gebhart/patrepeval huggingface dataset:
Direct genomic sequencing of bacterial DNA: the pyruvate kinase I gene of Escherichia coli. (1989)

The genomic sequencing procedure is applied to the direct sequencing of uncharacterized regions of bacterial DNA by a "multiplex walking" approach. Samples of bulk Escherichia coli DNA are cut with various restriction enzymes, subjected to chemical sequencing degradations, run in a sequencing gel, and transferred to nylon membranes. When a labeled oligomer is hybridized to a membrane, a sequence ladder appears wherever the probe lies near a restriction cut. New probes, based on sequence that lies beyond other restriction sites, are then synthesized, and the membranes are reprobed to reveal new sequence. Repeated cycles of oligomer probe synthesis and subsequent reprobing permit rapid sequence walking along the genome. This oligomer walking technique was used to sequence the pyruvate kinase (EC 2.7.1.40) gene in E. coli without resorting to cloning or to library construction. The sequenced region was amplified by the polymerase chain reaction and subsequently transcribed and translated using both in vivo and in vitro systems, and the resultant gene product characterized to show that the gene encodes the type I isoform of pyruvate kinase.
Deformation of carbon nanotubes in nanotube–polymer composites (1999)

Composites of uniaxially oriented multiwalled carbon nanotubes embedded in polymer matrices were fabricated and investigated by transmission electron microscopy. In strained composite films, buckling was ubiquitously observed in bent nanotubes with large curvatures. By analyses of a large number of bent nanotubes, the onset buckling strain and fracture strain were estimated to be ≈5% and ⩾18%, respectively. The buckling wavelengths are proportional to the dimensions of the nanotubes. Examination of the fracture surface showed adherence of the polymer to the nanotubes.
A Novel Method for the Fabrication of Fibrin-Based Electrospun Nanofibrous Scaffold for Tissue-Engineering Applications (2011)

In this study, fibrin, which is superior to fibrinogen in both structural and functional properties, has for the first time been electrospun successfully into uniform nano fibers resembling the extracellular matrix (ECM). The methods of fabrication and characterization of this unique scaffold are presented. Using poly (vinyl) alcohol as an "electrospinning-driving" polymer, we have developed a novel method for the fabrication of fibrin into a nanofibrous scaffold for various tissue-engineering applications starting from human-plasma-derived fibrinogen and thrombin and combining these ingredients within the syringe of an electrospinning setup under high voltage. In this fashion, fibrin nanofibrous scaffold is produced in a one-step approach without the need for subsequent cross-linking by synthetic agents that compromise the biological properties of the scaffold. Characterization of the electrospun membrane was done by scanning electron microscopy (SEM), Fourier transform infrared spectroscopy, and fibrin specific phosphotungstic acid hematoxylin staining. SEM data revealed the formation of bead-free fibers with a dimension ranging from 50-500 nm, which exactly mimics the fiber diameter of native ECM. Cell attachment and proliferation studies revealed that the scaffold supports the attachment, spreading, and proliferation of human umbilical cord blood-derived mesenchymal stem cells.
Preliminary Studies of Some 99mTc Labeled Potential Myocardial Metabolic Agents in Rabbits (1997)

SummaryFour groups of new ligands have been designed, synthetized and labeled with 99mTc. Each compound possesses either “active” carboxyl groups for interaction with coenzym-A, or are conjugate of glucose, aspartic acid or cystein. Gamma camera imaging in rabbits were carried out and the heart was chosen as target organ. Two compounds, “ASPEC” and “CEPHACYS” were taken up by the myocardium up to 1.1 and 1.63% of i.d., respectively.
Successful management of severe L‐asparaginase–associated pancreatitis by continuous regional arterial infusion of protease inhibitor and antibiotic (2008)

The current results indicated that early introduction of CRAI of protease inhibitor and antibiotic is suitable for treating severe AAP.
Rational Design of a Calcium-Binding Protein (2003)

Calcium ions play key roles as structural components in biomineralization and as a second messenger in signaling pathways. We have introduced a de novo designed calcium-binding site into the framework of a non-calcium-binding protein, domain 1 of CD2. The resulting protein selectively binds calcium over magnesium with calcium-binding affinity comparable to that of natural extracellular calcium-binding proteins (K(d) of 50 microM). This experiment is the first successful metalloprotein design that has a high coordination number (seven) metal-binding site constructed into a beta-sheet protein. Our results demonstrate the feasibility of designing a single calcium-binding site into a host protein, taking into account only local properties of a calcium-binding site obtained by a survey of natural calcium-binding proteins and chelators. The resulting site exhibits strong metal selectivity, suggesting that it should now be feasible to understand and manipulate signaling processes by designing novel calcium-modulated proteins with specifically desired functions and to affect their stability.
Chemical Protein Synthesis by Solid Phase Ligation of Unprotected Peptide Segments (1999)

In this paper we describe "solid phase chemical ligation" (SPCL), the application of the principles of polymer-supported organic synthesis to the construction of large polypeptide chains for the total chemical synthesis of proteins. In this method, each building block used is an unprotected peptide segment of 20 or more amino acids. These are consecutively reacted by chemical ligation, the chemoselective reaction of the unprotected peptide segments from aqueous solution, to make the polymer-supported target polypeptide. In a final step, the assembled full-length target polypeptide is released from the aqueous-compatible polymer support. Here we report chemistries for the attachment of the first segment to a polymer support, and for the assembly of the target polypeptide chain starting from the polymer-bound peptide segment. In this solid phase protein synthesis method, large target polypeptide chains can be built efficiently and rapidly by SPCL and, after release from the polymer support, folded to give functional protein molecules. Several examples of the application of SPCL are given: model peptides consisting of 27 and 68 amino acids, and polypeptides corresponding to the proteins C5a (74 amino acids) and MIF (115 amino acids), were each made in good yield and purity from the consecutive solid phase ligation of peptide segments. In addition, we report the total synthesis by SPCL of the enzyme "human group V secretory phospholipase A2" (GV-PLA2), which comprises a polypeptide of 118 amino acids containing 6 disulfide bonds. As demonstrated by these examples, SPCL is an important extension of our capabilities for total chemical protein synthesis.
Nature of respiratory stimulation in hyperthyroidism: the redox behaviour of cytochrome c (1995)

Hyperthyroid mitochondria show an increased Km and Vmax in the high affinity phase of cytochrome oxidase kinetics. During inhibitor titrations, cytochrome c shows a different redox behaviour in hyperthyroid with respect to protonophore-treated euthyroid mitochondria. The observations are discussed in terms of a different regulation of electron input and output into the respiratory chain during slip and leak types of uncoupling. In hyperthyroid mitochondria during inhibitor titrations, the pattern of the relationship between uncoupler-induced extra-respiration and membrane potential is highly non-linear. The complex nature of the respiratory stimulation in hyperthyroid mitochondria is discussed.
Effect of extracellular matrix topology on cell structure, function, and physiological responsiveness: hepatocytes cultured in a sandwich configuration (1996)

Extracellular matrix (ECM) geometry is an important modulator of cell polarity and function. For example, 3-dimensional matrices often more effectively induce differentiated cell function than traditional 2-dimensional substrates. The effect of ECM topology can be investigated in a controlled fashion using a technique whereby cells cultured on a single surface are overlaid with a second layer of ECM, thereby creating a "sandwich" configuration. Confluent monolayers of epithelial or endothelial cells overlaid in this fashion often reorganize into structures that are reminiscent of their native tissue. In the case of hepatocytes, the overlay causes a dramatic reorganization of the cytoskeleton, adoption of in vivo-like morphology and polarity, and expression of a wide array of liver-specific functions. In this short review, we use the sandwiched hepatocyte culture system to illustrate the effect of ECM geometry on cellular function. Pertinent studies are summarized in the context of defining the parallels, strengths, and limitations of this culture system as an in vitro model to study the physiology and morphogenesis of liver tissue. We also explore some of its potential uses as a model to study liver pharmacology and toxicology, and for the development of liver preservation techniques and liver-assist devices.
Novel Expanded Ring N-Heterocyclic Carbenes: Free Carbenes, Silver Complexes, And Structures (2008)

The addition of aromatic formamidines to dihaloalkanes proceeds in air under mildly basic conditions and in polar solvents to afford the corresponding amidinium salts in high yields. To demonstrate the wide scope of this methodology, several five-, six-, and seven-membered saturated N-heterocyclic amidinium salts have been prepared. The free carbenes 7-Mes, 7-Xyl, 7-Pri, 6-Mes, and 6-Xyl have also been isolated as stable white solids, and for the first time the solid state structures of free seven-membered N-heterocyclic carbenes have been determined (7-Mes and 7-Xyl). The syntheses and characterization of their Ag(I) halide complexes are also described and the X-ray structures for Ag(6-Pri)Br, Ag(7-Mes)Br, Ag(7-Xyl)I, and Ag(Xyl7-Mes)Br determined. On the basis of NMR data the silver halide species form either neutral, Ag(NHC)X, or ionic, [Ag(NHC)2][AgX2] complexes in solution. A feature of the expanded ring carbenes is the extremely large NCN angle (≥120°) and the consequential steric impact of the N-substituents on the metal center. For the free seven-membered ring carbenes the 13C NMR shifts are 258−260 ppm, well down field from those observed for the six- and five-membered ring carbenes.
Ionogels, ionic liquid based hybrid materials (2010)

The current interest in ionic liquids (ILs) is motivated by some unique properties, such as negligible vapour pressure, thermal stability and non-flammability, combined with high ionic conductivity and wide electrochemical stability window. However, for material applications, there is a challenging need for immobilizing ILs in solid devices, while keeping their specific properties. In this critical review, ionogels are presented as a new class of hybrid materials, in which the properties of the IL are hybridized with those of another component, which may be organic (low molecular weight gelator, (bio)polymer), inorganic (e.g. carbon nanotubes, silica etc.) or hybrid organic-inorganic (e.g. polymer and inorganic fillers). Actually, ILs act as structuring media during the formation of inorganic ionogels, their intrinsic organization and physicochemical properties influencing the building of the solid host network. Conversely, some effects of confinement can modify some properties of the guest IL, even though liquid-like dynamics and ion mobility are preserved. Ionogels, which keep the main properties of ILs except outflow, while allowing easy shaping, considerably enlarge the array of applications of ILs. Thus, they form a promising family of solid electrolyte membranes, which gives access to all-solid devices, a topical industrial challenge in domains such as lithium batteries, fuel cells and dye-sensitized solar cells. Replacing conventional media, organic solvents in lithium batteries or water in proton-exchange-membrane fuel cells (PEMFC), by low-vapour-pressure and non flammable ILs presents major advantages such as improved safety and a higher operating temperature range. Implementation of ILs in separation techniques, where they benefit from huge advantages as well, relies again on the development of supported IL membranes such as ionogels. Moreover, functionalization of ionogels can be achieved both by incorporation of organic functions in the solid matrix, and by encapsulation of molecular species (from metal complexes to enzymes) in the immobilized IL phase, which opens new routes for designing advanced materials, especially (bio)catalytic membranes, sensors and drug release systems (194 references).
Vertical compartmentation and cellular transformations in the germinal matrices of the embryonic rat cerebral cortex (1990)

Cellular compartmentation was studied in the germinal matrices (the primary neuroepithelium and the subventricular zone) of the rat cerebral cortex at successive stages of embryonic development. Three sets of materials were used: methacrylate-embedded brain sections from normal embryos, autoradiograms from embryos labeled with [3H]thymidine, and methacrylate-embedded sections from embryos exposed to 200 R X-ray. Examination of normal specimens showed that between Embryonic Day 12 (E12) and E15 the cortical germinal matrix consists only of a primary neuroepithelium. By Day E16, a subventricular zone has formed in the early developing ventrolateral aspect of the cortex. The subventricular zone grows in depth for several days, while at the same time the depth of the neuroepithelium decreases. Examination of short-survival thymidine radiograms revealed that the labeled cells do not form a continuous band in the neuroepithelium but aggregate in patches reminiscent of bunches of grapes strung one a line. It is postulated that this vertical periodicity is due to the alternation of cell aggregates with short and long cell cycle times. Finally, examination of the cortical neuroepithelium in rats exposed to 200 R X-ray showed that there is an alternation of radiosensitive (collapsing) and radioresistant (intact) patches that roughly correspond in size to the labeled and unlabeled patches seen in autoradiograms. Additional observations concern the onset of local cell proliferation in the white matter at late stages of fetal development and the transformation of the neuroepithelium into a matrix producing ependymal cells.
Micromachined high-Q inductors in a 0.18-μm copper interconnect low-k dielectric CMOS process (2002)

On-chip spiral micromachined inductors fabricated in a 0.18-/spl mu/m digital CMOS process with 6-level copper interconnect and low-K dielectric are described. A post-CMOS maskless micromachining process compatible with the CMOS materials and design rules has been developed to create inductors suspended above the substrate with the inter-turn dielectric removed. Such inductors have higher quality factors as substrate losses are eliminated by silicon removal and increased self-resonant frequency due to reduction of inter-turn and substrate parasitic capacitances. Quality factors up to 12 were obtained for a 3.2-nH micromachined inductor at 7.5 GHz. Improvements of up to 180% in maximum quality factor, along with 40%-70% increase in self-resonant frequency were seen over conventional inductors. The effects of micromachining on inductor performance was modeled using a physics-based model with predictive capability. The model was verified by measurements at various stages of the post-CMOS processing. Micromachined inductor quality factor is limited by series resistance up to a predicted metal thickness of between 6-10 /spl mu/m.
Synergistic and antagonistic effects of recombinant human interleukin (IL) 3, IL-1alpha, granulocyte and macrophage colony-stimulating factors (G-CSF and M-CSF) on the growth of GM-CSF-dependent leukemic cell lines. (1987)

Three human leukemia cell lines (TALL-101, AML-193, and MV4-11) that require granulocyte/macrophage-colony stimulating factor (GM-CSF) for growth in a chemically defined medium were examined for their response to recombinant human (rh) cytokines. Either rh interleukin (IL)-3 or rhGM-CSF alone supported the long term growth of all three cell lines, and the two growth factors acted synergistically to stimulate the proliferation of the early T lymphoblastic leukemia (TALL-101) and of the monocytic leukemia (AML-193) cells. However, IL-3 antagonized the proliferation of the biphenotypic B-myelomonocytic leukemia (MV4-11) cells in the presence of GM-CSF when both factors were used at very low concentrations. The rh granulocyte (G)-CSF independently supported the long and short term growth of AML-193 and MV4-11, respectively, and synergized with GM-CSF in inducing proliferation of these cells. By contrast, G-CSF did not stimulate TALL-101 cell growth and antagonized the effect of GM-CSF such that proliferation was arrested. Although neither rh macrophage (M)-CSF nor rhIL-1 alpha independently promoted proliferation of the three leukemia cell lines, these cytokines were able to either up- or down-regulate the GM-CSF-dependent growth of these cells. Taken together, these data demonstrate that leukemic cells often require the synergistic action of several cytokines for optimal growth, whereas other combinations of factors may be growth-inhibitory. This raises the possibility that multiple hemopoietic growth factors sustain or control leukemic cell proliferation also in vivo. In addition, the observation the G-CSF, M-CSF, and IL-1 alpha can, in some cases, arrest cell proliferation without inducing differentiation suggests that the programs of proliferative arrest and differentiation in leukemic cells can be dissociated.
An Accurate Analytical Model for 802.11e EDCA under Different Traffic Conditions with Contention-Free Bursting (2011)

Extensive research addressing IEEE 802.11e enhanced distributed channel access (EDCA) performance analysis, by means of analytical models, exist in the literature. Unfortunately, the currently proposed models, even though numerous, do not reach this accuracy due to the great number of simplifications that have been done. Particularly, none of these models considers the 802.11e contention free burst (CFB) mode which allows a given station to transmit a burst of frames without contention during a given transmission opportunity limit (TXOPLimit) time interval. Despite its influence on the global performance, TXOPLimit is ignored in almost all existing models. To fill in this gap, we develop in this paper a new and complete analytical model that (i) reflects the correct functioning of EDCA, (ii) includes all the 802.11e EDCA differentiation parameters, (iii) takes into account all the features of the protocol, and (iv) can be applied to all network conditions, going from nonsaturation to saturation conditions. Additionally, this model is developed in order to be used in admission control procedure, so it was designed to have a low complexity and an acceptable response time. The proposed model is validated by means of both calculations and extensive simulations.
FZD7 has a critical role in cell proliferation in triple negative breast cancer (2011)

Breast cancer is genetically and clinically heterogeneous. Triple negative breast cancer (TNBC) is a subtype of breast cancer that is usually associated with poor outcome and lack of benefit from targeted therapy. We used microarray analysis to perform a pathway analysis of TNBC compared with non-triple negative breast cancer (non-TNBC). Overexpression of several Wnt pathway genes, such as frizzled homolog 7 (FZD7), low density lipoprotein receptor-related protein 6 and transcription factor 7 (TCF7) was observed in TNBC, and we directed our focus to the Wnt pathway receptor, FZD7. To validate the function of FZD7, FZD7shRNA was used to knock down FZD7 expression. Notably, reduced cell proliferation and suppressed invasiveness and colony formation were observed in TNBC MDA-MB-231 and BT-20 cells. Study of the possible mechanism indicated that these effects occurred through silencing of the canonical Wnt signaling pathway, as evidenced by loss of nuclear accumulation of β-catenin and decreased transcriptional activity of TCF7. In vivo studies revealed that FZD7shRNA significantly suppressed tumor formation, through reduced cell proliferation, in mice bearing xenografts without FZD7 expression. Our findings suggest that FZD7-involved canonical Wnt signaling pathway is essential for tumorigenesis of TNBC, and thus, FZD7 shows promise as a biomarker and a potential therapeutic target for TNBC.
Cloning and expression of cDNA for a Na/Pi cotransport system of kidney cortex. (1991)

A cDNA library from rabbit kidney cortex was screened for expression of Na-dependent transport of phosphate (Pi) using Xenopus laevis oocytes as an expression system. A single clone was eventually isolated (designated NaPi-1) that stimulated expression of Na/Pi cotransport approximately 700-fold compared to total mRNA. The predicted sequence of the Na/Pi cotransporter consists of 465 amino acids (relative molecular mass, 51,797); hydropathy profile predictions suggest six (possibly eight) membrane-spanning segments. In vitro translation of NaPi-1/complementary RNA in the presence of pancreatic microsomes indicated NaPi-1 to be a glycosylated protein; four potential N-glycosylation sites are present in the amino acid sequence. Northern blot analysis demonstrated the presence of NaPi-1/mRNA in kidney cortex and liver; no hybridization signal was obtained with mRNA from other tissues (including small intestine). Kinetic analysis of Na/Pi cotransport expressed by NaPi-1/complementary RNA demonstrated characteristics (sodium interaction) similar to those observed in cortical apical membranes. The alignment of 5 amino acid residues (Gly342/Ala381-Xaa-Xaa-Xaa-Xaa-Leu386-Xaa-Xaa-Xaa-P ro390- Arg391) is consistent with a motif proposed for Na-dependent transport systems. We conclude that we have cloned a cDNA for a Na/Pi cotransport system present in rabbit kidney cortex.
Expression of functional (Na+ + K+)‐ATPase from cloned cDNAs (1987)

Functional (Na+ + K+)-ATPase is formed in Xenopus oocytes injected with alpha- and beta-subunit-specific mRNAs derived from cloned Torpedo californica cDNAs. Both the mRNAs are required for the expression of functional (Na+ + K+)-ATPase.