gebhart/patrepeval huggingface dataset:
Control of side-lobe intensity for attenuated phase-shifting mask in 157-nm lithography (2003)

The TaSiOx attenuated phase-shifting mask (Att-PSM) has strong potential for durability against laser irradiation and good lithographic performance in 157 nm lithography. However, the resist resolution limit and depth of focus (DOF) are deteriorated by side-lobe patterns generated near the contact hole. This is because the side-lobe intensity generated near the light-transmitting region becomes larger in sub 100 nm contact holes. To minimize the effect of side-lobes and improve lithographic performance, we evaluated an Att-PSM with a chrome light-shielding layer and optimized the transmittance of its attenuated phase-shifting film. In an optical simulation, we investigated the effect of the side-lobe intensity on the resist region (i.e., a reduction in resist thickness). The light-shielding film was placed on the attenuated phase-shifting film to prevent the side-lobe pattern, and its effect on the imaginary resist pattern was simulated. We found that the distance between the patterning edge of the hole and that of the light-shielding region must be greater than 90 nm to fabricate a 100 nm isolated hole without side-lobe patterns. The side-lobe intensity could be controlled using the chrome-shielding-type Att-PSM, and the lithographic performance (such as resolution limit and DOF) was enhanced.
Sparse dictionary learning from 1-BIT data (2014)

This work examines a sparse dictionary learning task - that of fitting a collection of data points, arranged as columns of a matrix, to a union of low-dimensional linear subspaces - in settings where only highly quantized (single bit) observations of the data matrix entries are available. We analyze a complexity penalized maximum likelihood estimation strategy, and obtain finite-sample bounds for the average per-element squared approximation error of the estimate produced by our approach. Our results are reminiscent of traditional parametric estimation tasks - we show here that despite the highly-quantized observations, the normalized per-element estimation error is bounded by the ratio between the number of “degrees of freedom” of the matrix and its dimension.
System design of reverse-powered G.fast (2012)

The continued growth of multimedia traffic pushes access network operators to further boost performance over their copper infrastructure network. As a result, digital subscriber line technology has evolved substantially. Field and lab trials have proven that recent innovations, such as crosstalk cancellation and phantom mode transmission, can push data rates of VDSL2 higher than 100 Mb/s on a single twisted pair and 300 Mb/s on two pairs. In ITU-T Q4, a new access technology to provide aggregate data rates in the range of 500 Mb/s to 1 Gb/s per copper loop of up to a few hundred meters is being defined under the G.fast project. G.fast enables the continued cost-effective deployment of fiber in the access network. In this paper, we give an overview of some key challenges this new access technology needs to overcome. By taking into account the expected access network topology, we give guidelines for the node architecture and deployment of G.fast.
Quality of Enzymatically Treated 72° Brix Orange Juice Stored at Refrigerated Temperatures (1986)

ABSTRACT Fresh Valencia orange juice was treated with 0, 70, and 350 ppm of commercial pectic enzymes, concentrated to 72° Brix and stored at –7°, –1°, 7°, and 13°C for up to 6 months. The 70 ppm enzyme treatment successfully reduced initial apparent viscosity by about 25%. For the 70 ppm enzyme treated samples after 6 months storage at all four temperatures, juice cloud remained acceptable, furfural remained below the significant level, and at −1°C, vitamin C levels were above 32 mg/100 mL. There was no significant difference in taste after 6 months storage at −7°C between control and 70 ppm enzyme treated samples. Product quality of enzymatically treated orange concentrate stored at refrigerated temperatures was of sufficient quality to realize potential savings of 17% in storage and 30% in refrigeration.
Randomized, Double‐Blinded, Placebo‐Controlled Trial of Fibrinogen Concentrate Supplementation After Complex Cardiac Surgery (2015)

URL: http://www.clinicaltrials.gov. Unique identifier: NCT01471730.
Properties of an Arcanobacterium haemolyticum strain isolated from a donkey. (2015)

The present study was designed to characterize phenotypically and genotypically an Arcanobacterium haemolyticum strain (A. haemolyticum P646) isolated from a purulent nasal discharge of a donkey. A. haemolyticum P646 showed, compared to sheep blood, an enhanced hemolytic reaction on rabbit blood agar, a synergistic CAMP-like reaction with Streptococcus agalactiae and Rhodococcus equi as indicator strains, a reverse CAMP reaction in the zone of Staphylococcus aureus beta-hemolysin and the typical biochemical properties of this species. The species identity could be confirmed by MALDI-TOF MS analysis, by sequencing the 16S rDNA and glyceraldehyde-3-phosphate dehydrogenase encoding gene gap and by amplification of A. haemolyticum specific parts of 16S-23S rDNA intergenic spacer region and 23S rDNA. A. haemolyticum P646 and the reference strain A. haemolyticum DSM 20595 were further characterized by amplification of the putative virulence genes encoding arcanolysin, phospholipase D, hemolysin A, CAMP factor family protein, a collagen binding protein and two neuraminidases which were present for A. haemolyticum DSM 20595. A. haemolyticum P646 showed a comparable gene spectrum but was negative for the genes encoding collagen binding protein and neuraminidase H. To our knowledge, the present study is the first phenotypic and genotypic characterization of an A. haemolyticum strain isolated from a donkey.
Halide-mediated dealkylation of phosphotriesters (2023)

In one embodiment, a method includes contacting a phosphotriester and a halogen salt in a polar solvent. In another embodiment, a method for dealkylating tributylphosphate includes contacting tributylphosphate and a halogen salt in a polar solvent.
“Addition” and “Subtraction”: Selectivity Design for Type II Maternal Embryonic Leucine Zipper Kinase Inhibitors (2017)

While adding the structural features that are more favored by on-target activity is the more common strategy in selectivity optimization, the opposite strategy of subtracting the structural features that contribute more to off-target activity can also be very effective. Reported here is our successful effort of improving the kinase selectivity of type II maternal embryonic leucine zipper kinase inhibitors by applying these two complementary approaches together, which clearly demonstrates the powerful synergy between them.
Development and Identification of a Novel Anti-HIV-1 Peptide Derived by Modification of the N-Terminal Domain of HIV-1 Integrase (2016)

The viral enzyme integrase (IN) is essential for the replication of human immunodeficiency virus type 1 (HIV-1) and represents an important target for the development of new antiretroviral drugs. In this study, we focused on the N-terminal domain (NTD), which is mainly involved into protein oligomerization process, for the development and synthesis of a library of overlapping peptide sequences, with specific length and specific offset covering the entire native protein sequence NTD IN 1-50. The most potent fragment, VVAKEIVAH (peptide 18), which includes a His residue instead of the natural Ser at position 39, inhibits the HIV-1 IN activity with an IC50 value of 4.5 μM. Amino acid substitution analysis on this peptide revealed essential residues for activity and allowed us to identify two nonapeptides (peptides 24 and 25), that show a potency of inhibition similar to the one of peptide 18. Interestingly, peptide 18 does not interfere with the dynamic interplay between IN subunits, while peptides 24 and 25 modulated these interactions in different manners. In fact, peptide 24 inhibited the IN-IN dimerization, while peptide 25 promoted IN multimerization, with IC50 values of 32 and 4.8 μM, respectively. In addition, peptide 25 has shown to have selective anti-infective cell activity for HIV-1. These results confirmed peptide 25 as a hit for further development of new chemotherapeutic agents against HIV-1.
Identification of Epstein-Barr Virus (EBV) Nuclear Antigen 2 (EBNA2) Target Proteins by Proteome Analysis: Activation of EBNA2 in Conditionally Immortalized B Cells Reflects Early Events after Infection of Primary B Cells by EBV (2004)

The Epstein-Barr virus (EBV) is a ubiquitous B-lymphotropic herpesvirus associated with several malignant tumors, e.g., Burkitt's lymphoma and Hodgkin's disease, and is able to efficiently immortalize primary B lymphocytes in vitro. The growth program of infected B cells is initiated and maintained by the viral transcription factor EBV nuclear antigen 2 (EBNA2), which regulates viral and cellular genes, including the proto-oncogene c-myc. In our study, patterns of protein expression in B cells with and without EBNA2 were analyzed by two-dimensional polyacrylamide gel electrophoresis and mass spectrometry. For this purpose, we used a conditional immortalization system for EBV, a B cell line (EREB2-5) that expresses an estrogen receptor-EBNA2 fusion protein. In order to discriminate downstream targets of c-Myc from c-Myc-independent EBNA2 targets, we used an EREB2-5-derived cell line, P493-6, in which c-Myc is expressed under the control of a tetracycline-regulated promoter. Of 20 identified EBNA2 target proteins, 11 were c-Myc dependent and therefore most probably associated with proliferation, and one of these proteins was a posttranslationally modified protein, i.e., hypusinylated eIF5a. Finally, to estimate the relevance of EBNA2 targets during early EBV infection, we analyzed the proteomes of primary B cells before and after infection with EBV. The protein expression pattern induced upon EBV infection was similar to that following EBNA2 activation. These findings underscore the value of EREB2-5 cells as an appropriate model system for the analysis of early events in the process of EBV-mediated B-cell immortalization.
Sm‐p80‐based schistosomiasis vaccine: double‐blind preclinical trial in baboons demonstrates comprehensive prophylactic and parasite transmission‐blocking efficacy (2018)

Schistosomiasis is of public health importance to an estimated one billion people in 79 countries. A vaccine is urgently needed. Here, we report the results of four independent, double-blind studies of an Sm-p80-based vaccine in baboons. The vaccine exhibited potent prophylactic efficacy against transmission of Schistosoma mansoni infection and was associated with significantly less egg-induced pathology, compared with unvaccinated control animals. Specifically, the vaccine resulted in a 93.45% reduction of pathology-producing female worms and significantly resolved the major clinical manifestations of hepatic/intestinal schistosomiasis by reducing the tissue egg-load by 89.95%. A 35-fold decrease in fecal egg excretion in vaccinated animals, combined with an 81.51% reduction in hatching of eggs into the snail-infective stage (miracidia), demonstrates the parasite transmission-blocking potential of the vaccine. Substantially higher Sm-p80 expression in female worms and Sm-p80-specific antibodies in vaccinated baboons appear to play an important role in vaccine-mediated protection. Preliminary analyses of RNA sequencing revealed distinct molecular signatures of vaccine-induced effects in baboon immune effector cells. This study provides comprehensive evidence for the effectiveness of an Sm-p80-based vaccine for schistosomiasis.
Covalent grafting of polythymidylic acid onto amine-containing polystyrene latex particles (2000)

The covalent grafting of a 35-base poly(thymidylic) acid (dT35) onto aminated polystyrene latex has been studied. The oligonucleotide was activated by 1,4-phenylene diisothiocyanate (PDC) prior to grafting reaction. The influence of various experimental conditions related either to the medium (pH, ionic strength) or to the latex (nature and surface charge density, presence of adsorbed nonionic surfactant) was studied. Discrimination between covalent grafting and adsorption was achieved by desorbing the non-covalently grafted dT35 induced by consecutive washings with a suitable buffer solution. The amount of covalently grafted oligonucleotide directly correlated to the concentration and accessible functional groups at the particle surface.
MP35-19 ASSOCIATION OF URINARY PCA3 AND TMPRSS2:ERG RISK GROUPS WITH DETECTION OF PROSTATE CANCER AT REPEAT BIOPSY IN MEN WITH AN INITIAL NEGATIVE PROSTATE BIOPSY (2018)

METHODS: We evaluated 519 patients treated with radical prostatectomy (RP) and extended pelvic lymph node (ePLND) for high risk PCa between 2011 and 2016. NLR was available in all cases and calculated from blood samples 1 week before RP. Univariable and multivariable logistic regression analyses evaluated the impact of NLR on adverse pathological outcomes (pT3b/pT4, LNI and Gleason score 8-10). Linear regression analyses examined the correlation of NLR and number of positive nodes. The best-cut off methodology was employed. The impact of NLR on the accuracy of the Briganti nomogram for LNI prediction was evaluated using the area under the curve (AUC) method. Kaplan-Meier curves and cox regression analyses tested the impact of NLR on biochemical recurrence (BCR).
Second Preimage Attacks on Dithered Hash Functions. (2007)

Abstract. The goal of this paper is to analyze the security of dithered variants of the Merkle-Damgård mode of operation that use a third input to indicate the position of a block in the message to be hashed. These modes of operation for hash functions have been proposed to avoid some structural weaknesses of the Merkle-Damgard paradigm, e.g. that second preimages can be constructed in much less than 2 n work, as pointed out by Kelsey and Schneier. Among the modes of operation that use such a third input are Rivest’s dithered hashing and Biham and Dunkelman’s Haifa proposal. We propose several new second preimage attacks on the Merkle-Damgård mode of operation, which can also attack Rivest’s dithered hash with almost the same complexity. When applied to Shoup’s UOWHF, these attacks can be shown to be optimal since their complexity matches Shoup’s security bound.
COMPUTER INFORMATION RETRIEVAL (2013)

Human–computer information retrieval (HCIR) is the study of information retrieval techniques that integrate human intelligence and algorithmic search to help people explore, understand, and use information. Since 2007, we have held an annual gathering of researchers and practitioners to advance the state of the art in this field. This meeting report summarizes the history of the HCIR symposium and emphasizes its relevance to the data science community.
Tuning of Surface Roughness and Lattice Constant in MgO(111)/Al2O3(0001) Grown by Laser Energy Controlled Pulsed Laser Deposition (2011)

We have studied the effect of variable laser energy on pulsed laser deposition (PLD) grown MgO(111) films on Al 2 O 3 (0001) substrates by X-ray diffraction and reflectivity measurements, atomic force microscopy and reflection high energy electron diffraction. In spite of the polar instability of MgO(111) surface, the surface roughness drastically decreases from ∼2 to ∼0.5 nm as the laser energy increases from ∼50 to ∼150 mJ. The in-plane lattice constant is larger than the bulk value at the smaller laser energy while it is smaller than the bulk value at the larger laser energy. This indicates that the balance between the electrostatic energy due to the polar structure, which favors a larger in-plane lattice constant, and the interface epitaxial strain, which favors a smaller in-plane lattice constant in MgO(111)/Al 2 O 3 (0001), can be tuned by varying the laser energy in PLD.
GenderMag: A Method for Evaluating Software's Gender Inclusiveness (2016)

In recent years, research into gender differences has established that individual differences in how people problem-solve often cluster by gender. Research also shows that these differences have direct implications for software that aims to support users' problem-solving activities, and that much of this software is more supportive of problem-solving processes favored (statistically) more by males than by females. However, there is almost no work considering how software practitioners—such as User Experience (UX) professionals or software developers—can find gender-inclusiveness issues like these in their software. To address this gap, we devised the GenderMag method for evaluating problem-solving software from a gender-inclusiveness perspective. The method includes a set of faceted personas that bring five facets of gender difference research to life, and embeds use of the personas into a concrete process through a gender-specialized Cognitive Walkthrough. Our empirical results show that a variety of practitioners who design software—without needing any background in gender research—were able to use the GenderMag method to find gender-inclusiveness issues in problem-solving software. Our results also show that the issues the practitioners found were real and fixable. This work is the first systematic method to find gender-inclusiveness issues in software, so that practitioners can design and produce problem-solving software that is more usable by everyone.
A Connective Tissue Growth Factor Signaling Receptor in Corneal Fibroblasts (2012)

CTGF binds to the M6P/IGF-2-R with high affinity, and the M6P/IGF-2-R is required for CTGF-stimulated proliferation in fibroblasts. These observations suggest that the M6P/IGF-2-R may be a new antifibrotic target.
CHAPTER 12. Discovery and Therapeutic Relevance of Small Molecule Modifiers of MicroRNA Function (2019)

MicroRNAs (miRNAs) are small, non-coding RNAs that predominantly regulate gene expression via translational repression. Dysregulation of miRNAs has been linked to various human diseases, including cancer, suggesting that targeting miRNAs with small molecules may hold therapeutic potential. As such, several approaches have been employed in order to discover small molecule modulators of miRNA function. Here we discuss recent methods used to identify small molecules that target miRNAs. Furthermore, considerations for experimental design as well as investigation into potential modes of action and pre-therapeutic evaluation of miRNA inhibitors are mentioned.
Synthetic repertoires derived from convalescent COVID-19 patients enable discovery of SARS-CoV-2 neutralizing antibodies and a novel quaternary binding modality (2021)

The ongoing evolution of SARS-CoV-2 into more easily transmissible and infectious variants has sparked concern over the continued effectiveness of existing therapeutic antibodies and vaccines. Hence, together with increased genomic surveillance, methods to rapidly develop and assess effective interventions are critically needed. Here we report the discovery of SARS-CoV-2 neutralizing antibodies isolated from COVID-19 patients using a high-throughput platform. Antibodies were identified from unpaired donor B-cell and serum repertoires using yeast surface display, proteomics, and public light chain screening. Cryo-EM and functional characterization of the antibodies identified N3-1, an antibody that binds avidly (K<sub>d,app</sub> = 68 pM) to the receptor binding domain (RBD) of the spike protein and robustly neutralizes the virus <i>in vitro</i>. This antibody likely binds all three RBDs of the trimeric spike protein with a single IgG. Importantly, N3-1 equivalently binds spike proteins from emerging SARS-CoV-2 variants of concern, neutralizes UK variant B.1.1.7, and binds SARS-CoV spike with nanomolar affinity. Taken together, the strategies described herein will prove broadly applicable in interrogating adaptive immunity and developing rapid response biological countermeasures to emerging pathogens.
Synthesis of 5H‐tetrazolo[5,1‐c][1,4]benzodiazepines (1985)

Abstract A three step synthesis of 5 H ‐tetrazolo[5,1‐ c ][1,4]benzodiazepin‐11‐ones 8a‐d via the reaction of a substituted benzyl azide and ethyl cyanoformate is described. The derived lactams are converted to the corresponding 11‐thiones 9a‐d and, through the S ‐methylated derivatives, to the 11‐amino analogs 11a‐f. All of the described compounds are representatives of a novel ring system.
Exploring Expressive Augmented Reality (2015)

We present "FingAR Puppet", an Augmented Reality (AR) system enhancing social pretend play by young children. Unlike goal-oriented AR systems that augment reality with informative instructions, FingAR Puppet helps children associate expressive interpretations with immediate reality. Empirical results show that FingAR Puppet promotes reasoning about emotional states, communication and divergent thinking during social pretend play for children 4-6 years old. We suggest that this study opens an interesting space for future AR systems to support complex cognitive and social development in early childhood. We also identify broader implications from using theories of cognitive development to guide the design of tangible and augmented interactions.
An Expiration Date for Pharmacogenetic Test Results and Prescribing Guidance? (2023)

Journal Article An Expiration Date for Pharmacogenetic Test Results and Prescribing Guidance? Get access Viviana Hernandez-Martinez, Viviana Hernandez-Martinez College of Pharmacy, Belmont University, Nashville, TN, United States Search for other works by this author on: Oxford Academic Google Scholar Jorge Duconge, Jorge Duconge School of Pharmacy, University of Puerto Rico, Medical Sciences Campus, San Juan, PR, United States Search for other works by this author on: Oxford Academic Google Scholar Gualberto Ruaño Gualberto Ruaño Institute of Living at Hartford Hospital, Hartford, CT, United States Address correspondence to this author at: Institute of Living at Hartford Hospital, 200 Retreat Ave, Hartford, CT 06102, United States. Tel: 860-972-3773. E-mail gualberto.ruano@hhchealth.org. Search for other works by this author on: Oxford Academic Google Scholar The Journal of Applied Laboratory Medicine, Volume 8, Issue 4, July 2023, Pages 826–830, https://doi.org/10.1093/jalm/jfad016 Published: 25 May 2023 Article history Received: 08 November 2022 Accepted: 17 February 2023 Published: 25 May 2023
Output facet heating mechanism for uncoated high power long wave infrared quantum cascade lasers (2020)

Output facet temperatures of an uncoated high power continuous-wave quantum cascade laser (QCL) emitting at 8.5 μm were measured by using micro-Raman thermometry. The rate of the measured temperature changes with the injected electrical power increased from 6.5 K/W below the laser threshold to 12.3 K/W above the threshold. In addition, the measured temperature rise exceeded 220 K at an optical power of 0.9 W, well above the model projections based only on Joule heating. Facet oxidation was characterized via x-ray photoelectron spectroscopy measurements at incremental etch depths. While the oxidation reactions of InP and Ga were observed only at the surface level, the measured penetration of native Al2O3 was ∼24 nm. COMSOL thermal modeling demonstrated that light reabsorption by the native Al2O3 layer could well explain the additional temperature rise above the threshold. These results suggest that facet oxidation must be addressed to ensure the reliability of high-power long wave infrared QCLs.