gebhart/patrepeval huggingface dataset:
New Insights and Faster Computations for the Graphical Lasso (2011)

We consider the graphical lasso formulation for estimating a Gaussian graphical model in the high-dimensional setting. This approach entails estimating the inverse covariance matrix under a multivariate normal model by maximizing the ℓ1-penalized log-likelihood. We present a very simple necessary and sufficient condition that can be used to identify the connected components in the graphical lasso solution. The condition can be employed to determine whether the estimated inverse covariance matrix will be block diagonal, and if so, then to identify the blocks. This in turn can lead to drastic speed improvements, since one can simply apply a standard graphical lasso algorithm to each block separately. Moreover, the necessary and sufficient condition provides insight into the graphical lasso solution: the set of connected nodes at any given tuning parameter value is a superset of the set of connected nodes at any larger tuning parameter value. This article has supplementary material online.
A fuzzy vehicle detection based on contour size similarity (2005)

In this paper, the obstacle detection for autonomous vehicle is carried out by a monocular camera, which is capable of detecting multiple obstacles, identifying the difference between obstacles and text or shadows on the road surface. The task of detection can be fulfilled under the circumstances of general brightness or in the presence of strong sunshine. An obstacle detection approach named contour size similarity (CSS) is developed in this paper. CSS is a way to make use of the contour size of objects and compare the similarity between objects and obstacles detected by means of fuzzy so as to judge whether the objects in the images are the obstacles we want to detect. The obstacles in this paper mainly refer to vehicles. Vehicles and obstacles with similar contour of vehicles can be detected by CSS. Then, we use section division to find out the nearest obstacle in separate section to provide necessary information for autonomous vehicles.
Identification of the lymphokines, interferon-gamma and interleukin-2, in inflammatory eye diseases. (1988)

The exact pathogenic mechanisms involved in autoimmune and inflammatory eye diseases are not known. However, studies during the past few years indicate that a T cell infiltrate, T cell sensitization to retinal antigens and expression of major histocompatibility complex (MHC) class II antigens are associated with this process. In this report we show that the lymphokines, IL-2 and IFN-gamma, are present in the human eye during inflammatory and autoimmune diseases. The presence of these lymphokines is associated with a lymphocyte infiltrate, predominantly of T cell origin, and with the expression of MHC class II antigens on both the infiltrating cells and ocular resident cells, that is, retinal pigment epithelial (rpe) cells and retinal vascular endothelial cells. Furthermore, in vitro studies demonstrate that IFN-gamma can enhance the expression of the HLA-DR determinant on both of these cell types. These observations suggest that lymphokine induced class II antigen expression may serve as a local amplification system in autoimmune and inflammatory eye diseases. A better understanding of the role of lymphokines in the mechanisms involved in the development of autoimmunity and inflammation may be beneficial in the treatment of these diseases.
Phosphorylation of Synthetic Peptides by a CDPK and Plant SNF1-Related Protein Kinase. Influence of Proline and Basic Amino Acid Residues at Selected Positions (2001)

Spinach (Spinacia oleracea L.) leaf sucrose-phosphate synthase (SPS) can be inactivated by phosphorylation of Ser-158 by calmodulin-like domain protein kinases (CDPKs) or SNF1-related protein kinases (SnRK1) in vitro. While the phosphorylation site sequence is relatively conserved, most of the deduced sequences of SPS from dicot species surrounding the Ser-158 regulatory phosphorylation site contain a Pro residue at P-4 (where P is the phosphorylated Ser); spinach is the exception and contains an Arg at P-4. We show that a Pro at P-4 selectively inhibits phosphorylation of the peptide by a CDPK relative to a SnRK1. The presence of a Pro at P-4, by allowing a tight turn in the peptide substrate, may interfere with proper binding of residues at P-5 and beyond. Both kinases had greater activity with peptides having basic residues at P-6 and P+5 (in addition to the known requirement for an Arg at P-3/P-4), and when the residue at P-6 was a His, the pH optimum for phosphorylation of the peptide was acid shifted. The results are used to predict proteins that may be selectively phosphorylated by SnRK1s (as opposed to CDPKs), such as SPS in dicot species, or may be phosphorylated in a pH-dependent manner.
A study of a new disease of cotton caused by the fungus Dematophora necatrix. (2004)

In August 2001, a new destructive disease of cotton was observed in Evia Island (central Greece), for the first time. Diseased plants with yellowish, wilted dry foliage, with a progressive growth decline, developed sudden wilt syndrome and eventually died. Underground, the main roots were rotted and covered with white, cottony-like mycelia. The first indications of the disease were observed during the middle of July in localized areas in one isolated field. From the diseased plants it was isolated a fungal species which gave growth to white septate mycelia and dark-brown sclerotia on PDA media, after two weeks of incubation at 22°C. The mycelia had pear-shaped swellings adjacent to the septa. In microscopic observations of infected root tissues, similar mycelial formations were found. Based on the morphological characteristics the pathogen was identified as Dematophora necatrix, the anamorphic stage of Rosellinia necatrix. The virulence of representative isolates on the three cotton cultivars Acala SJ2, Christina and Myrto, was confirmed by artificial inoculations. The isolates from cotton were found very pathogenic to cotton plants, irrespective of growth stage or cultivar. This study includes the report of a new disease of cotton, the isolation and identification of the pathogen and the susceptibility of different cultivars and stages in plant growth to selected D. necatrix isolates.
Heat Treatment Effect on Crystalline Structure and Photoelectrochemical Properties of Anodic TiO2 Nanotube Arrays Formed in Ethylene Glycol and Glycerol Based Electrolytes (2015)

The effect of annealing temperature on crystal structure of anodic titanium dioxide (ATO) layers prepared via anodization in the ethylene glycol and glycerol based electrolytes was studied. Then samples were annealed in air at the temperatures ranging from 400 to 1000 °C. The XRD measurements proved that a gradual phase change from anatase to rutile occurs with increasing annealing temperature. The anatase-to-rutile transformation occurs between 500 and 600 °C. The changes in the average crystallite sizes of anatase and rutile occurring during heat treatment of ATO layers were correlated with the mechanism of rutile phase nucleation. It was found also that the transition to the rutile phase in the samples formed in the ethylene glycol based electrolyte is considerably retarded and takes place at higher annealing temperatures due to the higher content of the embedded fluoride ions. The photoelectrochemical performance of ATO layers were studied under pulsed UV illumination. Photocurrent vs incident light wavelength and applied potential plots were recorded. The highest photocurrents were observed for the samples annealed at 400 °C, regardless of the electrolyte. It was demonstrated that the decrease in photocurrent values is related with the decreasing amount of the anatase phase in ATO samples. The enhanced photocurrent response was observed for ATO layers decorated with Ag nanoparticles. The highest photoconversion efficiencies, determined by incident photon-to-current efficiency (IPCE) calculations, were observed for the wavelength of 350 nm.
The cancer survivor’s companion Frances Goodhart The cancer survivor’s companion , Lucy Atkins Piatkus £14.99 278pp 9780749954857 074995485X (2012)

THIS BOOK sets out to be a companion to those recovering from cancer, and useful for lay and professional people who play a part in that recovery. The writers assume the reader has little knowledge of either cancer or medical terminology.
Human Embryonic Stem Cell-Derived “NET-Like” Structure Serves as a Hematopoietic Progenitor Niche and Favors Generation of Mature Megakaryocytes and Functional Platelets. (2006)

Abstract Human embryonic stem cells (hESCs) are proposed as an alternative source in regenerative medicine while being a promising tool to trace earliest ontogeny in vivo. Anucleate platelets can be irradiated to eliminate residual ESCs that potentially cause immunological rejection and teratoma formation in transplantation. Herein, we describe for the first time the generation of functional platelets from hESCs (Kyoto hES1, -2, and -3) by a novel method that is distinct from previously established OP9 co-culture. Exogenous combination of TPO, VEGF and IGF-II allowed hECSs to facilitate the differentiating kinetics of hematopoietic marker emergence when cultured on feeder cells, 10T1/2, whereas independent single administration had little effect on hematopoietic differentiation (P&lt;0.01). Consequently, unique “NET-like” structures expressing VE-cadherin low+, PECAM-1 high+, CD34 high+, CD45 + and VEGF-R2 + were observed around 14–15 days of culture. These structures contained hematopoietic progenitors capable of forming hematopoietic colonies in semisolid culture, or of differentiating into mature megakaryocytes in the presence of TPO, IL-6, and IL-11 (around 45 % of total cells displayed GPIbα +GPIX + by day 23). While totally 24–25 days culture was required for production of hESC-derived integrin αIIb +GPIX + platelets in this way, the platelets exhibited specific fibrinogen-bound to integrin αIIbβ3 in the presence of G-protein coupled receptor agonists in a dose-dependent manner. The efficiency of platelet production appeared to be well correlated with the frequency of “NET-like” structure. Thus, this structure may be a useful hallmark in our newly obtained culture method that may serve as an invaluable tool for not only generation of hESC-derived functional platelets but also studying niche machinery in hematopoiesis.
On the Thermally Reversible Dynamic Hydration Behavior of Oligo(ethylene glycol) Methacrylate-Based Polymers in Water (2012)

Dynamic thermally reversible hydration behavior of a well-defined thermoresponsive copolymer P(MEO2MA-co-OEGMA475) in D2O synthesized by ATRP random copolymerization of 2-(2-methoxyethoxy)ethyl methacrylate (MEO2MA) and oligo(ethylene glycol) methacrylate (Mn = 475 g/mol) was studied by means of IR spectroscopy in combination with perturbation correlation moving window (PCMW) technique and two-dimensional correlation spectroscopy (2DCOS). Largely different from poly(N-isopropylacrylamide) (PNIPAM), P(MEO2MA-co-OEGMA475) exhibits a sharp change below LCST and a gradual change above LCST due to the absence of strong intermolecular hydrogen bonding interactions between polymer chains, and the apparent phase transition is mainly arising from the multiple chain aggregation without a precontraction process of individual polymer chains. Additionally, the self-aggregation process of P(MEO2MA-co-OEGMA475) is found to be mainly dominated or driven by the conformation changes of oxyethylene side chains, which collapse first to get close to the hydrophobic backbones and then distort to expose hydrophilic ether oxygen groups to the “outer shell” of polymer chains as much as possible. On the other hand, PCMW easily determined the phase transition temperature to be ca. 32.5 °C during heating and ca. 31 °C during cooling as well as the transition temperature range to be 28.5–37 °C. 2DCOS was finally employed to discern the sequence order of all the group motions during heating and cooling. It is concluded that during the phase transition P(MEO2MA-co-OEGMA475) chains successively experience “hydrated chains–dehydrated chains–loosely aggregated micelles–densely aggregated micelles” four consecutive conformation changes. The results were further confirmed by temperature-variable 1H NMR analysis and molecular dynamics simulation.
Toehold of dsDNA exchange affects the hydrogel swelling kinetics of a polymer–dsDNA hybrid hydrogel (2010)

Hydrogel-based label-free nucleic acids sensor materials using high resolution interferometric readout of hydrogel swelling changes was prepared and characterized with respect to molecular design parameters. The DNA-sensitive hydrogel comprised sensing (S) and blocking (B) oligonucleotide pairs copolymerized with the network and formed reversible crosslinks in addition to stable covalent ones. Oligonucleotide probes (P) complementary to S with longer complementary regions comparing to B results in competitive replacement of S–B strands. The associated destabilization of DNA crosslinks results in changes of the hydrogel swelling. S–B dioligonucleotidic crosslinkers were designed with 8, 12 and 16 basepairs in complementary regions and were destabilized by probes with matching sequences with 2, 6 and 10 excess basepairs in the so-called “toe-hold” region. The kinetics of hydrogel swelling was tested at room and body temperature for hydrogels with different covalent crosslink densities. In general, the swelling kinetics was faster for longer “toe-holds” and slower for the longer and more stable blocking sequence. An increase of the covalent crosslink density resulted in a decrease of the swelling rate. The swelling of the hydrogel was faster the higher the temperature and closer to the S–B melting point. The following work shows direct correlation between the kinetics of strand displacement reaction and hydrogel swelling rates and provides a direction for further application of DNA-sensitive hydrogels.
Targeting protein–protein interactions by rational design: mimicry of protein surfaces (2006)

Protein-protein interactions play key roles in a range of biological processes, and are therefore important targets for the design of novel therapeutics. Unlike in the design of enzyme active site inhibitors, the disruption of protein-protein interactions is far more challenging, due to such factors as the large interfacial areas involved and the relatively flat and featureless topologies of these surfaces. Nevertheless, in spite of such challenges, there has been considerable progress in recent years. In this review, we discuss this progress in the context of mimicry of protein surfaces: targeting protein-protein interactions by rational design.
Preparation and Characterization of Fulleroid and Methanofullerene Derivatives (1995)

We describe the synthesis and complete characterization of soluble derivatives of C-60 for applications to physics and biology. The goal of the strategy was to have a ''modular'' approach in order to be able to easily vary a functional group attached indirectly to the cluster. The functionality could be hydrophilic (e.g., histamide) or hydrophobic (e.g., cholestanoxy). The former was prepared for biological studies and the latter for photophysical studies toward improvement of photoinduced electron transfer efficiencies in the fabrication of photodetectors and photodiodes. An important intermediate, a carboxylic acid, was found to be recalcitrant to characterization by the usual mass spectroscopic and elemental analysis techniques. This problem was solved by the use of MALDIMS. The carboxylic acid was easily converted to the key intermediate acid chloride, which in turn was convertible to a large variety of derivatives. Both isomeric forms ([5,6], fulleroid and [6,6], methanofullerene) of the C-61 clusters were prepared. The fulleroid formation could have given rise to a 50:50 mixture of phenyl-over-former pentagon phenyl-over-former hexagon isomers but, remarkably, afforded a 95:5 mixture of these isomers, respectively. The fulleroid and methano-fullerene gave different cyclic voltammograms, with the former being reduced at 34 mV more positive potential than the latter.
Spacing of palindromic half sites as a determinant of selective STAT (signal transducers and activators of transcription) DNA binding and transcriptional activity. (1995)

Signal transducers and activators of transcription (STAT proteins) bind to palindromic sequence elements related to interferon gamma (IFN-gamma) activation sites, which were first identified in the promoters of IFN-gamma-inducible genes. Although the sequences of the natural palindromic STAT-binding elements vary considerably, they conform to the general structure TT(N)5AA. We have systematically examined the effects of the spacing between the TT and AA core half sites on the binding of the STAT complexes activated by IFN-gamma, interleukin (IL) 6, granulocyte-macrophage colony-stimulating factor, and IL-4. We show that (i) as suggested earlier, a core palindromic TT--AA motif with a 5-bp spacing displays general STAT binding, (ii) a palindromic motif with a spacing of 4 bp selectively binds to complexes containing Stat3, and (iii) a motif with a 6-bp spacing selectively binds the STAT complexes activated by IL-4. We have examined natural elements in the promoters of cytokine-responsive genes that differ in half-site spacing and found that they display binding properties predicted from the synthetic binding sites. Furthermore, the observed differential selective binding characteristics for the most part correlate with the ability to mediate transcriptional activation of transfected test genes in response to the cytokines tested. Our results thus demonstrate that the specificity of STAT-directed transcription in response to particular cytokines or cytokine families depends in part on the spacing of half sites within the conserved response element sequence.
The volatile constituents of the scent gland reservoir of the fruit-spotting bug, Amblypelta nitida (1972)

Using combined gas chromatography and mass spectrometry, ten components of the scent-gland complex of the coreoid Amblypelta nitida Stal have been identified. Of specific interest is the presence in the gland reservoir of 2-n-butyloct-2-enal, the aldol condensation-dehydration product of hexanal.
Hematopoietic and Endothelial Differentiation of Human Induced Pluripotent Stem Cells (2009)

Induced pluripotent stem cells (iPSCs) provide an unprecedented opportunity for modeling of human diseases in vitro, as well as for developing novel approaches for regenerative therapy based on immunologically compatible cells. In this study, we employed an OP9 differentiation system to characterize the hematopoietic and endothelial differentiation potential of seven human iPSC lines obtained from human fetal, neonatal, and adult fibroblasts through reprogramming with POU5F1, SOX2, NANOG, and LIN28 and compared it with the differentiation potential of five human embryonic stem cell lines (hESC, H1, H7, H9, H13, and H14). Similar to hESCs, all iPSCs generated CD34(+)CD43(+) hematopoietic progenitors and CD31(+)CD43(-) endothelial cells in coculture with OP9. When cultured in semisolid media in the presence of hematopoietic growth factors, iPSC-derived primitive blood cells formed all types of hematopoietic colonies, including GEMM colony-forming cells. Human induced pluripotent cells (hiPSCs)-derived CD43(+) cells could be separated into the following phenotypically defined subsets of primitive hematopoietic cells: CD43(+)CD235a(+)CD41a(+/-) (erythro-megakaryopoietic), lin(-)CD34(+)CD43(+)CD45(-) (multipotent), and lin(-)CD34(+)CD43(+)CD45(+) (myeloid-skewed) cells. Although we observed some variations in the efficiency of hematopoietic differentiation between different hiPSCs, the pattern of differentiation was very similar in all seven tested lines obtained through reprogramming of human fetal, neonatal, or adult fibroblasts with three or four genes. Although several issues remain to be resolved before iPSC-derived blood cells can be administered to humans for therapeutic purposes, patient-specific iPSCs can already be used for characterization of mechanisms of blood diseases and for identification of molecules that can correct affected genetic networks.
In Vivo Blockade of the Programmed Cell Death-1 Pathway Using Soluble Recombinant PD-1-Fc Enhances CD4+ and CD8+ T Cell Responses but Has Limited Clinical Benefit (2013)

The programmed cell death-1 (PD-1)/programmed cell death ligand-1 pathway has been shown to limit cell-mediated effector functions during chronic viral infections impeding clearance of pathogens. As a strategy to reverse this exhaustion and increase T cell polyfunctionality, PD-1 ligands were blocked in vivo using a recombinant macaque PD-1 fused to a macaque Ig-Fc (rPD-1-Fc) in SIVmac239-infected rhesus macaques during the early chronic phase of infection, either alone or in combination with antiretroviral therapy. In vitro blockade showed improvement of Ag-specific CD4(+) and CD8(+) T cells from monkeys chronically infected with SIV. Of note, a prolonged 5-d blockade in culture was beneficial for both gag-specific CD4(+) and CD8(+) T cells based on proliferation and dual cytokine production. Although the in vivo administration of rPD-1-Fc induced enhanced SIV-specific CD4 and CD8 T cell proliferation both in the blood and gut, it failed to alter plasma viremia. However, rPD-1-Fc administration in the context of antiretroviral therapy interruption induced a significant delay of viral load rebound. In addition, rPD-1-Fc administration in MamuA*001(+) monkeys led to both an increase in the frequencies and Ki67 expression of GagCM9(+) CD8(+) T cells in the blood and rectal mucosa and polyfunctionality of GagCM9(+) CD8(+) T cells in blood. In conclusion, however, our data suggest that PD-1/programmed cell death ligand-1 blockade using soluble rPD-1-Fc instead of anti-PD-1 mAb, although effective in rescuing the effector function of SIV-specific CD4(+) and CD8(+) T cells during the early chronic phase of infection, has limited clinical benefit.
SNAP-25 Is Targeted to the Plasma Membrane through a Novel Membrane-binding Domain (1999)

SNAP-25, syntaxin, and synaptobrevin are SNARE proteins that mediate fusion of synaptic vesicles with the plasma membrane. Membrane attachment of syntaxin and synaptobrevin is achieved through a C-terminal hydrophobic tail, whereas SNAP-25 association with membranes appears to depend upon palmitoylation of cysteine residues located in the center of the molecule. This process requires an intact secretory pathway and is inhibited by brefeldin A. Here we show that the minimal plasma membrane-targeting domain of SNAP-25 maps to residues 85-120. This sequence is both necessary and sufficient to target a heterologous protein to the plasma membrane. Palmitoylation of this domain is sensitive to brefeldin A, suggesting that it uses the same membrane-targeting mechanism as the full-length protein. As expected, the palmitoylated cysteine cluster is present within this domain, but surprisingly, membrane anchoring requires an additional five-amino acid sequence that is highly conserved among SNAP-25 family members. Significantly, the membrane-targeting module coincides with the protease-sensitive stretch (residues 83-120) that connects the two alpha-helices that SNAP-25 contributes to the four-helix bundle of the synaptic SNARE complex. Our results demonstrate that residues 85-120 of SNAP-25 represent a protein module that is physically and functionally separable from the SNARE complex-forming domains.