gebhart/patrepeval huggingface dataset:
Human neural stem cells differentiate and promote locomotor recovery in spinal cord-injured mice (2005)

We report that prospectively isolated, human CNS stem cells grown as neurospheres (hCNS-SCns) survive, migrate, and express differentiation markers for neurons and oligodendrocytes after long-term engraftment in spinal cord-injured NOD-scid mice. hCNS-SCns engraftment was associated with locomotor recovery, an observation that was abolished by selective ablation of engrafted cells by diphtheria toxin. Remyelination by hCNS-SCns was found in both the spinal cord injury NOD-scid model and myelin-deficient shiverer mice. Moreover, electron microscopic evidence consistent with synapse formation between hCNS-SCns and mouse host neurons was observed. Glial fibrillary acidic protein-positive astrocytic differentiation was rare, and hCNS-SCns did not appear to contribute to the scar. These data suggest that hCNS-SCns may possess therapeutic potential for CNS injury and disease.
The clathrin adaptor Dab2 recruits EH domain scaffold proteins to regulate integrin β1 endocytosis (2012)

Endocytic adaptor proteins facilitate cargo recruitment and clathrin-coated pit nucleation. The prototypical clathrin adaptor AP2 mediates cargo recruitment, maturation, and scission of the pit by binding cargo, clathrin, and accessory proteins, including the Eps-homology (EH) domain proteins Eps15 and intersectin. However, clathrin-mediated endocytosis of some cargoes proceeds efficiently in AP2-depleted cells. We found that Dab2, another endocytic adaptor, also binds to Eps15 and intersectin. Depletion of EH domain proteins altered the number and size of clathrin structures and impaired the endocytosis of the Dab2- and AP2-dependent cargoes, integrin β1 and transferrin receptor, respectively. To test the importance of Dab2 binding to EH domain proteins for endocytosis, we mutated the EH domain-binding sites. This mutant localized to clathrin structures with integrin β1, AP2, and reduced amounts of Eps15. Of interest, although integrin β1 endocytosis was impaired, transferrin receptor internalization was unaffected. Surprisingly, whereas clathrin structures contain both Dab2 and AP2, integrin β1 and transferrin localize in separate pits. These data suggest that Dab2-mediated recruitment of EH domain proteins selectively drives the internalization of the Dab2 cargo, integrin β1. We propose that adaptors may need to be bound to their cargo to regulate EH domain proteins and internalize efficiently.
Micropump based on liquid marbles (2010)

A micropump based on a pair of liquid marbles coated with various powders and connected with a capillary tube is presented. The idea of the micropump is based on the difference of the Laplace pressures in the marbles. The initial stream was supported by the pressure instability developed under water overflow. The reported experiments validate the concept of the effective surface tension of liquid marbles. The micropump could be used for precise delivery of small quantities of liquids, the design of microreactors and microfluidics applications.
Compression of pulses of a few optical cycles through harmonic generation (2001)

Pulse compression through noncollinear sum-frequency generation in β-barium borate crystals is investigated. With dispersion to all orders taken into account, numerical calculations, carried out in the frequency domain, were performed for input pulse durations ranging from 10 to 50 fs. Fundamental pulses of a 10-fs duration at 800 nm were compressed down to 2.5 fs while a 2.5-fs second-harmonic signal was generated.
Intercellular Calcium Signaling Occurs between Human Osteoblasts and Osteoclasts and Requires Activation of Osteoclast P2X7 Receptors (2002)

Signaling between osteoblasts and osteoclasts is important in bone homeostasis. We previously showed that human osteoblasts propagate intercellular calcium signals via two mechanisms: autocrine activation of P2Y receptors, and gap junctional communication. In the current work we identified mechanically induced intercellular calcium signaling between osteoblasts and osteoclasts and among osteoclasts. Intercellular calcium responses in osteoclasts required P2 receptor activation but not gap junctional communication. Pharmacological studies and reverse transcriptase-PCR amplification demonstrated that human osteoclasts expressed functional P2Y1 receptors, but, unexpectedly, desensitization of P2Y1 did not block calcium signaling to osteoclasts. We also found that osteoclasts expressed functional P2X7 receptors and showed that pharmacological inhibition of these receptors blocked calcium signaling to osteoclasts. Thus these studies show that calcium signaling between osteoblasts and osteoclasts occurs via activation of P2 receptors, but that different families of P2 receptors are required for calcium signaling in these two cell types. Intercellular calcium signaling among bone cells is therefore amenable to pharmacological manipulation that will specifically affect only bone-forming or bone-resorbing cells. P2 receptors may be important drug targets for the modulation of bone turnover.
Reactome: a database of reactions, pathways and biological processes (2010)

Reactome (http://www.reactome.org) is a collaboration among groups at the Ontario Institute for Cancer Research, Cold Spring Harbor Laboratory, New York University School of Medicine and The European Bioinformatics Institute, to develop an open source curated bioinformatics database of human pathways and reactions. Recently, we developed a new web site with improved tools for pathway browsing and data analysis. The Pathway Browser is an Systems Biology Graphical Notation (SBGN)-based visualization system that supports zooming, scrolling and event highlighting. It exploits PSIQUIC web services to overlay our curated pathways with molecular interaction data from the Reactome Functional Interaction Network and external interaction databases such as IntAct, BioGRID, ChEMBL, iRefIndex, MINT and STRING. Our Pathway and Expression Analysis tools enable ID mapping, pathway assignment and overrepresentation analysis of user-supplied data sets. To support pathway annotation and analysis in other species, we continue to make orthology-based inferences of pathways in non-human species, applying Ensembl Compara to identify orthologs of curated human proteins in each of 20 other species. The resulting inferred pathway sets can be browsed and analyzed with our Species Comparison tool. Collaborations are also underway to create manually curated data sets on the Reactome framework for chicken, Drosophila and rice.
Protein Fouling of Virus Filtration Membranes: Effects of Membrane Orientation and Operating Conditions (2006)

The capacity of virus filters used in the purification of therapeutic proteins is determined by the rate and extent of membrane fouling. Current virus filtration membranes have a complex multilayer structure that can be used with either the skin-side up or with the skin-side facing away from the feed, but there is currently no quantitative understanding of the effects of membrane orientation or operating conditions on the filtration performance. Experiments were performed using Millipore's Viresolve 180 membrane under both constant pressure and constant flux operation with sulfhydryl-modified BSA used as a model protein. The capacity with the skin-side up was greater during operation with constant flux and at low transmembrane pressures, with the flux decline or pressure rise due primarily to osmotic pressure effects. In contrast, data obtained with the skin-side down showed a slower, steady increase in total resistance with the cumulative filtrate volume, with minimal contribution from osmotic pressure. The capacity with the skin-side down was significantly greater than that with the skin-side up, reflecting the different fouling mechanisms in the different membrane orientations. These results provide important insights for the design and operation of virus filtration membranes.
Confronting the next influenza pandemic with anti‐inflammatory and immunomodulatory agents: why they are needed and how they might work (2009)

Despite the best efforts of influenza scientists, companies and health officials to prepare for the next pandemic, most of the world's people will not have access to affordable supplies of vaccines and antiviral agents. They will have to rely on 19th century public health 'technologies' to see them through. In the 21st century, science ought to be able to provide something better. Influenza scientists study the molecular characteristics of influenza viruses and their signaling effects in cell culture and animal models of infection. While these studies have been enormously informative, they have been unable to explain the system-wide effects of influenza on the host, the increased mortality of younger adults in the 1918 influenza pandemic and the much lower mortality rates in children who were more commonly infected with the 1918 virus. Experiments by non-influenza scientists have defined common cell signaling pathways for acute lung injury caused by different agents, including inactivated H5N1 influenza virus. These pathways include several molecular targets that are up-regulated in acute lung injury and down-regulated by anti-inflammatory and immunomodulatory agents, including statins, fibrates, and glitazones. These agents also help reverse the mitochondrial dysfunction that accompanies multi-organ failure, something often seen in fatal Influenza. Observational studies suggest that statins are beneficial in treating patients with pneumonia (there are no such studies for fibrates and glitazones). Other studies suggest that these agents might be able to 'roll back' the self-damaging host response of young adults to the less damaging response of children and thus save lives. Research is urgently needed to determine whether these and other agents that modify the host response might be useful in managing H5N1 influenza and the next pandemic.
Targeted gene disruption of the endogenous c-abl locus by homologous recombination with DNA encoding a selectable fusion protein. (1990)

We have introduced a substitution mutation into the c-abl locus of murine embryonic stem cells by homologous recombination between exogenously added DNA and the endogenous gene. Model constructs were initially generated that consisted of a promoterless selectable neomycin resistance marker inserted into the v-abl gene of the complete Abelson murine leukemia virus genome, designed to be expressed either as a fusion protein or by translational restart. Tests of these viral genomes for transmission of v-abl and neo markers showed more stable coexpression in a protein fusion construct. The neo fusion was subcloned from this v-abl construct into a promoterless c-abl fragment, and the resulting DNA was used to transform embryonic stem cells. Direct screening of genomic DNAs showed that a high proportion of drug-resistant clones arose from homologous recombination into the endogenous c-abl locus.
Viscosupplementation for treatment of osteoarthritis: from initial discovery to current status and results. (2004)

Viscosupplementation is a therapeutic modality based on the replacement of synovial fluid or exudates with an elastoviscous hyaluronan solution. The first clinical trials were carried out on race horses with painful osteoarthritis of traumatic origin. In the early 1970s, the clinical trials were extended to painful osteoarthritis in humans. Analgesic effects lasting longer than the residence time of the injected hyaluronan in joints were reported both in horses and humans. The hyaluronan used was a noninflammatory fraction of the molecule with an average molecular weight of 2-3 million at a 1% concentration. The analgesic effect of this elastoviscous hyaluronan solution was demonstrated in behavioral animal pain models. Later it was shown that the elastoviscous properties of hyaluronan solutions are the determining factors in reducing pain-elicited nerve activity in both normal and inflamed cat and rat joints. It also was demonstrated in animal arthritis models that elastoviscous hyaluronan solutions promote the healing of traumatic intra-articular wounds. From the mid-1980s, several hyaluronan preparations of greatly varying average molecular weight but with the same concentration were introduced as viscosupplementation-based therapeutic agents. The elastoviscous properties of these solutions varied also, because of the greatly varying average molecular weights (0.5-6.0 million), imitating the rheological properties of either healthy or pathological synovial fluid. Currently, viscosupplementation products available worldwide vary greatly in their elastoviscous properties, and their dosage is not standardized in terms of frequency of injections required or in regard to the removal of exudates before injection. The question of which patient at what stage of the disease responds best with long-lasting pain relief to the many therapeutic products marketed with greatly varying elastoviscous properties has not yet been answered. At the same time, viscosupplementation was introduced, the same highly elastoviscous hyaluronan solutions also were applied in ophthalmic surgery as viscosurgical tools to protect sensitive tissues in the eye during surgery and to be used as soft instruments for tissue manipulation. Modified hyaluronan products (gels) also were introduced for augmentation of the intercellular matrix in tissues (viscoaugmentation) and for separating tissues to prevent adhesions and excessive scar formation (viscoseparation). Hyaluronan and its derivatives (gels) also have been used for drug delivery. The therapeutic use of highly elastoviscous solutions and gels of hyaluronan and its derivatives to build intercellular matrices for supplementation, regeneration, and developing new tissues introduced the concept of matrix engineering into medical practice.
Reduction of Nasopharyngeal Carriage ofStreptococcus pneumoniaeafter Administration of a 9‐Valent Pneumococcal Conjugate Vaccine to Toddlers Attending Day Care Centers (2002)

A double-blind, randomized study involving 264 toddlers attending day care centers was conducted to document the effect of a 9-valent pneumococcal conjugate vaccine on the carriage rate of pneumococci. Of 3750 cultures done on nasopharyngeal samples obtained from subjects during a 2-year follow-up period after vaccination, 65% were positive for Streptococcus pneumoniae. In all age windows, the rate of carriage of vaccine-type pneumococci was lower among subjects who received the pneumococcal vaccine than among control subjects, because the acquisition rate was lower in the former group. The effect was most pronounced among subjects aged < or =36 months. The sample size enabled us to study protection against carriage of S. pneumoniae serotypes 6B, 9V, 14, 19F, and 23F; significant protection against all serotypes except 19F was seen in the pneumococcal-vaccine group. The rate of carriage of serotype 6A (not included in the vaccine) was also reduced significantly, but the rate of carriage of serotype 19A (not included in the vaccine) was not. The rate of carriage of non-vaccine-type pneumococci (excluding serotype 6A) was higher in the pneumococcal-vaccine group than in the control group.
Ion channels formed in planar lipid bilayers by Bacillus thuringiensis toxins in the presence of Manduca sexta midgut receptors (1997)

A purified, GPI-linked receptor complex isolated from Manduca sexta midgut epithelial cells was reconstituted in planar lipid bilayers. CryIAa, CryIAc and CryIC, three Bacillus thuringiensis insecticidal proteins, formed channels at much lower doses (0.33-1.7 nM) than in receptor-free membranes. The non-toxic protein CryIB also formed channels, but at doses exceeding 80 nM. The channels of CrylAc, the most potent toxin against M. sexta, rectified the passage of cations. All other toxin channels displayed linear current-voltage relationships. Therefore, reconstituted Cry receptors catalyzed channel formation in phospholipid membranes and, in two cases, were involved in altering their biophysical properties.
Radioligand binding assay of epidermal growth factor receptor: causes of variability and standardization of the assay (1990)

Although experimental evidence indicates a probable role of epidermal growth factor receptor (EGFr) in clinical oncology, no standardized method for its determination has been yet described, and discrepant results have been reported in clinical studies. In standardizing a radioligand binding assay for EGFr, we evaluated the causes of variability in each step of the assay. Entrapment of EGFr in the nuclear fraction and contamination of the crude membrane fraction by cytosol protein were eliminated through preliminary purification steps. Both Scatchard and Rosenthal analysis of the saturation reaction of the membrane fraction with a wide range of concentrations of 125I-labeled EGF revealed a double class of binding sites. Study of the saturation reaction showed a partial exchange of 125I-labeled EGF with endogenous EGF within 20 h. The present method--incubation of partly purified membrane fraction with 125I-labeled EGF, 0.5 nmol/L, with and without 100-fold excess of cold EGF, for 20 h at 26 degrees C, followed by centrifugation at 5000 x g for 30 min to separate membrane-bound 125I-labeled EGF--shows good sensitivity, precision, and accuracy; is reasonably simple; and may be suitable for routine clinical use.
Myostatin Inhibition in Muscle, but Not Adipose Tissue, Decreases Fat Mass and Improves Insulin Sensitivity (2009)

Myostatin (Mstn) is a secreted growth factor expressed in skeletal muscle and adipose tissue that negatively regulates skeletal muscle mass. Mstn(-/-) mice have a dramatic increase in muscle mass, reduction in fat mass, and resistance to diet-induced and genetic obesity. To determine how Mstn deletion causes reduced adiposity and resistance to obesity, we analyzed substrate utilization and insulin sensitivity in Mstn(-/-) mice fed a standard chow. Despite reduced lipid oxidation in skeletal muscle, Mstn(-/-) mice had no change in the rate of whole body lipid oxidation. In contrast, Mstn(-/-) mice had increased glucose utilization and insulin sensitivity as measured by indirect calorimetry, glucose and insulin tolerance tests, and hyperinsulinemic-euglycemic clamp. To determine whether these metabolic effects were due primarily to the loss of myostatin signaling in muscle or adipose tissue, we compared two transgenic mouse lines carrying a dominant negative activin IIB receptor expressed specifically in adipocytes or skeletal muscle. We found that inhibition of myostatin signaling in adipose tissue had no effect on body composition, weight gain, or glucose and insulin tolerance in mice fed a standard diet or a high-fat diet. In contrast, inhibition of myostatin signaling in skeletal muscle, like Mstn deletion, resulted in increased lean mass, decreased fat mass, improved glucose metabolism on standard and high-fat diets, and resistance to diet-induced obesity. Our results demonstrate that Mstn(-/-) mice have an increase in insulin sensitivity and glucose uptake, and that the reduction in adipose tissue mass in Mstn(-/-) mice is an indirect result of metabolic changes in skeletal muscle. These data suggest that increasing muscle mass by administration of myostatin antagonists may be a promising therapeutic target for treating patients with obesity or diabetes.
In vivo and in vitro activities of point mutants of the bacteriophage T7 RNA polymerase promoter (1992)

Two compatible plasmids were recently reported [Ikeda et al. (1992) Nucleic Acids Res. 20, 2517-2524] that together can be used to determine whether a mutant T7 RNA polymerase promoter is active or inactive in vivo. The first plasmid, pKGP1-1, carries T7 gene 1 (the gene encoding T7 RNA polymerase) ligated to a tac promoter, while the second plasmid, pCM-X#, carries the gene encoding chloramphenicol acetyltransferase (CAT) ligated to potential T7 promoters. If the pCM-X# plasmid carries a potential T7 promoter that can be utilized by T7 RNA polymerase, then CAT is produced from transcripts generated by T7 RNA polymerase from the potential promoter on the pCM-X# plasmid. To determine whether Escherichia coli growth characteristics and chloramphenicol (cam) resistance produced by the plasmids pKGP1-1 and pCM-X# reflect the T7 promoter activity of the possible promoters carried by the pCM-X# plasmids, the in vivo and in vitro strengths of the potential T7 promoters were compared and correlated. In vivo promoter strength was determined by measuring the relative amounts of CAT present in E. coli extracts, while relative in vitro promoter strength was measured in transcription assays. The in vivo and in vitro strengths of 22 point mutants of the consensus T7 promoter were shown to correlate with the growth characteristics and cam resistance conferred to E. coli harboring the plasmid pKGP1-1 and the respective pCM-X# plasmid.(ABSTRACT TRUNCATED AT 250 WORDS)
CD59 protects glomerular endothelial cells from immune-mediated thrombotic microangiopathy in rats. (1998)

CD59 is a cell membrane-bound complement regulatory protein on glomerular cells that inhibits C5b-9 assembly and insertion. This report describes a recently developed model of immune thrombotic microangiopathy (TMA) induced by the renal artery perfusion of anti-glomerular endothelial cell (anti-GEN) antibody. To examine the role of CD59 in protecting the GEN from immune-mediated injury, rats underwent selective renal artery perfusion with F(ab')2 fragments of anti-CD59 monoclonal antibody to block CD59 activity or control mouse IgG followed by anti-GEN antibody or control goat IgG. Neutralization of CD59 in normal rats did not result in any significant functional or histologic changes. Perfusion with anti-CD59 did not change deposition of the pathogenic anti-GEN IgG used to induce the TMA model. However, neutralization of CD59 in the TMA model resulted in more C5b-9 formation in glomeruli, accompanied by increased platelet and fibrin deposition, more severe endothelial injury, and reduced renal function compared with the animals perfused with control F(ab')2 fragments. These results demonstrate directly that CD59 serves a protective role for GEN in this TMA model of rats, and confirm that C5b-9 formation has a critical pathogenic role in the mediation of the disease. CD59 may play an important role in protecting glomerular endothelium from other complement-mediated types of injury.
Evaluation of a combined index of optic nerve structure and function for glaucoma diagnosis (2011)

The SFI reflects the traditional clinical diagnosis of glaucoma by combining optic nerve structure and function. In doing so, it identifies a different subset of patients than either visual field testing or optic nerve head imaging alone. Analysis of prospective data will allow us to determine whether the combined index of structure and function can provide an improved standard for glaucoma diagnosis.