gebhart/patrepeval huggingface dataset:
ROR1 can interact with TCL1 and enhance leukemogenesis in Eµ-TCL1 transgenic mice (2013)

Receptor tyrosine kinase-like orphan receptor 1 (ROR1) is an oncoembryonic antigen found on chronic lymphocytic leukemia (CLL) B cells, but not on normal adult tissues. We generated transgenic (Tg) mice with human ROR1 regulated by the murine Ig promoter/enhancer. In contrast to nontransgenic littermates, such animals had B-cell-restricted expression of ROR1 and could develop clonal expansions of ROR1(bright)CD5(+)B220(low) B cells resembling human CLL at ≥ 15 mo of age. Because immune-precipitation and mass spectrometry studies revealed that ROR1 could complex with T-cell leukemia 1 (TCL1) in CLL, we crossed these animals with Eµ-TCL1-Tg (TCL1) mice. Progeny with both transgenes (ROR1 × TCL1) developed CD5(+)B220(low) B-cell lymphocytosis and leukemia at a significantly younger median age than did littermates with either transgene alone. ROR1 × TCL1 leukemia B cells had higher levels of phospho-AKT than TCL1 leukemia cells and expressed high levels of human ROR1, which we also found complexed with TCL1. Transcriptome analyses revealed that ROR1 × TCL1 leukemia cells had higher expression of subnetworks implicated in embryonic and tumor-cell proliferation, but lower expression of subnetworks involved in cell-cell adhesion or cell death than did TCL1 leukemia cells. ROR1 × TCL1 leukemia cells also had higher proportions of Ki-67-positive cells, lower proportions of cells undergoing spontaneous apoptosis, and produced more aggressive disease upon adoptive transfer than TCL1 leukemia cells. However, treatment with an anti-ROR1 mAb resulted in ROR1 down-modulation, reduced phospho-AKT, and impaired engraftment of ROR1 × TCL1 leukemia cells. Our data demonstrate that ROR1 accelerates development/progression of leukemia and may be targeted for therapy of patients with CLL.
The partial amino acid sequence of bovine cartilage proteoglycan, deduced from a cDNA clone, contains numerous Ser-Gly sequences arranged in homologous repeats (1987)

We have determined the sequence of a partial cDNA clone encoding the C-terminal region of bovine cartilage aggregating proteoglycan core protein. The deduced amino acid sequence contains a cysteine-rich region which is homologous with chicken hepatic lectin. This lectin-homologous region has previously been identified in rat and chicken cartilage proteoglycan. The bovine sequence presented here is highly homologous with the rat and chicken amino acid sequences in this apparently globular region. A region containing clusters of Ser-Gly sequences is located N-terminal to the lectin homology domain. These Ser-Gly-rich segments are arranged in tandemly repeated, approx. 100-residue-long, homology domains. Each homology domain consists of an approx. 75-residue-long Ser-Gly-rich region separated by an approx. 25-residue-long segment lacking Ser-Gly dipeptides. These dipeptides are arranged in 10-residue-long segments in the 100-residue-long homology domains. The shorter homologous segments are tandemly repeated some six times in each 100-residue-long homology domain. Serine residues in these repeats are potential attachment sites for chondroitin sulphate chains.
Effects of Natural Human Antibodies against a Nonhuman Sialic Acid That Metabolically Incorporates into Activated and Malignant Immune Cells (2005)

Humans are genetically incapable of producing the mammalian sialic acid N-glycolylneuraminic acid (Neu5Gc), due to an inactivating mutation in the enzyme synthesizing it. Despite this, human cells and tissues appear capable of metabolically incorporating Neu5Gc from exogenous sources, including dietary red meat and dairy products. All normal humans studied are now shown to have circulating Abs against Neu5Gc, with marked differences in isotype levels. The question arises whether such Abs can adversely affect Neu5Gc-expressing human cells or tissues. In this study, we show that although normal human PBMC do not incorporate Neu5Gc during in vitro incubation, activated T cells do. Primary human leukemia cells and human leukemic cell lines are even more efficient at incorporation. Human sera containing naturally high levels of anti-Neu5Gc IgG Abs (hereafter abbreviated GcIg) deposited complement on Neu5Gc-expressing leukemic cells and activated T cells, but not on normal cells. The binding of GcIg resulted in complement-mediated cytotoxicity, which was inhibited by heat inactivation. Low anti-Neu5Gc IgG-containing human sera did not mediate any of these effects. Mixed killing assays confirmed the 15-fold selective killing of leukemic cells over PBMC by GcIg following Neu5Gc feeding. This approach could potentially serve as novel way to target malignant cells for death in vivo using either natural Abs or anti-Neu5Gc Abs prepared for this purpose. Further studies are needed to determine whether deposition of natural GcIg and complement can also target healthy proliferating immune cells for death in vivo following incorporation of dietary Neu5Gc.
Lithium Aluminum Hydride (2004)

[16853-85-3] AlH4Li (MW 37.96) InChI = 1/Al.Li.4H/q-1;+1;;;;/rAlH4.Li/h1H4;/q-1;+1 InChIKey = OCZDCIYGECBNKL-PDCCDREHAZ (reducing agent for many functional groups;1 can hydroaluminate double and triple bonds;2 can function as a base3) Alternate Name: LAH. Physical Data: mp 125 °C; d 0.917 g cm−3. Solubility: soluble in ether (35 g/100 mL; conc of more dil soln necessary); soluble in THF (13 g/100 mL); modestly soluble in other ethers; reacts violently with H2O and protic solvents. Form Supplied in: colorless or gray solid; 0.5–1 M solution in diglyme, 1,2-dimethoxyethane, ether, or tetrahydrofuran; the LiAlH4·2THF complex is available as a 1 M solution in toluene. Analysis of Reagent Purity: Metal Hydrides Technical Bulletin No. 401 describes an apparatus and methodology for assay by means of hydrogen evolution. See also Rickborn and Quartucci.39a Handling, Storage, and Precaution: the dry solid and solutions are highly flammable and must be stored in the absence of moisture. Cans or bottles of LiAlH4 should be flushed with N2 and kept tightly sealed to preclude contact with oxygen and moisture. Lumps should be crushed only in a glove bag or dry box.
Packaging system for rapid production of murine leukemia virus vectors with variable tropism (1992)

A method for rapidly producing helper-free murine leukemia virus (MLV) without using packaging cell lines is described. Viruses bearing ecotropic or amphotropic MLV or Rous sarcoma virus envelope glycoprotein and containing various retroviral vector genomes have been prepared with titers 30 to 40-fold higher than those produced by transient transfection of standard packaging cells. This system can be used to alter the cellular tropism of MLV by incorporating other envelope glycoproteins and to prepare retroviral vector stocks without establishing stable producer cell lines. This method will be particularly useful for preparing viruses that encode toxic proteins and for the rapid analysis of panels of mutant envelope glycoproteins.
Hybrid modelling of low temperature plasmas for fundamental investigations and equipment design (2009)

The modelling of low temperature plasmas for fundamental investigations and equipment design is challenged by conflicting goals—having detailed, specialized algorithms which address sometimes subtle physical phenomena while also being flexible enough to address a wide range of process conditions. Hybrid modelling (HM) is a technique which provides many opportunities to address both fundamental physics and practical matters of equipment design. HM is a hierarchical approach in which modules addressing different physical processes on vastly disparate timescales are iteratively combined using time-slicing techniques. By compartmentalizing the physics in each module to accept given inputs and produce required outputs, different algorithms can be used to represent the same physical processes. In this manner, the algorithms best suited for the conditions of interest can be used without affecting other modules. In this paper, the basis and implementation of HM are discussed using examples from simulations of inductively coupled plasmas.
면적규모 및 공간해상도가 CA-Markov 기법에 의한 미래 토지이용 예측결과에 미치는 영향 (2007)

본 연구의 목적은 Landsat 시계열 영상으로 CA-Markov 기법에 의한 토지이용의 예측시 면적규모 및 공간해상도가 예측결과에 미치는 영향을 고려하여 미래의 토지이용 변화를 예측하는데 있다. 분석지역의 면적규모를 31.26km2부터 84.48km2까지 달리하면서 기법을 적용한 결과, 적용면적의 규모는 전체정확도에서 약 11% 차이를 보이면서 예측결과에 영향을 주었다. 공간해상도는 10m, 30m, 50m, 100m, 150m의 해상도에 대하여 비교한 결과, 30m의 공간해상도가 예측한 도심지의 총 면적과 도심지의 공간적인 분포 측면에서 가장 좋은 결과를 얻었다. 이와 같은 결과를 토대로, 1996년과 2001년의 토지피복도를 이용하여 CA-Markov기법으로 예측한 2004년의 토지피복결과와 2004년의 영상으로 최대우도법에 의한 토지피복결과를 비교하여 그 적용성을 평가한 후, 2030년, 2060년, 2090년에 대한 미래의 토지이용변화를 예측하였다. 현재를 기준으로 미래(2030, 2060, 2090)의 토지이용 면적변화는 도심지의 경우 지속적으로 증가하고, 산림의 경우는 크게 감소하는 일반적인 경향을 보이면서 예측되었다.
Variable-rate signalling in conjunction with coding for meteor burst communications (2002)

The author examines the use of variable-rate signaling in conjunction with error-correction coding for a meteor burst channel model which assumes that the received signal amplitude decays exponentially. The performance achievable with variable-rate signaling is quantified by calculating the cutoff rate. The average signal-to-noise ratio per bit required to support communications is calculated under the assumption that the code rate is equal to the cutoff rate. It is shown that the improvement of variable-rate signaling over fixed-rate signaling is large if the code rate is moderate to high, and that the improvement is small if the code rate is low and the decoder is provided with side information on the received signal level.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Airway Fibrosis and Angiogenesis due to Eosinophil Trafficking in Chronic Asthma (2008)

Asthma is characterized by the presence of increased numbers of inflammatory cells in the airway in particular eosinophils and Th2 lymphocytes. In addition to the presence of inflammatory cells, the airways of patients with asthma exhibit varying levels of structural changes termed airway remodeling. These structural changes include subepithelial fibrosis, smooth muscle hypertrophy/hyperplasia, epithelial cell mucus metaplasia, and increased angiogenesis. This review focuses on the potential role of the eosinophil in promoting features of airway remodeling including fibrosis and neovascularization in chronic asthma. Eosinophils may potentially contribute to airway remodeling through release of eosinophil derived mediators such as TGFβ which act directly upon target fibroblasts to promote fibrosis. In addition to the potential importance of the eosinophil to remodeling in asthma, eosinophilic esophagitis (EE) is another eosinophil associated disease that is associated with increased levels of esophageal eosinophils, increased levels of TGFβ expression, and increased levels of fibrosis, suggesting that a similar mechanism of remodeling may contribute to both of these eosinophil associated diseases. However, remodeling in both asthma and EE is likely complex involving both eosinophil dependent and eosinophil independent pathways. Further studies in both humans and animal models will help to increase our knowledge of the contribution of the eosinophil to remodeling in asthma as well as EE.
Activation of p38 Mitogen-Activated Protein Kinase In Vivo Selectively Induces Apoptosis of CD8+ but Not CD4+ T Cells (2000)

CD4(+) and CD8(+) T cells play specific roles during an immune response. Different molecular mechanisms could regulate the proliferation, death, and effector functions of these two subsets of T cells. The p38 mitogen-activated protein (MAP) kinase pathway is induced by cytokines and environmental stress and has been associated with cell death and cytokine expression. Here we report that activation of the p38 MAP kinase pathway in vivo causes a selective loss of CD8(+) T cells due to the induction of apoptosis. In contrast, activation of p38 MAP kinase does not induce CD4(+) T-cell death. The apoptosis of CD8(+) T cells is associated with decreased expression of the antiapoptotic protein Bcl-2. Regulation of the p38 MAP kinase pathway in T cells is therefore essential for the maintenance of CD4/CD8 homeostasis in the peripheral immune system. Unlike cell death, gamma interferon production is regulated by the p38 MAP kinase pathway in both CD4(+) and CD8(+) T cells. Thus, specific aspects of CD4(+) and CD8(+) T-cell function are differentially controlled by the p38 MAP kinase signaling pathway.
Endoplasmic reticulum stress response in cancer: molecular mechanism and therapeutic potential. (2010)

In eukaryotic cells, the endoplasmic reticulum (ER) is an organelle that is responsible for protein folding and assembly, lipid and sterol biosynthesis, and free calcium storage. In the past decade, intensive research effort has been focused on intracellular stress signaling pathways from the ER that lead to transcriptional and translational reprogramming of stressed cells. These signaling pathways, which are collectively termed Unfolded Protein Response (UPR), are critical for the cell to make survival or death decision under ER stress conditions. In recent years, research in the cancer field has revealed that ER stress and the UPR are highly induced in various tumors and are closely associated with cancer cell survival and resistance to anti-cancer treatments. Identifying the UPR components that are activated or suppressed in malignancy and exploring cancer therapeutic potentials by targeting the UPR are hot research spots. In this review, we summarize the recent progress in understating UPR signaling in cancer and its related therapeutic potential.
A model of secretory protein trafficking in recombinant AtT‐20 cells (1991)

After their synthesis, secretory proteins in animal cells undergo a series of transport and processing steps before they are secreted. The amount and quality of protein obtained in culture medium depends on the rates of these intracellular steps. We present a model of recombinant protein trafficking in mouse pituitary AtT-20 cells based on currently available biological knowledge, plausible hypotheses, and quantitative secretion results, and we use it to simulate the dynamics of basal and induced secretion and to predict the dynamics of intracellular trafficking events. Besides the endoplasmic reticulum and Golgi, the model recognizes a conversion compartment (CC) where final processing of protein occurs, a storage compartment from which protein is secreted only in the presence of secretion stimulus, and constitutive and pseudoregulated (PR) pathways of secretion. The model further assumes that the protein flux is split between CC and PR and that the storage compartment exerts a negative feedback on protein flux through CC. The model predictions are compared with experimental results on secretion of human growth hormone (hGH) and insulin related peptides and on accumulation of hGH upon removal of secretion stimulus. The model is in agreement with data when either of two hypotheses is implemented: (a) cells always exhibit a high sorting efficiency at the trans-Golgi, but CC has the capacity to process only a fraction of the protein flux leaving the Golgi compartment; (b) the processing capacity of CC never becomes saturated, but significant missorting at the trans-Golgi occurs; in the case, the protein flux toward the plasma membrane becomes split both at the trans-Golgi cisternae and between CC and PR. The usefulness of the type of model considered in providing a quantitative description of intracellular events and in designing new experiments is discussed.
Design, Synthesis, and Evaluation of Potent, Nonpeptidic Mimetics of Second Mitochondria-Derived Activator of Caspases (2009)

A series of new Smac mimetics have been designed, synthesized, and evaluated. The most potent compound 10 binds to XIAP, cIAP-1, and cIAP-2 BIR3 proteins with K(i) of 3.9, 0.37, and 0.25 nM, respectively. Compound 10 antagonizes XIAP in a cell-free functional assay and induces rapid cIAP-1 degradation in cancer cells. Compound 10 inhibits cell growth in the MDA-MB-231 cancer cell line with an IC(50) of 8.9 nM.
Neurodevelopmental Outcomes Following Bevacizumab Injections for Retinopathy of Prematurity (2016)

Preterm infants treated with bevacizumab versus laser had higher odds of severe neurodevelopmental disabilities. Further investigation on the long-term safety of antivascular endothelial growth factor treatment of ROP is needed.
A multilayer structured acoustic cloak with homogeneous isotropic materials (2008)

An acoustic cloak with concentric alternating layered structure is designed with homogeneous isotropic materials on the basis of effective medium theory. The cloak possesses low-reflection and power-flow bending properties for different shapes of wavefront both in far- and near-fields, which could perfectly approximate the ideal cloak with inhomogeneous and anisotropic distribution of material parameters.
Cellular Uptake Studies with -Peptides (2002)

Translocation across the membrane into cells is possible for certain peptides and proteins. To investigate the structural requirements of β-peptides for this process, a series of fluorescein-labeled β-peptides has been synthesized and their cellular uptake into 3T3 mouse fibroblast cells determined by fluorescence microscopy (see picture). Polycationic β-peptides have been shown to internalize into cells, and accumulation in the cytosol and nucleus is observed.
Superresolution by localization of quantum dots using blinking statistics (2005)

In microscopy, single fluorescence point sources can be localized with a precision several times greater than the resolution limit of the microscope. We show that the intermittent fluorescence or 'blinking' of quantum dots can analyzed by an Independent Component Analysis so as to identify the light emitted by each individual nanoparticle, localize it precisely, and thereby resolve groups of closely spaced (< lambda / 30) quantum dots. Both simulated and experimental data demonstrate that this technique is superior to localization based on Maximum Likelihood Estimation of the sum image under the assumption of point emitters. This technique has general application to any emitter with non-Gaussian temporal intensity distribution, including triplet state blinking. When applied to the labeling of structures, a high resolution "image" consisting of individually localized points may be reconstructed leading to the term "Pointillism".
Further improvement of the thermal stability of a partially stabilized Bacillus subtilis 3‐isopropylmalate dehydrogenase variant by random and site‐directed mutagenesis (1999)

A thermostabilized mutant of Bacillus subtilis 3-isopropylmalate dehydrogenase (IPMDH) obtained in a previous study contained a set of triple amino acid substitutions. To further improve the stability of the mutant, we used a random mutagenesis technique and identified two additional thermostabilizing substitutions, Thr22-->Lys and Met256-->Val, that separately endowed the protein with further stability. We introduced the two mutations into a single enzyme molecule, thus constructing a mutant with overall quintuple mutations. Other studies have suggested that an improved hydrophobic subunit interaction and a rigid type II beta-turn play important roles in enhancing the protein stability. Based on those observations, we successively introduced amino acid substitutions into the mutant with the quintuple mutations by site-directed mutagenesis: Glu253 at the subunit interface was replaced by Leu to increase the hydrophobic interaction between the subunits; Glu112, Ser113 and Ser115 that were involved in the formation of the turn were replaced by Pro, Gly and Glu, respectively, to make the turn more rigid. The thermal stability of the mutants was determined based on remaining activity after heat treatment and first-order rate constant of thermal unfolding, which showed gradual increases in thermal stability as more mutations were included.
Change-Centric Management of Versions in an XML Warehouse (2000)

We consider the management of changes in a Web Warehouse of XML data. Our approach is change-centric in that it focuses on deltas, i.e., the changes themselves vs. other approaches based on snapshots or integrated representations. We study a logical representation of changes based on deltas and some particular identifiers, XIDs. We consider implementation issues and analyze the advantages and disadvantages of several storage policies. Based on some requirements (certain functionalities that we want to support efficiently), we motivate the choice of our particular storage policy. It is based on storing the last version, &amp;quot;completed&amp;quot; forward deltas and on an original identification scheme for XML nodes. We report briefly on the status of an implementation within the Xyleme project.
FTY720, a Novel Immunosuppressant, Induces Sequestration of Circulating Mature Lymphocytes by Acceleration of Lymphocyte Homing in Rats. II. FTY720 Prolongs Skin Allograft Survival by Decreasing T Cell Infiltration into Grafts But Not Cytokine Production In Vivo (1998)

FTY720, a novel immunosuppressant, prolonged the survival of WKAH skin allografts transplanted into MHC-incompatible F344 rats. In this allograft model, the median survival time of the control group was 7 days, whereas those of the groups given FTY720 orally at 0.1 mg/kg and cyclosporin A (CsA) at 10 mg/kg were 10.5 and 11 days, respectively. In contrast, FTY720 (0.1 mg/kg) combined with CsA (10 mg/kg) synergistically prolonged allograft survival with a median survival time exceeding 70 days. To elucidate the mechanisms of this remarkable synergistic effect, mRNA expressions of IL-2 and IFN-gamma and that of CD3 (delta-chain), which reflects T cell infiltration, in allografts were temporally analyzed using a semiquantitative PCR method. In WKAH skin allografts, mRNA levels of IL-2, IFN-gamma, and CD3 were increased as compared with isograft controls, peaking on days 4 to 5. CsA (10 mg/kg) significantly inhibited elevations of IL-2 and IFN-gamma mRNA, while slightly inhibiting that of CD3 mRNA in allografts. On the contrary, FTY720 (0.1 mg/kg) markedly inhibited the elevation of CD3 mRNA, while slightly inhibiting those of IL-2 and IFN-gamma mRNA. FTY720 (0.1 mg/kg) combined with CsA (10 mg/kg) almost completely suppressed the intragraft expressions of mRNA for IL-2, IFN-gamma, and CD3. Immunohistochemical staining and flow cytometric analysis also confirmed that FTY720 decreased T cell infiltration into allografts. From these results, the synergistic effect of FTY720 combined with CsA on prolongation of allograft survival is presumably based on the respective inhibitions of T cell infiltration and cytokine production in grafts.