gebhart/patrepeval huggingface dataset:
Membrane protein stability can be compromised by detergent interactions with the extramembranous soluble domains (2014)

Detergent interaction with extramembranous soluble domains (ESDs) is not commonly considered an important determinant of integral membrane protein (IMP) behavior during purification and crystallization, even though ESDs contribute to the stability of many IMPs. Here we demonstrate that some generally nondenaturing detergents critically destabilize a model ESD, the first nucleotide-binding domain (NBD1) from the human cystic fibrosis transmembrane conductance regulator (CFTR), a model IMP. Notably, the detergents show equivalent trends in their influence on the stability of isolated NBD1 and full-length CFTR. We used differential scanning calorimetry (DSC) and circular dichroism (CD) spectroscopy to monitor changes in NBD1 stability and secondary structure, respectively, during titration with a series of detergents. Their effective harshness in these assays mirrors that widely accepted for their interaction with IMPs, i.e., anionic > zwitterionic > nonionic. It is noteworthy that including lipids or nonionic detergents is shown to mitigate detergent harshness, as will limiting contact time. We infer three thermodynamic mechanisms from the observed thermal destabilization by monomer or micelle: (i) binding to the unfolded state with no change in the native structure (all detergent classes); (ii) native state binding that alters thermodynamic properties and perhaps conformation (nonionic detergents); and (iii) detergent binding that directly leads to denaturation of the native state (anionic and zwitterionic). These results demonstrate that the accepted model for the harshness of detergents applies to their interaction with an ESD. It is concluded that destabilization of extramembranous soluble domains by specific detergents will influence the stability of some IMPs during purification.
Functions of SR proteins in the U12-dependent AT-AC pre-mRNA splicing pathway (2001)

SR proteins play critical roles in the major pre-mRNA splicing pathway. A second pathway processes U12-dependent AT-AC introns. We demonstrate, by biochemical complementation, the requirement for SR proteins in splicing of AT-AC introns. Whereas SR proteins were sufficient to activate splicing of a P120 AT-AC intron, splicing of a sodium channel AT-AC intron required an additional nuclear fraction. Individual recombinant SR proteins promoted splicing of both substrates, but displayed marked preferences. SR proteins supported basal AT-AC splicing, and also splicing stimulation via a downstream enhancer or conventional 5' splice site. Analysis of chimeric transcripts revealed that information dispersed throughout exons and introns dictates SR protein specificity and the requirement for the additional nuclear fraction. Thus, SR proteins function in both major and minor splicing pathways, and in coordinating the activities of both spliceosomes via exon definition. These results suggest that despite the substantial differences in intron consensus sequences and in four of the five snRNPs in each spliceosome, at least some of the interactions involving SR proteins are conserved between the two pathways.
Microelectrofluidic Systems (2018)

Composite systems that integrate microelectromechanical and microelectrofluidic (MEF) components with electronics are emerging as the next generation of system-on-a-chip (SOC) designs. However, there remains a pressing need for a structured methodology for MEFS design automation, including modeling techniques and simulation and optimization tools.Integrating top-down and bottom-up design philosophies, Microelectrofluidic Systems presents the first comprehensive design strategy for MEFS. This strategy supports hierarchical modeling and simulation from the component level to the system level. It leads to multi-objective optimization tools valuable in all phases of the design process, from conceptualization to final manufacturing. The authors begin by defining the basic variables and elements needed to describe MEFS behavior, then model that behavior across three layers of abstraction: the low-level component, high-level reconfigurable architecture, and bio/chemical application layers. They have developed a hierarchical integrated design environment with SystemC and present its architecture and associated functional packages.Microelectrofluidic Systems is visionary in its leverage of electronic design principles for microsystem design and heralds a new era of automated SOC design. The strategy it presents holds the potential for significant reductions in design time and life-cycle maintenance costs, and its techniques and tools for robust design and application flexibility can lead to the high-volume production needed for the inevitably growing product market.
Analog-to-Digital Conversion Using Sub-Nyquist Sampling Rate in Flexible Delay-Division Multiplexing OFDMA PONs (2016)

This paper details a delay-division multiplexing (DDM) scheme for orthogonal frequency-division multiple access (OFDMA) passive optical networks (PONs). Unlike detection in a conventional OFDMA PON, the detection of OFDM signals in the proposed scheme involves an analog-to-digital converter (ADC) operating at a sampling rate below the Nyquist rate for each optical network unit (ONU). Based on preallocated relative time delays among the ONUs, preprocessed signals sent from an optical line terminal can be detected as different downstream signals following spectral aliasing caused by ADCs operating at a sub-Nyquist sampling rate. It should be noted that the proposed scheme reduces the requirement of sampling rate, but not the analog bandwidth of an ADC, such that all sent subcarriers can be retained before spectral aliasing. Thus, the proposed DDM scheme can reduce computational complexity and power consumption in the demodulation process, leading to an improvement in cost efficiency. In experiments, we demonstrate that each ONU with an ADC operating at 1/2-1/32 of the Nyquist sampling rate is able to receive 1/2-1/32 of the downstream data, with an insignificant performance penalty. Furthermore, in the DDM scheme, the sampling instant of an ADC is a key parameter in the selection of required data. This paper also proposes a method for estimating the adjustments required in the sampling instant at ONUs. The proposed method is based on the use of deviations in the channel response, which provides the ability to identify with a high degree of precision the adjustments required for an ADC with sub-Nyquist sampling rate. Estimation error associated with the necessary adjustments has only negligible effects on performance, thereby confirming the reliability of the proposed method.
Tensor Train Decomposition for Efficient Memory Saving in Perceptual Feature-Maps (2019)

The perceptual loss functions have been used successfully in image transformation for capturing high-level features from images in pre-trained convolutional neural networks (CNNs). Standard perceptual losses require numerous parameters to compare differences in feature-maps on both an input image and a target image; thus, it is not affordable for resource-constrained devices in terms of utilizing a feature-maps. Hence, we propose a compressed perceptual losses oriented Tensor Train (TT) decomposition on the feature-maps. Additionally, to decide an optimal TT-ranks, the proposed algorithm used the global analytic solution of Variational Bayesian Matrix Factorization (VBMF). Therefore, in proposed method, the low-rank approximated feature-maps consist of salient features by virtue of these two techniques. To the best of our knowledge, we are the first to consider curtailing redundancies in feature-maps via low-rank TT-decomposition. Experimental results in style transfer tasks demonstrate that our method not only yields similar qualitative and quantitative results as that of the original version, but also reduces memory requirement by approximately 77%.
Protein Engineering for Cardiovascular Therapeutics (2013)

A number of new and innovative approaches for repairing damaged myocardium are currently undergoing investigation, with several encouraging results. In addition to the progression of stem cell-based approaches and gene therapy/silencing methods, evidence continues to emerge that protein therapeutics may be used to directly promote cardiac repair and even regeneration. However, proteins are often limited in their therapeutic potential by short local half-lives and insufficient bioavailability and bioactivity, and many academic laboratories studying cardiovascular diseases are more comfortable with molecular and cellular biology than with protein biochemistry. Protein engineering has been used broadly to overcome weaknesses traditionally associated with protein therapeutics and has the potential to specifically enhance the efficacy of molecules for cardiac repair. However, protein engineering as a strategy has not yet been used in the development of cardiovascular therapeutics to the degree that it has been used in other fields. In this review, we discuss the role of engineered proteins in cardiovascular therapies to date. Further, we address the promise of applying emerging protein engineering technologies to cardiovascular medicine and the barriers that must be overcome to enable the ultimate success of this approach.
Automatic projector calibration with embedded light sensors (2004)

Projection technology typically places several constraints on the geometric relationship between the projector and the projection surface to obtain an undistorted, properly sized image. In this paper we describe a simple, robust, fast, and low-cost method for automatic projector calibration that eliminates many of these constraints. We embed light sensors in the target surface, project Gray-coded binary patterns to discover the sensor locations, and then prewarp the image to accurately fit the physical features of the projection surface. This technique can be expanded to automatically stitch multiple projectors, calibrate onto non-planar surfaces for object decoration, and provide a method for simple geometry acquisition.
CHLORPROPAMIDE AND LIPID METABOLISM OF RAT AND HUMAN ADIPOSE TISSUE IN VITRO1 (1970)

Abstract. Lipolysis measured as glycerol release from rat adipose tissue in vitro was inhibited by chlorpropamide. This antilipolytic effect was independent of the addition of glucose to the incubation medium. At the same time chlorpropamide decreased the re‐esterification of FFA formed by lipolysis. This inhibitory effect was more pronounced in tissue incubated in medium with glucose present. Since lipolysis as well as re‐esterification of FFA is accelerated by glucose, present data would indicate that chlorpropamide primarily interferes with the glucose metabolism or the stimulatory action of glucose on the two pathways of the triglyceride‐FFA cycle. Chlorpropamide (1 mg/ml) had no effect on the glycerol release and lipogenesis of human omental tissue. The present findings lend no support to the recent theory that sulfonylureas decrease the plasma levels of FFA and glycerol in man by direct action of the drug on adipose tissue.
Ultrafast dynamics in waveguide saturable absorbers (2002)

Summary form only given. The results of a model of differential transmission measurements in GaAs-GaAlAs waveguide saturable absorbers indicate that high field effects, spectral hole burning and carrier heating are important mechanisms governing absorption dynamics.
Supplementary Figure 1 from DiSCoVERing Innovative Therapies for Rare Tumors: Combining Genetically Accurate Disease Models with <i>In Silico</i> Analysis to Identify Novel Therapeutic Targets (2023)

&lt;p&gt;Detailed diagram of the workflow of the DiSCoVER work flow&lt;/p&gt;
Point-of-Use Sweat Biosensor to Track the Endocrine–Inflammation Relationship for Chronic Disease Monitoring (2020)

This wearable system is designed to be a point of use, chronic disease self-monitoring and management platform.
Leveraging Locality in Abstractive Text Summarization (2022)

Neural attention models have achieved significant improvements on many natural language processing tasks. However, the quadratic memory complexity of the self-attention module with respect to the input length hinders their applications in long text summarization. Instead of designing more efficient attention modules, we approach this problem by investigating if models with a restricted context can have competitive performance compared with the memory-efficient attention models that maintain a global context by treating the input as a single sequence. Our model is applied to individual pages which contain parts of inputs grouped by the principle of locality during both encoding and decoding. We empirically investigated three kinds of locality in text summarization at different levels of granularity, ranging from sentences to documents. Our experimental results show that our model has a better performance compared with strong baselines with efficient attention modules, and our analysis provides further insights into our locality-aware modeling strategy.
Characteristics of Self-Aligned Si/Ge T-Gate Poly-Si Thin-Film Transistors With High on/off Current Ratio (2007)

In this paper, we have successfully developed and fabricated self-aligned Si/Ge T-gate poly-Si thin-film transistors (Si/Ge T-gate TFTs) with a thick gate oxide at the gate edges near the source and drain for the first time. The Si/Ge T-gate was formed by selective wet etching of Ge gate layer. The thick gate oxide layer at the gate edges and passivation oxide layer were deposited simultaneously in passivation process. The thick gate oxide at the gate edges effectively reduces the drain vertical and lateral electric fields without additional mask, lightly doped drain, spacer, or subgate bias. The Si/Ge T-gate TFTs not only reduce the off-state leakage current but also maintain a high on-state current. Experimental results show that the Si/Ge T-gate TFTs have low off-state leakage currents, improved on/off current ratio, and more saturated output characteristics compared with conventional TFTs
Anodized Film for Vacuum Equipment. (2002)

We developed new methods for anodizing aluminum surfaces of plasma process chambers, one in sulfuric acid, and another in oxalic acid, in order to reduce particulate generation. The anodized films show a lower density of cracks than conventionally anodized films even after exposing to high temperature. Therefore, they have a better performance of small number in particulate. Analysis by X-ray diffraction, scanning electron microscopy, infrared spectroscopy and electron probe microanalysis reveals that both films are amorphous and that a cracking mechanism depends on the electrolyte and anodizing process. It is also found that number of cracks and total amount of outgassing increase after sealing process.
Angular analysis of B0 d → K∗μ+μ− decays in pp collisions at $$ \sqrt{s}=8 $$ TeV with the ATLAS detector (2018)

A bstract An angular analysis of the decay B d 0 → K ∗ μ + μ − is presented, based on proton-proton collision data recorded by the ATLAS experiment at the LHC. The study is using 20.3 fb −1 of integrated luminosity collected during 2012 at centre-of-mass energy of $$ \sqrt{s}=8 $$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:msqrt><mml:mi>s</mml:mi></mml:msqrt><mml:mo>=</mml:mo><mml:mn>8</mml:mn></mml:math> TeV. Measurements of the K * longitudinal polarisation fraction and a set of angular parameters obtained for this decay are presented. The results are compatible with the Standard Model predictions.
Fabrication, Characterization, and Printing of Conductive Ink Based on Multi Core–Shell Nanoparticles Synthesized by RAPET (2013)

Abstract In the current research, conductive patterns are deposited on different substrates by direct inkjet printing of conductive inks based on metal@carbon and bimetal@carbon core–shell nanoparticles synthesized by the RAPET (reaction under autogenic pressure at elevated temperatures) technique. Various co‐solvents and additives are examined for production of stable conductive ink. The morphology of the deposited layers is characterized by optical and scanning electron microscopy measurements. The stability of the prepared inks is examined by dynamic light scattering measurements. The electrical resistivity is measured by a four‐point probe system and calculated using the geometric dimensions. The results obtained are very promising and indicate that the conductivity of the deposited layers is close to that of bulk metals and higher than most results published so far. Moreover, the importance and advantages of the protective carbon layer that prevents metal oxidation is demonstrated.
Superior Hypogastric Plexus Block to Reduce Pain After Laparoscopic Hysterectomy (2021)

ClinicalTrials.gov, NCT03283436.
ChemInform Abstract: Synthesis of the Simple Peptide Model Ac‐Abu(PO3H2)‐NHMe. (1992)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Pulse energy limits of the femtosecond Ti:sapphire osillators (2006)

In this paper we analyze an alternative approach to the stabilization of the extra-high energy ultrashort pulses and explore the pulse energy limits of low-repetition rate Ti:sapphire oscillators operating within the positive GDD region. The numerical analysis based on the distributed generalized Ginzburg-Landau model has demonstrated that a source of the pulse stabilization is the negative passive feed-back caused by the spectral loss maintained by the chirp due to self-phase modulation.
CompoundProtein Interaction Prediction Within Chemogenomics: Theoretical Concepts, Practical Usage, and Future Directions (2013)

With advancements in high-throughput technologies and open availability of bioassay data, computational methods to generate models, that zoom out from a single protein with a focused ligand set to a larger and more comprehensive description of compound-protein interactions and furthermore demonstrate subsequent translational validity in prospective experiments, are of prime importance. In this article, we discuss some of the new benefits and challenges of the emerging computational chemogenomics paradigm, particularly with respect to compound-protein interaction. Examples of experimentally validated computational predictions and recent trends in molecular feature extraction are presented. In addition, analyses of cross-family interactions are considered. We also discuss the expected role of computational chemogenomics in contributing to increasingly expansive network-level modeling and screening projects.
Variant-selective stereopure oligonucleotides protect against pathologies associated with C9orf72-repeat expansion in preclinical models (2021)

A large G<sub>4</sub>C<sub>2</sub>-repeat expansion in C9orf72 is the most common genetic cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Neuronal degeneration associated with this expansion arises from a loss of C9orf72 protein, the accumulation of RNA foci, the expression of dipeptide repeat (DPR) proteins, or all these factors. We report the discovery of a new targeting sequence that is common to all C9orf72 transcripts but enables preferential knockdown of repeat-containing transcripts in multiple cellular models and C9BAC transgenic mice. We optimize stereopure oligonucleotides that act through this site, and we demonstrate that their preferential activity depends on both backbone stereochemistry and asymmetric wing design. In mice, stereopure oligonucleotides produce durable depletion of pathogenic signatures without disrupting protein expression. These oligonucleotides selectively protect motor neurons harboring C9orf72-expansion mutation from glutamate-induced toxicity. We hypothesize that targeting C9orf72 with stereopure oligonucleotides may be a viable therapeutic approach for the treatment of C9orf72-associated neurodegenerative disorders.
Crystal structure ofO-ethylN-(ethoxycarbonyl)thiocarbamate (2015)

The title compound, C6H11NO3S, provides entries to novel carbamoyl disulfanes and related compounds of inter-est to our laboratory. The atoms of the central O(C=S)N(C=O)O fragment have an r.m.s. deviation of 0.1077 Å from the respective least-squares plane. While several conformational orientations are conceivable, the crystal structure shows only the one in which the carbonyl and the thio-carbonyl moieties are anti to each other across the central conjugated C-N-C moiety. Pairs of 2.54 Å N-H⋯S=C hydrogen bonds between adjacent mol-ecules form centrosymmetric dimers in the crystal.
Asymptotic analysis and design of iterative receivers for non linear ISI channels (2014)

In this paper, iterative receiver analysis and design for non linear satellite channels is investigated. To do so, an EXtrinsic Information Transfer (EXIT) chart-based optimization is applied using two major assumptions: the equalizer outputs follow a Gaussian Mixture distribution since we use non-binary modulations and partial interleavers are used between the Low Density Parity Check (LDPC) code and the mapper. Achievable rates, performance and thresholds of the optimized receiver are analysed. The objective in fine is to answer the question: Is it worth optimizing an iterative receiver for non linear satellite channels?
Prognostic Value of Numerical Chromosome Aberrations in Multiple Myeloma: A FISH Analysis of 15 Different Chromosomes (1998)

Recent observations indicate that chromosome aberrations are important prognostic factors in patients with multiple myeloma (MM) treated with high-dose chemotherapy. Nevertheless, the inherent problems of conventional cytogenetics have hampered the systematic evaluation of this parameter in series of patients treated with conventional chemotherapy. Fluorescence in situ hybridization (FISH) analysis is an attractive alternative for evaluation of numerical chromosomal changes. In the present study, we analyze the relationship between aneuploidies of 15 different chromosomes assessed by FISH and prognosis in a series of 63 patients with MM treated with conventional chemotherapy. After a median follow-up of 61 months (range, 6 to 109), 49% of patients are still alive with a median survival of 33 months. The overall incidence of numerical chromosome abnormalities was 70%. This incidence significantly increased when seven or more chromosomes were analyzed (53 patients), reaching 81%. Trisomies of chromosomes 6, 9, and 17 were associated with prolonged survival (P = .033, P = .035, and P = .026, respectively); by contrast, overall survival (OS) was lower in cases with monosomy 13 (as assessed by deletion of Rb gene,P = .0012). From the clinical point of view, loss of Rb gene was associated with a poor performance status; low hemoglobin levels; high creatinine, C-reactive protein, and lactic dehydrogenase serum levels; high percentage of bone marrow plasma cells (BMPC); extensive bone lytic lesions; and advanced clinical stage. Other chromosome abnormalities such as trisomy of chromosome 9 and 17 were associated with good prognostic features including high hemoglobin levels, early clinical stage, β2microglobulin less than 6 μg/mL, and low percentage of BMPC. A multivariate analysis for OS showed that S-phase PC greater than 3% (P = .010) and β2microglobulin serum levels greater than 6 μg/mL (P = .024), together with monosomy of chromosome 13 (P = .031) and nontrisomy of chromosome 6 (P = .048) was the best combination of independent parameters for predicting survival in patients with MM. According to these results, chromosomal analysis is of great use in patients with MM at diagnosis to have a correct prognostic evaluation for clinical decision making.
Session details: Variation-aware and reconfigurable design (2010)

No abstract available.