gebhart/patrepeval huggingface dataset:
When and where will a target go? A behavioural and electrophysiological study of expectation in primates (2008)

In a rapidly changing visual environment, the delay between perception and action might impair the probability of survival of a prey or the efficiency of a predator. In order to compensate for delays associated with sensory-motor processing, primates often make predictions about future events and initiate anticipatory movements. To prepare an anticipatory movement, an estimation of when and where to a target is likely to move is necessary. Such an internal representation is often termed 'expectation'.\nThe aim of this thesis was to investigate the gradual changes of a subject's expectation at the behavioral and electrophysiological levels. Anticipatory smooth pursuit was used in order to study temporal and directional changes in expectation.\nWe found that temporal uncertainty strongly modulated the latency and the velocity of anticipatory movements suggesting that monkeys could estimate the hazard rate of target motion onset in order to decide when to initiate an anticipatory movement. In addition, we have shown that monkeys could use prior directional information in order to voluntarily initiate anticipatory responses in the direction of expected target motion. This prior directional information significantly affected the latency and velocity of these movements. Finally, we have shown that the majority of recorded supplementary eye field (SEF) neurons encoded expected target motion direction. The presence of a directional cue induced an increase of activity in the preferred direction of the neuron. Moreover, a large sub-population of neurons encoded the direction of future anticipatory movement.\nThese results suggest that the SEF could be involved in the cognitive control of anticipatory pursuit eye movements when prior temporal and directional information is provided.
Properties of Lewis Lung Carcinoma Cells Surviving Curcumin Toxicity (2012)

The anti-inflammatory agent curcumin can selectively eliminate malignant rather than normal cells. The present study examined the effects of curcumin on the Lewis lung carcinoma (LLC) cell line and characterized a subpopulation surviving curcumin treatments. Cell density was measured after curcumin was applied at concentrations between 10 and 60 μM for 30 hours. Because of the high cell loss at 60 μM, this dose was chosen to select for surviving cells that were then used to establish a new cell line. The resulting line had approximately 20% slower growth than the original LLC cell line and based on ELISA contained less of two markers, NF-κB and ALDH1A, used to identify more aggressive cancer cells. We also injected cells from the original and surviving lines subcutaneously into syngeneic C57BL/6 mice and monitored tumor development over three weeks and found that the curcumin surviving-line remained tumorigenic. Because curcumin has been reported to kill cancer cells more effectively when administered with light, we examined this as a possible way of enhancing the efficacy of curcumin against LLC cells. When LLC cells were exposed to curcumin and light from a fluorescent lamp source, cell loss caused by 20 μM curcumin was enhanced by about 50%, supporting a therapeutic use of curcumin in combination with white light. This study is the first to characterize a curcumin-surviving subpopulation among lung cancer cells. It shows that curcumin at a high concentration either selects for an intrinsically less aggressive cell subpopulation or generates these cells. The findings further support a role for curcumin as an adjunct to traditional chemical or radiation therapy of lung and other cancers.
High-Temperature Performance of AlGaN/GaN Metal–Oxide–Semiconductor Heterostructure Field-Effect-Transistors (2001)

The characteristics of novel AlGaN/GaN Metal–Oxide–Semiconductor Heterostructure Field Effect Transistors (MOSHFETs) were measured in the temperature range of 20–300 °C. At 300 °C the leakage current of MOSHFET remains four orders of magnitude lower than that of regular HFET. The saturation current and transconductance for both types of transistors follow the temperature dependence of electron velocity in the channel. The recovery of the current collapse at elevated temperatures compensates the effect of the decrease of the steady-state saturation current with temperature. As a consequence, the saturation microwave power remains fairly constant in the temperature range 20–200 °C, varying only by about 20% or so. These results show high potential of MOSHFETs for high-temperature microwave, digital and switching applications.
Deep Graph Unfolding for Beamforming in MU-MIMO Interference Networks (2023)

We develop an efficient and near-optimal solution for beamforming in multi-user multiple-input-multiple-output single-hop wireless ad-hoc interference networks. Inspired by the weighted minimum mean squared error (WMMSE) method, a classical approach to solving this problem, and the principle of algorithm unfolding, we present unfolded WMMSE (UWMMSE) for MU-MIMO. This method learns a parameterized functional transformation of key WMMSE parameters using graph neural networks (GNNs), where the channel and interference components of a wireless network constitute the underlying graph. These GNNs are trained through gradient descent on a network utility metric using multiple instances of the beamforming problem. Comprehensive experimental analyses illustrate the superiority of UWMMSE over the classical WMMSE and state-of-the-art learning-based methods in terms of performance, generalizability, and robustness.
Accelerating Recurrent Neural Networks for Gravitational Wave Experiments (2021)

This paper presents novel reconfigurable architectures for reducing the latency of recurrent neural networks (RNNs) that are used for detecting gravitational waves. Gravitational interferometers such as the LIGO detectors capture cosmic events such as black hole mergers which happen at unknown times and of varying durations, producing time-series data. We have developed a new architecture capable of accelerating RNN inference for analyzing time-series data from LIGO detectors. This architecture is based on optimizing the initiation intervals (II) in a multi-layer LSTM (Long Short-Term Memory) network, by identifying appropriate reuse factors for each layer. A customizable template for this architecture has been designed, which enables the generation of low-latency FPGA designs with efficient resource utilization using high-level synthesis tools. The proposed approach has been evaluated based on two LSTM models, targeting a ZYNQ 7045 FPGA and a U250 FPGA. Experimental results show that with balanced II, the number of DSPs can be reduced up to 42% while achieving the same IIs. When compared to other FPGA-based LSTM designs, our design can achieve about 4.92 to 12.4 times lower latency.
Influence of PEG length on conformational and binding properties of CCK peptides exposed by supramolecular aggregates (2014)

Five novel peptide amphiphiles (PAs), with common formula (C18)2-PEGx-CCK8 in which the CCK8 peptide and the (C18)2-hydrophobic moiety are spaced by polyethylene linkers of different length (PEG moieties with molecular weights of 700, 1000, 1500, 2000, and 3000 Daltons) are described. They act as potential target-selective nanocarriers towards tumor cells overexpressing cholecistokynin receptors. PAs self-assemble in supramolecular aggregates, with hydrodynamic radius ranging between 63 and 104 nm, as indicated by DLS measurements. Fluorescence studies suggested that, irrespective from the PEG length, the tryptophan residue located at the center of the CCK8 sequence is completely surrounded by water molecules at high mobility. This result indicates a potential capability of all formulated nanovectors to recognize the overexpressed CCK-2 receptors. CD data suggest that CCK8 peptide, in most of PAs in their aggregate form, adopts a conformation allowing the interaction with the receptor. Anyway, biological data obtained by flow cytometry analysis indicate that the five PAs have a different binding ability towards the CCK-2 receptors, with higher binding properties shown by PA containing PEG with MW of 2000 Dalton. Therefore, PEG2000 can be considered as the best spacer in the formulation of nanovectors based on CCK8 peptide amphiphiles.
Factors Affecting the Formation of 2:1 Host:Guest Inclusion Complexes of 2-[(R-Phenyl)amine]-1,4-naphthalenediones (PAN) in β- and γ-Cyclodextrins (2016)

The molecular hosts cyclodextrins form inclusion complexes with a wide variety of guests, resulting in complexes with various host:guest stoichiometries. In the case of a series of 19 1,4-naphthoquinolines as guests with either β- or γ-cyclodextrin studied using electrospray mass spectroscopy, in most cases only 1:1 complexes were observed, with 2:1 host:guest complexes observed in just 6 out of 38 host:guest combinations. It is shown that these higher-order complexes were observed only in the case of small (or no) electronically withdrawing substituents, and were much less likely in the case of the larger γ-cyclodextrin host. The size and electronic properties of the substituents involved shows that both steric and electronic factors must be taken into account in predicting which cyclodextrin host:guest stoichiometries will be stable enough to form (or once formed, be robust enough to be observed in the ESI-MS experiments). It is clear that the prediction of host-guest stoichiometry for a specific host-guest pair is complicated, and involves a subtle interplay of both electronic and steric factors. However, there are definite trends, which can be used to help predict host:guest stoichiometry for a given host-guest pair.
Dual genetic tracing reveals a unique fibroblast subpopulation modulating cardiac fibrosis (2023)

After severe heart injury, fibroblasts are activated and proliferate excessively to form scar, leading to decreased cardiac function and eventually heart failure. It is unknown, however, whether cardiac fibroblasts are heterogeneous in respect of their degree of activation, proliferation, and function during cardiac fibrosis. Here, by dual recombinases-mediated genetic lineage tracing, we found that endocardium-derived fibroblasts (EndoFb) preferentially proliferate and expand in response to pressure overload. Fibroblast-specific proliferation tracing revealed highly regional expansion of activated fibroblasts after injury, the pattern of which mirrors that of EndoFb distribution in the heart. Specific ablation of EndoFb alleviates cardiac fibrosis and reduces the decline of heart function after pressure overload injury. Mechanistically, Wnt signaling promotes activation and expansion of EndoFb during cardiac remodeling. Our study identified EndoFb as a key fibroblast subpopulation accounting for severe cardiac fibrosis after pressure overload injury, and as a potential therapeutic target against cardiac fibrosis.
Magnetic Targeting of Magnetoliposomes to Solid Tumors with MR Imaging Monitoring in Mice: Feasibility (2006)

Magnetic targeting of sterically stabilized magnetoliposomes after they are intravenously injected is feasible in vivo.
Data from Copper Chelation Enhances Antitumor Efficacy and Systemic Delivery of Oncolytic HSV (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; Copper in serum supports angiogenesis and inhibits replication of wild-type HSV-1. Copper chelation is currently being investigated as an antiangiogenic and antineoplastic agent in patients diagnosed with cancer. Herpes simplex virus–derived oncolytic viruses (oHSV) are being evaluated for safety and efficacy in patients, but several host barriers limit their efficacy. Here, we tested whether copper inhibits oHSV infection and replication and whether copper chelation would augment therapeutic efficacy of oHSV.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental Design:&lt;/b&gt; Subcutaneous and intracranial tumor-bearing mice were treated with oHSV ± ATN-224 to evaluate tumor burden and survival. Virus replication and cell killing was measured in the presence or absence of the copper chelating agent ATN-224 and in the presence or absence of copper &lt;i&gt;in vitro&lt;/i&gt;. Microvessel density and changes in perfusion were evaluated by immunohistochemistry and dynamic contrast enhanced MRI (DCE-MRI). Serum stability of oHSV was measured in mice fed with ATN-224. Tumor-bearing mice were injected intravenously with oHSV; tumor burden and amount of virus in tumor tissue were evaluated.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; Combination of systemic ATN-224 and oHSV significantly reduced tumor growth and prolonged animal survival. Immunohistochemistry and DCE-MRI imaging confirmed that ATN-224 reduced oHSV-induced blood vessel density and vascular leakage. Copper at physiologically relevant concentrations inhibited oHSV replication and glioma cell killing, and this effect was rescued by ATN-224. ATN-224 increased serum stability of oHSV and enhanced the efficacy of systemic delivery.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusion:&lt;/b&gt; This study shows that combining ATN-224 with oHSV significantly increased serum stability of oHSV and greatly enhanced its replication and antitumor efficacy. &lt;i&gt;Clin Cancer Res; 18(18); 4931–41. ©2012 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
Electrons imitating light: Frustrated supercritical collapse in charged arrays on graphene (2018)

The photon-like electronic dispersion of graphene bestows its charge carriers with unusual confinement properties that depend strongly on the geometry and strength of the surrounding potential. Here we report bottom-up synthesis of atomically-precise one-dimensional (1D) arrays of point charges aimed at exploring supercritical confinement of carriers in graphene for new geometries. The arrays were synthesized by arranging F4TCNQ molecules into a 1D lattice on back-gated graphene devices, allowing precise tuning of both the molecular charge state and the array periodicity. Dilute arrays of ionized F4TCNQ molecules are seen to behave like isolated subcritical charges but dense arrays show emergent supercriticality. In contrast to compact supercritical clusters, extended 1D charge arrays exhibit both supercritical and subcritical characteristics and belong to a new physical regime termed frustrated supercritical collapse. Here carriers in the far-field are attracted by a supercritical charge distribution, but have their fall to the center frustrated by subcritical potentials in the near-field, similar to the trapping of light by a dense cluster of stars in general relativity.
Adequately Defining the Amino Acid Requirements of Fish: The Case Example of Lysine (2006)

A critical review of the literature highlights significant discrepancies in the estimates and modes of expression ofamino acid requirements. Using lysine as a case example, this paper highlights some of these discrepancies andpotential limitations of current approaches.Published estimates of lysine requirements for rainbow trout varied from 1.3 – 2.9 % of the diet and NRC (1993)estimated lysine requirement at 1.8% of the diet. Results from recent studies and detailed data analysis suggest thatlysine requirement to maximize weight gain is about 2.3% of the diet in rainbow trout, where requirement tomaximize protein gain of this species appears to be closer to 2.7% of the diet. These estimates are significantlyhigher and appear more appropriate (robust) than the lysine requirement proposed by NRC (1993).Different modes of expression of lysine requirement are used, often interchangeably, in the literature. It is importantto understand that these different modes of expression are based on different assumptions and that the use ofdifferent modes of expression will result in dramatically different recommendations, especially since aquaculturefeeds are formulated to widely different nutritional specifications (protein, energy, etc.). Studies suggest thatexpressing lysine requirement as a function of digestible energy or protein contents of the diet is not appropriate.Studies have also indicated that “newer” approaches of estimating amino acid requirements (e.g., factorial aminoacid requirement, ideal protein concept), widely used in poultry and swine nutrition, may have significant pitfallswhen used in fish nutrition.
Antigen unmasking for immunoelectron microscopy: labeling is improved by treating with sodium ethoxide or sodium metaperiodate, then heating on retrieval medium. (1995)

To optimize the ultrastructural localization of immunoglobulin G in corneal crystalloid deposits, we compared a range of antigen unmasking techniques. A human corneal biopsy specimen was fixed in formalin, post-osmicated, and embedded in epoxy resin for electron microscopy. Thin sections were immunogold-labeled for IgG after treatment with sodium ethoxide or sodium metaperiodate. Sections were also treated by heating them at 95 degrees C while they floated on water, 0.01 M citrate buffer (pH 6.0), or sodium metaperiodate. The treatments were applied separately and combined. After labeling, crystalloids in untreated sections had a probe density of 5 particles/microns2. Crystalloids in sections treated only with sodium ethoxide or sodium metaperiodate had probe densities of 15-20 particles/microns2. Sodium ethoxide combined with heating on water, or citrate buffer, gave probe densities of 140-160 particles/microns2. Sodium metaperiodate combined with heating on citrate buffer gave the highest probe density (195 particles/microns2). Although sodium ethoxide coupled with heating increased probe density, the ethoxide etched the sections and caused unacceptable damage. Treatment with sodium metaperiodate followed by heating on citrate buffer is recommended for antigen unmasking. This combination gave a high probe density and sections remained intact, with good ultrastructural detail.
Demyelination, Astrogliosis, and Accumulation of Ubiquitinated Proteins, Hallmarks of CNS Disease inhsf1-Deficient Mice (2007)

The heat shock transcription factors (Hsfs) are responsible for the heat shock response, an evolutionarily conserved process for clearance of damaged and aggregated proteins. In organisms such as Caenorhabditis elegans, which contain a single Hsf, reduction in the level of Hsf is associated with the appearance of age-related phenotypes and increased accumulation of protein aggregates. Mammalian cells express three hsfs (hsf1, hsf2, hsf4) and their role in CNS homeostasis remains unclear. In this study, we examined the effects of deletion of single or multiple hsf genes in the CNS using mutant mice. Our results show that hsf1-/- mice display progressive myelin loss that accompanies severe astrogliosis and this is exacerbated in the absence of either the hsf2 or hsf4 gene. Magnetic resonance imaging and behavioral studies indicate reduction in the white matter tracts of the corpus callosum, and deficiencies in motor activity, respectively, in aged hsf1-/- mice. Concomitantly, hsf1-/- aged CNS exhibit increased activated microglia and apoptotic cells that are mainly positive for GFAP, an astrocyte-specific marker. Studies based on the expression of short-lived ubiquitinated green fluorescent protein (GFPu) in living hsf1-/- cells indicate that they exhibit reduced ability to degrade ubiquitinated proteins, accumulate short-lived GFPu, and accumulate aggregates of the Huntington's model of GFP containing trinucleotide repeats (Q103-GFP). Likewise, hsf1-/- brain and astrocytes exhibit higher than wild-type levels of ubiquitinated proteins, increased levels of protein oxidation, and increased sensitivity to oxidative stress. These studies indicate a critical role for mammalian hsf genes, but specifically hsf1, in the quality control mechanisms and maintenance of CNS homeostasis during the organism's lifetime.
Effect of Pectin, a Soluble Dietary Fiber, on Functional and Morphological Parameters of the Small Intestine in Rats (1989)

We investigated the effects of pectin, a soluble dietary fiber, on functional and morphological parameters of the small intestine in rats. A control group and a pectin-fed group were given a fiber-free elemental liquid diet and an elemental liquid diet containing 2.5% (w/w) pectin, respectively, for 2 weeks. The ileal mucosal specific activities of maltase, sucrase and alkaline phosphatase increased significantly in the pectin-fed group. Maltose absorption of the ileum, studied in vitro by the method of everted sacs and disaccharide-dependent potential difference, increased significantly in the pectin-fed group. The length of the small intestine as well as the villus height and crypt depth of both the jejunum and the ileum were significantly greater in the pectin-fed group. The crypt cell production rate of the jejunum and the ileum was also significantly greater in the pectin-fed group. Plasma enteroglucagon, but not gastrin, increased significantly in the pectin-fed group. These data suggest that pectin feeding results in hyperplasia of the small-intestinal mucosa and a significant increase in the enzyme activities of the brush border membrane of the ileum.
Using SONAR-based Gas Volume Fraction Meter for Improved Net Oil Rate Measurement (2005)

The impa ct of entrained gases on net oil measurement is addressed and quantified for three common approaches for determining net oil: coriolis meters, resonant microwave oscillators and microwave absorption devices. Entrained gases are often encountered in the liquid leg of gas – liquid separator based measurement approaches and, if unrecognized, can result in significant error in net oil. The measurement principles of the three types of watercut meters considered are described. Each watercut measurement device continues to provide a measurement in the presence of gas. However, the interpretation of net oil content of an oil / water mixture with free gas present can be significantly impacted without specific knowledge of the gas volume fraction. The errors in oil cut introduced by unrecognized entrained gases are outlined using simplified models for each type of watercut measurement device considered. An approach is proposed to utilize SONAR-based gas volume fraction meters in conjunction with the watercut devices to provide accurate net oil determination in the presence of entrained gas. Laboratory and field data evaluating the proposed approach are presented, demonstrating both the impact of entrained gases on net oil measurement and the practicality of accounting for the free gas to enable accurate net oil measurement, independent of small gas volume fraction levels.
Characterization of normal peripheral blood lymphocyte colony-forming cells: cell cycle status, surface markers, and cellular growth requirements (1983)

We performed a series of studies to further clarify the nature of lymphocyte colony-forming cells (CFC) from normal peripheral blood. Mononuclear cells were separated into E-rosette-enriched (E+) and E-rosette-depleted (E-) populations and cultured in methylcellulose with conditioned media and irradiated mononuclear cells. Linear plating relationships were obtained with plating efficiencies of 0.26% +/- .02% (mean +/- SE) for E+ CFC and 0.18% +/- .02% for E- CFC. Cells in E+ colonies were T lymphocytes and in E- colonies were B lymphocytes as determined by cell surface marker analysis. Using the thymidine suicide technique, approximately one-half of CFC were found to be in cycle at any moment, and plating efficiencies and cell cycle status of E+ CFC were not changed by preincubation with PHA in liquid culture for 48 hr. Using antibody complement-mediated cytotoxicity, E+ CFC were found to be T101+, OKT3+, and Ia-, while E- CFC were OKT3- and Ia+. Using monocyte-depleted populations obtained by sedimentation at unit gravity, lymphocyte colony growth was absent in monocyte-depleted fractions, and optimal growth occurred with 40% monocytes in culture. In contrast to some previous studies, we find that lymphocyte CFC originate from a small, cycling population of cells bearing mature T or B lymphocyte markers. Entry into cell division, however, does not confer colony-forming capacity on lymphocytes. Monocytes are critical to growth of E+ CFC, and cultures severely depleted of monocytes would not be expected to form colonies.