gebhart/patrepeval huggingface dataset:
Plasma Mannoheptulose Kinetics in Adult Domestic Short-Haired Felines (2018)

Mannoheptulose (MH), a sugar found in avocados that inhibits glycolysis, has been investigated as a functional feed ingredient for canines. However, no studies have sought to feed MH to felines. The purpose of this study was to assess whether ingested MH appears in peripheral circulation of adult domestic short-hair felines (N = 10, 4.1 ± 0.1 kg, 1.6 y) fed a MH containing diet. The study was designed as a randomized cross-over with each cat receiving dietary treatments, control and MH. Each study period lasted 28 d and a meal challenge was performed on d 28. Felines were fasted overnight, anaesthetized, and a catheter was inserted into the jugular vein for repeated blood sampling. A fasting blood sample was collected six hours after catheter placement. Subsequently, felines were offered their full daily ration of test diet and blood was collected every 2 h during the 24 h post-prandial period for analysis of plasma MH. Ingested MH appeared in the plasma within 2 h of ingestion confirming that dietary MH is absorbed and available for cellular uptake. Circulating MH was cleared from plasma within 24 h of ingestion. The differences in plasma MH kinetics between species are likely attributed to differences in feline carbohydrate metabolism relative to other mammals. No MH was detected in cats fed the control diet. These results suggest that MH is digested, absorbed and available from peripheral circulation in adult cats. Finally, MH remains in circulation longer than in dogs and may suggest that cats would only need a lower dose or fewer doses of MH per day.
Human resident gut microbe Bacteroides thetaiotaomicron regulates colonic neuronal innervation and neurogenic function (2020)

Bt, common gut bacteria, is critical in regulating enteric neuronal and enteroendocrine cell populations, and neurogenic colonic activity. This highlights the potential use of this resident gut bacteria for maintaining healthy gut function.
A Text Retrieval Approach To Content-Based Audio Hashing. (2008)

[TODO] Add abstract here.
Latent sensitivity to Fas-mediated apoptosis after CD40 ligation may explain activity of CD154 gene therapy in chronic lymphocytic leukemia (2002)

Patients with chronic lymphocytic leukemia (CLL) treated with adenovirus (Ad)-CD154 (CD40L) gene therapy experience reductions in leukemia cell counts and lymph node size associated with induction of the death receptor Fas (CD95). CD4 T cell lines can induce apoptosis of CD40-activated CLL cells via a CD95 ligand (CD95-L)-dependent mechanism. To examine whether CD95-L was sufficient to induce cytolysis of CD40-activated CLL cells, we used Chinese hamster ovary cells transfected with CD95-L as cytotoxic effector cells. CD40-activated CLL cells were initially resistant to CD95-mediated apoptosis despite high-level expression of CD95. However, after 72 h, CLL cells from seven of seven patients became increasingly sensitive to CD95-mediated apoptosis. This sensitivity correlated with a progressive decline in Flice-inhibitory protein (FLIP), which was induced within 24 h of CD40 ligation. Down-regulation of FLIP with an antisense oligonucleotide or a pharmacologic agent, however, was not sufficient to render CLL cells sensitive to CD95-mediated apoptosis in the 24-72 h after CD40 activation. Although the levels of pro-Caspase-8 appeared sufficient, inadequate levels of Fas-associated death domain protein (FADD) and DAP3 may preclude assembly of the death-inducing signaling complex. Seventy-two hours after CD40 ligation, sensitivity to CD95 and a progressive increase in FADD and DAP3 were associated with the acquired ability of FADD and FLIP to coimmunoprecipitate with the death-inducing signaling complex after CD95 ligation. Collectively, these studies reveal that CD40 ligation on CLL B cells induces a programmed series of events in which the cells initially are protected and then sensitized to CD95-mediated apoptosis through shifts in the balance of the anti- and proapoptotic proteins FLIP and FADD.
Spectral dependence of noise and gain in Er-doped fiber preamplifier at 980 nm (1993)

We investigated the gain and noise figure dependence on signal wavelength for erbium doped fiber amplifiers (EDFA) counter-pumped at 980 nm. Using a two level modeling technique, we found a good agreement between our experimental measurements and the corresponding theoretical predictions for EDFAs operating under or far from full population inversion. Finally, we describe design trade-offs between small signal gain and noise figure for a range of active fiber length EDFAs at wavelengths of 1531 nm and 1548 nm.
Physiological Significance and Expression of P450s in the Developing Eye (2006)

Expression of 10 CYP orthologs (Families 1–3) in developing mouse conceptus is constitutive. These forms have specific temporal and spatial expression. Studies on CYP1B1 indicate its requirement for normal eye development, both in human and mouse. The distribution of the enzyme in the mouse eye is in three regions, which may reflect three different, perhaps equally important, functions in this organ. Its presence in the inner ciliary and lens epithelia appears to be necessary for normal development of the trabecular meshwork and its function in regulating intraocular pressure. Its expression in the retinal ganglion and inner nuclear layers may reflect a role in maintenance of the visual cycle. Its expression in the corneal epithelium may indicate a function in metabolism of environmental xenobiotics.
The effects of conventional extracorporeal circulation versus miniaturized extracorporeal circulation on microcirculation during cardiopulmonary bypass-assisted coronary artery bypass graft surgery (2012)

OBJECTIVES To reduce the complications associated with cardiopulmonary bypass (CPB) during cardiac surgery, many modifications have been made to conventional extracorporeal circulation systems. This trend has led to the development of miniaturized extracorporeal circulation systems. Cardiac surgery using conventional extracorporeal circulation systems has been associated with significantly reduced microcirculatory perfusion, but it remains unknown whether this could be prevented by an mECC system. Here, we aimed to test the hypothesis that microcirculatory perfusion decreases with the use of a conventional extracorporeal circulation system and would be preserved with the use of an miniaturized extracorporeal circulation system. METHODS Microcirculatory density and perfusion were assessed using sublingual side stream dark-field imaging in patients undergoing on-pump coronary artery bypass graft (CABG) surgery before, during and after the use of either a conventional extracorporeal circulation system (n = 10) or a miniaturized extracorporeal circulation system (n = 10). In addition, plasma neutrophil gelatinase-associated lipocalin and creatinine levels and creatinine clearance were assessed up to 5 days post-surgery to monitor renal function. RESULTS At the end of the CPB, one patient in the miniaturized extracorporeal circulation-treated group and five patients in the conventional extracorporeal circulation-treated group received one bag of packed red blood cells (300 ml). During the CPB, the haematocrit and haemoglobin levels were slightly higher in the miniaturized extracorporeal circulation-treated patients compared with the conventional extracorporeal circulation-treated patients (27.7 ± 3.3 vs 24.7 ± 2.0%; P = 0.03; and 6.42 ± 0.75 vs 5.41 ± 0.64 mmol/l; P < 0.01). The density of perfused vessels with a diameter <25 µm (i.e. perfused vessel density) decreased slightly in the conventional extracorporeal circulation-treated group from 16.4 ± 3.8 to 12.8 ± 3.3 mm/mm(2) (P < 0.01) and remained stable in the miniaturized extracorporeal circulation-treated group (16.3 ± 2.7 and 15.2 ± 2.9 mm/mm(2) before and during the pump, respectively). Plasma neutrophil gelatinase-associated lipocalin levels were increased following the use of extracorporeal circulation in both groups, and no differences were observed between the groups. Plasma creatinine levels and creatinine clearance were not affected by CABG surgery or CPB. CONCLUSIONS The results from this relatively small study suggest that the use of the miniaturized extracorporeal circulation system is associated with a statistically significant (but clinically insignificant) reduction in haemodilution and microcirculatory hypoperfusion compared with the use of the conventional extracorporeal circulation system.
Abstract B19: Discovery of novel tubulin inhibitor ABI-274 whose synergistic combination with vemurafenib overcome acquired vemurafenib resistance in BRAF mutated melanoma (2015)

Abstract Acquired clinical resistance to BRAF inhibitors such as vemurafenib or dabrafefnib arises frequently after short term of these targeted therapy. We hypothesized that a combined therapy using vemurafenib with a G2/M phase blocking agent will arrest resistant cells and overcome vemurafenib resistance. To test this hypothesis, we performed combination studies using our recently discovered tubulin inhibitor ABI-274 and vemurafenib on both vemurafenib-sensitive cells and a resistant A375RF21 sub line. The combination showed strong synergy in vitro, synergistically arrested cells in G1/G2/M phase, and significantly enhanced cancer cell apoptosis. In vivo co-administration of vemurafenib with ABI-274 showed strong synergistic efficacy in the vemurafenib-resistant xenograft model in nude mice. Overall, these results offer a rational combination strategy to significantly enhance the therapeutic benefit in melanoma patients who inevitably become resistant to current vemurafenib therapy. This work was supported by NIH grants R01CA148706, 1S10OD010678-01 and 1S10RR026377-01. Citation Format: Jin Wang, Jianjun Chen, Duane D. Miller, Wei Li. Discovery of novel tubulin inhibitor ABI-274 whose synergistic combination with vemurafenib overcome acquired vemurafenib resistance in BRAF mutated melanoma. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Melanoma: From Biology to Therapy; Sep 20-23, 2014; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(14 Suppl):Abstract nr B19.
Momentum Coefficient Governing Discrete Jet Actuation for Separation Control (2021)

Amplitude scaling laws for active control of boundary layer separation using discrete jet forcing are not fully established. Momentum coefficient is the most widely accepted scaling parameter, but accurate measurement and assessment of the employed assumptions are often not documented or even attempted. This work discusses various methods for experimentally determining the momentum coefficient produced by fluidic oscillators. Complementary simulations of the actuator are performed using delayed detached eddy simulations to validate the methods and offer explanations for shortcomings in the experiments. Scaling methods are applied to the experimental study of separation control on the suction side of a type II Glauert airfoil, otherwise known as the NASA hump model. An array of fluidic oscillators is located at and used to control separation over a range of Reynolds numbers for various actuator sizes and spacings . Integrated surface pressure measurements are used to determine the suitability of various momentum coefficient definitions for scaling the flow control efficacy. It is found that the momentum coefficients obtained using direct measurements of actuator plenum or throat pressure govern scaling with respect to both Reynolds number and actuator size. This is independent of the sweeping frequency in the range surveyed.
Millisecond dynamics of BTK reveal kinome-wide conformational plasticity within the apo kinase domain (2017)

Abstract Bruton tyrosine kinase (BTK) is a key enzyme in B-cell development whose improper regulation causes severe immunodeficiency diseases. Design of selective BTK therapeutics would benefit from improved, in-silico structural modeling of the kinase’s solution ensemble. However, this remains challenging due to the immense computational cost of sampling events on biological timescales. In this work, we combine multi-millisecond molecular dynamics (MD) simulations with Markov state models (MSMs) to report on the thermodynamics, kinetics, and accessible states of BTK’s kinase domain. Our conformational landscape links the active state to several inactive states, connected via a structurally diverse intermediate. Our calculations predict a kinome-wide conformational plasticity, and indicate the presence of several new potentially druggable BTK states. We further find that the population of these states and the kinetics of their inter-conversion are modulated by protonation of an aspartate residue, establishing the power of MD &amp; MSMs in predicting effects of chemical perturbations.
Supplementary Table S2 from Single-Cell Transcriptome Analysis Reveals Gene Signatures Associated with T-cell Persistence Following Adoptive Cell Therapy (2023)

&lt;p&gt;Supplementary Table S2&lt;/p&gt;
Exploring Conditional Text Generation for Aspect-Based Sentiment\n Analysis (2021)

Aspect-based sentiment analysis (ABSA) is an NLP task that entails processing\nuser-generated reviews to determine (i) the target being evaluated, (ii) the\naspect category to which it belongs, and (iii) the sentiment expressed towards\nthe target and aspect pair. In this article, we propose transforming ABSA into\nan abstract summary-like conditional text generation task that uses targets,\naspects, and polarities to generate auxiliary statements. To demonstrate the\nefficacy of our task formulation and a proposed system, we fine-tune a\npre-trained model for conditional text generation tasks to get new\nstate-of-the-art results on a few restaurant domains and urban neighborhoods\ndomain benchmark datasets.\n
Calibration and testing of wide‐field UV instruments (2017)

Abstract As with all optical systems the calibration of wide‐field ultraviolet (UV) systems includes three main areas: sensitivity, imaging quality, and imaging capability. The one thing that makes UV calibrations difficult is the need for working in vacuum substantially extending the required time and effort compared to visible systems. In theory a ray tracing and characterization of each individual component of the optical system (mirrors, windows, and grating) should provide the transmission efficiency of the combined system. However, potentially unknown effects (contamination, misalignment, and measurement errors) can make the final error too large and unacceptable for most applications. Therefore, it is desirable to test and measure the optical properties of the whole system in vacuum and compare the overall response to the response of a calibrated photon detector. A proper comparison then allows the quantification of individual sources of uncertainty and ensures that the whole instrument performance is within acceptable tolerances or pinpoints which parts fail to meet requirements. Based on the experience with the IMAGE Spectrographic Imager, the Wide‐band Imaging Camera, and the ICON Far Ultraviolet instruments, we discuss the steps and procedures for the proper radiometric sensitivity and passband calibration, spot size, imaging distortions, flatfield, and field of view determination.
Blend encapsulation by random copolymers: C/B/A-ran-B and C/D/A-ran-B systems (1998)

Random copolymers with the same monomeric units as blended homopolymers A and B have a strong tendency to encapsulate the minor phase in A/B/A-ran-B ternary systems. In this study we investigate encapsulation when one or both monomeric units in the random copolymer are chemically distinct from, but completely or partially miscible with, the other blend components, i.e., a C/D/A-ran-B blend. As model polymers, a styrene/methyl methacrylate random copolymer (70% styrene by weight) (SMMA), and polystyrene (PS), poly(methyl methacrylate) (PMMA), polycarbonate (PC), and poly(phenylene oxide) (PPO) homopolymers are chosen; PPO is completely miscible with PS and PC is partially miscible with PMMA. Three blend systems were prepared by melt mixing: PS/PC/SMMA, PPO/PMMA/SMMA, and PPO/PC/SMMA. Transmission electron microscopy demonstrated that for all cases SMMA moves to the interface between the matrix and dispersed phases during melt mixing, and forms an encapsulating layer. However, the resulting average size of a dispersed phase droplet is not significantly decreased by the addition of SMMA. Moreover, this size increased significantly upon further annealing, except for the blend with a PPO matrix which has a very high melt viscosity, demonstrating that encapsulation by SMMA does not provide stability against static coalescence.
Capstan: A Vector RDA for Sparsity (2021)

This paper proposes Capstan: a scalable, parallel-patterns-based, reconfigurable dataflow accelerator (RDA) for sparse and dense tensor applications. Instead of designing for one application, we start with common sparse data formats, each of which supports multiple applications. Using a declarative programming model, Capstan supports application-independent sparse iteration and memory primitives that can be mapped to vectorized, high-performance hardware. We optimize random-access sparse memories with configurable out-of-order execution to increase SRAM random-access throughput from 32% to 80%.
Codelivery of CRISPR-Cas9 and chlorin e6 for spatially controlled tumor-specific gene editing with synergistic drug effects (2020)

Controlled release of CRISPR-Cas9 ribonucleoprotein (RNP) and codelivery with other drugs remain a challenge. We demonstrate controlled release of CRISPR-Cas9 RNP and codelivery with antitumor photosensitizer chlorin e6 (Ce6) using near-infrared (NIR)- and reducing agent-responsive nanoparticles in a mouse tumor model. Nitrilotriacetic acid-decorated micelles can bind His-tagged Cas9 RNP. Lysosomal escape of nanoparticles was triggered by NIR-induced reactive oxygen species (ROS) generation by Ce6 in tumor cells. Cytoplasmic release of Cas9/single-guide RNA (sgRNA) was achieved by reduction of disulfide bond. Cas9/sgRNA targeted the antioxidant regulator <i>Nrf2</i>, enhancing tumor cell sensitivity to ROS. Without NIR irradiation, Cas9 was degraded in lysosomes and gene editing failed in normal tissues. The synergistic effects of Ce6 photodynamic therapy and <i>Nrf2</i> gene editing were confirmed in vivo. Controlled release of CRISPR-Cas9 RNP and codelivery with Ce6 using stimuli-responsive nanoparticles represent a versatile strategy for gene editing with potentially synergistic drug effects.
Gallbladder varices: imaging findings in patients with portal hypertension. (1991)

A retrospective review of the medical and imaging records of 50 patients with portal hypertension examined in the authors' department during a 2-year period identified six patients with gallbladder wall varices. Imaging studies performed in these patients included computed tomography (CT) (four patients), duplex and color Doppler flow (five patients), and magnetic resonance (MR) (four patients). Five of six patients with gallbladder varices had portal vein thrombosis. Anechoic areas within the gallbladder wall detected with ultrasonography could be distinguished from intramural edema by using duplex or color Doppler flow imaging in all five patients in whom it was used. Contrast material enhancement of these varices was detected with CT in three patients, two of whom also had adjacent mesenteric collaterals. Gradient-echo MR imaging (fast imaging in steady precession/fast low-angle shot) showed flow-related enhancement within the gallbladder wall in two patients. The presence of gallbladder wall varices may imply the presence of portal vein thrombosis. Since these varices can be a source of major blood loss, surgeons must be made aware of them when operating on patients with portal hypertension.
ChemInform Abstract: Catalyst‐Free, One Pot and Three‐Component Synthesis of 4′‐Phenyl‐1′H‐spiro[indoline‐3,2′‐quinazolin]‐2‐ones and 2,4‐Diphenyl‐1,2‐dihydroquinazolines. (2016)

Abstract A simple, mild, efficient and environmentally benign method for the synthesis of the title compounds is developed without using any catalyst in ethanol.
Analysis of Single Factor on the Low Temperature Compressive Characteristics of Sulphate Saline Soil (2014)

According to the experiments study of sulfuric acid saline soil, the formula of compression coefficient with the changes of moisture content, salt content, initial dry density and temperature is presented, and the law of single influencing factor on sulfuric acid saline soil compression are analyzed in the paper.
Identification of cutaneous lymphocyte-associated antigen as sialyl 6-sulfo Lewis X, a selectin ligand expressed on a subset of skin-homing helper memory T cells (2005)

We previously identified the carbohydrate determinant sialyl 6-sulfo Lewis X (Le(x)) as the major L-selectin ligand on high endothelial venules of peripheral lymph nodes. In this study, we examined the distribution of the sialyl 6-sulfo Le(x) determinant among peripheral lymphocytes. The determinant was expressed on a subset of helper memory T and NK cells. The helper memory T cells expressing sialyl 6-sulfo Le(x) were CD45RO(bright+) PSGL-1(high+) CCR4+ L-selectin+ CCR7+ but did not express alpha4beta7 integrin or CCR9, indicating that they were the skin-homing population of central memory T cells. The T-cell subset significantly expressed mRNA for 6-sulfotransferase HEC-GlcNAc6ST and fucosyltransferase Fuc-T VII, responsible for the synthesis of sialyl 6-sulfo Le(x). Characteristics of the T-cell population were similar to those previously described for cutaneous lymphocyte-associated antigen (CLA)-positive T cells defined by the HECA-452 or 2F3 antibody. The binding of the T-cell subset with the specific anti-sialyl 6-sulfo Le(x) antibody G152 was almost completely abrogated by HECA-452 or 2F3. Binding of recombinant E-, P-, and L-selectins to the T-cell subset was significantly inhibited by G152 and by HECA-452 antibodies. We propose that CLA, which is expressed without any activation stimuli on peripheral skin-homing helper memory T cells in healthy persons, is at least partly the sialyl 6-sulfo Le(x) determinant.
Anti-CD19 CAR T-Cell Therapy for Patients with Richter Syndrome: A Lysa Study from the Descar-T Registry (2022)

International audience
Magnetic Field Strength Measurements in Heat-Assisted Magnetic Recording (2019)

A method for measuring the magnetic field strength of the magnetic writer used in heat-assisted magnetic recording (HAMR) is presented. The measurement, termed write current assist percentage (WCAP), compares the laser current needed to erase a narrow data track (a micro-track) with the laser current needed when the magnetic writer is assisting with the erasure. The difference is related to the temperature difference in the recording medium. If the temperature dependence of the medium's magnetic anisotropy is known, the erasure field can be determined. The method is useful for comparing the magnetic response of different write pole geometries, for comparing frequency responses of different designs, and for comparing media.
Evaluation of berberine/bovine serum albumin nanoparticles for liver fibrosis therapy (2014)

Use of non-hazardous materials in pharmaceutical formulation avoids the emergence of toxic potential to the environment.
Synthesis and Structural Characterization of a γ-Keggin-Type Dimeric Silicotungstate with a Bis(μ-hydroxo) Dizirconium Core [(γ-SiW10O36)2Zr2(μ-OH)2]10- (2007)

A novel dinuclear zirconium sandwich-type silicotungstate cluster of [(gamma-SiW(10)O(36))(2)Zr(2)(mu-OH)(2)](10-) (1) was synthesized by the reaction of a divacant lacunary gamma-Keggin silicotungstate [gamma-SiW(10)O(36)](8-) with ZrOCl(2).8H(2)O. The anion consisted of two [gamma-SiW(10)O(36)](8-) units sandwiching a diamond Zr(2)(mu-OH)(2) core, and each zirconium atom in 1 was six-coordinated to two mu-OH ligands and four oxygen atoms of two [gamma-SiW(10)O(36)](8-) units. The Zr(2)(mu-OH)(2) core in 1 reacted with methanol to give the corresponding monomethoxo derivative [(gamma-SiW(10)O(36))(2)Zr(2)(mu-OH)(mu-OCH(3))](10-) (2).