gebhart/patrepeval huggingface dataset:
Vertex Channel Field Effect Transistor (VC-FET) Technology Featuring High Performance and Highly Manufacturable Trench Capacitor DRAM (2006)

Vertex channel (VC) transistor is applied to both support devices and array transistor of trench capacitor DRAM for the first time. On-current of VC-FETs is much higher than that of conventional planar devices with keeping sufficiently small off-current. They achieve 15% or much smaller propagation delay (Tpd) of fan-out 3 than planar devices. Furthermore, 1.6 times of on-current as a planar array transistor is achieved by the combination of VCAT and P+poly gate without degradation of retention characteristics
On the impedance modeling of switched capacitor converters with arbitrary output nodes (2013)

Demand for high power density and miniaturization are pushing the application limits of Switched Capacitor Converters (SCCs) to new areas. Their benefit has up to now been used only in low power application ICs such as memories, or mobile phone backlighting where efficiency is not critical and magnetic components are not available. Recently, research in SCCs is demonstrating that their benefits can be extended to high power density systems, achieving efficiency levels comparable to classical inductive SMPS. These new concepts consider advanced control schemes or hybrid combinations of SCCs and inductive switching, and require better understandings of the SCC and its appropriate models. This work presents a new methodology to model hybrid combinations of SCCs and inductors. The well-known vector charge flow analysis for Switched Capacitor Converters is reviewed and extended in order to accurately model the behavior of a SCC when any of the internal nodes is loaded and controlled by Pulse-Width-Modulation. Results of the analysis compare favorably to behavioral simulations.
Enhanced and controlled chromatin extraction from FFPE tissues and the application to ChIP-seq (2019)

This study provided a new method that achieves efficient extraction of high-quality chromatin suitable for chromatin-based epigenetic assays with less damage on chromatin. This approach may provide a way to circumvent the over-fixed nature of FFPE tissues for future technology development.
Structure-Activity Relationships of Diastereomeric Lysine Ring Size Analogs of the Antimicrobial Peptide Gramicidin S (2004)

Structure-activity relationships were examined in seven gramicidin S analogs in which the ring-expanded analog GS14 [cyclo-(VKLKVdYPLKVKLdYP)] is modified by enantiomeric inversions of its lysine residues. The conformation, amphiphilicity, and self-association propensity of these peptides were investigated by circular dichroism spectroscopy and reversed phase high performance liquid chromatography. (31)P nuclear magnetic resonance spectroscopic and dye leakage experiments were performed to evaluate the capacity of these peptides to induce inverse nonlamellar phases in, and to permeabilize phospholipid bilayers; their growth inhibitory activity against the cell wall-less mollicute Acholeplasma laidlawii B was also examined. The amount and stability of beta-sheet structure, effective hydrophobicity, propensity for self-association in water, ability to disrupt the organization of phospholipid bilayers, and ability to inhibit A. laidlawii B growth are strongly correlated with the facial amphiphilicity of these GS14 analogs. Also, the magnitude of the parameters segregate these peptides into three groups, consisting of GS14, the four single inversion analogs, and the two multiple inversion analogs. The capacity of these peptides to differentiate between bacterial and animal cell membranes exhibits a biphasic relationship with peptide amphiphilicity, suggesting that there may only be a narrow range of peptide amphiphilicity within which it is possible to achieve the dual therapeutic requirements of high antibiotic effectiveness and low hemolytic activity. These results were rationalized by considering how the physiochemical properties of these GS14 analogs are likely to be reflected in their partitioning into lipid bilayer membranes.
Interaction between the genomes of Lactococcus lactis and phages of the P335 species (2013)

Phages of the P335 species infect Lactococcus lactis and have been particularly studied because of their association with strains of L. lactis subsp. cremoris used as dairy starter cultures. Unlike other lactococcal phages, those of the P335 species may have a temperate or lytic lifestyle, and are believed to originate from the starter cultures themselves. We have sequenced the genome of L. lactis subsp. cremoris KW2 isolated from fermented corn and found that it contains an integrated P335 species prophage. This 41 kb prophage (Φ KW2) has a mosaic structure with functional modules that are highly similar to several other phages of the P335 species associated with dairy starter cultures. Comparison of the genomes of 26 phages of the P335 species, with either a lytic or temperate lifestyle, shows that they can be divided into three groups and that the morphogenesis gene region is the most conserved. Analysis of these phage genomes in conjunction with the genomes of several L. lactis strains shows that prophage insertion is site specific and occurs at seven different chromosomal locations. Exactly how induced or lytic phages of the P335 species interact with carbohydrate cell surface receptors in the host cell envelope remains to be determined. Genes for the biosynthesis of a variable cell surface polysaccharide and for lipoteichoic acids (LTAs) are found in L. lactis and are the main candidates for phage receptors, as the genes for other cell surface carbohydrates have been lost from dairy starter strains. Overall, phages of the P335 species appear to have had only a minor role in the adaptation of L. lactis subsp. cremoris strains to the dairy environment, and instead they appear to be an integral part of the L. lactis chromosome. There remains a great deal to be discovered about their role, and their contribution to the evolution of the bacterial genome.
Nuclear Factor-κB Nuclear Localization Is Predictive of Biochemical Recurrence in Patients with Positive Margin Prostate Cancer (2004)

In univariate and multivariate analysis, NF-kappaB nuclear expression was strongly predictive of biochemical recurrence in patients with positive surgical margins after RP. We propose that nuclear NF-kappaB may serve as a useful independent molecular marker for stratifying patients at risk for recurrence.
HapSense (2019)

We present HapSense, a single-volume soft haptic I/O device with uninterrupted dual functionalities of force sensing and vibrotactile actuation. To achieve both input and output functionalities, we employ a ferroelectric electroactive polymer as core functional material with a multilayer structure design. We introduce a haptic I/O hardware that supports tunable high driving voltage waveform for vibrotactile actuation while insitu sensing a change in capacitance from contact force. With mechanically soft nature of fabricated structure, HapSense can be embedded onto various object surfaces including but not limited to furniture, garments, and the human body. Through a series of experiments and evaluations, we characterized physical properties of HapSense and validated the feasibility of using soft haptic I/O with real users. We demonstrated a variety of interaction scenarios using HapSense.
Insulin action on activity and cell surface disposition of human HepG2 glucose transporters expressed in Chinese hamster ovary cells. (1990)

Complementary DNA encoding a facilitative glucose transporter was isolated from a human hepatoma cell line (HepG2) cDNA library and subcloned into a metal-inducible mammalian expression vector, pLEN (California Biotechnology) containing human metallothionein gene II promoter sequences. Chinese hamster ovary (CHO) cells transfected with this transporter expression vector, pLENGT, exhibited a 2-17-fold increase in immunoreactive HepG2-type glucose transporter protein, as measured by protein immunoblotting with antipeptide antibodies directed against the HepG2-type glucose transporter C-terminal domain. Expression of the human glucose transporter was verified by protein immunoblotting with a mouse polyclonal antiserum that recognizes the human but not the rodent HepG2-type transporter. 2-Deoxy-D-glucose uptake was increased 2-7-fold in transfected cell lines. Polyclonal antisera directed against purified red blood cell glucose transporter were raised in several rabbits. Antiserum from one rabbit, delta, was found to bind to the surface of intact red cells but not to inside-out red cell ghosts. Using this delta-antiserum in intact cell-binding assays, 1.6-9-fold increases in cell surface expression of the human glucose transporter were measured in CHO-K1 cell lines transfected with the transporter expression vector. Measurements of total cellular glucose transporter immunoreactive protein using anti-HepG2 transporter C-terminal peptide serum, cell surface glucose transporter protein using delta-antiserum and 2-deoxyglucose uptake revealed proportional relationships among these parameters in transfected cell lines expressing different levels of transporter protein. Insulin increased 2-deoxyglucose uptake 40% in control CHO-K1 cells and in CHO-K1 cells expressing modest levels of the human glucose transporter protein. However, stimulation of sugar-uptake by insulin was only 10% in cells overexpressing human glucose transporter protein 9-fold, and no effect of insulin on sugar uptake was detected in several cell lines expressing very high levels (12-17-fold over controls) of human HepG2 glucose transporter protein. No insulin stimulation of anti-cell surface glucose transporter antibody binding was detected in any control or transfected CHO-K1 cell lines. These data indicate that a glucose transporter protein that is insensitive to insulin in HepG2 cells is regulated by insulin when expressed at low but not at high levels in insulin-response CHO-K1 cells. Additionally, the results suggest that insulin does not increase 2-deoxyglucose uptake by increasing the number of cell surface HepG2-type glucose transporters in CHO-K1 fibroblasts.
Considerations of beta and electron transport in internal dose calculations (1990)

Ionizing radiation has broad uses in modern science and medicine. These uses often require the calculation of energy deposition in the irradiated media and, usually, the medium of interest is the human body. Energy deposition from radioactive sources within the human body and the effects of such deposition are considered in the field of internal dosimetry. In July of 1988, a three-year research project was initiated by the Nuclear Engineering Department at Texas A M University under the sponsorship of the US Department of Energy. The main thrust of the research was to consider, for the first time, the detailed spatial transport of electron and beta particles in the estimation of average organ doses under the Medical Internal Radiation Dose (MIRD) schema. At the present time (December of 1990), research activities are continuing within five areas. Several are new initiatives begun within the second or third year of the current contract period. They include: (1) development of small-scale dosimetry; (2) development of a differential volume phantom; (3) development of a dosimetric bone model; (4) assessment of the new ICRP lung model; and (5) studies into the mechanisms of DNA damage. A progress report is given for each of these tasks within the Comprehensive Report. In each case, preliminary results are very encouraging and plans for further research are detailed within this document.
Operation Guidance System for Rotary Snowplow on Sidewalk Using HUD (2005)

In winter, Japan has very deep and heavy snow, and faces a problem of freezing of the road surface. It is therefore difficult for people to walk along a sidewalk and conveniently move from place to place in winter. This study aims to achieve efficient wintertime sidewalk administrator by applying developed ITS technologies to the snowplow. This paper describes the analysis of snow removal task, the mechanical type of snowplow in Japan, and the proposed operation guidance system using Head-Up-Display for rotary snowplow on sidewalk, which are expected to be practically used in the near future.
Carbon Microspheres as Ball Bearings in Aqueous-Based Lubrication (2011)

We present an exploratory study on a suspension of uniform carbon microspheres as a new class of aqueous-based lubricants. The surfactant-functionalized carbon microspheres (∼0.1 wt %) employ a rolling mechanism similar to ball bearings to provide low friction coefficients (μ ≈ 0.03) and minimize surface wear in shear experiments between various surfaces, even at high loads and high contact pressures. The size range, high monodispersity, and large yield stress of the C(μsphere), as well as the minimal environmental impact, are all desirable characteristics for the use of a C(μsphere)-SDS suspension as an alternative to oil-based lubricants in compatible devices and machinery.
Mitigating Doppler effects on physical-layer network coding in VANET (2015)

This paper considers physical-layer network coding (PNC) in vehicular ad-hoc network (VANET) to solve the problem of short contact time between fast-moving vehicles. PNC enables data exchange between nodes in a relay network within a short airtime, e.g., twice faster than relay networks based on traditional communication, and can be a powerful performance booster in VANET. One of the most important challenges in applying PNC to VANET, however, is the Doppler shift caused by vehicular motions. Doppler shift leads to carrier frequency offset (CFO) that induces inter-carrier interference (ICI) in OFDM systems. The ICI destroys the orthogonality of modulated symbols, causing degradation in PNC signal detection. This paper puts forth a detection method to mitigate the CFO/ICI effect on PNC. The method, referred to as BP-VPNC, makes use of a belief propagation (BP) algorithm to process the outputs of the OFDM correlators. BP extracts useful hidden information embedded in ICI to improve signal detection in VANET PNC. Our study shows that the BER performance of PNC VANET operated with BP-VPNC can be achieved close to that of traditional VANET at various CFO levels. These results suggest that with BP-VPNC, a potential shortcoming of PNC, vulnerability to CFO, can be circumvented, and that PNC can be used to overcome the short vehicular contact time in VANET.
Serum lipoprotein (a) predicts acute coronary syndromes in patients with severe carotid stenosis (2018)

Lp (a) determination could be a useful tool to predict ACS in patients with severe carotid stenosis.
Synthesis of nano-sized Leucite Glass-ceramics (2010)

Objectives: The objectives of the study were to synthesize nano-sized leucite glass-ceramics. Methods: An aluminosilicate glass was ball milled using Attritor (AM) and high speed milling (HM) methods. A starting glass powder was wet ground in an Attritor Mill (1-S Lab, Union Process, USA) at 400 rpm with 5mm YTZ grinding media for 120mins and 2mm YTZ media for 120mins (AM4). A second Attritor milling regimen was 0.65mm YTZ media (90mins) and 0.40mm YTZ media for 480mins (AM9.5). The starting glass was also wet milled (Pulverisette P7, Fritsch, Germany) at 1000 rpm with 1mm YTZ for 30(HM0.5), 60(HM1), 120(HM2) and 240mins (HM4). Powders were subjected to crystallization heat treatments and characterised using Scanning Electron Microscopy and X-ray Diffraction. Ceramco-3 glass-ceramic was used as a control. Photomicrographs (AM:x2200, HM:x15000 magnification) were scanned using a light pen and image analysis software. Groups within milling methods were compared for significant differences (p&lt;0.05) in median crystal size using a One Way ANOVA. Results: The median leucite crystal sizes (25%,75% percentiles, µm2) and significant differences (p&lt;0.001) between groups are listed below. Glass-ceramic group Median Crystal size (µm2) 25%,75% Percentiles Crystallite number Starting 0.836 a 0.589,1.190 558 AM4 0.345 b 0.251,0.457 1434 AM9.5 0.140 c 0.102,0.196 3378 HM0.5 0.085 d 0.055,0.127 790 HM1 0.055 e 0.038,0.086 1076 HM2 0.055 e 0.036,0.081 1315 HM4 0.048 f 0.030,0.070 1718 Ceramco-3 had a median leucite crystal size (25%,75% percentile) of 2.50(0.52,6.71) µm2. The experimental groups had significantly smaller median leucite particle sizes than Ceramco-3 (p&lt;0.001). Tetragonal leucite was found in all the test groups. Attritor and high speed milling of glasses increased the number of crystallites and reduced the crystal size following heat treatments. Conclusions: Attritor and high speed milling of aluminosilicate glasses produced fine and nano-scale tetragonal leucite glass-ceramics with minimal matrix microcracking following crystallization heat treatments.
Computational Reverse-Engineering Analysis for Scattering Experiments on Amphiphilic Block Polymer Solutions (2019)

In this paper, we present a computational reverse-engineering analysis for scattering experiments (CREASE) based on genetic algorithms and molecular simulation to analyze the structure within self-assembled amphiphilic polymer solutions. For a given input comprised of scattering intensity profiles and information about the amphiphilic polymers in solution, CREASE outputs the structure of the self-assembled micelles (e.g., core and corona diameters, aggregation number) as well as the conformations of the amphiphilic polymer chains in the micelle (e.g., blocks' radii of gyration, chain radii of gyration, monomer concentration profiles). First, we demonstrate CREASE's ability to reverse-engineer self-assembled nanostructures for scattering profiles obtained from molecular simulations (or <i>in silico</i> experiments) of generic coarse-grained bead-spring polymer chains in an implicit solvent. We then present CREASE's outputs for scattering profiles obtained from small-angle neutron scattering (SANS) experiments of poly(d-glucose carbonate) block copolymers in solution that exhibit assembly into spherical nanoparticles. The success of this method is demonstrated by its ability to replicate, quantitatively, the results from <i>in silico</i> experiments and by the agreement in micelle core and corona sizes obtained from microscopy of the <i>in vitro</i> solutions. The primary strength of CREASE is its ability to analyze scattering profiles without an off-the-shelf scattering model and the ability to provide chain and monomer level structural information that is otherwise difficult to obtain from scattering and microscopy alone.
Hell Hath No Fury? Correcting Bias in the NRC Emotion Lexicon (2021)

There have been several attempts to create an accurate and thorough emotion lexicon in English, which identifies the emotional content of words. Of the several commonly used resources, the NRC emotion lexicon (Mohammad and Turney, 2013b) has received the most attention due to its availability, size, and its choice of Plutchik's expressive 8-class emotion model. In this paper we identify a large number of troubling entries in the NRC lexicon, where words that should in most contexts be emotionally neutral, with no affect (e.g., lesbian, stone, mountain), are associated with emotional labels that are inaccurate, nonsensical, pejorative, or, at best, highly contingent and context-dependent (e.g., lesbian labeled as DISGUST and SADNESS, stone as ANGER, or mountain as ANTICIPATION). We describe a procedure for semi-automatically correcting these problems in the NRC, which includes disambiguating POS categories and aligning NRC entries with other emotion lexicons to infer the accuracy of labels. We demonstrate via an experimental benchmark that the quality of the resources is thus improved. We release the revised resource and our code to enable other researchers to reproduce and build upon results 1 .
Single-nucleus RNA-seq identifies Huntington disease astrocyte states (2020)

Huntington Disease (HD) is an inherited movement disorder caused by expanded CAG repeats in the Huntingtin gene. We have used single nucleus RNASeq (snRNASeq) to uncover cellular phenotypes that change in the disease, investigating single cell gene expression in cingulate cortex of patients with HD and comparing the gene expression to that of patients with no neurological disease. In this study, we focused on astrocytes, although we found significant gene expression differences in neurons, oligodendrocytes, and microglia as well. In particular, the gene expression profiles of astrocytes in HD showed multiple signatures, varying in phenotype from cells that had markedly upregulated metallothionein and heat shock genes, but had not completely lost the expression of genes associated with normal protoplasmic astrocytes, to astrocytes that had substantially upregulated glial fibrillary acidic protein (GFAP) and had lost expression of many normal protoplasmic astrocyte genes as well as metallothionein genes. When compared to astrocytes in control samples, astrocyte signatures in HD also showed downregulated expression of a number of genes, including several associated with protoplasmic astrocyte function and lipid synthesis. Thus, HD astrocytes appeared in variable transcriptional phenotypes, and could be divided into several different "states", defined by patterns of gene expression. Ultimately, this study begins to fill the knowledge gap of single cell gene expression in HD and provide a more detailed understanding of the variation in changes in gene expression during astrocyte "reactions" to the disease.
Circadian rhythms in Neurospora crassa on a polydimethylsiloxane microfluidic device for real-time gas perturbations (2013)

Racetubes, a conventional system employing hollow glass tubes, are typically used for monitoring circadian rhythms from the model filamentous fungus, Neurospora crassa. However, a major technical limitation in using a conventional system is that racetubes are not amenable for real-time gas perturbations. In this work, we demonstrate a simple microfluidic device combined with real-time gas perturbations for monitoring circadian rhythms in Neurospora crassa using bioluminescence assays. The developed platform is a useful toolbox for investigating molecular responses under various gas conditions for Neurospora and can also be applied to other microorganisms.
An integrated approach to reduced‐order control theory (1983)

Abstract Linear‐Quadratic‐Gaussian (LQG) theory generally requires the use of a full‐order dynamic observer whose dimension is often prohibitive in applications so that reduced‐order controller design techniques are needed. A general formalism is presented here for the optimal design of controllers of arbitrary prescribed order with the usual quadratic cost functionals. The gradients of the cost functional are obtained in explicit form and involves Liapunov equations. A fundamental aspect of this paper is a unifying formalism; direct output feedback and reduced‐order controllers, stochastic and deterministic systems, infinite‐time and finite‐time problems and time‐invariant and time‐varying problems are considered. Optimization of sensor and actuator locations and parameter‐variation‐insensitive controller design are also considered within this framework. Examples are treated.