gebhart/patrepeval huggingface dataset:
Quantifying data retention of perpendicular spin-transfer-torque magnetic random access memory chips using an effective thermal stability factor method (2015)

The thermal stability of perpendicular Spin-Transfer-Torque Magnetic Random Access Memory (STT-MRAM) devices is investigated at chip level. Experimental data are analyzed in the framework of the Néel-Brown model including distributions of the thermal stability factor Δ. We show that in the low error rate regime important for applications, the effect of distributions of Δ can be described by a single quantity, the effective thermal stability factor Δeff, which encompasses both the median and the standard deviation of the distributions. Data retention of memory chips can be assessed accurately by measuring Δeff as a function of device diameter and temperature. We apply this method to show that 54 nm devices based on our perpendicular STT-MRAM design meet our 10 year data retention target up to 120 °C.
Translation of New Experimental Test Methods for the Evaluation and Design of Shaped Charge Perforators to Field Applications (2011)

Abstract Perforation performance evaluation has come under scrutiny in several recent publications. For most shaped charge perforators sold, performance is evaluated in cement targets, from which downhole performance is extrapolated. This method has been shown to generally over-predict downhole performance, with broad implications for perforating systems and shaped charge design, and well completion design. Advanced test methodologies are an order of magnitude more complex than the simplified cement penetration tests. This paper details a set of experimental shaped charge development programs with specific geometry and/or flow performance requirements and examples of their corresponding field performance. Tests have been performed with full simulation of single shot perforation, and simplified perforating simulations into stressed rock. Results are reported for shale, sandstone, and high permeability sandstone targets. Designs tested include both conventional and reactive shaped charges. In one example from 2008-2009, CNX completed fourteen wells using both conventional and reactive perforating systems to evaluate any impact on completion performance. Stimulation and production data have been analyzed for 81 stimulation stages. When comparing wells perforated with reactive shaped charges to conventionally perforated offsets, a reduction in breakdown pressure gradient of between 13% and 29% is observed. Subsequent treating pressures are reduced by 6% to 15%. The wells perforated with reactive shaped charges have also exhibited significantly slower productivity decline over the first nine months. In addition, near-perforation permeability has been mapped using advanced digital imaging techniques. This allows the grain structure and permeability distribution of a perforated rock target to be accurately measured as a function of radial distance away from the perforation wall and longitudinal position along the perforation tunnel. The paper describes important improvements in our understanding of perforation damage distribution, and provides techniques for use in conjunction with API RP 19B Section 2 and 4 tests to design perforating shaped charges and systems.
Extensive dissemination and intraclonal maturation of HIV Env vaccine-induced B cell responses (2019)

Well-ordered HIV-1 envelope glycoprotein (Env) trimers are prioritized for clinical evaluation, and there is a need for an improved understanding about how elicited B cell responses evolve following immunization. To accomplish this, we prime-boosted rhesus macaques with clade C NFL trimers and identified 180 unique Ab lineages from ∼1,000 single-sorted Env-specific memory B cells. We traced all lineages in high-throughput heavy chain (HC) repertoire (Rep-seq) data generated from multiple immune compartments and time points and expressed several as monoclonal Abs (mAbs). Our results revealed broad dissemination and high levels of somatic hypermutation (SHM) of most lineages, including tier 2 virus neutralizing lineages, following boosting. SHM was highest in the Ab complementarity determining regions (CDRs) but also surprisingly high in the framework regions (FRs), especially FR3. Our results demonstrate the capacity of the immune system to affinity-mature large numbers of Env-specific B cell lineages simultaneously, supporting the use of regimens consisting of repeated boosts to improve each Ab, even those belonging to less expanded lineages.
Interplay between reversible phosphorylation and irreversible ADP-ribosylation of eukaryotic translation elongation factor 2 (2018)

The functionality of eukaryotic translation elongation factor 2 (eEF2) is modulated by phosphorylation, eEF2 is simultaneously the molecular target of ADP-ribosylating toxins. We analyzed the interplay between phosphorylation and diphthamide-dependent ADP-ribosylation. Phosphorylation does not require diphthamide, eEF2 without it still becomes phosphorylated. ADP-ribosylation not only modifies the H715 diphthamide but also inhibits phosphorylation of S595 located in proximity to H715, and stimulates phosphorylation of T56. S595 can be phosphorylated by CDK2 and CDK1 which affects EEF2K-mediated T56-phosphorylation. Thus, ADP-ribosylation and S595-phosphorylation by kinases occur within the same vicinity and both trigger T56-phosphorylation. Diphthamide is surface-accessible permitting access to ADP-ribosylating enzymes, the adjacent S595 side chain extends into the interior. This orientation is incompatible with phosphorylation, neither allowing kinase access nor phosphate attachment. S595 phosphorylation must therefore be accompanied by structural alterations affecting the interface to ADP-ribosylating toxins. In agreement with that, replacement of S595 with Ala, Glu or Asp prevents ADP-ribosylation. Phosphorylation (starvation) as well as ADP-ribosylation (toxins) inhibit protein synthesis, both affect the S595/H715 region of eEF2, both trigger T57-phosphorylation eliciting similar transcriptional responses. Phosphorylation is short lived while ADP-ribosylation is stable. Thus, phosphorylation of the S595/H715 'modifier region' triggers transient interruption of translation while ADP-ribosylation arrests irreversibly.
A Role for the Proton-coupled Folate Transporter (PCFT-SLC46A1) in Folate Receptor-mediated Endocytosis (2008)

Recently, this laboratory identified a proton-coupled folate transporter (PCFT), with optimal activity at low pH. PCFT is critical to intestinal folate absorption and transport into the central nervous system because there are loss-of-function mutations in this gene in the autosomal recessive disorder, hereditary folate malabsorption. The current study addresses the role PCFT might play in another transport pathway, folate receptor (FR)-mediated endocytosis. FRalpha cDNA was transfected into novel PCFT(+) and PCFT(-) HeLa sublines. FRalpha was shown to bind and trap folates in vesicles but with minimal export into the cytosol in PCFT(-) cells. Cotransfection of FRalpha and PCFT resulted in enhanced folate transport into cytosol as compared with transfection of FRalpha alone. Probenecid did not inhibit folate binding to FR, but inhibited PCFT-mediated transport at endosomal pH, and blocked FRalpha-mediated transport into the cytosol. FRalpha and PCFT co-localized to the endosomal compartment. These observations (i) indicate that PCFT plays a role in FRalpha-mediated endocytosis by serving as a route of export of folates from acidified endosomes and (ii) provide a functional role for PCFT in tissues in which it is expressed, such as the choroid plexus, where the extracellular milieu is at neutral pH.
A novel comparative robustness index for evaluating the performance of grid-tied PV inverters (2016)

Increasing the integration of PV systems requires more reliable and more robust PV inverter architectures. This paper presents a novel index called Smart Inverter Robustness Index (SIRI) to evaluate the robustness of grid-tied PV inverters. Proposed index considering four major operational characteristics such as efficiency, Total Harmonic Distortion (THD), Maximum Power Point Tracking (MPPT) effectiveness and Power Factor (PF) compliance provides a comparative evaluation of PV inverters. Robustness of a single-phase grid-tied PV inverter under varying manufacturing inaccuracies is analyzed by using SIRI index and a boundary for robust operation is determined. Statistical analysis and Random Latin Hypercube Sampling (RLHS) algorithm are used to model the impact of physical variations of passive components on PV inverter operation with minimum sampling points. Effectiveness and feasibility of proposed index is verified by simulation and experimental results of a single-phase grid-tied PV inverter.
Nanotube memories for space applications (2004)

The radiation hardness characteristics of nano-electromechanical single-walled carbon nanotube (SWNT) memory elements has been studied. The NRAM bits have been exposed to 100 krad, 1 Mrad and 10 Mrad of gamma-radiation. Initial test results indicate that NRAM is an extremely radiation hard memory.
The opioid crisis and … reconsidering the use of drugs that affect body temperature (2018)

The New York Times recently reported that opioids are now the leading cause of death of Americans under the age of 50 [1]. This shocking statistic is a current assessment of the deadly effects of o...
Modeling geminate pair dissociation in organic solar cells: high power conversion efficiencies achieved with moderate optical bandgaps (2012)

We propose a model for geminate electron–hole dissociation in organic photovoltaic (OPV) cells and show how power conversion efficiencies greater than those currently achieved might be realized via design strategies employing moderate optical bandgaps and enhanced charge delocalization near the donor–acceptor interface. Applying this model to describing geminate electron–hole dissociation via charge transfer (CT) states, we find good agreement with recently published high-efficiency experimental data. The optimal bandgap for current-generation organic active layer materials is argued to be ∼1.7 eV – significantly greater than in previous analyses, including the Shockley–Queisser approach based upon non-excitonic solar cell dynamics. For future higher efficiency OPVs, the present results show that the optimal bandgap should be slightly lower, ∼1.6 eV. Finally, these results support design strategies aimed at enhancing mobility near the donor–acceptor interface and reducing the electron–hole binding energy, rather than striving to further reduce the bandgap.
Data from Isolation of T-Cell Receptors Specifically Reactive with Mutated Tumor-Associated Antigens from Tumor-Infiltrating Lymphocytes Based on CD137 Expression (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; The adoptive transfer of lymphocytes genetically modified to express tumor reactive T-cell receptors (TCR) can mediate tumor regression. Some tumor-infiltrating lymphocytes (TIL) recognize somatic mutations expressed only in the patient's tumors, and evidence suggests that clinically effective TILs target tumor-specific neoantigens. Here we attempted to isolate neoantigen-reactive TCRs as a prelude to the treatment of patients with autologous T cells genetically modified to express such TCRs.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental Design:&lt;/b&gt; Mutations expressed by tumors were identified using whole-exome and RNA sequencing. Tandem minigene (TMG) constructs encoding 12–24 mutated gene products were synthesized, each encoding the mutated amino acid flanked by 12 amino acids of the normal protein sequence. TILs were cultured with autologous dendritic cells (DC) transfected with &lt;i&gt;in vitro&lt;/i&gt; transcribed (IVT) mRNAs encoding TMGs and were evaluated for IFNγ secretion and CD137 expression. Neoantigen-reactive T cells were enriched from TILs by sorting for CD137&lt;sup&gt;+&lt;/sup&gt; CD8&lt;sup&gt;+&lt;/sup&gt; T cells and expanded &lt;i&gt;in vitro&lt;/i&gt;. Dominant TCR α and β chains were identified in the enriched populations using a combination of 5′ rapid amplification of cDNA ends, deep sequencing of genomic DNA, PairSeq analysis, and single-cell RT-PCR analysis. Human PBL retrovirally transduced to express the TCRs were evaluated for recognition of relevant neoantigens.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; We identified 27 TCRs from 6 patients that recognized 14 neoantigens expressed by autologous tumor cells.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusions:&lt;/b&gt; This strategy provides the means to generate T cells expressing neoantigen-reactive TCRs for use in future adoptive cell transfer immunotherapy trials for patients with cancer. &lt;i&gt;Clin Cancer Res; 23(10); 2491–505. ©2016 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
Precision Carbon Deposition Using Pyrolytic Laser Chemical Vapor Deposition (LCVD) 73 (2000)

Laser Chemical Vapor Deposition (LCVD) can be used to rapid prototype many different metals and ceramics. The spatial resolution is potentially very fine, depending on the accuracy of stage or laser movement, and the size of the laser spot used for the localized heating. This paper describes a set of experiments performed using an LCVD system powered with a 100 Watt CO2 laser. The laser was focused to 200 mm onto a graphite substrate to deposit pyrolytic carbon. The morphologies of the carbon deposits were studied while varying laser power, reagent concentration, scanning speeds, and scanning patterns.
Boholamide A, an APD-Class, Hypoxia-Selective Cyclodepsipeptide (2020)

Calcium homeostasis is implicated in some cancers, leading to the possibility that selective control of calcium might lead to new cancer drugs. On the basis of this idea, we designed an assay using a glioblastoma cell line and screened a collection of 1000 unique bacterial extracts. Isolation of the active compound from a hit extract led to the identification of boholamide A (<b>1</b>), a 4-amido-2,4-pentadieneoate (APD)-class peptide. Boholamide A (<b>1</b>) applied in the nanomolar range induces an immediate influx of Ca<sup>2+</sup> in glioblastoma and neuronal cells. APD-class natural products are hypoxia-selective cytotoxins that primarily target mitochondria. Like other APD-containing compounds, <b>1</b> is hypoxia selective. Since APD natural products have received significant interest as potential chemotherapeutic agents, <b>1</b> provides a novel APD scaffold for the development of new anticancer compounds.
DYRK1A antagonists rescue degeneration and behavioural deficits of in vivo models based on amyloid-β, Tau and DYRK1A neurotoxicity (2022)

Alzheimer's disease (AD) involves pathological processing of amyloid precursor protein (APP) into amyloid-β and microtubule associated protein Tau (MAPT) into hyperphosphorylated Tau tangles leading to neurodegeneration. Only 5% of AD cases are familial making it difficult to predict who will develop the disease thereby hindering our ability to treat the causes of the disease. A large population who almost certainly will, are those with Down syndrome (DS), who have a 90% lifetime incidence of AD. DS is caused by trisomy of chromosome 21 resulting in three copies of APP and other AD-associated genes, like dual specificity tyrosine-phosphorylation-regulated kinase 1A (DYRK1A) overexpression. This implies that DYRK1a inhibitors may have therapeutic potential for DS and AD, however It is not clear how overexpression of each of these genes contributes to the pathology of each disease as well as how effective a DYRK1A inhibitor would be at suppressing any of these. To address this knowledge gap, we used Drosophila models with human Tau, human amyloid-β or fly DYRK1A (minibrain (mnb)) neuronal overexpression resulting in photoreceptor neuron degeneration, premature death, decreased locomotion, sleep and memory loss. DYRK1A small molecule Type 1 kinase inhibitors (DYR219 and DYR533) were effective at suppressing these disease relevant phenotypes confirming their therapeutic potential.
Vasoactive intestinal peptide receptor antagonist [4Cl-D-Phe6, Leu17] VIP (1986)

From structure-activity relationship studies of rat growth hormone-releasing factor (rGFR) on the vasoactive intestinal peptide (VIP) receptor in an in vitro preparation of exocrine pancreas, we predicted that [4Cl-D-Phe6, Leu17]VIP would be a competitive antagonist for the action of VIP. Micromolar concentrations of synthetic [4Cl-D-Phe6, Leu17]VIP competitively antagonized VIP-stimulated amylase release in the pancreatic preparation and VIP-stimulated short-circuit current changes in a colonic tumor cell line. In addition, [4Cl-D-Phe6, Leu17]VIP inhibited amylase release stimulated by rGRF, high concentrations of secretin (agents that act through the VIP receptor), and peptide contaminants in a preparation of natural glucagon. Finally, [4Cl-D-Phe6, Leu17]VIP did not inhibit the action of agonists for the secretin, GRF, or glucagon receptors.
New digital predistortion design based on mixed-signal cartesian feedback training for 3G homodyne transmitter (2012)

In this paper, a smart adaptive RF power amplifier linearization technique is presented. We invest a Mixed-Signal Cartesian Feedback Loop design to train an embedded Random Access Memory in order to overcome digital-stage latency and bandwidth limitation. The new design consists of a traditional analog stage including filters, I/Q modulator, feedback I/Q demodulator and an improved digital stage which adjusts the phase misalignment around the loop and updates the RAM. We used a not fully-pipelined CORDIC design for the digital part in order to improve the system operating frequency without increasing the silicon surface area. We implemented this design for the UMTS standard using ASIC 65nm low power technology. We reached 230 MHz with system power consumption less than 6 mw which is better than a fully analog system (8.8 mW).
Multimerization and DNA Binding Properties of INI1/hSNF5 and Its Functional Significance (2009)

INI1/hSNF5/BAF47/SMARCB1 is an HIV-1 integrase (IN)-binding protein that modulates viral replication in multiple ways. A minimal IN-binding domain of INI1, S6 (amino acids 183-294), transdominantly inhibits late events, and down-modulation of INI1 stimulates early events of HIV-1 replication. INI1 both stimulates and inhibits in vitro integration depending on IN concentration. To gain further insight into its role in HIV-1 replication, we purified and biochemically characterized INI1. We found that INI1 forms multimeric structures. Deletion analysis indicated that the Rpt1 and Rpt2 motifs form the minimal multimerization domain. We isolated mutants of INI1 that are defective for multimerization using a reverse yeast two-hybrid system. Our results revealed that INI1 residues involved in multimerization overlap with IN-binding and nuclear export domains and are required for nuclear retention and co-localization with IN. Multimerization-defective mutants are also defective for mediating the transdominant effect of INI1-S6-(183-294). Furthermore, we found that INI1 is a minor groove DNA-binding protein. Although IN binding and multimerization are required for INI1-mediated inhibition, the acceptor DNA binding property of INI1 may be required for stimulation of in vitro strand transfer activities of IN. Binding of INI1 to IN results in the formation of presumably inactive high molecular weight IN-INI1 complexes, and the multimerization-defective mutant was unable to form these complexes. These results indicate that the multimerization and IN binding properties of INI1 are necessary for its ability to both inhibit integration and influence assembly and particle production, providing insights into the mechanism of INI1-mediated effects in HIV-1 replication.
Gas-Pressure Sintering of β-Silicon Nitride Containing Y<sub>2</sub>O<sub>3</sub> and Nd<sub>2</sub>O<sub>3</sub> (1992)

Y2O3-Nd2O3-doped β-Si3N4 was sintered at 1700° to 1900°C for 4h in 10MPa N2, and the effect of the amount of the additives and sintering temperatures on stength, fracture toughness and the microstructure was investigated. A dense material (>98% of the theoretical) was obtained by firing at 1900°C with addition of 1 to 10mol% of oxides. Rod-like β-Si3N4 grains developed by firing at 1900°C increased the fracture toughness up to 7.8MPa√m because of the pull-out and the crack-deflection mechanism. The material made from β-Si3N4 powder had a high Weibull modules than that from α-Si3N4 powder.
Rare de novo deletion of metabotropic glutamate receptor 7 (GRM7) gene in a patient with autism spectrum disorder (2015)

GRM7, the gene encoding metabotropic glutamate receptor 7 (mGluR7), have been implicated in multiple neuropsychiatric disorders and shown to mediate excitatory synaptic neurotransmitter signaling and plasticity in the mammalian brain. Here we report a 303 kb de novo deletion at band 3p26.1, disrupting five coding exons of GRM7 in a proband with autism spectrum disorder, and hyperactivity. Our exon transcriptome-mutation contingency index method shows that three of the exons within the breakpoint boundaries are under purifying selection and highly expressed in prenatal brain regions. Based on our results and a thorough review of the literature, we propose that haploinsufficiency of the GRM7 product (mGluR7) contributes to autism spectrum disorders and hyperactivity phenotype as seen in the patient described here.
Feature-enhancing zoom to facilitate Ki-67 hot spot detection (2014)

Image processing algorithms in pathology commonly include automated decision points such as classifications. While this enables efficient automation, there is also a risk that errors are induced. A different paradigm is to use image processing for enhancements without introducing explicit classifications. Such enhancements can help pathologists to increase efficiency without sacrificing accuracy. In our work, this paradigm has been applied to Ki-67 hot spot detection. Ki-67 scoring is a routine analysis to quantify the proliferation rate of tumor cells. Cell counting in the hot spot, the region of highest concentration of positive tumor cells, is a method increasingly used in clinical routine. An obstacle for this method is that while hot spot selection is a task suitable for low magnification, high magnification is needed to discern positive nuclei, thus the pathologist must perform many zooming operations. We propose to address this issue by an image processing method that increases the visibility of the positive nuclei at low magnification levels. This tool displays the modified version at low magnification, while gradually blending into the original image at high magnification. The tool was evaluated in a feasibility study with four pathologists targeting routine clinical use. In a task to compare hot spot concentrations, the average accuracy was 75&plusmn;4.1% using the tool and 69&plusmn;4.6% without it (n=4). Feedback on the system, gathered from an observer study, indicate that the pathologists found the tool useful and fitting in their existing diagnostic process. The pathologists judged the tool to be feasible for implementation in clinical routine.