gebhart/patrepeval huggingface dataset:
String Current in Decananometer nand Flash Arrays: A Compact-Modeling Investigation (2012)

This paper presents a detailed compact-modeling investigation of the string current in decananometer nand Flash arrays. This investigation allows, first of all, to highlight the role of velocity saturation, low-field mobility, and drain-induced barrier lowering on the string current versus read voltage characteristics. Results are validated on a 41-nm technology for different positions of the selected cell along the nand string, different pass voltages, and different array background patterns. The effect of cycling on the string current is then investigated by means of postcycling bake experiments, showing that the impact of charge trapping/detrapping and interface state generation/annealing varies as a function of the read current level. Compact-modeling results display that, at low read currents, charge trapping/detrapping represents the main damage mechanism for the cells, while interface states come into play for read currents close to the string saturation level via mobility degradation.
Pitch‐Tunable Size Reduction Patterning with a Temperature‐Memory Polymer (2012)

A scalable and pitch-tunable size reduction patterning method is introduced by exploiting the temperature memory effect of shape memory polymer and replica molding of UV-curable materials.
Immunogenicity and Efficacy of a Novel Multi-Antigenic Peptide Vaccine Based on Cross-Reactivity between Feline and Human Immunodeficiency Viruses (2019)

For the development of an effective HIV-1 vaccine, evolutionarily conserved epitopes between feline and human immunodeficiency viruses (FIV and HIV-1) were determined by analyzing overlapping peptides from retroviral genomes that induced both anti-FIV/HIV T cell-immunity in the peripheral blood mononuclear cells from the FIV-vaccinated cats and the HIV-infected humans. The conserved T-cell epitopes on p24 and reverse transcriptase were selected based on their robust FIV/HIV-specific CD8⁺ cytotoxic T lymphocyte (CTL), CD4⁺ CTL, and polyfunctional T-cell activities. Four such evolutionarily conserved epitopes were formulated into four multiple antigen peptides (MAPs), mixed with an adjuvant, to be tested as FIV vaccine in cats. The immunogenicity and protective efficacy were evaluated against a pathogenic FIV. More MAP/peptide-specific CD4⁺ than CD8⁺ T-cell responses were initially observed. By post-third vaccination, half of the MAP/peptide-specific CD8⁺ T-cell responses were higher or equivalent to those of CD4⁺ T-cell responses. Upon challenge, 15/19 (78.9%) vaccinated cats were protected, whereas 6/16 (37.5%) control cats remained uninfected, resulting in a protection rate of 66.3% preventable fraction (<i>p</i> = 0.0180). Thus, the selection method used to identify the protective FIV peptides should be useful in identifying protective HIV-1 peptides needed for a highly protective HIV-1 vaccine in humans.
Abstract LB-098: Sequential azacitidine and histone deacetylase inhibition induces a potent antitumor response in Kras G12D mouse model of NSCLC (2017)

Abstract Combination epigenetic treatment as a therapeutic approach holds much promise. However, to unlock the true potential of these combinatorial paradigms, further optimization is required. We have elucidated in our current study, a treatment schedule combining Azacitidine with Histone Deacetylase Inhibition (HDACi) which considers both schedule and isoform specificity. We have deployed a sequential schedule with HDACi administered post Azacitidine in a chronic low dose manner. This schedule takes advantage of two key parameters altered by Azacitidine: dsRNA induced immune signature and MYC depletion. In our system, HDACis amplify an existing immune signature and the MYC depleted environment acts as a potent sensitizer. HDACi induced augmentation of immune gene transcription seems driven predominantly through the inhibition of HDAC1/2 and HDAC6 isoforms, with broad spectrum HDACi inhibitors demonstrating the greatest potency. While the combination treatment induced perturbation of proliferation is driven by inhibition of HDAC1/2/3 isoforms. Applying this concept to a genetically engineered mouse model of NSCLC we observe a potent anti-tumor response as evidenced by a reduction in tumor burden, progression and proliferation. These phenotypic parameters are correlated with modification of both immune and proliferative gene signatures as well as alteration of key immune populations in the tumor microenvironment. We propose that this combinatorial alteration of both immune and proliferative parameters holds the promise to be a more robust treatment for NSCLC. Note: This abstract was not presented at the meeting. Citation Format: Michael Topper, Michelle Vaz, Katherine Chiappinelli, Christina DeStefano Shields, Alyssa Wenzel, Cynthia Zahnow, Pam Strissel, Reiner Strick, Stephen Baylin. Sequential azacitidine and histone deacetylase inhibition induces a potent antitumor response in Kras G12D mouse model of NSCLC [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr LB-098. doi:10.1158/1538-7445.AM2017-LB-098
Qualification and performance of a high-efficiency laser transmitter for deep-space optical communications (2022)

A high-power Laser Transmitter Assembly (LTA) was developed to support the Deep Space Optical Communications (DSOC) technology demonstration being developed by the Jet Propulsion Laboratory. NASA’s Psyche Mission plans to host the DSOC flight subsystem for testing space-to-ground high-bandwidth laser communications en route to the 16-Psyche asteroid. We review the design, performance, and qualification of the LTA Engineering Model and Flight Model (EM and FM) delivered to JPL. The LTA uses a master-oscillator power amplifier (MOPA) design and delivers up to 4.5 W at 1550 nm, with a highly efficient, cladding-pumped, polarization-maintaining erbium-ytterbium fiber amplifier. The master oscillator generates a range of pulse widths and repetition rates to support modulation formats from 16- to 128-PPM for optical data transmission at &lt;100 Mbps. The LTA was designed for high reliability and radiation hardness, and includes redundant signal and pumping paths to reduce single points of failure, hardware interlocks to ensure safe operation and protection against damage, closed-loop control of optical power, and detailed health and status via telemetry. The LTA EM and FM were subjected to unit-appropriate space qualification testing. We describe the performance testing of the EM and FM, for the characterization of key metrics such as wavelength stability, signal linewidth, optical pulse width, jitter, and extinction ratio, and polarization extinction ratio. The management of optical nonlinearities (selfphase modulation, Brillouin scattering, or pulse-to-pulse energy variation), which could result in an optical link penalty or damage to the LTA, is also detailed, and factors affecting the power efficiency are discussed.
In Vitro Selection of a Single-Stranded DNA Molecular Recognition Element against Atrazine (2014)

Widespread use of the chlorotriazine herbicide, atrazine, has led to serious environmental and human health consequences. Current methods of detecting atrazine contamination are neither rapid nor cost-effective. In this work, atrazine-specific single-stranded DNA (ssDNA) molecular recognition elements (MRE) were isolated. We utilized a stringent Systematic Evolution of Ligands by Exponential Enrichment (SELEX) methodology that placed the greatest emphasis on what the MRE should not bind to. After twelve rounds of SELEX, an atrazine-specific MRE with high affinity was obtained. The equilibrium dissociation constant (Kd) of the ssDNA sequence is 0.62 ± 0.21 nM. It also has significant selectivity for atrazine over atrazine metabolites and other pesticides found in environmentally similar locations and concentrations. Furthermore, we have detected environmentally relevant atrazine concentrations in river water using this MRE. The strong affinity and selectivity of the selected atrazine-specific ssDNA validated the stringent SELEX methodology and identified a MRE that will be useful for rapid atrazine detection in environmental samples.
Euplotes Telomerase:  Evidence for Limited Base-Pairing during Primer Elongation and dGTP as an Effector of Translocation (1998)

The telomeric sequence repeats at the ends of eukaryotic chromosomes are maintained by the ribonucleoprotein enzyme telomerase. Telomeric DNA primers are bound by telomerase both at the active site, which includes base-pairing with the RNA template, and at a second anchor site. The stabilities of Euplotes aediculatus primer-telomerase complexes were determined by measuring their dissociation rates (koff), using an assay involving photo-cross-linking at the anchor site. The primer length was varied, and mismatched substitutions were introduced in a systematic manner. We observed that koff does not scale with primer length as expected for accumulated primer-template base-pairing. This suggests that telomerase maintains a more-or-less constant number of base pairs, similar to the transcription bubble maintained by RNA polymerase. An upper limit was estimated by comparing the experimental koff for the primer-telomerase complex to that of a model DNA-RNA duplex. All the binding energy could be attributed to 10 or 11 base pairs; alternatively, there could be <10 base pairs, with the remaining energy contributed by other parts of telomerase. Most primers exhibited biphasic dissociation kinetics, with variations in both the amount in each phase and the rate for each phase. Since the cross-links monitored in the dissociation assay were all formed with the 5' region of the primer, the two phases may arise from different base-pairing registers with the RNA template, possibly representing pre- and post-translocation complexes. A shift from slow phase to fast phase dissociation was observed in the presence of dGTP, which may implicate dGTP as a positive effector of translocation.
Combustion Chamber Deposits and Knock in a Spark Ignition Engine - Some Additive and Fuel Effects (1996)

&lt;div class="htmlview paragraph"&gt;A four-cylinder engine with a slice between the head and the block carrying instrumented plugs has been used to study the growth of combustion chamber deposits and knock. Deposit thicknesses vary substantially at different locations, the thickness generally being greatest at the coolest surfaces. If a dirty engine is run on a low-boiling-point fuel such as a primary reference fuel, deposits are removed and octane requirement is reduced rapidly. Of the head deposits, those in the cooler squish region where the end gas is likely to be situated affect knock more than the deposits in the hotter regions. Different fuel additives have different effects on deposits in different areas. For instance, an additive might cause a substantial increase in deposit thickness in the hotter areas and a slight increase in total deposit weight but can control deposits in the cooler squish regions and so reduce octane requirement increase (ORI) compared to the base fuel alone. Different fuels respond to the same deposits to different extents in terms of knock. Knock ratings can depend on the fuel the deposits have been exposed to just prior to the rating. Low octane, low-boiling-point fuels appear to make the engine more prone to knock probably by facilitating the release of pro-knock species trapped in the deposits. This “chemical” ORI can be alleviated by running the engine on a full boiling range gasoline for a short time.&lt;/div&gt;
Circulating microRNA profile predicts disease progression in patients receiving second-line treatment of lapatinib and capecitabine for metastatic pancreatic cancer (2016)

Patients exhibiting pancreatic cancer possess poor rates of survival. Therefore, the identification of a biomarker that can be measured non-invasively and be used to predict patient outcomes is required for the successful treatment of pancreatic cancer. The present study evaluated serum microRNA (miRNA/miR) profiles in patients exhibiting pancreatic cancer, who were treated with lapatinib and capecitabine in a phase II trial. Serum samples were collected for the measurement of a panel of miRNAs (miR-21, miR-210, miR-221 and miR-7) associated with the epidermal growth factor receptor (EGFR)1 and human epidermal growth factor receptor (HER)2 pathways. Preclinically, human pancreatic cancer PANC-1, MIA PaCa-2 and BXCP-3 cell lines were utilized for miRNA and drug resistance studies. In total, 6/17 patients treated experienced disease progression following 2 cycles of treatment [non-responders (NRS)], while another 6/17 patients exhibited a stable disease state and received >4 cycles of treatment [responders (RS); range, 4-22 cycles]. Five patients withdrew from the study due to severe toxicity or mortality. The mean overall survival time was 6.5 vs. 10.4 months for NRS and RS, respectively. Significant upregulation of serum miRNAs at earlier time points (3-6 weeks) was observed in NRS. miRNA levels increased with cancer progression, and lapatinib and 5-fluorouracil (5-FU; the active form of capecitabine) treatment increased the miRNA levels (specifically miR-210 and miR-221) in the treatment-resistant pancreatic cancer PANC-1 and MIA PaCa-2 cell lines. However, lapatinib and 5-FU treatment did not increase the miRNA levels in the treatment-sensitive BXPC-3 cell line. Inhibition of miR-221 increased the sensitivity of the PANC-1 cells to treatment. In conclusion, an increase in specific serum miRNAs was associated with resistance to lapatinib and capecitabine treatment. Additional investigation is required with regard to the application of the miRNA panel investigated in the present study as a potential predictor of patient responses to anti-EGFR/HER2 treatment.
Molecular archeology of L1 insertions in the human genome (2002)

The sequence data give no indication that the creation of L1 structural variants depends on characteristics of the insertion locus. In addition, the formation of 5' truncated and 5' inverted L1s are probably not due to the action of the L1 endonuclease.
Analysis of Single Cells with Capillary Electrophoresis Electrospray Ionization Fourier Transform Ion Cycloton Resonance Mass Spectrometry (1996)

Recent results with on-line capillary electrophoresis (CE) electrospray ionization (ESI) Fourier transform ion cyclotron resonance (FTICR) mass spectrometry suggest that CE/ESI-FTICR can provide a powerful technique for micro-sample analyses owing to the inherent sensitivity of the technique and the enhanced information content derived from high-performance mass measurements. Using micro-sampling methods and ion accumulation techniques based on quadrupolar excitation, we demonstrate that adequate sensitivity exists to characterize the hemoglobin from a single human erythrocyte (approximately 450 amol). In these studies mass spectra with average mass resolution in excess of 45 000 (FWHM) were obtained for both the alpha- and beta chain of hemoglobin following in-column lysing of a single erythrocyte.
Mid-infrared Ge-on-Si electro-absorption modulator (2017)

We present the first waveguide electro-absorption modulator in germanium-on-silicon material platform at 3.8 μm wavelength, based on free-carrier injection into a straight waveguide. The fabricated 1 mm long device has modulation depth of >35 dB at 7 V.
Scaling 100G QPSK links for reliable network development (2010)

Nonlinearities are a performance limitation in coherent optical links, and efforts have been made to understand the tradeoffs between launch power and the penalties related to nonlinearities. Using both simulation and experimental results from our 100G testbed we investigate the use of a nonlinear phase criterion that quantifies the total nonlinear phase accumulation within a 112 Gb/s PDM-QPSK link. We examine the nonlinear effects of self-phase (SPM) and cross-phase modulation (XPM) on a 112 Gb/s PM-QPSK channel propagating between four 10 Gb/s OOK aggressor channels on a 50 GHz grid and quantify the launch power and span count scaling behavior. In order to assess the applicability of a nonlinear phase criterion on real-world links, we determine the launch power that yields a 1.5 dB OSNR penalty at a BER of 10<sup>-3</sup> for each configuration. This launch power then allows the identification of a Nonlinear Threshold Power (number of spans times launch power) that fully incorporates the increasing nonlinear penalties with further transmission distance. This metric allows for the determination of a set of engineering rules for deployment of 100 Gb/s PDM-QPSK in linear links with arbitrary number of spans and span distances. We find that this nonlinear threshold is constant in dispersion-compensated links. These experimental results are validated with simulations.
Field and bias dependence of high-frequency magnetic noise in MgO-based magnetic tunnel junctions (2009)

We present room-temperature measurements of high-frequency magnetization fluctuation (mag noise) in MgO-based nanopillar magnetic tunnel junctions (MTJs) biased with a direct current (dc). In the frequency range of 1–13 GHz, double mag-noise peaks are observed for some MTJs while others only show a single mag-noise peak. The in-plane field dependence of the mag-noise peak frequency is consistent with the Kittel formula. For all MTJs measured, the bias-dependent shift in the mag-noise peak frequency has a pronounced asymmetry. In addition, we find nonmonotonic variations in peak linewidth as a function of the external in-plane magnetic field and of the dc bias current. These suggest the possible involvement of nonmacrospin modes in spin-torque-dependent thermal mag-noise generation.
Targeting hepatocarcinogenesis model in C56BL6 mice with pan-aurora kinase inhibitor Danusertib (2018)

<b>Background</b>: To elucidate the expression of Aurora kinases (AURK) and the anticancer effects of pan-aurora kinase inhibitor Danusertib in hepatocarcinogenesis model in C56Bl6 mice. <b>Methods</b>: Thirty mice C56Bl6 were randomly divided into Group A or control, Group B animals who underwent experimental hepatocarcinogenesis with diethylnitrosamine (DEN), and Group C animals with DEN-induced hepatocarcinogenenesis that treated with pan-aurora kinase inhibitor Danusertib. Primary antibodies for immunochistochemistry (IHC) included rabbit antibodies against Ki-67, DKK1, INCENP, cleaved caspase-3, NF-κB p65, c-Jun, β-catenin. Hepatocyte growth factor receptor (C-MET/HGFR) and Bcl-2 antagonist of cell death (BAD) serum levels were determined using a quantitative sandwich enzyme immunoassay technique. <b>Results</b>: Inhibition of AURK reduced the number of DEN-induced liver tumours. Apoptosis and proliferation was very low in both DEN-induced and anti- AURK groups respectively. The hepatocellular adenoma cells of DEN-treated mice uniformly had ample nuclear INCENP whereas in anti- AURK markedly decreased. Expression of β-catenin, NF-kB and c-Jun did not differ in liver tumors of both AURK -depleted and non-depleted mice. <b>Conclusions:</b> Depletion of AURK reduced the number of DEN-induced hepatic tumours. However, their size did not differ significantly between the groups.
2165. Surveillance of Severe Viral Respiratory Infections among Children Presenting to Hôpital Saint Damien in Haiti (2022)

Abstract Background Learning the burden and seasonality of respiratory viral infections in children in resource-limited settings is critical for hospital infection care and prevention and national public health programs. We built a prospective surveillance program of severe acute respiratory illness (SARI) in hospitalized children at Hôpital Saint Damien - Nos Petits Frères et Soeurs to gather local evidence and support informed clinical and policy decision-making. The COVID-19 pandemic erupted as we were launching our project, requiring the use of available point-of-care diagnostics. Methods Children &amp;lt; 18 years of age with cough, history of fever ≥ 38 C°, of &amp;lt; 10 days evolution, and requiring hospitalization were included in the study. We obtained a nasopharyngeal swab and collected demographic and clinical data for eligible patients. Samples were tested using antigen test on-site for influenza A (Flu A) and B (Flu B), respiratory syncytial virus (RSV), and SARS-CoV-2. Afterwards, all specimens (both negative and positive) were stored and shipped for molecular studies. Results We obtained and tested 167 samples from patients since April 30, 2021, through January 31, 2022. Single isolates were detected in 88 samples (53%), multiple isolates in 20 samples (12%), and no isolates in 59 samples (35%). Positive cases for RSV, Flu A, and Flu B peaked between November and January. Rhinovirus 1A (RhV) was detected throughout the study period, with peaks around August-September and was the most often detected viral isolate (49, 38%), followed by RSV (37, 29%). Co-infections were seen with RSV, Flu A, RhV, and SARS-CoV-2. Molecular studies detected 7 isolates of Flu A not detected by rapid test, 1 isolate of Flu B, and 1 isolate of SARS-CoV-2. However, it failed to detect 2 isolates of Flu A detected by rapid test, 1 isolate of Flu B, and 1 isolate of SARS-CoV-2. Conclusion Our study captured circulating respiratory viruses in children with SARI in Haiti during the COVID-19 pandemic. Preliminary data suggest an increase in respiratory viruses between August and January. Improving point-of-care diagnostics can better inform providers of the local epidemiology of respiratory viruses and support clinical decision-making, such as good use of antibiotics. However, we confirmed the sensitivity of molecular testing. Disclosures All Authors: No reported disclosures.
The Rocky 7 Mars rover prototype (2002)

This paper provides a system overview of a new Mars rover prototype, Rocky 7. We describe all system aspects: mechanical and electrical design, computer and software infrastructure, algorithms for navigation and manipulation, science data acquisition, and outdoor rover testing. In each area, the improved or added functionality is explained in a context of its path to flight, and need within the constraints of desired science missions.
Bacterial rhamnolipids and their 3-hydroxyalkanoate precursors activate Arabidopsis innate immunity through two independent mechanisms (2021)

Plant innate immunity is activated upon perception of invasion pattern molecules by plant cell-surface immune receptors. Several bacteria of the genera <i>Pseudomonas</i> and <i>Burkholderia</i> produce rhamnolipids (RLs) from l-rhamnose and (<i>R</i>)-3-hydroxyalkanoate precursors (HAAs). RL and HAA secretion is required to modulate bacterial surface motility, biofilm development, and thus successful colonization of hosts. Here, we show that the lipidic secretome from the opportunistic pathogen <i>Pseudomonas aeruginosa</i>, mainly comprising RLs and HAAs, stimulates <i>Arabidopsis</i> immunity. We demonstrate that HAAs are sensed by the bulb-type lectin receptor kinase LIPOOLIGOSACCHARIDE-SPECIFIC REDUCED ELICITATION/S-DOMAIN-1-29 (LORE/SD1-29), which also mediates medium-chain 3-hydroxy fatty acid (mc-3-OH-FA) perception, in the plant <i>Arabidopsis thaliana</i> HAA sensing induces canonical immune signaling and local resistance to plant pathogenic <i>Pseudomonas</i> infection. By contrast, RLs trigger an atypical immune response and resistance to <i>Pseudomonas</i> infection independent of LORE. Thus, the glycosyl moieties of RLs, although abolishing sensing by LORE, do not impair their ability to trigger plant defense. Moreover, our results show that the immune response triggered by RLs is affected by the sphingolipid composition of the plasma membrane. In conclusion, RLs and their precursors released by bacteria can both be perceived by plants but through distinct mechanisms.