gebhart/patrepeval huggingface dataset:
Search for Leptoquarks Decaying to $\mu$ + $X$ Meson with the D0 Detector at the Fermilab Tevatron Collider (1999)

We describe a search for the pair production of second generation leptoquarks that decay to muons plus other particles in 94 $pb^{-1}$ of data taken with the D0 detector at the Fermilab Tevatron (center-of-mass energy $\sqrt{s}$ = 1.8 TeV) from 1993{96. The search places limits on the cross sections and mass of second generation leptoquarks for various branching ratios and couplings. For both scalar leptoquarks decaying into a muon and a quark the mass limit is 200 GeV/$c^2$ while for one scalar leptoquark decaying into a muon and a quark with the other scalar leptoquark decaying into a neutrino and a quark the mass limit is 160 GeV/$c^2$ at the 95% confidence level.
A 35-GHz differential distributed loss-compensation amplifier (2008)

The demand for 40+ Gb/s broadband drivers and equalizers for electrical and optical links compels the use of distributed circuit techniques and on-chip loss compensation. A distributed loss-compensation scheme is presented for synthetic transmission lines. The distributed loss-compensated amplifier is implemented in a 120 nm BiCMOS process using only NMOS devices. A 3 dB bandwidth of 35 GHz is measured with gain ripple of +/-1 dB while consuming only 18 mW.
Dissipation Indicates Memory Formation in Driven Disordered Systems (2023)

Disordered and amorphous materials often retain memories of perturbations they have experienced since preparation. Studying such memories is a gateway to understanding this challenging class of systems. However, it often requires the ability to measure local structural changes in response to external drives. Here, we show that dissipation is a generic macroscopic indicator of the memory of the largest perturbation. Through experiments in crumpled sheets under cyclic drive, we show that dissipation transiently increases when first surpassing the largest perturbation due to irreversible structural changes with unique statistics. This finding is used to devise novel memory readout protocols based on global observables only. The general applicability of this approach is demonstrated by revealing a similar memory effect in a three-dimensional amorphous solid.
Proteomic profiling of the autoimmune response to breast cancer antigens uncovers a suppressive effect of hormone therapy (2013)

Our findings suggest occurrence of a global altered immune response to breast cancer-derived proteins associated with HT. Thus a full understanding of factors that modulate the immune response is necessary to translate autoantibody panels into clinical applications.
Single-cell characterization and metabolic profiling of in vitro cultured human skeletal progenitors with enhanced in vivo bone forming capacity (2019)

Cell populations and their interplay provide the basis of a cell-based regenerative construct. Serum-free preconditioning can overcome the less predictable behavior of serum expanded progenitor cells, but the underlying mechanism and how this is reflected in vivo remains unknown. Herein, the cellular and molecular changes associated with a cellular phenotype shift induced by serum-free preconditioning of human periosteum-derived cells were investigated. Following BMP-2 stimulation, preconditioned cells displayed enhanced in vivo bone forming capacity, associated with an adapted cellular metabolism together with an elevated expression of BMPR2. Single-cell RNA sequencing confirmed the activation of pathways and transcriptional regulators involved in bone development and fracture healing, providing support for the augmentation of specified skeletal progenitor cell populations. The reported findings illustrate the importance of appropriate in vitro conditions for the in vivo outcome. In addition, BMPR2 represents a promising biomarker for the enrichment of skeletal progenitor cells for in vivo bone regeneration.
Strain relaxation effect by nano-pattern etching in InGaN/GaN quantum well structures grown by rf-plasma assisted molecular beam epitaxy. (2008)

The IQE of InGaN quantum-wells emit from green to red is not so high due to spatial separation of electrons and holes by strain-induced piezo-electric-field. The strain relaxation in InGaN-QWs by nano etching is discussed.
Data from Small-Molecule Polθ Inhibitors Provide Safe and Effective Tumor Radiosensitization in Preclinical Models (2023)

&lt;div&gt;AbstractPurpose:&lt;p&gt;DNA polymerase theta (Polθ, encoded by the &lt;i&gt;POLQ&lt;/i&gt; gene) is a DNA repair enzyme critical for microhomology mediated end joining (MMEJ). Polθ has limited expression in normal tissues but is frequently overexpressed in cancer cells and, therefore, represents an ideal target for tumor-specific radiosensitization. In this study we evaluate whether targeting Polθ with novel small-molecule inhibitors is a feasible strategy to improve the efficacy of radiotherapy.&lt;/p&gt;Experimental Design:&lt;p&gt;We characterized the response to Polθ inhibition in combination with ionizing radiation in different cancer cell models &lt;i&gt;in vitro&lt;/i&gt; and &lt;i&gt;in vivo&lt;/i&gt;.&lt;/p&gt;Results:&lt;p&gt;Here, we show that ART558 and ART899, two novel and specific allosteric inhibitors of the Polθ DNA polymerase domain, potently radiosensitize tumor cells, particularly when combined with fractionated radiation. Importantly, noncancerous cells were not radiosensitized by Polθ inhibition. Mechanistically, we show that the radiosensitization caused by Polθ inhibition is most effective in replicating cells and is due to impaired DNA damage repair. We also show that radiosensitization is still effective under hypoxia, suggesting that these inhibitors may help overcome hypoxia-induced radioresistance. In addition, we describe for the first time ART899 and characterize it as a potent and specific Polθ inhibitor with improved metabolic stability. &lt;i&gt;In vivo&lt;/i&gt;, the combination of Polθ inhibition using ART899 with fractionated radiation is well tolerated and results in a significant reduction in tumor growth compared with radiation alone.&lt;/p&gt;Conclusions:&lt;p&gt;These results pave the way for future clinical trials of Polθ inhibitors in combination with radiotherapy.&lt;/p&gt;&lt;/div&gt;
Persistence of Zinc-Binding Bacterial Superantigens at the Surface of Antigen-Presenting Cells Contributes to the Extreme Potency of These Superantigens as T-Cell Activators (2005)

Bacterial superantigen intoxication causes massive overactivation of T cells, which can result in potentially lethal toxic shock. Superantigens fall into two groups: superantigens such as staphylococcal enterotoxin B (SEB) that contain a single generic binding site for major histocompatibility complex class II (MHC-II) and more potent superantigens such as SEA with a second, zinc-dependent MHC-II binding site that enables them to cross-link adjacent MHC-II molecules. We found that although all superantigens bound rapidly to the surface of human B cells, zinc-binding superantigens largely remained at the cell surface for at least 40 h. In contrast, single-binding-site superantigens were greatly depleted from the surface by 4 h. Subcellular fractionation and confocal microscopy revealed that some SEB entered lysosomal compartments, but SEA remained almost undetectable inside cells at 20 h. SEA and SEB mutants that do not bind MHC-II were trafficked rapidly to lysosomal compartments. Our findings suggest that the persistence of SEA and other zinc-dependent, cross-linking superantigens on the surface of antigen-presenting cells contributes to their potency as T-cell activators.
S-1 architecture manual (1979)

This manual provides a complete description of the instruction-set architecture of the S-1 Uniprocessor (Mark IIA), exclusive of vector operations. It is assumed that the reader has a general knowledge of computer architecture. The manual was designed to be both a detailed introduction to the S-1 and an architecture reference manual. Also included are user manuals for the FASM Assembler and the S-1 Formal Description Syntax.
Stimulation of exosome release by extracellular DNA is conserved across multiple cell types (2018)

Exosomes are distinguished from other types of extracellular vesicles by their small and relatively uniform size (30-100 nm) and their composition which reflects their endo-lysosomal origin. Involvement of these extracellular organelles in intercellular communication and their implication in pathological conditions has fuelled intensive research on mammalian exosomes; however, currently, very little is known about exosomes in lower vertebrates. Here we show that, in primary cultures of head kidney leukocytes from Atlantic salmon (Salmo salar), phosphorothioate CpG oligodeoxynucleotides induce secretion of vesicles with characteristics very similar to these of mammalian exosomes. Further experiments revealed that the oligonucleotide-induced exosome secretion did not depend on the CpG motifs but it relied on the phosphorothioate modification of the internucleotide linkage. Exosome secretion was also induced by genomic bacterial and eukaryotic DNA in toll-like receptor 9-negative piscine and human cell lines demonstrating that this is a phylogenetically conserved phenomenon which does not depend on activation of immune signaling pathways. In addition to exosomes, stimulation with phosphorothioate oligonucleotides and genomic DNA induced secretion of LC3B-II, an autophagosome marker, which was associated with vesicles of diverse size and morphology, possibly derived from autophagosome-related intracellular compartments. Overall, this work reveals a previously unrecognized biological activity of phosphorothioate ODNs and genomic DNA - their capacity to induce secretion of exosomes and other types of extracellular vesicles. This finding might help shed light on the side effects of therapeutic phosphorothioate oligodeoxynucleotides and the biological activity of extracellular genomic DNA which is often upregulated in pathological conditions.
Flexible complementary circuits operating at sub-0.5 V via hybrid organic–inorganic electrolyte-gated transistors (2021)

Electrolyte-gated transistors (EGTs) hold great promise for next-generation printed logic circuitry, biocompatible integrated sensors, and neuromorphic devices. However, EGT-based complementary circuits with high voltage gain and ultralow driving voltage (<0.5 V) are currently unrealized, because achieving balanced electrical output for both the p- and n-type EGT components has not been possible with current materials. Here we report high-performance EGT complementary circuits containing p-type organic electrochemical transistors (OECTs) fabricated with an ion-permeable organic semiconducting polymer (DPP-g2T) and an n-type electrical double-layer transistor (EDLT) fabricated with an ion-impermeable inorganic indium-gallium-zinc oxide (IGZO) semiconductor. Adjusting the IGZO composition enables tunable EDLT output which, for In:Ga:Zn = 10:1:1 at%, balances that of the DPP-g2T OECT. The resulting hybrid electrolyte-gated inverter (HCIN) achieves ultrahigh voltage gains (>110) under a supply voltage of only 0.7 V. Furthermore, NAND and NOR logic circuits on both rigid and flexible substrates are realized, enabling not only excellent logic response with driving voltages as low as 0.2 V but also impressive mechanical flexibility down to 1-mm bending radii. Finally, the HCIN was applied in electrooculographic (EOG) signal monitoring for recording eye movement, which is critical for the development of wearable medical sensors and also interfaces for human-computer interaction; the high voltage amplification of the present HCIN enables EOG signal amplification and monitoring in which a small ∼1.5 mV signal is amplified to ∼30 mV.
Overcoming cisplatin resistance in non-small cell lung cancer with Mad2 silencing siRNA delivered systemically using EGFR-targeted chitosan nanoparticles (2016)

Lung cancer remains one of the leading killers in the United States and around the world. Platinum agents, including cisplatin, are the first line treatment in lung cancer, including non-small cell lung cancer (NSCLC), which is the predominant form of lung cancer. In this study, we have evaluated Mad2 cell-cycle checkpoint gene silencing using small interfering RNA (siRNA) delivered systemically using epidermal growth factor receptor-targeted chitosan nanoparticles in drug sensitive and resistant models of NSCLC. Our results show that Mad2 gene silencing using targeted chitosan nanoparticles has tremendous potential in overcoming platinum resistance in NSCLC.
Enabling low-cost QCL by large scale fabrication on CMOS pilot line (2020)

The costs of manufacturing QCL are still a major bottleneck for the adoption of this technology for chemical sensing. The integration of MIR sources on Si substrate based on CMOS technology paves the way for high-volume low-cost fabrication. Furthermore, the use of Si-based fabrication platform open the way to the co-integration of QCL MIR sources with Si-based waveguides, allowing realization optical sensors fully integrated on planar substrate. We report the fabrication of DFB QCL sources operating at 7.4&mu;m on silicon substrate within 200 mm CMOS/MEMS pilot line. To do so, we have developed an appropriate fabrication process flow that fully respects the design and the process rules of a standard CMOS manufacturing line. Moreover, we have developed wafer level electro-optic characterization on prober station. The characterizations done at wafer level on thousands devices have demonstrated average threshold current densities close to between 3 kA/cm<sup>2</sup> and 2.5 kA/cm<sup>2</sup> with a relative dispersion around 5%. The optical power can reach 1 mW at ambient temperature, 1.5% duty cycle. This fabrication run achieves performance at the state of the art, that are comparable with those of QCL fabricated on InP substrate. With a yield of 98% on the wafer central fields, this work give perspectives to address application fields needing low cost MIR laser sources.
ESAT-6-Like Protein Secretion inBacillus anthracis (2008)

Proteins of the WXG100 family represent the prototypical substrates of bacterial type VII secretion systems that typically encompass 100 residues, lack canonical signal peptides, and form helix-turn-helix hairpin structures with WXG positioned in the turn element. Bacillus anthracis encodes six WXG100 proteins, herein referred to as EsxB, EsxL, EsxP, EsxQ, EsxV, and EsxW. With the exception of EsxB, B. anthracis proteins harbor C-terminal extensions that are appended to canonical WXG domains. When cultured in liquid broth, B. anthracis secretes two substrates, EsxB and EsxW, into the extracellular environment. EsxB is required for the stability and secretion of EsxW; however, EsxW is dispensable for EsxB secretion. In agreement with the hypothesis that EsxB binding to substrates promotes recognition and secretion by the type VII pathway, EsxB is reported to interact with EsxB and EsxW. Unlike deletions in mycobacterial EsxB, deletion of five N- or C-terminal residues does not affect the ability of mutant B. anthracis EsxB to travel the type VII pathway and initiate secretion of EsxW. Translational fusion of ubiquitin to the N or C terminus of EsxB also had no effect, while ubiquitin insertion into the center turn abrogated secretion. Anthrax-infected guinea pigs mounted humoral immune responses to EsxB, EsxP, and EsxW, which suggests that B. anthracis activates the type VII secretion pathway during infection.
Banding Reduction in Electrophotographic Process Using Piezoelectric Actuated Laser Beam Deflection Device (2000)

Banding is an image artifact that appears as peroidic light and dark bands across a page. This paper presents an experimental study on the application of a piezoelectric laser beam deflection device to reduce banding in the electrophotographic process. Banding is characterized using several different measurement techniques. An empirical model of the actuator is obtained using system identification techniques by measuring the laser beam position on-line using an optical sensor. An open loop control strategy is then proposed and implemented. Experimental results showed significant improvements with the images printed using beam deflection control.
Coenzyme-A-Independent Transacylation System; Possible Involvement of Phospholipase A2 in Transacylation (2017)

The coenzyme A (CoA)-independent transacylation system catalyzes fatty acid transfer from phospholipids to lysophospholipids in the absence of cofactors such as CoA. It prefers to use C20 and C22 polyunsaturated fatty acids such as arachidonic acid, which are esterified in the glycerophospholipid at the <i>sn</i>-2 position. This system can also acylate alkyl ether-linked lysophospholipids, is involved in the enrichment of arachidonic acid in alkyl ether-linked glycerophospholipids, and is critical for the metabolism of eicosanoids and platelet-activating factor. Despite their importance, the enzymes responsible for these reactions have yet to be identified. In this review, we describe the features of the Ca<sup>2+</sup>-independent, membrane-bound CoA-independent transacylation system and its selectivity for arachidonic acid. We also speculate on the involvement of phospholipase A2 in the CoA-independent transacylation reaction.
Ignition of Nanoscale Titanium/Potassium Perchlorate Pyrotechnic Powder: Reaction Mechanism Study (2018)

The reaction mechanism and ignition characteristics of the pyrotechnic composite of titanium nanoparticles and micron-sized potassium perchlorate was investigated under rapid heating conditions (∼5 × 105 K/s) by temperature jump (T-Jump) time-of-flight mass spectrometry. X-ray photoelectron spectroscopy surface analysis and transmission electron microscopy (TEM) characterization of titanium nanoparticles show a reactive oxide layer (∼6 nm) composed of amorphous TiO2 and roughly 20% crystalline TiN and titanium oxynitride. The T-Jump and thermogravimetric analysis reveals the oxide layer to be responsible for catalysis of oxygen release from KClO4, resulting in ignition temperatures as low as 720 K in atmospheric pressure argon. Fast and slow in situ heating TEM corroborate the findings of oxygen atmosphere ignition characteristics, which illustrate KClO4 melting and coating of titanium nanoparticles immediately before oxidizer decomposition and titanium oxidation. Unlike aluminum, which has been shown to have a rapid loss of surface area before combustion as a result of sintering, Ti retained its high surface area. A combination of a reactive shell and the preservation of titanium nanostructure under rapid heating may lead to enhanced oxygen diffusion and increased potential for transient energy release.
Abstract P1017: Tissue Engineered Human Acellular Blood Vessels For Coronary Artery Bypass Grafting (2022)

Objective: Conduit for coronary artery bypass grafting (CABG) can be limited due to poor quality or prior removal of saphenous veins. A human acellular vessel (HAV) bioengineered from vascular cells and then decellularized for implantation may provide a readily available, off-the-shelf conduit for CABG. Here we evaluate the use of small diameter HAV for CABG in a non-human primate model. Methods: Adult male baboons (n=7; 26.8 - 37.0 kg) were imaged by left heart catheterization and computed tomography angiography. CABG was performed using a 3.5 mm diameter HAV to the left anterior descending (LAD) or right coronary artery (RCA) via sternotomy with cardiopulmonary bypass. The proximal coronary artery was ligated to prevent competitive flow and graft transit time flowmetry (TTFM) was assessed after implant. Angiography at 2 weeks, 1, 3, and 6 months evaluated graft patency and heart function. HAVs explanted at 6 months were assessed by immunohistochemistry for host cellular response and remodeling. Results and Conclusion: Baboons underwent CABG using a 3.5 mm HAV from the ascending aorta to the LAD (n=2) or RCA (n=5). The diminutive LAD led to early graft loss due to size mismatch and poor runoff. HAV bypass to the dominant RCA (TTFM: 22 ± 7.7 mL/min) resulted in sustained graft patency for up to 6 months post-implantation. HAV explant histology revealed infiltration of multiple host cell populations with formation of a neoadventitial layer and evidence of luminal endothelization. HAV conduits retained structural integrity with no evidence of mechanical failure throughout the study. These results demonstrate that tissue-engineered HAVs may provide an off-the-shelf conduit for CABG.
Determination of a HLA II Promiscuous Peptide Cocktail as Potential Vaccine Against EBV Latency II Malignancies. (2005)

Abstract The Epstein-Barr virus (EBV) is associated with several malignant diseases which can be distinguished by their patterns of viral latent gene expression. The latency II program is limited to the expression of the non-immunodominant antigens EBNA1, LMP1 and LMP2 and is seen in EBV-positive Hodgkin’s disease, nasopharyngeal carcinomas and peripheral T/NK-cell lymphomas. CD4+ T cells may play a crucial role in controlling these EBV latency II malignancies. The aim of this study was to determine a peptide cocktail containing highly promiscuous MHC class II epitopes derived from the EBV latency II antigens. Using the prediction software TEPITOPE, we selected 24 potential MHC II promiscuous peptides derived from the EBV latency II antigens EBNA1, LMP1 and LMP2. The predicted peptides were then submitted to peptide-binding assays on HLA II purified molecules, which allowed the selection of 6 peptides (EBNA1: 3; LMP1: 1; LMP2: 2) with a highly promiscuous capability of binding. This peptide cocktail was immunogenic in a model of HLA-DR1 transgenic mice, leading to a specific cellular and humoral Th1 response. To determine whether the peptides of the cocktail were recognized by human CD4+ T cells, we stimulated CD8-depleted PBMCs from 12 healthy EBV-seropositive donors expressing various HLA genotypes. A proliferative response was observed in all of the donors tested. Significant levels of IFN-gamma and IL-10 secretion were observed in 7/12 and 4/12 donors, respectively, using ELISA method. We also found a relatively low but significant number of IFN-gamma-secreting memory cells in 8 of the 10 donors tested using ELISPOT assay (range, 22 to 167 SFC per 106 CD8-depleted PBMCs). Finally, we analyzed by ELISPOT the responses obtained using PBMCs from 5 EBV-seropositive Hodgkin patients at different stages of the disease. No significant response was observed in the 2 patients at diagnosis. By contrast, a highly significant response was observed in a patient with EBV-associated Hodgkin lymphoma in remission. In conclusion, we have determined an HLA II promiscuous peptide cocktail containing epitopes from EBV latency II antigens. This promiscuous peptide cocktail may be immunogenic in the majority of the population and could be used in immunotherapeutic approaches (as peptide-based vaccine or cellular therapy) against EBV latency II malignancies.
Evaluation of Audio Beat Tracking and Music Tempo Extraction Algorithms (2007)

Abstract This is an extended analysis of eight different algorithms for musical tempo extraction and beat tracking. The algorithms participated in the 2006 Music Information Retrieval Evaluation eXchange (MIREX), where they were evaluated using a set of 140 musical excerpts, each with beats annotated by 40 different listeners. Performance metrics were constructed to measure the algorithms' abilities to predict the most perceptually salient musical beats and tempi of the excerpts. Detailed results of the evaluation are presented here and algorithm performance is evaluated as a function of musical genre, the presence of percussion, musical meter and the most salient perceptual tempo of each excerpt.