gebhart/patrepeval huggingface dataset:
CC chemokine receptor 2 promotes recruitment of myeloid cells associated with insulin resistance in nonalcoholic fatty liver disease (2018)

Nonalcoholic fatty liver disease (NAFLD) is a common disease, closely associated with obesity and insulin resistance. We investigated the presence of a subset of myeloid cells associated with metabolic disturbance in the liver of patients with NAFLD and a murine model of obesity-induced liver disease. Gene and protein expression in liver and serum was investigated with RT-PCR or ELISA and correlated to clinical disease. Liver-infiltrating immune cells were isolated from normal or diseased human liver for flow cytometric analysis. In animal experiments, mice were fed a high-fat diet (60% of calories from fat) for 16 wk, or high-fat diet with 30% fructose for 32 wk to induce steatohepatitis and fibrosis. A small molecule inhibitor of CC chemokine receptor 2 (CCR2), CCX872, was administered to some mice. A subset of CD11c<sup>+</sup>CD206<sup>+</sup> immune cells was enriched in human liver tissue, and greater infiltration was observed in NAFLD. The presence of CD11c<sup>+</sup>CD206<sup>+</sup> myeloid cells correlated with systemic insulin resistance. CD11c<sup>+</sup>CD206<sup>+</sup> cells expressed high levels of CCR2, and liver CC chemokine ligand 2 (CCL2) expression was increased in nonalcoholic steatohepatitis and correlated with disease activity. In mice, CCR2 inhibition reduced infiltration of liver CD11b<sup>+</sup>CD11c<sup>+</sup>F4/80<sup>+</sup> monocytes, which are functional homologs of human CD11c<sup>+</sup>CD206<sup>+</sup> cells, and improved liver injury and glycemic control. A role for CCR2/CCL2 in human NAFLD has long been postulated. These data confirm a role for this chemokine/receptor axis, through mediating adipose and hepatic infiltration of myeloid cells. Inhibition of CCR2 improved hepatic inflammation and fibrosis in murine models of NAFLD. These data confirm the rationale for targeting CCR2 to treat NAFLD. NEW & NOTEWORTHY These data show for the first time that CD11c<sup>+</sup>CD206<sup>+</sup> myeloid cells, previously associated with human adipose tissue inflammation, infiltrate into liver tissue in nonalcoholic fatty liver disease. These cells express CCR2. Inhibition of CCR2 in mice inhibits hepatic inflammation caused by a murine homolog of these myeloid cells and improves experimental liver disease.
A Novel Precision Die Attach Technique for Opto-Electronics Packaging (2011)

Semiconductor Laser diodes that emit visible light have various interesting applications such as sensing, high density optical storage and projection displays. In any opto-electronic package, the laser diode chips are typically attached or soldered to metal or ceramic substrates that have good thermal conductivity and are well-matched in coefficient of thermal expansion using solder. Some applications require a critical alignment of the front facet of the laser diode to the front edge of the substrate onto which the laser diode chip is attached to. Depending on the application, the alignment precision could be varying from 20 μm to being as stringent as 0.5 to 1 μm. In many of these applications, the cost of packaging is also a very important factor. In such applications, it is essential to develop a laser diode chip bonding process that can meet such stringent die alignments along with a low cost manufacturing process. Therefore, the objective of this research work is to provide a low cost alternative solution for die attach process that can guarantee alignment precision of 0.5 to 1 microns and can be easily adapted to high volume manufacturing. The novel technique proposed in this work uses primarily gravity force for the facet alignments between the two components. In this passive-gravity assisted precision (P-GAP) assembly process, the laser diode (LD) chip is placed on the substrate using a traditional pick and place machine and later the substrate and the chip are tilted such that the chip slides on the substrate due to the gravity and touches a mechanical stop in-front of them. This does not involve any active alignment. In addition, we have provided few ideas to improve the sliding when gravity is used. This technique has been implemented on several samples and the feasibility of achieving the alignment precision to within a micron was demonstrated.
Characterization of the Products of a Gene Expressed During Androgen-Programmed Cell Death and their Potential use as a Marker of Urogenital Injury (1990)

Regression of the rat ventral prostate gland following castration is accompanied by the induced expression of messenger RNA encoding Testosterone Repressed Prostate Message-2 (TRPM-2). Subsequent studies have shown that this gene is also induced during renal injury. In each of these tissues, the TRPM-2 RNA products are expressed by cells undergoing programmed death as a result of the hormonal stimuli or the traumatic insult. In an attempt to characterize this gene and its products, we partially sequenced complementary DNAs for TRPM-2 isolated from a recombinant library constructed using RNA of a hydronephrotic kidney. The sequence of these clones showed close homology with the sulfated glycoprotein-2 (SGP-2/clusterin) gene, expressed constitutively by mammalian Sertoli cells. Antibody recognition studies confirm this homology. Antiserum made against rat clusterin recognized TRPM-2 encoded polypeptides in extracts of regressing rat ventral prostate glands. Western blot analysis allowed us to demonstrate large increases in the concentration of these proteins in extracts of regressing ventral prostate gland and in rat serum and urine during the acute period of prostatic regression. These results indicate that proteins are synthesized from the large amount of TRPM-2 RNA produced by dying prostate cells and imply that these proteins are shed into the serum and urine. Based on the intense synthesis of TRPM-2 gene products by dying cells in the urogenital tract and the ability to assay for these products in serum and urine, we suggest that an assay for TRPM-2 products might allow us to monitor the extent of cellular damage associated with specific urogenital disease states.
Microwave-Assisted Sample Treatment in a Fully Automated Flow-Based Instrument:  Oxidation of Reduced Technetium Species in the Analysis of Total Technetium-99 in Caustic Aged Nuclear Waste Samples (2004)

An automated flow-based instrument for microwave-assisted treatment of liquid samples has been developed and characterized. The instrument utilizes a flow-through reaction vessel design that facilitates the addition of multiple reagents during sample treatment and removal of the gaseous reaction products and enables quantitative removal of liquids from the reaction vessel for carryover-free operations. Matrix modification and speciation control chemistries that are required for the radiochemical determination of total (99)Tc in caustic aged nuclear waste samples have been investigated. A rapid and quantitative oxidation procedure using peroxydisulfate in acidic solution was developed to convert reduced technetium species to pertechnetate in samples with high content of reducing organics. The effectiveness of the automated sample treatment procedures has been validated in the radiochemical analysis of total (99)Tc in caustic aged nuclear waste matrixes from the Hanford site.
Solution structure of the autophagy-related protein LC3C reveals a polyproline II motif on a mobile tether with phosphorylation site (2019)

(Macro-)autophagy is a compartmental degradation pathway conserved from yeast to mammals. The yeast protein Atg8 mediates membrane tethering/hemifusion and cargo recruitment and is essential for autophagy. The human MAP1LC3/GABARAP family proteins show high sequence identity with Atg8, but MAP1LC3C is distinguished by a conspicuous amino-terminal extension with unknown functional significance. We have determined the high-resolution three-dimensional structure and measured the backbone dynamics of MAP1LC3C by NMR spectroscopy. From Ser18 to Ala120, MAP1LC3C forms an α-helix followed by the ubiquitin-like tertiary fold with two hydrophobic binding pockets used by MAP1LC3/GABARAP proteins to recognize targets presenting LC3-interacting regions (LIRs). Unlike other MAP1LC3/GABARAP proteins, the amino-terminal region of MAP1LC3C does not form a stable helix α<sub>1</sub> but a "sticky arm" consisting of a polyproline II motif on a flexible linker. Ser18 at the interface between this linker and the structural core can be phosphorylated in vitro by protein kinase A, which causes additional conformational heterogeneity as monitored by NMR spectroscopy and molecular dynamics simulations, including changes in the LIR-binding interface. Based on these results we propose that the amino-terminal polyproline II motif mediates specific interactions with the microtubule cytoskeleton and that Ser18 phosphorylation modulates the interplay of MAP1LC3C with its various target proteins.
Resonant Two-Laser Spin-State Spectroscopy of a Negatively Charged Quantum-Dot–Microcavity System with a Cold Permanent Magnet (2023)

A high-efficiency spin-photon interface is an essential piece of quantum hardware necessary for various quantum technologies. Self-assembled ($\mathrm{In}$,$\mathrm{Ga}$)$\mathrm{As}$ quantum dots have excellent optical properties: if embedded in an optical microcavity, they can show near-deterministic spin-photon entanglement and spin readout. To address the individual spin states, an external magnetic field is required, and a superconducting magnet is usually used. Here we show a compact cryogenically compatible $\mathrm{Sm}$-$\mathrm{Co}$ magnet design that delivers a 475-mT in-plane (Voigt-geometry) magnetic field at $5\phantom{\rule{0.2em}{0ex}}\mathrm{K}$, which is suitable for lifting the energy degeneracy of the electron spin states and trion transitions of a single ($\mathrm{In}$,$\mathrm{Ga}$)$\mathrm{As}$ quantum dot. This quantum dot is embedded in a birefringent high-finesse optical microcavity that enables efficient collection of single photons emitted by the quantum dot. We demonstrate spin-state manipulation by addressing the trion transitions with a single laser field and two laser fields. The experimental data agree well with our model, which covers single- and two-laser cross-polarized resonance fluorescence, Purcell enhancement in a birefringent cavity, and variation of the laser powers.
Joint User Activity and Non-Coherent Data Detection in mMTC-Enabled Massive MIMO Using Machine Learning Algorithms (2018)

Machine-type communication (MTC) services are expected to be an integral part of the future cellular systems. A key challenge of MTC, especially for the massive MTC (mMTC), is the detection of active devices among a large number of devices. The sparse characteristics of mMTC makes compressed sensing (CS) approaches a promising solution to the device detection problem. CS-based techniques are shown to outperform conventional device detection approaches. However, utilizing CS-based approaches for device detection along with channel estimation and using the acquired estimates for coherent data transmission may not be the optimal approach, especially for the cases where the goal is to convey only a few bits of data. In this work, we propose a non-coherent transmission technique for the mMTC uplink and compare its performance with coherent transmission. Furthermore, we demonstrate that it is possible to obtain more accurate channel state information by combining the conventional estimators with CS-based techniques.
Al-2.62 Lift-Off Process (2021)

As increasingly smaller molecular materials and material structures are devised or developed for technological applications, the demands on the processes of lithography now routinely include feature sizes that are of the order of 10 nm. In reaching such a fine level of resolution, the methods of lithography have increased markedly in sophistication and brought into play 2terminology that is unfamiliar, on the one hand, to scientists tasked with the development of new lithographic materials or, on the other, to the engineers who design and operate the complex equipment that is required in modern-day processing. Publications produced by scientists need to be understood by engineers and vice versa, and these commonly arise from collaborative research that draws heavily on the terminology of two or more of the traditional disciplines. It is developments in polymer science and material science that lead progress in areas that cross traditional boundaries, such as microlithography. This document provides the exact definitions of a selection of unfamiliar terms that researchers and practitioners from different disciplines might encounter.
Neural net diagnostics for VLSI test (1990)

This paper discusses the application of neural network pattern analysis algorithms to the IC fault diagnosis problem. A fault diagnostic is a decision rule combining what is known about an ideal circuit test response with information about how it is distorted by fabrication variations and measurement noise. The rule is used to detect fault existence in fabricated circuits using real test equipment. Traditional statistical techniques may be used to achieve this goal, but they can employ unrealistic a priori assumptions about measurement data. Our approach to this problem employs an adaptive pattern analysis technique based on feedforward neural networks. During training, a feedforward network automatically captures unknown sample distributions. This is important because distributions arising from the nonlinear effects of process variation can be more complex than is typically assumed. A feedforward network is also able to extract measurement features which contribute significantly to making a correct decision. Traditional feature extraction techniques employ matrix manipulations which can be particularly costly for large measurement vectors. In this paper we discuss a software system which we are developing that uses this approach. We also provide a simple example illustrating the use of the technique for fault detection in an operational amplifier.
Open Entity Extraction from Web Search Query Logs (2010)

In this paper we propose a completely unsupervised method for open-domain entity extraction and clustering over query logs. The underlying hypothesis is that classes defined by mining search user activity may significantly differ from those typically considered over web documents, in that they better model the user space, i.e. users ’ perception and interests. We show that our method outperforms state of the art (semi-)supervised systems based either on web documents or on query logs (16 % gain on the clustering task). We also report evidence that our method successfully supports
Analysis of DC-link current harmonics for unconventional PWM strategies — Application of the double Fourier integral Method (2015)

This paper presents a numerical approach for determining the theoretical harmonic components of unconventional pulse width modulation (PWM) strategies such as the Unified-Double Carrier PWM (Uni-DC PWM). The method uses a double Fourier integral formulation to analyze the inverter DC-link current harmonic components, by establishing inner and outer integral limits of this formulation. The provided results of the investigated modulation strategy are demonstrated by comparing with those obtained by Fast Fourier Transform (FFT) analysis of simulated switched waveforms for selected conditions. 3D graphics and general cartographies for global variation of the DC bus RMS current are also presented, together with a comparison of the harmonic performance of a classic PWM strategy and the Uni-DC PWM.
Active Tracking System with Rapid Eye Movement Involving Simultaneous Top-down and Bottom-up Attention Control (2008)

Active Tracking System with Rapid Eye Movement Involving Simultaneous Top-down and Bottom-up Attention Control
Inhibition of spontaneous GABAergic transmission by trimethylolpropane phosphate. (1999)

Trimethylolpropane phosphate (TMPP) is a neuroactive organophosphate generated during partial pyrolysis of a synthetic ester turbine engine lubricant. While TMPP had been shown to have little affinity for acetylcholinesterase, previous binding studies and 6Cl- flux measurements have implicated TMPP as an antagonist of GABA, receptor/Cl- channels. Using the whole-cell patch clamp method, spontaneous inhibitory postsynaptic currents (sIPSCs) mediated by bicuculline-sensitive GABA(A) receptors were measured in neurons cultured from the rat embryonic hippocampus for 13-21 days. Experiments were conducted in the presence of tetrodotoxin and 6-cyano-7-nitroquinoxaline to inhibit spontaneous presynaptic action potentials and glutamate transmission, respectively, thus isolating GABAergic sIPSCs for study. TMPP induced a concentration-dependent inhibition of sIPSC amplitude and frequency suggesting both postsynaptic and presynaptic actions. Administration of 5 microM TMPP reversibly diminished sIPSC amplitude by 23 +/- 8% (mean SEM, n=5 cells) while markedly decreasing the mean sIPSC frequency by 40 +/- 2% (n=5). The mean time constant of sIPSC decay was reversibly decreased by 20 +/- 4% (n=3) in the presence of 20 microM TMPP, suggesting an increase in the rate of inactivation. To directly verify the blockade of ionotropic GABA receptors by TMPP, the effects of TMPP were examined on whole-cell Cl- current responses activated by exogenous GABA. Administration of TMPP (5 microM) depressed peak whole-cell GABA-induced currents to 73 1% (n=4) of control levels, consistent with the results on sIPSC amplitude. Our data directly demonstrate that TMPP directly inhibits GABA(A) receptor function, as indicated by the blockade of whole-cell GABA-mediated Cl- current and the reduction in sIPSC amplitude. Furthermore, TMPP exerts a presynaptic effect on GABAergic transmission, as evidenced by the reduction in sIPSC frequency, which may be independent of a GABA(A) receptor. The molecular basis for the presynaptic action of TMPP remains to be elucidated.
Retinoid Induced Apoptosis in Leukemia Cells Through a Retinoic Acid Nuclear Receptor-Independent Pathway (1997)

Trans retinoic acid (RA) has proven to be a potent therapeutic agent in the treatment of acute promyelocytic leukemia. Unfortunately, other subtypes of acute myelogenous leukemia are resistant to the antiproliferative and differentiating effects of RA. In this report, we describe a novel retinoid 6-[3-(1-adamantyl)-4-hydroxyphenyl]-2-naphthalene carboxylic acid (AHPN; CD437) that not only totally inhibits the proliferation of RA-resistant leukemic cell lines HL-60R and K562 but also induces apoptosis in these cells. Exposure of HL-60R to CD437 results in the rapid (within 30 minutes) increase of the cyclin-dependent kinase inhibitor p21(waf1/cip1) as well as GADD45 mRNA. Manifestations of CD437-mediated programmed cell death are noted within 2 hours, as indicated by both the cleavage and activation of the CPP32 protease and cleavage of poly (ADP-ribose) polymerase. This is followed by cleavage of bcl-2 and internucleosomal DNA degradation. HL-60R cells do not express the retinoid nuclear receptor RAR beta and RAR gamma and express a truncated RAR alpha. Thus, CD437 induction of p21(waf1/cip1) and GADD45 mRNAs and apoptosis occurs through a unique mechanism not involving the retinoid nuclear receptors. CD437 represents a unique retinoid with therapeutic potential in the treatment of myeloid leukemia.
A modern biomaterial for adhesion prevention (2006)

A biomaterial composed of carboxymethylcellulose, poly(ethylene oxide), and calcium can be prepared in a variety of ways to reduce fibrin deposition and adhesion formation. This biomaterial platform can be formulated into a flowable gel with tissue adherence appropriate for use in minimally invasive surgery. The device remains at the site of placement even in gravitationally dependent areas. A peridural formulation was shown in preclinical studies to be safe and effective in reducing adhesions to dura following spinal surgery. A peritoneal formulation used on pelvic organs following peritoneal cavity surgery was also shown to be safe and effective. A clinical feasibility study showed that patients with severe back pain and lower extremity weakness treated with the peridural formulation, applied over their nerve roots following laminectomy or laminotomy, experienced significantly reduced symptoms when compared with surgery-only controls. The peritoneal formulation was shown in two multicenter feasibility studies of women undergoing pelvic surgery to significantly reduce adhesion formation when compared with surgery-only controls. Confirmation of the feasibility studies awaits results from pivotal clinical trials. These formulations were safe, effective, and easy to use. This biomaterial provided a benefit to patients undergoing surgery where postsurgical adhesion formation is a concern.
Synthetically Programmable DNA Binding Domains in Aggregates of DNA‐Functionalized Gold Nanoparticles (2009)

Nanoparticles that assemble into core/shell aggregate structures comprising thermally addressable, phase-separated DNA binding domains are designed. Since the strength of the DNA binding in these domains differs, these aggregate systems exhibit two distinct melting transitions upon dehybridization (see image) resulting from the stepwise disassociation of the entire structure. These materials are ideal for probing the structure–function relationship of DNA-linked nanoparticle aggregates.
Post-traitement de champs de vitesse instantanée et éparse à l'aide de réseaux de neurones informés par la physique (2022)

International audience
Threshold in Stage-specific Embryonic Glycotypes Uncovered by a Full Portrait of Dynamic N-Glycan Expression during Cell Differentiation (2009)

Although various glycoforms appear to participate independently in multiple molecular interactions in cellular adhesion that contribute to embryogenesis and organogenesis, a full portrait of the glycome diversity and the effect of the structural variations of cellular glycoforms on individual cell stages in proliferation and differentiation remain unclear. Here we describe a novel concept for the characterization of dynamic glycoform alteration during cell differentiation by means of "glycoblotting-based cellular glycomics," the only method allowing for rapid and quantitative glycan analysis. We demonstrated that processes of dynamic cellular differentiation of mouse embryonic carcinoma cells, P19CL6 and P19C6, and mouse embryonic stem cells into cardiomyocytes or neural cells can be monitored and characterized quantitatively by profiling entire N-glycan structures of total cell glycoproteins. Whole N-glycans enriched and identified by the glycoblotting method (67 glycans for P19CL6, 75 glycans for P19C6, and 72 glycans for embryonic stem cells) were profiled and bar-coded quantitatively with respect to the ratio of subgroups composed of characteristic glycoforms, namely glycotypes.
Simulation of gate lag and current collapse in gallium nitride field-effect transistors (2004)

Results of two-dimensional numerical simulations of gate lag and current collapse in GaN heterostructure field-effect transistors are presented. Simulation results clearly show that current collapse takes place only if an enhanced trapping occurs under the gate edges. Hot electrons play an instrumental role in the collapse mechanism. The simulation results also link the current collapse with electrons spreading into the buffer layer and confirm that a better electron localization (as in a double heterostructure field-effect transistor) can dramatically reduce current collapse.