gebhart/patrepeval huggingface dataset:
Essential Regulation of CNS Angiogenesis by the Orphan G Protein–Coupled Receptor GPR124 (2010)

The orphan G protein-coupled receptor (GPCR) GPR124/tumor endothelial marker 5 is highly expressed in central nervous system (CNS) endothelium. Here, we show that complete null or endothelial-specific GPR124 deletion resulted in embryonic lethality from CNS-specific angiogenesis arrest in forebrain and neural tube. Conversely, GPR124 overexpression throughout all adult vascular beds produced CNS-specific hyperproliferative vascular malformations. In vivo, GPR124 functioned cell-autonomously in endothelium to regulate sprouting, migration, and developmental expression of the blood-brain barrier marker Glut1, whereas in vitro, GPR124 mediated Cdc42-dependent directional migration to forebrain-derived, vascular endothelial growth factor-independent cues. Our results demonstrate CNS-specific angiogenesis regulation by an endothelial receptor and illuminate functions of the poorly understood adhesion GPCR subfamily. Further, the functional tropism of GPR124 marks this receptor as a therapeutic target for CNS-related vascular pathologies.
Differential Phospholipid Substrates and Directional Transport by ATP-binding Cassette Proteins ABCA1, ABCA7, and ABCA4 and Disease-causing Mutants (2013)

ABCA1, ABCA7, and ABCA4 are members of the ABCA subfamily of ATP-binding cassette transporters that share extensive sequence and structural similarity. Mutations in ABCA1 cause Tangier disease characterized by defective cholesterol homeostasis and high density lipoprotein (HDL) deficiency. Mutations in ABCA4 are responsible for Stargardt disease, a degenerative disorder associated with severe loss in central vision. Although cell-based studies have implicated ABCA proteins in lipid transport, the substrates and direction of transport have not been firmly established. We have purified and reconstituted ABCA1, ABCA7, and ABCA4 into liposomes for fluorescent-lipid transport studies. ABCA1 actively exported or flipped phosphatidylcholine, phosphatidylserine, and sphingomyelin from the cytoplasmic to the exocytoplasmic leaflet of membranes, whereas ABCA7 preferentially exported phosphatidylserine. In contrast, ABCA4 transported phosphatidylethanolamine in the reverse direction. The same phospholipids stimulated the ATPase activity of these ABCA transporters. The transport and ATPase activities of ABCA1 and ABCA4 were reduced by 25% in the presence of 20% cholesterol. Nine ABCA1 Tangier mutants and the corresponding ABCA4 Stargardt mutants showed significantly reduced phospholipid transport activity and subcellular mislocalization. These studies provide the first direct evidence for ABCA1 and ABCA7 functioning as phospholipid transporters and suggest that this activity is an essential step in the loading of apoA-1 with phospholipids for HDL formation.
The Role of Biofilms in Airway Disease (2003)

Biofilms are defined as collections of microorganisms attached to a surface and embedded in a matrix. This attached state is the primary mode of microbial growth in the environment and within the body. However, biofilms represent a significant clinical concern because they are recalcitrant to antimicrobial agents. This is particularly troublesome in the respiratory tract where biofilms clearly complicate traditional therapies. This review focuses on the biology, development, and antimicrobial resistance properties of biofilms formed by three significant respiratory tract pathogens; Pseudomonas aeruginosa, Staphylococcus aureus, and Haemophilus influenzae. Recent research has begun to shed light on the molecular events governing biofilm formation and antimicrobial resistance mechanisms with these organisms. A deeper understanding of these concepts will be necessary for the development of rational strategies to control biofilms in the future.
Miniaturization and Geometry Optimization of a Polymer-Based Rectilinear Ion Trap (2007)

The fabrication, operation, and characterization of a polymer-based rectilinear ion trap mass analyzer is discussed. A novel, fast prototyping technique, stereolithography (SLA)-based fabrication, traditionally reserved for end use production parts and to fabricate master molds for rubber products, is applied here as a tool to create precise, arbitrary geometries. Taking full advantage of the SLA methodology, an open corner, polymer-based ion trap has been fabricated and tested. The use of a custom resin, Nanoform 15120 (DSM Somos, New Castle, DE), has resulted in a polymer with high heat deflection temperature and greater structural stability at higher temperatures and lower capacitance. The mass analyzer was mounted in a polymer holder and tested in a custom vacuum system using modified LCQ Duo (Thermo Fisher Corp.) electronics. The resolution, mass/charge range, and MS/MS capabilities were examined using electrospray ionization as well as atmospheric pressure chemical ionization. In the course of this study, three traps of different sizes were fabricated, beginning with a "full size" device measuring 10 x 8 x 50 mm. The next two traps were scaled down by linear factors of a half and a third. SLA is shown to allow fabrication of light, small rectilinear ion traps, which are less expensive and have the same performance as traditional machined devices of the same size. In addition, smaller traps can be built just as easily, and they show unit mass resolution to mass 300, tandem mass spectrometry capabilities, and low power consumption.
The novel BTB-kelch protein, KBTBD8, is located in the Golgi apparatus and translocates to the spindle apparatus during mitosis (2013)

Proteins of the BTB-kelch family are known to be involved in multiple biological processes such as migration, cytoskeleton arrangement, regulation of cell morphology, protein ubiquitination and gene expression. KBTBD8 is a new member of this family. The gene was found in a comparative transcriptome analysis of pluripotent stem cells and was therefore suggested to play a role in the regulation of pluripotency. Comparative analysis of the gene and protein sequences revealed a high conservation throughout evolution especially in the characteristic domains of BTB, BACK and kelch. We identified the Golgi apparatus as the subcellular localization of the KBTBD8 protein in non-dividing cells and could show that KBTBD8 co-localizes with α-tubulin on the spindle apparatus of mitotic cells suggesting a role in cell proliferation. In conclusion, KBTBD8 is a new member of the BTB-kelch superfamily that is located in the Golgi apparatus and translocates to the spindle apparatus during mitosis.
Random Forest Architectures on FPGA for Multiple Applications (2017)

A random forest is a widely used machine learning classifier. An FPGA is a good platform for performance acceleration of random forests due to their inherent concurrent memory accesses and computational parallelism. Amortizing the cost of an FPGA implementation among different applications is desirable, but the context switch time between applications significantly influences the forest architecture. Several architectures for random forests implemented within an FPGA are described, and the area-reconfiguration tradeoffs that determine the suitability of each for multiple applications are characterized. We show that each architecture can maximize the area utilization efficiency of an FPGA given a constraint on the context switch time.
Immunohistochemical expression of T, Tn and sialyl-Tn antigens and clinical outcome in human breast carcinoma. (2001)

Our data suggested that the expression of T, Tn and sialyl-Tn antigens does not appear to predict the outcome of patients with breast carcinoma in a long-term run. Moreover, the findings signified a potential value for a negative or low Tn antigen expression in prognostic stratification of breast carcinomas.
Medical oncology management of advanced hepatocellular carcinoma 2019: a reality check (2019)

In terms of global cancer-related deaths, hepatocellular carcinoma (HCC) has the fourth highest mortality rate. Up until 2017, treatment of advanced HCC was largely limited to sorafenib, an oral tyrosine kinase inhibitor, with little to no success in the development of alternative treatment options. However, in the past two years, there has been an unprecedented increase in both the number and type of treatment options available for HCC. As of 2019, the US FDA has approved four oral tyrosine kinase inhibitors, two immune checkpoint inhibitors, and one anti-angiogenesis antibody for the treatment of HCC. Even with this new variety, systemic treatment of advanced HCC remains largely unsatisfactory, and the median survival rate stands at approximately one year. The expected breakthrough of using immune checkpoint inhibitors in advanced HCC did not materialize in 2019. The use of immune checkpoint inhibitors in conjunction with oral tyrosine kinase inhibitors or anti-angiogenesis medications is the current clinical research trend, the results of which are eagerly anticipated. Despite limited progress in survival, HCC research is currently experiencing a period of growth and innovation, and there is hope for significant advances in the treatment of advanced HCC as the field continues to develop.
Mechanistic Studies of Substrate-assisted Inhibition of Ubiquitin-activating Enzyme by Adenosine Sulfamate Analogues (2011)

Ubiquitin-activating enzyme (UAE or E1) activates ubiquitin via an adenylate intermediate and catalyzes its transfer to a ubiquitin-conjugating enzyme (E2). MLN4924 is an adenosine sulfamate analogue that was identified as a selective, mechanism-based inhibitor of NEDD8-activating enzyme (NAE), another E1 enzyme, by forming a NEDD8-MLN4924 adduct that tightly binds at the active site of NAE, a novel mechanism termed substrate-assisted inhibition (Brownell, J. E., Sintchak, M. D., Gavin, J. M., Liao, H., Bruzzese, F. J., Bump, N. J., Soucy, T. A., Milhollen, M. A., Yang, X., Burkhardt, A. L., Ma, J., Loke, H. K., Lingaraj, T., Wu, D., Hamman, K. B., Spelman, J. J., Cullis, C. A., Langston, S. P., Vyskocil, S., Sells, T. B., Mallender, W. D., Visiers, I., Li, P., Claiborne, C. F., Rolfe, M., Bolen, J. B., and Dick, L. R. (2010) Mol. Cell 37, 102-111). In the present study, substrate-assisted inhibition of human UAE (Ube1) by another adenosine sulfamate analogue, 5'-O-sulfamoyl-N(6)-[(1S)-2,3-dihydro-1H-inden-1-yl]-adenosine (Compound I), a nonselective E1 inhibitor, was characterized. Compound I inhibited UAE-dependent ATP-PP(i) exchange activity, caused loss of UAE thioester, and inhibited E1-E2 transthiolation in a dose-dependent manner. Mechanistic studies on Compound I and its purified ubiquitin adduct demonstrate that the proposed substrate-assisted inhibition via covalent adduct formation is entirely consistent with the three-step ubiquitin activation process and that the adduct is formed via nucleophilic attack of UAE thioester by the sulfamate group of Compound I after completion of step 2. Kinetic and affinity analysis of Compound I, MLN4924, and their purified ubiquitin adducts suggest that both the rate of adduct formation and the affinity between the adduct and E1 contribute to the overall potency. Because all E1s are thought to use a similar mechanism to activate their cognate ubiquitin-like proteins, the substrate-assisted inhibition by adenosine sulfamate analogues represents a promising strategy to develop potent and selective E1 inhibitors that can modulate diverse biological pathways.
Clinical Procedures in Anesthesia and Intensive Care (1992)

Part 1: Preparing and using the anaesthesia machine and monitors. Part 2: Respiratory procedures. Part 3: Cardiovascular procedures. Part 4: central nervous system procedures. Part 5: Peripheral nerve procedures. Part 6: Gastrointestinal, obstetrical, and renal procedures.
Bone formation enhanced by induction: Bone growth in titanium implants in rats (1985)

Bone-inducing materials have been investigated for the purpose of augmenting bone formation in implants made of porous fiber titanium. The bone-inducing materials used were: (1) Bone from the iliac crest of inbred rats (isografts), (2) Antigen-extracted, autolyzed, demineralized bone from outbred rats (AAA bone a.m. Urist), and (3) AAA bone combined with bone marrow from inbred rats. Tubes of fiber titanium were packed with bone-inducing materials and implanted in the back musculature of inbred rats. Bone formation was assessed by labelling with 3H-proline (collagen synthesis) and 47Ca (mineral deposit) and by content of calcium of the harvested implants. Isografts and AAA bone with marrow yielded a substantial amount of new bone. Without the marrow, AAA bone yielded very small amounts of new bone.
Protective Cytotoxic T-Cell Responses Induced by Venezuelan Equine Encephalitis Virus Replicons Expressing Ebola Virus Proteins (2005)

Infection with Ebola virus causes a severe disease accompanied by high mortality rates, and there are no licensed vaccines or therapies available for human use. Filovirus vaccine research efforts still need to determine the roles of humoral and cell-mediated immune responses in protection from Ebola virus infection. Previous studies indicated that exposure to Ebola virus proteins expressed from packaged Venezuelan equine encephalitis virus replicons elicited protective immunity in mice and that antibody-mediated protection could only be demonstrated after vaccination against the glycoprotein. In this study, the murine CD8(+) T-cell responses to six Ebola virus proteins were examined. CD8(+) T cells specific for Ebola virus glycoprotein, nucleoprotein, and viral proteins (VP24, VP30, VP35, and VP40) were identified by intracellular cytokine assays using splenocytes from vaccinated mice. The cells were expanded by restimulation with peptides and demonstrated cytolytic activity. Adoptive transfer of the CD8(+) cytotoxic T cells protected filovirus naïve mice from challenge with Ebola virus. These data support a role for CD8(+) cytotoxic T cells as part of a protective mechanism induced by vaccination against six Ebola virus proteins and provide additional evidence that cytotoxic T-cell responses can contribute to protection from filovirus infections.
Feature Detector for DVB-T Signal in Multipath Fading Channel (2007)

In this paper, detection of digital TV signals is studied since there is strong motivation to better utilize the idle TV channels to improve spectral efficiency, as seen in the efforts of IEEE 802.22 Wireless Regional Area Networks (WRAN) international standard activities. Cyclostationary feature of DVB signals is explored so that the robust single-cycle detector (SCD) can be employed to handle the problem of noise uncertainty, to which the widely used energy detector (ED) is susceptible. Due to complexity concerns for real-time implementation, a blind twin peak (BTP) detector is proposed to approximate the performance of SCD while keep the complexity as low as ED.
Chemically Modified Firefly Luciferase Is an Efficient Source of Near-Infrared Light (2010)

Bioluminescence and bioluminescence resonance energy transfer (BRET) are two naturally occurring light emission phenomena that have been adapted to a wide variety of important research applications including in vivo imaging and enzyme assays. The luciferase enzyme from the North American firefly, which produces yellow-green light, is a key component of many of these applications. Recognizing the heightened interest in the potential of near-infrared (nIR) light to improve these technologies, we have demonstrated that spectral emissions with maxima of 705 and 783 nm can be efficiently produced by a firefly luciferase variant covalently labeled with nIR fluorescent dyes. In one case, an outstanding BRET ratio of 34.0 was achieved emphasizing the importance of selective labeling with fluorescent dyes and the efficiency provided by the intramolecular BRET process. Additionally, we constructed a biotinylated fusion protein that similarly produced nIR light. This novel material was immobilized on solid supports containing streptavidin, demonstrating, in principle, that it may be used for receptor-based imaging. Also, the matrix-bound labeled fusion protein was used to measure factor Xa activity at physiological concentrations in blood. We believe this to be the first report of bright nIR light sources produced by chemical modification of a beetle luciferase.
AlGaN/GaN HFETs on 100 mm Silicon Substrates for Commercial Wireless Applications (2002)

GaN grown on Si is currently the only pathway towards high volume manufacturing of GaN based RF devices. In this paper we present the technological status of GaN grown on 100 mm Si substrates. Optimised growth, accounting for the lattice and thermal coefficient of expansion mismatch results in device quality GaN layers that exhibit excellent uniformity over the 100 mm Si substrate. The electrical characteristics of the fabricated devices reflect the high quality of the layers, leading to saturated power levels of 3.3 W/mm, the highest power densities reported to date for GaN on Si. Large periphery devices are shown to achieve up to 27 W of output power.
A light and electron microscopic study of Scherffelia dubia, a new member of the scaly green flagellates (Prasinophyceae) (1986)

In clonal culture Scherffelia dubia (Perty) Pascher shows a considerable range of morphological variation, with different cell shapes being produced including those typical for three other species of Scherffelia Pascher ( S. opisthostigma Skuja, S. ovata Pascher, S. pelagica Skuja) and one species of Tetraselmis Stein ( T. bichlora Ettl &amp; Ettl). It is concluded these taxa should be reduced to the synonymy of S. dubia , the type species of Scherffelia. The general cell morphology of S. dubia is described in detail, including a serial section and absolute configuration analysis of the flagellar apparatus. S. dubia is compared with species of Tetraselmis of which ultrastructural details are known and it is shown that both genera are very similar but the generic distinction is nevertheless justified. Main features of distinction include the pyrenoid (present in Tetraselmis but lacking in Scherffelia ) and the chloroplast (single and more or less cup‐shaped in Tetraselmis , two separate lateral chloroplasts in Scherffelia ). Both genera are accommodated in the same family, the correct name being Chlorodendraceae and not Tetraselmidaceae or Platymonadaceae which have often been used.
Macrophage Migration Inhibitory Factor May Be Used as an Early Diagnostic Marker in Colorectal Carcinomas (2008)

Recent genetic studies have identified many differentially expressed genes in colorectal carcinomas. For validation of up-regulated genes in colorectal carcinomas, we performed an enzyme-linked immunosorbent assay. Candidate markers were selected from gene expression data for 40 colorectal cancers and 35 matched normal mucosal samples. Based on intensive filtering, 9 genes were selected for the further evaluations. Among them, macrophage migration inhibitory factor (MIF), inhibin betaA, and chemokine ligand 10 were screened, and the results were compared with carcinoembryonic antigen (CEA) in serum samples of 129 patients with colon cancer and 53 healthy control subjects. We found that the serum MIF level was significantly increased in patients with colorectal cancer. Compared with CEA, MIF was more sensitive in early cancer detection (47.3% vs 29.5%). However, the specificity was not as high as that of CEA (90.6% vs 100.0%). Our findings indicate that MIF may be used as a diagnostic marker in colorectal carcinomas.
Binding ofEscherichia coliadhesin AfaE to CD55 triggers cell-surface expression of the MHC class I-related molecule MICA (2002)

MICA are distant homologs of MHC class I molecules expressed in the normal intestinal epithelium. They are ligands of the NKG2D activating receptor expressed on most gammadelta T cells, CD8+ alphabeta T cells, and natural killer cells and therefore play a critical role in innate immune responses. We investigated MICA cell-surface expression on infection of epithelial cell lines by enteric bacteria and show here that MICA expression can be markedly increased by bacteria of the diffusely adherent Escherichia coli diarrheagenic group. This effect is mediated by the specific interaction between bacterial adhesin AfaE and its cellular receptor, CD55, or decay-accelerating factor. It is extremely rapid after AfaE binding, consistent with a stress-induced signal. MICA induction on epithelial cells triggered IFN-gamma release by the NKG2D expressing natural killer cell line NKL. This host-bacteria interaction pathway could play a role in the pathogenesis of inflammatory bowel disease, a condition that implicates a bacterial trigger in genetically susceptible individuals. This was supported by the increased MICA expression at the surface of epithelial cells in colonic biopsies from Crohn's disease-affected patients compared with controls.
Recent studies on asymmetric hydrogenation. New catalysts and synthetic applications in organic synthesis (2002)

Abstract CODRu(h3methylallyl)2 is a versatile starting material for the preparation of a wide range of chiral bisphosphines ruthenium(II) complexes: (P*P)Ru(h3methylallyl)2 2, Ru[X4(P*P)2] 3, and cationic monohydride ruthenium complex 4. A facile synthesis of new C2 electron-rich chiral phosphines, bis(phosphetano)benzene 8 and 1,1¢bis(phosphetano)ferrocene 10 is presented. Dynamic kinetic resolution was used for efficient syntheses of key components of the hexahydroazepane core 16 of balanol and of optically pure Boc-(2S,3R,3S)-iso-dolaproïne 19. Catalyst 4 was used in asymmetric hydrogenation of 22 to give (+)-cis-methyl dihydrojasmonate in high enantioselectivity.
Isolation and Characterization of Multipotent Human Keloid-Derived Mesenchymal-Like Stem Cells (2008)

In this study, we report the isolation and characterization of a population of multipotent keloid-derived mesenchymal-like stem cells (KMLSCs) from keloid scalp tissues. These KMLSCs expressed the typical mesenchymal stem cell marker proteins CD13, CD29, CD44, CD90, fibronectin, and vimentin when they were cultured in serum-containing medium and when subsequent exposure to various differentiation media resulted in their differentiation into adipocytes, osteoblasts, chondrocytes, smooth muscle cells, and angiogenic endothelial cells. When KMLSCs were cultured in neural stem culture conditions (i.e., in the presence of epidermal growth factor and fibroblast growth factor 2 in substrate-free conditions), they produced large numbers of neurospheres containing nestin-, CD133-, and SOX2-positive cells that expressed neural-crest stem cell markers. Subsequent exposure of these cells to different differentiation conditions resulted in cells that expressed neuronal cell-, astrocyte-, oligodendrocyte-, or Schwann cell-specific markers. Our study suggests that KMLSCs may be an alternative adult stem cell resource for regenerative tissue repair and auto-transplantation.