gebhart/patrepeval huggingface dataset:
Virtualized Reality: Perspectives on 4D Digitization of Dynamic Events (2007)

Digitally recording dynamic events, such as sporting events, for experiencing in a spatio-temporally distant and arbitrary setting requires 4D capture: three dimensions for their geometry and appearance over the fourth dimension of time. Today's computer vision techniques make 4D capture possible. The virtualized reality system serves as an example on the general problem of digitizing dynamic events. In this article, we present the virtualized reality system's details from a historical perspective
Transdifferentiation of glioblastoma cells into vascular endothelial cells (2011)

Glioblastoma (GBM) is the most malignant brain tumor and is highly resistant to intensive combination therapies and anti-VEGF therapies. To assess the resistance mechanism to anti-VEGF therapy, we examined the vessels of GBMs in tumors that were induced by the transduction of p53(+/-) heterozygous mice with lentiviral vectors containing oncogenes and the marker GFP in the hippocampus of GFAP-Cre recombinase (Cre) mice. We were surprised to observe GFP(+) vascular endothelial cells (ECs). Transplantation of mouse GBM cells revealed that the tumor-derived endothelial cells (TDECs) originated from tumor-initiating cells and did not result from cell fusion of ECs and tumor cells. An in vitro differentiation assay suggested that hypoxia is an important factor in the differentiation of tumor cells to ECs and is independent of VEGF. TDEC formation was not only resistant to an anti-VEGF receptor inhibitor in mouse GBMs but it led to an increase in their frequency. A xenograft model of human GBM spheres from clinical specimens and direct clinical samples from patients with GBM also showed the presence of TDECs. We suggest that the TDEC is an important player in the resistance to anti-VEGF therapy, and hence a potential target for GBM therapy.
Asthma Therapies Revisited: What Have We Learned? (2009)

Asthma is a heterogenous disorder related to numerous biologic, immunologic, and physiologic components that generate multiple clinical phenotypes. Further, genetic and environmental factors interact in ways that produce variability in both disease onset and severity and differential expression based on both the age and sex of the patient. Thus, the natural history of asthma is complex in terms of disease expression, remission, relapse, and progression. As such, therapy for asthma is complicated and has been approached from the standpoints of primary, secondary, and tertiary prevention. Presently, asthma cannot be cured but can be controlled in most patients, an indication that most of the success clinical research strategies have realized has been in the area of tertiary prevention. Since for many adult patients with asthma their disease had its roots in early life, much recent research has focused on events during early childhood that can be linked to subsequent asthma development with the hopes of creating appropriate interventions to alter its natural history of expression. These research approaches can be categorized into three questions. Who is the right patient to treat? When is the right time to begin treatment? And finally, what is the appropriate treatment to prescribe?
AlphaMbeta2 (CD11b/CD18, Mac-1) integrin activation by a unique monoclonal antibody to alphaM I domain that is divalent cation-sensitive. (2000)

The beta2 (CD18) leukocyte integrins play a key role in normal and inflammatory immune responses. In resting leukocytes, these receptors do not bind ligands. However, when leukocytes are exposed to an appropriate agonist, high-affinity ligand binding is achieved, presumably as a result of conformational changes in the integrin. In this study, we describe a novel monoclonal antibody, mAb 6C1, directed against the alphaM subunit, which directly induces adhesion of alphaMbeta2-transfected CHO cells to fibrinogen, ICAM-1, and iC3b. Induction of binding could also be accomplished by monovalent Fab fragments of mAb 6C1 at concentrations similar to that observed with intact IgG, demonstrating stimulation of adhesion was not because of receptor cross-linking at the cell surface. The binding of mAb 6C1 induces conformational changes in the receptor, as evidenced by the expression of an "activation reporter" epitope recognized by mAb 24. The binding of mAb 6C1 is modulated by divalent cations. Mn2+ promoted high levels of 6C1 binding, and Mg2+ supported low levels of binding, however Ca2+ failed to support binding. A unique distinction of mAb 6C1 is localization of its epitope to the alphaM I domain. The alphaM I domain is essential for ligand binding, can directly bind divalent cations, and participates in the regulation of alphaMbeta2 ligand-binding affinity. Thus, these studies have identified a novel alphaM I domain activation epitope of alphaMbeta2 and support the idea that the I domain modulates the activational state of the beta2 integrins.
BRET3: a red‐shifted bioluminescence resonance energy transfer (BRET)‐based integrated platform for imaging protein‐protein interactions from single live cells and living animals (2009)

Taking advantage of the bioluminescence resonance energy transfer (BRET) phenomenon, we report the development of a highly photon-efficient, self-illuminating fusion protein combining a mutant red fluorescent protein (mOrange) and a mutant Renilla reniformis luciferase (RLuc8). This new BRET fusion protein (BRET3) exhibits severalfold improvement in light intensity in comparison with existing BRET fusion proteins. BRET3 also exhibits the most red-shifted light output (564-nm peak wavelength) of any reported bioluminescent protein that utilizes its natural substrate coelenterazine, a benefit of which is demonstrated at various tissue depths in small animals. The imaging utility of BRET3 at the single-cell level is demonstrated using an intramolecular sensor incorporating two mammalian target of rapamycin pathway proteins (FKBP12 and FRB) that dimerize only in the presence of rapamycin. With its increased photon intensity, red-shifted light output, and good spectral resolution (approximately 85 nm), BRET3 shows improved spatial and temporal resolution for measuring intracellular events in single cells and in living small animal models. The development of further BRET3-based assays will allow imaging of protein-protein interactions using a single assay directly scalable from intact living cells to small living subjects, allowing accelerated drug discovery.
A Silicon CMOS Monolithic RF and Microwave Switching Element (1997)

RF and microwave switching elements using silicon CMOS technology are being investigated and show promise as an alternative to the traditional PIN diode and GaAs MESFET devices. Silicon CMOS RF switching elements are attractive because of their potential application in all-silicon monolithic CMOS solutions for completely integrated baseband and RF functions in low cost wireless, mobile satellite and personal communications systems. Initial results of an SPDT switch show 1 dB insertioni loss and 44 dB isolation at 200 MHz on a developmental device with switch performance characterized to 2.0 GHz.
Potential of human induced pluripotent stem cells in studies of liver disease (2014)

Liver disease is a leading cause of death in the Western world. However, our insight into the underlying disease mechanisms and the development of novel therapeutic agents has been hindered by limited availability of primary tissue, intraspecies variability associated with the use of animal models, and reduced long-term viability of isolated and diseased liver cells. The emergence of human induced pluripotent stem cells and differentiation protocols to generate hepatocyte-like cells has opened the possibility of addressing these issues. Here, we discuss the recent progress and potential in the production of various cell types constituting the liver and their applications to model liver diseases and test drug toxicity in vitro.
OATL1, a novel autophagosome-resident Rab33B-GAP, regulates autophagosomal maturation (2011)

Macroautophagy is a bulk degradation system conserved in all eukaryotic cells. A ubiquitin-like protein, Atg8, and its homologues are essential for autophagosome formation and act as a landmark for selective autophagy of aggregated proteins and damaged organelles. In this study, we report evidence demonstrating that OATL1, a putative Rab guanosine triphosphatase-activating protein (GAP), is a novel binding partner of Atg8 homologues in mammalian cells. OATL1 is recruited to isolation membranes and autophagosomes through direct interaction with Atg8 homologues and is involved in the fusion between autophagosomes and lysosomes through its GAP activity. We further provide evidence that Rab33B, an Atg16L1-binding protein, is a target substrate of OATL1 and is involved in the fusion between autophagosomes and lysosomes, the same as OATL1. Because both its GAP activity and its Atg8 homologue-binding activity are required for OATL1 to function, we propose a model that OATL1 uses Atg8 homologues as a scaffold to exert its GAP activity and to regulate autophagosomal maturation.
Circuit QED and engineering charge-based superconducting qubits (2009)

The last two decades have seen tremendous advances in our ability to generate and manipulate quantum coherence in mesoscopic superconducting circuits. These advances have opened up the study of quantum optics of microwave photons in superconducting circuits as well as providing important hardware for the manipulation of quantum information. Focusing primarily on charge-based qubits, we provide a brief overview of these developments and discuss the present state of the art. We also survey the remarkable progress that has been made in realizing circuit quantum electrodynamics (QED) in which superconducting artificial atoms are strongly coupled to individual microwave photons.
Soluble TNF receptors in vitreoretinal proliferative disease. (2001)

These observations suggest the existence of TNF inhibitory mechanisms within the eye during retinal processes of inflammation and angiogenesis. That high vitreous levels of sTNF-Rs relate to severity of retinopathy suggests that these molecules may constitute reactive products of inflammation. Effective control of TNFalpha activity by sTNF-Rs within the retinal microenvironment may determine the outcome and severity of retinal proliferative conditions.
Minimizing observer metamerism in display systems (2009)

Abstract Observer metamerism has long been known to be an issue of concern for color engineers. With the advent and mass proliferation of narrow‐band display devices, this article addresses the issue of observer metamerism and puts it in the context of first understanding the implication of interobserver variations in the color matching functions (CMFs) and additionally designing the ideal set of primary illuminant spectral power distributions (SPDs) such that observer metamerism is minimized. The article also suggests the use of the Full Width Half Maximum (FWHM) and the number of modes (peaks) in the primary SPDs as a means of assessing the susceptibility to observer‐to‐observer variations between various modern display technologies. © 2009 Wiley Periodicals, Inc. Col Res Appl, 34, 391–398, 2009
The design and implementation of a log-structured file system (1991)

This paper presents a new technique for disk storage management called a log-structured file system. A log-structured file system writes all modifications to disk sequentially in a log-like structure, thereby speeding up both file writing and crash recovery. The log is the only structure on disk; it contains indexing information so that files can be read back from the log efficiently. In order to maintain large free areas on disk for fast writing, we divide the log into segments and use a segment cleaner to compress the live information from heavily fragmented segments. We present a series of simulations that demonstrate the efficiency of a simple cleaning policy based on cost and benefit. We have implemented a prototype log-structured file system called Sprite LFS; it outperforms current Unix file systems by an order of magnitude for small-file writes while matching or exceeding Unix performance for reads and large writes. Even when the overhead for cleaning is included, Sprite LFS can use 70% of the disk bandwidth for writing, whereas Unix file systems typically can use only 5--10%.
The Role of Annexin A5 in the Modulation of the Immune Response Against Dying and Dead Cells (2007)

Annexins are characterized by the ability to bind phospholipids of membranes in the presence of Ca2+. Annexin A5 represents a typical member of this protein family and is a natural occurring highly specific ligand for phosphatidylserine (PS). The exposure of PS is one major "eat me" signal for phagocytes of apoptotic and necrotic cells. Apoptotic cells are normally cleared via an anti-inflammatory pathway. In contrast, the uptake and removal of necrotic cells normally involves inflammation and an immune response. Interestingly, the lack of endogenous annexin A5 also leads to a reduced inflammatory potential of necrotic cells. Annexin A5 may interfere in vivo with the immunosuppressive effects of apoptotic cells since it preferentially binds PS with high affinity and inhibits apoptotic cell uptake by macrophages. In this review we focus on how defects in the clearance process can lead to chronic autoimmunity. Furthermore, the role of annexin A5 as important adjuvant for apoptotic cell-based tumour vaccines is discussed. The mechanism of how the immunogenicity of apoptotic cells can be restored by blocking their PS-dependent clearance is outlined in detail. Taken together, annexin A5 is an important modulator of the immune response against PS-exposing particles like apoptotic cells, necrotic cells, and certain viruses.
Formation and Morphology of Calcium Sulfate Nanoparticles and Nanowires in Water-in-Oil Microemulsions (1999)

Nanosized insoluble metal sulfate aggregates, predominantly CaSO4, have been prepared in a variety of water-in-oil (w/o) microemulsions stabilized by either nonionic or ionic surfactants. Particles were visualized by transmission electron microscopy (TEM) and the identities of the aggregates confirmed by energy-dispersive X-ray analysis (EDXA). BaSO4 prepared in n-heptane microemulsions stabilized by the sodium salt of Aerosol-OT (AOT) appeared as slightly irregular aggregates, 8−50 nm in diameter. In contrast, BaSO4 in n-heptane microemulsions stabilized by ammonium diethylhexyl phosphate (NH4DEHP) existed in the form of submicron-sized "flocs" comprising nanospheres 5−7 nm in diameter. BaSO4 synthesis in cyclohexane microemulsions stabilized by tetraethylene glycol monododecyl ether (C12E4), produced discrete essentially monodisperse nanospheres 8−10 nm in diameter. A wider variety of morphologies were encountered in the synthesis of CaSO4 which produced nanospheres, ellipsoids, rods, nanohairs, nanowires, and nanobundles. The greatest structural diversity was obtained in systems stabilized by C12E4 where product morphology was sensitive to the mole ratio of water to surfactant (ω0) in the reaction medium, the overall water content, surfactant concentration, reactant concentration, and incubation time. The growth of CaSO4 nanowires was monitored as a function of time and was fastest at high overall reactant concentrations. Nanowires and nanobundles were often observed to span completely the individual sections of the copper grid used in TEM measurements, indicating lateral growth potential on the order of hundreds of microns. In contrast, CaSO4 formed in microemulsion systems stabilized by AOT in dodecane yielded only nanospheres whose size was largely independent of composition and reaction conditions.
Egan's Fundamentals of Respiratory Care (1990)

Section 1: Foundations of Respiratory Care. Quality Respiratory Care. Patient Safety, Communication, And Recordkeeping. Principles of Infection Control. Ethical and Legal Implications of Practice. Section 2: Technological Bases for Respiratory Care. Physical Principles in Respiratory Care. Computers Applications in Respiratory Care. Section 3: Applied Anatomy & Physiology. The Respiratory Care System. The Cardiovascular System. Ventilation. Oxygen Transport and Delivery (Gas Exchange). Solutions, Body Fluids, And Electrolytes. Acid-Base Balance. Regulation of Breathing. Section 4: Assessment of Respiratory Disorders. Bedside Assessment. Ecg and Laboratory Assessment. Analysis and Monitoring of Gas Exchange. Pulmonary Function Testing. Thoracic Imaging: Chest X-Ray, Ct, And Mri. Section 5: Synopsis of Cardiopulmonary Disease. Pulmonary Infections. Obstructive Lung Disease: Copd, Asthma, Bronchiectasis, And Related Conditions. Interstitial Diseases. Pleural Disease. Pulmonary Vascular Disease. Acute Lung Injury, Pulmonary Edema, And Multiple System Organ Failure. Lung Neoplasms. Neuromuscular and Other Diseases of the Chest Wall. Disorders of Sleep. Section 6: Basic Therapeutics. Airway Pharmacology. Airway Management. Emergency Life Support. Humidity and Bland Aerosol Therapy. Aerosol Drug Administration. Storage and Delivery of Medical Gases. Medical Gas Therapy. Lung Expansion Therapy. Airway Clearance Techniques. Section 7: Acute and Critical Care. Respiratory Therapy and the Need for Ventilatory Support. Ventilatory Modes and Functions. Physics/Physiology of Ventilatory Support. Initiating and Adjusting Ventilatory Support. Patient Management and Monitoring. Discontinuing Ventilatory Support. Neonatal and Pediatric Critical Care. Section 8: Preventive and Long Term Care. Patient Education and Health Promotion. Nutritional Aspects of Health and Disease. Cardiopulmonary Rehabilitation. Respiratory Care in Alternative Settings. Appendices.
The eosinophil and airway remodelling in asthma (2010)

Several clinical and experimental studies indicate that eosinophils contribute to airways remodelling not only through their secretion of cationic proteins such as ECP and cytokines such as TGF-beta1, but also through interactions with mast cells and epithelial cells.
The Arabidopsis Cupin Domain Protein AtPirin1 Interacts with the G Protein α-Subunit GPA1 and Regulates Seed Germination and Early Seedling Development (2003)

Heterotrimeric G proteins are implicated in diverse signaling processes in plants, but the molecular mechanisms of their function are largely unknown. Finding G protein effectors and regulatory proteins can help in understanding the roles of these signal transduction proteins in plants. A yeast two-hybrid screen was performed to search for proteins that interact with Arabidopsis G protein α-subunit (GPA1). One of the identified GPA1-interacting proteins is the cupin-domain protein AtPirin1. Pirin is a recently defined protein found because of its ability to interact with a CCAAT box binding transcription factor. The GPA1–AtPirin1 interaction was confirmed in an in vitro binding assay. We characterized two atpirin1 T-DNA insertional mutants and established that they display a set of phenotypes similar to those of gpa1 mutants, including reduced germination levels in the absence of stratification and an abscisic acid–imposed delay in germination and early seedling development. These data indicate that AtPirin1 likely functions immediately downstream of GPA1 in regulating seed germination and early seedling development.
Microbial Community Development in a Dynamic Gut Model Is Reproducible, Colon Region Specific, and Selective forBacteroidetesandClostridiumCluster IX (2010)

Dynamic, multicompartment in vitro gastrointestinal simulators are often used to monitor gut microbial dynamics and activity. These reactors need to harbor a microbial community that is stable upon inoculation, colon region specific, and relevant to in vivo conditions. Together with the reproducibility of the colonization process, these criteria are often overlooked when the modulatory properties from different treatments are compared. We therefore investigated the microbial colonization process in two identical simulators of the human intestinal microbial ecosystem (SHIME), simultaneously inoculated with the same human fecal microbiota with a high-resolution phylogenetic microarray: the human intestinal tract chip (HITChip). Following inoculation of the in vitro colon compartments, microbial community composition reached steady state after 2 weeks, whereas 3 weeks were required to reach functional stability. This dynamic colonization process was reproducible in both SHIME units and resulted in highly diverse microbial communities which were colon region specific, with the proximal regions harboring saccharolytic microbes (e.g., Bacteroides spp. and Eubacterium spp.) and the distal regions harboring mucin-degrading microbes (e.g., Akkermansia spp.). Importantly, the shift from an in vivo to an in vitro environment resulted in an increased Bacteroidetes/Firmicutes ratio, whereas Clostridium cluster IX (propionate producers) was enriched compared to clusters IV and XIVa (butyrate producers). This was supported by proportionally higher in vitro propionate concentrations. In conclusion, high-resolution analysis of in vitro-cultured gut microbiota offers new insight on the microbial colonization process and indicates the importance of digestive parameters that may be crucial in the development of new in vitro models.
Oxidative Stress and Redox Modulation Potential in Type 1 Diabetes (2011)

Redox reactions are imperative to preserving cellular metabolism yet must be strictly regulated. Imbalances between reactive oxygen species (ROS) and antioxidants can initiate oxidative stress, which without proper resolve, can manifest into disease. In type 1 diabetes (T1D), T-cell-mediated autoimmune destruction of pancreatic β-cells is secondary to the primary invasion of macrophages and dendritic cells (DCs) into the islets. Macrophages/DCs, however, are activated by intercellular ROS from resident pancreatic phagocytes and intracellular ROS formed after receptor-ligand interactions via redox-dependent transcription factors such as NF-κB. Activated macrophages/DCs ferry β-cell antigens specifically to pancreatic lymph nodes, where they trigger reactive T cells through synapse formation and secretion of proinflammatory cytokines and more ROS. ROS generation, therefore, is pivotal in formulating both innate and adaptive immune responses accountable for islet cell autoimmunity. The importance of ROS/oxidative stress as well as potential for redox modulation in the context of T1D will be discussed.