gebhart/patrepeval huggingface dataset:
Membrane protein-regulated networks across human cancers (2019)

Alterations in membrane proteins (MPs) and their regulated pathways have been established as cancer hallmarks and extensively targeted in clinical applications. However, the analysis of MP-interacting proteins and downstream pathways across human malignancies remains challenging. Here, we present a systematically integrated method to generate a resource of cancer membrane protein-regulated networks (CaMPNets), containing 63,746 high-confidence protein-protein interactions (PPIs) for 1962 MPs, using expression profiles from 5922 tumors with overall survival outcomes across 15 human cancers. Comprehensive analysis of CaMPNets links MP partner communities and regulated pathways to provide MP-based gene sets for identifying prognostic biomarkers and druggable targets. For example, we identify CHRNA9 with 12 PPIs (e.g., ERBB2) can be a therapeutic target and find its anti-metastasis agent, bupropion, for treatment in nicotine-induced breast cancer. This resource is a study to systematically integrate MP interactions, genomics, and clinical outcomes for helping illuminate cancer-wide atlas and prognostic landscapes in tumor homo/heterogeneity.
Control of Convective Heat Transfer in a Confined Laminar Impinging Jet by Low Amplitude Forcing (2002)

A numerical finite-difference model, derived using a control-volume approach, was used to compute the flow and heat transfer characteristics in a two-dimensional confined laminar air jet impinging on an isothermal surface. Several cases were considered with Re=650, 750, and nozzle to plate spacing, H/W=5. The behavior of the jet and the attendant heat transfer from the target wall were investigated when the jet was forced by fluidic excitation at the nozzle exit. At Re between 585 and 610, the unforced jet exhibits a transition to an unsteady regime leading to asymmetric vortex shedding and jet flapping [1, 2]. Investigation of the velocity spectra indicate three distinct dominant modes; the lowest frequency is associated with the jet flapping while the highest frequency is associated with the asymmetric vortex formation which causes buckling of the jet column. As a result of the two combined modes, the peak heat transfer is enhanced and the lateral cooling extent is broadened. The jet was subjected to forcing by introduction of numerical excitation at each side of the jet that modeled fluidic excitation. The jet was forced on both opposing sides at its exit, both with in-phase and out-of-phase modes. Under some conditions, out of phase forcing at Re=650 at the highest frequency leads to stabilization of the normally separated flow on one side only. This unusual asymmetric flow field is unsteady but repeatable, and results in an enhancement of the heat transfer. At Reynolds number of 750, forcing with an out of phase mode at the highest frequency leads to a complete stabilization of the jet. The forcing suppresses the high-amplitude low frequency flapping mode leaving only a high frequency vortex formation mode. The suppression of the jet flapping leads to a decrease in the peak heat transfer, but because separation is suppressed, the average wall heat transfer is enhanced.
Refractory Depression (Advances in Neuropsychiatry and Psychopharmacology, Volume 2). Edited by Jay D. Amsterdam. New York: Raven Press. 1991. 265 pp. $75.00. (1992)

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Evaluation of thresholding methods for activation likelihood estimation meta‐analysis via large‐scale simulations (2022)

In recent neuroimaging studies, threshold-free cluster enhancement (TFCE) gained popularity as a sophisticated thresholding method for statistical inference. It was shown to feature higher sensitivity than the frequently used approach of controlling the cluster-level family-wise error (cFWE) and it does not require setting a cluster-forming threshold at voxel level. Here, we examined the applicability of TFCE to a widely used method for coordinate-based neuroimaging meta-analysis, Activation Likelihood Estimation (ALE), by means of large-scale simulations. We created over 200,000 artificial meta-analysis datasets by independently varying the total number of experiments included and the amount of spatial convergence across experiments. Next, we applied ALE to all datasets and compared the performance of TFCE to both voxel-level and cluster-level FWE correction approaches. All three multiple-comparison correction methods yielded valid results, with only about 5% of the significant clusters being based on spurious convergence, which corresponds to the nominal level the methods were controlling for. On average, TFCE's sensitivity was comparable to that of cFWE correction, but it was slightly worse for a subset of parameter combinations, even after TFCE parameter optimization. cFWE yielded the largest significant clusters, closely followed by TFCE, while voxel-level FWE correction yielded substantially smaller clusters, showcasing its high spatial specificity. Given that TFCE does not outperform the standard cFWE correction but is computationally much more expensive, we conclude that employing TFCE for ALE cannot be recommended to the general user.
Fusion between Newcastle disease virus and erythrocyte ghosts using octadecyl Rhodamine B fluorescence assay produces dequenching curves that fit the sum of two exponentials (1994)

The kinetics of fusion between Newcastle disease virus and erythrocyte ghosts has been investigated with the octadecyl Rhodamine B chloride assay [Hoekstra, De Boer, Klappe, and Wilschut (1984) Biochemistry 23, 5675-5681], and the data from the dequenching curves were fitted by non-linear regression to currently used kinetic models. We used direct computer-assisted fitting of the dequenching curves to the mathematical equations. Discrimination between models was performed by statistical analysis of different fits. The experimental data fit the exponential model previously published [Nir, Klappe, and Hoekstra (1986) Biochemistry 25, 2155-2161] but we describe for the first time that the best fit was achieved for the sum of two exponential terms: A1[1-exp(-k1t)]+A2[1-exp(-k2t)]. The first exponential term represents a fast reaction and the second a slow dequenching reaction. These findings reveal the existence of two independent, but simultaneous, processes during the fusion assay. In order to challenge the model and to understand the meaning of both equation, fusion experiments were carried out under different conditions well known to affect viral fusion (changes in pH, temperature and ghost concentration, and the presence of disulphide-reducing agents or inhibitors of viral neuraminidase activity), and the same computer fitting scheme was followed. The first exponential equation represents the viral protein-dependent fusion process itself, because it is affected by the assay conditions. The second exponential equation accounts for a nonspecific reaction, because it is completely independent of the assay conditions and hence of the viral proteins. An interpretation of this second process is discussed in terms of probe transfer between vesicles.
Exploration of the Mechanism of the Activation of ClONO2by HCl in Small Water Clusters Using Electronic Structure Methods (2000)

High-level electronic structure calculations were used to study the mechanism of the reaction of ClONO2 with HCl in neutral water clusters containing one to five solvating water molecules. For the reaction between molecular HCl and ClONO2, the barrier decreases from 42 kcal mol-1 (uncatalyzed) to essentially zero when catalyzed by only two water molecules, where the reaction products involve Cl2 and HONO2. The calculations thus predict that the gas-phase reaction may be important in the stratospheric reactivation of ClONO2. The reaction between ClONO2 and solvated H3O+Cl-, as on the polar stratospheric cloud (PSC) surface, was investigated with clusters involving up to seven water molecules. The ice-catalyzed reaction involves an ionic mechanism whereby charge transfer to ClONO2 from the attacking nucleophile leads to significant ionization along the Cl−ONO2 bond. The effect of the size of the first solvation shell of Cl- is addressed by our calculations. In a cluster containing three waters and a five-water cluster structurally related to hexagonal ice, ClONO2 reacts spontaneously with HCl to yield Cl2/HONO2 in the three-water reaction and Cl2/H3O+NO3- in the five-water-catalyzed reaction. The calculations thus predict that the reaction of ClONO2 with HCl on PSC ice aerosols can proceed spontaneously via an ionic pathway.
Explicit evaluation of the equivalent degrees of freedom of smoothing splines: A spectral factorization approach (1998)

Smoothing splines are commonly used to reconstruct an unknown continuous function given n discrete noisy samples. In the tuning of the regularization parameter, which controls the balance between smoothness and datafit, the most computerintensive part is the evaluation of the socalled ''equivalent degrees of freedom'' (EDOF) as a function of the regularization parameter. In the paper a closedform expression of the asymptotic (as n goes to infinity) EDOF is obtained for the case of equally spaced data. The derivation is based on the reformulation of the spline smoothing problem as a Bayesian estimation prob lem. Statespace methods, Kalman filtering, and spectral factorization techniques are used to show that the asymp totic EDOF can be obtained as the variance of a suitably defined stationary process. As a byproduct of the main result, it is found that the asymptotic EDOF depend on the cube of the sampling interval.
Preparation and magnetic properties of hollow nano-spheres of cobalt and cobalt oxide: Drastic cooling-field effects on remnant magnetization of antiferromagnet (2004)

We investigate the making of magnetic hollow spheres of Co3O4 (2) and fcc Co (3) with diameter 500 nm and thickness 40 nm, using polystyrene-bead templates. The spheres are characterized by scanning electron microscope, transmission electron microscope, electron diffraction, and x-ray diffraction. Magnetic measurements on 2 reveal a drastic enhancement of remnant magnetization below TN induced by cooling-field, while measurements on 3 indicate a soft ferromagnetism similar to that of bulk fcc Co.
Within-class and unsupervised clustering improve accuracy and extract local structure for supervised classification (2006)

Deterministic clustering methods at different levels of granularity such as within classes, at the class level and across classes are investigated for their effect on classification performance in a series of empirical studies. Specifically I have found that clustering within classes, by extracting local structure, can improve supervised learning performance in many cases. This approach, and unsupervised clustering across entire data sets are usually better for prediction than clustering or grouping within-class clusters across classes, or even global classifier approaches. These conclusions are supported by more than 3000 experiments on four benchmark datasets, using some of the most powerful automated classification methods such as regularized logistic regression and Support Vector Machines (SVMs). 
I have used a simple combination of unsupervised clustering and classification methods to search for local structure in the data and detect locally significant features. The approach is illustrated by analysis of lung cancer survival data from records of 200,000 patients.
A first course in electronics (2012)

A top-down circuits course introduces students to electronic circuit design, teaching the formulation, evaluation and implementation of design objectives and solutions. Course topics include analog and digital signals and circuits, conversion, sensors, and energy storage and are introduced on the basis of concrete design examples. A comprehensive design project and custom PCB design expose students to physical aspects of design. The syllabus emphasizes topics of critical importance such power dissipation limits and is relation to technology and Moore's Law, relegating topics such as semiconductor device operation to follow-up elective courses.
Discovery of Sulforaphane as a Potent BACE1 Inhibitor Based on Kinetics and Computational Studies (2020)

BACE1 is the rate-limiting enzyme involved in the production and deposition of β-amyloid (Aβ). Since neurotoxic Aβ plays a critical role in Alzheimer's disease (AD) pathogenesis, BACE1 has emerged as a key target for preventing AD. In the present study, the potential of sulforaphane, an isothiocyanate found in cruciferous vegetables, as a BACE1 inhibitor has been investigated. Sulforaphane exhibited six times more potent activity against BACE1 compared to well-known positive controls including resveratrol and quercetin. Sulforaphane presented selective and non-competitive BACE1 inhibitory activity with low off-target inhibition of BACE2 and other aspartic and serine proteases. In addition, sulforaphane presented negative binding energy, suggesting that the compound had a high affinity for BACE1. It interacted with locations other than the active binding sites of BACE1 through van der Waals forces. Overall, sulforaphane appeared to be a promising candidate with potent and selective BACE1 inhibitory properties that play an important role in AD prevention.
Peptide‐Directed DNA‐Templated Protein Labelling for The Assembly of a Pseudo‐IgM (2019)

The development of methods for conjugation of DNA to proteins is of high relevance for the integration of protein function and DNA structures. Here, we demonstrate that protein-binding peptides can direct a DNA-templated reaction, selectively furnishing DNA-protein conjugates with one DNA label. Quantitative conversion of oligonucleotides is achieved at low stoichiometries and the reaction can be performed in complex biological matrixes, such as cell lysates. Further, we have used a star-like pentameric DNA nanostructure to assemble five DNA-Rituximab conjugates, made by our reported method, into a pseudo-IgM antibody structure that was subsequently characterized by negative-stain transmission electron microscopy (nsTEM) analysis.
Chemically Sensitive Interfaces on Surface Acoustic Wave Devices (1994)

Using surface acoustic wave (SAW) devices, three approaches to the effective use of chemically sensitive interfaces that are not highly chemically selective have been examined: (1) molecular identification from time-resolved permeation transients; (2) using multifrequency SAW devices to determine the frequency dependence of analyte/film interactions; (3) use of an array of SAW devices bearing diverse chemically sensitive interfaces to produce a distinct response pattern for each analyte. In addition to their well-known sensitivity to mass changes (0.0035 monolayer of N2 can be measured), SAW devices respond to the mechanical and electronic properties of thin films, enhancing response information content but making a thorough understanding of the perturbation critical. Simultaneous measurement of changes in frequency and attenuation, which can provide the information necessary to determine the type of perturbation, are used as part of the above discrimination schemes.
White‐Light‐Emitting Diodes Based on Iridium Complexes via Efficient Energy Transfer from a Conjugated Polymer (2006)

Abstract Efficient white‐light‐emitting diodes (WLEDs) have been developed using a polyfluorene‐type blue‐emitting conjugated polymer doped with green and red phosphorescent dyes. The emission spectrum of the conjugated polymer, which has a very high luminescent efficiency, shows a large spectral overlap with the absorbance of green and red iridium complexes. Also, efficient energy transfer from the conjugated polymer to the iridium complexes is observed. Poly( N ‐vinyl carbazole) is used to improve the miscibility between conjugated polymer and iridium complexes because of their poor chemical compatibility and phase separation. A white emission spectrum is easily obtained by varying the contents of the three materials and controlling the phase morphology. Moreover, these WLEDs show a voltage‐independent electroluminescence owing to the threshold and driving voltage of the three materials being similar as a result of energy transfer.
Overview of Ohmic Heating (2014)

In 1827, Georg Ohm published his treatise: Die galvanische Kette, mathematisch bearbeite (The Galvanic Circuit Investigated Mathematically) where he described what is today known as Ohm’s law. Thereafter, in 1841, James Prescott Joule showed that electricity flowing through a conductor resulted in the generation of heat. Although both these investigators faced skepticism and initial lack of acceptance of their results, their work has contributed directly to the development of today’s embodiments of Ohmic, or joule effect heating.
Crops with target‐site herbicide resistance for Orobanche and Striga control (2009)

It is necessary to control root parasitic weeds before or as they attach to the crop. This can only be easily achieved chemically with herbicides that are systemic, or with herbicides that are active in soil. Long-term control can only be attained if the crops do not metabolise the herbicide, i.e. have target-site resistance. Such target-site resistances have allowed foliar applications of herbicides inhibiting enol-pyruvylshikimate phosphate synthase (EPSPS) (glyphosate), acetolactate synthase (ALS) (e.g. chlorsulfuron, imazapyr) and dihydropteroate synthase (asulam) for Orobanche control in experimental conditions with various crops. Large-scale use of imazapyr as a seed dressing of imidazolinone-resistant maize has been commercialised for Striga control. Crops with two target-site resistances will be more resilient to the evolution of resistance in the parasite, if well managed.
A Variation Tolerant Current-Mode Signaling Scheme for On-Chip Interconnects (2012)

Current-mode signaling (CMS) with dynamic overdriving is one of the most promising scheme for high-speed low-power communication over long on-chip interconnects. However, they are sensitive to parameter variations due to reduced voltage swings on the line. In this paper, we propose a variation tolerant dynamic overdriving CMS scheme. The proposed CMS scheme and a competing CMS scheme (CMS-Fb) are fabricated in 180-nm CMOS technology. Measurement results show that the proposed scheme offers 34% reduction in energy/bit and 42% reduction in energy-delay-product over CMS-Fb scheme for a 10 mm line operating at 0.64 Gbps of data rate. Simulations indicate that the proposed CMS scheme consumes 0.297 pJ/bit for data transfer over the 10 mm line at 2.63 Gb/s. Measurements indicate that the delay of CMS-Fb becomes 2.5 times its nominal value in the presence of intra-die variations whereas the delay of the proposed scheme changes by only 5% for the same amount of intra-die variations. Measurement and simulation results show that both the schemes are robust against inter-die variations. Experiments and simulations also indicate that the proposed CMS scheme is more robust against practical variations in supply and temperature as compared to CMS-Fb scheme.
Standards of medical informatics in Japan. (1993)

Standardization activities related to medical informatics in Japan are briefly introduced in this paper. Because two kinds of portable media that are MODs (Magneto Optical Disk) and IC cards are supposed to be practically used in medicine, standardization works are currently supported by Japanese government. With an introduction of the organizations their standards and policy are explained.
Competition Between Two MHC Binding Registers in a Single Peptide Processed from Myelin Basic Protein Influences Tolerance and Susceptibility to Autoimmunity (2003)

Experimental allergic encephalomyelitis (EAE) is an animal model for multiple sclerosis induced by stimulating myelin basic protein (MBP)-specific T cells. The MBP-specific repertoire in B10.PL mice is shaped by tolerance mechanisms that eliminate MBP121-150-specific T cells. In contrast, MBPAc1-11-specific T cells escape tolerance and constitute the encephalitogenic repertoire. To determine if this differential tolerance is caused by differences in the abundance of MBP epitopes generated by processing, MBP peptides were eluted from I-Au complexes and analyzed by mass spectrometry. Peptides were identified from both the NH2-terminal and MBP121-150 regions. Unexpectedly, MBPAc1-18 and Ac1-17, which contain the MBPAc1-11 epitope, were much more abundant than MBP121-150 peptides. The results demonstrate that competition between two I-Au binding registers, a low affinity register defined by MBPAc1-11 and a high affinity register defined by MBP5-16, prevents most of the NH2-terminal naturally processed peptides from binding in the MBPAc1-11 register. The small fraction of MBPAc1-18 bound in the MBPAc1-11 register is not sufficient to induce tolerance but provides a ligand for MBPAc1-11-specific T cells during disease. These results provide a basis for both the lack of tolerance to MBPAc1-11 and the ability of this epitope to become a target during autoimmunity.
Hierarchical RNNs for Waveform-Level Speech Synthesis (2018)

Speech synthesis technology has a wide range of applications such as voice assistants. In recent years waveform-level synthesis systems have achieved state-of-the-art performance, as they overcome the limitations of vocoder-based synthesis systems. A range of waveform-level synthesis systems have been proposed; this paper investigates the performance of hierarchical Recurrent Neural Networks (RNNs) for speech synthesis. First, the form of network conditioning is discussed, comparing linguistic features and vocoder features from a vocoder-based synthesis system. It is found that compared with linguistic features, conditioning on vocoder features requires less data and modeling power, and yields better performance when there is limited data. By conditioning the hierarchical RNN on vocoder features, this paper develops a neural vocoder, which is capable of high quality synthesis when there is sufficient data. Furthermore, this neural vocoder is flexible, as conceptually it can map any sequence of vocoder features to speech, enabling efficient synthesizer porting to a target speaker. Subjective listening tests demonstrate that the neural vocoder outperforms a high quality baseline, and that it can change its voice to a very different speaker, given less than 15 minutes of data for fine tuning.
Development of the Hypothalamic-Pituitary-Thyroid Axis in the Neonatal Rat (1975)

The hypothalmic content of thyrotropin-releasing hormone (TRH), the pituitary concentration of thyroid-stimulating hormone (TSH), and the serum concentrations of TSH, thyroxine (T4), and triiodothyronine (T3) have been determined at different intervals during the first 50 days following birth in the rat. From a minimum concentration of 1 pg/mug protein at birth, the hypothalamic concentration of TRH increased to a maximum of 5 to 6 pg between 16 and 28 days of age. Serum and pituitary TSH concentrations increased to maximum levels by the end of the first post-natal week; the elevated hormone levels were then maintained to the end of the third post-natal week. Circulating thyroid hormone concentrations were very low at birth. T4 increased rapidly between days 4 and 16 to reach a peak concentration of 6 mug/100 ml, while T3 followed a parallel pattern with a peak concentration of 108 ng/100 ml obtained only at day 28. These data indicate that, in the rat, components of the hypothalamic-pituitary-thyroid axis develop simultaneously during the post-natal period.