gebhart/patrepeval huggingface dataset:
The balance between intrinsic and ecological fitness reveals hidden regimes in eco-evolutionary population dynamics (2023)

Understanding how populations evolve requires accounting for both intrinsic fitness, defined by genotype and environment, and ecological interactions that emerge in mixed communities. While evolutionary experiments typically assess fitness in isolation, such monoculture measures may misrepresent dynamics in realistic, interacting populations. Here, we present a game-theoretic framework that explicitly separates intrinsic and ecological contributions to fitness, allowing us to map how ecological interactions can mask, mirror, maintain, or mimic selection driven by genetic differences. We derive analytical conditions for these regimes using deterministic replicator dynamics and validate them in stochastic Wright-Fisher models with mutation and drift. Applying our model to published microbial and cancer co-culture data, we show that real systems span both intrinsic-dominant and ecology-dominant regimes, with ecological effects sometimes reversing or neutralizing intrinsic fitness advantages. These results expose a critical blind spot in experimental design and interpretation, emphasizing the need to account for ecological interactions when inferring evolutionary dynamics and designing therapeutic strategies.
Layout-Aware Delay Variation Optimization for CNTFET-Based Circuits (2014)

Carbon Nanotube Field Effect Transistors (CNTFETs) are attractive alternatives to MOSFET devices as CNTFETs benefit from higher on-current, better gate control and faster switching response. However CNTFET-based technologies suffer from higher process variations compared to MOSFET devices. The CNT density variation is one of the most important sources of variation and directly impacts gate delay variation. The density variations of different gates in the layout are asymmetrically correlated according to their positions with respect to CNT growth direction. In this paper, we take advantage of this asymmetric correlation of CNT density to optimize the circuit layout to reduce the total variation of circuit delay using two heuristic placement methods. Simulation results on ISCAS85 Benchmark circuits show a reduction in total delay variation up to 30%. Our proposed Path Healing technique is up to five orders of magnitude faster than Simulated Annealing placement.
A simple phase-shifting cell for reflectarray using a slot loaded with a ferroelectric capacitor (2014)

A tunable reflectarray phase-shifting cell, designed for a resonance frequency of 5.6 GHz, is presented. The cell is based on a simple slot topology and loaded by a ferroelectric thin film capacitor of 60% tunability under 400 kV/cm bias electric field. The cell provides 245 degrees of phase-shifting.
Pilot test results for internal multiples attenuation on land data from northern Kuwait (2017)

We review a processing sequence for data conditioning and predicting surface and internal multiples that was applied with success on Kuwaiti datasets and, in particular, is favored for conditioning the data prior to amplitude variation with azimuth inversions and fracture characterization. We report on enhancements to this processing sequence evaluated by testing on a pilot dataset. Our tests suggest that improved preprocessing (geometry regularization and near-offsets reconstruction) and more flexible parametrizations of the generators of multiples, with particular attention to multiples generated in the near surface, can have a significant contribution to improved results from multiple attenuation. Presentation Date: Wednesday, September 27, 2017 Start Time: 3:30 PM Location: 370A Presentation Type: ORAL
Tamoxifen Attenuates Glucocorticoid Actions on Bone Formation in Vitro (1997)

Tamoxifen is a synthetic estrogen analog which may regulate osteogenesis in vivo by virtue of its antiglucocorticoid properties. We have examined tamoxifen regulation of glucocorticoid-induced osteogenesis in two different in vitro bone systems: the chicken periosteal osteogenesis model (CPO) and rat bone marrow stromal cells (RBMC). Hormone uptake studies were conducted with the osteosarcoma cell line, ROS 17/2.8. In the CPO model, alkaline phosphatase (AP) activity and collagen synthesis were stimulated by the glucocorticoid dexamethasone (Dex; 0.1μ m). These Dex-mediated effects were inhibited by increasing concentrations of tamoxifen (10–100 μm). Similarly, in the RBMC model, Dex-dependent (0.01 μm Dex) mineralized tissue formation and AP activity were blocked by tamoxifen (0.1 μm). Although tamoxifen inhibited Dex-mediated increases of AP activity in ROS 17/2.8 cells, it did not inhibit uptake of 3H-Dex or of 3H-estrogen. Northern analyses showed that tamoxifen did not affect messenger RNAs (mRNAs) for AP. Tamoxifen did seem to reduce mRNA for collagen type I, but not bone sialoprotein, osteopontin, and osteocalcin. Dex-induced increases for all proteins mRNAs in the RBMC model were not reduced by tamoxifen. Similarly, tamoxifen had no effects on cellular proliferation. We conclude that tamoxifen has no direct effect on gene expression of bone-related proteins of osteoblastic cells. Further, in the ROS 17/2.8 cell line, the antiglucocorticoid properties of tamoxifen do not appear to be mediated through either Dex or estrogen receptors.
Occupational Illness (1995)

Workplace exposures to hazardous materials cause or aggravate diseases as common and diverse as asthma, cancer, dermatitis, and tuberculosis.1 Crude estimates of the number of new cases of occupational disease in the United States range from 125,000 to 350,000 per year,24 in addition to 5.3 million work-related injuries. The economic cost is estimated to exceed $60 billion annually.2,57 Occupational disorders occur in industry and agriculture, both as underrecognized endemic diseases and in sporadic epidemics. With modernization, occupational hazards have shifted from factories and mines to include hospitals and office buildings.Patients perceive industrial toxins as threatening their . . .
Three-dimensional Contrast-enhanced MR Angiography (1996)

Three-dimensional contrast-enhanced magnetic resonance (MR) angiography is a relatively new technique that uses the transient shortening in blood T1 following the intravenous injection of gadolinium chelates to image blood vessels irrespective of flow. For many applications, 3D contrast-enhanced MR angiography is developing into a safe, fast, and cost-effective alternative to conventional diagnostic angiography. One of its biggest advantages over other MR angiography techniques (and CT angiography) is the ability to image in a plane parallel to the vessel of interest. This feature, combined with the inherent properties of a 3D gradient refocused sequence, make 3D contrast-enhanced MR angiography intrinsically fast, high resolution and free from saturation and turbulence-related artifacts. This article is designed to familiarize the reader with the theory of 3D contrast-enhanced MR angiography and the application of the technique to different vascular territories. Contrast agents, relaxation effects, contrast bolus effects, pulse sequences, artifacts, and post-processing, as well as the present state of thinking with regard to optimal contrast injection timing/detection and Fourier space mapping are discussed. Patient preparation and techniques and imaging parameters for body applications of gadolinium-enhanced MR angiography, including aorta, renal arteries, mesenteric arteries, portal venous system, pelvis and legs, pulmonary arteries, and carotid arteries are included.
Rhodothalassiales (2021)

Abstract Rho.do.tha.las.si.a'les. N.L. neut. n. Rhodothalassium , type genus of the order; suff. ‐ales, ending denoting an order; N.L. fem. pl. n. Rhodothalassiales , the Rhodothalassium order. The order currently comprises a single family and genus, which is characterized by halophilic anoxygenic phototrophic bacteria having spiral‐shaped cells and containing lamellar photosynthetic membranes. The properties of the order are determined by the characteristics of the Rhodothalassiaceae family. Taxonomic and Nomenclature Notes According to the List of Prokaryotic names with Standing in Nomenclature (LPSN), the taxonomic status of the order Rhodothalassiales is: correct name (last update, February 2025) * . LPSN classification: Bacteria / Pseudomonadati / Pseudomonadota / Alphaproteobacteria / Rhodothalassiales The order Rhodothalassiales can also be recovered in the Genome Taxonomy Database (GTDB) as o__Sphingomonadales (version v220) ** . GTDB classification: d__Bacteria / p__Pseudomonadota / c__Alphaproteobacteria / o__Sphingomonadales * Meier‐Kolthoff et al. ( 2022 ). Nucleic Acids Res , 50 , D801 – D807 ; DOI: 10.1093/nar/gkab902 ** Parks et al. ( 2022 ). Nucleic Acids Res , 50 , D785 – D794 ; DOI: 10.1093/nar/gkab776
ParSPIKE-a parallel DSP-accelerator for dynamic simulation of large spiking neural networks (2003)

The fast simulation of large networks of spiking neurons is a major task for the examination of biology inspired vision systems. Networks of this type are labelling features by synchronization of spikes and there is strong demand to simulate those effects in a real world environment. Because of the quite complex calculations for one model neuron the simulation of thousands or millions of these neurons is not efficient on existing hardware platforms. In order to simulate closer to the real time requirement, it is necessary to implement a dedicated hardware. Our aim is a hardware system mainly consisting of standard components which is as flexible as possible concerning the model neuron but as specialized as necessary to meet our performance requirements. Thus we decided to implement a parallel system with Digital Signal Processors (DSP) offering a large on-chip-memory. One main task of this work is the optimization of the simulation algorithm for the neurons distributed to the DSP which means the sequential part of simulation. This optimization benefits from the fact that there is only a very low percentage of simultaneously active neurons in vision networks. For communication between the nodes only spikes are distributed via a spike switching network. Processing of the network topology is realized by two different concepts. One idea is to compute the synapses autonomously on the processing node by representing a regular connection scheme with one connection mask for many neurons. Additional connections requiring adaptability and irregular connection schemes are stored in a shared memory. To avoid a bottleneck a synapse caching is used within each processing node. This paper describes the architecture of a DSP accelerator and shows the advantages with simulation results from a typical large vision network.
African Trypanosomiasis: Naturally Occurring Regulatory T Cells Favor Trypanotolerance by Limiting Pathology Associated with Sustained Type 1 Inflammation (2007)

Tolerance to African trypanosomes requires the production of IFN-gamma in the early stage of infection that triggers the development of classically activated macrophages controlling parasite growth. However, once the first peak of parasitemia has been controlled, down-regulation of the type 1 immune response has been described. In this study, we have evaluated whether regulatory T cells (Tregs) contribute to the limitation of the immune response occurring during Trypanosoma congolense infection and hereby influence the outcome of the disease in trypanotolerant C57BL/6 host. Our data show that Foxp3+ Tregs originating from the naturally occurring Treg pool expanded in the spleen and the liver of infected mice. These cells produced IL-10 and limited the production of IFN-gamma by CD4+ and CD8+ effector T cells. Tregs also down-regulated classical activation of macrophages resulting in reduced TNF-alpha production. The Treg-mediated suppression of the type 1 inflammatory immune response did not hamper parasite clearance, but was beneficial for the host survival by limiting the tissue damages, including liver injury. Collectively, these data suggest a cardinal role for naturally occurring Tregs in the development of a trypanotolerant phenotype during African trypanosomiasis.
Complementary surrounds explain diverse contextual phenomena across visual modalities. (2018)

Context is known to affect how a stimulus is perceived. A variety of illusions have been attributed to contextual processing-from orientation tilt effects to chromatic induction phenomena, but their neural underpinnings remain poorly understood. Here, we present a recurrent network model of classical and extraclassical receptive fields that is constrained by the anatomy and physiology of the visual cortex. A key feature of the model is the postulated existence of near- versus far- extraclassical regions with complementary facilitatory and suppressive contributions to the classical receptive field. The model accounts for a variety of contextual illusions, reveals commonalities between seemingly disparate phenomena, and helps organize them into a novel taxonomy. It explains how center-surround interactions may shift from attraction to repulsion in tilt effects, and from contrast to assimilation in induction phenomena. The model further explains enhanced perceptual shifts generated by a class of patterned background stimuli that activate the two opponent extraclassical regions cooperatively. Overall, the ability of the model to account for the variety and complexity of contextual illusions provides computational evidence for a novel canonical circuit that is shared across visual modalities. (PsycINFO Database Record (c) 2018 APA, all rights reserved).
Joint Source Localization and Dereverberation by Sound Field Interpolation Using Sparse Regularization (2018)

In this paper, source localization and dereverberation are formulated jointly as an inverse problem. The inverse problem consists in the interpolation of the sound field measured by a set of microphones by matching the recorded sound pressure with that of a particular acoustic model. This model is based on a collection of equivalent sources creating either spherical or plane waves. In order to achieve meaningful results, spatial, spatio-temporal and spatio-spectral sparsity can be promoted in the signals originating from the equivalent sources. The inverse problem consists of a large-scale optimization problem that is solved using a first order matrix-free optimization algorithm. It is shown that once the equivalent source signals capable of effectively interpolating the sound field are obtained, they can be readily used to localize a speech sound source in terms of Direction of Arrival (DOA) and to perform dereverberation in a highly reverberant environment.
Supplemental Table S5 from Impact of Emergent Circulating Tumor DNA <i>RAS</i> Mutation in Panitumumab-Treated Chemoresistant Metastatic Colorectal Cancer (2023)

&lt;p&gt;Plasma-SelectTM Sequence Mutations Gene List&lt;/p&gt;
ChemInform Abstract: BUILDING UNITS FOR OLIGOSACCHARIDES. XXIX. SYNTHESIS OF TRISACCHARIDE FROM N‐ACETYLGLUCOSAMINE, GALACTOSE AND RHAMNOSE OF AN O‐DETERMINANT CHAIN FROM ESCHERICHIA COLI. DEPENDENCE OF STEREOSELECTIVITY OF THE α‐GLYCOSIDE SYNTHESIS ON THE REACTIVITY OF THE PYRANOSYL HALIDE (1981)

Abstract Die Hg‐Salz‐katalysierte α‐Glycosidsynthese durch Reaktion der Halogenide (I) bzw. (VI) (Darstellung jeweils beschrieben) mit den aktiven OH‐Gruppen der Rhamnoside (II) unter Bildung der Produkte (IV) und/oder (III), (VIIa) bzw. (VIIb) + (VIII) wird untersucht.
A CMOS implementation of a Connex memory (2002)

The Connex Memory was introduced as a physical support for efficient symbolic processing. CM allows a significant speed-up over conventional CAMs in applications such as string matching with don't cares in time related to the size of the string, regardless the size of the CM content. This paper presents a parametrical implementation of an enhanced version of CM at algorithmic-level, as well as gate-level, using VHDL language and Cadence software package. The basic cell is dynamically implemented and the electric analysis is performed in the Mietec 2 /spl mu/m technology. The behavior of all the other blocks is validated by logic simulation using the 'leapfrog' simulator from Cadence. Schemes, programs in VHDL and complexity issues are illustrated and discussed in the paper. In addition, applications of the CM are presented, including support for functional and logical programming, relational databases, DNA computing (splicing operation) and others.
Regulation of hydraulic conductivity in response to sustained changes in pressure (2005)

The present study addresses the effect of a sustained change in pressure on microvascular permeability assessed by hydraulic conductivity (Lp) measurements from microvessels of the rat mesentery. With a microperfusion technique, transvascular filtration (normalized to surface area; Jv/S) and Lp were measured in small arterioles (baseline Lp= 0.26 x 10(-7) cm.s(-1).cmH2O(-1)) and venules (baseline Lp= 2.88 x 10(-7) cm.s(-1).cmH2O(-1)). The main finding of this study is that step increases in microvascular pressure led to time-dependent alterations of L(p). Immediately after a twofold step increase in pressure, Jv/S increased in proportion to the pressure change. This observation is consistent with Starling's law that predicts filtration proportional to the overall pressure gradient when Lp is constant. However, when Jv/S measurements continued for 60-90 min past the step in pressure, there was an initial decrease in Jv/S for 30 min ("sealing effect") followed by a substantial increase in Jv/S out to 90 min. The sustained increase in Jv/S suggests an increase in Lp of 36 +/- 7% for small arterioles and 42 +/- 5% for small venules (P < 0.05 for both). In addition, the increase in Lp in response to an increase in pressure was attenuated significantly by nitric oxide synthase inhibition. These results indicate that a pressure-induced mechanical stimulus (possibly Jv) activates a NO-dependent biochemical response that leads to an increase in hydraulic conductivity.
Using ANS FOTRAN (1980)

The National Bureau of Standards' was established by an act of Congress on March 3, 1901. The Bureau's overall goal is to strengthen and advance the Nation's science and technology and facilitate their effective application
Breaking the Concentration Limit in Fluorescence Fluctuation Spectroscopy with Camera-Based Detection (2022)

Fluorescence correlation spectroscopy (FCS) is an extremely versatile tool that has been widely used to measure chemical reaction rates, protein binding, nanoparticle-protein interactions, and biomolecular dynamics in vitro and in vivo. As an inherently micro-sized approach, FCS is compatible with high-throughput screening applications, as demanded for drug design, but typically limited to nanomolar concentrations, which restricts possible applications. Here, we show how massively parallel camera-based detection with side illumination can extend the usable concentration range of FCS more than 100-fold to measure low affinity processes. Our line illumination (LIM) approach is robust, fast (1 s acquisition times), and does not require any reference measurements to characterize the observation volume size.
Characterization of G-Quadruplexes in Chlamydomonas reinhardtii and the Effects of Polyamine and Magnesium Cations on Structure and Stability (2018)

Chlamydomonas reinhardtii is a green alga with a very GC-rich genome (67%) and a high density of potential G-quadruplex-forming sequences (PQSs). Using the Ensembl Plants DNA database, 19 PQSs were selected, and their ability to fold in vitro was examined using four experimental methods. Our results support in vitro folding of 18 of the 19 PQSs selected for study. The high physiological polyamine concentrations in C. reinhardtii create unique conditions for studying G4 folding. We investigated whether high polyamine concentrations affect the stability and structural fold of two polymorphic G4s selected from the cohort of PQSs. The two polymorphic G4s selected were found to be greatly stabilized when studied at the physiologically high polyamine concentrations. Lastly, the effects of physiologically relevant Mg<sup>2+</sup> concentrations were tested on both of the polymorphic G4s, and one of the G4s shifted from a dynamic mixture of folds to favor a parallel fold in the presence of Mg<sup>2+</sup>. Our work supports the concept of folding of G4s under the unique conditions observed in C. reinhardtii, and these structures, being located in promoter regions of DNA repair and photosynthetic genes, might be relevant structures in the physiology of C. reinhardtii.
Role of Dopamine Receptors in the Anticancer Activity of ONC201 (2017)

ONC201/TIC10 is a first-in-class small molecule inducer of TRAIL that causes early activation of the integrated stress response. Its promising safety profile and broad-spectrum efficacy in vitro have been confirmed in Phase I/II trials in several advanced malignancies. Binding and reporter assays have shown that ONC201 is a selective antagonist of the dopamine D2-like receptors, specifically, DRD2 and DRD3. We hypothesized that ONC201's interaction with DRD2 plays a role in ONC201's anticancer effects. Using cBioportal and quantitative reverse-transcription polymerase chain reaction analyses, we confirmed that DRD2 is expressed in different cancer cell types in a cell type-specific manner. On the other hand, DRD3 was generally not detectable. Overexpressing DRD2 in cells with low DRD2 levels increased ONC201-induced PARP cleavage, which was preceded and correlated with an increase in ONC201-induced CHOP mRNA expression. On the other hand, knocking out DRD2 using CRISPR/Cas9 in three cancer cell lines was not sufficient to abrogate ONC201's anticancer effects. Although ONC201's anticancer activity was not dependent on DRD2 expression in the cancer cell types tested, we assessed the cytotoxic potential of DRD2 blockade. Transient DRD2 knockdown in HCT116 cells activated the integrated stress response and reduced cell number. Pharmacological antagonism of DRD2 significantly reduced cell viability. Thus, we demonstrate in this study that disrupting dopamine receptor expression and activity can have cytotoxic effects that may at least be in part due to the activation of the integrated stress response. On the other hand, ONC201's anticancer activity goes beyond its ability to antagonize DRD2, potentially due to ONC201's ability to activate other pathways that are independent of DRD2. Nevertheless, blocking the dopamine D1-like receptor DRD5 via siRNA or the use of a pharmacological antagonist promoted ONC201-induced anticancer activity.
<title>AI techniques and object-oriented technology for VLSI design-space representation, optimization, and management</title> (1990)

The VLSI design process consists of many highly specialized tasks. Algorithmic, compute-intensive and mundane tasks which used to be performed manually, have been automated by traditional VLSI CAD tools. These tools have automated many aspects of VLSI design synthesis, analysis, optimization and verification. However, the successful and efficient utilization of these tools has proved to be very knowledge intensive requiring the interaction and guidance of domain experts. In recent years many expert systems for VLSI design have been reported but these stand-alone expert systems have to be integrated with traditional CAD tools to be able to provide automated decision-making, judgment-based opportunity ranking and tighter data source integration. Furthermore, an integrated and distributed knowledge-base is essential for rapid prototyping of expert design assistants, design techniques and optimization heuristics. We report an experimental VLSI design environment based on a central object-oriented model-base. The object-oriented design kernel is capable of accommodating traditional CAD tools as well as knowledge-based tools.