gebhart/patrepeval huggingface dataset:
Telomerase activity in human germline and embryonic tissues and cells (1996)

Telomerase is a ribonucleoprotein that synthesizes telomere repeats onto chromosome ends and is involved in maintaining telomere length in germline tissues and in immortal and cancer cells. In the present study, the temporal regulation of expression of telomerase activity was examined in human germline and somatic tissues and cells during development. Telomerase activity was detected in fetal, newborn, and adult testes and ovaries, but not in mature spermatozoa or oocytes. Blastocysts expressed high levels of telomerase activity as did most human somatic tissues at 16–20 weeks of development with the exception of human brain tissue. This activity could no longer be detected in the somatic tissues examined from the neonatal period onward. Neither placenta nor cultured fetal amniocytes contained detectable telomerase activity. Fetal tissues explanted into primary cell culture showed a dramatic decline in telomerase activity which became undetectable after the first passage in vitro. Elucidation of the regulatory pathways involved in the repression of telomerase activity during development may lead to the ability to manipulate telomerase levels and explore the consequences both for cellular aging and for the survival of cancer cells. © 1996 Wiley-Liss, Inc.
The Escherichia coli heat-stable enterotoxin is a long-lived superagonist of guanylin (1993)

The mechanism by which bacterial heat-stable enterotoxins (ST I STA) cause diarrhea in humans and animals has been linked to the activation of an intestinal membrane-bound guanylate cyclase. Guanylin, a recently discovered rat intestinal peptide, is homologous in structure to ST I and can activate guanylate cyclase present on the human colonic carcinoma cell line T84. To directly test the mechanistic association of guanylate cyclase activation with diarrhea, we synthesized guanylin and a guanylin analog termed N9P10 guanylin and compared their biological activities with those of a synthetic ST I analog, termed ST Ib(6-18). We report that guanylin is able to inhibit the binding of a radiolabeled ST I analog to rat intestinal cells but causes diarrhea in infant mice only at doses at least 4 orders of magnitude higher than that of ST Ib(6-18). In contrast, N9P10 guanylin was enterotoxic in mice at much lower doses than guanylin but proved to be a weaker inhibitor of radiolabeled ST I than guanylin in the receptor binding assay. The pattern of guanylate cyclase activation observed for ST Ib(6-18) and the two guanylin analogs parallels the results observed in the receptor binding assay rather than those observed in the diarrheal assay. Treatment of guanylin with chymotrypsin or lumenal fluid derived from newborn mouse intestines resulted in a rapid loss of binding activity. Together, these results suggest that ST I enterotoxins may represent a class of long-lived superagonists of guanylin.
Correlation of AMPA Receptor Subunit Composition with Synaptic Input in the Mammalian Cochlear Nuclei (2001)

The composition of AMPA receptors in patches excised from somata and dendrites of six cell types in the mammalian cochlear nuclei was probed and compared electrophysiologically and pharmacologically with the rapid application of glutamate. Cells excited predominantly by auditory nerve fibers had AMPA receptors with exceptionally rapid gating (submillisecond deactivation and desensitization time constants). The nonlinear current-voltage relationship in the presence of spermine showed that few of these receptors had GluR2 subunits, and the insensitivity of desensitization to cyclothiazide indicated that they contained mostly flop splice variants. At synapses made by parallel fibers, AMPA receptors were slowly gating (time constants of deactivation and desensitization >1 msec) and contained higher levels of GluR2 and flip isoforms. However, receptors at auditory nerve synapses on cells that also receive parallel fiber input, the fusiform cells, had intermediate properties with respect to kinetics and contained GluR2 and flip isoforms. Given the diverse biophysical properties, patterns of innervation, patterns of electrical activity, and targets of each cell type in vivo, these data indicate that the kinetics and permeation properties of AMPA receptors are linked to factors associated with synaptic connectivity.
Inorganic Halide Perovskites for Efficient Light-Emitting Diodes (2015)

Lead-halide perovskites have transcended photovoltaics. Perovskite light-emitting diodes (PeLEDs) emerge as a new field to leverage on these fascinating semiconductors. Here, we report the first use of completely inorganic CsPbBr3 thin films for enhanced light emission through controlled modulation of the trap density by varying the CsBr-PbBr2 precursor concentration. Although pure CsPbBr3 films can be deposited from equimolar CsBr-PbBr2 and CsBr-rich solutions, strikingly narrow emission line (17 nm), accompanied by elongated radiative lifetimes (3.9 ns) and increased photoluminescence quantum yield (16%), was achieved with the latter. This is translated into the enhanced performance of the resulting PeLED devices, with lower turn-on voltage (3 V), narrow electroluminescence spectra (18 nm) and higher electroluminescence intensity (407 Cd/m(2)) achieved from the CsBr-rich solutions.
Identification of the membrane receptor of a class XIV myosin in Toxoplasma gondii (2004)

Apicomplexan parasites exhibit a unique form of substrate-dependent motility, gliding motility, which is essential during their invasion of host cells and during their spread between host cells. This process is dependent on actin filaments and myosin that are both located between the plasma membrane and two underlying membranes of the inner membrane complex. We have identified a protein complex in the apicomplexan parasite Toxoplasma gondii that contains the class XIV myosin required for gliding motility, TgMyoA, its associated light chain, TgMLC1, and two novel proteins, TgGAP45 and TgGAP50. We have localized this complex to the inner membrane complex of Toxoplasma, where it is anchored in the membrane by TgGAP50, an integral membrane glycoprotein. Assembly of the protein complex is spatially controlled and occurs in two stages. These results provide the first molecular description of an integral membrane protein as a specific receptor for a myosin motor, and further our understanding of the motile apparatus underlying gliding motility in apicomplexan parasites.
Archipelago: an Island-based file system for highly available and scalable internet services (2000)

Maintaining availability in the face of failures is a critical requirement for Internet services. Existing approaches in cluster-based data storage rely on redundancy to survive a small number of failures, but the system becomes entirely unavailable if more failures occur. We describe an approach that allows a cluster file server to isolate failures so that the system can continue to serve most clients. Our approach is complementary to existing redundancy-based methods: redundancy can mask the first few failures, and failure isolation can take over and maintain availability for the majority of clients if more failures occur. The building blocks of our design are selfcontained and load-balanced file servers called islands. The main idea underlying island-based design is the one-island principle: as many operations as possible should involve exactly one island. The one-island principle provides failure isolation because each island can function independently of other islands&amp;apos; failures. ...
The N-Terminal Cyclophilin-Homologous Domain of a 150-Kilodalton Tumor Recognition Molecule Exhibits Both Peptidylprolyl cis-trans-Isomerase and Chaperone Activities (1994)

A cyclophilin-related protein has recently been found to be involved in tumor recognition by natural killer cells. The N-terminal end of this 150-kDa surface molecule (NK-TR) is homologous to cyclophilin/peptidylprolyl cis-trans-isomerase. We have constructed a soluble bacterial fusion protein between the cyclophilin-homologous domain of the NK-TR molecule and glutathione S-transferase (GST) to test for the presence of peptidylprolyl cis-trans-isomerase and chaperone activities and for cyclosporin A binding. The purified NK-cyp-GST fusion protein is shown to accelerate the isomerization of the prolyl peptide bond of the substrate N-succinyl-Ala-Ala-Pro-Phe-p-nitroanilide with a kcat/KM value of 7.4 x 10(5) M-1 s-1. The isomerase activity of the NK-TR cyclophilin homolog has been determined to be relatively insensitive to inhibition by the immunosuppressive drug cyclosporin A, with an IC50 value of 770 nM as compared to 19 nM for human cyclophilin. Furthermore, the NK-cyp-GST fusion protein has been found to participate in the protein folding process as a chaperone by preventing the aggregation of early folding intermediates of carbonic anhydrase. The implications of the finding of both peptidylprolyl cis-trans-isomerase and chaperone activities within the N-terminal domain of a large, cell type-restricted, surface molecule are discussed.
Cellular and molecular mechanisms of endothelial cell dysfunction. (1997)

repeated observation that it is altered by a variety of pathophysiological conditions. Such alterations of NO production and/or bioavailability have been shown to occur both in experimental animal models and in human subjects, in the setting of such diverse disorders as hypertension, hypercholesterolemia, aging, cigarette smoking, diabetes, and heart failure (1). The mechanisms underlying the alteration of this important function of the endothelium are varied and likely multifactorial. During the past several years an enormous amount of research has been devoted to understanding these abnormalities, which has led to new insights into regulation of vascular tone, redox state, inflammation, growth, and the prothrombotic/antithrombotic properties of the vessel wall. This Perspective will highlight some of these important new observations, as they relate to the pathology of the endothelial cell L -arginine/NO synthase (NOS) system. In addition, future directions of research that may be particularly informative will be indicated. Alterations of the substrate for the NOS enzyme The substrate for NOS is the basic amino acid L -arginine (with a K m of approximately 5 m M, reference 2). L -Arginine is syn
Metal‐Ion‐Mediated Tuning of Duplex DNA Binding by Bis(2‐(2‐pyridyl)‐1H‐benzimidazole) (2007)

Studies of double-stranded-DNA binding have been performed with three isomeric bis(2-(n-pyridyl)-1H-benzimidazole)s (n=2, 3, 4). Like the well-known Hoechst 33258, which is a bisbenzimidazole compound, these three isomers bind to the minor groove of duplex DNA. DNA binding by the three isomers was investigated in the presence of the divalent metal ions Mg(2+), Co(2+), Ni(2+), Cu(2+), and Zn(2+). Ligand-DNA interactions were probed with fluorescence and circular dichroism spectroscopy. These studies revealed that the binding of the 2-pyridyl derivative to DNA is dramatically reduced in the presence of Co(2+), Ni(2+), and Cu(2+) ions and is abolished completely at a ligand/metal-cation ratio of 1:1. Control experiments done with the isomeric 3- and 4-pyridyl derivatives showed that their binding to DNA is unaffected by the aforementioned transition-metal ions. The ability of 2-(2-pyridyl)benzimidazole to chelate metal ions and the conformational changes of the ligand associated with ion chelation probably led to such unusual binding results for the ortho isomer. The addition of ethylenediaminetetraacetic acid (EDTA) reversed the effects completely.
ITAMs: immunoregulatory scaffolds that link immunoreceptors to their intracellular signaling pathways. (1998)

Antigen receptors on the surface of T and B lymphocytes and various immunoglobulin Fc receptors are complexed multi-subunit structures that possess unique cytoplasmic modules, termed immunoreceptor tyrosine-based activation motif (ITAM). These modules consist of two repeats of the conserved sequence Tyr-X-X-Leu/lle spaced by six-to-eight residues and they function as 'on and off' switches that link the receptors to their intracellular signaling machinery. Thus, engagement of ITAM-containing receptors results in a rapid and transient phosphorylation of the ITAMs' tyrosine residues that function as temporal scaffolds for Src homology 2 (SH2) domains of downstream effector molecules. Recruitment and binding of these molecules to phospho-ITAMs initiate a cascade of biochemical events that lead to cell proliferation, differentiation, and acquisition of unique effector functions.
Stenting and Medical Therapy for Atherosclerotic Renal-Artery Stenosis (2013)

Renal-artery stenting did not confer a significant benefit with respect to the prevention of clinical events when added to comprehensive, multifactorial medical therapy in people with atherosclerotic renal-artery stenosis and hypertension or chronic kidney disease. (Funded by the National Heart, Lung and Blood Institute and others; ClinicalTrials.gov number, NCT00081731.).
The Role of Src Kinase in Macrophage-Mediated Inflammatory Responses (2012)

Src kinase (Src) is a tyrosine protein kinase that regulates cellular metabolism, survival, and proliferation. Many studies have shown that Src plays multiple roles in macrophage-mediated innate immunity, such as phagocytosis, the production of inflammatory cytokines/mediators, and the induction of cellular migration, which strongly implies that Src plays a pivotal role in the functional activation of macrophages. Macrophages are involved in a variety of immune responses and in inflammatory diseases including rheumatoid arthritis, atherosclerosis, diabetes, obesity, cancer, and osteoporosis. Previous studies have suggested roles for Src in macrophage-mediated inflammatory responses; however, recently, new functions for Src have been reported, implying that Src functions in macrophage-mediated inflammatory responses that have not been described. In this paper, we discuss recent studies regarding a number of these newly defined functions of Src in macrophage-mediated inflammatory responses. Moreover, we discuss the feasibility of Src as a target for the development of new pharmaceutical drugs to treat macrophage-mediated inflammatory diseases. We provide insights into recent reports regarding new functions for Src that are related to macrophage-related inflammatory responses and the development of novel Src inhibitors with strong immunosuppressive and anti-inflammatory properties, which could be applied to various macrophage-mediated inflammatory diseases.
Subdomains of the octopine synthase upstream activating element direct cell-specific expression in transgenic tobacco plants. (1992)

Previous work has shown that the octopine synthase (ocs) gene encoded by the Agrobacterium tumefaciens Ti-plasmid contains an upstream activating sequence necessary for its expression in plant cells. This sequence is composed of an essential 16-bp palindrome and flanking sequences that modulate the level of expression of the ocs promoter in transgenic tobacco calli. In this study, we have used RNA gel blot analysis of RNA extracted from transgenic tobacco plants to show that the octopine synthase gene is not constitutively expressed in all plant tissues and organs. This tissue-specific pattern of expression is determined, to a large extent, by the 16-bp palindrome. Histochemical analysis, using an ocs-lacZ fusion gene, has indicated that the 16-bp palindrome directs the expression of the ocs promoter in specific cell types in the leaves, stems, and roots of transgenic tobacco plants. This expression is especially strong in the vascular tissue of the leaves, leaf mesophyll cells, leaf and stem guard cells, and the meristematic regions of the shoots and roots. Sequences surrounding the palindrome in the upstream activating sequence restrict the expression of the ocs promoter to fewer cell types, resulting in a reduced level of expression of beta-galactosidase activity in the central vascular tissue of leaves, certain types of leaf trichomes, and the leaf primordia.
Calculation of protein backbone geometry from α‐carbon coordinates based on peptide‐group dipole alignment (1993)

An algorithm is proposed for the conversion of a virtual-bond polypeptide chain (connected C alpha atoms) to an all-atom backbone, based on determining the most extensive hydrogen-bond network between the peptide groups of the backbone, while maintaining all of the backbone atoms in energetically feasible conformations. Hydrogen bonding is represented by aligning the peptide-group dipoles. These peptide groups are not contiguous in the amino acid sequence. The first dipoles to be aligned are those that are both sufficiently close in space to be arranged in approximately linear arrays termed dipole paths. The criteria used in the construction of dipole paths are: to assure good alignment of the greatest possible number of dipoles that are close in space; to optimize the electrostatic interactions between the dipoles that belong to different paths close in space; and to avoid locally unfavorable amino acid residue conformations. The equations for dipole alignment are solved separately for each path, and then the remaining single dipoles are aligned optimally with the electrostatic field from the dipoles that belong to the dipole-path network. A least-squares minimizer is used to keep the geometry of the alpha-carbon trace of the resulting backbone close to that of the input virtual-bond chain. This procedure is sufficient to convert the virtual-bond chain to a real chain; in applications to real systems, however, the final structure is obtained by minimizing the total ECEPP/2 (empirical conformational energy program for peptides) energy of the system, starting from the geometry resulting from the solution of the alignment equations. When applied to model alpha-helical and beta-sheet structures, the algorithm, followed by the ECEPP/2 energy minimization, resulted in an energy and backbone geometry characteristic of these alpha-helical and beta-sheet structures. Application to the alpha-carbon trace of the backbone of the crystallographic 5PTI structure of bovine pancreatic trypsin inhibitor, followed by ECEPP/2 energy minimization with C alpha-distance constraints, led to a structure with almost as low energy and root mean square deviation as the ECEPP/2 geometry analog of 5PTI, the best agreement between the crystal and reconstructed backbone being observed for the residues involved in the dipole-path network.
Application of Strain-Promoted Azide–Alkyne Cycloaddition and Tetrazine Ligation to Targeted Fc-Drug Conjugates (2012)

We have previously described an approach whereby antibody Fc fragments harboring a single C-terminal selenocysteine residue (Fc-Sec) are directed against a variety of targets by changing the peptide or small molecule to which they are conjugated. In the present work, we describe methodology for improving the efficacy of these Fc-Sec conjugates by incorporating cytotoxic drugs. The Fc-Sec protein is first programmed to target specific tumor cell types by attachment of a bifunctional linker that contains a "clickable" handle (e.g., cyclobutane or cyclooctyne) in addition to a tumor cell-binding peptide or small molecule. Following Fc-Sec conjugation, a cytotoxic warhead is then attached by cycloaddition reactions of tetrazine or azide-containing linker. To validate this approach, we used a model system in which folic acid (FA) is the targeting moiety and a disulfide-linked biotin moiety serves as a cytotoxic drug surrogate. We demonstrated successful targeting of Fc-Sec proteins to folate-receptor expressing tumor cells. Tetrazine ligation was found to be an efficient method for biotin "arming" of the folate-targeted Fc-Sec proteins. We also report novel bioconjugation methodologies that use [4 + 2] cycloaddition reactions between tetrazines and cyclooctynes.
An algorithm for the machine calculation of complex Fourier series (1965)

An efficient method for the calculation of the interactions of a 2m factorial experiment was introduced by Yates and is widely known by his name.The generalization to 3m was given by Box et al. [1].Good [2] generalized these methods and gave elegant algorithms for which one class of applications is the calculation of Fourier series.In their full generality, Good's methods are applicable to certain problems in which one must multiply an JV-vector by an JV X N matrix which can be factored into m sparse matrices, where m is proportional to log JV.This results in a procedure requiring a number of operations proportional to JV log JV rather than JV2.These methods are applied here to the calculation of complex Fourier series.They are useful in situations where the number of data points is, or can be chosen to be, a highly composite number.The algorithm is here derived and presented in a rather different form.Attention is given to the choice of JV.It is also shown how special advantage can be obtained in the use of a binary computer with JV = 2m and how the entire calculation can be performed within the array of JV data storage locations used for the given Fourier coefficients.Consider the problem of calculating the complex Fourier series
Microvascular basement membranes in diabetes mellitus (2003)

The alterations in the microvascular system of diabetes mellitus patients are responsible for the most devastating complications of this widespread disease. In the kidney, the microangiopathy leads to thickening of the glomerular capillary basement membrane but also to the expansion of the mesangial matrix and thickening of the tubular basement membrane. Several mechanisms are implicated in the pathogenesis of diabetic renal microangiopathy. These include increased synthesis of type IV collagen following hyperglycaemia-induced alteration of the pattern of podocyte-integrin expression, decreased expression of matrix metalloproteinases (MMP-2 and 3), and increased expression of tissue inhibitor of metalloproteinase (TIMP). An altered morphology of podocytes accompanies these basement membrane alterations. Other factors which may contribute to renal matrix accumulation include vascular endothelial growth factor (VEGF), since treatment with anti-VEGF antibodies attenuates glomerular basement membrane thickening, platelet-derived growth factor (PDGF) (B chain) and its receptor, which appear to be highly expressed in mesangial and visceral epithelial cells and might play a role in the development of diabetic nephropathy. Also oxygen radicals/oxidative stress may play a role in matrix accumulation in diabetic nephropathy as aminoguanidine, an inhibitor of the formation of advanced glycation end-products but with antioxidant properties, attenuates diabetic nephropathy. Retinal diabetic microangiopathy follows much the same principles, be it that microvascular proliferation is a distinctive element in the retina. Nephropathy and retinopathy occur frequently but not always together, indicating that in their multifactorial pathogenesis much remains to be clarified.
Asymmetric Ni(II)/Cr(II)-Mediated Coupling Reaction:  Stoichiometric Process (2002)

[reaction: see text] Via an X-ray analysis, the sulfonamide bearing R(1) = i-Pr, R(2) = Me, and R(3) = Me is shown to be a tridentate ligand to a Cr(III) salt. This class of ligands, represented by R(1) = t-Bu, R(2) = 2-naphthyl, and R(3) = Me, is effective to achieve an asymmetric Ni/Cr-mediated coupling reaction and, with the C14-C38 segment of halichondrins, its synthetic potential has been demonstrated. A possible mechanism is suggested for the process.
Three-dimensional imaging systems: a new development (1988)

An optical system which produces 3-D images exhibiting continuous parallax with no flipping or cardboarding is described. Both integral and lenticular images can be recorded on photographic film without recourse to a specialized environment. Standard photographic processing and enlarging techniques are used to obtain hard copy. Measurements on commercially available retrodirective screens and a new retroscreen arrangement show that the new screen developed gives significant advantages. A retrodirective and a transmission version of the system have been constructed.