereof for processing the incident light. The optical apparatus may be formed, at least in part, by a micromachining process.
Characterization of Circulating Insulin in Insulin Autoimmune Syndrome* (1986)

We examined the forms of circulating insulin in three patients with the insulin autoimmune syndrome by a method combining gel filtration and reverse phase high performance liquid chromatography (RP-HPLC). Insulin bound to circulating antibody was dissociated by molecular sieve chromatography at acid pH. The free insulin peak eluted from a Sephadex G-50 column was subsequently chromatographed on a Bio-Gel P-30 column. In all three patients, insulin coeluted with normal human insulin. However, when the partially purified insulins, obtained by gel filtration, were applied to RP-HPLC, an abnormally migrating insulin was found in two of three patients. The insulins were more hydrophobic than normal human, porcine, or bovine insulin, but were different from each other. A third patient had only a single insulin peak on RP-HPLC which corresponded to normal insulin. In contrast, the insulin from insulin-treated diabetic patients with antibodies to exogenous insulin corresponded to either porcine or bovine and normal human insulin. The antibodies in the circulation of these patients with the autoimmune syndrome were of the immunoglobulin G type and contained kappa and lambda-chains in the same proportions as antibodies in insulin-treated patients. Autoantibodies could not be distinguished from those secondary to exogenous insulin treatment on the basis of displacement of binding by human, beef, or pork insulin. These results suggest that in certain patients with the insulin autoimmune syndrome, there may be a molecular abnormality of circulating insulin. Whether this comprises a cause for the syndrome or is a result of posttranslational processing of insulin remains to be determined.
Response to “Comment on Nanometer-Scale Corrosion of Copper in De-Aerated Deionized Water” [J. Electrochem. Soc., 161, C107 (2014)] (2015)

This response is provided to comments by Spahiu and Puigdomenech criticizing the conclusion of Cleveland et al. [J. Electrochem. Soc., 161, C107 (2014)] that, in the absence of hydrogen, copper will corrode in deaerated deionized water. Spahiu and Puigdomenech base their critique on anomalies in the Pourbaix diagram presented by Cleveland et al., on concerns that the experimental system was inadequately deaerated, and on differences between the corrosion rates predicted in our work and in the work of Hultquist et al. [Proceedings of the 2008 International Corrosion Congress, Paper 3884, p. 1 (2008)]. In the present work, explanations are provided supporting our thermodynamic analysis and the experimental results. New numerical simulations show that the difference in estimated corrosion rates between our system and that published by Hultquist et al. are the natural consequence of scale and transport differences between the two systems. Thus, the comment that the difference in estimated corrosion rates between our system and that of Hultquist somehow invalidates our results is without basis. The concerns raised by Spahiu and Puigdoimenech do not invalidate the conclusions presented in Cleveland et al.
Odin: Microsoft’s Scalable Fault-Tolerant {CDN} Measurement System (2018)

Content delivery networks (CDNs) are critical for delivering high performance Internet services. Using world-wide deployments of front-ends, CDNs can direct users to the front-end that provides them with the best latency and availability. The key challenges arise from the heterogeneous connectivity of clients and the dynamic nature of the Internet that influences latency and availability. Without continuous insight on performance between users, front-ends, and external networks, CDNs will not be able to attain their full potential performance. We describe Odin, Microsoft’s Internet measurement platform for its first-party and third-party customers. Odin is designed to handle Microsoft’s large user base and need for large-scale measurements from users around the world. Odin integrates with Microsoft’s varied suite of web-client and thick-client applications, all while being mindful of the regulatory and privacy concerns of enterprise customers. Odin has been operational for 2 years. We present the first detailed study of an Internet measurement platform of this scale and complexity.
The structure of mouse tumour-necrosis factor at 1.4 Å resolution: towards modulation of its selectivity and trimerization (1999)

The 1.4 A resolution structure of recombinant mouse tumour-necrosis factor alpha (mTNF) at 100 K has been determined. The crystals are triclinic, space group P1, with unit-cell parameters a = 48.06, b = 48.18, c = 51.01 A, alpha = 114.8, beta = 103.6, gamma = 91.1 degrees. The structure was refined to a final crystallographic R value of 19.7% (Rfree = 23.3%), including 3477 protein atoms, one 2-propanol molecule, one Tris molecule and 240 water molecules. Throughout the crystal lattice, the trimers are differently packed compared with human TNF, which was crystallized in the tetragonal space group P41212 and refined to 2.6 A resolution. The structures of mTNF and human TNF are very similar, diverging mainly in regions that are either flexible and/or involved in crystal packing. Some loops in mTNF which contain residues important for receptor binding are better resolved than in human TNF, such as the surface-exposed loops 30-34 and 144-147, which are also important for receptor specificity. Compared with human TNFs, the channel formed by the three monomers in mTNF is narrower. One 2-propanol molecule trapped in the trimeric channel could be a lead compound for the design of TNF inhibitors.
Repeatable retinal imaging independent of posture and head pose with robotically-aligned optical coherence tomography (2023)

Ophthalmic optical coherence tomography (OCT) has achieved remarkable clinical success but remains sequestered in ophthalmology specialty offices. Recently introduced robotic OCT systems seek to expand patient access but fall short of their full potential due to significant imaging workspace and motion planning restrictions. Here, we present a next-generation robotic OCT system capable of imaging in any configuration that is mechanically reachable. This system overcomes prior restrictions by eliminating fixed-base tracking components, extending robot reach, and planning alignment in six degrees of freedom. With this robotic system, we show repeatable subject imaging independent of posture under widely varying head orientations.
Novel fluorinated poly(aryl ether ketone)s (1995)

Abstract Two novel fluorinated monomers were prepared and polymerized with biphenols to produce amorphous, thermally stable poly(aryl ether ketone)s. The properties of the fluorinated polymers are compared to those of unfluorinated, amorphous poly(aryl ether ketone)s. The presence of fluorine in the polymers was found to cause a decrease in glass transition temperature and Young's moduli, however, no increase in thermal stability was observed. The fluorinated polymers are soluble in common organic solvents such as chloroform and methylene chloride at room temperature, and also show solubility in solvents containing a ketonic moiety, such as acetone. Evidence of polymer branching through fluorines considered to be unreactive under the polymerization conditions was found. Efforts were made to evaluate the reactivity of fluorine atoms under the polymerization conditions using both molecular modeling and 19 F‐NMR to ascertain if such branching could be avoided. © 1995 John Wiley &amp; Sons, Inc.
Beam preshaping in a Vlasov antenna launcher using wall perturbations (2017)

Vlasov antennas are widely used for transforming the whispering gallery mode (WGM) output of gyrotrons to a free space TEM mode. To improve the overall efficiency of a Vlasov antenna system, we have investigated the use of wall perturbations inside the Vlasov launcher to transform the TEmn WGM to a Gaussian beam. In this paper, we will discuss the design methodology and present some experimental and theoretical results.
Hardware Validation Test of the Advanced Plant Habitat (2018)

An automated plant growth facility for conducting plant research supporting space biology and food production project on the International Space Station (ISS).
Combining Temporal And Spectral Features In Hmm-Based Drum Transcription. (2007)

[TODO] Add abstract here.
Synthesis of Sulfoximines and Sulfilimines with Aryl and Pyrazolylmethyl Substituents (2010)

Abstract Sulfoximines bearing pyrazolylmethyl and aryl substituents, which are relevant to the crop protection industry, and their corresponding sulfilimine intermediates, have been prepared from sulfide precursors by either iron‐catalyzed nitrogen transfer reactions or metal‐free imination procedures. Whereas the former approach leads to N ‐nosyl‐substituted products, the latter affords N ‐cyano derivatives.
Gender Bias and Universal Substitution Adversarial Attacks on Grammatical Error Correction Systems for Automated Assessment (2022)

Grammatical Error Correction (GEC) systems perform a sequence-to-sequence task, where an input word sequence containing grammatical errors, is corrected for these errors by the GEC system to output a grammatically correct word sequence. With the advent of deep learning methods, automated GEC systems have become increasingly popular. For example, GEC systems are often used on speech transcriptions of English learners as a form of assessment and feedback - these powerful GEC systems can be used to automatically measure an aspect of a candidate's fluency. The count of \textit{edits} from a candidate's input sentence (or essay) to a GEC system's grammatically corrected output sentence is indicative of a candidate's language ability, where fewer edits suggest better fluency. The count of edits can thus be viewed as a \textit{fluency score} with zero implying perfect fluency. However, although deep learning based GEC systems are extremely powerful and accurate, they are susceptible to adversarial attacks: an adversary can introduce a small, specific change at the input of a system that causes a large, undesired change at the output. When considering the application of GEC systems to automated language assessment, the aim of an adversary could be to cheat by making a small change to a grammatically incorrect input sentence that conceals the errors from a GEC system, such that no edits are found and the candidate is unjustly awarded a perfect fluency score. This work examines a simple universal substitution adversarial attack that non-native speakers of English could realistically employ to deceive GEC systems used for assessment.
Gene Expression Ratios Lead to Accurate and Translatable Predictors of DR5 Agonism across Multiple Tumor Lineages (2015)

Death Receptor 5 (DR5) agonists demonstrate anti-tumor activity in preclinical models but have yet to demonstrate robust clinical responses. A key limitation may be the lack of patient selection strategies to identify those most likely to respond to treatment. To overcome this limitation, we screened a DR5 agonist Nanobody across >600 cell lines representing 21 tumor lineages and assessed molecular features associated with response. High expression of DR5 and Casp8 were significantly associated with sensitivity, but their expression thresholds were difficult to translate due to low dynamic ranges. To address the translational challenge of establishing thresholds of gene expression, we developed a classifier based on ratios of genes that predicted response across lineages. The ratio classifier outperformed the DR5+Casp8 classifier, as well as standard approaches for feature selection and classification using genes, instead of ratios. This classifier was independently validated using 11 primary patient-derived pancreatic xenograft models showing perfect predictions as well as a striking linearity between prediction probability and anti-tumor response. A network analysis of the genes in the ratio classifier captured important biological relationships mediating drug response, specifically identifying key positive and negative regulators of DR5 mediated apoptosis, including DR5, CASP8, BID, cFLIP, XIAP and PEA15. Importantly, the ratio classifier shows translatability across gene expression platforms (from Affymetrix microarrays to RNA-seq) and across model systems (in vitro to in vivo). Our approach of using gene expression ratios presents a robust and novel method for constructing translatable biomarkers of compound response, which can also probe the underlying biology of treatment response.
Dereverberation and Signal Separation of Speech Signal Mixtures (2022)

This paper contributes to the dereverberation and signal separation problem of speech signal mixtures in reverberant environments by comparing the performance of different subband transform techniques, namely PolyPhase Filter Banks (PPFB) and weighted overlap-add short-term Fourier transform (WOLA STFT). The subband techniques allow large deconvolution problem to be subdivided into many smaller problems, which are feasible to solve. The critical finding is that the PPFB has better performance measures when compared with the WOLA STFT while having a lower computational complexity due to a lower subsampling rate. From the evaluation study, it can be seen that both the signal separation and the de-reverberation perform well even for high levels of background noise (SNR=0dB).
On Learning the $cμ$ Rule in Single and Parallel Server Networks (2018)

We consider learning-based variants of the $c μ$ rule for scheduling in single and parallel server settings of multi-class queueing systems. In the single server setting, the $c μ$ rule is known to minimize the expected holding-cost (weighted queue-lengths summed over classes and a fixed time horizon). We focus on the problem where the service rates $μ$ are unknown with the holding-cost regret (regret against the $c μ$ rule with known $μ$) as our objective. We show that the greedy algorithm that uses empirically learned service rates results in a constant holding-cost regret (the regret is independent of the time horizon). This free exploration can be explained in the single server setting by the fact that any work-conserving policy obtains the same number of samples in a busy cycle. In the parallel server setting, we show that the $c μ$ rule may result in unstable queues, even for arrival rates within the capacity region. We then present sufficient conditions for geometric ergodicity under the $c μ$ rule. Using these results, we propose an almost greedy algorithm that explores only when the number of samples falls below a threshold. We show that this algorithm delivers constant holding-cost regret because a free exploration condition is eventually satisfied.