gebhart/patrepeval huggingface dataset:
Application of Markov random fields to formant extraction (2002)

The theory of Markov random fields (MRFs) is used to extract formants from linear predictive coding (LPC) pole locations. In this model, the spectral peaks are presented in a time-frequency plot, using LPC poles as noisy indications of these peaks, and the formants are represented as lines connecting the spectral peaks. The spectral peaks and formants are modeled by a site process MRF and a line process MRF, respectively. The a posteriori probability of the spectral peaks and formants, given the LPC poles, quantifies the continuity constraints on the formants, the relationship between spectral peaks and formant locations, and the noise of the LPC poles. The formants are chosen by maximizing the a posteriori probability using simulated annealing. The parameters characterizing the MRFs are estimated by maximizing a pseudolikelihood function derived from LPC pole data with correctly labeled formants.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Characterization of functional residues in the interfacial recognition domain of lecithin cholesterol acyltransferase (LCAT) (1999)

Lecithin cholesterol acyltransferase (LCAT) is an interfacial enzyme active on both high-density (HDL) and low-density lipoproteins (LDL). Threading alignments of LCAT with lipases suggest that residues 50-74 form an interfacial recognition site and this hypothesis was tested by site-directed mutagenesis. The (delta56-68) deletion mutant had no activity on any substrate. Substitution of W61 with F, Y, L or G suggested that an aromatic residue is required for full enzymatic activity. The activity of the W61F and W61Y mutants was retained on HDL but decreased on LDL, possibly owing to impaired accessibility to the LDL lipid substrate. The decreased activity of the single R52A and K53A mutants on HDL and LDL and the severer effect of the double mutation suggested that these conserved residues contribute to the folding of the LCAT lid. The membrane-destabilizing properties of the LCAT 56-68 helical segment were demonstrated using the corresponding synthetic peptide. An M65N-N66M substitution decreased both the fusogenic properties of the peptide and the activity of the mutant enzyme on all substrates. These results suggest that the putative interfacial recognition domain of LCAT plays an important role in regulating the interaction of the enzyme with its organized lipoprotein substrates.
Relation of spatial learning of rats in the Morris water maze task to the number of viable CA1 neurons following four-vessel occlusion. (1994)

Male Wistar rats were tested in the Morris water maze task 1 week after 6, 9, or 12 min of transient global ischemia. The 9-min and 12-min ischemia groups were significantly impaired in the acquisition and the reversal experiment. A systematic counting of CA1 neurons in the whole hippocampal formation revealed a unilateral number of CA1 neurons of 286,000 in the sham group, of which 2/3 were located in the dorsal hippocampus. The ischemia groups showed a significant decline in the number of dorsal CA1 neurons, whereas only the 12-min ischemia group showed a significant but minor decline (10%-15%) in the number of ventral CA1 neurons. A correlation analysis showed that the escape distance declined with increasing number of viable CA1 neurons, but poor correlation coefficients were obtained. Thus, some of the ischemic rats with even very few viable CA1 neurons in the dorsal hippocampus were capable of performing this spatial learning task at sham-group level.
ChemInform Abstract: Spongistatin Synthetic Studies. Part 3. Construction of the C(1—17) Spiroketal. (1998)

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.
Resonant Internal Transverse‐Mode Coupling in InGaN/GaN/AlGaN Lasers (2007)

This chapter contains sections titled: Introduction Internal Mode Coupling and the Concept of “Ghost Modes” Device Structure and Material Parameters Calculation Technique Results of Calculations Resonant Conditions Spatial Characteristics of Laser Emission under the Resonant Internal Mode Coupling Spectral Effects of the Resonant Internal Mode Coupling Carrier-Induced Resonant Internal Mode Coupling Discussion and Conclusions References
ENDOGENOUS CYTOKININS, AUXINS, AND ABSCISIC ACID IN RED ALGAE FROM BRAZIL1 (2010)

Endogenous cytokinins, auxins, and abscisic acid (ABA) were identified and quantified in 11 red algae collected from the Brazilian coast. Field materials and two isolates cultured in the laboratory were extracted with various solvents and buffers containing a mixture of appropriate internal standards, purified by solid‐phase extraction followed by immunoaffinity chromatography, and analyzed by liquid chromatography–tandem mass spectrometry. Isoprenoid cytokinins (free and conjugated forms of isopentenyladenine [iP], cis ‐zeatin [ c Z], and trans ‐zeatin [ t Z]) were detected in all species with concentrations of c Z and iP forms being higher than t Z forms. Dihydrozeatin (DHZ) and its metabolites were only detected at very low levels in nine of the studied species. Aromatic cytokinins (6‐benzylaminopurine [BA], ortho ‐ and meta ‐topolin [ o T and m T]) were not detected in any of the samples. The cytokinin profile of Chondracanthus teedei (Mert. ex Roth) Kütz. was distinct in comparison to other species with para ‐topolin ( p T) derivatives detected in low concentrations. The main auxins present in all species were free indole‐3‐acetic acid (IAA) and indole‐3‐acetamide (IAM). Indole‐3‐ethanol (IEt), indole‐3‐acetyl glutamic acid (IAGlu), and indole‐3‐acetyl leucine (IALeu) were detected in a few species at low concentrations. ABA was present in all species analyzed except for Hypnea nigrescens Grev. ex J. Agardh. No ABA conjugates were detected in any species. These results confirm that cytokinins, auxins, and ABA were common constituents in red seaweeds, with this being the first report of the occurrence of ABA in Rhodophyta. The complexity of the hormone profiles suggests that plant hormones play a role in regulating physiological processes in Rhodophyta.
9H‐Xanthene‐9‐carboxylic Acid [1,2,4]Oxadiazol‐3‐yl‐ and (2H‐Tetrazol‐5‐yl)‐amides as Potent, Orally Available mGlu1 Receptor Enhancers. (2005)

Abstract For Abstract see ChemInform Abstract in Full Text.
COMPARATIVE13C NMR STUDIES OF COMPLEXATION OF IMIDAZOLIDINE-2-SELENONE AND ITS ANALOGOUS THIONE TO GOLD(I) THIOMALATE (1996)

Abstract The interaction of gold(I) thiomalate (AuStm)n (Myocrisin) with imidazolidine-2-selenone (SeImt) was studied in an aqueous solution at pH 7.40 using 13C NMR spectroscopy. It was found that SeImt binds more strongly to (AuStm)n than imidazolidine-2-thione and its derivatives as determined by 13C NMR spectroscopy. SeImt reacts differently with Au(Stm)2 −, as compared to (AuStm)n. With (AuStm)n, SeImt forms a ternary complex of ImtSe-Au-Stm, releasing free Stm− to solution. Redox reaction of gold(I) to metallic gold and free thiomalate (Stm−) to disulfide (Stm)2 occurs when Au(Stm)2 − reacts with SeImt.
Nutraceuticals and cataract prevention. (2008)

Cataract refers to any opacity developing in the lens or capsule of the eye, causing impairment of vision or blindness. Since cataract is a normal part of ageing, it becomes a major issue in public health with the growth of an ageing population. Other risk factors are genetics, excessive exposure to sunlight, cigarette smoking, diabetes mellitus, hormonal medication and eye injury. The most effective and common treatment is cataract surgery to remove the cloudy lens but this is medically expensive. On the other hand, diet has a significant impact on cataract development; high intake of fruit and vegetables may reduce the risk of cataract based upon epidemiology data. However, preventive methods using nutraceutical intervention have not been widely studied in clinical trials. This chapter presents the most recent results on various nutraceuticals including carotenoids, flavonoids, herbs and functional foods in cataract research, which suggest the potential for nutraceuticals to be an efficacious cataract preventative agent. It will also provide a comprehensive strategy for cataract prevention in the light of literature reviews.
Towards automating the security compliance value chain (2015)

Information security is of paramount importance in this digital era. While businesses strive to adopt industry-accepted system-hardening standards such as benchmarks recommended by the Center for Internet Security (CIS) to combat threats, they are confronted with an additional challenge of ever-evolving regulations that address security concerns. These create additional requirements, which must be incorporated into software systems. In this paper, we present a generic approach towards automating different activities of the Security Compliance Value Chain (SCVC) in organizations. We discuss the approach in the context of the Payment Card Industry Data Security Standard (PCI-DSS) regulations. Specifically, we present automation of (1) interpretation of PCI-DSS regulations to infer system requirements, (2) traceability of the inferred system requirements to CIS security controls (3) implementation of appropriate security controls, and finally, (4) verification and reporting of compliance.
Fluid Dynamics of the Open Port Interface for High-Speed Nanoliter Volume Sampling Mass Spectrometry (2021)

The open port interface (OPI) coupled to an atmospheric pressure ion source is used to capture, dilute, focus, and transport nanoliter volume sample droplets for high-speed mass spectrometric analysis. For typical applications, the system has been optimized to achieve 1 Hz nanoliter volume sample transfer rates while simultaneously diluting the sample >1000-fold to minimize sample matrix-induced ionization suppression. Geometric, flow, and dispensing alterations to the system presented here demonstrate that sample transfer rates for the OPI of at least 15 Hz are possible. The fluid dynamic processes that enable sampling rates of 1 Hz and greater are examined in detail by correlating computational fluid dynamics simulations, analytic calculations, experimental data, photographic footage, and reference to the fluid dynamics literature. The resulting models and experimental results provide the rationale underlying the design and tuning of the system as well as information for developing optimized analytical methods. In combination with acoustic droplet dispensing, referred to as acoustic ejection mass spectrometry (AEMS), this system can be considered to be a special case of flow injection analysis with unique features that control the peak width, symmetry, and segregation of the samples transported in a fluid while simultaneously enabling their mixing and dilution with carrier fluids. In addition, conditions are established to prevent direct contact of the sample with a surface enabling, in combination with a contact-free dispenser like acoustic ejection, a dramatic reduction in sample-to-sample carry-over.
Improving server power management in research and development data centers (2011)

Research data centers are often composed of thousands of diverse computer systems used for ongoing research, development, software regression and hardware compatibility testing. The usage patterns of many of these systems result in periodic non-use and extended periods of idleness. Users routinely fail to ensure that idle machines are powered down prior to overnight or extended absence periods. The annual amount of wasted energy in the HP Bangalore development data center is estimated at 14400 MWh resulting in over 8600 tons of CO2 emissions per year. In this paper, we propose Idle Machine Power Savings (IMPS), which seeks to address potential power cost savings and minimize environmental impact. IMPS consists of a low overhead, highly scalable data acquisition framework enabling the development of algorithms (an artificial neural network is used in the initial prototype) for automatic "extended idle" notifications and optional automatic shutdown of unused computers in data centers. This paper describes our approach, the framework, a prototype implementation and provides preliminary results. The results show an enormous potential for energy savings that translate directly into financial savings and lowered greenhouse gas emissions.
Zeitdiskrete Signalverarbeitung (1998)

Wer die Methoden der digitalen Signalverarbeitung erlernen oder anwenden will, kommt ohne das weltweit bekannte, neu gefaßte Standardwerk "Oppenheim/Schafer" nicht aus. Die Beliebtheit des Buches beruht auf den didaktisch hervorragenden Einführungen, der umfassenden und tiefgreifenden Darstellung der Grundlagen, der kompetenten Berücksichtigung moderner Weiterentwicklungen und der Vielzahl verständnisfördernder Aufgaben.
Automated sequential affinity chromatography of sea urchin embryo DNA binding proteins. (1992)

An automated method of running a tandem sequence of oligonucleotide affinity columns was used to purify factors that interact specifically with cis-regulatory sites of the CyIIIa cytoskeletal actin gene of the sea urchin embryo (Strongylocentrotus purpuratus). The method allows quantitative enrichment in a single chromatographic run of up to 12 different sequence-specific DNA binding proteins, each of which may then be readily purified to homogeneity by methods such as preparative gel electrophoresis. The affinity chromatography and identification of six different CyIIIa-regulatory factors is described, and the general utility of the method is discussed.
Asymmetric Construction of Quaternary Carbon Stereocenters:  High Stereoselection in Mukaiyama Aldol Reactions of 2-Siloxyindoles with Chiral Aldehydes (2005)

[reaction: see text] A new synthesis of enantiopure 3,3-disubstituted oxindoles by stereoselective Mukaiyama aldol reaction of 3-substituted 2-siloxyindoles and chiral, enantiopure aldehydes having nitrogen or oxygen substituents at the alpha carbon is described. When the C3 substituent of the prochiral nucleophile is aryl or heteroaryl, stereoselectivity is high (10-80:1).
Rapid Weight Loss, Central Obesity Improvement and Blood Glucose Reduction Are Associated with a Stronger Adaptive Immune Response Following COVID-19 mRNA Vaccine (2022)

Obesity is associated with a poor COVID-19 prognosis, and it seems associated with reduced humoral response to vaccination. Public health campaigns have advocated for weight loss in subjects with obesity, hoping to eliminate this risk. However, no evidence proves that weight loss leads to a better prognosis or a stronger immune response to vaccination. We aimed to investigate the impact of rapid weight loss on the adaptive immune response in subjects with morbid obesity. Twenty-one patients followed a hypocaloric, very-low-carbohydrate diet one week before to one week after the two mRNA vaccine doses. The diet's safety and efficacy were assessed, and the adaptive humoral (anti-SARS CoV-2 S antibodies, Abs) and cell-mediated responses (IFNγ secretion on stimulation with two different SARS CoV-2 peptide mixes, IFNγ-1 and IFNγ-2) were evaluated. The patients lost ~10% of their body weight with metabolic improvement. A high baseline BMI correlated with a poor immune response (R -0.558, <i>p</i> = 0.013 for IFNγ-1; R -0.581, <i>p</i> = 0.009 for IFNγ-2; R -0.512, <i>p</i> = 0.018 for Abs). Furthermore, there was a correlation between weight loss and higher IFNγ-2 (R 0.471, <i>p</i> = 0.042), and between blood glucose reduction and higher IFNγ-1 (R 0.534, <i>p</i> = 0.019), maintained after weight loss and waist circumference reduction adjustment. Urate reduction correlated with higher Abs (R 0.552, <i>p</i> = 0.033). In conclusion, obesity is associated with a reduced adaptive response to a COVID-19 mRNA vaccine, and weight loss and metabolic improvement may reverse the effect.
Temporal-Context-Based Video Browsing Interface for PVR-Enabled High-Definition Television Systems (2006)

We describe an implementation of our previously developed temporal-context-based video browsing interface, on a PVR-enabled high-definition television system. The implementation poses significant challenges such as consuming minimal computational resources so as to avoid disrupting any of the existing functionalities, sampling the stored video frames using a 1394 AV/C connection, and rendering the sampled images in a visually pleasing and useful way. Our implementation successfully addresses the aforementioned challenges by taking advantage of the target platform's facilities for high-quality video scaling and frame sampling.
Introducing folding stability into the score function for computational design of RNA‐binding peptides boosts the probability of success (2016)

A computational strategy that integrates our peptide search algorithm with atomistic molecular dynamics simulation was used to design rational peptide drugs that recognize and bind to the anticodon stem and loop domain (ASL(Lys3)) of human tRNAUUULys3 for the purpose of interrupting HIV replication. The score function of the search algorithm was improved by adding a peptide stability term weighted by an adjustable factor λ to the peptide binding free energy. The five best peptide sequences associated with five different values of λ were determined using the search algorithm and then input in atomistic simulations to examine the stability of the peptides' folded conformations and their ability to bind to ASL(Lys3). Simulation results demonstrated that setting an intermediate value of λ achieves a good balance between optimizing the peptide's binding ability and stabilizing its folded conformation during the sequence evolution process, and hence leads to optimal binding to the target ASL(Lys3). Thus, addition of a peptide stability term significantly improves the success rate for our peptide design search.
True Concurrent Modulation of a Multi-Channel Ring Modulator Transmitter Driven by a Comb Laser (2017)

This paper presents experimental data of concurrent modulation of a multi-channel transmitter that uses carrier-injection ring modulators at 10Gb/s/channel that is optically driven by a quantum-dot comb laser with 50GHz channel spacing.
Orthogonal Design of Unitary Constellations for Uncoded and Trellis-Coded Noncoherent Space–Time Systems (2004)

We construct unitary noncoherent space-time constellations, which can be considered as a concatenation of a training block with an orthogonal design. With a simple construction, our constellations are easy to design, enjoy full antenna diversity, allow for a simplified maximum-likelihood (ML) detector, and achieve error performance comparable to existing designs that rely on computer search. To exploit the constellation structures and improve coding gains, we further pursue a trellis-coded modulation (TCM) approach. Based on the sequence pairwise error analysis, we identify two simple parameters to quantify the asymptotic error performance, which enables us to compare among different TCM schemes or uncoded alternatives.
Antagonists of Anaphase-promoting Complex (APC)-2-Cell Cycle and Apoptosis Regulatory Protein (CARP)-1 Interaction Are Novel Regulators of Cell Growth and Apoptosis (2011)

CARP-1/CCAR1, a perinuclear phosphoprotein, is a regulator of cell growth and apoptosis signaling. Although CARP-1 is a regulator of chemotherapy-dependent apoptosis, it is also a part of the NF-κB proteome and a co-activator of steroid/thyroid nuclear receptors as well as β-catenin signaling. Our yeast two-hybrid screen revealed CARP-1 binding with the anaphase-promoting complex/cyclosome E3 ubiquitin ligase component APC-2 protein. CARP-1 also binds with anaphase-promoting complex/cyclosome co-activators Cdc20 and Cdh1. Following mapping of the minimal epitopes involved in CARP-1 binding with APC-2, a fluorescence polarization assay was established that indicated a dissociation constant (K(d)) of 480 nm for CARP-1/APC-2 binding. Fluorescence polarization assay-based high throughput screening of a chemical library yielded several small molecule antagonists of CARP-1/APC-2 binding, termed CARP-1 functional mimetics. CFM-4 (1(2-chlorobenzyl)-5'-phenyl-3'H-spiro[indoline-3,2'-[1,3,4]thiadiazol]-2-one), a lead compound, binds with and stimulates CARP-1 expression. CFM-4 prevents CARP-1 binding with APC-2, causes G(2)M cell cycle arrest, and induces apoptosis with an IC(50) range of 10-15 μm. Apoptosis signaling by CFM-4 involves activation of caspase-8 and -9 and caspase-mediated ubiquitin-proteasome pathway-independent loss of cyclin B1 and Cdc20 proteins. Depletion of CARP-1, however, interferes with CFM-4-dependent cell growth inhibition, activation of caspases, and apoptosis. Because CFM-4 also suppresses growth of drug-resistant human breast cancer cells without affecting the growth of human breast epithelial MCF-10A cells, elevating CARP-1 by CFM-4 and consequent apoptosis could in principle be exploited to further elucidate, and perhaps effectively target, often deregulated cell cycle pathways in pathological conditions, including cancer.
Origin of oblique optical axis of electrically tunable focusing lenses arising from initial anisotropic molecular tilts under a symmetric electric field. I (2020)

The optical axes of electrically tunable liquid crystal (LC) lenses are usually tilted, and the corresponding asymmetric wavefront aberrations hinder the lenses from being diffraction-limited. Looking back at the literature studies since 1979, researchers used different approaches to compensate the tilting of the optical axis for achieving a perfect lens, or they utilized the intrinsically asymmetric wavefront aberration as a physical-planar free-form optics. However, the physics behind axis tilting has not been discussed yet, and the origin of the oblique optical axes of LC lenses in terms of anisotropic properties of molecules requires an investigation. In this paper, we study the origin of the asymmetrical tilting of optical axes of LC lenses. We found that the initial anisotropic molecular tilts (the so-called pretilt angle) result in the dielectric torque difference even under a rotationally symmetric electric field. Moreover, it is discovered that the rotational symmetry of the wavefront can be broken by generating uneven tilt angles of the LC molecules even though the electric potential is rotationally symmetric. Numerical results are presented and discussed to illustrate the mechanism.
Indirect Performance Sensing for On-Chip Self-Healing of Analog and RF Circuits (2014)

The advent of the nanoscale integrated circuit (IC) technology makes high performance analog and RF circuits increasingly susceptible to large-scale process variations. On-chip self-healing has been proposed as a promising remedy to address the variability issue. The key idea of on-chip self-healing is to adaptively adjust a set of on-chip tuning knobs (e.g., bias voltage) in order to satisfy all performance specifications. One major challenge with on-chip self-healing is to efficiently implement on-chip sensors to accurately measure various analog and RF performance metrics. In this paper, we propose a novel indirect performance sensing technique to facilitate inexpensive-yet-accurate on-chip performance measurement. Towards this goal, several advanced statistical algorithms (i.e., sparse regression and Bayesian inference) are adopted from the statistics community. A 25 GHz differential Colpitts voltage-controlled oscillator (VCO) designed in a 32 nm CMOS SOI process is used to validate the proposed indirect performance sensing and self-healing methodology. Our silicon measurement results demonstrate that the parametric yield of the VCO is significantly improved for a wafer after the proposed self-healing is applied.