gebhart/patrepeval huggingface dataset:
In vitro phosphorylated bovine milk fat globule membrane proteins (1997)

Incubation of the milk fat globule membrane (MFGM) with [γ-32P]ATP, in the presence of protein phosphatase inhibitors and MgCl2 and/or MnCl2, led to protein phosphorylation within this membrane. Analysis of the 32P-labeled proteins of bovine MFGM, by SDSPAGE and autoradiography, showed at least 15 radioactive bands with relative molecular masses in the range of 10 to 200 kDa. Bovine MFGM had four bands (66–67, 51, 33, and 24 kDa) labeled more intensively than others. Calcium could not substitute for Mg2+ and Mn2+ in the phosphorylation reaction. Genistein (100 μmol/L) reduced protein phosphorylation by 50 to 70%, whereas daidzein and heparin did not. The 66–67 and 15 kDa in vitro phosphorylated bovine MFGM proteins were butyrophilin and fatty-acid-binding protein (FABP), respectively. Phosphoamino acid analysis of 32P-labeled 66, 51, and 15 kDa polypeptide acid hydrolyzates revealed radiolabeled phosphotyrosine, -threonine, and -serine in the 66 kDa protein, radiolabeled phosphotyrosine and -threonine in the 51 kDa protein, and radiolabeled phosphotyrosine in the 15 kDa protein. FABP appeared to be in a complex with its putative kinase. The analysis of in vitro phosphorylated human MFGM revealed 13–15 radioactive protein bands in the range of 20 to 200 kDa. The 65 and 50 kDa radiolabeled bands were prominent in all five individual samples of human MFGM analyzed. FAK, insulin β-subunit receptor, c-src60 and MAPK, were detected in the bovine and human MFGM using Western immunoblotting. MAPKAPK was also found in the bovine MFGM.
segDeepM: Exploiting segmentation and context in deep neural networks for object detection (2015)

In this paper, we propose an approach that exploits object segmentation in order to improve the accuracy of object detection. We frame the problem as inference in a Markov Random Field, in which each detection hypothesis scores object appearance as well as contextual information using Convolutional Neural Networks, and allows the hypothesis to choose and score a segment out of a large pool of accurate object segmentation proposals. This enables the detector to incorporate additional evidence when it is available and thus results in more accurate detections. Our experiments show an improvement of 4.1% in mAP over the R-CNN baseline on PASCAL VOC 2010, and 3.4% over the current state-of-the-art, demonstrating the power of our approach.
Characterization and decomposition of self-aligned quadruple patterning friendly layout (2012)

Self-aligned quadruple patterning (SAQP) lithography is one of the major techniques for the future process requirement after 16nm/14nm technology node. In this paper, based on the existing knowledge of current 193nm lithography and process flow of SAQP, we will process an early study on the definition of SAQP-friendly layout. With the exploration of the feasible feature regions and possible combinations of adjacent features, we will define several simple but important geometry rules to help define the SAQP-friendliness. Then, we will introduce a conflicting graph algorithm to generate the feature region assignment for SAQP decomposition. Our experimental results validate our SAQP-friendly layout definition, and basic circuit building blocks in the low level metal layer are analyzed.
Hyperacidification of Trans‐Golgi Network and Endo/Lysosomes in Melanocytes by Glucosylceramide‐Dependent V‐ATPase Activity (2011)

Sphingolipids are considered to play a key role in protein sorting and membrane trafficking. In melanocytic cells, sorting of lysosomal and melanosomal proteins requires the sphingolipid glucosylceramide (GlcCer). This sorting information is located in the lumenal domain of melanosomal proteins. We found that two processes dependent on lumenal pH, protein sialylation and lysosomal acid lipase (LAL) activity were aberrant in GM95 melanocyte cells, which do not produce glycosphingolipids. Using fluorescence lifetime imaging microscopy (FLIM), we found that the lumenal pH in the trans-Golgi network and lysosomes of wild-type melanocyte MEB4 cells are >1 pH unit lower than GM95 cells and fibroblasts. In addition to the lower pH found in vivo, the in vitro activity of the proton pump, the vacuolar-type H(+) -translocating ATPase (V-ATPase), was twofold higher in MEB4 compared to GM95 cells. The apparent K(i) for inhibition of the V-ATPase by concanamycin A and archazolid A, which share a common binding site on the c-ring, was lower in glycosphingolipid-deficient GM95 cells. No difference between the MEB4 and GM95 cells was found for the V-ATPase inhibitors apicularen A and salicylihalimide. We conclude that hyperacidification in MEB4 cells requires glycosphingolipids and propose that low pH is necessary for protein sorting and melanosome biogenesis. Furthermore, we suggest that glycosphingolipids are indirectly involved in protein sorting and melanosome biogenesis by stimulating the proton pump, possibly through binding of GlcCer. These experiments establish, for the first time, a link between pH, glycosphingolipids and melanosome biogenesis in melanocytic MEB4 cells, to suggest a role for glycosphingolipids in hyperacidification in melanocytes.
Prostate specific antigen kinetics following robotic stereotactic body radiotherapy for localized prostate cancer (2014)

At a median follow-up of 3 years, 70% of patients achieved a PSA nadir below 0.5 ng/ml with a median PSA nadir of 0.3 ng/ml at a median time to nadir of 30 months. In our cohort, 36.2% experienced a benign PSA bounce. Absence of PSA bounce, initial PSA, and testosterone at the time of nadir proved to be significant predictors of achieving a PSA nadir below threshold. PSA kinetics after prostate SBRT were well described with a functional volume model with fitted half-lives of 4.4 and 14.8 months for malignant and benign sources of PSA, respectively. Patients treated with prostate SBRT experience an initial period of rapid PSA decline followed by a slow decline which will likely result in lower PSA nadirs after longer follow-up. The long-term disease specific impacts of these results remain to be determined.
Automatic Generation and Validation of Compact Network Models for a Fine Pitch BGA Package (2003)

A methodology for automatically generating compact thermal network models of increasing complexity, for use in numerical simulations of general semiconductor integrated circuit (IC) packages is presented. The method is based on the multi-grid agglomeration of the underlying mesh used in the finite volume discretization of the energy conservation equation of the package. The method is applied to a 196-pin fine pitch ball grid array (FBGA) package. Various network topologies and the corresponding network conductances were automatically extracted for this package. These networks were then used in computational fluid dynamics (CFD) simulations for a range of boundary conditions corresponding to single-phase natural and forced convective cooling. Results show good agreement with the detailed package simulations.
RAPID DISEASE PROGRESSION IS THE PRIMARY REASON PATIENTS FAIL TO RECEIVE SYSTEMIC THERAPY FOLLOWING CYTOREDUCTIVE NEPHRECTOMY (CN) (2009)

You have accessJournal of Urology1 Apr 2009RAPID DISEASE PROGRESSION IS THE PRIMARY REASON PATIENTS FAIL TO RECEIVE SYSTEMIC THERAPY FOLLOWING CYTOREDUCTIVE NEPHRECTOMY (CN) Alexander Kutikov, Robert G. Uzzo, Brian L. Egleston, Stephen A. Blakely, Kevan Iffrig, David Y.T. Chen, Rosalia Viterbo, Richard E. Greenberg, Yu-Ning Wong, and Stephen A Boorjian Alexander KutikovAlexander Kutikov More articles by this author , Robert G. UzzoRobert G. Uzzo More articles by this author , Brian L. EglestonBrian L. Egleston More articles by this author , Stephen A. BlakelyStephen A. Blakely More articles by this author , Kevan IffrigKevan Iffrig More articles by this author , David Y.T. ChenDavid Y.T. Chen More articles by this author , Rosalia ViterboRosalia Viterbo More articles by this author , Richard E. GreenbergRichard E. Greenberg More articles by this author , Yu-Ning WongYu-Ning Wong More articles by this author , and Stephen A BoorjianStephen A Boorjian More articles by this author View All Author Informationhttps://doi.org/10.1016/S0022-5347(09)61404-XAboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail "RAPID DISEASE PROGRESSION IS THE PRIMARY REASON PATIENTS FAIL TO RECEIVE SYSTEMIC THERAPY FOLLOWING CYTOREDUCTIVE NEPHRECTOMY (CN)." The Journal of Urology, 181(4S), p. 497 © 2009 by American Urological AssociationFiguresReferencesRelatedDetails Volume 181Issue 4SApril 2009Page: 497 Advertisement Copyright & Permissions© 2009 by American Urological AssociationMetricsAuthor Information Alexander Kutikov More articles by this author Robert G. Uzzo More articles by this author Brian L. Egleston More articles by this author Stephen A. Blakely More articles by this author Kevan Iffrig More articles by this author David Y.T. Chen More articles by this author Rosalia Viterbo More articles by this author Richard E. Greenberg More articles by this author Yu-Ning Wong More articles by this author Stephen A Boorjian More articles by this author Expand All Advertisement PDF downloadLoading ...
The vasopressin-regulated urea transporter in renal inner medullary collecting duct (1990)

The terminal part of the inner medullary collecting duct (terminal IMCD) is unique among collecting duct segments in part because its permeability to urea is regulated by vasopressin. The urea permeability can rise to extremely high levels (greater than 100 x 10(-5) cm/s) in response to vasopressin. Recent studies in isolated perfused IMCD segments have established that the rapid movement of urea across the tubule epithelium occurs via a specialized urea transporter, presumably an intrinsic membrane protein, present in both the apical and basolateral membranes. This urea transporter has properties similar to those of the urea transporters in mammalian erythrocytes and in toad urinary bladder, namely, inhibition by phloretin, inhibition by urea analogues, saturation kinetics in equilibrium-exchange experiments, and regulation by vasopressin. The urea transport pathway is distinct from and independent of the vasopressin-regulated water channel. The increase in transepithelial urea transport in response to vasopressin is mediated by adenosine 3',5'-cyclic monophosphate and is associated with an increase in the urea permeability of the apical membrane. However, little is known about the physical events associated with the activation or insertion of urea transporters in the apical membrane. Because of the importance of this transporter to the urinary concentrating mechanism, efforts toward understanding its molecular structure and the molecular basis of its regulation appear to be justified.
Phased nanopore assembly with Shasta and modular graph phasing with GFAse (2023)

As a step towards simplifying and reducing the cost of haplotype resolved <i>de novo</i> assembly, we describe new methods for accurately phasing nanopore data with the Shasta genome assembler and a modular tool for extending phasing to the chromosome scale called GFAse. We test using new variants of Oxford Nanopore Technologies' (ONT) PromethION sequencing, including those using proximity ligation and show that newer, higher accuracy ONT reads substantially improve assembly quality.
Extracellular vesicles biogenesis, isolation, manipulation and genetic engineering for potential in vitro and in vivo therapeutics: An overview (2022)

The main goals of medicine consist of early detection and effective treatment of different diseases. In this regard, the rise of exosomes as carriers of natural biomarkers has recently attracted a lot of attention and managed to shed more light on the future of early disease diagnosis methods. Here, exosome biogenesis, its role as a biomarker in metabolic disorders, and recent advances in state-of-art technologies for exosome detection and isolation will be reviewed along with future research directions and challenges regarding the manipulation and genetic engineering of exosomes for potential <i>in vitro</i> and <i>in vivo</i> disease diagnosis approaches.
Bacterial Cellulose-Binding Domain Modulates in Vitro Elongation of Different Plant Cells1 (1998)

Recombinant cellulose-binding domain (CBD) derived from the cellulolytic bacterium Clostridium cellulovorans was found to modulate the elongation of different plant cells in vitro. In peach (Prunus persica L.) pollen tubes, maximum elongation was observed at 50 &mgr;g mL-1 CBD. Pollen tube staining with calcofluor showed a loss of crystallinity in the tip zone of CBD-treated pollen tubes. At low concentrations CBD enhanced elongation of Arabidopsis roots. At high concentrations CBD dramatically inhibited root elongation in a dose-responsive manner. Maximum effect on root hair elongation was at 100 &mgr;g mL-1, whereas root elongation was inhibited at that concentration. CBD was found to compete with xyloglucan for binding to cellulose when CBD was added first to the cellulose, before the addition of xyloglucan. When Acetobacter xylinum L. was used as a model system, CBD was found to increase the rate of cellulose synthase in a dose-responsive manner, up to 5-fold compared with the control. Electron microscopy examination of the cellulose ribbons produced by A. xylinum showed that CBD treatment resulted in a splayed ribbon composed of separate fibrillar subunits, compared with a thin, uniform ribbon in the control.
Development of dual-function ELISA for effective antigen and antibody detection against H7 avian influenza virus (2013)

This is the first dual-function ELISA reported for either antigen or antibody detection against H7 AIVs. The assay was highly sensitive and 100% specific in both functions rendering it effective for H7 diagnosis.
Emerging Therapeutic Strategies to Restore Regulatory T Cell Control of Islet Autoimmunity in Type 1 Diabetes (2021)

Despite many decades of investigation uncovering the autoimmune mechanisms underlying Type 1 Diabetes (T1D), translating these findings into effective therapeutics has proven extremely challenging. T1D is caused by autoreactive T cells that become inappropriately activated and kill the β cells in the pancreas, resulting in insulin insufficiency and hyperglycemia. A large body of evidence supports the idea that the unchecked activation and expansion of autoreactive T cells in T1D is due to defects in immunosuppressive regulatory T cells (Tregs) that are critical for maintaining peripheral tolerance to islet autoantigens. Hence, repairing these Treg deficiencies is a much sought-after strategy to treat the disease. To accomplish this goal in the most precise, effective and safest way possible, restored Treg functions will need to be targeted towards suppressing the autoantigen-specific immune responses only and/or be localized in the pancreas. Here we review the most recent developments in designing Treg therapies that go beyond broad activation or expansion of non-specific polyclonal Treg populations. We focus on two cutting-edge strategies namely <i>ex vivo</i> generation of optimized Tregs for re-introduction in T1D patients vs direct <i>in situ</i> stimulation and restoration of endogenous Treg function.
Autonomic Regulation Therapy to Enhance Myocardial Function in Heart Failure Patients: The ANTHEM-HFpEF Study (2017)

The ANTHEM-HFpEF study is likely to provide valuable information intended to expand our understanding of the potential role of ART in patients with chronic symptomatic HFpEF and HFmrEF.
Functional mimicry of tumor-associated antigens by antiidiotypic antibodies. (1988)

Antiidiotypic antibodies (Ab2) have been shown to induce specific immunity against murine and human tumors. Studies in murine tumor systems also have shown that Ab2 immunizations can induce protective immunity against a challenge with tumor cells. Antibodies and cytotoxic/regulatory T cells have been implicated as mediators of the antitumor effects induced by Ab2 immunization in mice. In recent clinical trials, cancer patients immunized with Ab2 that functionally mimic a gastrointestinal tumor-associated antigen developed highly specific antitumor immune responses. Thus Ab2 are promising vaccine candidates in immunotherapy approaches to cancer. The choice of Ab2 as well as optimization of immunization procedures with Ab2 are important considerations in future studies.
The Tao of IGF-1: Insulin-Like Growth Factor Receptor Activation Increases Pain by Enhancing T-Type Calcium Channel Activity (2014)

T-type calcium channels are important players in the transmission of pain signals in the primary afferent pathway. Indeed, inhibiting or depleting T-type calcium channels in dorsal root ganglion (DRG) neurons mediates analgesia. Conversely, nerve injury or peripheral inflammation have been shown to induce T-type calcium channel activity in DRG neurons, and this in turn has been linked to the development of chronic pain states. The mechanisms that underlie this enhancement of T-type channels remain incompletely understood and may include changes in channel stability in the plasma membrane or alterations in channel function. In this issue of Science Signaling, Zhang and colleagues identify a cell signaling pathway that potently regulates T-type calcium channel activity in afferent neurons and link this process to pain hypersensitivity. Specifically, they show that insulin-like growth factor-1 receptors in DRG neurons mediate a protein kinase C α (PKCα)-dependent enhancement of T-type calcium currents and that interfering with this pathway reduces both mechanical and thermal pain hypersensitivity in rodents. Targeting this process offers a new avenue for developing pain therapeutics.
The COMQUAD Component Container Architecture and Contract Negotiation (2004)

Component-based applications require runtime support to be able to guarantee non-functional properties. This report proposes an architecture for a real-time-capable, component-based runtime environment, which allows to separate non-functional and functional concerns in component-based software development. The architecture is presented with particular focus on three key issues: the conceptual architecture, an approach including implementation issues for splitting the runtime environment into a real-time-capable and a real-time-incapable part, and details of contract negotiation. The latter includes selecting component implementations for instantiantion based on their non-functional properties.
Cardiovascular magnetic resonance evidence of myocardial fibrosis and its clinical significance in adolescent and adult patients with Ebstein's anomaly (2018)

Both focal and diffuse myocardial fibrosis were observed in adolescent and adult patients with Ebstein's anomaly. Increased diffuse fibrosis is associated with worse LV function, increased Ebstein's severity, and worse clinical status.
STEM and HRTEM studies of accumulated deposits on human tooth surface (2017)

The aim of this study was to clarify the fine structure of accumulated deposits on the surface of teeth that are considered to affect the gloss of teeth. The study was carried out using, as specimens, human incisor teeth having gloss, which were extracted from teenage donors and those incapable of showing gloss even by brushing which were extracted from donors in their 50s. Thin longitudinal sections of tooth enamel with accumulated deposits on the surface were prepared by focused ion beam (FIB) milling, and the fine structure was analyzed using a scanning transmission electron microscope (STEM) and a high resolution transmission electron microscope (HRTEM). By FIB, thin longitudinal sections could be prepared from tooth enamel together with organic and inorganic substances accumulated on the surface without artifacts. The accumulated deposits on the surface of teeth having gloss were composed of organic substances. However, it was first revealed by STEM observation that the accumulated solid deposits on the surface of teeth having no gloss had a complicated structure wherein inorganic and organic substances coexisted. It is suggested that the organic substances contain proteins derived from saliva. The inorganic substances were spherical and needle-like hydroxyapatites (HAs). It is considered that amino acids constituting the proteins affected the nucleus formation and the crystal formation of HA. It is considered that the unevenness of the accumulated deposits existing on the surface of tooth enamel having no gloss causes the decrease in gloss of teeth due to diffuse reflection of light.
High active nitrogen flux growth of GaN by plasma assisted molecular beam epitaxy (2015)

In the present study, the authors report on a modified Riber radio frequency (RF) nitrogen plasma source that provides active nitrogen fluxes more than 30 times higher than those commonly used for plasma assisted molecular beam epitaxy (PAMBE) growth of gallium nitride (GaN) and thus a significantly higher growth rate than has been previously reported. GaN films were grown using N2 gas flow rates between 5 and 25 sccm while varying the plasma source's RF forward power from 200 to 600 W. The highest growth rate, and therefore the highest active nitrogen flux, achieved was ∼7.6 μm/h. For optimized growth conditions, the surfaces displayed a clear step-terrace structure with an average RMS roughness (3 × 3 μm) on the order of 1 nm. Secondary ion mass spectroscopy impurity analysis demonstrates oxygen and hydrogen incorporation of 1 × 1016 and ∼5 × 1017, respectively. In addition, the authors have achieved PAMBE growth of GaN at a substrate temperature more than 150 °C greater than our standard Ga rich GaN growth regime and ∼100 °C greater than any previously reported PAMBE growth of GaN. This growth temperature corresponds to GaN decomposition in vacuum of more than 20 nm/min; a regime previously unattainable with conventional nitrogen plasma sources. Arrhenius analysis of the decomposition rate shows that samples with a flux ratio below stoichiometry have an activation energy greater than decomposition of GaN in vacuum while samples grown at or above stoichiometry have decreased activation energy. The activation energy of decomposition for GaN in vacuum was previously determined to be ∼3.1 eV. For a Ga/N flux ratio of ∼1.5, this activation energy was found to be ∼2.8 eV, while for a Ga/N flux ratio of ∼0.5, it was found to be ∼7.9 eV.
Chromosome workshop: Chromosomes 11, 14, and 15 (1999)

This report describes linkage data presented at the Workshop on Chromosomes 11, 14, and 15 at the Sixth World Congress of Psychiatric Genetics in Bonn, Germany, together with relevant linkage data submitted to the chair and co-chair, and it is presented in the context of the previous literature concerning these chromosomes. We have attempted to collate current linkage data to provide a guide to potentially interesting findings on chromosomes 11, 14, and 15 for the phenotypes of bipolar disorder, schizophrenia, alcoholism, autism, and spelling and reading disability. We discuss methodological limitations and provide chromosome ideograms and tables summarizing findings to date. The most promising region currently appears to be 15q13-q15 in the region of the alpha 7 nicotinic receptor for the phenotype of schizophrenia (and, perhaps, more generally for functional psychosis). Additionally, 15q11-q13 in the region of GABRB3 holds interest as a potential site of a susceptibility gene for autism. Two regions on chromosome 11, 11p15 in the region of tyrosine hydroxylase gene and 11q22-q23 in the region of DRD2, continue to retain some interest for functional psychosis.