gebhart/patrepeval huggingface dataset:
Bead‐Based Extracellular Vesicle Analysis Using Flow Cytometry (2020)

Extracellular vesicles (EVs) represent promising circulating biomarkers for cancers, but their high-throughput analyses in clinical settings prove challenging due to lack of simple, fast, and robust EV assays. Here, a bead-based EV assay detected by flow cytometry is described, which integrates EV capture using microbeads with EV protein analyses by flow cytometry. The assay is fast (<4 h for 48 samples), robust, and compatible with conventional flow cytometry instruments for high-throughput EV analysis. With the method, a panel of pancreatic cancer biomarkers in EVs from plasma samples of pancreatic cancer patients is successfully analyzed. The assay is readily translatable to other biomarkers or cancer types and can be run with standard materials on conventional flow cytometers, making it highly flexible and adaptable to diverse research and clinical needs.
Authoring learning environments using an embedded pedagogical model (1996)

For computer-based learning environments to make a major impact on education, we need tools to scale up construction of these systems in order to deploy the technology. On the one hand, commercial authoring tools can be used by educators to ease construction of learning environments. However, these tools provide no guidance in terms of pedagogy. On the other hand, construction tools for intelligent tutoring systems (ITSs) can assist educators in authoring tutoring systems by helping them encode instructional content, but many require authors to specify explicit models such as teaching strategies and student models. Although the resulting software is pedagogically principled, encoding these models is cumbersome. For educators to create quality tutoring programs with relative ease, our approach combines the commitment to pedagogy of the ITS tools, with the ease of authoring of off-the-shelf tools. by embedding a pedagogical model implicitly in a tool. The embedded model ensures that the resulting learning environments will be pedagogically sound, while freeing educators to concentrate on curriculum content. We demonstrate this with a case study of a prototype authoring tool, Investigative Goal-Based Scenario (IGBS) Builder, intended for educators building multimedia learning environments using an embedded pedagogical model of situated instruction.
Enhancing a QUBO solver via data driven multi-start and its application to vehicle routing problem (2022)

Quadratic unconstrained binary optimization (QUBO) models have garnered growing interests as a strong alternative modelling framework for solving combinatorial optimization problems. A wide variety of optimization problems that are usually studied using conventional Operations Research approaches can be formulated as QUBO problems. However, QUBO solvers do not guarantee optimality when solving optimization problems. Instead, obtaining high quality solutions using QUBO solvers entails tuning of multiple parameters. Here in our work, we conjecture that the initial states adjustment method used in QUBO solvers can be improved, where careful tuning will yield overall better results. We propose a data-driven multi-start algorithm that complements the QUBO solver (namely Fujitsu Digital Annealer) in solving constrained optimization problems. We implemented our algorithm on a variety of capacitated vehicle routing problem instances, and empirical results show that different initial state adjustment methods do make a difference in the quality of solutions obtained by the QUBO solver.
Nanovaccine Impact on Dendritic Cells: Transcriptome Analysis Enables New Insights Into Antigen and Adjuvant Effects (2020)

<b>Aim:</b> For vaccines the combination between an antigen and adjuvants are both crucially important to trigger an effective immune response in dendritic cells. Innovative adjuvants like resiquimod or muramyldipeptide have their target protein inside the cell. <b>Materials & methods:</b> Up/downregulation and proteome expression was investigated for the adjuvant combination resiquimod and muramyldipeptide in a soluble form versus encapsulated into a nanocarrier. <b>Results:</b> We found that 1225 genes were upregulated after nanocarrier treatment while 478 genes were downregulated. Most prominent were interferon-stimulated genes with more than 25-times higher expression after nanocarrier treatment, for example <i>RSAD2</i> and <i>ISG15</i>, which were recently found to have antiviral or antitumor effects. <b>Conclusion:</b> Encapsulation gives a more effective upregulation of vaccine-related genes.
Metalloporphyrin heterodimers, molecular bilayer fibers and monolayer leaflets (1996)

Abstract Amphiphilic metalloporphyrins assemble in water to form supramolecular fibers, which have been characterized by transmission electron microscopy. Loose octopus porphyrin fibers can be doped with hydrophobic electron acceptors, metalloporphyrin monomolecular sheets are crystalline. Charge separation occurs in amino porphyrin fibers without added electron acceptors. Bolaamphiphilic porphyrins with four pyridinyl or methyl pyridinium groups in β‐pyrrolic positions have been synthesized. The regioisomer mixture is very soluble in water (≌ 0.1 M) and is ideally suited to form heterodimers with negatively charged ms‐tetrasubstituted porphyrins. Bimetallic porphyrinate pairs are described. The zinc complex is stable down to pH 1.0. Regioisomer II forms well‐defined molecular monolayer leaflets in bulk water at pH 2.5. The surface structure of such monolayers is discussed. It consists of a large cationic plane and hydrophobic edges. Possible applications are discussed shortly.
A hybrid adaptive fuzzy approach for the control of cooperative manipulators (2003)

We examine in this article the complex problem of simultaneous position and internal force control in multiple cooperative manipulator systems. This is done in the presence of unwanted parametric and modeling uncertainties as well as external disturbances. A decentralized adaptive hybrid intelligent control scheme is proposed here. The controller makes use of a multi-input multi-output fuzzy logic engine and a systematic online adaptation mechanism. Unlike conventional adaptive controllers, the proposed one does not require a precise model of the system's dynamics. The performance of the proposed controller is compared to that of a well known conventional adaptive controller.
Temperature dependence of photoinduced valence changes in rubidium manganese hexacyanoferrate probed by Raman spectroscopy (2009)

Temperature dependence of the photoinduced charge transfer process in Rb0.94Mn[Fe(CN)6]0.98·0.2H2O was investigated by observing the pair valence states of adjacent metal ions by Raman spectroscopy. After irradiation by 395 nm light in resonance with ligand-to-metal charge transfer band (CN- → Fe(III)), the photoinduced phase containing low-temperature-like phase was generated as a result of the charge transfer from Mn(II) to Fe(III). Since this process was suppressed upon cooling, it was suggested that the charge transfer process was assisted by a thermal-activated process.
Control of catalytic nanoparticle synthesis: general discussion (2018)

Déborah De Masi opened the discussion of the paper by Laura Prati: Can you explain why you have better results with ruthenium nanoparticles than with bimetallic RuAu NPs? Is it due to a change of the crystallinity of Ru when it is on the surface of Au? Laura Prati replied: There
Using USAF DATCOM to Predict Nonlinear Aerodynamics of Structurally Impaired Aircraft (2009)

This paper presents an approach to predict the nonlinear aerodynamics of a structurally damaged aircraft model based on the engineering level aerodynamic prediction methods, DATCOM. Raw results from the code provide good correlation with wind tunnel data at very low angles of attack, but accuracy deteriorates rapidly as the angle of attack increases. A new methodology is then proposed which combines the experimental results of healthy aircraft with the predicted aerodynamics of the damaged cases, to yield better correlation between experimental and predicted aerodynamic coefficients for damaged aircraft. Three damage- configurations are studied at supersonic speeds. The methodology can be used to quickly generate aerodynamic model for damaged aircraft for simulation and reconfigurable control. Copyright © 2010 Praise Worthy Prize S.r.l. - All rights reserved.
Pulmonary vasodilation in acute pulmonary embolism – a systematic review (2019)

Acute pulmonary embolism is the third most common cause of cardiovascular death. Pulmonary embolism increases right ventricular afterload, which causes right ventricular failure, circulatory collapse and death. Most treatments focus on removal of the mechanical obstruction caused by the embolism, but pulmonary vasoconstriction is a significant contributor to the increased right ventricular afterload and is often left untreated. Pulmonary thromboembolism causes mechanical obstruction of the pulmonary vasculature coupled with a complex interaction between humoral factors from the activated platelets, endothelial effects, reflexes and hypoxia to cause pulmonary vasoconstriction that worsens right ventricular afterload. Vasoconstrictors include serotonin, thromboxane, prostaglandins and endothelins, counterbalanced by vasodilators such as nitric oxide and prostacyclins. Exogenous administration of pulmonary vasodilators in acute pulmonary embolism seems attractive but all come with a risk of systemic vasodilation or worsening of pulmonary ventilation-perfusion mismatch. In animal models of acute pulmonary embolism, modulators of the nitric oxide-cyclic guanosine monophosphate-protein kinase G pathway, endothelin pathway and prostaglandin pathway have been investigated. But only a small number of clinical case reports and prospective clinical trials exist. The aim of this review is to give an overview of the causes of pulmonary embolism-induced pulmonary vasoconstriction and of experimental and human investigations of pulmonary vasodilation in acute pulmonary embolism.
Abstract B39: MYC, a downstream target of BRD-NUT, is necessary and sufficient for the blockade of differentiation in NUT midline carcinoma (2013)

Abstract NUT midline carcinoma (NMC) is an aggressive type of squamous cell carcinoma that is defined by the presence of BRD-NUT fusion oncogenes, which encode chimeric proteins that block differentiation and maintain tumor growth. BRD-NUT oncoproteins contain two bromodomains whose binding to acetylated histones is required for the blockade of differentiation in NMC, but the mechanisms by which BRD-NUT act remain uncertain. Here we provide evidence that MYC is a key downstream target of BRD4-NUT. Expression profiling of NMCs show that the set of genes whose expression is maintained by BRD4-NUT is highly enriched for MYC upregulated genes, and MYC and BRD4-NUT protein expression is strongly correlated in primary NMCs. More directly, we find that BRD4-NUT associates with the MYC promoter and is displaced by acetyl histone mimetic BET inhibitor, JQ1, which prevents binding of BET bromodomains to acetylated histones. BRD4-NUT is also required to maintain MYC expression in NMC cell lines, as shown by a dramatic decrease in MYC expression upon JQ1 treatment and knockdown of BRD4-NUT with NUT specific siRNAs. Moreover, both siRNA knockdown of MYC and a dominant-negative form of MYC, omomyc, induce differentiation of NMC cells. Conversely, differentiation of NMC cells induced by knockdown of BRD4-NUT is abrogated by enforced expression of MYC. Together, these findings suggest that MYC is a downstream target of BRD4-NUT that is required for maintenance of NMC cells in an undifferentiated, proliferative state. Our findings support a model in which dysregulation of MYC by BRD-NUT fusion proteins has a central role in the pathogenesis of NMC. Citation Format: Erica M. Walsh, Adlai R. Grayson, Michael J. Cameron, Jernej Godec, Todd Ashworth, Alexandra B. Aserlind, Hongfang Wang, Gerard Evan, Michael J. Kluk, James E. Bradner, Jon C. Aster, Christopher A. French. MYC, a downstream target of BRD-NUT, is necessary and sufficient for the blockade of differentiation in NUT midline carcinoma. [abstract]. In: Proceedings of the AACR Precision Medicine Series: Synthetic Lethal Approaches to Cancer Vulnerabilities; May 17-20, 2013; Bellevue, WA. Philadelphia (PA): AACR; Mol Cancer Ther 2013;12(5 Suppl):Abstract nr B39.
Adherence to Oral Antihyperglycemic Agents (Dipeptidyl Peptidase-4 Inhibitors and Biguanides) and Its Associated Factors in Patients with Type 2 Diabetes (2019)

To investigate medication adherence to oral antihyperglycemic agents and its associated factors in Japanese type 2 diabetic patients, a questionnaire survey was conducted in 983 adult patients receiving once-daily (QD) or twice-daily (BID) dipeptidyl peptidase-4 inhibitors (DPP-4 inhibitor) or BID biguanides (BG) as monotherapy at 502 pharmacies in Japan. The percentage of patients with good adherence (the proportion of days in which patients took all pills as prescribed in the past 7 days ≥80%) was high (≥90%) in any dosing regimen with no significant difference among the groups. The following factors were identified as associating with good adherence: the longer duration of type 2 diabetes (≥1 year) (p=0.002), "Feeling your disease gets worse if you don't take medications" (p=0.031), "Not forgetting to bring along your medicine when you leave home" (p=0.007), "Feeling anxiety on taking medications for long period of time" (p=0.042), "Neither feeling nor not feeling anxiety on taking medications for a long period of time" (p=0.004), "Never run out of your medicine because you get a refill on time" (p=0.035), and the lower MMAS-4 score (p<0.001). Subgroup analyses revealed that adherence of younger patients (<65 years) with BG (BID) was lower than those with DPP-4 inhibitor (QD) (p=0.021). Additionally, around 60% of patients currently prescribed with QD preferred QD regimen, and ≥80% patients prescribed with BID equally preferred once-weekly or QD regimen, suggesting a large discrepancy exists between their preference and the actual regimen in patients on BID.
Expression of AMPA Receptor Subunit Proteins in Purified Retinal Ganglion Cells (2003)

Purpose
To determine whether α-amino-3-hydroxy-5-methylisoxazole-4-propioate (AMPA) receptor (AMPAR) subunit proteins are expressed in cultured retinal ganglion cells (RGCs).
Investigation of Measurement Conditions of Metastable De-excitation Spectroscopy of MgO Thin Films Used for Plasma Display Panels (2011)

The measurement conditions of metastable de-excitation spectroscopy (MDS) were investigated in order to apply MDS to the study of the electronic structure of MgO films used for plasma display panels (PDPs). It was demonstrated that positive charging induced on the surface of the MgO film of 50 nm thickness during the MDS measurement can be avoided by employing a low flux of primary metastable He atoms. The positive charges accumulated by successive MDS measurements were found to be completely removed by irradiation of keV electrons, in which the neutralization by the re-distribution of secondary electrons emitted by the keV electron irradiation plays an important role [J. Surf. Anal. 12, 284 (2005)]. The changes in the MDS spectra due to the heating treatment of the MgO film, which is one of the processes employed in the fabrication of PDPs, was investigated, and the ionization potential given as a sum of the band gap and the electron affinity was found to decrease with the increase in the heating temperature. Heating the MgO film at 500 °C in vacuum is effective to clean the surface but not sufficient to completely remove contaminations on the surface, and repeating sputtering and heating at 500 °C is required to clean the MgO film surface. The electronic structure of the clean surface of the MgO film of 50 nm thickness was found to be the same as that of 500 nm thickness, the thickness of which is a typical value for the MgO film used in PDPs. This result revealed that 50 nm thick MgO films, in which effects of charging is much less than those for 500 nm thick films, can be used to evaluate the electronic structure of the MgO film surface. The present results confirmed that MDS is one of the effective techniques to evaluate properties of MgO films used for PDPs.
Generating memory with vaccination (2009)

The goal of vaccination is to induce long-lasting protective immune memory. Although most vaccines induce good memory responses, the type of memory induced by different vaccines may be considerably different. In addition, memory responses to the same vaccine may be influenced by age, environmental and genetic factors. Results emerging from detailed and integrated profiling of immune-responses to natural infection or vaccination suggest that the type and duration of immune memory are largely determined by the magnitude and complexity of innate immune signals that imprint the acquired immune primary responses. Here we summarize results obtained from analyzing human immune memory responses to different types of vaccines. We will also discuss how extending clinical investigation to events occurring early after vaccination can help identify early predictive markers of protective memory and thus contribute to faster development of better and safer vaccines.
Neurogenic Bladder: The Effect of Neurologic Lesions on Micturition (2007)

This chapter contains section titled: Suggested Reading
Probabilistic 3D Contrast-Ultrasound Tractography Based on a a Convective-Dispersion Finite-Element Scheme (2018)

Three-dimensional dynamic contrast-enhanced ultrasound imaging opens the door for the characterisation of vascular networks. This work focusses on a stable finite-element algorithm to retrieve local properties of the vascularity based on the convection-dispersion equation. We show that, even at low spatial and temporal resolution, local convective-dispersion behaviour can be captured. Moreover, we present a probabilistic tractography strategy to visualise convective pathways and provide an in-vivo example.
Anticholeretic effect of somatostatin in anesthetized dogs (1978)

Summary. Somatostatin, 0.2‐1.0 β g . kg ‐l min ‐1 , was administered i.v. in 5 anesthetized dogs. Following 9‐min infusions, hepatic bile output was found to decrease by approximately 50% after a latency of 6 min. The mode of action suggests that somatostatin inhibits hormone‐induced bile output.
A Learning Framework for Robust Bin Picking by Customized Grippers (2018)

Customized grippers have specifically designed fingers to increase the contact area with the workpieces and improve the grasp robustness. However, grasp planning for customized grippers is challenging due to the object variations, surface contacts and structural constraints of the grippers. In this paper, we propose a learning framework to plan robust grasps for customized grippers in real-time. The learning framework contains a low-level optimization-based planner to search for optimal grasps locally under object shape variations, and a high-level learning-based explorer to learn the grasp exploration based on previous grasp experience. The optimization-based planner uses an iterative surface fitting (ISF) to simultaneously search for optimal gripper transformation and finger displacement by minimizing the surface fitting error. The high-level learning-based explorer trains a region-based convolutional neural network (R-CNN) to propose good optimization regions, which avoids ISF getting stuck in bad local optima and improves the collision avoidance performance. The proposed learning framework with RCNN-ISF is able to consider the structural constraints of the gripper, learn grasp exploration strategy from previous experience, and plan optimal grasps in clutter environment in real-time. The effectiveness of the algorithm is verified by experiments.
COMPACT FUSION PUMP SYSTEM OF CPB AND PCPS (2001)

PURPOSE CPB and/or PCPS are important tools in circulatory support in proportion to the patients' situation. In the execution of CPB for open heart surgery, complicated works, large equipments and large area have been required PCPS using preconnected circuit can be easily and quickly set-up. Many works are needed for operation of these 2 systems and for conversion between these 2 systems. We have developed a new compact fusion system of CPB and PCPS to dissolve these problems. METHOD 1. A preconnected CPB circuit was used. 2. All devices for CPB - 1 centrifugal pump controller, 2 suction roller pumps, digital monitor for vital signs, camera for operation field, ACT measuring device and blood gas analyzer - were compacted to a rack of which base area is 55 × 40cm. 3. A venous bypass circuit to the original CPB circuit, which enabled us to change drainage mode of venous blood by gravity or by negative pressure easily. 4. An additional module for selective cerebral perfusion was available with another 2 small roller pumps. RESULT All set-up work from the opening of box to starting CPB could be done within 3 minutes by one staff. It was possible to change the mode of extracorporeal circulation, CPB or PCPS, easily. It was possible to manage all the patients in various situation with this compact CPB circuit without modification at use. CONCLUSIONS New compact fusion pump system which adopted the merit of both CPB and PCPS enabled us to manage all the various situation only with one core circuit, quickly, without expert staff.
Long-term ingrowth and apposition of porous hydroxylapatite implants (1997)

Bone implant materials are often used to fill in bone gaps that frequently result from orthognathic and craniofacial reconstruction. The substrate hydroxylapatite (HA) is commonly implanted into the bone voids, resulting from these conditions due to its established biocompatibility and osteoconductive properties. The porous structure of HA provides a three-dimensional guideline for fibrovascular ingrowth, facilitating the process that ultimately results in the deposition of new bone. Porous HA (Interpore, 200) implants were implanted in the mandible or maxilla of nine humans and removed after 14-30 months (19.1-month mean). There was no evidence of an inflammatory response. The sample composition and apposition against the implant were determined using point counting and a digitizing tablet and software. Percent ingrowth in available space (%IAS) was defined as %Bone/(%Bone + %Void). A new measure of implant saturation (%IAS-%Apposition of bone) was established to help determine the fundamental manner in which long-term HA implants incorporate bone. In the mean, the samples were composed of 27% bone, 21% void, and 53% implant. The apposition percentages averaged 60% bone, 16% void, and 24% soft tissue. The %IAS averaged 58%, and implant saturation averaged -3%, indicating that a near-balance between the implant and surrounding bone has been established.