gebhart/patrepeval huggingface dataset:
Direct observations of ultrasound microbubble contrast agent interaction with the microvessel wall (2007)

Many thousands of contrast ultrasound studies have been conducted in clinics around the world. In addition, the microbubbles employed in these examinations are being widely investigated to deliver drugs and genes. Here, for the first time, the oscillation of these microbubbles in small vessels is directly observed and shown to be substantially different than that predicted by previous models and imaged within large fluid volumes. Using pulsed ultrasound with a center frequency of 1 MHz and peak rarefactional pressure of 0.8 or 2.0 MPa, microbubble expansion was significantly reduced when microbubbles were constrained within small vessels in the rat cecum (p<0.05). A model for microbubble oscillation within compliant vessels is presented that accurately predicts oscillation and vessel displacement within small vessels. As a result of the decreased oscillation in small vessels, a large resting microbubble diameter resulting from agent fusion or a high mechanical index was required to bring the agent shell into contact with the endothelium. Also, contact with the endothelium was observed during asymmetrical collapse, not during expansion. These results will be used to improve the design of drug delivery techniques using microbubbles.
Progress and Challenges in the Design and Clinical Development of Antibodies for Cancer Therapy (2018)

The remarkable progress in engineering and clinical development of therapeutic antibodies in the last 40 years, after the seminal work by Köhler and Milstein, has led to the approval by the United States Food and Drug Administration (FDA) of 21 antibodies for cancer immunotherapy. We review here these approved antibodies, with emphasis on the methods used for their discovery, engineering, and optimization for therapeutic settings. These methods include antibody engineering <i>via</i> chimerization and humanization of non-human antibodies, as well as selection and further optimization of fully human antibodies isolated from human antibody phage-displayed libraries and immunization of transgenic mice capable of generating human antibodies. These technology platforms have progressively led to the development of therapeutic antibodies with higher human content and, thus, less immunogenicity. We also discuss the genetic engineering approaches that have allowed isotype switching and Fc modifications to modulate effector functions and bioavailability (half-life), which together with the technologies for engineering the Fv fragment, have been pivotal in generating more efficacious and better tolerated therapeutic antibodies to treat cancer.
Amyotrophic Lateral Sclerosis (2001)

Charcot described amyotrophic lateral sclerosis (ALS) in 1874. Despite progress, this creeping paralysis, known colloquially as Lou Gehrig's disease, is still not visibly affected by available therapies. However, advances in genetics have accelerated the pace of ALS research in the past decade, promising more effective treatment.Definition of the DiseaseALS has two meanings. In one sense, it refers to several adult-onset conditions characterized by progressive degeneration of motor neurons (Figure 1). In the United Kingdom, the term motor neuron disease is used for these disorders. In the second sense, ALS refers to one specific form of motor neuron disease . . .
Rigid Rod Conjugated Polymers for Nonlinear Optics. 3. Intramolecular H Bond Effects on Poly(phenyleneethynylene) Chains (1997)

This paper describes the synthesis and the X-ray and the optical characterization of conjugated soluble polymers in which the planarity of the backbone has been improved by intramolecular H bonds. The solubility of the polymers was enhanced by increasing the number of alkyl chains on the aryl group. The electron density on the phenyl ring was also modified by the amino and ester groups, introducing electron-donor or electron-acceptor groups, which also increase the polarizability. The polymers have been synthesized by polycondensation using a palladium-catalyzed coupling reaction, between a bromoaryl and an ethynylaryl unit, with HBr elimination. This method allows the insertion of a triple bond between two phenyl groups. It was initially used in our laboratory to obtain oligomers or high molecular weight polymers, having important nonlinear susceptibilities. The new polymers have been characterized by UV−visible and Raman spectroscopies, as well as nonlinear optical measurements of the third-order susceptibilities (χ(3)). These measurements allowed us to show the influence of the H bonds between the aryl groups on the absorption wavelength. In addition, the nonlinear optical measurements show that the χ(3) value of the pPY (6.8 × 10-10 esu) is close to the highest values obtained in acetylenic polymers such as polydiacetylenes.
Correction of Diabetic Erectile Dysfunction with Adipose Derived Stem Cells Modified with the Vascular Endothelial Growth Factor Gene in a Rodent Diabetic Model (2013)

The aim of this study was to determine whether adipose derived stem cells (ADSCs) expressing vascular endothelial growth factor (VEGF) gene can improve endothelial function, recover the impaired VEGF signaling pathway and enhance smooth muscle contents in a rat diabetic erectile dysfunction (DED) model. DED rats were induced via intraperitoneal injection of streptozotocin (40 mg/kg), and then screened by apomorphine (100 µg/kg). Five groups were used (n = 12/group)-Group 1 (G1): intracavernous injection of lentivirus-VEGF; G2: ADSCs injection; G3: VEGF-expressing ADSCs injection; G4: Phosphate buffered saline injection; G1-G4 were DED rats; G5: normal rats. The mean arterial pressure (MAP) and intracavernosal pressure (ICP) were measured at days 7 and 28 after the injections. The components of the VEGF system, endothelial, smooth muscle, pericytes markers in cavernoursal tissue were assessed. On day 28 after injection, the group with intracavernosum injection of ADSCs expressing VEGF displayed more efficiently and significantly raised ICP and ICP/MAP (p<0.01) than those with ADSCs or lentivirus-VEGF injection. Western blot and immunofluorescent analysis demonstrated that improved erectile function by ADSCs-VEGF was associated with increased expression of endothelial markers (VEGF, VEGF R1, VEGF R2, eNOS, CD31 and vWF), smooth muscle markers (a-actin and smoothelin), and pericyte markers (CD146 and NG2). ADSCs expressing VEGF produced a therapeutic effect and restored erectile function in diabetic rats by enhancing VEGF-stimulated endothelial function and increasing the contents of smooth muscle and pericytes.
Differential expression of two fibroblast growth factor-receptor genes is associated with malignant progression in human astrocytomas. (1994)

Malignant astrocytomas, which are highly invasive, vascular neoplasms, compose the majority of nervous system tumors in humans. Elevated expression of fibroblast growth factors (FGFs) in astrocytomas has implicated the FGF family of mitogens in the initiation and progression of astrocyte-derived tumors. In this study, we demonstrated that human astrocytomas undergo parallel changes in FGF-receptor (FGFR) expression during their progression from a benign to a malignant phenotype. FGFR type 2 (BEK) expression was abundant in normal white matter and in all low-grade astrocytomas but was not seen in malignant astrocytomas. Conversely, FGFR type 1 (FLG) expression was absent or barely detectable in normal white matter but was significantly elevated in malignant astrocytomas. Malignant astrocytomas also expressed an alternatively spliced form of FGFR-1 (FGFR-1 beta) containing two immunoglobulin-like disulfide loops, whereas normal human adult and fetal brains expressed a receptor form (FGFR-1 alpha) containing three immunoglobulin-like disulfide loops. Intermediate grades of astrocytic tumors exhibited a gradual loss of FGFR-2 and a shift in expression from FGFR-1 alpha to FGFR-1 beta as they progressed from benign to malignant phenotype. These results suggest that differential expression and alternative splicing of FGFRs may be critical in the malignant progression of astrocytic tumors.
Genetically encoded fluorescent reporters of protein tyrosine kinase activities in living cells (2001)

The complexity and specificity of many forms of signal transduction are widely believed to require spatial compartmentation of protein kinase and phosphatase activities, yet existing methods for measuring kinase activities in cells lack generality or spatial or temporal resolution. We present three genetically encoded fluorescent reporters for the tyrosine kinases Src, Abl, and epidermal growth factor (EGF) receptor. The reporters consist of fusions of cyan fluorescent protein (CFP), a phosphotyrosine binding domain, a consensus substrate for the relevant kinase, and yellow fluorescent protein (YFP). Stimulation of kinase activities in living cells with addition of growth factors causes 20-35% changes in the ratios of yellow to cyan emissions because of phosphorylation-induced changes in fluorescence resonance energy transfer (FRET). Platelet-derived growth factor (PDGF) stimulated Abl activity most strongly in actin-rich membrane ruffles, supporting the importance of this tyrosine kinase in the regulation of cell morphology. These results establish a general strategy for nondestructively imaging dynamic protein tyrosine kinase activities with high spatial and temporal resolution in single living cells.
Growth hormone stimulates insulin‐like growth factor I actions on adult articular chondrocytes (1989)

We report effects of adding insulin-like growth factor I (IGF-I) and methionyl human growth hormone (GH), alone or in combination, to adult bovine articular chondrocytes plated at high density. Purified human and synthetic IGF-I stimulated chondrocyte DNA and proteoglycan synthesis. GH had no effect on either process. However, GH added in combination with IGF-I increased proteoglycan, cell-associated proteoglycan, and keratan sulfate synthesis over levels observed with IGF-I alone. IGF-I and GH did not alter the hydrodynamic size of proteoglycans or synthesis of collagen. Our results show that GH and IGF-I act together to stimulate adult chondrocyte extracellular matrix synthesis.
Identification of a 33-Kd protein associated with the alpha-granule membrane (GMP-33) that is expressed on the surface of activated platelets (1992)

To identify antigens on the platelet plasma membrane that are exposed after activation, we developed a monoclonal antibody (MoAb) designated RUU-SP 1.77. The RUU-SP 1.77 antigen is present on the membrane of resting platelets at a basal level and is strongly expressed on the plasma membrane after thrombin activation. Freshly fixed platelets bound 4,150 +/- 1,935 (mean +/- SD) RUU-SP 1.77 molecules per platelet; on fixed thrombin-stimulated platelets the number of binding sites was upregulated to 19,050 +/- 5,120 (kd 4.5 +/- 0.8 nmol/L). MoAb RUU-SP 1.77 recognized a major protein of 33 Kd and a minor 28-Kd protein, both under nonreduced and reduced conditions. Immunoelectron microscopic studies showed the presence of the protein associated with the membrane of alpha-granules. Due to the localization associated with the alpha-granule membrane, we have designated it GMP-33 (granule membrane protein with a molecular weight of 33 Kd). Based on structural properties, we conclude that GMP-33 is a protein associated with the alpha-granule membrane that has not been described before.
Bacterial glycoproteins: Functions, biosynthesis and applications (2003)

Although widely distributed in eukaryotic cells glycoproteins appear to be rare in prokaryotic organisms. The prevalence of the misconception that bacteria do not glycosylate their proteins has been a subject matter of discussion for a long time. Glycoconjugates that are linked to proteins or peptides, generated by the ribosomal translational mechanism have been reported only in the last two to three decades in a few prokaryotic organisms. Most studied prokaryotic glycoproteins are the S-layer glycoproteins of Archeabacteria. Apart from these, membrane-associated, surface-associated, secreted glycoproteins and exoenzymes glycoproteins are also well documented in both, Archea and Eubacteria. From the recent literature, it is now clear that prokaryotes are capable of glycosylating proteins. In general, prokaryotes are deprived of the cellular organelles required for glycosylation. In prokaryotes many different glycoprotein structures have been observed that display much more variation than that observed in eukaryotes. Besides following similar mechanisms in the process of glycosylation, prokaryotes have also been shown to use mechanisms that are different from those found in eukaryotes. The knowledge pertaining to the functional aspects of prokaryotic glycoproteins is rather scarce. This review summarizes developments and understanding relating to characteristics, synthesis, and functions of prokaryotic glycoproteins. An extensive summary of glycosylation that has been reported to occur in bacteria has also been tabulated. Various possible applications of these diverse biomolecules in biotechnology, vaccine development, pharmaceutics and diagnostics are also touched upon.
Reduced Circulating GDF11 Is Unlikely Responsible for Age-Dependent Changes in Mouse Heart, Muscle, and Brain (2015)

Recent high-profile studies report conflicting data on the age-related change in circulating growth/differentiation factor 11 (GDF11) and myostatin as well as the former's influence on muscle regeneration. Both ligands bind and activate ActRIIB receptors with similar affinities and should therefore have similar actions, yet these studies suggest that GDF11 activates muscle regeneration whereas myostatin is well known to inhibit it. They also suggest that circulating GDF11 levels, but not those of myostatin, decline with age. We performed a careful assessment of the ELISA used to quantify circulating myostatin in these studies and determined that assay reagents significantly cross react with each protein, each of which is highly homologous. Circulating myostatin levels decreased with age and estimates of GDF11 levels using myostatin null mice indicate that they were almost 500 times lower than those for myostatin. This suggests that circulating GDF11 has little physiological relevance as it could not outcompete myostatin for ActRIIB binding sites. Together, these results further suggest that the previously reported aging muscle, heart, and brain phenotypes attributed to reduced circulating GDF11 should be reconsidered.
Multi-valued Decision Diagrams for the Verification of Consistency in Automotive Product Data (2012)

Highly customizable products and mass customization - as increasing trends of the last years - are mainly responsible for an immense growth of complexity within the digital representations of knowledge of car manufacturers. We developed a method to detect and analyze inconsistencies by employing a Multi-Valued Decision Diagram (MDD) which issued to encode the set of all valid product configurations. On this basis, we stated a number of rules of consistency that are checked by a set-based verification scheme.
Mutations and Response to Epidermal Growth Factor Receptor Inhibitors (2009)

Novel therapeutic agents targeting the epidermal growth factor receptor (EGFR) have improved outcomes for a subgroup of patients with colorectal, lung, head and neck, and pancreatic cancers. In these tumors, the EGFR activation turns on at least five different signaling pathways (RAS/mitogen-activated protein kinase, phospholipase C, phosphatidylinositol 3-kinase/AKT, signal transducer and activator of transcription, and SRC/FAK pathways), which are intimately interconnected, and frequent mutations involving either the receptor itself or downstream effectors have been found. Up to now, it seems that alterations at the EGFR level has major importance in EGFR tyrosine kinase inhibitor response, whereas modifications of downstream effectors could lead to treatment resistance. Furthermore, our understanding of the mechanism of the EGFR network activation provides new hypotheses on potential new anticancer drugs that may be effective.
Prostaglandin F2α Formation from Prostaglandin H2 by Prostaglandin F Synthase (PGFS):  Crystal Structure of PGFS Containing Bimatoprost, (2006)

Prostaglandin H(2) (PGH(2)) formed from arachidonic acid is an unstable intermediate and is efficiently converted into more stable arachidonate metabolites by the action of enzymes. Prostaglandin F synthase (PGFS) has dual catalytic activities: formation of PGF(2)(alpha) from PGH(2) by the PGH(2) 9,11-endoperoxide reductase activity and 9alpha,11beta-PGF(2) (PGF(2)(alphabeta)) from PGD(2) by the PGD(2) 11-ketoreductase activity in the presence of NADPH. Bimatoprost (BMP), which is a highly effective ocular hypotensive agent, is a PGF(2)(alpha) analogue that inhibits both the PGD(2) 11-ketoreductase and PGH(2) 9,11-endoperoxide reductase activities of PGFS. To examine the catalytic mechanism of PGH(2) 9,11-endoperoxide reductase, a crystal structure of PGFS[NADPH + BMP] has been determined at 2.0 A resolution. BMP binds near the PGD(2) binding site, but the alpha- and omega-chains of BMP are locate on the omega- and alpha-chains of PGD(2), respectively. Consequently, the bound BMP and PGD(2) direct their opposite faces of the cyclopentane moieties toward the nicotinamide ring of the bound NADP. The alpha- and omega-chains of BMP are involved in H-bonding with protein residues, while the cyclopentane moiety is surrounded by water molecules and is not directly attached to either the protein or the bound NADPH, indicating that the cyclopentane moiety is movable in the active site. From the complex structure, two model structures of PGFS containing PGF(2)(alpha) and PGH(2) were built. On the basis of the model structures and inhibition data, a putative catalytic mechanism of PGH(2) 9,11-endoperoxide reductase of PGFS is proposed. Formation of PGF(2)(alpha) from PGH(2) most likely involves a direct hydride transfer from the bound NADPH to the endoperoxide of PGH(2) without the participation of specific amino acid residues.
Transformation of Tetrahymena thermophila by microinjection of a foreign gene. (1993)

Tetrahymena thermophila has been transformed to paromomycin-resistant phenotypes by microinjection of an aminoglycoside 3'-phosphotransferase (neo) gene under the control of the T. thermophila histone H4-I promoter. This chimeric neo gene, by itself or on a vector containing a rRNA-encoding DNA (rDNA) origin of replication, transforms T. thermophila. In cells transformed with the rDNA origin vector, the neo gene is usually found integrated into the endogenous rDNA molecules and is present in high copy number. In transformants obtained by microinjecting only the linear chimeric gene, the neo gene is found to have replaced the histone H4-I gene or is found integrated into the 5' flanking region of the H4-I gene. The relative transcript levels of the neo gene in T. thermophila transformed by the linear chimeric gene are much higher than in cells transformed with the vector. The neo gene provides an effective selectable marker for transformation of T. thermophila.
394. Generation of a Novel Allogeneic CAR T Cell Platform Utilizing an Engineered Meganuclease and AAV Donor Template to Achieve Efficient Disruption of T Cell Receptor Expression and Simultaneous Homology-Directed Insertion of a CD19 CAR (2016)

Chimeric antigen receptor (CAR) T cell therapies have achieved dramatic results treating hematological malignancies by redirecting the specificity of T cells to target CD19 expressing cancer cells. Clinical trials reporting these impressive results have used autologous therapies, which pose significant manufacturing, logistical, and cost issues, complicating the implementation of such therapies on a larger scale. Furthermore, CAR T cells are typically generated by using Lenti- or Retro- viral vectors, resulting in random integration of the CAR gene, heterogeneous expression of the CAR on the cell surface, and the potential for insertional mutagenesis. We have developed a platform to address these issues by using a streamlined process to insert a CAR gene into the T cell receptor (TCR) alpha chain locus of T cells obtained from healthy donors using a highly optimized engineered meganuclease. The resulting gene-edited allogeneic CAR T cells do not express an endogenous TCR and therefore should not be capable of eliciting graft versus host disease upon adoptive transfer. We first produced and validated an engineered meganuclease targeting TCRα, and developed a scalable process for electroporating T cells with meganuclease mRNA that routinely results in greater than 60% knockout of the TCR, as measured by flow cytometry. To test our gene knock-in approach, we treated cells with our meganuclease to induce a double-strand break (DSB) in TCRα. We then transduced these cells using an AAV6 vector containing a donor DNA template consisting of a second generation CD19 CAR driven by an exogenous promoter and flanked by homology arms to the target site in the TCRα sequence. Homology directed repair of the DSB utilizing this donor template results in insertion of the CD19 CAR at this site in the genome. Incorporating this process into a 14 day procedure for generation and expansion of TCR knockout CAR T cells, we successfully generated a large population of TCR knockout cells with >70% of those cells stably expressing the CD19 CAR. Importantly, these CAR T cells proliferated when co-cultured with CD19+ target cells, released cytokines including IFN-γ and IL-2, and exhibited potent cytotoxic activity against CD19+ target cells. Studies to confirm in vivo antitumor activity are currently being conducted. In summary, we describe a novel, highly efficient, and scalable method to produce allogeneic CAR T cells in a streamlined process using an engineered meganuclease in combination with an AAV6 donor template.
Proliferation and differentiation of goat bone marrow stromal cells in 3D scaffolds with tunable hydrophilicity (2009)

We have synthesized methacrylate-endcapped caprolactone networks with tailored water sorption ability, poly(CLMA-co-HEA), in the form of three-dimensional (3D) scaffolds with the same architecture but exhibiting different hydrophilicity character (x(HEA)=0, 0.3, 0.5), and we investigated the interaction of goat bone marrow stromal cells (GBMSCs) with such structures. For this purpose, GBMSCs were seeded and cultured for 3, 7, 14, 21, and 28 days onto the developed scaffolds. Cells have proliferated throughout the whole scaffold volume. Cell adhesion and morphology were analyzed by SEM, whereas cell viability and proliferation was assessed by MTS test and DNA quantification concluding that numbers of cells increased as a function of the culturing time (until day 14) and also with the hydrophobic content in the samples (from 50 to 100% of CLMA). No significant difference between samples with 100% and 70% of CLMA were detected in some cases. Osteoblastic differentiation was followed by assessing the alkaline phosphatase activity of cells, as well as type I collagen and osteocalcin expressions levels until day 21. The three markers were positive at days 14 and 21 when cells were cultured in 100% CLMA substrates which suggests osteoblastic differentiation of mesenchymal stem cells within these scaffolds. On the other hand, when the CLMA content decreases (until 50%), type I collagen and osteocalcin were positive but ALP was negative indicating that the differentiation process is affected by hydrophilic content. We suggest that such system may be useful to extract information on the effect of materials' wettability on the corresponding biological performance in a 3D environment. Such general insights may be relevant in the context of biomaterials selection for tissue engineering strategies.