gebhart/patrepeval huggingface dataset:
A structure-derived snap-trap mechanism of a multispecific serpin from the dysbiotic human oral microbiome (2017)

Enduring host-microbiome relationships are based on adaptive strategies within a particular ecological niche. <i>Tannerella forsythia</i> is a dysbiotic member of the human oral microbiome that inhabits periodontal pockets and contributes to chronic periodontitis. To counteract endopeptidases from the host or microbial competitors, <i>T. forsythia</i> possesses a serpin-type proteinase inhibitor called miropin. Although serpins from animals, plants, and viruses have been widely studied, those from prokaryotes have received only limited attention. Here we show that miropin uses the serpin-type suicidal mechanism. We found that, similar to a snap trap, the protein transits from a metastable native form to a relaxed triggered or induced form after cleavage of a reactive-site target bond in an exposed reactive-center loop. The prey peptidase becomes covalently attached to the inhibitor, is dragged 75 Å apart, and is irreversibly inhibited. This coincides with a large conformational rearrangement of miropin, which inserts the segment upstream of the cleavage site as an extra β-strand in a central β-sheet. Standard serpins possess a single target bond and inhibit selected endopeptidases of particular specificity and class. In contrast, miropin uniquely blocked many serine and cysteine endopeptidases of disparate architecture and substrate specificity owing to several potential target bonds within the reactive-center loop and to plasticity in accommodating extra β-strands of variable length. Phylogenetic studies revealed a patchy distribution of bacterial serpins incompatible with a vertical descent model. This finding suggests that miropin was acquired from the host through horizontal gene transfer, perhaps facilitated by the long and intimate association of <i>T. forsythia</i> with the human gingiva.
Improvement of the Transmission Spectra of Tunable Wavelength-Selective Liquid Crystal Fabry-Perot Interferometer Filters (1993)

A reflection-type tunable liquid-crystal Fabry-Perot filter, in which the input light beam passes through a cell twice after reflection by a mirror, is shown to have improved transmission characteristics. Simulation and experimental results show that this is an effective way to decrease the cross talk between neighboring channels, even though there is a slight increase in loss due to the double pass and the mirror. When these filters are applied to wavelength division multiplexing systems with analog-amplitude modulation, they increase the channel capacity to three times the original value.
Reduction of Low Molecular Weight Protein-tyrosine Phosphatase Expression Improves Hyperglycemia and Insulin Sensitivity in Obese Mice (2007)

To investigate the role of low molecular weight protein-tyrosine phosphatase (LMW-PTP) in glucose metabolism and insulin action, a specific antisense oligonucleotide (ASO) was used to reduce its expression both in vitro and in vivo. Reduction of LMW-PTP expression with the ASO in cultured mouse hepatocytes and in liver and fat tissues of diet-induced obese (DIO) mice and ob/ob mice led to increased phosphorylation and activity of key insulin signaling intermediates, including insulin receptor-beta subunit, phosphatidylinositol 3-kinase, and Akt in response to insulin stimulation. The ASO-treated DIO and ob/ob animals showed improved insulin sensitivity, which was reflected by a lowering of both plasma insulin and glucose levels and improved glucose and insulin tolerance in DIO mice. The treatment did not decrease body weight or increase metabolic rate. These data demonstrate that LMW-PTP is a key negative regulator of insulin action and a potential novel target for the treatment of insulin resistance and type 2 diabetes.
Phylogenetic Relationships Between Mycoplasmas and Other Procaryotes Based upon the Electrophoretic Behavior of Their Ribosomal Ribonucleic Acids (1977)

The migration of ribosomal ribonucleic acids (rRNA&apos;s) from bacteria, bacterial L forms, mycoplasmas, and acholeplasmas in nondenaturing and formamide gels has been examined. Mycoplasmal and acholeplasmal RNAs migrate in a pattern distinct from each other and from bacteria in nondenaturing gels. The differences observed appear to be mainly due to conformational differences in the molecules. When examined under denaturing conditions in formamide gels, the 23S RNAs of all organisms examined comigrated. The 16S RNAs of mycoplasmas and acholeplasmas comigrated and appear to be of a smaller molecular weight than bacterial 16S RNA. It is suggested that the differences observed are indicative of significant phylogenetic divergence between mycoplasmas and bacteria or bacterial L forms.
Hybrid template and block matching algorithm for image intra prediction (2012)

Template matching has been shown to outperform the H.264 prediction modes for Intra video coding thanks to better spatial prediction and no additional ancillary data to transmit. The method indeed works well when the template and the block to be predicted are highly correlated, e.g., in homogenous image areas, however, it obviously fails in areas with non homogeneous textures. This paper explores the idea of using a block-matching intra prediction algorithm which, thanks to a Rate-Distorsion (RD) based decision mechanism, will naturally be used in image areas when template matching (TM) fails. This new method offers a significant coding gain compared to H.264 Intra prediction modes and the template matching based prediction. Indeed, the TM-based algorithm and the proposed hybrid algorithm lead, with the Bjontergaard measure, to rate gains of up to respectively 38.02% and 48.38% at low bitrates when compared with H.264 Intra only.
Human Intravenous Immunoglobulin Preparation and Virus Inactivation by Pasteurization and Solvent Detergent Treatment (2000)

ABSTRACT Human intravenous immunoglobulin (IVIG) solutions were prepared by two different methods and compared to each other. The crude immunoglobulin fraction obtained from Cohn-Oncley fractionation of plasma was further purified and subjected to virus inactivation, either by polyethylene glycol precipitation and pasteurization at 60°C for 10 hours, or by ion exchange chromatography and solvent/detergent treatment.
HIGH EFFICIENCY BIFACIAL SOLAR CELL DEVELOPPED ON MONOCRISTALLINE SI AND TRANSFERED TO MULTICRISTALLINE SI (2011)

An alternative process to the aluminium full back side is necessary to realize high efficiency solar cell on thin wafers. Even if metallization paste manufacturers deliver paste that minimize the wafer bowing to 1.5 mm for wafer lower than 200 μm, it is more and more critical to process wafers thinner than 150 μm with full aluminium back side. The objective of this work is to demonstrate on monocristalline silicon wafer that boron back surface field (BSF), diffused from BCl3 gas source or from oxide doped layer like Boron Silicon Glass (BSG), is as efficient as full back side aluminium BSF. In addition this work deal with integration of different passivation layer optimised to passivate high boron doped layer at the backside of a bifacial solar cell. The best efficiency obtained on monocristalline wafers shows an increase in efficiency of 0.9% absolute compare to our standard process with full aluminium back side. According to the process optimised for monocristalline wafers, the process was transferred on multicristalline wafer. Even if the gain in current, for bifacial solar cell, compared to standard process is confirmed, the high temperature process for boron diffusion, activate electrically lot of intra-grain defects and decrease the solar cell performance. A correlation between Light Beam Induced Current (LBIC) and electroluminescence highlight local shunt and explain why the solar cell performance with boron BSF diffused at the back side is impacted. An alternative solution is also proposed to reduce the thermal budget of boron diffusion and improve the solar cell efficiency.
EMI Noise Prediction for Electronic Ballasts (2010)

The design of electromagnetic (EM) interference filters for converter systems is usually based on measurements with a prototype during the final stages of the design process. Predicting the conducted EM noise spectrum of a converter by simulation in an early stage has the potential to save time/cost and to investigate different noise reduction methods, which could, for example, influence the layout or the design of the control integrated circuit. Therefore, the main sources of conducted differential-mode (DM) and common-mode (CM) noise of electronic ballasts for fluorescent lamps are identified in this paper. For each source, the noise spectrum is calculated and a noise propagation model is presented. The influence of the line impedance stabilizing network (LISN) and the test receiver is also included. Based on the presented models, noise spectrums are calculated and validated by measurements.
Beamforming Tradeoffs for Initial UE Discovery in Millimeter-Wave MIMO Systems (2016)

Millimeter-wave (mmW) multi-input multi-output (MIMO) systems have gained increasing traction toward the goal of meeting the high data-rate requirements in next-generation wireless systems. The focus of this work is on low-complexity beamforming approaches for initial user equipment (UE) discovery in such systems. Toward this goal, we first note the structure of the optimal beamformer with per-antenna gain and phase control and establish the structure of good beamformers with per-antenna phase-only control. Learning these right singular vector (RSV)type beamforming structures in mmW systems is fraught with considerable complexities such as the need for a non-broadcast system design, the sensitivity of the beamformer approximants to small path length changes, inefficiencies due to power amplifier backoff, etc. To overcome these issues, we establish a physical interpretation between the RSV-type beamformer structures and the angles of departure/arrival (AoD/AoA) of the dominant path(s) capturing the scattering environment. This physical interpretation provides a theoretical underpinning to the emerging interest on directional beamforming approaches that are less sensitive to small path length changes. While classical approaches for direction learning such as MUltiple SIgnal Classification (MUSIC) have been well-understood, they suffer from many practical difficulties in a mmW context such as a non-broadcast system design and high computational complexity. A simpler broadcast-based solution for mmW systems is the adaptation of limited feedback-type directional codebooks for beamforming at the two ends. We establish fundamental limits for the best beam broadening codebooks and propose a construction motivated by a virtual subarray architecture that is within a couple of dB of the best tradeoff curve at all useful beam broadening factors. We finally provide the received SNR loss-UE discovery latency tradeoff with the proposed beam broadening constructions. Our results show that users with a reasonable link margin can be quickly discovered by the proposed design with a smooth roll-off in performance as the link margin deteriorates. While these designs are poorer in performance than the RSV learning approaches or MUSIC for cell-edge users, their low-complexity that leads to a broadcast system design makes them a useful candidate for practical mmW systems.
Power Allocation for Space-Terrestrial Cooperation Systems with Statistical CSI (2022)

This paper studies an integrated network design that boosts system capacity through cooperation between wireless access points (APs) and a satellite. By coherently combing the signals received by the central processing unit from the users through the space and terrestrial links, we mathematically derive an achievable throughput expression for the uplink (UL) data transmission over spatially correlated Rician channels. A closed-form expression is obtained when maximum ratio combining is employed to detect the desired signals. We formulate the max-min fairness and total transmit power optimization problems relying on the channel statistics to perform power allocation. The solution of each optimization problem is derived in form of a low-complexity iterative design, in which each data power variable is updated based on a closed-form expression. The mathematical analysis is validated with numerical results showing the added benefits of considering a satellite link in terms of improving the ergodic data throughput.
Multiple mechanisms of apoptosis induction by the histone deacetylase inhibitor PCI-24781 lead to predictive efficacy biomarkers (2008)

AACR Annual Meeting-- Apr 12-16, 2008; San Diego, CA

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PCI-24781 is a novel orally bioavailable broad-spectrum HDAC inhibitor that is currently in clinical trials in patients with solid and hematologic malignancies. PCI-24781 inhibits growth and induces apoptosis in most tumor cell lines tested, but, as with other broad-spectrum HDAC inhibitors, there are multiple mechanisms of action for this compound, that are cell- and tumor- type dependent. We have previously shown that PCI-24781 can upregulate tumor suppressor genes including the CDK inhibitors p21 and p19, induce cell cycle arrest in G1 or G2/M, upregulate death receptors including TRAIL and LIGHT, and inhibit homologous recombination by downregulation of RAD51 and BRCA1 (Adimoolam S. et al, 2007, PNAS, epub Nov 27). In this work, we identify clinically useful biomarkers based on early events in the mechanism of caspase-dependent induction of apoptosis by PCI-24781 in tumor cell lines. In HCT-116, OVCAR-3, PC-3, CEM, and Jurkat cells, the pan-caspase inhibitor qVD-OPh blocked 70-90% of PCI-24781-induced apoptosis, whereas inhibitors of individual caspases reduced it by only 20-30%, with caspase-9 inhibitor LEHD-fmk showing the most activity. Caspase activation assays show that while caspases 2, 3, 6 and 9 are activated at 48 hours, only caspase-9 activation is observed at 16 hours, indicating an early activation of the intrinsic apoptosis pathway. Accordingly, mitochondrial outer-membrane permeability (MOMP) and cytochrome c release from mitochondria are observed at 12 hours in all the cell lines sensitive to PCI-24781. However, events preceding this, including death receptor activation, Bid cleavage, calcium efflux and ROS production, vary in importance for apoptotic sensitivity to PCI-24781 in different lines. Interestingly, while Bid cleavage is observed in most cell lines, PCI-24781 does not activate caspase-8 nor is apoptosis inhibited by the caspase-8 inhibitor IETD-fmk. Some of these early events appear are found to be conserved in multiple sensitive cell lines as well as in primary human tumors treated ex vivo , and could be broadly useful as predictors of PCI-24781 sensitivity in the clinic.
Helix Persistence and Breakdown in Oligoureas of Metaphenylenediamine: Apparent Diastereotopicity as a Spectroscopic Marker of Helix Length in Solution (2008)

Oligomeric ureas derived from m-phenylenediamine with chain lengths of up to seven urea linkages were made by iterative synthetic pathways. Three families were synthesized: 4 and 20, bearing a terminal chiral sulfinyl group; 24, bearing a terminal rotationally restricted amide group, and 30 bearing a terminal achiral bromophenyl group. The distal end of the oligomers was capped with an N-benzyl group to act as a diastereotopic probe. With a terminal sulfinyl group, the 1H NMR signals arising from the CH2 group of the diastereotopic probe remained anisochronous even when separated from the stereogenic center by up to 24 bonds (in 20c). With a rotationally restricted amide, anisochronicity was no longer apparent beyond 17 bond lengths (in 24c). No anisochronicity was observable with a terminal bromophenyl group. We interpret these results as indicating that the oligoureas of short lengths adopt a defined helical secondary structure in solution, but that in longer oligomers the helicity breaks down and transmission of chirality in these systems is limited to about 24 bond lengths. We propose that "apparent diastereotopicity" (anisochronicity) provides a general empirical method for identifying secondary structure in solution.
Optimization of the KOH Texturing Process: Benchmarking on Minority Carrier Lifetime and on n-PERT Solar Cell Performance (2015)

We report on the progress of wet chemical process development for saw damage removal and silicon surface texturing in n-type passivated emitter with rear totally diffused (n-PERT) solar cells. A KOH based saw damage removal (SDR) and texturing process sequence has been developed which provides both, improved solar cell efficiency and reduction in cost of ownership. On the bases of our best electrical and optical performance we were able to define our optimized KOH based wet process (5 μm SDR + 4.5 μm texturing) in comparison with the reference KOH wet process (0 μm SDR + 9 μm texturing). The optimized texturing wet process provides a reflectance value of less than 10% with a process time of 8 min in 2% KOH solution. The emitter saturation current density (Joe) using the optimized KOH process is extracted from a symmetric lifetime vehicle to be between 30-40 fA/cm2 for BBr3 emitter passivated with ALD-Al2O3. The Best Known Process (BKP) for SDR + TEX is determined to be, SDR: 5 μm (3.5 min) KOH 20%, 70C and TEX: 4.5 μm (8 min) KOH 2%, 80C. This BKP has been implemented in an n-type PERT with rear emitter and resulted in conversion cell efficiency of 20.6% (average cells) and 20.8% (best cell) as a fist attempt on large area (156x156 mm2) CZ-Si based cells.
Effect of Grinding-Induced Stress on Interface State Density of SiC/SiO<sub>2</sub> (2019)

Back-grinding process was applied to the 4H-SiC (0001) epitaxial wafers. We found that the parameters about stress increased after back-grinding process. In our work, the characterization of stress on interface state density (D it ) of SiC/SiO 2 was investigated. Furthermore, the absorption of peak frequencies was also observed by fourier transform infrared spectroscopy attenuated total reflection (ATR-FTIR) analysis, and the D it of SiC/SiO 2 was obtained by quasi-static capacitance voltage (QSCV) measurement as well as C-φ s method. The above results suggested that the D it increased with the increasing grinding-induced stress.
Simultaneous Balanced DPSK Demodulation of Multiple 40 Gbit/s WDM Channels using a Single Periodic FBG (2007)

We demonstrate simultaneous balanced DPSK demodulation of 40 Gb/s WDM channels using a single periodic sampled fiber-Bragg-grating. The reflection (transmission) spectrum serves as the constructive (destructive) port of a traditional delay-line-interferometer. We observe approximately 0.5 dB required OSNR variation across the band of the FBG.
Bound Analysis using Backward Symbolic Execution (2009)

A fundamental problem that arises frequently in quantita-tive program analysis (e.g., resource usage analysis) is that of computing an upper bound for a given arithmetic expres-sion at a given program location in terms of the procedure inputs. We refer to this problem as bound analysis. The problem is theoretically as well as practically challenging because of variable updates inside loops and presence of vir-tual methods. Our solution to the bound analysis problem involves an inter-procedural (goal-directed) backward analysis built on top of an SMT solver. The analysis has the advantage of dealing with arbitrary operators that are understood by the underlying SMT solver. The analysis uses novel proof-rule based non-iterative technique to reason about updates inside loops, which makes it quite scalable. It uses user-defined ab-stract implementations to trace back across virtual methods arising from use of interfaces or extensible types. We have implemented the analysis inside the SPEED tool, which computes symbolic computational complexity bounds for procedures. Our analysis is used to translate bounds on number of loop iterations and cost of method calls to respec-tive bounds in terms of procedure inputs. We have evaluated the precision and scalability of the analysis over 4.NET as-semblies that together contained thousands of methods and resulted in 9152 queries to the analysis. The analysis was able to answer 90 % of the queries on an average of 0.23 seconds per query. 1.
Studies of Z-scan with "ring"-shaped beams (2003)

Summary form only given. A variety of experimental techniques for measuring nonlinear refractive and absorptive coefficients has been invented and developed during the last two decades. Here we concentrate on perhaps the simplest of these methods-the so-called Z-scan technique. By varying the position of a sample with respect to the focal plane of an input lens and detecting the energy transmitted through an aperture placed in the far field, one can determine the nonlinearly induced phase shift. In the absence of the aperture the nonlinear loss is measured. From these measurements, and knowledge of the underlying physics describing the nonlinear optical (NLO) response of the material, the nonlinear refractive index and absorption coefficient can be obtained.
Rare‐Cell Enrichment by a Rapid, Label‐Free, Ultrasonic Isopycnic Technique for Medical Diagnostics (2014)

One significant challenge in medical diagnostics lies in the development of label-free methods to separate different cells within complex biological samples. Here we demonstrate a generic, low-power ultrasonic separation technique, able to enrich different cell types based upon their physical properties. For malaria, we differentiate between infected and non-infected red blood cells in a fingerprick-sized drop of blood. We are able to achieve an enrichment of circulating cells infected by the ring stage of the parasite over nonparasitized red blood cells by between two and three orders of magnitude in less than 3 seconds (enabling detection at parasitemia levels as low as 0.0005%). In a second example, we also show that our methods can be used to enrich different cell types, concentrating Trypanosoma in blood at very low levels of infection, on disposable, low-cost chips.
Effects of Methyl and Halogens in Analgesic Peptide Molecules for Their Potent Agonist Activities at MOR/DOR and Antagonist Activity at NK1R (2015)

Treating pain has been always challenging, especially when it becomes chronic in nature. Current drugs (e.g. opioid drugs) cannot treat this problem effectively. In addition, constant use of these drugs has deadly side effects including drowsiness and mental clouding, nausea and emesis, and constipation [1]. Development of analgesic tolerance and hyperalgesia in many patients as the results of taking these drugs are also a serious concern. Overexpression of substance P and its receptor has been observed during prolonged pain states. Studies revealed that co-administration of cocktails of drugs containing μ/δ opioid agonist and NK1 antagonist can provide better analgesic effects in rat model while reducing side effects [2-4]. Herein, we report design, synthesis and SARs of few multifunctional ligands having μ/δ opioid agonist (μ-preferring) and NK1 antagonist activities. The detail of this study has already been communicated to J. Med. Chem. for publication [5]. We anticipate that these ligands will show better analgesia while reducing the adverse side effects. Our drug design principle is based on overlapping and adjacent pharmacophores (Figure 1) and we considered our previously published μ-selective (binding) ligand TY012 (H-Tyr-D-Ala-Gly-Phe-Pro-Leu-Trp-NH-Bn(3ʹ,5ʹ-(CF3)2)) [6].
The nonlinear Compton scattering experiment (2002)

We constructed an experimental system to observe the nonlinear Compton scattering. As a test experiment, we measure the Compton scattering in a linear region and had a reasonable-agreement with simulation.