gebhart/patrepeval huggingface dataset:
Blood flow distribution in a polymyxin coated fibrous bed for endotoxin removal. Effect of a new blood path design (2001)

The analysis of flow distribution in cartridges designed for hemoperfusion is extremely important. Taking advantage of a new imaging technique, based on the analysis of a helical scanner-generated imaging sequence, we studied the blood flow distribution in a series of cartridges for extracorporeal removal of endotoxin. Cartridges with improved design were compared to cartridges with a standard design. The improved design consists in a different structure of the holes of the distributor of the flow within the adsorbent unit. Cartridges were studied in vitro with human blood from voluntary donors at blood flows of 100 and 250 ml/min. The progression of density in specific regions of interest (ROI) was analyzed to detect the distribution of the dye injected in the blood circuit. The study demonstrates that both at 100 ml/min and at 250 ml/min of blood flow, the progression of flow appears more homogeneous in the devices with improved design. In detail, the flow distribution measured by the incremental density values detected in the ROIs of the proximal comers (close to the arterial port) and in the ROIs of the central region of the device (close to the inner wall of the case) displays a significant difference between the standard and the improved device. The ROIs studied in the standard devices display a slower increase in density and significantly lower absolute values expressed in Hounsfield units. The experimental method utilized to analyze flow distribution seems to represent an important means to study the performance and design of this type of device.
Supplementary Figure 4 from CD4<sup>+</sup> T-Cell Help in the Tumor Milieu Is Required for Recruitment and Cytolytic Function of CD8<sup>+</sup> T Lymphocytes (2023)

Supplementary Figure 4 from CD4&lt;sup&gt;+&lt;/sup&gt; T-Cell Help in the Tumor Milieu Is Required for Recruitment and Cytolytic Function of CD8&lt;sup&gt;+&lt;/sup&gt; T Lymphocytes
Ultra-fine pitch individually addressable visible laser arrays for high speed digital printing applications (2008)

An individually addressable visible semiconductor laser diode array with a 20 μm pitch is demonstrated that is highly suited for deployment in next-generation digital print systems. The array, operating at 660 nm, comprises 22 single mode lasers fabricated on a single GaInP/AlGaInP/GaAs substrate. The laser array is flip-chip bonded onto a patterned ceramic submount that enables the individual elements to be driven independently and is integrated into a 26-pin butterfly package. Arrays tested CW exhibit low threshold current (&amp;lt;20 mA per emitter), up to 50 mW output power per channel with a high slope efficiency (0.9 W/A) and a high characteristic temperature of over 100 K.
Coherent power combination of two Master-oscillator-power-amplifier (MOPA) semiconductor lasers using optical phase lock loops (2007)

Using heterodyne Optical Phase-Locked Loops (OPLLs), two 1W high power 1550 nm master-oscillator-power-amplifier (MOPA) semiconductor lasers operating as current controlled oscillators are phase-locked to a 1 mW reference laser. The signals of the two MOPAs are then coherently combined and their mutual coherence is studied. In each OPLL, the acquisition range is increased to +/-1.1GHz with the help of an aided- acquisition circuit. Control of the phase of a single slave MOPA is demonstrated using a RF phase shifter. The differential phase error between two MOPAs locked to the common reference laser is typically 22 degrees.
Human knowledge models: Learning applied knowledge from the data (2022)

Artificial intelligence and machine learning have demonstrated remarkable results in science and applied work. However, present AI models, developed to be run on computers but used in human-driven applications, create a visible disconnect between AI forms of processing and human ways of discovering and using knowledge. In this work, we introduce a new concept of “Human Knowledge Models” (HKMs), designed to reproduce human computational abilities. Departing from a vast body of cognitive research, we formalized the definition of HKMs into a new form of machine learning. Then, by training the models with human processing capabilities, we learned human-like knowledge, that humans can not only understand, but also compute, modify, and apply. We used several datasets from different applied fields to demonstrate the advantages of HKMs, including their high predictive power and resistance to noise and overfitting. Our results proved that HKMs can efficiently mine knowledge directly from the data and can compete with complex AI models in explaining the main data patterns. As a result, our study reveals the great potential of HKMs, particularly in the decision-making applications where “black box” models cannot be accepted. Moreover, this improves our understanding of how well human decision-making, modeled by HKMs, can approach the ideal solutions in real-life problems.
Ashtech XII GPS Receiver, The All-In-One All-In-View (1988)

Ashtech XII, the all-in-one, all-in-view GPS (global positioning system) receiver is introduced. The term all-in-one denotes that navigation, survey, and time transfer capabilities are all combined in one receiver. Furthermore, for survey applications the required equipment all fits in one small carrying case. The all-in-view term denotes that the receiver can track all the satellites in view, even when the 24-satellite constellation is complete and the existing healthy satellites are operational. The architecture of the Ashtech XII technology is presented, and automatic operation of the receiver is discussed. >
FoldGPCR: Structure prediction protocol for the transmembrane domain of G protein‐coupled receptors from class A (2010)

Building reliable structural models of G protein-coupled receptors (GPCRs) is a difficult task because of the paucity of suitable templates, low sequence identity, and the wide variety of ligand specificities within the superfamily. Template-based modeling is known to be the most successful method for protein structure prediction. However, refinement of homology models within 1-3 A C alpha RMSD of the native structure remains a major challenge. Here, we address this problem by developing a novel protocol (foldGPCR) for modeling the transmembrane (TM) region of GPCRs in complex with a ligand, aimed to accurately model the structural divergence between the template and target in the TM helices. The protocol is based on predicted conserved inter-residue contacts between the template and target, and exploits an all-atom implicit membrane force field. The placement of the ligand in the binding pocket is guided by biochemical data. The foldGPCR protocol is implemented by a stepwise hierarchical approach, in which the TM helical bundle and the ligand are assembled by simulated annealing trials in the first step, and the receptor-ligand complex is refined with replica exchange sampling in the second step. The protocol is applied to model the human beta(2)-adrenergic receptor (beta(2)AR) bound to carazolol, using contacts derived from the template structure of bovine rhodopsin. Comparison with the X-ray crystal structure of the beta(2)AR shows that our protocol is particularly successful in accurately capturing helix backbone irregularities and helix-helix packing interactions that distinguish rhodopsin from beta(2)AR.
An Elastomeric Poly(Thiophene‐EDOT) Composite with a Dynamically Variable Permeability Towards Organic and Water Vapors (2012)

Abstract An interpenetrating polymer network (IPN) material with controllable nanoporosity is developed for applications such as chemical protection. The IPN material is based on a conducting polymer backbone consisting of thiophene and 3,4 ethylenedioxythiophene (EDOT) repeat units–poly(thiophene‐EDOT)–formed within a soft polyurethane support. The IPN demonstrates reversible, electrochemically switchable nanoporosity in the absence of standard liquid electrolyte, with the oxidized state being the open (high porosity) state and the reduced state being the closed (low porosity) state. The switching of the IPN between its oxidized (open) and reduced (closed) states is actuated using application of ±1.0 V. The variability in the IPN porosity, induced by the electrochemical switching, is revealed by large changes in water vapor diffusivity, as well as changes in the diffusivities of the chemical agent simulants chloroethyl ethyl sulfide (CEES) and methyl salicylate (MeS). The closed state of the IPN is able to decrease CEES diffusivity by ≈99% compared to expanded Teflon (ePTFE), while the open state allows high MVT rates comparable to ePTFE. The IPN's ability to allow high MVT under non‐threat conditions (open state) and high protection from agents under threat conditions (closed state) is a unique and desirable characteristic of this novel IPN material.
Identification and characterization of leukotriene D4 receptors and signal transduction processes in rat basophilic leukemia cells. (1987)

The leukotriene D4 (LTD4) receptor on rat basophilic leukemia (RBL-1) cell membranes was characterized using a radioligand binding assay. [3H]LTD4 binding to RBL-1 membrane receptors was stereoselective, specific, and saturable. The binding affinity and maximum binding density of [3H]LTD4 to RBL-1 membrane receptors were 0.9 +/- 0.2 nM and 800 +/- 125 fmol/mg protein, respectively. Binding of [3H]LTD4 to the receptors was enhanced by divalent cations (Ca2+, Mg2+, and Mn2+) and inhibited by guanine nucleotides and sodium ions, specifically, indicating that a guanine nucleotide-binding protein may regulate the agonist-receptor interaction. LTD4, LTE4 agonist and antagonist analogs competed with the radioligand in binding to the RBL-1 LTD4 receptors. The binding affinities of these analogs correlated with (a) those determined from the guinea pig lung LTD4 receptors and (b) the pharmacological activities in smooth muscle contraction. LTD4 and related agonists also induced time- and concentration-dependent phosphatidylinositol hydrolysis in RBL-1 cells. The LTD4 induction of inositol 1-phosphate was potent, stereoselective, specific, and was blocked by LTD4 receptor antagonists. The rank order potency of agonist-induced inositol 1-phosphate formation in RBL-1 cells was equivalent to the receptor binding affinity determined using either RBL-1 cell or guinea pig lung membranes. These studies have demonstrated the G protein coupled LTD4 receptors on RBL-1 cell membranes. Binding of agonists to the receptor may activate the G protein-regulated phospholipase C to induce hydrolysis of phosphatidylinositol. The hydrolytic products of phosphatidylinositol, possibly inositol trisphosphate and diacylglycerol, may be the intracellular messengers for LTD4 receptors in RBL-1 cells.
Effects of Sideritis euboea (Lamiaceae) Aqueous Extract on IL-6, OPG and RANKL Secretion by Osteoblasts (2011)

The water extract obtained from the aerial parts of Sideritis euboea (Lamiaceae), which is known in Greece as 'mountain tea', was investigated by determining the in vitro effect of this extract on the IL-6, OPG and RANKL secretion by osteoblasts, three important molecules in osteoblast-osteoclast interplay. The results showed that this extract reduced significantly the secretion of IL-6 by KS-483 osteoblasts, while it also suppressed RANKL secretion, with both effects being dose-dependent and more potent at the higher concentrations tested (50, 100 microg/mL). We further determined the chemical profile of the extract by applying an analytical U-HPLC-DAD-ESI-MS/MS method using the high resolution hybrid LTQ-Orbitrap Discovery spectrometer. An ESI source in negative mode was employed. The analysis indicated that the water extract of S. euboea is rich in flavonoid glycosides, and phenylpropanoid glycosides.
Rhamnolipids from Pseudomonas aeruginosa disperse the biofilms of sulfate-reducing bacteria (2018)

Biofilm formation is an important problem for many industries. <i>Desulfovibrio vulgaris</i> is the representative sulfate-reducing bacterium (SRB) which causes metal corrosion in oil wells and drilling equipment, and the corrosion is related to its biofilm formation. Biofilms are extremely difficult to remove since the cells are cemented in a polymer matrix. In an effort to eliminate SRB biofilms, we examined the ability of supernatants from <i>Pseudomonas aeruginosa</i> PA14 to disperse SRB biofilms. We found that the <i>P</i>. <i>aeruginosa</i> supernatants dispersed more than 98% of the biofilm. To determine the biochemical basis of this SRB biofilm dispersal, we examined a series of <i>P</i>. <i>aeruginosa</i> mutants and found that mutants <i>rhlA</i>, <i>rhlB</i>, <i>rhlI</i>, and <i>rhlR</i>, defective in rhamnolipids production, had significantly reduced levels of SRB biofilm dispersal. Corroborating these results, purified rhamnolipids dispersed SRB biofilms, and rhamnolipids were detected in the <i>P</i>. <i>aeruginosa</i> supernatants. Hence, <i>P</i>. <i>aeruginosa</i> supernatants disperse SRB biofilms via rhamnolipids. To determine the genetic basis of how the <i>P</i>. <i>aeruginosa</i> supernatants disperse SRB biofilms, a whole transcriptomic analysis was conducted (RNA-seq); based on this analysis, we identified four proteins (DVUA0018, DVUA0034, DVUA0066, and DVUA0084) of the <i>D</i>. <i>vulgaris</i> megaplasmid that influence biofilm formation, with production of DVUA0066 (a putative phospholipase) reducing biofilm formation 5.6-fold. In addition, the supernatants of <i>P</i>. <i>aeruginosa</i> dispersed the SRB biofilms more readily than protease in M9 glucose minimum medium and were also effective against biofilms of <i>Escherichia coli</i> and <i>Staphylococcus aureus</i>.
Supplementary Figure 5 from Chimeric Antigen Receptor T Cells with Dissociated Signaling Domains Exhibit Focused Antitumor Activity with Reduced Potential for Toxicity <i>In Vivo</i> (2023)

&lt;p&gt;PDF file - 854K, Figure S5. F-28z CART cells produce dramatically less IFN-γ in response to stimulation with A1847 (M+/F-) cells compared to A1847 (M+/F+) cells. A. F-28z CAR expression on human CD3+ T cells upon transduction with lentivirus compared to untransduced T cells. F-28z CART transduced T cells were detected using biotinylated-protein L followed by SA-PE. B. Transduced T cells (1 x 105 T cells) were cultured alone (none) or stimulated overnight with an equal number of either FRa-negative PEO-1 cells or A1847 (M+/F-) cells, or FRa-positive A1847 (M+/F+) cancer cells. Cell-free supernatant was harvested after ~20 hours of incubation and the IFN-γ levels were measured with ELISA. Mean IFN-γ concentration plus-minus SEM (pg/ml) from triplicate cultures is shown. ***P &lt; 0.001 comparing the IFN-γ secretion produced by M-z/F-28 CART cells against A1847M+/F+ versus A1847M+/F- or PEO cells.&lt;/p&gt;
Dynamic Changes of EGFR Activating Mutations as an Early Predictor of Progression in Non–Small Cell Lung Cancer Patients Treated with EGFR Tyrosine Kinase Inhibitors (2020)

Serial monitoring of circulating tumor DNA may predict resistance to first-line epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors before CT-confirmed progression. Our objective was to evaluate dynamic changes in plasma EGFR-activating mutations as an early predictor of disease progression before clinical or radiological evidence. For this observational study, 35 patients with advanced, EGFR-positive, nonsquamous, non-small cell lung cancer were enrolled. All patients were initiating or receiving EGFR tyrosine kinase inhibitors and had received at least one follow-up CT scan. Peripheral blood samples were collected at each clinical visit, and CT scans were scheduled every 8 to 16 weeks after tyrosine kinase inhibitor initiation and upon clinical/symptom progression. Of the 35 patients, 16 experienced reappearance of EGFRactivating mutations and disease progression. Of these, 12 patients experienced reappearance of EGFR-activating mutations before CT-confirmed progression, 3 had CT-confirmed progression one visit (8 weeks) before detectable EGFR-activating mutations, and 1 had EGFR-activating mutations reappear concurrently with CT-confirmed progression. EGFR-activating mutations reappeared at a mean of 10 weeks (median, 16 weeks) before routinely scheduled CT-confirmed progression. Using study-specific definitions, we observed 5 false positives and no false negatives. This study demonstrates that dynamic changes in circulating tumor DNA can predict resistance to EGFR-TKIs before CT-confirmed progression. Further prospective trials of this promising approach with potential benefits to patient care should be considered.
Analysis of White Noise on Power Frequency Estimation by DFT-Based Frequency Shifting and Filtering Algorithm (2019)

The frequency shifting and filtering (FSF) algorithm, a variant of DFT, has the merit of high efficiency for frequency analysis thanks to its simple implementation in the time domain. However, the inevitable white noise injected by various factors leads to inaccurate frequency estimation in practical measurement. This article investigates the influence of a stationary white noise on FSF-based frequency estimation of the power system. The variance expression of the frequency estimator is derived theoretically and compared to its unbiased Cramer-Rao lower bound (CRLB). The obtained results are validated by several computer simulations.
MINIMAL SIDE‐CHAIN PROTECTION CAN BE A SUCCESSFUL STRATEGY IN SOLID‐PHASE PEPTIDE SYNTHESIS (1979)

The N-terminal tyrosine residue of Met-enkephalin could be readily incorporated without protection of its phenolic hydroxylgroup. Furthermore, the HF-cleaved product contained fewer impurities than that derived from hydroxyl-protected material. Despite the presence of Tyr in the center of the chain, an LH-RH antagonist, [D-Phe2, D-Trp3, D-Phe6]-LH-RH, could also be made in normal yield by incorporation of free Boc-Tyr. Syntheses of the same model peptide without protection of the Ser residue and protection of the Arg residue as the guanidine HCl salt also gave excellent yields of analog. Finally, the LH-RH inhibitor and a highly active agonist, [D-Leu6, desGly-NH2(10)]-LH-RH ethylamide, were synthesized without protection of Tyr, Ser and Arg, which enabled free peptides to be generated directly by ammonolysis and ethylaminolysis, respectively, without HF treatment. In all examples, no evidence emerged to suggest reaction of side-chains during synthesis.
Unsupervised Feature Learning from Temporal Data (2015)

Current state-of-the-art classification and detection algorithms rely on supervised training. In this work we study unsupervised feature learning in the context of temporally coherent video data. We focus on feature learning from unlabeled video data, using the assumption that adjacent video frames contain semantically similar information. This assumption is exploited to train a convolutional pooling auto-encoder regularized by slowness and sparsity. We establish a connection between slow feature learning to metric learning and show that the trained encoder can be used to define a more temporally and semantically coherent metric. Our main assumption is that data samples that are temporal neighbors are also likely to be neighbors in the latent space. For example, adjacent frames in a video sequence are more likely to be semantically similar than non-adjacent frames. This assumption naturally leads to the slowness prior on features which was introduced in SFA (Wiskott & Sejnowski (2002)). Temporal coherence can be exploited by assuming a prior on the features extracted from the temporal data sequence. One such prior is that the features should vary slowly with respect to time. In the discrete time setting this prior corresponds to minimizing an L p norm of the difference of feature vectors for temporally adjacent inputs. Consider a video sequence withT frames, ifzt represents the feature vector extracted from the frame at timet then the slowness prior corresponds to minimizing PT t=1 kzt zt 1kp. To avoid the degenerate solution zt = z0 for t = 1:::T , a second term is introduced which encourages data samples that are not temporal neighbors to be separated by at least a distance ofm-units in feature space, wherem is known as the margin. In the temporal setting this corresponds to minimizing max(0;mk zt zt0kp), wherejt t 0 j > 1. Together the two terms form the loss function introduced in Hadsell et al. (2006) as a dimension reduction and data visualization algorithm known as DrLIM. Assume that there is a differentiable mapping from input space to feature space which operates on individual temporal samples. Denote this mapping by G and assume it is parametrized by a set of trainable coefficients denoted byW . That is,zt = GW(xt). The per-sample loss function can be written as:
Topside distributed acoustic sensing in subsea developments (2020)

Lowering total cost of ownership (TCO) has been a significant driver for adopting distributed acoustic sensing (DAS) over alternative surveillance techniques. For subsea wells, topside DAS requires optical engineering solutions to compensate for the reduced acoustic bandwidth, optical losses and back reflections accumulated through umbilicals, multiple wet- and dry-mate optical connectors, splices, optical feedthrough systems, and downhole fibers and wet mates. To obviate these problems, we describe a subsea fiber topology with two transmission fibers from the topside to an optical circulator deployed in the optical flying lead at the subsea tree equipped with an optical feedthrough system. This limits the sensing fiber portion of the total fiber length to only be the fiber located below the subsea tree, while eliminating all back reflections from the multiple subsea connectors above the remote circulator. The acoustic sampling frequency is only constrained by the fiber length below the subsea tree; thus enabling dry-tree equivalent sensing of both upper and lower completions regardless of the tie-back distance. This implies that the various spectral-based DAS processing algorithms developed for sand control, inflow profiling, well integrity, and seismic imaging on dry-tree wells can be equally and readily applied to DAS data acquired from subsea wells going forward. Results from various laboratory and field trials which validate system performance are presented, and deployment in subsea projects is discussed. Presentation Date: Monday, October 12, 2020 Session Start Time: 1:50 PM Presentation Time: 2:40 PM Location: 361F Presentation Type: Oral