gebhart/patrepeval huggingface dataset:
The Three-dimensional Structures of Antagonistic and Agonistic Forms of the Glucocorticoid Receptor Ligand-binding Domain (2003)

Here we describe the three-dimensional crystal structures of human glucocorticoid receptor ligand-binding domain (GR-LBD) in complex with the antagonist RU-486 at 2.3 A resolution and with the agonist dexamethasone ligand together with a coactivator peptide at 2.8 A. The RU-486 structure was solved in several different crystal forms, two with helix 12 intact (GR1 and GR3) and one with a protease-digested C terminus (GR2). In GR1, part of helix 12 is in a position that covers the co-activator pocket, whereas in the GR3, domain swapping is seen between the crystallographically identical subunits in the GR dimer. An arm consisting of the end of helix 11 and beyond stretches out from one molecule, and helix 12 binds to the other LBD, partly blocking the coactivator pocket of that molecule. This type of GR-LBD dimer has not been described before but might be an artifact from crystallization. Furthermore, the subunits of the GR3 dimers are covalently connected via a disulfide bond between the Cys-736 residues in the two molecules. All three RU-486 GR-LBD structures show that GR has a very flexible region between the end of helix 11 and the end of helix 12.
Hypocrea jecorina Cellobiohydrolase I Stabilizing Mutations Identified Using Noncontiguous Recombination (2013)

Noncontiguous recombination (NCR) is a method to identify pieces of structure that can be swapped among homologous proteins to create new, chimeric proteins. These "blocks" are encoded by elements of sequence that are not necessarily contiguous along the polypeptide chain. We used NCR to design a library in which blocks of structure from Hypocrea jecorina cellobiohydrolase I (Cel7A) and its two thermostable homologues from Talaromyces emersonii and Chaetomium thermophilum are shuffled to create 531,438 possible chimeric enzymes. We constructed a maximally informative subset of 35 chimeras to analyze this library and found that the blocks contribute additively to the stability of a chimera. Within two highly stabilizing blocks, we uncovered six single amino acid substitutions that each improve the stability of H. jecorina cellobiohydrolase I by 1-3 °C. The small number of measurements required to find these mutations demonstrates that noncontiguous recombination is an efficient strategy for identifying stabilizing mutations.
Two‐dimensional electrophoresis reveals a nuclear matrix‐associated nucleolin complex of basic isoelectric point (1997)

A monoclonal antibody was raised against a salt-extractable fraction of nuclear matrix / intermediate filament scaffolds of polarized MDCK cells. The antibody recognized an approximately 100 kDa protein in total cell lysates and nuclear matrices of various human cells and tissues and stained nucleolar structures in immunofluorescence microscopy. By partial sequencing of five peptides derived from immunoprecipitated protein, the targeted antigen was found to be homologous to human nucleolin. After two-dimensional electrophoresis of total HeLa cell lysates, immunoreactive bands were detected at isoelectric point (pI) 5.5--6.1, characteristic for nucleolin, and at pI 8.5--9. Whereas the protein focusing at acidic pI was found in Triton X-100-soluble cellular fractions, the antigen focusing at basic pI was exclusively contained in the residual nuclear fraction and was solubilized upon treatment of nuclear matrices with RNAse. The component solubilized by RNAse treatment was still detected at basic pI in two-dimensional electrophoresis. However, upon immunoprecipitation of the antigen from the RNAse-released fraction in the presence of sodium dodecyl sulfate (SDS), the nuclear matrix-derived antigen was positioned at pI 5--6. The present data indicate that the nuclear matrix-bound nucleolin is associated with ribonucleoproteins and a basic component resisting dissociation under conditions of isoelectric focusing.
Phospholipases introduced into the hypophase affect the surfactant film outlining a bubble (1992)

The hypophase exchanger is a recently developed device that makes it possible to replace the liquid in the sample chamber of a pulsating bubble surfactometer, after a bubble has been formed, without changing the size of the bubble. A surfactant film outlining the bubble will retain its surface properties, provided the liquid entering the sample chamber and replacing the hypophase is inert. If, on the other hand, the new hypophase consists of a phospholipase solution, the physical properties of the film are seriously affected. It was found that when phospholipase C, even at low concentration, entered the sample chamber, the physical properties were significantly changed. Phospholipase A2 had to be added at a higher concentration to exert a similar effect. It is postulated that the site of action of phospholipase A2 may be partly protected in the hydrophobic region of the tightly packed surfactant film.
Chronic pudendal nerve neuromodulation in women with idiopathic refractory detrusor overactivity incontinence: Results of a pilot study with a novel minimally invasive implantable mini‐stimulator (2005)

Chronic pudendal nerve stimulation may reduce the degree of detrusor overactivity incontinence, even in patients in whom sacral neuromodulation fails. Bion therapy is relatively simple and minimally invasive and is well tolerated by the patient.
Monoclonal antibodies to poly(adenosine diphosphate ribose) recognize different structures (1984)

Two hybridomas producing monoclonal antibodies to poly(adenosine diphosphate ribose) [poly(ADP-Rib)] were established. One antibody, 10H (IgG3, kappa), bound to most of the poly(ADP-Rib) preparation, which consisted of molecules of various sizes of more than 20 ADP-Rib residues. The binding of this antibody was inhibited by not only poly-(ADP-Rib) but also a monomer unit of poly(ADP-Rib), Ado(P)-Rib-P. The sites protected by antibody 10H were isolated and analyzed by hydrolysis with alkaline phosphomonoesterase and then snake venom phosphodiesterase. The sites contained the same amounts of monomer units and branched portions [Ado(P)-Rib(P)-Rib-P] as the original poly(ADP-Rib) molecules but a lower average number of branched portions per molecule than in the original molecules. The other antibody, 16B (IgM, lambda), reacted with only 50% of the radioactive poly(ADP-Rib), and its binding was not inhibited by a monomer unit. This antibody protected 25% of all the poly(ADP-Rib) molecules from hydrolysis by snake venom phosphodiesterase. The protected sites contained twice as many branched portions per molecule as the original poly(ADP-Rib) molecules. These results show that the two monoclonal antibodies recognize different structures of poly-(ADP-Rib); 10H antibody recognizes the linear structure with ribose-ribose linkages, and 16B antibody may recognize specific structures, including the branched portions of poly-(ADP-Rib).
Oxydation ungesättigter Verbindungen mittels organischer Superoxyde (1909)

g HzO.(C€J~.CH~.CHZ
Multi-functional DNA nanostructures that puncture and remodel lipid membranes into hybrid materials (2018)

Synthetically replicating key biological processes requires the ability to puncture lipid bilayer membranes and to remodel their shape. Recently developed artificial DNA nanopores are one possible synthetic route due to their ease of fabrication. However, an unresolved fundamental question is how DNA nanopores bind to and dynamically interact with lipid bilayers. Here we use single-molecule fluorescence microscopy to establish that DNA nanopores carrying cholesterol anchors insert via a two-step mechanism into membranes. Nanopores are furthermore shown to locally cluster and remodel membranes into nanoscale protrusions. Most strikingly, the DNA pores can function as cytoskeletal components by stabilizing autonomously formed lipid nanotubes. The combination of membrane puncturing and remodeling activity can be attributed to the DNA pores' tunable transition between two orientations to either span or co-align with the lipid bilayer. This insight is expected to catalyze the development of future functional nanodevices relevant in synthetic biology and nanobiotechnology.
CD19-CAR Trials (2014)

CD19 is a B-lineage-specific transmembrane glycoprotein, the expression of which is maintained on more than 95% B-cell malignancies. This strict lineage restriction makes CD19 an ideal target for immune therapies using chimeric antigen receptors (CARs). Here, we review published phase 1 trials of T cells expressing CARs targeting CD19 and describe briefly the biological questions that they addressed. All patients treated in these trials had relapsed B-cell malignancies, which in many cases were chemorefractory. Nonetheless, major responses have been observed, especially in patients with chronic lymphocytic leukemia and acute lymphoblastic leukemia. Many of these responses were accompanied by a systemic inflammatory reaction syndrome that could be life threatening but was almost always reversible with adequate medical management. Given their remarkable activity, CD19-CAR T cells are likely to be quickly incorporated into the management of B-cell neoplasms; these cells have become the paradigm for similar strategies targeting other cancers.
Megahertz OCT for ultrawide-field retinal imaging with a 1050nm Fourier domain mode-locked laser (2011)

We demonstrate ultrahigh speed swept source retinal OCT imaging using a Fourier domain mode locked (FDML) laser. The laser uses a combination of a semiconductor optical amplifier and an ytterbium doped fiber amplifier to provide more than 50 mW output power. The 1050 nm FDML laser uses standard telecom fiber for the km long delay line instead of two orders of magnitude more expensive real single mode fiber. We investigate the influence of this "oligo-mode" fiber on the FDML laser performance. Two design configurations with 684,400 and 1,368,700 axial scans per second are investigated, 25x and 50x faster than current commercial instruments and more than 4x faster than previous single spot ophthalmic results. These high speeds enable the acquisition of densely sampled ultrawide-field data sets of the retina within a few seconds. Ultrawide-field data consisting of 1900 x 1900 A-scans with ~70° angle of view are acquired within only 3 and 6 seconds using the different setups. Such OCT data sets, more than double as large as previously reported, are collapsed to a 4 megapixel high definition fundus image. We achieve good penetration into the choroid by hardware spectral shaping of the laser output. The axial resolution in tissue is 12 µm (684 kHz) and 19 µm (1.37 MHz). A series of new data processing and imaging extraction protocols, enabled by the ultrawide-field isotropic data sets, are presented. Dense isotropic sampling enables both, cross-sectional images along arbitrary coordinates and depth-resolved en-face fundus images. Additionally, we investigate how isotropic averaging compares to the averaging of cross-sections along the slow axis.
Protecting Communities in Biomedical Research (2006)

Holloway's article on race, emergency medicine and clinical trials for the blood substitute PolyHeme® (Northfield Laboratories, Inc., Evanston, IL) calls attention to problematic applications of “c...
Inhibition of 17 -Hydroxysteroid Oxidoreductase by Flavonoids in Breast and Prostate Cancer Cells (1998)

Several flavonoids and isoflavonoids were found to inhibit 17beta-oxidoreduction of estrogens by the purified 17beta-HSOR type 1, or in cell lines expressing 17beta-HSOR type 1 enzyme (T-47D breast cancer cells) or type 2 (PC-3 prostate cancer cells). The structural demands for the inhibition of estrone (E1) reduction and estradiol (E2) oxidation catalyzed by 17beta-HSOR types 1 and 2, respectively, were not identical. Flavones, flavanones, and isoflavones hydroxylated at both the double ring (positions 5 and 7) and ring B (position 4') were the most potent inhibitors of E1 reduction in T-47D cells, and by the purified type 1 enzyme whereas flavones hydroxylated at positions 3, 5, and 7 of rings A and C, with or without a hydroxyl group in ring B, were capable of inhibiting E2 oxidation in PC-3 cells. Change to flavanone structure, or hydroxylation at position 3 of ring C of flavones, or methylation of the hydroxyl group at position 4' of ring B of flavones and isoflavones reduced or abolished their inhibitory activity on E1 reduction in T-47D cells. On the contrary, hydroxyl group at position 3 of flavones (flavonol structure) markedly increased the inhibition of E2 oxidation in PC-3 cells. Thus, changes in the number and location of hydroxyl groups may discriminate inhibition of E1 reduction and E2 oxidation. Some of the differences may be due to differences in pharmacokinetics of these compounds in T-47D and PC-3 cells. Inhibition of 17beta-HSORs could lead to an alteration in the availability of the highly active endogenous estrogen, but the effects of these compounds in vivo cannot be predicted on the basis of these results alone. Some of these compounds (isoflavones) are estrogenic per se, and they may replace endogenous estrogens, whereas flavones are only very weakly estrogenic or nonestrogenic. Regarding prevention or treatment of estrogen-related diseases, apigenin, coumestrol, and genistein raise special interest.
Learning in Implicit Generative Models (2016)

Generative adversarial networks (GANs) provide an algorithmic framework for constructing generative models with several appealing properties: they do not require a likelihood function to be specified, only a generating procedure; they provide samples that are sharp and compelling; and they allow us to harness our knowledge of building highly accurate neural network classifiers. Here, we develop our understanding of GANs with the aim of forming a rich view of this growing area of machine learning---to build connections to the diverse set of statistical thinking on this topic, of which much can be gained by a mutual exchange of ideas. We frame GANs within the wider landscape of algorithms for learning in implicit generative models--models that only specify a stochastic procedure with which to generate data--and relate these ideas to modelling problems in related fields, such as econometrics and approximate Bayesian computation. We develop likelihood-free inference methods and highlight hypothesis testing as a principle for learning in implicit generative models, using which we are able to derive the objective function used by GANs, and many other related objectives. The testing viewpoint directs our focus to the general problem of density ratio estimation. There are four approaches for density ratio estimation, one of which is a solution using classifiers to distinguish real from generated data. Other approaches such as divergence minimisation and moment matching have also been explored in the GAN literature, and we synthesise these views to form an understanding in terms of the relationships between them and the wider literature, highlighting avenues for future exploration and cross-pollination.
Characterization of the stability of recombinant protein production in the GS‐NS0 expression system (2001)

The GS-NS0 system is an important mammalian expression system used largely within industry for the high-level expression of recombinant proteins for therapeutic use. It is essential that the productivity of this system remains stable throughout culture expansion for the successful long-term production of recombinant proteins. Here we present a study of the stability of recombinant protein production from unamplified GS-NS0 cell lines over extended period of continuous culture. The cell lines used in this study were generated by the transfection of NS0 cells with DNA encoding for a secreted recombinant protein and by two subsequent rounds of limiting dilution cloning prior to analysis of stability. The stability of recombinant protein production was assessed at intervals over a period of 134 days using repeated batch culture in shake flasks. Heterogeneous stability was identified. The productivity of some clones remained consistent throughout 134 days of continuous culture. Others exhibit rapid and progressive loss of productivity. Analysis of the causal relationships underlying stability indicates that the initial transfectant determines the susceptibility to loss or retention of productivity. Selection of production clones on the basis of growth and productivity alone will not predict stability during long-term culture. Our research indicates that stable high-producing clones can readily be obtained from use of the GS-NS0 system in the absence of amplification but there may be molecular features of the original transfectants that could serve as very important predictive indicators of the stability of recombinant protein production.
Feline immunodeficiency virus vectors persistently transduce nondividing airway epithelia and correct the cystic fibrosis defect (1999)

Several problems limit the application of gene transfer to correct the cystic fibrosis (CF) Cl(-) transport defect in airway epithelia. These include inefficient transduction with vectors applied to the apical surface, a low rate of division by airway epithelial cells, failure of transgene expression to persist, and immune responses to vectors or vector-encoded proteins. To address these issues, we used a feline immunodeficiency virus-based (FIV-based) vector. FIV vector formulated with a calcium chelator transduced fully differentiated, nondividing human airway epithelia when applied to the apical surface. FIV-based vector encoding the cystic fibrosis transmembrane conductance regulator cDNA corrected the Cl(-) transport defect in differentiated CF airway epithelia for the life of the culture (>3 months). When this approach was applied in vivo, FIV vector expressing beta-galactosidase transduced 1-14% of adult rabbit airway epithelia. Transduced cells were present in the conducting airways, bronchioles, and alveoli. Importantly, gene expression persisted, and cells with progenitor capacity were targeted. FIV-based lentiviral vectors may be useful for the treatment of genetic lung diseases such as CF. This article may have been published online in advance of the print edition.
Practical screening of purified cellobiohydrolases and endoglucanases with α-cellulose and specification of hydrodynamics (2010)

α-Cellulose is an excellent substrate to screen for CBHs and EGs. This current investigation shows in detail, for the first time, the adsorption of purified cellulases onto α-cellulose, the effect of hydrodynamics on cellulase adsorption and the correlation between the adsorption and the activity of cellulases at different hydrodynamic conditions. Complete suspension of the substrate has to be ensured in order to optimize the cellulase attack. In the future, screenings should be conducted with α-cellulose so that proper cellulases are selected to best hydrolyze the real alkaline-pretreated biomass used in biorefineries.
Managing application services over service provider networks: architecture and dependency analysis (2002)

This paper proposes a novel approach for managing IP-based services and applications, reflecting the authors' experience with the IBM Global Network. It describes how one can extend the existing network and systems management paradigms to address problems in the management of application services hosted by network service providers (NSP). We introduce the concept of "service management domains" which are virtual domains built from resources and dependency relationships pertaining to physically monitored domains in the network management layer. They form the basis for managing fault, performance and service level agreements related to application service offerings.
Assembly of large genomic segments in artificial chromosomes by homologous recombination in Escherichia coli (2001)

We developed a method for the reconstruction of a 100 kb DNA fragment into a bacterial artificial chromosome (BAC). The procedure makes use of iterative rounds of homologous recombination in Escherichia coli. Smaller, overlapping fragments of cloned DNA, such as cosmid clones, are required. They are transferred first into a temperature-sensitive replicon and then into the BAC of choice. We demonstrated the usefulness of this procedure by assembling a 90 kb genomic segment into an E.coli-STREPTOMYCES: artificial chromosome (ESAC). Using this procedure, ESACs are easy to handle and remarkably more stable than the starting cosmids.
Colloidosomes: Selectively Permeable Capsules Composed of Colloidal Particles (2002)

We present an approach to fabricate solid capsules with precise control of size, permeability, mechanical strength, and compatibility. The capsules are fabricated by the self-assembly of colloidal particles onto the interface of emulsion droplets. After the particles are locked together to form elastic shells, the emulsion droplets are transferred to a fresh continuous-phase fluid that is the same as that inside the droplets. The resultant structures, which we call "colloidosomes," are hollow, elastic shells whose permeability and elasticity can be precisely controlled. The generality and robustness of these structures and their potential for cellular immunoisolation are demonstrated by the use of a variety of solvents, particles, and contents.
Regulation of signal transduction by HDL (2013)

High density lipoprotein (HDL) cholesterol has direct effects on numerous cell types that influence cardiovascular and metabolic health. These include endothelial cells, vascular smooth-muscle cells, leukocytes, platelets, adipocytes, skeletal muscle myocytes, and pancreatic β cells. The effects of HDL or apoA-I, its major apolipoprotein, occur through the modulation of intracellular calcium, oxygen-derived free-radical production, numerous kinases, and enzymes, including endothelial nitric-oxide synthase (eNOS). ApoA-I and HDL also influence gene expression, particularly genes encoding mediators of inflammation in vascular cells. In many paradigms, the change in intracellular signaling occurs as a result of cholesterol efflux, with the cholesterol acceptor methyl-β-cyclodextrin often invoking responses identical to HDL or apoA-I. The ABC transporters ABCA1 and ABCG1 and scavenger receptor class B, type I (SR-BI) frequently participate in the cellular responses. Structure-function relationships are emerging for signal initiation by ABCA1 and SR-BI, with plasma membrane cholesterol binding by the C-terminal transmembrane domain of SR-BI uniquely enabling it to serve as a sensor of changes in membrane cholesterol. Further investigation of the processes underlying HDL and apoA-I modulation of intracellular signaling will potentially reveal new prophylactic and therapeutic strategies to optimize both cardiovascular and metabolic health.
STAT3-Mediated Metabolic Reprograming in Cellular Transformation and Implications for Drug Resistance (2015)

Signal transducer and activator of transcription (STAT)3 mediates the signaling downstream of cytokine and growth factor receptors, regulating the expression of target genes. It is constitutively phosphorylated on tyrosine (Y-P) in many tumors, where its transcriptional activity can induce a metabolic switch toward aerobic glycolysis and down-regulate mitochondrial activity, a prominent metabolic feature of most cancer cells, correlating with reduced production of ROS, delayed senescence, and protection from apoptosis. STAT3 can, however, also localize to mitochondria, where its serine-phosphorylated (S-P) form preserves mitochondrial oxidative phosphorylation and controls the opening of the mitochondrial permeability transition pore, also promoting survival and resistance to apoptosis in response to specific signals/oncogenes such as RAS. Thus, downstream of different signals, both nuclear, Y-P STAT3, and mitochondrial, S-P STAT3, can act by promoting cell survival and reducing ROS production. Here, we discuss these properties in the light of potential connections between STAT3-driven alterations of mitochondrial metabolism and the development of drug resistance in cancer patients.