gebhart/patrepeval huggingface dataset:
Tissue Engineering of Bone: Material and Matrix Considerations (2008)

When the normal physiologic reaction to fracture does not occur, such as in fracture nonunions or large-scale traumatic bone injury, surgical intervention is warranted. Autografts and allografts represent current strategies for surgical intervention and subsequent bone repair, but each possesses limitations, such as donor-site morbidity with the use of autograft and the risk of disease transmission with the use of allograft. Synthetic bone-graft substitutes, developed in an effort to overcome the inherent limitations of autograft and allograft, represent an alternative strategy. These synthetic graft substitutes, or matrices, are formed from a variety of materials, including natural and synthetic polymers, ceramics, and composites, that are designed to mimic the three-dimensional characteristics of autograft tissue while maintaining viable cell populations. Matrices also act as delivery vehicles for factors, antibiotics, and chemotherapeutic agents, depending on the nature of the injury to be repaired. This intersection of matrices, cells, and therapeutic molecules has collectively been termed tissue engineering. Depending on the specific application of the matrix, certain materials may be more or less well suited to the final structure; these include polymers, ceramics, and composites of the two. Each category is represented by matrices that can form either solid preformed structures or injectable forms that harden in situ. This article discusses the myriad design considerations that are relevant to successful bone repair with tissue-engineered matrices and provides an overview of several manufacturing techniques that allow for the actualization of critical design parameters.
Purification of human gamma interferon receptors by sequential affinity chromatography on immobilized monoclonal antireceptor antibodies and human gamma interferon. (1987)

mAbs against human IFN-gamma (huIFN-gamma) receptors were obtained by immunizing a BALB/c mouse with eluates from immobilized recombinant huIFN-gamma (rhuIFN-gamma) on which lysates of enriched Raji cell membranes had been adsorbed. mAbs were selected for competitive inhibition of receptor binding of 125I-labeled rhuIFN-gamma. The following additional properties suggest that these antibodies are specific for huIFN-gamma receptors: they bind to the surface of human cells expressing IFN-gamma receptors but not to heterologous cells; this binding is inhibited competitively by addition of rhuIFN-gamma; the number of binding sites revealed by direct binding of 125I-labeled rhuIFN-gamma correlates with the amount of antigen recognized by the mAbs on different cell lines. A Triton X-100 extract of a membrane-enriched fraction of human Raji cells was affinity purified with these mAbs and the eluates from such columns were further purified on immobilized rhuIFN-gamma. As revealed by SDS-PAGE, the final eluate contained two major protein bands with approximate Mr of 90,000 (p90) and 50,000 (p50), respectively. Both proteins were able to specifically bind 125I-labeled rhuIFN-gamma upon electroblotting to nitrocellulose. This binding could be inhibited by the huIFN-gamma receptor mAbs, suggesting that the same epitopes are recognized on p90, p50, and on the cell surface. Therefore, these proteins most likely represent at least a part of huIFN-gamma receptors.
Mechanistic studies on the phosphoramidite coupling reaction in oligonucleotide synthesis. I. Evidence for nudeophilic catalysis by tetrazole and rate variations with the phosphorus substituents (1987)

Tetrazole catalyzed reactions of a series of phosphoramidites, 5'-O-DMTdT-3'-O-P(OR1)NR2(2) (1a-h), with 3'-O-SiButPh2-6-N-benzoyl-dA (2a) in acetonitrile solution have been studied. It is found that the coupling rate depends very much on whether tetrazole is added before or after 2a, and that dialkylammonium tetrazolide salts are inhibitors. These and other facts are evidence that the reactions are subjected to nucleophilic catalysis by tetrazole, in addition to acid catalysis. The rate variations with phosphorus substituents of 1a-h are NEt2 greater than NPri2 greater than N(CH2CH2)O greater than NMePh, and OMe greater than OCH2CH2CN greater than OCHMeCH2CN greater than OCMe2CH2CN much greater than OC6H4Cl. The inhibitor properties of dialkylammonium tetrazolides have practical consequences for the efficiency of DNA syntheses, when in situ prepared phosphoramidites are used; the same would apply for segmented, simultaneous syntheses or syntheses where recycling is performed.
Increased tolerance and conversion of inhibitors in lignocellulosic hydrolysates by Saccharomyces cerevisiae (2007)

Abstract During hydrolysis of lignocellulosic biomass, monomeric sugars and a broad range of inhibitory compounds are formed and released. These inhibitors, which can be organized around three main groups, furans, weak acids and phenolics, reduce ethanol yield and productivity by affecting the microorganism performance during the fermentation step. Among the microorganisms that have been evaluated for lignocellulosic hydrolysate ethanol fermentation, the yeast Saccharomyces cerevisiae appears to be the least sensitive. In order to overcome the effect of inhibitors, strategies that include improvement of natural tolerance of microorganism and use of fermentation control strategies have been developed. An overview of the origin, effects and mechanisms of action of known inhibitors on S. cerevisiae is given. Fermentation control strategies as well as metabolic, genetic and evolutionary engineering strategies to obtain S. cerevisiae strains with improved tolerance are discussed. Copyright © 2007 Society of Chemical Industry
Evaluation of 2,3,5-triphenyltetrazolium chloride as a stain for detection and quantification of experimental cerebral infarction in rats. (1986)

We have evaluated the use of 2,3,5-triphenyltetrazolium chloride (TTC) as an histopathologic stain for identification of infarcted rat brain tissue. The middle cerebral artery (MCA) of 35 normal adult rats was occluded surgically. At various times after surgical occlusion, rats were sacrificed and brain slices were obtained and stained with TTC or hematoxolin and eosin (H & E); the size of the area of infarcted tissue stained by each method was quantified. In rats sacrificed 24 hr after occlusion of the MCA, the size of the area of infarction was 21 +/- 2% of the coronal section for TTC, and 21 +/- 2% for H & E (mean +/- S.D., N = 13). The size of areas of infarction determined by either staining method was not significantly different in area by the paired test, and a significant correlation between sizes determined by each method was found by linear regression analysis (r = 0.91, slope = 0.89, and the y intercept = 4.4%). Staining with TTC is a rapid, convenient, inexpensive, and reliable method for the detection and quantification of cerebral infarction in rats 24 hr after the onset of ischemia.
Modulation of RANTES production by human cytomegalovirus infection of fibroblasts (1997)

Chemokines play a major role in inflammatory responses and affect hematopoiesis both negatively and positively. We show that fresh isolates and laboratory strains (Towne and Ad-169) of human cytomegalovirus (HCMV) induce production of the CC chemokine RANTES in fibroblasts. Induction of extracellular RANTES production occurred as early as 8 h after infection, peaked around 24 h after infection, and was almost undetectable by 48 and 72 h. Upregulation occurred in the absence of viral DNA synthesis, suggesting that it was due to immediate-early-early HCMV gene expression. CMV infection stimulated RANTES transcription, since reverse transcription-PCR detected a sharp increase in RANTES RNA which persisted even when extracellular RANTES was no longer detected. Induction of RANTES in fibroblasts was not due to prior induction of tumor necrosis factor alpha or interleukin 1 beta. Down-regulation required an active viral genome. Decrease of RANTES in culture supernatants may be associated with the appearance of the HCMV CC chemokine receptor US28, since we show that this gene is transcribed as early as 8 h after infection. Modulation of CC chemokine production early during CMV infection might have a regulatory effect on viral replication, as well as affect immune surveillance.
Definition of a bacterial virulence factor: sialylation of the group B streptococcal capsule. (1989)

Sialylation of bacterial capsules has been proposed as an important virulence factor for several species of encapsulated pathogens, including group B Streptococcus. We have constructed a transposon mutant strain of type III group B Streptococcus that expresses a capsular polysaccharide differing from the wild type only in that the mutant strain's capsule lacks sialic acid. The mutant polysaccharide is antigenically identical to the capsular polysaccharide of type 14 Streptococcus pneumoniae, as predicted by the structures of the type III group B Streptococcus and S. pneumoniae polysaccharides. Loss of capsular sialic acid was associated with loss of virulence in the mutant strain in a neonatal rat model of lethal group B Streptococcus infection. These studies demonstrate directly that capsular sialic acid is a critical virulence determinant for type III group B Streptococcus and support the general hypothesis that surface sialylation aids pathogenic microorganisms in evading host defenses.
Monounsaturated Fatty Acids Prevent the Deleterious Effects of Palmitate and High Glucose on Human Pancreatic β-Cell Turnover and Function (2003)

Glucotoxicity and lipotoxicity contribute to the impaired beta-cell function observed in type 2 diabetes. Here we examine the effect of saturated and monounsaturated fatty acids at different glucose concentrations on human beta-cell turnover and secretory function. Exposure of cultured human islets to saturated fatty acid and/or to an elevated glucose concentration for 4 days increased beta-cell DNA fragmentation and decreased beta-cell proliferation. In contrast, the monounsaturated palmitoleic acid or oleic acid did not affect DNA fragmentation and induced beta-cell proliferation. Moreover, each monounsaturated fatty acid prevented the deleterious effects of both palmitic acid and high glucose concentration. The cell-permeable ceramide analogue C(2)-ceramide mimicked both the palmitic acid-induced beta-cell apoptosis and decrease in proliferation. Furthermore, the ceramide synthetase inhibitor fumonisin B1 blocked the deleterious effects of palmitic acid on beta-cell turnover. In addition, palmitic acid decreased Bcl-2 expression and induced release of cytochrome c from the mitochondria into the cytosol, which was prevented by fumonisin B1 and by oleic acid. Finally, each monounsaturated fatty acid improved beta-cell secretory function that was reduced by palmitic acid and by high glucose. Thus, in human islets, the saturated palmitic acid and elevated glucose concentration induce beta-cell apoptosis, decrease beta-cell proliferation, and impair beta-cell function, which can be prevented by monounsaturated fatty acids. The deleterious effect of palmitic acid is mediated via formation of ceramide and activation of the apoptotic mitochondrial pathway, whereas Bcl-2 may contribute to the protective effect of monounsaturated fatty acids.
Propagation in Tissue Cultures of Cytopathogenic Agents from Patients with Measles. (1954)

Conclusion and SummaryThe findings just summarized support the presumption that this group of agents is composed of representatives of the viral species responsible for measles.Eight agents exhibiting the properties of viruses have been isolated in cultures of human or simian renal cells from the blood or throat washings of five cases of typical measles. Multiplication of the agents in vitro is accompanied by characteristic changes in the cells. Primarily these changes consist in the formation of syncytial giant cells wherein the chromatin assumes a marginal position and is replaced centrally by an acidophilic substance of unknown nature. The cytopathogenic effect of at least one of the agents is inhibited by convalescent phase measles sera from other patients with measles. Antigen appears during cultivation in vitro of the measles agents that reacts specifically in complement fixation tests with convalescent phase measles sera.
Nickel Ethylene Polymerization Catalysts Based on Phosphorus Ligands (2001)

Nickel(II) complexes of ligands of the type Ar-2- PN(Me)PAr2 (Ar = ortho-substituted phenyl group) are highly active and poison-tolerant catalysts for the polymerization of ethylene.
Modified Starches Properties and Uses (1986)

SECTION I: MODIFIED STARCHES-THEIR CHEMISTRY AND PROPERTIES. Converted Starches. Cross-Linked Starches. Acetylated Starch and Miscellaneous Organic Esters. Hydrox-yethylated Starches. Hydroxypropylated Starches. Phosphory-lated Starches and Miscellaneous Inorganic Esters. Cationic Starches. Succinate and Substituted Succinate Derivates of Starch. Grafted Starches. Miscellaneous Modifications. SECTION II: USES OF MODIFIED STARCHES. Food Industry. Paper Industry. Textile Industry. Corrugating and Adhesive Industries. Index.
Differential gene expression in mammary carcinoma cell lines: identification of DRIM, a new gene down-regulated in metastasis. (1998)

Differential display technique was applied to a pair of cell lines derived from human breast carcinoma cell line MDA-MB 435 with metastatic and non-metastatic properties in the nude mouse system, with the objective to isolate genes involved in metastasis. DRIM (Down-Regulated In Metastasis) was the only gene found to be differentially expressed in this system. DRIM encodes a protein comprising 2785 amino acids with significant homology to a protein in yeast and C. elegans. The protein contains a conserved positively charged tail and several HEAT repeats, designated after four functionally characterized proteins in which the repeat was detected. Most of the hydrophobic regions of DRIM can be assigned to HEAT repeats. Expression of DRIM at the RNA level was investigated in several normal tissues and tumor cell lines.
TensorLayer: A Versatile Library for Efficient Deep Learning Development (2017)

Deep learning has enabled major advances in the fields of computer vision, natural language processing, and multimedia among many others. Developing a deep learning system is arduous and complex, as it involves constructing neural network architectures, managing training/trained models, tuning optimization process, preprocessing and organizing data, etc. TensorLayer is a versatile Python library that aims at helping researchers and engineers efficiently develop deep learning systems. It offers rich abstractions for neural networks, model and data management, and parallel workflow mechanism. While boosting efficiency, TensorLayer maintains both performance and scalability. TensorLayer was released in September 2016 on GitHub, and has helped people from academia and industry develop real-world applications of deep learning.
EXPERIMENTAL STUDIES ON HEADACHE (1940)

Studies on man and lower animals have shown that the cranial blood vessels are pain-sensitive structures, capable under special circumstances of giving rise to headache.<sup>1</sup>The distention of cerebral arteries is primarily responsible for the headache produced by certain chemical agents, of which histamine is representative;<sup>2</sup>the headache associated with septicemia and fever is in the same category.<sup>3</sup>It has been shown that the afferent fibers from the pain-sensitive cerebral arteries above the tentorium enter the brain stem primarily through the fifth cranial nerve, whereas the fibers from the arteries below the tentorium enter the nervous system chiefly through the upper cervical nerves.<sup>4</sup>The distention of certain branches of the external carotid arteries is chiefly responsible for migraine headache and the headache associated with arterial hypertension.<sup>5</sup> Thus, data about the great variety of headaches resulting from distention of cranial arteries are specific, but there is
Expression of Endothelin-1 in the Lungs of Patients with Pulmonary Hypertension (1993)

Pulmonary hypertension is associated with the increased expression of endothelin-1 in vascular endothelial cells, suggesting that the local production of endothelin-1 may contribute to the vascular abnormalities associated with this disorder.
Prospective Clinical Study on Digital Nerve Repair with Collagen Nerve Conduits and Review of Literature (2013)

Little data are available concerning conduit repair of digital nerve lesions. We are presenting a prospective two-center cohort study on digital nerve reconstruction with collagen nerve conduits. The data are put into the context of a comprehensive review of existing literature. Over a period of 3 years, all consecutive digital nerve lesions that could not be repaired by tensionless coaptation with a gap length of less than 26 mm were reconstructed with nerve conduits made from bovine collagen I. Sensibility was assessed 1 week, 3, 6, and 12 months postoperatively by static and moving 2-point-discrimination (2PD) and monofilament testing. Forty-nine digital nerve lesions in 40 patients met the inclusion criteria. The mean nerve gap was 12.3 ± 2.3 mm (span 5-25 mm). Forty nerve reconstructions could be included in the 12-month follow-up. Three cases, assessed 12 months postoperatively, showed excellent sensibility (static 2PD <6 mm). Seventeen achieved good (2PD 6-10 mm), 5 fair (2PD 11-15 mm), 6 poor (2PD >15 mm, but protective sensibility), and 9 achieved no sensibility. Monofilament test results were significantly better if gap length was shorter than 12 mm. Our results confirm tubulization as one possible technique in nerve reconstruction for gap lengths of 5 to 25 mm.
Cap-Independent Translation of Picornavirus RN As:Structure and Function of the Internal Ribosomal Entry Site (1990)

Picornaviruses are mammalian plus-strand RNA viruses whose genomes serve as mRNA. A study of the structure and function of these viral mRNAs has revealed differences among them in events leading to the initiation of protein synthesis. A large segment of the 5' nontranslated region, approximately 400 nucleotides in length, promotes 'internal' entry of ribosomes independent of the non-capped 5' end of the mRNA. This segment, which we have called the internal ribosome entry site (IRES), maps approximately 200 nt down-stream from the 5' end and is highly structured. IRES elements of different picornaviruses, although functionally similar in vitro and in vivo, are not identical in sequence or structure. However, IRES elements of the genera entero- and rhinoviruses, on the one hand, and cardio- and aphthoviruses, on the other hand, reveal similarities corresponding to phylogenetic kinship. All IRES elements contain a conserved Yn-Xm-AUG unit (Y, pyrimidine; X, nucleotide) which appears essential for IRES function. The IRES elements of cardio-, entero- and aphthoviruses bind a cellular protein, p57. In the case of cardioviruses, the interaction between a specific stem-loop of the IREs is essential for translation in vitro. The IRES elements of entero- and cardioviruses also bind the cellular protein, p52, but the significance of this interaction remains to be shown. The function of p57 or p52 in cellular metabolism is unknown. Since picornaviral IRES elements function in vivo in the absence of any viral gene products, we speculate that IRES-like elements may also occur in specific cellular mRNAs releasing them from cap-dependent translation. IRES elements are useful tools in the construction of high yield expression vectors, or for tagging cellular genetic elements.
Vectorization in an oncolytic vaccinia virus of an antibody, a Fab and a scFv against programmed cell death -1 (PD-1) allows their intratumoral delivery and an improved tumor-growth inhibition (2016)

We report here the successful vectorization of a hamster monoclonal IgG (namely J43) recognizing the murine Programmed cell death-1 (mPD-1) in Western Reserve (WR) oncolytic vaccinia virus. Three forms of mPD-1 binders have been inserted into the virus: whole antibody (mAb), Fragment antigen-binding (Fab) or single-chain variable fragment (scFv). MAb, Fab and scFv were produced and assembled with the expected patterns in supernatants of cells infected by the recombinant viruses. The three purified mPD-1 binders were able to block the binding of mPD-1 ligand to mPD-1 <i>in vitro</i>. Moreover, mAb was detected in tumor and in serum of C57BL/6 mice when the recombinant WR-mAb was injected intratumorally (IT) in B16F10 and MCA 205 tumors. The concentration of circulating mAb detected after IT injection was up to 1,900-fold higher than the level obtained after a subcutaneous (SC) injection (i.e., without tumor) confirming the virus tropism for tumoral cells and/or microenvironment. Moreover, the overall tumoral accumulation of the mAb was higher and lasted longer after IT injection of WR-mAb1, than after IT administration of 10 µg of J43. The IT injection of viruses induced a massive infiltration of immune cells including activated lymphocytes (CD8<sup>+</sup> and CD4<sup>+</sup>). Interestingly, in the MCA 205 tumor model, WR-mAb1 and WR-scFv induced a therapeutic control of tumor growth similar to unarmed WR combined to systemically administered J43 and superior to that obtained with an unarmed WR. These results pave the way for next generation of oncolytic vaccinia armed with immunomodulatory therapeutic proteins such as mAbs.
Update: Affibody Molecules for Molecular Imaging and Therapy for Cancer (2007)

Affibody molecules are scaffold proteins, having a common frame of amino acids determining the overall fold or tertiary structure, but with each member characterized by a unique amino acid composition in an exposed binding surface determining binding specificity and affinity for a certain target. Affibody molecules represent a new class of affinity proteins based on a 58-amino acid residue protein domain, derived from one of the IgG binding domains of staphylococcal protein A. They combine small size ( approximately 6.5 kDa) with high affinity and specificity. Affibody molecules with nanomolar affinities were selected from an initial library (3 x 10(9) members) and, after affinity maturation, picomolar binders were obtained. The small size and simple structure of affibody molecules allow their production by chemical synthesis with homogeneous site-specific incorporation of moieties for further labeling using a wide range of labeling chemistries. The robustness and the refolding properties of affibody molecules make them amenable to labeling conditions that denature most proteins, including incubation at pH 11 at 60 degrees C for up to 60 minutes. Affibody molecules meet the requirements which are key for successful clinical use as imaging agents: high-affinity binding to the chosen target; short plasma half-life time; rapid renal clearance for nonbound drug substance and, high, continuously increasing tumor-to-organ ratios, resulting in high-contrast in vivo images shortly after injection of the diagnostic agent.