gebhart/patrepeval huggingface dataset:
IL-4 Expression and Constitutive Activation of Erk Signaling In Vivo in Follicular Lymphoma. (2007)

Abstract Follicular lymphoma (FL) is characterized by constitutive expression of the Bcl-2 oncoprotein as a consequence of the t(14;18) BCL2/JH translocation in germinal center B-cells. While Bcl-2 confers survival advantage through anti-apoptosis mechanisms, the t(14;18) alone is not sufficient for lymphomagenesis. Evidence suggests that additional factors in the lymph node microenvironment, related to tumor infiltrating T-cells and macrophages, may cooperate with Bcl-2 in orchestrating the malignant phenotype in vivo. In this study we generated proteomic cytokine profiles of patient lymph node tissue lysates from FL (N=53) grades 1–3, and the non-malignant normal counterpart follicular hyperplasia (FH; N=24). Using an ultrasensitive multiplex elisa system we assayed a panel of 11 cytokines known to be secreted by T-cells and/or macrophages including IL-1beta, IL-2, IL-4, IL-5, IL-6, IL-8, IL-10, IL-13, IL-12p70, TNF-alpha, and INF gamma. With the exception of IL-4, all cytokines measured showed higher concentrations in FH than FL. In particular, IL-1 beta demonstrated levels 20 times higher in FH; IL-8 levels were 30 times higher; and IL-13 levels were 9 times higher in FH than in FL (p values &lt; 0.005). In contrast, IL-4 levels were 5 times higher in FL than in FH (p &lt; 0.0054). Interestingly, IL-4 levels were highest in FL grade 1 (N=20) in comparison to grade 2 (N=18) and grade 3 (N=12). Immunohistochemical stains for CD3 showed no significant difference in the numbers of CD3+ T-cells in FL samples over FH lymph nodes; or in FL grade 1 vs. grade 2 or grade 3. Hence the differences observed are not due to numerical differences in the total number of T-cells present in FL and FH. We evaluated the activation state of the mitogen activated protein (MAP) kinase signaling pathway, which is activated in response to stimulation by most cytokines in our panel via PI3Kinase. Western blot analysis showed that Erk was constitutively phosphorylated in 14 out of 15 (93%) of FL cases in contrast to only 3 out of 9 (33%) of FH cases. These findings demonstrate that tumor growth in FL is characterized overall by low levels of cytokines within the lymph node microenvironment in comparison to growth associated with the benign counterpart FH. The T-cell secreted cytokine, IL-4, which drives B-cell proliferation, was the only cytokine that showed statistically significant higher expression in the lymph node microenvironment of FL in comparison to FH. Moreover, the intracellular MAP kinase signaling pathway was constitutively activated in vivo in patient FL samples as compared to FH, despite higher overall cytokine levels in FH. These findings suggest that the IL-4 cytokine, and intracellular Erk activation in FL cells, may 1) play a role, in cooperation with Bcl-2, in driving the malignant phenotype in FL and 2) may serve as effective molecular targets for future therapies in FL.
Punching Shear Behavior of GFRP-RC Slab-Column Edge Connections (2018)

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Immunogenicity and Safety of the Quadrivalent Human Papillomavirus Vaccine in HIV-1-Infected Women (2014)

The quadrivalent HPV vaccine targeted at types 6, 11, 16, and 18 was safe and immunogenic in HIV-infected women aged 13-45 years. Women with HIV RNA load >10 000 copies/mL and/or CD4 count <200 cells/µL had lower rates of seroconversion rates. Clinical Trials Registration. NCT00604175.
Waste Management of a Microemulsion Using Electrolyte Addition at Increased Temperatures (1999)

Laboratory and field experiments were conducted to examine an intermediate waste treatment process that involves adding an electrolyte (NaCl) at increased temperatures to a single-phase microemulsion (SPME) waste. An in situ flushing test performed at a Superfund site at Hill AFB, UT, was the source of the SPME waste. The produced fluids from extraction wells included constituents of a complex nonaqueous phase liquid (NAPL) extracted from the shallow aquifer, as well as the surfactant–cosurfactant mixture (3.0% Brij 97, 2.5% n-pentanol) injected to enhance NAPL solubility. The treatment method is based on separation of the SPME waste into two immiscible phases: a hydrophobic oil-rich phase, and a hydrophilic water-rich phase. Laboratory data indicated that at higher temperatures, lower amounts of salt were required to produce similar levels of volumetric phase separation of the SPME waste. The volumetric separations (aqueous/total) were on the order of ∼0.95 ±0.01 for samples taken during the first pore volume, and a composite volume of the flushing experiment. Partitioning of several NAPL constituents into the organic phase was usually greater than 96% of the mass present in the effluent SPME waste. A cost analysis suggests potential economic advantages of this intermediate waste management process. Key words: site remediation; waste treatment; NAPL; salt; in situ flushing.
Flat pulse-amplitude rational-harmonic-mode-locking fiber lasers with GHz pulse repetition rates (2013)

Rational harmonic mode locking (RHML) in an active mode-locked fiber laser can increase the output pulse repetition rate a number of times the modulation frequency of an optical modulator in a cavity when driven by gigahertz (GHz) RF. The amplitudes of the output optical pulse train in a high order RHML operation are not equalized and flat due to the GHz RF drive signals. A modified RHML technique using standard instrumentation that generates 1 GHz electrical square wave signals to accomplish up to 6<sup>th</sup> order RHML in fiber lasers is presented for improving the flatness of the amplitudes of the output optical pulse train at the pulse repetition rate of up to 12 GHz.
Detectors for Cooperative Mesh Networks With Decode-and-Forward Relays (2014)

We consider mesh networks composed of groups of relaying nodes which operate in decode-and-forward mode. Each node from a group relays information to all the nodes in the next group. We study these networks in two setups, one where the nodes have complete state information about the channels through which they receive the signals, and another when they only have the statistics of the channels. We derive recursive expressions for the probabilities of errors of the nodes and present several implementations of detectors used in these networks. We compare the mesh networks with multihop networks formed by a set of parallel sections of multiple relaying nodes. We demonstrate with numerous simulations that there are significant improvements in performance of mesh over multihop networks in various scenarios.
Quantitative Assay of Endotoxin by the Use of Ammonia Electrode and Purified Factor C (1992)

Factor C, an endotoxin-sensitive serine-protease zymogen, was prepared by cation-exchange chromatography using SP Toyopearl 650C. This preparation exhibited a single band on sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The endotoxine-dependent Factor C activity was determined from the amount of released ammonium ions by cleavage of N-tert-butoxy-carbonl Val-Pro-Arg-NH2 using an ammonia electrode. The sensitivity towards the endotoxin was approximately 5×10-8 g/ml.
Magnetic resonance imaging for detection and analysis of mouse phenotypes (2005)

With the enormous and growing number of experimental and genetic mouse models of human disease, there is a need for efficient means of characterizing abnormalities in mouse anatomy and physiology. Adaptation of magnetic resonance imaging (MRI) to the scale of the mouse promises to address this challenge and make major contributions to biomedical research by non-invasive assessment in the mouse. MRI is already emerging as an enabling technology providing informative and meaningful measures in a range of mouse models. In this review, recent progress in both in vivo and post mortem imaging is reported. Challenges unique to mouse MRI are also identified. In particular, the needs for high-throughput imaging and comparative anatomical analyses in large biological studies are described and current efforts at handling these issues are presented.
Design of 3D-printable nasopharyngeal swabs in Matlab for COVID-19 testing (2020)

As an important diagnostic device for detecting respiratory infections, the nasopharyngeal swab is running out of supply due to the fast spread of COVID-19. In this short paper, we present a novel design platform in Matlab for realizing patient-specific nasopharyngeal swabs that can be quickly 3D-printed to fill the swabs’ shortage. Firstly, the swab is realized with our geometry modeling tool using the size derived from the patient’s CT data. Then, Selective-Laser-Sintering (SLS) is employed to print the swab using polyamide as biocompatible material. A printed swab is also presented to demonstrate the performance of the proposed design platform.
MYC Instructs and Maintains Pancreatic Adenocarcinoma Phenotype (2020)

The signature features of pancreatic ductal adenocarcinoma (PDAC) are its fibroinflammatory stroma, poor immune activity, and dismal prognosis. We show that acute activation of <i>Myc</i> in indolent pancreatic intraepithelial neoplasm (PanIN) epithelial cells <i>in vivo</i> is, alone, sufficient to trigger immediate release of instructive signals that together coordinate changes in multiple stromal and immune-cell types and drive transition to pancreatic adenocarcinomas that share all the characteristic stromal features of their spontaneous human counterpart. We also demonstrate that this <i>Myc</i>-driven PDAC switch is completely and immediately reversible: <i>Myc</i> deactivation/inhibition triggers meticulous disassembly of advanced PDAC tumor and stroma and concomitant death of tumor cells. Hence, both the formation and deconstruction of the complex PDAC phenotype are continuously dependent on a single, reversible <i>Myc</i> switch. SIGNIFICANCE: We show that <i>Myc</i> activation in indolent <i>Kras</i> <sup>G12D</sup>-induced PanIN epithelium acts as an immediate pleiotropic switch, triggering tissue-specific signals that instruct all the diverse signature stromal features of spontaneous human PDAC. Subsequent <i>Myc</i> deactivation or inhibition immediately triggers a program that coordinately disassembles PDAC back to PanIN.<i>See related commentary by English and Sears, p. 495</i>.
Production, bioavailability and health benefits of dairy peptides (2016)

Resumen del trabajo presentado al III National and II International Student Congress of Food Science and Technology: "Bioactive compounds of natural origin in Food Science and Technology", celebrado en Valencia del 3 al 4 de marzo de 2016.
GloServ: global service discovery using the OWL Web ontology language (2005)

Due to the growth in ubiquitous computing technology in the past few years, the need for contextaware service discovery across wide area networks is becoming prevalent.Current service discovery protocols lack in the ability to scale to large networks as well as semantically describe services.Thus, we propose GloServ, which is a global service discovery architecture that locates services throughout wide and local area networks.Intelligent agents within GloServ use the OWL Web Ontology Language to provide detailed service descriptions, and provide users with automatic registration and querying.This paper discusses a revision of GloServ that uses the OWL Web Ontology Language, as its ontology for describing services instead of the Resource Description Framework Schema (RDFS).We will describe how OWL is used for automated registration and querying of services throughout a global network.
Quadrilateral Meshing with Directionality Control through the Packing of Square Cells. (1998)

This paper proposes a computational method for fully automated quadrilateral meshing. Unlike previous methods, this new scheme can create a quadrilateral mesh whose directionality is precisely controlled. Given as input: (1) a 2D geometric domain, (2) a desired node spacing distribution as a scalar function defined over the domain, and (3) a desired mesh directionality as a vector field defined over the domain, the proposed method first packs square cells closely in the domain. The centers of the squares are then connected by Delaunay triangulation, yielding a triangular mesh topology. The triangular mesh is further converted into a quad-dominant mesh or an all-quad mesh that satisfies the given mesh directionality. Since the closely packed square cells mimic a pattern of Voroni polygons corresponding to a well-shaped graded quadrilateral mesh, the proposed method generates a high quality mesh whose element sizes and mesh directionality conform well to the given input. Keywords: quadri...
Task-Based Functional Connectivity and Blood-Oxygen-Level-Dependent Activation During Within-Scanner Performance of Lumbopelvic Motor Tasks: A Functional Magnetic Resonance Imaging Study (2022)

There are a limited number of neuroimaging investigations into motor control of the lumbopelvic musculature. Most investigation examining motor control of the lumbopelvic musculature utilize transcranial magnetic stimulation (TMS) and focus primarily on the motor cortex. This has resulted in a dearth of knowledge as it relates to how other regions of the brain activate during lumbopelvic movement. Additionally, task-based functional connectivity during lumbopelvic movements has not been well elucidated. Therefore, we used functional magnetic resonance imaging (fMRI) to examine brain activation and ROI-to-ROI task-based functional connectivity in 19 healthy individuals (12 female, age 29.8 ± 4.5 years) during the performance of three lumbopelvic movements: modified bilateral bridge, left unilateral bridge, and right unilateral bridge. The whole brain analysis found robust, bilateral activation within the motor regions of the brain during the bilateral bridge task, and contralateral activation of the motor regions during unilateral bridging tasks. Furthermore, the ROI-to-ROI analysis demonstrated significant connectivity of a motor network that included the supplemental motor area, bilateral precentral gyrus, and bilateral cerebellum regardless of the motor task performed. These data suggest that while whole brain activation reveals unique patterns of activation across the three tasks, functional connectivity is very similar. As motor control of the lumbopelvic area is of high interest to those studying low back pain (LBP), this study can provide a comparison for future research into potential connectivity changes that occur in individuals with LBP.
Localization of Propionibacterium acnes in granulomas supports a possible etiologic link between sarcoidosis and the bacterium (2012)

Sarcoidosis likely results from the exposure of a genetically susceptible subject to an environmental agent, possibly an infectious one. Mycobacterial and propionibacterial organisms are the most commonly implicated potential etiologic agents. Propionibacterium acnes is the only microorganism, however, found in sarcoid lesions by bacterial culture. To evaluate the pathogenic role of this indigenous bacterium, we screened for the bacterium in sarcoid and non-sarcoid tissues using immunohistochemical methods with novel P. acnes-specific monoclonal antibodies that react with cell-membrane-bound lipoteichoic acid (PAB antibody) and ribosome-bound trigger-factor protein (TIG antibody). We examined formalin-fixed and paraffin-embedded samples of lungs and lymph nodes from 196 patients with sarcoidosis, and corresponding control samples from 275 patients with non-sarcoidosis diseases. The samples were mostly from Japanese patients, with 64 lymph node samples from German patients. Immunohistochemistry with PAB antibody revealed small round bodies within sarcoid granulomas in 20/27 (74%) video-assisted thoracic surgery lung samples, 24/50 (48%) transbronchial lung biopsy samples, 71/81 (88%) Japanese lymph node samples, and 34/38 (89%) German lymph node samples. PAB antibody did not react with non-sarcoid granulomas in any of the 45 tuberculosis samples or the 34 samples with sarcoid reaction. In nongranulomatous areas, small round bodies detected by PAB antibody were found in alveolar macrophages of lungs and paracortical macrophages of lymph nodes from many sarcoid and some non-sarcoid patients. Large-spheroidal acid-fast bodies, Hamazaki-Wesenberg bodies, which were found in 50% of sarcoid and 15% of non-sarcoid lymph node samples, reacted with both PAB and TIG antibodies. Electron microscopy revealed that these Hamazaki-Wesenberg bodies had a single bacterial structure and lacked a cell wall with occasional protrusions from the body. The high frequency and specificity of P. acnes, detected by PAB antibody within sarcoid granulomas, indicates that this indigenous bacterium might be the cause of granuloma formation in many sarcoid patients.
Investigating P2X7R-mediated inflammatory signalling in Alzheimer's disease (2021)

BACKGROUND: Neuroinflammation is thought to contribute to the onset and/or progression of Alzheimer´s disease (AD). Astrocytes and microglia sense danger-associated molecules (e.g. Aβ species, ATP) through membrane receptors including the purinergic receptor P2X7 (P2X7R). These interactions activate pro-inflammatory pathways and lead to the release of cytokines that participate in damaging inter-cellular cascades. Inhibition of P2X7R in AD models ameliorates cognitive deficits, pointing towards a neuroprotective effect of P2X7R blockade in vivo potentially associated with the modulation of inflammatory responses. However, the action of P2X7R and downstream signals on tau-mediated neurodegeneration in AD remains elusive. METHOD: We used biochemical and immunohistochemical methods in combination with in-situ hybridization technology (RNAscope) in post-mortem AD and control (Braak 0-VI) BA9 prefrontal cortex to examine early changes in P2X7R expression, determine the spatial pattern of P2X7R activation relative to Aβ and pathological tau accumulation, and evaluate the association between P2X7R and local inflammatory responses. Primary glial and organotypic slice cultures are being used to model glial responses to physiological Aβ species and assess downstream effects on neurons, including alterations in tau and synapse health. RESULT: We found elevated levels of P2X7R from Braak stage II relative to controls accompanied by an increased amyloid burden, synaptic mislocalization of tau and an altered astrocyte reactivity. P2X7R was markedly expressed in astrocytes surrounding AD hallmarks and also in disease-associated microglia neighbouring Aβ plaques. Investigation of inflammatory mediators linked with P2X7R-positive glia revealed higher activation of the NLRP3 inflammasome and NFkB pathways with disease progression. Preliminary data from in vitro and ex vivo models show inflammatory changes and tau redistribution to the synapses following stimulation with oligomeric Aß. CONCLUSION: These data suggest that P2X7R expression and activation are altered in the early stages of AD, prior to marked synapse loss. Ongoing studies aim to determine if the blockade of P2X7R-mediated inflammatory signals has benefits for tau-associated neurodegeneration in AD models.
Hierarchical self-assembly of complex polyhedral microcontainers (2009)

The concept of self-assembly of a two-dimensional (2D) template to a three-dimensional (3D) structure has been suggested as a strategy to enable highly parallel fabrication of complex, patterned microstructures. We have previously studied the surface tension based self-assembly of patterned, microscale polyhedral containers (cubes, square pyramids and tetrahedral frusta). In this paper, we describe the observed hierarchical self-assembly of more complex, patterned polyhedral containers in the form of regular dodecahedra and octahedra. The hierarchical design methodology, combined with the use of self-correction mechanisms, was found to greatly reduce the propagation of self-assembly error that occurs in these more complex systems. It is a highly effective way to mass-produce patterned, complex 3D structures on the microscale and could also facilitate encapsulation of cargo in a parallel and cost-effective manner. Furthermore, the behavior that we have observed may be useful in the assembly of complex systems with large numbers of components.
Attempted hybridization of Zea and Sorghum (1973)

Major Problems in Plant breeding programs are the maintenance of adequate genetic variability and the discovery of desirable traits. Wide Crosses (Interspecific or intergeneric) are potential solution of these problems. Generally Interspecific crosses have been more success than Intergeneric crosses.......
Response Vectors for the Sender and Receiver across Three Pairs (2015)

&lt;p&gt;. Each vertical tick represents a trial; long lines represent behavioral responses. Experimental blocks are marked by a red background; control blocks by a grey background. The blue dashed line represents the block-specific value of the regression coefficient β (see text for details); the red line represents the block-specific value of the mutual information between the two vectors. Note that in all six experimental blocks, the value of β was significantly greater than zero while in all control blocks, the value was zero. Likewise, about 4 to 13 bits of information (see &lt;a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0111332#pone-0111332-t003" target="_blank"&gt;Table 3&lt;/a&gt;) were transferred from one brain to another during experimental blocks, compared to zero bits in the control blocks.&lt;/p&gt;