gebhart/patrepeval huggingface dataset:
Topological insulators with inversion symmetry (2007)

Topological insulators are materials with a bulk excitation gap generated by the spin-orbit interaction that are different from conventional insulators. This distinction is characterized by ${Z}_{2}$ topological invariants, which characterize the ground state. In two dimensions, there is a single ${Z}_{2}$ invariant that distinguishes the ordinary insulator from the quantum spin-Hall phase. In three dimensions, there are four ${Z}_{2}$ invariants that distinguish the ordinary insulator from ``weak'' and ``strong'' topological insulators. These phases are characterized by the presence of gapless surface (or edge) states. In the two-dimensional quantum spin-Hall phase and the three-dimensional strong topological insulator, these states are robust and are insensitive to weak disorder and interactions. In this paper, we show that the presence of inversion symmetry greatly simplifies the problem of evaluating the ${Z}_{2}$ invariants. We show that the invariants can be determined from the knowledge of the parity of the occupied Bloch wave functions at the time-reversal invariant points in the Brillouin zone. Using this approach, we predict a number of specific materials that are strong topological insulators, including the semiconducting alloy ${\mathrm{Bi}}_{1\ensuremath{-}x}{\mathrm{Sb}}_{x}$ as well as $\ensuremath{\alpha}\text{\ensuremath{-}}\mathrm{Sn}$ and HgTe under uniaxial strain. This paper also includes an expanded discussion of our formulation of the topological insulators in both two and three dimensions, as well as implications for experiments.
NEGATIVE INDOCYANINE GREEN STAINING OF EPIRETINAL MEMBRANES (2002)

FOSTER, ROBERT E. MD; PETERSEN, MICHAEL R. MD, PhD; DA MATA, ANDREA P. MD; BURK, SCOTT E. MD, PhD; ROSA, ROBERT H. Jr MD; RIEMANN, CHRISTOPHER D. MD Author Information
Molecular Cloning and Expression of a Second Chondroitin N-Acetylgalactosaminyltransferase Involved in the Initiation and Elongation of Chondroitin/Dermatan Sulfate (2003)

We identified a novel human chondroitin N-acetylgalactosaminyltransferase, designated chondroitin GalNAcT-2 after a BLAST analysis of the GenBank(TM) data base using the sequence of a previously described human chondroitin N-acetylgalactosaminyltransferase (chondroitin GalNAcT-1) as a probe. The new cDNA sequence contained an open reading frame encoding a protein of 542 amino acids with a type II transmembrane protein topology. The amino acid sequence displayed 60% identity to that of human chondroitin GalNAcT-1. Like chondroitin GalNAcT-1, the expression of a soluble form of the protein in COS-1 cells produced an active enzyme, which not only transferred beta1,4-N-acetylgalactosamine (GalNAc) from UDP-[(3)H]GalNAc to a polymer chondroitin representing growing chondroitin chains (beta-GalNAc transferase II activity) but also to GlcUA beta 1-3Gal beta 1-O-C(2)H(4)NHCbz, a synthetic substrate for beta-GalNAc transferase I that transfers the first GalNAc to the core tetrasaccharide in the protein-linkage region of chondroitin sulfate. In contrast, the tetrasaccharide serine (GlcUA beta 1-3Gal beta 1-3Gal beta 1-4Xyl beta 1-O-Ser) derived from the linkage region, which is an inert acceptor substrate for chondroitin GalNAcT-1, served as an acceptor substrate. The coding region of this enzyme was divided into seven discrete exons, which is similar to the genomic organization of the chondroitin GalNAcT-1 gene, and was localized to chromosome 10q11.22. Northern blot analysis revealed that the chondroitin GalNAcT-2 gene exhibited a ubiquitous but differing expression in human tissues, and the expression pattern differed from that of chondroitin GalNAcT-1. Thus, we demonstrated redundancy in the chondroitin GalNAc transferases involved in the biosynthetic initiation and elongation of chondroitin sulfate, which is important for understanding the biosynthetic mechanisms leading to the selective chain assembly of chondroitin/dermatan sulfate on the linkage region tetrasaccharide common to various proteoglycans containing chondroitin/dermatan sulfate and heparin/heparan sulfate chains.
Synthesis and Evaluation of Insulin−Human Serum Albumin Conjugates (2005)

A series of human insulin maleimido derivatives with short and long linkers was synthesized by exploiting the variations in the pK(a) values and environment of the three amino groups present in the protein. The syntheses were accomplished in organic solvent because of maleimide's instability in basic aqueous media. The derivatives thus obtained were conjugated to the free thiol on Cys34 of human serum albumin (HSA) and purified. A structure-activity relationship based on in vitro receptor binding and activation results for this series of insulin-HSA conjugates showed that the best compounds were attached at the B1 position of insulin with either short or long linkers. Two conjugates were administered subcutaneously to streptozotocin-induced diabetic rats and found to possess blood glucose normalizing activity up to 8 h post-administration. The return to diabetic plasma glucose levels was not observed within the time frame of the experiment (48 h). In comparison, the insulin-treated group's normalization activity lasted 2 h and returned to a diabetic level at 8 h. The onset of the conjugate activities were delayed by 1 h when compared to the activity of human insulin. The study results led to the identification of CJC-1575 as a potent and long lasting human insulin analogue.
Early Experience with an Internet Broadcast System Based on Overlay Multicast (2003)

Abstract: "In this paper, we report on experience in building and deploying an operational Internet broadcast system based on Overlay Multicast. In over a year, the system has been providing a cost-effective alternative for Internet broadcast, used by over 3600 users spread across multiple continents in home, academic and commercial environments. Technical conferences and special interest groups are the early adopters. Our experience confirms that Overlay Multicast can be easily deployed and can provide reasonably good application performance. The experience has led us to identify first-order issues that are guiding our future efforts and are of importance to any Overlay Multicast protocol or system. Our key contributions are (i) enabling a real Overlay Multicast application and strengthening the case for overlays as a viable architecture for enabling group communication applications on the Internet, (ii) the details in engineering and operating a fully functional streaming system, addressing a wide range of real-world issues that are not typically considered in protocol design studies, and (iii) the data, analysis methodology, and experience that we are able to report given our unique standpoint."
Rho-mediated Contractility Exposes a Cryptic Site in Fibronectin and Induces Fibronectin Matrix Assembly (1998)

Many factors influence the assembly of fibronectin into an insoluble fibrillar extracellular matrix. Previous work demonstrated that one component in serum that promotes the assembly of fibronectin is lysophosphatidic acid (Zhang, Q., W.J. Checovich, D.M. Peters, R.M. Albrecht, and D.F. Mosher. 1994. J. Cell Biol. 127:1447–1459). Here we show that C3 transferase, an inhibitor of the low molecular weight GTP-binding protein Rho, blocks the binding of fibronectin and the 70-kD NH2-terminal fibronectin fragment to cells and blocks the assembly of fibronectin into matrix induced by serum or lysophosphatidic acid. Microinjection of recombinant, constitutively active Rho into quiescent Swiss 3T3 cells promotes fibronectin matrix assembly by the injected cells. Investigating the mechanism by which Rho promotes fibronectin polymerization, we have used C3 to determine whether integrin activation is involved. Under conditions where C3 decreases fibronectin assembly we have only detected small changes in the state of integrin activation. However, several inhibitors of cellular contractility, that differ in their mode of action, inhibit cell binding of fibronectin and the 70-kD NH2-terminal fibronectin fragment, decrease fibronectin incorporation into the deoxycholate insoluble matrix, and prevent fibronectin's assembly into fibrils on the cell surface. Because Rho stimulates contractility, these results suggest that Rho-mediated contractility promotes assembly of fibronectin into a fibrillar matrix. One mechanism by which contractility could enhance fibronectin assembly is by tension exposing cryptic self-assembly sites within fibronectin that is being stretched. Exploring this possibility, we have found a monoclonal antibody, L8, that stains fibronectin matrices differentially depending on the state of cell contractility. L8 was previously shown to inhibit fibronectin matrix assembly (Chernousov, M.A., A.I. Faerman, M.G. Frid, O.Y. Printseva, and V.E. Koteliansky. 1987. FEBS (Fed. Eur. Biochem. Soc.) Lett. 217:124–128). When it is used to stain normal cultures that are developing tension, it reveals a matrix indistinguishable from that revealed by polyclonal anti-fibronectin antibodies. However, the staining of fibronectin matrices by L8 is reduced relative to the polyclonal antibody when the contractility of cells is inhibited by C3. We have investigated the consequences of mechanically stretching fibronectin in the absence of cells. Applying a 30–35% stretch to immobilized fibronectin induced binding of soluble fibronectin, 70-kD fibronectin fragment, and L8 monoclonal antibody. Together, these results provide evidence that self-assembly sites within fibronectin are exposed by tension.
Frequent Identification of HIV-1 DNA in Bronchoalveolar Lavage Cells Obtained from Individuals with the Acquired Immunodeficiency Syndrome (1991)

Tissue macrophages are recognized as a cellular target for infection with the human immunodeficiency virus type 1 (HIV-1). To characterize the nature of this cell-retrovirus interaction within the lower respiratory tract we analyzed fluid and cells obtained by bronchoalveolar lavage (BAL) of eight individuals with acquired immunodeficiency syndrome (AIDS) who were undergoing diagnostic fiberoptic bronchoscopy. Of these eight individuals, seven had active infection with Pneumocystis carinii; one had suspected cytomegalovirus pneumonitis. At the time of study two were receiving the antiretroviral drug zidovudine (azidothymidine [AZT]). HIV-1 could not be isolated from any of the eight samples of BAL fluid concentrated by ultracentrifugation through 20% sucrose. HIV-1 antigen (p24) was detected in one of eight samples of concentrated BAL fluid but could not be found in eight samples of media conditioned by overnight incubation with adherent BAL cells. Despite the infrequent detection of HIV-1 antigen it was possible to identify HIV-1 genomic sequences by the use of a DNA amplification technique, the polymerase chain reaction, in all eight BAL cell preparations. In BAL cells adherent for up to 5 days in culture this method detected retroviral DNA that hybridized to a complementary pair of primers located in the env and gag gene regions of HIV-1. These studies demonstrate the uniform presence of HIV-1 harboring cells within the airways of the lung in individuals with AIDS and active respiratory infection and may have implications for local organ defense.(ABSTRACT TRUNCATED AT 250 WORDS)
Improved management of lysosomal glucosylceramide levels in a mouse model of type 1 Gaucher disease using enzyme and substrate reduction therapy (2010)

Gaucher disease is caused by a deficiency of the lysosomal enzyme glucocerebrosidase (acid beta-glucosidase), with consequent cellular accumulation of glucosylceramide (GL-1). The disease is managed by intravenous administrations of recombinant glucocerebrosidase (imiglucerase), although symptomatic patients with mild to moderate type 1 Gaucher disease for whom enzyme replacement therapy (ERT) is not an option may also be treated by substrate reduction therapy (SRT) with miglustat. To determine whether the sequential use of both ERT and SRT may provide additional benefits, we compared the relative pharmacodynamic efficacies of separate and sequential therapies in a murine model of Gaucher disease (D409V/null). As expected, ERT with recombinant glucocerebrosidase was effective in reducing the burden of GL-1 storage in the liver, spleen, and lung of 3-month-old Gaucher mice. SRT using a novel inhibitor of glucosylceramide synthase (Genz-112638) was also effective, albeit to a lesser degree than ERT. Animals administered recombinant glucocerebrosidase and then Genz-112638 showed the lowest levels of GL-1 in all the visceral organs and a reduced number of Gaucher cells in the liver. This was likely because the additional deployment of SRT following enzyme therapy slowed the rate of reaccumulation of GL-1 in the affected organs. Hence, in patients whose disease has been stabilized by intravenously administered recombinant glucocerebrosidase, orally administered SRT with Genz-112638 could potentially be used as a convenient maintenance therapy. In patients naïve to treatment, ERT followed by SRT could potentially accelerate clearance of the offending substrate.
C4d Deposition without Rejection Correlates with Reduced Early Scarring in ABO-Incompatible Renal Allografts (2008)

C4d deposition in peritubular capillaries is a specific marker for the presence of antidonor antibodies in renal transplant recipients and is usually associated with antibody-mediated rejection (AMR) in conventional allografts. In ABO-incompatible grafts, however, peritubular capillary C4d is often present on protocol biopsies lacking histologic features of AMR; the significance of C4d in this setting remains unclear. For addressing this, data from 33 patients who received ABO-incompatible renal allografts (after desensitization) were retrospectively reviewed. Protocol biopsies were performed at 1 and/or 3 and 6 mo after transplantation in each recipient and at 12 mo in 28 recipients. Twenty-one patients (group A) had strong, diffuse peritubular capillary C4d staining without histologic evidence of AMR or cellular rejection on their initial protocol biopsies. The remaining 12 patients (group B) had negative or weak, focal peritubular capillary C4d staining. Three grafts (two in group B) were lost but not as a result of AMR. Excluding these three patients, serum creatinine levels were similar in the two groups at 6 and 12 mo after transplantation and at last follow-up; however, recipients in group A developed significantly fewer overall chronic changes, as scored by the sum of Banff chronic indices, than group B during the first year after transplantation. These results suggest that diffuse peritubular capillary C4d deposition without rejection is associated with a lower risk for scarring in ABO-incompatible renal allografts; the generalizability of these results to conventional allografts remains unknown.
New Piezoelectric Polymers (1998)

Four kinds of piezoelectric polymers are introduced. Submicron thin films of polyurea are prepared by vapor deposition polymerization. Poled films of aromatic polyurea exhibit the piezoelectric constant d 31 =20 pC/N, which is almost independent of temperature in the range of 100 to 200°C. Aliphatic polyureas show a ferroelectric hysteresis with a coercive field of about 100 MV/m. Single crystalline films of a copolymer of vinylidene fluoride and trifluoroethylene were prepared by annealing elongated films at a paraelectric temperature range avoiding the side surface contacts. No lamella structures were present and the crystallinity was near 100%. The large electromechanical coupling factors k 33 =0.3 and k 31 =0.1 were observed. A large electrostrictive constant R =2.6×10 -17 m 2 /V 2 was observed for polyurethane. With a dc bias field of 15 MV/m, a piezoelectric constant of d 33 =600 pC/N was obtained, which was larger than that of PZT. A shear piezoelectric constant d 14 =-10 pC/N was obtained for oriented films of poly-L-lactic acid, which were optically active and biodegradable. After poling, this polymer showed the tensile piezoelectricity and pyroelectricity.
The Effect on Subtilisin Activity of Oxidizing a Methionine Residue (1969)

Abstract The effects of hydrogen peroxide on a bacterial serine protease, subtilisin Carlsberg (EC 3.4.4.16), were investigated. Of the 5 methionine residues in this molecule, only 1, Residue 222, was oxidized to methionine sulfoxide. No other changes in amino acid composition were found. The oxidized enzyme was enzymatically active, but the efficiency was less than that of the native subtilisin. The extent of decrease in kcat was between 57 and 92%, depending on the substrate used. Km(app) increased for most substrates used, but it decreased for the N-benzyloxycarbonylglycine p-nitrophenyl ester. The change in individual reaction rate parameters was investigated using N-cinnamoylimidazole. The dissociation constant of the ES complex, K8, was greater for oxidized subtilisin than for native subtilisin, while the rate constants for the acylation step, k2, and the deacylation step, k3, were decreased.
Development of a Telemanipulator for Dexterity Enhanced (1995)

The precision and stability of motion achievable with the human hand limits current microsurgical practice. Were it possible to overcome these natural limits, better procedures of the eye, ear, hand, brain, and spin would result. Such issues of dexterity enhancement lie not only with scaling down surgical skills of the most gifted, but also addressing widely variable skills of the entire surgical community.
Demonstration of waveguide couplers fabricated using microtransfer molding (1997)

Arrays of single-mode optical waveguides, couplers, and interferometers were fabricated from a UV curable prepolymer using microtransfer molding. The coupling between the waveguides was reproducible and consistent across the array and was controlled after fabrication by additional UV exposure.
A comparison of post‐receptor signal transduction events in Jurkat cells transfected with either IL‐8R1 or IL‐8R2 Chemokine mediated activation of p42/p44 MAP‐kinase (ERK‐2) (1995)

The CXC chemokine, IL-8, is a potent chemoattractant of neutrophils and binds to two distinct receptors, termed IL-8R1 and IL-8R2. These receptors share high affinity for IL-8, however, only IL-8R1 is specific for IL-8 whereas IL-8R2 binds other related chemokines, including GRO alpha with high affinity. Stable Jurkat transfectants were generated expressing either functional IL-8R1 or IL-8R2 (J-IL8R1 and J-IL8R2). Both J-IL8R1 and J-IL8R2 exhibited high affinity IL-8 binding (Kd 3-5 nM) with respective receptor densities of 23,000 +/- 3,000 and 18,500 +/- 1,500. Pre-treatment of both transfectants with 1.0 micrograms/ml B. pertussis toxin (PTx) resulted in inhibition of IL-8 mediated intracellular Ca2+ mobilisation and chemotaxis, without altering the receptor's affinity for its ligand. This indicates that both receptors couple to a PTx-sensitive G-protein. Further studies showed that IL-8R1 and IL-8R2 could mediate time-dependent phosphorylation of p42/p44 MAP-kinase. In both transfectants, phosphorylation was maximal at 1-2 min after IL-8 stimulation and could be inhibited by PTx. Stimulation of J-IL8R1 and J-IL8R2 with GRO alpha revealed that this chemokine was a more potent activator of MAP-kinase in J-IL8R2, an observation reflected in the high affinity binding of GRO alpha to IL-8R2. These studies indicate that chemokines are capable of activating protein kinases and with regards to PTx-sensitivity and MAP-kinase stimulation, no significant differences between IL-8R1 and IL-8R2 post-receptor signalling occur during cell activation by IL-8.
Synthetic studies of the antitumor antibiotic streptonigrin. I. Synthesis of the A‐B ring portion of streptonigrin (1976)

Abstract Bromination of 6‐methoxy‐5,8‐quinolinedione gave the 7‐bromo derivative in quantitative yield. Treatment of the bromo compound with sodium azide followed by hydrogenation yielded 7‐amino‐6‐methoxy‐5,8‐quinolinedione, the A‐B ring portion of the antitumor antibiotic strep tonigrin. The corresponding 2‐methyl homolog was prepared in a similar manner from 6‐methoxy‐2‐methyl‐8‐nitroquinoline, which in turn, was obtained by a Skraup synthesis from 2‐nitro‐anisidine and crotonaldehyde.
Delivery systems for siRNA drug development in cancer therapy (2014)

Since the discovery of the Nobel prize-winning mechanism of RNA interference (RNAi) ten years ago, it has become a promising drug target for the treatment of multiple diseases, including cancer. There have already been some successful applications of siRNA drugs in the treatment of age-related macular degeneration and respiratory syncytial virus infection. However, significant barriers still exist on the road to clinical applications of siRNA drugs, including poor cellular uptake, instability under physiological conditions, off-target effects and possible immunogenicity. The successful application of siRNA for cancer therapy requires the development of clinically suitable, safe and effective drug delivery systems. Herein, we review the design criteria for siRNA delivery systems and potential siRNA drug delivery systems for cancer therapy, including chemical modifications, lipid-based nanovectors, polymer-mediated delivery systems, conjugate delivery systems, and others.
Water-Soluble Poly(ethylenimine)-Based Nitric Oxide Donors:  Preparation, Characterization, and Potential Application in Hemodialysis (2006)

A novel approach to potentially resolve serious thrombosis issues associated with kidney dialysis (hemodialysis) therapies is described. New water-soluble polymeric nitric oxide (NO) donors, based on the diazeniumdiolated branched poly(ethylenimine)s and their derivatives, are prepared and characterized. These macromolecular NO donors (with up to 4.15 micromol/mg of total NO release) are utilized as additives to the dialysate solution of model dialysis filters. The presence of these species can create a localized increase in NO levels at the high surface area dialysis fiber/blood interface within the hemodialyzers. Nitric oxide is a naturally occurring and potent anti-platelet agent and is expected to greatly decrease the risk of thrombosis in the dialysis units.
Effect of fatty acids and their derivatives on mitochondrial structures. (1989)

Reye's Syndrome (RS) is characterized by encephalopathy, fatty degeneration of viscera and high levels of free fatty acids which are implicated in cellular toxicity. We have examined the effects of octanoic acid (C8:0), palmitic acid (C16:0) and oleic acid (C18:1) on rat liver mitochondrial swelling by spectroscopic and microscopic techniques. Of the fatty acids tested oleic acid had a greater effect than palmitic acid while octanoic acid had no effect. Acyl-CoA derivatives produced greater mitochondrial swelling than either acyl-carnitine or free fatty acids. However, identical amounts of palmitoyl-CoA and oleoyl-CoA were required to produce the same degree of swelling. Addition of carnitine (2mM) to oleoyl-CoA reduced the mitochondrial swelling significantly thus suggesting that the toxicity of the fatty acids may be reduced by conversion to their carnitine derivatives. Twice the concentration of oleoyl-carnitine was required to produce half the maximum swelling as compared to oleoyl-CoA. Ultrastructural profiles of mitochondria treated with oleic acid, oleoyl-CoA and oleoyl-carnitine demonstrated greater swelling with oleoyl-CoA than with oleic acid or oleoyl-carnitine. These results suggest that carnitine may protect the mitochondria from damage by the fatty acids and their acyl-CoA derivatives in Reye's Syndrome.