gebhart/patrepeval huggingface dataset:
Conditional targeting of Ispd using paired Cas9 nickase and a single DNA template in mice (2014)

CRISPR/Cas9 technology is a highly promising genome editing tool in the mouse, potentially overcoming the costs and time required for more traditional gene targeting methods in embryonic stem (ES) cells. Recently, compared to the wildtype nuclease, paired Cas9 nickase (Cas9n) combined with single guide RNA (sgRNA) molecules has been found to enhance the specificity of genome editing while reducing off-target effects. Paired Cas9n has been shown to be as efficient as Cas9 for generating insertion and deletion (indel) mutations by non-homologous end joining and targeted deletion in the genome. However, an efficient and reliable approach to the insertion of loxP sites flanking critical exon(s) to create a conditional allele of a target gene remains an elusive goal. In this study, we microinjected Cas9n RNA with sgRNAs together with a single DNA template encoding two loxP sites flanking (floxing) exon 2 of the isoprenoid synthase containing domain (Ispd) into the pronucleus and cytoplasm of C57BL/6NCr one-cell stage zygotes. After surgical transfer, one F0 mouse expressing a conditional allele was produced (at a frequency of ∼8% of live pups born). The floxed allele was transmitted through the germline to F1 progeny, and could be successfully recombined using Cre recombinase. This study indicates that conditional targeting can be accomplished effectively using paired Cas9n and a single DNA template.
Efficacy and safety of HOE 901 versus NPH insulin in patients with type 1 diabetes. The European Study Group of HOE 901 in type 1 diabetes. (2000)

This study indicates that HOE 901 achieves better control of fasting glucose and HbA1c levels over 4 weeks, and HOE 901 has a possible safety benefit in terms of nocturnal hypoglycemia.
Structurally Diverse Cyclisation Linkers Impose Different Backbone Conformations in Bicyclic Peptides (2012)

Combinatorial libraries of structurally diverse peptide macrocycles offer a rich source for the development of high-affinity ligands to targets of interest. In this work we have developed linkers for the generation of genetically encoded bicyclic peptides and tested whether the peptides cyclised by them have significant variations in their backbone conformations. Two new cyclisation reagents, each containing three thiol-reactive groups, efficiently and selectively cyclised linear peptides containing three cysteine moieties. When the mesitylene linker of the bicyclic peptide PK15, a potent inhibitor of plasma kallikrein (K(i)=2 nM), was replaced by the new linkers, its inhibitory activity dropped by a factor of more than 1000, suggesting that the linkers impose different conformations on the peptide. Indeed, structural analysis by solution-state NMR revealed different NOE constraints in the three bicyclic peptides, indicating that these relatively small linkers at the centres of bicyclic peptide structures significantly influence the conformations of the peptides. These results demonstrate the prominent structural role of linkers in peptide macrocycles and suggest that application of different cyclisation linkers in a combinatorial fashion could be an attractive means to generate topologically diverse macrocycle libraries.
β-Tubulin Binds Src Homology 2 Domains through a Region Different from the Tyrosine-phosphorylated Protein-recognizing Site (1996)

Src homology 2 (SH2) domains have been demonstrated to bind tyrosine-phosphorylated proteins that participate in signaling by growth factors and oncogenes by recognizing amino acid sequences containing phosphotyrosine residue. We found that SH2 domains such as Ash/Grb2, the 85-kDa subunit of phosphatidylinositol 3-kinase, and phospholipase Cgamma1 also bind beta-tubulin through a different region that recognizes phosphotyrosine in vitro and in vivo. Furthermore, binding occurs even when the SH2 domain is occupied by tyrosine-phosphorylated epidermal growth factor receptors. Using deleted constructs of Ash/Grb2 SH2, we found that carboxyl-terminal beta strands E and F, and alpha helix B (region "c") are required for binding. A synthetic peptide (FLWVVKFNSLNELVDYH) composed of region c inhibited the binding of beta-tubulin to the SH2 domains of Ash/Grb2, phosphatidylinositol 3-kinase, and phospholipase Cgamma1. The co-localization of SH2 proteins and microtubules is also confirmed by immunostaining. These data suggest that microtubules play important roles in the assembly of signaling molecules complexes containing SH2 proteins.
[A global glimpse at the development and future of family planning research]. (1990)

Contraceptive research is a time-consuming and expensive endeavor. It takes 15 to 25 years and 15 million US dollars to develop a new contraceptive method. Such an expensive investment made it inhibitive for developing countries to have their own contraceptive research. Most of them have to use foreign currency to import contraceptives. Besides a few pharmaceutical companies, there are 7 important organizations and agencies in the world that are engaged in sponsoring or organizing contraceptive research. Among these organizations, WHO/HRP and UNFPA have had more involvement in contraceptive research in China. The emphasis of funding from HRP in recent years has switched from supporting organizational building of research institutes to finding specific research projects. HRP has 10 task forces which reviews research proposals from over the world and funding is provided to the projects approved. UNFPA has allocated 4.5 million US dollars in contraceptive research in its 1990-1994 assistance programs to China. 3 important issues that need basic research are 1. male contraceptives 2. male infertility and 3. mechanism of female menstrual disturbance. In the past number of years, international organizations have placed great emphasis on social and behavior research related to contraceptive practice. Attention has also been given to the development of management skills in the research institutes so that the scarce resources could be used efficiently. Training of personnel has also been a major component of assistance from both HRP and UNFPA. It has been suggested that a training center be established in China to serve the need of China and Asia and Pacific region.
Reverse thermogelling biodegradable polymer aqueous solutions (2009)

A reverse thermogelling polymer aqueous solution is a free-flowing sol at a low temperature and becomes a semisolid gel as the temperature increases. It is expected to be a very promising biomaterial as a minimally invasive injectable system for drug delivery and tissue engineering applications. The principles of materials design are (1) balancing the hydrophobicity and hydrophilicty of a polymer, (2) controlling the topology of a polymer, (3) matching the degradation kinetics of a polymer with a specific biomedical application, and (4) controlling the biocompatibility of the material with a drug as well as a host. This article covers recent progress of reverse theromogelling biodegradable polymers based on aliphatic polyesters, polyphosphazenes, poloxamer derivatives, polysaccharides, polypeptides, poly(propylene phosphate)s, polyorthoesters, polycarbonates, polycyanoacrylates, and poly(N-(2-hydroxyethyl) methacrylamide-lactate)s. The material characteristics, driving forces or mechanism for sol-gel transition, and their biomedical applications are summarized. In addition, the authors' perspectives on future reverse theromogelling materials design are suggested.
Si→SiO2transformation: Interfacial structure and mechanism (1987)

We show that the c-Si\ensuremath{\rightarrow}a-${\mathrm{SiO}}_{2}$ transformation takes place via an ordered crystalline oxide layer \ensuremath{\simeq}5 A\r{} thick. Modeling of high-resolution transmission electron-microscope lattice images in two projections suggests the crystalline oxide to be tridymite, a stable, bulk form of ${\mathrm{SiO}}_{2}$.
Small-molecule activator of glutamate transporter EAAT2 translation provides neuroprotection (2014)

Glial glutamate transporter EAAT2 plays a major role in glutamate clearance in synaptic clefts. Several lines of evidence indicate that strategies designed to increase EAAT2 expression have potential for preventing excitotoxicity, which contributes to neuronal injury and death in neurodegenerative diseases. We previously discovered several classes of compounds that can increase EAAT2 expression through translational activation. Here, we present efficacy studies of the compound LDN/OSU-0212320, which is a pyridazine derivative from one of our lead series. In a murine model, LDN/OSU-0212320 had good potency, adequate pharmacokinetic properties, no observed toxicity at the doses examined, and low side effect/toxicity potential. Additionally, LDN/OSU-0212320 protected cultured neurons from glutamate-mediated excitotoxic injury and death via EAAT2 activation. Importantly, LDN/OSU-0212320 markedly delayed motor function decline and extended lifespan in an animal model of amyotrophic lateral sclerosis (ALS). We also found that LDN/OSU-0212320 substantially reduced mortality, neuronal death, and spontaneous recurrent seizures in a pilocarpine-induced temporal lobe epilepsy model. Moreover, our study demonstrated that LDN/OSU-0212320 treatment results in activation of PKC and subsequent Y-box-binding protein 1 (YB-1) activation, which regulates activation of EAAT2 translation. Our data indicate that the use of small molecules to enhance EAAT2 translation may be a therapeutic strategy for the treatment of neurodegenerative diseases.
Expression and crystallization of the complex of HLA-DR2 (DRA, DRB1*1501) and an immunodominant peptide of human myelin basic protein (1998)

HLA-DR2 is associated with susceptibility to multiple sclerosis (MS). A peptide from human myelin basic protein (MBP, residues 85-99) was previously found to bind to purified HLA-DR2 (DRA, DRB1*1501) and to be recognized by human MBP-specific T cell clones. Soluble HLA-DR2 was expressed in the baculovirus system by replacing the hydrophobic transmembrane regions and cytoplasmic segments of DRalpha and DRbeta with leucine zipper dimerization domains from the transcription factors Fos and Jun. In the expression construct, the MBP(85-99) sequence was covalently linked to the N terminus of the mature DRbeta chain. The recombinant protein was secreted by Sf9 cells infected with the recombinant baculovirus and purified by affinity chromatography. The leucine zipper dimerization domains were then cleaved from the assembled HLA-DR2/MBP peptide complex with V8 protease, and the protein was further purified by anion-exchange HPLC. Analysis by HPLC gel filtration indicated that the HLA-DR2/MBP peptide complex did not have a tendency to aggregate. The purified HLA-DR2/MBP peptide complex readily crystallized by the hanging drop method in 15-18% polyethylene glycol 6000/100 mM glycine, pH 3.5. At a synchrotron radiation source, a crystal with a tetragonal space group diffracted to a resolution of 2.6 A. The expression of such homogenous HLA-DR/peptide complexes may facilitate cocrystallization with T cell receptors as well as other molecules involved in T cell receptor recognition and signaling.
Improved antitumor activity of a recombinant anti-Lewis(y) immunotoxin not requiring proteolytic activation. (1996)

B1(dsFv)-PE33 is a recombinant immunotoxin composed of a mutant form of Pseudomonas exotoxin (PE) that does not need proteolytic activation and a disulfide-stabilized Fv fragment of the anti-Lewis(y) monoclonal antibody B1, which recognizes a carbohydrate epitope on human carcinoma cells. In this molecule, amino acids 1-279 of PE are deleted and domain Ib (amino acids 365-394) is replaced by the heavy chain variable region (VH) domain of monoclonal antibody B1. The light chain (VL) domain is connected to the VH domain by a disulfide bond. This recombinant toxin, termed B1(dsFv)-PE33, does not require proteolytic activation and it is smaller than other immunotoxins directed at Lewis(y), all of which require proteolytic activation. Furthermore, it is more cytotoxic to antigen-positive cell lines. B1(dsFv)-PE38 has the highest antitumor activity of anti-Lewis(y) immunotoxins previously constructed. B1(dsFv)-PE33 caused complete regression of tumors when given at 12 micrograms/kg (200 pmol/kg) every other day for three doses, whereas B1(dsFv)-PE38 did not cause regressions at 13 micrograms/kg (200 pmol/kg). By bypassing the need for proteolytic activation and decreasing molecular size we have enlarged the therapeutic window for the treatment of human cancers growing in mice, so that complete remissions are observed at 2.5% of the LD50.
Hydrophobin HFBII in detail: ultrahigh-resolution structure at 0.75 Å (2006)

Hydrophobins are small proteins secreted by filamentous fungi that have a unique ability to spontaneously form amphiphilic layers. Hydrophobins have only recently been structurally characterized through the first crystal structure determination of a protein of this class, Trichoderma reesei hydrophobin HFBII [Hakanpää, Paananen et al. (2004), J. Biol. Chem. 279, 534-539]. The resolution of the HFBII structure has now been extended to an ultrahigh resolution of 0.75 A. The structure was refined conventionally and multipole refinement has been initiated. The ultrahigh-resolution structure is analyzed here in detail and comparison is made to the previous atomic resolution structure of the same protein as well as to other ultrahigh-resolution structures found in the Protein Data Bank.
Role of the Ras-Association Domain Family 1 Tumor Suppressor Gene in Human Cancers (2005)

In recent years, the list of tumor suppressor genes (or candidate TSG) that are inactivated frequently by epigenetic events rather than classic mutation/deletion events has been growing. Unlike mutational inactivation, methylation is reversible and demethylating agents and inhibitors of histone deacetylases are being used in clinical trails. Highly sensitive and quantitative assays have been developed to assess methylation in tumor samples, early lesions, and bodily fluids. Hence, gene silencing by promoter hypermethylation has potential clinical benefits in early cancer diagnosis, prognosis, treatment, and prevention. The hunt for a TSG located at 3p21.3 resulted in the identification of the RAS-association domain family 1, isoform A gene (RASSF1A). RASSF1A falls into the category of genes frequently inactivated by methylation rather than mutational events. This gene is silenced and frequently inactivated by promoter region hypermethylation in many adult and childhood cancers, including lung, breast, kidney, gastric, bladder, neuroblastoma, medulloblastoma, gliomas and it has homology to a mammalian Ras effector (i.e., Nore1). RASSF1A inhibits tumor growth in both in vitro and in vivo systems, further supporting its role as a TSG. We and others identified the gene in 2000, but already there are over a 150 publications demonstrating RASSF1A methylation in a large number of human cancers. Many laboratories including ours are actively investigating the biology of this novel protein family. Thus far, it has been shown to play important roles in cell cycle regulation, apoptosis, and microtubule stability. This review summarizes our current knowledge on genetic, epigenetic, and functional analysis of RASSF1A tumor suppressor gene and its homologues.
ChAdOx1 nCoV-19 (AZD1222) protects Syrian hamsters against SARS-CoV-2 B.1.351 and B.1.1.7. (2021)

We investigated ChAdOx1 nCoV-19 (AZD1222) vaccine efficacy against SARS-CoV-2 variants of concern (VOCs) B.1.1.7 and B.1.351 in Syrian hamsters. We previously showed protection against SARS-CoV-2 disease and pneumonia in hamsters vaccinated with a single dose of ChAdOx1 nCoV-19. Here, we observed a 9.5-fold reduction of virus neutralizing antibody titer in vaccinated hamster sera against B.1.351 compared to B.1.1.7. Vaccinated hamsters challenged with B.1.1.7 or B.1.351 did not lose weight compared to control animals. In contrast to control animals, the lungs of vaccinated animals did not show any gross lesions. Minimal to no viral subgenomic RNA (sgRNA) and no infectious virus was detected in lungs of vaccinated animals. Histopathological evaluation showed extensive pulmonary pathology caused by B.1.1.7 or B.1.351 replication in the control animals, but none in the vaccinated animals. These data demonstrate the effectiveness of the ChAdOx1 nCoV-19 vaccine against clinical disease caused by B.1.1.7 or B.1.351 VOCs.
Interplay between Vascular Endothelial Growth Factor (VEGF) and Nuclear Factor Erythroid 2-related Factor-2 (Nrf2) (2011)

Several recently published studies have suggested that decreasing VEGF levels result in placental oxidative stress in preeclampsia, although the question as to how decreased VEGF concentrations increase oxidative stress still remains unanswered. Here, we show that VEGF activated Nrf2, the main regulating factor of the intracellular redox balance, in the cytotrophic cell line BeWo. In turn, this activated the production of antioxidative enzymes thioredoxin, thioredoxin reductase, and heme oxygenase-1, which showed a decrease in their expression in the placentas of preeclamptic women. Nevertheless, this activation occurred without oxidative stress stimulus. As a consequence, the activation of Nrf2 protected BeWo cells against H(2)O(2)/Fe(2+)-induced oxidative damage. We further show that VEGF up-regulated the expression of itself. A positive feedback loop was described in which VEGF activated Nrf2 in an ERK1/2-dependent manner; the up-regulation of HO-1 expression by Nrf2 augmented the production of carbon monoxide, which in turn up-regulated VEGF expression. In conclusion, VEGF induces the Nrf2 pathway to protect against oxidative stress and, via a positive feedback loop, to elevate VEGF expression. Therefore, decreased VEGF bioavailability during preeclampsia may result in higher vulnerability to placental oxidative cell damage and a further reduction of VEGF bioavailability, a vicious circle that may end up in preeclampsia.
Association of chronic inflammation, not its treatment, with increased lymphoma risk in rheumatoid arthritis (2006)

Risk of lymphoma is substantially increased in a subset of patients with RA, those with very severe disease. High inflammatory activity, rather than its treatment, is a major risk determinant.
Genetic ablation of Nrf2 enhances susceptibility to cigarette smoke–induced emphysema in mice (2004)

Although inflammation and protease/antiprotease imbalance have been postulated to be critical in cigarette smoke-induced (CS-induced) emphysema, oxidative stress has been suspected to play an important role in chronic obstructive pulmonary diseases. Susceptibility of the lung to oxidative injury, such as that originating from inhalation of CS, depends largely on its upregulation of antioxidant systems. Nuclear factor, erythroid-derived 2, like 2 (Nrf2) is a redox-sensitive basic leucine zipper protein transcription factor that is involved in the regulation of many detoxification and antioxidant genes. Disruption of the Nrf2 gene in mice led to earlier-onset and more extensive CS-induced emphysema than was found in wild-type littermates. Emphysema in Nrf2-deficient mice exposed to CS for 6 months was associated with more pronounced bronchoalveolar inflammation; with enhanced alveolar expression of 8-oxo-7,8-dihydro-2'-deoxyguanosine, a marker of oxidative stress; and with an increased number of apoptotic alveolar septal cells--predominantly endothelial and type II epithelial cells--as compared with wild-type mice. Microarray analysis identified the expression of nearly 50 Nrf2-dependent antioxidant and cytoprotective genes in the lung that may work in concert to counteract CS-induced oxidative stress and inflammation. The responsiveness of the Nrf2 pathway may act as a major determinant of susceptibility to tobacco smoke-induced emphysema by upregulating antioxidant defenses and decreasing lung inflammation and alveolar cell apoptosis.
Combining Fluorinated Polymers with Ag Nanoparticles as a Route to Enhance Optical Properties of Composite Materials (2020)

Polymer-based nanocomposites have recently received considerable attention due to their unique properties, which makes them feasible for applications in optics, sensors, energy, life sciences, etc. The present work focuses on the synthesis of nanocomposites consisting of a polytetrafluorethylene-like matrix in which metallic nano-silver are embedded, by using multiple magnetron plasmas. By successively exposing the substrate to separate RF magnetrons using as combination of target materials polytetrafluorethylene (PTFE) and silver, individual control of each deposition process is insured, allowing obtaining of structures in which silver nanoparticles are entrapped in-between two PTFE layers with given thicknesses. The topographical and morphological characteristics investigated by means of Scanning Electron Microscopy and Atomic Force Microscopy techniques evidenced the very presence of Ag nanoparticles with typical dimension 7 nm. The chemical composition at various depositing steps was evaluated through X-ray Photoelectron Spectroscopy. We show that the presence of the top PTFE layer prevents silver oxidation, while its thickness allows the tailoring of optical properties, as evidenced by spectroellipsometry. The appearance of chemical bonds between silver atoms and PTFE atoms at interfaces is observed, pointing out that despite of pure physical deposition processes, a chemical interaction between the polymeric matrix and metal is promoted by plasma.
An experimental system for creating and presenting interactive graphical documents (1982)

An experimental system is described for the design, development, and presentation of computer-based documents that combine pictures and text on a high-resolution color raster display. Such documents can be used, for example, for maintenance and repair tasks, videotex databases, or computer-aided instruction.
Protein cages, rings and tubes: useful components of future nanodevices? (2008)

There is a great deal of interest in the possibility that complex nanoscale devices can be designed and engineered. Such devices will lead to the development of new materials, electronics and smart drugs. Producing complex nanoscale devices, however will present many challenges and the components of such devices will require a number of special features. Devices will be engineered to incorporate desired functionalities but, because of the difficulties of controlling matter precisely at the nanoscale with current technology, the nanodevice components must self-assemble. In addition, nanocomponents that are to have wide applicability in various devices must have enough flexibility to integrate into a large number of potentially very different environments. These challenges are daunting and complex, and artificial nanodevices have not yet been constructed. However, the existence of nanomachines in nature in the form of proteins (eg, enzymes) suggests that they will be possible to produce. As the material from which nature's nanomachines are made, proteins seem ideal to form the basis of engineered components of such nanodevices. Initially, engineering projects may focus on building blocks such as rings, cages and tubes, examples of which exist in nature and may act as a useful start point for modification and further development. This review focuses on the recent research and possible future development of such protein building blocks.
Effect of Introduction of the Pneumococcal Conjugate Vaccine on Drug-Resistant Streptococcus pneumoniae (2006)

The rate of antibiotic-resistant invasive pneumococcal infections decreased in young children and older persons after the introduction of the conjugate vaccine. There was an increase in infections caused by serotypes not included in the vaccine.