gebhart/patrepeval huggingface dataset:
Imaging of Bioelectric Sources in the Heart Using a Cellular Automaton Model (2005)

The approach to solve the inverse problem of electrocardiography presented here is using a computer model of the individual heart of a patient. It is based on a 3D-MRI dataset. Electrophysiologically important tissue classes are incorporated using rules. Source distributions inside the heart are simulated using a cellular automaton. Finite Element Method is used to calculate the corresponding body surface potential map. Characteristic parameters like duration and amplitude of transmembrane potential or velocity of propagation are optimized for selected tissue classes or regions in the heart so that simulated data fit to the measured data. This way the source distribution and its time course of an individual patient can be reconstructed.
De Novo Insertions and Deletions of Predominantly Paternal Origin Are Associated with Autism Spectrum Disorder (2014)

Whole-exome sequencing (WES) studies have demonstrated the contribution of de novo loss-of-function single-nucleotide variants (SNVs) to autism spectrum disorder (ASD). However, challenges in the reliable detection of de novo insertions and deletions (indels) have limited inclusion of these variants in prior analyses. By applying a robust indel detection method to WES data from 787 ASD families (2,963 individuals), we demonstrate that de novo frameshift indels contribute to ASD risk (OR = 1.6; 95% CI = 1.0-2.7; p = 0.03), are more common in female probands (p = 0.02), are enriched among genes encoding FMRP targets (p = 6 × 10(-9)), and arise predominantly on the paternal chromosome (p < 0.001). On the basis of mutation rates in probands versus unaffected siblings, we conclude that de novo frameshift indels contribute to risk in approximately 3% of individuals with ASD. Finally, by observing clustering of mutations in unrelated probands, we uncover two ASD-associated genes: KMT2E (MLL5), a chromatin regulator, and RIMS1, a regulator of synaptic vesicle release.
Ant colony search algorithm for unit commitment (2004)

In this paper, the ant colony search algorithm (ACSA) is proposed to solve the thermal unit commitment problem. ACSA is a new cooperative agents approach, which is inspired by the observation of the behaviors of real ant colonies on the topic of ant trial formation and foraging methods. In the ACSA, a set of cooperating agents called "ants" cooperates to find good solution for unit commitment problem of thermal units. The merits of ACSA are parallel search and optimization capabilities. The problem is decomposed in two sub-problems. The unit commitment sub-problem is solved by the ant colony search algorithm method and the economic dispatch sub-problem is solved by the lambda-iteration method. The unit commitment problem is formulated as the minimization of the performance index, which is the sum of objectives (fuel cost, start-up cost) and some constraints (power balance, generation limits, spinning reserve, minimum up time and minimum down time). This proposed approach is tested and compared to conventional Lagrangian relaxation (LR), genetic algorithm (GA), evolutionary programming (EP), Lagrangian relaxation and genetic algorithm (LRGA) on the 10 unit system.
Protein Kinase C Deficiency Blocks Recovery from Agonist-induced Desensitization (1996)

Protein phosphorylation is central to agonist-induced attenuation of the function of G-protein-linked receptors. Stable expression of RNA antisense to specific protein kinase mRNAs permitted analysis of loss-of-function mutants of A431 human epidermoid carcinoma cells, lacking protein kinase A, protein kinase C, or beta-adrenergic receptor kinase. Deficiency of protein kinase C, but not the others, amplified rather than attenuated agonist-induced desensitization. In wild-type cells, the t1/2 for recovery from desensitization was approximately 25 min following removal of agonist. In the protein kinase C-deficient cells, no resensitization was observed even 60 min after agonist removal. Like protein kinase C-deficiency, inhibition of protein kinase C with bisindolylmaleimide or calphostin C blocked resensitization. Resensitization was suppressed by FK506, an inhibitor of protein phosphatase 2B, mimicking protein kinase C-deficiency, but in a non-additive manner. The data reveal protein kinase C and protein phosphatase 2B to be critical elements of resensitization.
A multiagent urban traffic simulation Part I: dealing with the ordinary (2009)

We describe in this article a multiagent urban traffic simulation, as we believe individual-based modeling is necessary to encompass the complex influence the actions of an individual vehicle can have on the overall flow of vehicles. We first describe how we build a graph description of the network from purely geometric data, ESRI shapefiles. We then explain how we include traffic related data to this graph. We go on after that with the model of the vehicle agents: origin and destination, driving behavior, multiple lanes, crossroads, and interactions with the other vehicles in day-to-day, ?ordinary? traffic. We conclude with the presentation of the resulting simulation of this model on the Rouen agglomeration.
Photonic Crystals Based on Periodic Arrays of Aligned Carbon Nanotubes (2002)

We demonstrate here that large area periodic arrays of well-aligned carbon nanotubes can be fabricated inexpensively on Ni dots made by the process of self-assembly nanosphere lithography. These periodic arrays appear colorful due to their efficient reflection and diffraction of visible light. In addition, due to their honeycomb lattice structure, these arrays can act as photonic band gap crystals in the visible frequency range. In this report, we present the initial exploration of the optical properties of such arrays. Here we show that these potential 2D photonic band gap crystal arrays might find very important applications in optoelectronics.
Clinical and pathologic correlation of the activated form of the estrogen receptor beta (ERβ) in breast cancer (BC). (2014)

3046 Background: ERβ is antagonized by anti-estrogens and has been associated with a better prognosis although its role is unclear. Experimentally, ERβ has a nuclear biology common to the steroid nuclear receptors. In the absence of estrogenic ligand, it is evenly distributed in nuclei; when exposed to ligand, ERβ migrates to form sub-nuclear aggregates that can be detected by immunofluorescence microscopy. Thus, two distinct nuclear patterns, diffuse (D) or aggregated (A) are observed which correspond to the receptors’ functional states. Similarly to previous work on ERα and PR (ASCO 2013 abstr.# e11535 & 593), an immunohistochemistry (IHC) method has been developed to characterize the nuclear distribution patterns which may indicate whether ERβ is transcriptionally active or not in PEFF tissues. The goal of the study is to analyze whether activated ERβ is associated with anti-estrogen treatment outcome. Methods: 662 archived BC biopsies have been obtained along with clinical and pathological data. Biopsies were analyzed for standard HES, ERα, ERβ, PR and Ki67. ERβ positivity was determined with the 14C8 antibody (Abcam) and the nuclear distribution pattern analyzed at x1000 magnification. Results: 392 cases have been analyzed to date. Mean Age: 57 (17-89). Median follow up 36 months (mo). Histology: ductal 82% lobular 15% other 3%; ERαpos 78% PRpos 78%. Adjuvant chemotherapy 46%, Hormone therapy 85%. Stage I 44%, II 48%, III 8%. Grade I 25%, II 50%, III 25%. ERβ was positive in 57% of the cases (ERβpos). ERβ was activated (A- ERβ) in 35% of the ERβpos biopsies, and non-activated (D- ERβ) in 65% ERβpos . A-ERβ was associated with higher grade (p < 0.000, p = 0.007); ERβ, PR, HER2, Ki67, staging were not associated with ERβpos nor A-ERβ. Local or distant Progressive disease (PD) was evident in 19% of cases and was not associated with ERβpos or A-ERβ (p=0.87). With DFS defined as time to PD or death (5 year cut-off), neither ERβposnor A-ERβ were associated with a better DFS (HR: 1.02 and 0.98). Conclusions: In contrast to ERα, preliminary results show that ERβ positivity and ERβ activation status were associated with higher pathological grade but not with other pathological or clinical variables.
Tandem CAR T cells targeting HER2 and IL13Rα2 mitigate tumor antigen escape (2016)

In preclinical models of glioblastoma, antigen escape variants can lead to tumor recurrence after treatment with CAR T cells that are redirected to single tumor antigens. Given the heterogeneous expression of antigens on glioblastomas, we hypothesized that a bispecific CAR molecule would mitigate antigen escape and improve the antitumor activity of T cells. Here, we created a CAR that joins a HER2-binding scFv and an IL13Rα2-binding IL-13 mutein to make a tandem CAR exodomain (TanCAR) and a CD28.ζ endodomain. We determined that patient TanCAR T cells showed distinct binding to HER2 or IL13Rα2 and had the capability to lyse autologous glioblastoma. TanCAR T cells exhibited activation dynamics that were comparable to those of single CAR T cells upon encounter of HER2 or IL13Rα2. We observed that TanCARs engaged HER2 and IL13Rα2 simultaneously by inducing HER2-IL13Rα2 heterodimers, which promoted superadditive T cell activation when both antigens were encountered concurrently. TanCAR T cell activity was more sustained but not more exhaustible than that of T cells that coexpressed a HER2 CAR and an IL13Rα2 CAR, T cells with a unispecific CAR, or a pooled product. In a murine glioblastoma model, TanCAR T cells mitigated antigen escape, displayed enhanced antitumor efficacy, and improved animal survival. Thus, TanCAR T cells show therapeutic potential to improve glioblastoma control by coengaging HER2 and IL13Rα2 in an augmented, bivalent immune synapse that enhances T cell functionality and reduces antigen escape.
Universal space-time coding (2003)

A universal framework is developed for constructing full-rate and full-diversity coherent space-time codes for systems with arbitrary numbers of transmit and receive antennas. The proposed framework combines space-time layering concepts with algebraic component codes optimized for single-input-single-output (SISO) channels. Each component code is assigned to a "thread" in the space-time matrix, allowing it thus full access to the channel spatial diversity in the absence of the other threads. Diophantine approximation theory is then used in order to make the different threads "transparent" to each other. Within this framework, a special class of signals which uses algebraic number-theoretic constellations as component codes is thoroughly investigated. The lattice structure of the proposed number-theoretic codes along with their minimal delay allow for polynomial complexity maximum-likelihood (ML) decoding using algorithms from lattice theory. Combining the design framework with the Cayley transform allows to construct full diversity differential and noncoherent space-time codes. The proposed framework subsumes many of the existing codes in the literature, extends naturally to time-selective and frequency-selective channels, and allows for more flexibility in the tradeoff between power efficiency, bandwidth efficiency, and receiver complexity. Simulation results that demonstrate the significant gains offered by the proposed codes are presented in certain representative scenarios.
Characterization of a 5-fluorouracil-enriched osteoprogenitor population of the murine bone marrow (1993)

In the presence of beta-glycerophosphate and vitamin C, cultures of normal mouse bone marrow cells form three-dimensional structures that stain positive with the Von Kossa technique and express alkaline phosphatase (ALP), collagen type I, and osteocalcin. Little is known about the characteristics and frequency of the cells that contribute to this phenomenon. Most likely, mature osteoblastic cells do not contribute to the nodule formation because no osteocalcin expressing cells are detected in the flushed marrow by in situ hybridization. Limiting dilution analysis shows that, in normal bone marrow, 1 of 2.2 x 10(5) cells has the potency to form a bone nodule and to express ALP, collagen, and osteocalcin in a temporal fashion. Upon in vivo treatment with 5-fluorouracil (5-FU), this frequency increases 12-fold, eg, 1 in 1.75 x 10(4) cells shows osteogenic activity. In comparison, fibroblast colony forming cells occur at a frequency of 1 of 2.5 x 10(4) or 1 of 5 x 10(3) plated cells in normal or 5-FU-treated marrow, respectively. Using density centrifugation, the majority of the osteoprogenitor cells in 5-FU marrow are found in the low-density (1.066 to 1.067 g/mL) fractions. In addition, these cells bind to nylon wool but not to plastic and aggregate in the presence of wheat germ agglutinin and soybean agglutinin. Scanning and transmission electron microscopy shows that the bone nodules in 5-FU marrow cultures are composed of fibroblastoid cells embedded in a mineralized collagen matrix. In conclusion, our results show that a quiescent cell population in the murine bone marrow with fibroblastoid characteristics contributes to the formation of bone-like nodules in vitro.
Fading channels: information-theoretic and communications aspects (1998)

In this paper we review the most peculiar and interesting information-theoretic and communications features of fading channels. We first describe the statistical models of fading channels which are frequently used in the analysis and design of communication systems. Next, we focus on the information theory of fading channels, by emphasizing capacity as the most important performance measure. Both single-user and multiuser transmission are examined. Further, we describe how the structure of fading channels impacts code design, and finally overview equalization of fading multipath channels.
2.4F/sup 2/ memory cell technology with stacked-surrounding gate transistor (S-SGT) DRAM (2001)

This paper proposes 2.4F/sup 2/ memory cell technology with stacked-surrounding gate transistor (S-SGT) DRAM. One unit of the S-SGT DRAM is formed by stacking several SGT-type cells in series vertically. The SGT-type cell itself arranges gate, source, drain and plate on a silicon pillar vertically. Both gate and plate electrode surround the silicon pillar. Subsequently applied trench etching and sidewall spacer formation during S-SGT DRAM formation causes a step-like silicon pillar structure. Due to these steps, gate, plate and diffusion layer in one S-SGT DRAM unit are fabricated vertically by a self-aligned process. The cell size dependence of the self-aligned-type S-SGT DRAM was analyzed with regard to the above step widths and the number of cells in one unit. As a result, the cell design for minimizing the cell size of this device has been formulated. By using the proposed cell design, it is demonstrated by process simulation that the S-SGT DRAM in 0.5 /spl mu/m design rule can achieve a cell size of 2.4F/sup 2/, which is half of the cell size of a conventional SGT DRAM cell (4.8F/sup 2/). Therefore, the S-SGT DRAM is a promising candidate for future ultra high density DRAMs.
Metabolic effects of the incretin mimetic exenatide in the treatment of type 2 diabetes (2006)

Interventional studies have demonstrated the impact of hyperglycemia on the development of vascular complications associated with type 2 diabetes, which underscores the importance of safely lowering glucose to as near-normal as possible. Among the current challenges to reducing the risk of vascular disease associated with diabetes is the management of body weight in a predominantly overweight patient population, and in which weight gain is likely with many current therapies. Exenatide is the first in a new class of agents termed incretin mimetics, which replicate several glucoregulatory effects of the endogenous incretin hormone, glucagon-like peptide-1 (GLP-1). Currently approved in the US as an injectable adjunct to metformin and/or sulfonylurea therapy, exenatide improves glycemic control through multiple mechanisms of action including: glucose-dependent enhancement of insulin secretion that potentially reduces the risk of hypoglycemia compared with insulin secretagogues; restoration of first-phase insulin secretion typically deficient in patients with type 2 diabetes; suppression of inappropriately elevated glucagon secretion to reduce postprandial hepatic output; and slowing the rate of gastric emptying to regulate glucose appearance into the circulation. Clinical trials in patients with type 2 diabetes treated with subcutaneous exenatide twice daily demonstrated sustained improvements in glycemic control, evidenced by reductions in postprandial and fasting glycemia and glycosylated hemoglobin (HbA(1c)) levels. Notably, improvements in glycemic control with exenatide were coupled with progressive reductions in body weight, which represents a distinct therapeutic benefit for patients with type 2 diabetes. Acute effects of exenatide on beta-cell responsiveness along with significant reductions in body weight in patients with type 2 diabetes may have a positive impact on disease progression and potentially decrease the risk of associated long-term complications.
CMOS Ultrasound Transceiver Chip for High-Resolution Ultrasonic Imaging Systems (2009)

The proposed CMOS ultrasound transceiver chip will enable the development of portable high resolution, high-frequency ultrasonic imaging systems. The transceiver chip is designed for close-coupled MEMS transducer arrays which operate with a 3.3-V power supply. In addition, a transmit digital beamforming system architecture is supported in this work. A prototype chip containing 16 receive and transmit channels with preamplifiers, time-gain compensation amplifiers, a multiplexed analog-to-digital converter with 3 kB of on-chip SRAM, and 50-MHz resolution time delayed excitation pulse generators has been fabricated. By utilizing a shared A/D converter architecture, the number of A/D converter and SRAM is cut down to one, unlike typical digital beamforming systems which need 16 A/D converters for 16 receive channels. The chip was fabricated in a 0.35-mum standard CMOS process. The chip size is 10 mm(2), and its average power consumption in receive mode is approximately 270 mW with a 3.3-V power supply. The transceiver chip specifications and designs are described, as well as measured results of each transceiver component and initial pulse-echo experimental results are presented.
Regeneration of skeletal muscle fibers from autologous satellite cells multiplied in vitro. An experimental model for testing cultured cell myogenicity (1989)

An experimental model used to test in vivo myogenicity of autologous satellite cells multiplied in vitro is described. Free muscle autotransplantation served as the basis and was combined with x-irradiation. Administration of 1500, 2500, and 3500 rad doses 24 hours before or after ischemia showed that inhibition of spontaneous regeneration is dose dependent and more efficient when irradiation was applied before injury. A single dose of 2500 rad before injury resulted in the formation of a cystic structure ideal for cell implantation. FITC-latex beads and/or carbocyanine dyes were internalized by mononucleated satellite cells in vitro. Labeling did not affect survival or development of these cells. No sign of marker release or spreading from labeled to unlabeled cells was detectable unless by the fusion process. These labels were retained for several weeks. Grafting of labeled dense cellular suspensions into x-irradiated ischemic muscles indicated that satellite cells retain their myogenic characteristic and are able to reform fully differentiated muscle fibers.
A Splitting-Based Iterative Algorithm for Accelerated Statistical X-Ray CT Reconstruction (2011)

Statistical image reconstruction using penalized weighted least-squares (PWLS) criteria can improve image-quality in X-ray computed tomography (CT). However, the huge dynamic range of the statistical weights leads to a highly shift-variant inverse problem making it difficult to precondition and accelerate existing iterative algorithms that attack the statistical model directly. We propose to alleviate the problem by using a variable-splitting scheme that separates the shift-variant and ("nearly") invariant components of the statistical data model and also decouples the regularization term. This leads to an equivalent constrained problem that we tackle using the classical method-of-multipliers framework with alternating minimization. The specific form of our splitting yields an alternating direction method of multipliers (ADMM) algorithm with an inner-step involving a "nearly" shift-invariant linear system that is suitable for FFT-based preconditioning using cone-type filters. The proposed method can efficiently handle a variety of convex regularization criteria including smooth edge-preserving regularizers and nonsmooth sparsity-promoting ones based on the l(1)-norm and total variation. Numerical experiments with synthetic and real in vivo human data illustrate that cone-filter preconditioners accelerate the proposed ADMM resulting in fast convergence of ADMM compared to conventional (nonlinear conjugate gradient, ordered subsets) and state-of-the-art (MFISTA, split-Bregman) algorithms that are applicable for CT.
Brainstem auditory evoked potentials in the fetal sheep, in utero. (1987)

We studied brainstem auditory evoked potentials (BAEPs) in 8 fetal sheep in utero, ranging in gestational age from 105 to 142 days gestation (normal term 147 days). We could not elicit BAEPs prior to 117 days of gestation. After this age rapid maturation was seen, with three discernible peaks observed prior to 120 days and five peaks after 120 days. A significant (P less than 0.05) gestational age related fall in peak latencies and interpeak latencies was observed. The rate of stimulus presentation that could be tolerated without significant changes in wavepeak latency or amplitude also increased with advancing gestational age. In older fetuses (greater than 125 days), where a differentiated electrocorticogram (ECOG) was observed, differences were seen in latency and amplitude of several of the BAEP wavepeaks dependent upon the state. In high voltage ECOG states the amplitudes of wave IV and V were significantly (P less than 0.05) greater than in the low voltage ECOG state and the latencies of wave I, II and V were significantly (P less than 0.05) longer in low as compared to high voltage ECOG state. The BAEP, being obtainable over very short periods of time, appears to provide a useful indice of neural maturation for the sheep fetus in utero.
Interference issues in multi-code CDMA networks (2002)

Multi-code direct-sequence code division multiple access (MC-CDMA) has been proposed as a flexible multiple access scheme for wireless packet networks that support a large variety of mobiles with different and even time-varying rates. However, the interference model typically used with conventional DS-CDMA cellular systems - a large number of low-power mobiles uniformly distributed in cells - may not hold. In MC-CDMA cellular systems, it is possible for a high-rate mobile, perhaps near the boundary of a cell, to have all the codes for high-rate transmission - therefore transmitting at high power and causing significant interference to the neighboring cell. In this study, we analyze the effects of MC-CDMA intercell interference on the reverse link (i.e., mobile to cell site) and investigate a maximum capacity power allocation (MCPA) criterion that exploits the sub-code concatenation property of MC-CDMA transmission. When the transmission rate is high, power control with MCPA criterion can significantly reduce reverse-link MC-CDMA intercell interference. However, with only four codes per mobile (e.g., as in IS-95), the reduction in intercell interference is less than 1 dB.