gebhart/patrepeval huggingface dataset:
Proteolytic activity in wound fluids and tissues derived from chronic venous leg ulcers (2009)

Venous leg ulcers affect approximately 1% of the general population and 3.6% of those over the age of 65. The goal of the research described herein is to shorten the time to healing by developing wound care alternatives that are based on a comprehensive understanding of the venous ulcer wound environment. The proteolytic and inflammatory components in wound fluids and tissue biopsy samples were characterized in subjects with documented long-standing venous ulcers that had showed resistance to standard therapy. All wounds showed polymicrobial colonization with greater than 10(6) CFU/g. Myeloperoxidase, a measure of leukocyte infiltration, was also markedly elevated in these wounds. Zymography revealed the presence of both pro-matrix metalloproteinase (MMP)-2 and pro-MMP-9 in wound fluids and to a lesser extent in tissue biopsies. Using an immunocapture activity assay we reveal a sevenfold excess of MMP-9 in wound fluid as compared to tissue, with 73% in the activated form. In contrast, MMP-8 total protein levels were nearly equal in wound fluids and biopsies. Fibronectin, a critical component of the extracellular matrix, was shown to be degraded in both wound fluids and biopsy samples. Finally, the potential of a novel wound dressing to neutralize several constituents of this hostile wound environment is shown.
The Fate of Fresh and Preserved, Noncrushed and Crushed Autogenous Cartilage in the Rabbit Model (1994)

This study was conducted to investigate volume retention and chondrocyte survival rate in autogenous fresh noncrushed, fresh crushed, preserved noncrushed, and preserved crushed cartilage grafts in rabbits. During the first phase of this investigation, cartilage was harvested from the right ear of 20 New Zealand white rabbits, then preserved. Four months later during the second phase, two 6-mm discs of previously harvested and preserved cartilage, one crushed and one noncrushed, were applied to the right ear. At the same time, two 6-mm discs of fresh cartilage graft were harvested from the left ear and then placed at a higher level on the same side, one crushed and one noncrushed. Three months after implantation, the rabbits were sacrificed and the grafts were evaluated. The preserved noncrushed cartilage retained 91.34% of the volume (SD = 2.46). Although most of the chondrocytes were nonviable, vascular ingrowth occurred with a significant repopulation of chondrocytes peripherally, in association with vascular endothelial ingrowth. The preserved crushed cartilage retained 74.19% of the volume (SD = 3.06). Most of the original chondrocytes were lost, but vascular ingrowth did occur and some osteoid formation occurred on the crushed cartilages. All chondrocytes on the fresh noncrushed cartilage grafts were viable and the grafts retained 94.54% of the volume (SD = 2.46). Crushed fresh cartilage retained 69.73% of its volume and the amount of viable chondrocytes ranged from 70% to 90% in the specimens evaluated (SD = 5.15). Although there is no question that noncrushed cartilage is superior, crushed cartilage can be used with a fair degree of predictability to attain the aesthetic goal.(ABSTRACT TRUNCATED AT 250 WORDS)
Effect of cyclic dipeptides containing histidine on pentobarbital narcosis. (1981)

We examined the effect of cyclo (His-Pro) and its analogs on pentobarbital narcosis in mice. Cyclo (His-Pro), 500 nmol/mouse, administered via intracerebroventricular (i.c.v.) route significantly prolonged the sleeping time. Methylation of histidine in the structure of cyclo (His-Pro) did not increase the activity of cyclo (His-Pro). Some of other cyclo (His-Pro) analogs, of which proline was replaced with other amino acids, cyclo (His-Phe), cyclo (His-Tyr), cyclo (His-His) and cyclo (D-His-Leu) produced significant prolongation of the sleeping time as compared with cyclo (His-Pro). These results suggest that cyclo (His-Pro) has opposing effect to that of thyrotropin releasing hormone (TRH) and the prolongation of pentobarbital narcosis by cyclic dipeptides might be caused by their central action.
Sonic Hedgehog signaling limits atopic dermatitis via Gli2-driven immune regulation (2019)

Hedgehog (Hh) proteins regulate development and tissue homeostasis, but their role in atopic dermatitis (AD) remains unknown. We found that on induction of mouse AD, Sonic Hedgehog (Shh) expression in skin, and Hh pathway action in skin T cells were increased. Shh signaling reduced AD pathology and the levels of Shh expression determined disease severity. Hh-mediated transcription in skin T cells in AD-induced mice increased Treg populations and their suppressive function through increased active transforming growth factor-β (TGF-β) in Tregs signaling to skin T effector populations to reduce disease progression and pathology. RNA sequencing of skin CD4+ T cells from AD-induced mice demonstrated that Hh signaling increased expression of immunoregulatory genes and reduced expression of inflammatory and chemokine genes. Addition of recombinant Shh to cultures of naive human CD4+ T cells in iTreg culture conditions increased FOXP3 expression. Our findings establish an important role for Shh upregulation in preventing AD, by increased Gli-driven Treg cell-mediated immune suppression, paving the way for a potential new therapeutic strategy.
Radiosynthesis and Evaluation of [18F]Selectfluor bis(triflate) (2010)

Selectfluor, one of the most reactive and commonly used electrophilic fluorinating N–F reagents, has been radiolabeled with 18F. The resulting new [18F]-labeled N–F reagent is safe, nontoxic, and easy to handle. The combined use of [18F]Selectfluor bis(triflate) and AgOTf allows for the preparation of electron-rich 18F-aromatic compounds through a simple “shake and mix” protocol at room temperature (see scheme; SA=specific activtiy).
Phytoestrogens Inhibit Growth and MAP Kinase Activity in Human Aortic Smooth Muscle Cells (1999)

-Estrogens are known to induce cardioprotective effects by inhibiting smooth muscle cell (SMC) growth and neointima formation. However, the use of estrogens as cardioprotective agents is limited by carcinogenic effects in women and feminizing effects in men. If noncarcinogenic and nonfeminizing estrogenlike compounds, such as natural phytoestrogens, afford cardioprotection, this would provide a safe method for prevention of cardiovascular disease in both men and women. Therefore, we evaluated and compared in human aortic SMCs the effects of phytoestrogens (formononetin, genistein, biochanin A, daidzein, and equol) on 2.5% fetal calf serum-induced proliferation (3H-thymidine incorporation and cell number), collagen synthesis (3H-proline incorporation), and total protein synthesis (3H-leucine incorporation) and on PDGF-BB (25 ng/mL)-induced migration (modified Boydens chambers). Moreover, the effects of phytoestrogens on PDGF-BB (25 ng/mL)-induced mitogen-activated protein kinase (MAP kinase) activity in SMCs was also studied. Phytoestrogens inhibited proliferation, collagen and total protein synthesis, migration, and MAP kinase activity in a concentration-dependent manner and in the following order of potency: biochanin A>genistein>equol>daidzein>formononetin. In conclusion, our studies provide the first evidence that in human aortic SMCs phytoestrogens inhibit mitogen-induced proliferation, migration and extracellular matrix synthesis and inhibit/downregulate MAP kinase activity. Thus, phytoestrogens may confer protective effects on the cardiovascular system by inhibiting vascular remodeling and neointima formation and may be clinically useful as a safer substitute for feminizing estrogens in preventing cardiovascular disease in both women and men.
Developing a programmed restriction endonuclease for highly specific DNA cleavage (2005)

Specific cleavage of large DNA molecules at few sites, necessary for the analysis of genomic DNA or for targeting individual genes in complex genomes, requires endonucleases of extremely high specificity. Restriction endonucleases (REase) that recognize DNA sequences of 4-8 bp are not sufficiently specific for this purpose. In principle, the specificity of REases can be extended by fusion to sequence recognition modules, e.g. specific DNA-binding domains or triple-helix forming oligonucleotides (TFO). We have chosen to extend the specificity of REases using TFOs, given the combinatorial flexibility this fusion offers in addressing a short, yet precisely recognized restriction site next to a defined triple-helix forming site (TFS). We demonstrate here that the single chain variant of PvuII (scPvuII) covalently coupled via the bifunctional cross-linker N-(gamma-maleimidobutryloxy) succinimide ester to a TFO (5'-NH2-[CH2](6 or 12)-MPMPMPMPMPPPPPPT-3', with M being 5-methyl-2'-deoxycytidine and P being 5-[1-propynyl]-2'-deoxyuridine), cleaves DNA specifically at the recognition site of PvuII (CAGCTG) if located in a distance of approximately one helical turn to a TFS (underlined) complementary to the TFO ('addressed' site: 5'-TTTTTTTCTCTCTCTCN(approximately 10)CAGCTG-3'), leaving 'unaddressed' PvuII sites intact. The preference for cleavage of an 'addressed' compared to an 'unaddressed' site is >1000-fold, if the cleavage reaction is initiated by addition of Mg2+ ions after preincubation of scPvuII-TFO and substrate in the absence of Mg2+ ions to allow triple-helix formation before DNA cleavage. Single base pair substitutions in the TFS prevent addressed DNA cleavage by scPvuII-TFO.
Role of Yersinia Murine Toxin in Survival of Yersinia pestis in the Midgut of the Flea Vector (2002)

Transmission by flea bite is a relatively recent adaptation that distinguishes Yersinia pestis, the plague bacillus, from closely related enteric bacteria. Here, a plasmid-encoded phospholipase D (PLD), previously characterized as Yersinia murine toxin (Ymt), was shown to be required for survival of Y. pestis in the midgut of its principal vector, the rat flea Xenopsylla cheopis. Intracellular PLD activity appeared to protect Y. pestis from a cytotoxic digestion product of blood plasma in the flea gut. By enabling colonization of the flea midgut, acquisition of this PLD may have precipitated the transition of Y. pestis to obligate arthropod-borne transmission.
High-Efficiency 352 nm Quaternary InAlGaN-Based Ultraviolet Light-Emitting Diodes Grown on GaN Substrates (2004)

We demonstrated high-efficiency ultraviolet (UV) light-emitting diodes (LEDs) with an emission wavelength of 352 nm using a quaternary InAlGaN multiple-quantum-well (MQW) emitting region. GaN substrates were used in order to eliminate the effects of threading dislocations. Emission fluctuation due to In segregation was clearly observed even in a dislocation-free area by a cathode luminescence (CL) image of a quaternary InAlGaN MQW, which is considered to contribute to the achievement of a high-efficiency UV emission. The maximum UV output power obtained was as high as 7.4 mW under room temperature (RT) CW operation. The maximum external quantum efficiency (EQE) was 1.1% with an injection current of 50 mA, which is the highest EQE ever obtained for 350-nm-band UV LEDs with a top-emission geometry.
Monoclonal Antibody "Gold Rush" (2007)

The market, sales and regulatory approval of new human medicines, during the past few years, indicates increasing number and share of new biologics and emergence of new multibillion dollar molecules. The global sale of monoclonal antibodies in 2006 were $20.6 billion. Remicade had annual sales gain of $1 billion during the past 3 years and five brands had similar increase in 2006. Rituxan with 2006 sales of $4.7 billion was the best selling monoclonal antibody and biological product and the 6th among the top selling medicinal brand. It may be the first biologic and monoclonal antibody to reach $10 billion annual sales in the near future. The strong demand from cancer and arthritis patients has surpassed almost all commercial market research reports and sales forecast. Seven monoclonal antibody brands in 2006 had sales exceeding $1 billion. Humanized or fully human monoclonal antibodies with low immunogenicity, enhanced antigen binding and reduced cellular toxicity provide better clinical efficacy. The higher technical and clinical success rate, overcoming of technical hurdles in large scale manufacturing, low cost of market entry and IND filing, use of fully human and humanized monoclonal antibodies has attracted funds and resources towards R&D. Review of industry research pipeline and sales data during the past 3 years indicate a real paradigm shift in industrial R&D from pharmaceutical to biologics and monoclonal antibodies. The antibody bandwagon has been joined by 200 companies with hundreds of new projects and targets and has attracted billions of dollars in R&D investment, acquisitions and licensing deals leading to the current Monoclonal Antibody Gold Rush.
Higher plants possess two structurally different poly(ADP‐ribose) polymerases (1998)

One of the immediate reactions of the mammalian cell to many environmental stresses is a massive synthesis of poly(ADP-ribose), catalyzed by poly(ADP-ribose) polymerase (PARP). Most of the biological functions attributed to PARP are inferred from experimentation with mammalian cells. In plants, the biology of PARP may be more complicated and diverse than was previously thought. Two poly(ADP-ribose) polymerase homologues were found in plants, the classical Zn-finger-containing polymerase (ZAP) and the structurally non-classical PARP proteins (APP and NAP), which lack the characteristic N-terminal Zn-finger domain. By enzymatic and cytological experiments the recombinant APP protein was shown to be located in the nucleus and to possess DNA-dependent poly(ADP-ribose) polymerase activity in yeast. The nuclear localization was further confirmed by the analysis of transgenic tobacco plants that expressed a translational gene fusion between APP and the bacterial beta-glucuronidase. The app promoter was transcriptionally up-regulated in cells pre-determined to die because of deficiency in a DNA ligase I.
Intestinal T Cell Responses to Gluten Peptides Are Largely Heterogeneous: Implications for a Peptide-Based Therapy in Celiac Disease (2009)

The identification of gluten peptides eliciting intestinal T cell responses is crucial for the design of a peptide-based immunotherapy in celiac disease (CD). To date, several gluten peptides have been identified to be active in CD. In the present study, we investigated the recognition profile of gluten immunogenic peptides in adult HLA-DQ2(+) celiac patients. Polyclonal, gliadin-reactive T cell lines were generated from jejunal mucosa and assayed for both proliferation and IFN-gamma production in response to 21 peptides from wheat glutenins and alpha-, gamma-, and omega-gliadins. A magnitude analysis of the IFN-gamma responses was performed to assess the hierarchy of peptide potency. Remarkably, 12 of the 14 patients recognized a different array of peptides. All alpha-gliadin stimulatory peptides mapped the 57-89 N-terminal region, thus confirming the relevance of the known polyepitope 33-mer, although it was recognized by only 50% of the patients. By contrast, gamma-gliadin peptides were collectively recognized by the great majority (11 of 14, 78%) of CD volunteers. A 17-mer variant of 33-mer, QLQPFPQPQLPYPQPQP, containing only one copy of DQ2-alpha-I and DQ2-alpha-II epitopes, was as potent as 33-mer in stimulating intestinal T cell responses. A peptide from omega-gliadin, QPQQPFPQPQQPFPWQP, although structurally related to the alpha-gliadin 17-mer, is a distinct epitope and was active in 5 out of 14 patients. In conclusion, these results showed that there is a substantial heterogeneity in intestinal T cell responses to gluten and highlighted the relevance of gamma- and omega-gliadin peptides for CD pathogenesis. Our findings indicated that alpha-gliadin (57-73), gamma-gliadin (139-153), and omega-gliadin (102-118) are the most active gluten peptides in DQ2(+) celiac patients.
Identification of a Novel Binding Motif in Pyrococcus furiosus DNA Ligase for the Functional Interaction with Proliferating Cell Nuclear Antigen (2006)

DNA ligase is an essential enzyme for all organisms and catalyzes a nick-joining reaction in the final step of the DNA replication, repair, and recombination processes. Herein, we show the physical and functional interaction between DNA ligase and proliferating cell nuclear antigen (PCNA) from the hyperthermophilic Euryarchaea Pyrococcus furiosus. The stimulatory effect of P. furiosus PCNA on the enzyme activity of P. furiosus DNA ligase was observed not at low ionic strength, but at a high salt concentration, at which a DNA ligase alone cannot bind to a nicked DNA substrate. On the basis of mutational analyses, we identified the amino acid residues that are critical for PCNA binding in a loop structure located in the N-terminal DNA-binding domain of P. furiosus DNA ligase. We propose that the pentapeptide motif QKSFF is involved in the PCNA-interacting motifs, in which Gln and the first Phe are especially important for stable binding with PCNA.
Comparative transcriptome analysis of embryonic and adult stem cells with extended and limited differentiation capacity (2007)

Multivariate analysis techniques clustered stem cells on the basis of their expressed gene profile, and the genes determining this clustering reflected the stem cells' differentiation potential in vitro. This comparative transcriptome analysis should significantly aid the isolation and culture of MAPCs and MAPC-like cells, and form the basis for studies to gain insights into genes that confer on these cells their greater developmental potency.
A high-throughput cellulase screening system based on droplet microfluidics (2014)

A new ultra-high-throughput screening assay for the detection of cellulase activity was developed based on microfluidic sorting. Cellulase activity is detected using a series of coupled enzymes leading to the formation of a fluorescent product that can be detected on a chip. Using this method, we have achieved up to 300-fold enrichments of the active population of cells and greater than 90% purity after just one sorting round. In addition, we proved that we can sort the cellulase-expressing cells from mixtures containing less than 1% active cells.
The GLI Gene Encodes a Nuclear Protein Which Binds Specific Sequences in the Human Genome (1990)

The GLI gene is amplified in a subset of human tumors and encodes a protein product with five zinc finger DNA-binding motifs. In this study, we show that the GLI gene product has a predominantly nuclear localization and binds DNA in a sequence-specific fashion. Three GLI binding sites were identified by using a novel procedure in which total human DNA was bound to a GLI recombinant fusion protein, and the polymerase chain reaction was used to amplify and recover the bound sequences. The GLI protein protected a 23- to 24-base region within all three binding sites, and the protected region in each case included the 9-base-pair sequence 5'-GACCACCCA-3'. One of the binding sites was contained within a 63-base-pair repeat of the variable number of tandem repeat type, whereas the other two sites were represented once in the genome. The approach used here to identify GLI binding sites should be applicable to the characterization of other zinc finger proteins.
Life‐cycle seismic for turbidite fields in deepwater Nigeria (2011)

Seismic data plays a critical role throughout the life‐cycle of most modern oil and gas fields. Typically, seismic data is acquired when a new subsurface problem presents itself, requiring a local investment in a seismically‐defined answer. This reactive approach to subsurface problem solving is often inefficient for optimizing value from producing fields. Turbidite fields in Offshore Deepwater Nigeria share a series of common characteristics that allow us to anticipate many of these important subsurface questions in advance, and facilitate the proactive planning of an efficient seismic program for the potential life of an opportunity. This paper discusses the key considerations necessary for planning such life‐cycle seismic and suggests recommendations for types of seismic acquisitions to be considered for this arena.
Characterization and purification of a phage phi 29-encoded DNA polymerase required for the initiation of replication. (1984)

The phage phi 29 protein p2, required for the formation of the protein p3-dAMP initiation complex, has been purified from Escherichia coli cells harboring a gene 2-containing recombinant plasmid. The purified protein p2, of molecular weight 68,000, had a specific DNA polymerase activity that elongated the p3-dAMP initiation complex when phi 29 DNA-protein p3 was used as template. In addition, the purified protein p2 was active in catalyzing the initiation reaction when complemented with phi 29 mutant sus2-infected Bacillus subtilis or plasmid-containing E. coli extracts providing protein p3, in the presence of phi 29 DNA-protein p3 as template. However, when purified protein p3 was used in the complementation assay, a very low amount of initiation complex was formed; addition of extracts from uninfected B. subtilis or E. coli strongly stimulated the initiation reaction, indicating that, in addition to proteins p2 and p3 and the phi 29 DNA-protein p3 template, some host factor(s) is required for the formation of the p3-dAMP initiation complex. The results show that phage phi 29 encodes a DNA polymerase that is required at the initiation step of protein-primed DNA synthesis.
The Solid-Phase Enzyme Inhibitor Library Assay (2003)

Synthesis of a portion mixing library of putative inhibitors in a resin already containing a good fluorescence-quenched substrate, which may have been defined with substrate libraries as described in Chapter 8, provides a method for direct detection of inhibitory activity (1). Beads containing potential inhibitors remained dark while enzyme cleaved the substrate in beads containing noninhibitors, resulting in a dramatic increase in fluorescence. The dark beads can be collected and analyzed by sequence analysis.
Erythropoietin in Friedreich ataxia (2013)

In Friedreich ataxia (FRDA), several candidate substances including erythropoietin (EPO) focus on increase in the amount of frataxin and aim to counteract the consequences of frataxin deficiency. Evidence for recombinant human erythropoietin (rHuEPO) in FRDA is based on in vitro studies using mouse neuronal cell lines, human fibroblasts, cardiomyocytes, and primary lymphocytes from FRDA patients or control subjects which showed a dose-dependent increase of frataxin after incubation with different erythropoietins. The mechanism by which EPO induces frataxin increase remains to be elucidated, but may involve post-transcriptional and/or post-translational modifications of frataxin or alterations in frataxin half-life and metabolism. In vivo data on rHuEPO's ability to increase frataxin in FRDA patients is contradictory as studies on the effect of EPO derivatives in FRDA differ in treatment regimen, sample size, and duration. Open-label studies indicate for sustained frataxin increase, decrease of oxidative stress, and clinical improvement in FRDA patients after administration of rHuEPO. Two randomized controlled studies found acceptable safety and tolerability of EPO derivatives in FRDA. Secondary outcome measures, however, such as frataxin up-regulation and clinical efficacy were not met. This review will focus on (i) pre-clinical work on erythropoietins in FRDA and (ii) clinical studies in FRDA patients exposed to erythropoietins.