gebhart/patrepeval huggingface dataset:
SINGLE-CELL LEVEL INVESTIGATION OF CYTOSKELETAL/CELLULAR RESPONSE TO EXTERNAL STIMULI (2007)

A detailed understanding of the molecular mechanisms by which chemical signals control cell behavior is needed if the complex biological processes of embryogenesis, development, health and disease are to be completely understood. Yet, if we are to fully understand the molecular mechanisms controlling cell behavior, measurements at the single cell level are needed to supplement information gained from population level studies. One of the major challenges to accomplishing studies at the single cell level has been a lack of physical tools to complement the powerful molecular biological assays which have provided much of what we currently know about cell behavior. The goal of this exploratory project is the development of an experimental platform that facilitates integrated observation, tracking and analysis of the responses of many individual cells to controlled environmental factors (e.g. extracellular signals). Toward this goal, we developed chemically-patterned microarrays of both adherent and suspension mammalian cell types. A novel chemical patterning methodology, based on photocatalytic lithography, was developed to construct biomolecule and cell arrays that facilitate analysis of biological function. Our patterning techniques rely on inexpensive stamp materials and visible light, and do not necessitate mass transport or specified substrates. Patterned silicon and glass substrates are modified such that there is a non-biofouling polymer matrix surrounding the adhesive regions that target biomolecules and cells. Fluorescence and reflectance microscopy reveal successful patterning of proteins and single to small clusters of mammalian cells. In vitro assays conducted upon cells on the patterned arrays demonstrate the viability of cells interfacing with this synthetic system. Hence, we have successfully established a versatile cell measurement platform which can be used to characterize the molecular regulators of cellular behavior in a variety of important biological processes. The achievements realized in this project have enabled presentations and publication within the international scientific community, new collaborations with researchers at the University of California, and successful competition for three additional, separate research grants on studies of stem cell fate commitment and pathogen-host cell interactions.
Automatic Detection of Off-Task Behaviors in Intelligent Tutoring Systems with Machine Learning Techniques (2009)

Identifying off-task behaviors in intelligent tutoring systems is a practical and challenging research topic. This paper proposes a machine learning model that can automatically detect students' off-task behaviors. The proposed model only utilizes the data available from the log files that record students' actions within the system. The model utilizes a set of time features, performance features, and mouse movement features, and is compared to 1) a model that only utilizes time features and 2) a model that uses time and performance features. Different students have different types of behaviors; therefore, personalized version of the proposed model is constructed and compared to the corresponding nonpersonalized version. In order to address data sparseness problem, a robust Ridge Regression algorithm is utilized to estimate model parameters. An extensive set of experiment results demonstrates the power of using multiple types of evidence, the personalized model, and the robust Ridge Regression algorithm.
Turkish Tombul Hazelnut (<i>Corylus avellana</i> L.). 2. Lipid Characteristics and Oxidative Stability (2003)

The quality of crude hazelnut oil extracted from Tombul (Round) hazelnut, grown in the Giresun province of Turkey, was determined by measuring lipid classes, fatty acids, and fat soluble bioactives (tocopherols and phytosterols). Oxygen uptake, peroxide value, thiobarbituric acid reactive substances, and alpha-tocopherol levels of stripped and crude hazelnut oils in bulk and oil-in-water (o/w) emulsion systems were also evaluated as indices of lipid oxidation over a 21 day storage period at 60 degrees C in the dark. The total lipid content of Tombul hazelnut was 61.2%, of which 98.8% were nonpolar and 1.2% polar constituents. Triacylglycerols were the major nonpolar lipid class and contributed nearly 100% to the total amount. Phosphatidylcholine, phosphatidylethanolamine, and phosphatidylinositol were the most abundant polar lipids, respectively. Sixteen fatty acids were identified, among which oleic acid contributed 82.7% to the total, followed by linoleic, palmitic, and stearic acids. Unsaturated fatty acids accounted for 92.2% of the total fatty acids present. Among oil soluble bioactives, alpha-tocopherol (38.2 mg/100 g) and beta-sitosterol (105.5 mg/100 g) were predominant in hazelnut oil and comprised 88 and 93% of the total tocopherols and phytosterols present, respectively. The results also showed that both stripped and crude hazelnut oils were more stable in terms of lipid oxidation in the bulk oil as compared to those in an o/w emulsion.
BETA GRANULE FORMATION IN ISOLATED ISLETS OF LANGERHANS (1969)

The distribution of radioautographic grains over organelles within the beta cells of rat islets of Langerhans was investigated at various times after pulse labeling of the isolated islets with tritium-labeled amino acids. Ten minutes after the start of labeling most of the grains were situated over the endoplasmic reticulum and cytoplasm; by contrast, 60 min from the start of labeling the majority of the grains were associated with the beta granules. At 20, 30, and 45 minutes after pulse labeling the proportion of grains associated with the Golgi complex was increased two- to three-fold over the 10- or 60-minute values. The distribution of radioautographic grains over granules in the intact cells did not suggest that the electron-lucent type of secretory granules were precursors of the electron-opaque granules. Furthermore, studies of the pattern of grains over granules isolated by centrifugation 60 min after pulse labeling showed no preferential labeling of the electron-lucent type of granule. It is concluded that labeled amino acids are incorporated initially in the endoplasmic reticulum, and that the label subsequently appears in the beta granules. The Golgi complex participates either in the formation of the beta granule or in the translocation of the granule through the cytoplasm of the cell.
Spatial distribution and interaction of defects in spinel, based on optical studies of x-ray irradiation induced processes (2001)

Kinetic studies of optical center accumulation and decay, together with the growth and decay of radioluminescence (RL) in magnesium aluminate spinel MgAl{sub 2}O{sub 4}, were performed at room temperature. We observed two stages of defect accumulation during prolonged X-ray irradiation, as evidenced by changes in absorption bands at 3.78 and 4.15 eV related to antisite defects, and bands at 4.75 and 5.3 eV due to F-type centers. A correlation was found between optical absorption band growth and the intensities of RL bands at 4.86 and 5.02 eV, the latter of which originate: from electron-hole recombination processes. The rate of decay of absorption centers and RL intensities is dependent on time after X-ray irradiation. Also both decay rates could be described by a two-stage exponential law. Results are discussed using a model that includes tunneling and recombination of electron and hole centers on spatially correlated defects located at different distances from one another.
The Inverse Type II β‐Turn on <scp>D</scp>‐Trp‐Phe, a Pharmacophoric Motif for MOR Agonists (2011)

Herein we propose the D-Trp-Phe sequence within an inverse type II β-turn as a new kind of pharmacophoric motif for μ-opioid receptor (MOR) cyclopeptide agonists. Initially, we observed that c[Tyr-D-Pro-D-Trp-Phe-Gly] (4), an analogue of endomorphin-1 (H-Tyr-Pro-Trp-Phe-NH₂) lacking the crucial protonatable amino group of Tyr 1, is a MOR agonist with 10⁻⁸ M affinity. Molecular docking analysis suggested that the relevant interactions with the receptor involve D-Trp-Phe. The bioactive conformation of this region was investigated by selected derivatives of 4 designed to adopt an inverse type II β-turn. These efforts led to c[Tyr-Gly-D-Trp-Phe-Gly] (14) and to the cyclotetrapeptide c[D-Asp-1-amide-β-Ala-D-Trp-Phe] (15), showing improved nanomolar affinity. Both 14 and 15 selectively bind MOR, as they have negligible affinity for the κ- and δ-opioid receptors. Both 14 and 15 behave as partial MOR agonists in functional assays. Conformational and docking analyses confirm the role of the inverse β-turn in binding. These results indicate that the D-Trp-Phe inverse β-turn structure can be used for designing non-endomorphin-like peptidomimetic opioid agonists in general, characterized by an atypical mechanism of interaction between ligand and receptor.
A Trust Region Spectral Bundle Method for Nonconvex Eigenvalue Optimization (2008)

International audience
Genistein inhibits tumor invasion by suppressing multiple signal transduction pathways in human hepatocellular carcinoma cells (2014)

Gen and its inhibition of multiple signal transduction pathways can control the invasiveness and metastatic potential of HCC.
Influence of temperature and impact velocity on the coefficient of restitution (1994)

Tests were performed on a variety of material combinations to understand the effects of temperature and impact velocity on the coefficient of restitution (COR). The tests, performed in a vacuum at room and liquid nitrogen temperatures, consisted of dropping a ball onto a target plate and recording the impact time history of the ball's bounce-down. Time intervals between successive impacts were measured from the time history and used to calculate the coefficient of restitution and impact velocity for each impact. Maximum impact velocities ranged from approximately 33 (0.84) to 52 in./s (1.32 m/s). Five ball-target plate combinations were evaluated: type 316 stainless steel (316 SS) on 316 SS; M50 tool steel on Armalon; M50 on 4340 steel; 410C steel on Armalon; and copper on copper. The coefficient of restitution for the 316 SS-316 SS, M50-Armalon, 410C-Armalon, and copper-copper combinations increased as the temperature and impact velocity decreased. The coefficient for the hard steel combination, M50-4340, was not greatly influenced by temperature or variations in impact velocity.
Recurrent Neural Networks with Longitudinal Pooling and Consistency Regularization (2020)

Most neurological diseases are characterized by gradual deterioration of brain structure and function. To identify the impact of such diseases, studies have been acquiring large longitudinal MRI datasets and applied deep-learning to predict diagnosis label(s). These learning models apply Convolutional Neural Networks (CNN) to extract informative features from each time point of the longitudinal MRI and Recurrent Neural Networks (RNN) to classify each time point based on those features. However, they neglect the progressive nature of the disease, which may result in clinically implausible predictions across visits. In this paper, we propose a framework that injects the extracted features from CNNs at each time point to the RNN cells considering the dependencies across different time points in the longitudinal data. On the feature level, we propose a novel longitudinal pooling layer to couple features of a visit with those of proceeding ones. On the prediction level, we add a consistency regularization to the classification objective in line with the nature of the disease progression across visits. We evaluate the proposed method on the longitudinal structural MRIs from three neuroimaging datasets: Alzheimer's Disease Neuroimaging Initiative (ADNI, N=404), a dataset composed of 274 healthy controls and 329 patients with Alcohol Use Disorder (AUD), and 255 youths from the National Consortium on Alcohol and NeuroDevelopment in Adolescence (NCANDA). All three experiments show that our method is superior to the widely used methods. The code is available at this https URL
Simultaneous Human detection and action recognition employing 2DPCA-HOG (2011)

In this paper a novel algorithm for Human detection and action recognition in videos is presented. The algorithm is based on Two-Dimensional Principal Components Analysis (2DPCA) applied to Histogram of Oriented Gradients (HOG). Due to simultaneous Human detection and action recognition employing the same algorithm, the computational complexity is reduced to a great deal. Experimental results applied to public datasets confirm these excellent properties compared to most recent methods.
Capillary flow responses in a soil–plant system for modified subsurface precision irrigation (2013)

Water movement in a soil–plant system was evaluated based on capillary flow in a modified subsurface irrigation system that incorporates a plant-water measuring device. Water from a reservoir tank located underneath the plant pot was supplied to the root zone through a fibrous medium. Evapotranspiration was measured from the water uptake and evaluations were performed based on soil moisture distribution and mass balance. Potential evapotranspiration was used as a reference for the plant–water uptake. Data were obtained from a test plant provided with the modified subsurface irrigation system. The plant was grown in a phytotron under controlled air temperature and humidity, and a comparison was made for different levels of soil moisture condition. The experimental results confirmed the operational efficiency of the modified subsurface irrigation system for precision irrigation.
Numerical study of ultra-high speed wavelength conversion using a Gain-Clamped SOA in combination with optical filtering (2006)

Using numerical simulations, we demonstrate that wavelength conversion of 40 Gb/s and 160 Gb/s RZ signals is feasible using only a gain-clamped SOA (GCSOA) and optical filters. The signal is converted to the lasing wavelength of the GCSOA and no extra CW probe is thus required. The scheme is based on the optical filtering of the chirp of the lasing field induced by the input signal.
Designing high speed controllers for high speed local area networks (2003)

Performance requirements for bridges interconnecting LANs (local area networks) and HSLANs (high-speed LANs) were studied. It turned out that, in many cases, state-of-the-art bridges are much more likely to be the bottleneck than the medium access protocol used in the HSLAN. Thus, speeding up network controllers will be inevitable. This holds even more for the implementation of more complex functions required for gateways and direct interconnection of high-speed devices. Working in parallel will probably be the only solution for speeding up network controllers.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Reflex-arc on a chip: An in silico cell culture analogue (2006)

Treatment and understanding of traumatic spinal cord injury (SCI) and neurodegenerative diseases have been problematic due in part to difficulties associated with the various models used to test new drug therapies. Animal studies are expensive, time consuming, and can raise ethical issues. In vitro studies avoid many of the issues associated with animal studies and can allow the use of human cells, but such data are too incomplete to be predictors of human response due to the lack of interaction between tissues and differences between culture and physiological dynamics. To overcome the shortcomings of existing models we are developing a microscopic cell culture analogue (microCCA) of the spinal reflex-arc. This system will provide a model which can accurately reflect important aspects of in vivo behavior of animal models, but retain the cost effectiveness of in vitro models as well as the ability to perform large numbers of tests in parallel
The grand canonical ensemble in generalized thermostatistics (2004)

We study the grand-canonical ensemble with a fluctuating number of degrees of freedom in the context of generalized thermostatistics. Several choices of grand-canonical entropy functional are considered. The ideal gas is taken as an example.
Disjoint-path routing: Efficient communication for streaming applications (2009)

Streaming is emerging as an important programming model for multicores. Streaming provides an elegant way to express task decomposition and inter-task communication, while hiding laborious orchestration details such as load balancing, assignment (of stream computation to nodes) and computation/communication scheduling from the programmer. This paper develops a novel communication optimization for streaming applications based on the observation that streaming computations typically involve large, systematic data transfers between known communicating pairs of nodes over extended periods of time. From the above observation, we advocate a family of routing algorithms that expend some over overheads to compute disjoint paths for stream communication. Disjoint-path routing is an attractive design point because (a) the overheads of discovering disjoint paths are amortized over large periods of time and (b) the benefits of disjoint path routing are significant for bandwidth-sensitive streaming applications. We develop one instance of disjoint-path routing called tentacle routing-a backtracking, best-effort technique. On a 4 times 4 (6 times 6) system, tentacle routing results in 55% (84%) and 28% (41%) mean throughput improvement for high-network-contention streaming applications, and for all streaming applications, respectively.
On test set preservation of retimed circuits (1995)

Abstract| Recently, it has been shown that retiming has a very strong impact on the run time of sequential, structural automatic test pattern generators (ATPGs), as well as the levels of fault coverage and fault eciency attained. In this paper, we show that retiming preserves testability with respect to a single stuck-at fault test set by adding a prex sequence of a pre-determined number of arbitrary input vectors. Experimental results show that high fault coverages can be achieved on high performance circuits optimized by retiming with a much less CPU time (a reduction of two orders of magnitude in several instances) than if ATPG is attempted directly on those circuits.
Multiuser receiver aware multicast protocols for wireless ad-hoc networks (2001)

Most existing multicast protocols for wireless ad-hoc networks operate at the network layer and make no assumption about the underlying link and physical layer protocols. This results in inefficiency in the usage of bandwidth and power. In this paper, we assume a DS-CDMA based wireless ad-hoc network and propose two schemes, Centralized-Tree Distributed-Power (CTDP) and Distributed-Tree Distributed-Power (DTDP), tailored to the link and physical layer protocols. Both schemes seek to construct a multicast tree and determine the power levels at which the nodes should transmit to satisfy the SINR requirements of all receiving nodes with the least total transmit power. Empirical evaluation shows that CTDP is more efficient than DTDP in terms of consumed transmit power but at significantly higher computation cost. On the other hand, DTDP is fully distributed and thus may be better suited for mobile wireless ad-hoc networks.
Acceleration of wound healing in healing‐impaired <i>db/db</i> mice with a photocrosslinkable chitosan hydrogel containing fibroblast growth factor‐2 (2005)

Application of ultraviolet light irradiation to a photocrosslinkable chitosan (Az-CH-LA) aqueous solution including fibroblast growth factor-2 (FGF-2) results within 30 seconds in an insoluble, flexible hydrogel. The FGF-2 molecules retained in the chitosan hydrogel remain biologically active and are released from the chitosan hydrogel upon in vivo biodegradation of the hydrogel. To evaluate the accelerating effect on wound healing of this hydrogel, full-thickness skin incisions were made in the backs of healing-impaired diabetic (db/db) mice and their normal (db/+) littermates. The mice were later killed, and histological sections of the wound were prepared. The degree of wound healing was evaluated using several histological parameters such as the rate of contraction, epithelialization, and tissue filling. Application of the chitosan hydrogel significantly advanced the rate of contraction on Days 0 to 2 in db/db and db/+ mice. Although the addition of FGF-2 into the chitosan hydrogel in db/+ mice had little effect, application of the chitosan hydrogel-containing FGF-2 further accelerated the adjusted tissue filling rate (Days 2 to 4 and Days 4 to 8) in db/db mice. Furthermore, the chitosan hydrogel-containing FGF-2 markedly increased the number of CD-34-positive vessels in the wound areas of db/db mice on Day 4. Thus, the application of chitosan hydrogel-containing FGF-2 onto a healing-impaired wound induces significant wound contraction and accelerates wound closure and healing.
Ozone effects on root‐disease susceptibility and defence responses in mycorrhizal and non‐mycorrhizal seedlings of Scots pine (<i>Pinus sylvestris</i> L.) (1993)

Interactions between ozone and biotic stress caused by a pathogen, Heterobasidion annosum (Fr.) Bref., in mycorrhizal [Hegeloma crustuliniforme (Bull, ex St. Am.) Quel.] and non-mycorrhizal Scots pine seedlings were investigated using a semi-axenic model system. Ozone exposure (200 nl 1<sup>-1</sup> , 8 h d<sup>-1</sup> for 28 d) increased disease incidence significantly, but mycorrhizal infection completely prevented this negative effect. The presence of the pathogen on the root systems was necessary for the induction of changes in the soluble and wall-bound secondary compounds of roots and needles; ozone alone did not induce such changes. Mycorrhizal infection appeared to have a dampening effect on the induction of these compounds. H. annosum induced a significant accumulation of the two pine stilbenes both locally and systemically in the more susceptible seedlings. In these seedlings ozone had a significant positive effect on the accumulation of both stilbenes in the roots, but it reduced pinosylvin and had no effect on pinosylvin 3-methyl ether in the needles. The catechin content of the roots decreased in the same infected seedlings, but to a larger degree upon ozone treatment. One compound of as yet unknown structure accumulated gradually in the infected roots over the experimental period, and could thus be associated with resistance. Its accumulation was little affected by ozone treatment. Among the root cell wall-bound phenolics analyzed, only lignin-like material showed significant changes. The presence of the pathogen was again necessary for induction, but ozone had an inhibitory effect on this response. Pure pinosylvin applied through the hypocotyls of excised seedlings was shown to be phytotoxic, with the needles displaying discoloration and wilting as observed after pathogenic inoculation, and being characterized by a lower chlorophyll content and increased transpiration. Accumulation of pinosylvin in the needles was detected at amounts comparable to those found in the main experiment.