gebhart/patrepeval huggingface dataset:
Dysregulation of miRNA-9 in a Subset of Schizophrenia Patient-Derived Neural Progenitor Cells (2017)

(Cell Reports 15, 1024–1036; May 3, 2016) In the originally published version of this article, the concentration of dual-SMAD inhibitors used was incorrectly reported in the Supplemental Experimental Procedures as “0.1 mM LDN193189 (Stemgent) and 10 mM SB431542 (Tocris)” instead of “0.1 μM LDN193189 (Stemgent) and 10 μM SB431542 (Tocris).” The Supplemental Experimental Procedures section has now been corrected online. The authors regret this error. Dysregulation of miRNA-9 in a Subset of Schizophrenia Patient-Derived Neural Progenitor CellsTopol et al.Cell ReportsApril 21, 2016In BriefTopol et al. examine the role of decreased miR-9 levels in a subset of schizophrenia patient-derived neural progenitor cells from two independent cohorts. They observe a strong correlation between miR-9 expression and miR-9 regulatory activity. Manipulation of miR-9 impacts neural migration most likely through changes to many indirect miR-9 targets. Full-Text PDF Open Access
Design Effect of Metallic (Durable) and Polymeric (Resorbable) Stents on Blood Flow and Platelet Activation (2018)

Bioresorbable vascular scaffolds (BVS) provide transient vessel support for occluded coronary arteries while resorbing over time, potentially allowing vessel restoration approximating the native, healthy state. Clinical trials indicate that the Absorb BVS (Abbott Vascular, Santa Clara, CA) performance was similar to that of the Xience metallic drug-eluting stent (DES), with low long-term complications rates. However, when under-deployed in very small vessels (diameter < 2.25 mm), the thrombosis rate of BVS was higher, possibly due to the effect of strut thickness on the hemodynamics (157 μm BVS vs. 81 μm DES). This study aims to determine the influence of BVS design in vessels of varying diameter on the potential platelet activation. Sixteen computational fluid dynamics models of vessels of varying diameter (1.8-3.0 mm), strut thickness (81-157 μm), and BVS/DES designs were compared. Platelet stress accumulation (SA), a metric for the activation potential, was calculated along platelet flow trajectories and their probability distribution was compared. The models were consistent with clinical observations, indicating that devices deployed in very small vessels exhibited increased probability for platelet activity as compared to the same devices deployed in nominal sized vessels. Deployment, although with residual stenosis, increased probability for higher SA than in similar diameter straight vessels. Reducing BVS struts thickness while maintaining their pattern improved performance closer to that of DES. Our findings highlight the importance of appropriate vessel sizing and deployment technique for BVS, and may help designing future BVS with thinner struts, ultimately improving performance in very small vessels.
Chiral Zirconium Catalysts for Enantioselective Synthesis (2004)

Abstract For Abstract see ChemInform Abstract in Full Text.
Improving Antibody Therapeutics by Manipulating the Fc Domain: Immunological and Structural Considerations (2022)

Interactions between the crystallizable fragment (Fc) domain of antibodies and a plethora of cellular Fc receptors (FcRs) or soluble proteins form a critical link between humoral and innate immunity. In particular, the immunoglobulin G Fc domain is critical for the clearance of target cells by processes that include (<i>a</i>) cytotoxicity, phagocytosis, or complement lysis; (<i>b</i>) modulation of inflammation; (<i>c</i>) antigen presentation; (<i>d</i>) antibody-mediated receptor clustering; and (<i>e</i>) cytokine release. More than 30 Fc-engineered antibodies aimed primarily at tailoring these effects for optimal therapeutic outcomes are in clinical evaluation or have already been approved. Nonetheless, our understanding of how FcR engagement impacts various immune cell phenotypes is still largely incomplete. Recent insights into FcR biology coupled with advances in Fc:FcR structural analysis, Fc engineering, and mouse models that recapitulate human biology are helping to fill in existing knowledge gaps. These advances will provide a blueprint on how to fine-tune the Fc domain to achieve optimal therapeutic efficacy.
SEM simulation for 2D and 3D inspection metrology and defect review (2014)

Advanced SEM simulation has become a key element in the ability of SEM inspection, metrology and defect review to meet the challenges of advanced technologies. It grants additional capabilities to the end user, such as 3D height measurements, accurate virtual metrology, and supports Design Based Metrology to bridge the gap between design layout and SEM image. In this paper we present SEM simulations capabilities, which take into consideration all parts of the SEM physical and electronic path, interaction between Electron beam and material, multi perspective SEM imaging and shadowing derived from proximity effects caused by the interaction of the Secondary Electrons signal with neighboring pattern edges. Optimizing trade-off between simulation accuracy, calibration procedures and computational complexity, the simulation is running in real-time with minimum impact on throughput. Experiment results demonstrate Height measurement capacities, and CAD based simulated pattern is compared with SEM image to evaluate simulated pattern fidelity.
A comparative study on system combination schemes for LVCSR (2010)

We present a comparative study on combination schemes for large vocabulary continuous speech recognition by incorporating long-span class posterior probability features into conventional short-time cepstral features. System combination can improve the overall speech recognition performance when multiple systems exhibit different error patterns and multiple knowledge sources encode complementary information. A variety of combination approaches are investigated in this paper, e.g., feature concatenation single stream system, model combination multi-stream system, lattice rescoring and ROVER. These techniques work at different levels of a LVCSR system and have different computational cost. We compared their performance and analyzed their advantages and disadvantages on large vocabulary English broadcast news transcription tasks. Experimental results showed that model combination with independent tree consistently outperforms ROVER, feature concatenation and lattice rescoring. In addition, the phoneme posterior probability features do provide complementary information to short-time cepstral features.
Fast Search Method for Image Vector Quantization Based on Equal-Average Equal-Variance and Partial Sum Concept (2005)

The encoding process of image vector quantization (VQ) is very heavy due to it performing a lot of k-dimensional Euclidean distance computations. In order to speed up VQ encoding, it is most important to avoid unnecessary exact Euclidean distance computations as many as possible by using features of a vector to estimate how large it is first so as to reject most of unlikely codewords. The mean, the variance, L2 norm and partial sum of a vector have been proposed as effective features in previous works for fast VQ encoding. Recently, in the previous work [6], three features of the mean, the variance and L2 norm are used together to derive an EEENNS search method, which is very search efficient but still has obvious computational redundancy. This paper aims at modifying the results of EEENNS method further by introducing another feature of partial sum to replace L2 norm feature so as to reduce more search space. Mathematical analysis and experimental results confirmed that the proposed method is more search efficient compared to [6].
Wildfires in the Lab: Simple Experiment and Models for the Exploration of Excitable Dynamics (2015)

Wildfires lead to the loss of life and property in many parts of the world. Understanding their dangers and, more particularly, the underlying dynamics which lead to fires of catastrophic scale contributes to better awareness as well as prevention and firefighting capabilities within the affected areas. In order to enable a basic understanding of the mechanisms of fire propagation for high school and college students, we present here simple model experiments using match sticks that demonstrate the dangers of spatial coupling between individual reactive (combustible) elements leading to rapid spreading of the combustion reaction. Supplemented with easy-to-grasp numerical simulations, our work illustrates the dynamics of wildfires in impressive but controllable ways and puts wildfire propagation into the fascinating framework of excitable active media which have many equivalents in chemical, ecological, biological or societal systems.
The Thioredoxin TRX-1 Modulates the Function of the Insulin-Like Neuropeptide DAF-28 during Dauer Formation in Caenorhabditis elegans (2011)

Thioredoxins comprise a conserved family of redox regulators involved in many biological processes, including stress resistance and aging. We report that the C. elegans thioredoxin TRX-1 acts in ASJ head sensory neurons as a novel modulator of the insulin-like neuropeptide DAF-28 during dauer formation. We show that increased formation of stress-resistant, long-lived dauer larvae in mutants for the gene encoding the insulin-like neuropeptide DAF-28 requires TRX-1 acting in ASJ neurons, upstream of the insulin-like receptor DAF-2. Genetic rescue experiments demonstrate that redox-independent functions of TRX-1 specifically in ASJ neurons are needed for the dauer formation constitutive (Daf-c) phenotype of daf-28 mutants. GFP reporters of trx-1 and daf-28 show opposing expression patterns in dauers (i.e. trx-1 is up-regulated and daf-28 is down-regulated), an effect that is not observed in growing L2/L3 larvae. In addition, functional TRX-1 is required for the down-regulation of a GFP reporter of daf-28 during dauer formation, a process that is likely subject to DAF-28-mediated feedback regulation. Our findings demonstrate that TRX-1 modulates DAF-28 signaling by contributing to the down-regulation of daf-28 expression during dauer formation. We propose that TRX-1 acts as a fluctuating neuronal signaling modulator within ASJ neurons to monitor the adjustment of neuropeptide expression, including insulin-like proteins, during dauer formation in response to adverse environmental conditions.
Approximate reverse k-nearest neighbor queries in general metric spaces (2006)

In this paper, we propose an approach for efficient approximative RkNN search in arbitrary metric spaces where the value of k is specified at query time. Our method uses an approximation of the nearest-neighbor-distances in order to prune the search space. In several experiments, our solution scales significantly better than existing non-approximative approaches while producing an approximation of the true query result with a high recall.
Identification of Reference Proteins for Western Blot Analyses in Mouse Model Systems of 2,3,7,8-Tetrachlorodibenzo-P-Dioxin (TCDD) Toxicity (2014)

Western blotting is a well-established, inexpensive and accurate way of measuring protein content. Because of technical variation between wells, normalization is required for valid interpretation of results across multiple samples. Typically this involves the use of one or more endogenous controls to adjust the measured levels of experimental molecules. Although some endogenous controls are widely used, validation is required for each experimental system. This is critical when studying transcriptional-modulators, such as toxicants like 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD).To address this issue, we examined hepatic tissue from 192 mice representing 47 unique combinations of strain, sex, Ahr-genotype, TCDD dose and treatment time. We examined 7 candidate reference proteins in each animal and assessed consistency of protein abundance through: 1) TCDD-induced fold-difference in protein content from basal levels, 2) inter- and intra- animal stability, and 3) the ability of each candidate to reduce instability of the other candidates. Univariate analyses identified HPRT as the most stable protein. Multivariate analysis indicated that stability generally increased with the number of proteins used, but gains from using >3 proteins were small. Lastly, by comparing these new data to our previous studies of mRNA controls on the same animals, we were able to show that the ideal mRNA and protein control-genes are distinct, and use of only 2-3 proteins provides strong stability, unlike in mRNA studies in the same cohort, where larger control-gene batteries were needed.
The influence of the shallot shape on the sound of Trompete reed pipes (2014)

The focus of investigations was the influence of certain shallot parameters on the sound of reed pipes. Since the dimensioning of organ pipes is mainly based on the experience of organ builders at present, the aim is to provide scientific data for organ builders explaining the influence of various shallot parameters on the sound. Due to this knowledge, it would be possible to realize the desired ideas of sound of organ pipes by targeted adjustment of these parameters during the dimensioning of the pipes. The investigated Trompete shallots differ in the termination angle of the shallot. To analyze the parameter of the shallot termination, angle measurements were carried out at a simple shallot model, which provide findings on the dependence of the reflection properties on various termination angles. The results show that the findings due to the model comply with the analyses of the sound spectra of the Trompete shallot.
Splice variants of human FOXP3 are functional inhibitors of human CD4+ T‐cell activation (2006)

FOXP3 has been identified as a key regulator of immune homeostasis. Mutations within the FOXP3 gene result in dysregulated CD4+ T-cell function and elevated cytokine production, leading to lymphoproliferative disease. FOXP3 expression in CD4+ T cells is primarily detected with the CD4+ CD25+ regulatory T-cell population. In humans the protein is detected as a doublet following immunoblot analysis. The lower band of the doublet has been identified as a splice isoform lacking a region corresponding to exon 2. The aim of this study was to investigate whether the splice variant form lacking exon 2 and a new novel splice variant lacking both exons 2 and 7, were functional inhibitors of CD4+ T-cell activation. The data generated showed that full-length FOXP3 and both splice variant forms of the protein were functional repressors of CD4+ T-cell activation.
Predicting the Integral Heat of Adsorption for Gas Physisorption on Microporous and Mesoporous Adsorbents (2014)

We have developed two predictive methods for the heats of adsorption that stem from isotherm models and benchmarked them against the Clausius–Clapeyron equation. These are the Tóth potential function model and the modified Clapeyron equation. Three adsorbate/adsorbent working pairs are used as examples: n-butane/BAX 1500 activated carbon, isobutane/BAX 1500 activated carbon, and ammonia/Fuji Davison type RD silica gel, all of which are examples of gas physisorption on adsorbents with both micro- and mesopores. Isotherms and corresponding integral heats of adsorption were measured in the range 298–348 K. For n-butane and isobutane, the pressures were up to 235 kPa, and for ammonia, the pressures were up to 835 kPa. Our two predictive methods consistently offer significant improvements over the Clausius–Clapeyron equation. Between the two predictive methods, the Tóth model is more robust across all three working pairs studied with predictions generally falling within 10–15% of the values of the measured heats.
Continental biogenic species in the Greenland Ice Core Project ice core: Tracing back the biomass history of the North American continent (1997)

Ammonium, nitrate, and organic acid records from the Greenland Ice Core Project deep ice core are discussed. All species have a continental biogenic source that is situated predominantly on the North American continent for species deposited in Summit, central Greenland. The record therefore can be used to trace back the biomass history of the North American continent. Difficulty in the interpretation of these records arises from their unknown transfer behavior in a more alkaline atmosphere, which characterizes glacial time periods compared to interglacial stadials. This may have implications not only for weak acids such as formate and acetate, but also possibly for the transport and incorporation of HNO 3 into aerosols, whereas ammonium is probably not affected by the alkalinity change of the atmosphere. Our approach is to compare samples with similar H + concentrations throughout the record. From the records we infer several significant fluctuations in the extent of the Laurentide Ice Sheet during the last glaciation. We find evidence against the occurrence of an extensive Younger Dryas event in North America.
The effect of elastomer chain length on properties of silicone-modified polyimide adhesives (1981)

A series of polyimides containing silicone elastomers was synthesized in order to study the effects of the elastomer chain length on polymer properties. The elastomer with repeat units varying from n=10 to 105 was chemically reacted into the backbone of an addition polyimide oligomer via reactive aromatic amine groups. Glass transition temperatures of the elastomer and polyimide phases were observed by torsional braid analysis. The elastomer-modified polyimides were tested as adhesives for bonding titanium in order to determine their potential for aerospace applications. Adhesive lap shear tests were performed before and after aging bonded specimens at elevated temperatures.
Silicon integrated nanophotonic high-radix switch arrays for next generation computer systems (2010)

We review results on design and development of 4×4 silicon nanophotonic non-blocking switch arrays integrated with driving analog CMOS circuits for circuit-switched optical networks. Such high-radix optical routers are envisioned for future Exascale computer systems.
A multi-channel EEG system featuring single-wire data aggregation via FM-FDM techniques (2016)

Conventional EEG systems are extremely power hungry due to a reliance on high resolution analog-to-digital converters (ADCs) to cover their required dynamic range. This paper presents a novel architecture for acquiring multi-channel high-resolution EEG using low power techniques. Instead of digitizing the output of each analog front-end (AFE) amplifier with an individual ADC, a voltage-controlled oscillator is used to generate an up-converted frequency-modulated (FM) signal at a unique carrier frequency. All channels then share a single wire via frequency-domain multiplexing (FDM), enabling a rugged mechanical design. The composite FM signal is then digitized with a single ADC optimized for time-domain resolution (1 MHz, 12 bits) rather than employing multiple ADCs optimized for voltage-domain resolution (1 kHz, 16–24 bits), thereby enabling a low-power implementation. To validate this approach, a discrete prototype is developed and achieves 75 dB of dynamic range per channel.
Radical Polymerization of New Functional Monomers: Mono- and Di-methacryloyl Isocyanate Containing Bisphenol-S and its Derivatives (1996)

New functional monomers mono- and di-methacryloyl isocyanate containing bisphenol-S were prepared on reaction of methacryloyl isocyanate (MAI) with bisphenol-S (BPS) and its derivatives at low temperature. The monomers thus obtained were characterized with elemental analysis, infrared, ultraviolet, 1H and 13C-NMR (nuclear magnetic resonance) spectra. Radical polymerization of mono- and di-methacryloyl isocyanate containing bisphenol-S and its derivatives was studied in terms of the rate of polymerization, solvent effect, thermal properties and kinetic measurements of photocrosslinking. Polar solvents such as dimethyl sulfoxide and dimethylacetamide (DMAc) were found to slow the polymerization. Functional polymers containing the vinyl group of MAI were successfully modified and photocrosslinked on irradiation in the presence of benzoin isopropyl ether. The photocrosslinking process follows second-order kinetics.
Stable gene transfer and expression in human primary T cells by the Sleeping Beauty transposon system (2005)

The Sleeping Beauty (SB) transposon system is a nonviral DNA delivery system in which a transposase directs integration of an SB transposon into TA-dinucleotide sites in the genome. To determine whether the SB transposon system can mediate stable gene expression in human T cells, primary peripheral blood lymphocytes (PBLs) were nucleofected with SB vectors carrying a DsRed reporter gene. Plasmids containing the SB transposase on the same molecule as (cis) or on a molecule separate from (trans) the SB transposon mediated long-term and stable reporter gene expression in human primary T cells. Sequencing of transposon:chromosome junctions confirmed that stable gene expression was due to SB-mediated transposition. In other studies, PBLs were successfully transfected using the SB transposon system and shown to stably express a fusion protein consisting of (1) a surface receptor useful for positive T-cell selection and (2) a "suicide" gene useful for elimination of transfected T cells after chemotherapy. This study is the first report demonstrating that the SB transposon system can mediate stable gene transfer in human primary PBLs, which may be advantageous for T-cell-based gene therapies.
Rigorous and practical vector model for phase-shifting masks in optical lithography (1992)

A new vector (true two-dimensional) optical lithography modeling program, METROPOLE, is presented which incorporates arbitrary mask geometries. This rigorous model is thus ideally suited for the simulation of phase shifting masks. The efficiency of the electric field calculations, both within the mask and on the substrate structures, allows its use on accessible engineering workstations. Several simulation examples are presented, and include the new phase shifting on the substrate technique (POST).
Turbine combustor configured for high-frequency dynamics mitigation and related method (2023)

A turbomachine combustor includes a combustion chamber; a plurality of micro-mixer nozzles mounted to an end cover of the combustion chamber, each including a fuel supply pipe affixed to a nozzle body located within the combustion chamber, wherein fuel from the supply pipe mixes with air in the nozzle body prior to discharge into the combustion chamber; and wherein at least some of the nozzle bodies of the plurality of micro-mixer nozzles have axial length dimensions that differ from axial length dimensions of other of the nozzle bodies.
Electron Paramagnetic Resonance (1998)

Specialist Periodical Reports provide systematic and detailed review coverage of progress in the major areas of chemical research. Written by experts in their specialist fields the series creates a unique service for the active research chemist, supplying regular critical in-depth accounts of progress in particular areas of chemistry. For over 80 years the Royal Society of Chemistry and its predecessor, the Chemical Society, have been publishing reports charting developments in chemistry, which originally took the form of Annual Reports. However, by 1967 the whole spectrum of chemistry could no longer be contained within one volume and the series Specialist Periodical Reports was born. The Annual Reports themselves still existed but were divided into two, and subsequently three, volumes covering Inorganic, Organic and Physical Chemistry. For more general coverage of the highlights in chemistry they remain a 'must'. Since that time the SPR series has altered according to the fluctuating degree of activity in various fields of chemistry. Some titles have remained unchanged, while others have altered their emphasis along with their titles; some have been combined under a new name whereas others have had to be discontinued. The current list of Specialist Periodical Reports can be seen on the inside flap of this volume.