gebhart/patrepeval huggingface dataset:
Diversity Observed in the Nanostructure of Protic Ionic Liquids (2010)

The nanostructure of a series of 20 protic ionic liquids (PILs) has been investigated using small- and wide-angle X-ray scattering (SAXS and WAXS). The PILs contained alkylammonium, dialkylammonium, trialkylammonium, and cyclic ammonium cations combined with organic or inorganic anions. The presence of hydroxyl and methoxy substituents on the alkyl chains of the cations was also explored. Many of the PILs showed a nanostructure resulting from segregation of the polar and nonpolar components of the ionic liquid. It was found that this segregation was enhanced for longer alkyl chains, with a corresponding increase in the length scale, whereas the presence of hydroxyl groups on the alkyl chains led to much less ordered liquids. The broad range of protic ionic liquids studied allowed several structure-property relationships to be established. The solvophobic effect was shown to be dependent on the nanostructure of the PILs. These PILs support amphiphile self-assembly, and it was shown that the less structured PILs had more "water-like" behavior in the diversity of lyotropic liquid-crystal phases supported, and the thermal stability ranges for these phases.
Direct correlation between hyperoxaluria/oxalate stone disease and the absence of the gastrointestinal tract-dwelling bacterium Oxalobacter formigenes: possible prevention by gut recolonization or enzyme replacement therapy. (1999)

Oxalobacter formigenes is a specific oxalate-degrading, anaerobic bacterium inhabiting the gastrointestinal tracts of vertebrates, including humans. This bacterium maintains an important symbiotic relationship with its host by regulating oxalate homeostasis, primarily by preventing enteric absorption. Increased absorption of oxalate can lead to multiple complications associated with hyperoxaluria, especially recurrent calcium oxalate urolithiasis. Detection of O. formigenes in the gastrointestinal tract has attracted attention because the absence of this bacterium appears to be a risk factor for development of hyperoxaluria and/or recurrent calcium oxalate kidney stone disease. In the present study, epidemiologic studies with patients at high risk for calcium oxalate urolithiasis showed a direct correlation between the number of recurrent kidney stone episodes and the lack of O. formigenes colonization. As expected, the lack of O. formigenes revealed a clear association with prophylactic antibiotic therapy. To confirm the importance of O. formigenes in regulating hyperoxaluria, laboratory rats known to be noncolonized were colonized with live bacteria or treated with a preparation of oxalate-degrading enzymes derived from O. formigenes to determine any subsequent increased resistance to high oxalate challenge. Rats receiving either bacteria or enzyme replacement therapy excreted far lower levels of oxalate, did not develop the crystalluria observed with control rats, and resisted the formation of calcium oxalate crystals in their nephrons. These observations, taken together, support the concept that O. formigenes is important in maintaining oxalate homeostasis, that its absence from the gut increases the risk for hyperoxaluria and recurrent kidney stone disease, and that replacement therapy is an efficient procedure to prevent hyperoxaluria and its complications.
Yersiniasignals macrophages to undergo apoptosis and YopJ is necessary for this cell death (1997)

Pathogenic Yersinia spp. carry a large common plasmid that encodes a number of essential virulence determinants. Included in these factors are the Yersinia-secreted proteins called Yops. We analyzed the consequences of wild-type and mutant strains of Yersinia pseudotuberculosis interactions with the macrophage cell line RAW264. 7 and murine bone marrow-derived macrophages. Wild-type Y. pseudotuberculosis kills approximately 70% of infected RAW264.7 macrophages and marrow-derived macrophages after an 8-h infection. We show that the cell death mediated by Y. pseudotuberculosis is apoptosis. Mutant Y. pseudotuberculosis that do not make any Yop proteins no longer cause host cell death. Attachment to host cells via invasin or YadA is necessary for the cell death phenotype. Several Yop mutant strains that fail to express one or more Yop proteins were engineered and then characterized for their ability to cause host cell death. A mutant with a polar insertion in YpkA Ser/Thr kinase that does not express YpkA or YopJ is no longer able to cause apoptosis. In contrast, a mutant no longer making YopE or YopH (a tyrosine phosphatase) induces apoptosis in macrophages similar to wild type. When yopJ is added in trans to the ypkAyopJ mutant, the ability of this strain to signal programmed cell death in macrophages is restored. Thus, YopJ is necessary for inducing apoptosis. The ability of Y. pseudotuberculosis to promote apoptosis of macrophages in cell culture suggests that this process is important for the establishment of infection in the host and for evasion of the host immune response.
Aminoacids as Chiral Synthons1: Preparation of Enantiomerically Pure (R) and (S) Malic Acids and its Application to the Synthesis of 3-Hydroxy 4-Butanolide (1986)

Abstract Malic acid has been proved to be an extremely valuable chiral synthon for enantiospecific synthesis of complex molecules such as monensin2, amphotericin B3, variou s hydroxytetrahydrofurans4, lactones5,6 and pheromones7. However the (S) isomer only is easily available8; the (R) isomer is more difficult to obtain and is generally prepared by a synthetic way9.
Right on target (2014)

Barras talks about sequencing genomes, which has become easy. Understanding them remains incredibly hard. Last month, two groups announced that they had performed a mind-boggling feat. They targeted and disabled nearly everyone of the genes in cell growing in a dish. They didn't knock out all the genes in each cell at once, a course, but one gene at a time.
Chromosomal Integration of Heterologous DNA in Escherichia coli with Precise Removal of Markers and Replicons Used during Construction (1999)

A set of vectors which facilitates the sequential integration of new functions into the Escherichia coli chromosome by homologous recombination has been developed. These vectors are based on plasmids described by Posfai et al. (J. Bacteriol. 179:4426-4428, 1997) which contain conditional replicons (pSC101 or R6K), a choice of three selectable markers (ampicillin, chloramphenicol, or kanamycin), and a single FRT site. The modified vectors contain two FRT sites which bracket a modified multiple cloning region for DNA insertion. After integration, a helper plasmid expressing the flippase (FLP) recombinase allows precise in vivo excision of the replicon and the marker used for selection. Sites are also available for temporary insertion of additional functions which can be subsequently deleted with the replicon. Only the DNA inserted into the multiple cloning sites (passenger genes and homologous fragment for targeting) and a single FRT site (68 bp) remain in the chromosome after excision. The utility of these vectors was demonstrated by integrating Zymomonas mobilis genes encoding the ethanol pathway behind the native chromosomal adhE gene in strains of E. coli K-12 and E. coli B. With these vectors, a single antibiotic selection system can be used repeatedly for the successive improvement of E. coli strains with precise deletion of extraneous genes used during construction.
Fast Nearest Neighbor Search in Medical Image Databases (2018)

We examine the problem of finding similar tumor shapes. Starting from a natural similarity function (the so-called `max morphological distance'), we showed how to lower-bound it and how to search for nearest neighbors in large collections of tumor-like shapes. Specifically, we used state-of-the-art concepts from morphology, namely the `pattern spectrum' of a shape, to map each shape to a point in n-dimensional space. Following [16, 30], we organized the n-d points in an R-tree. We showed that the L∞ (=max) norm in the n-d space lower-bounds the actual distance. This guarantees no false dismissals for range queries. In addition, we developed a nearest-neighbor algorithm that also guarantees no false dismissals. Finally, we implemented the method, and we tested it against a testbed of realistic tumor shapes, using an established tumor- growth model of Murray Eden [13]. The experiments showed that our method is roughly an order of magnitude faster than the straightforward sequential scanning.
International Intervention is Not the Only Way to Save Depleting Resources (2005)

Growing concerns over biodiversity and environmental conservation are causing some cultures to abandon the harvesting of wild foods. Among Asian wild food harvesting cultures, the harvest of such resources as whale, tuna, shark's fin, and bird's nests has provoked grave concern. International organizations such as IWC (International Whaling Commission), CITES (Convention on International Trade in Endangered Species of Wild Fauna and Flora) and FAO (Food and Agriculture Organization of the United Nations) tried to regulate the harvest and trade of those animals and products. Any conservation policy, however, must consider the cultural history of the exploitation of each of these resources. Trepang, haishen, or holothurian may be one of the resources nearing depletion. Interestingly enough, while the trepang market is almost exclusively Chinese, it has been a major export product from Japan and Southeast Asia to China for at least three hundred years. Currently, tropical countries such as the Philippines export some twenty species of trepang, and temperate countries including Japan, one or two. A question that must be asked is what kinds of changes have been observed in ecological, political, economical and cultural spheres over the past three hundred years. In this paper, I will first present my view against the trend for international trepang trade regulation. Second, an overview of the history of trepang exploitation and trade, focusing primarily on that of the Philippines will be provided. Furthermore, the present situation in the Philippines will be described, based on my five-year survey on the expansion of the trepang industry. On the basis of information flow and interrelationships between Chinese traders in Hong Kong and the Philippines, I will emphasize that 1) the trepang industry has established multi-ethnic network chains from producers to consumers, and therefore, 2) the management of trepang resources needs commitment and support from trepang traders.
Hypusine: its post-translational formation in eukaryotic initiation factor 5A and its potential role in cellular regulation. (1993)

The amino acid, hypusine [N epsilon-(4-amino-2-hydroxybutyl) lysine], a unique component of one cellular protein, eukaryotic translation initiation factor 5A (eIF-5A, old terminology eIF-4D), is formed post-translationally in two enzymatic steps: (i) transfer of the 4-aminobutyl moiety of the polyamine spermidine to the epsilon-amino group of a single specific lysine residue in the eIF-5A precursor protein to form an intermediate, deoxyhypusine, and (ii) subsequent hydroxylation in this 4-aminobutyl portion. Hypusine is produced soon after the translation of eIF-5A mRNA; the modification is essentially irreversible. Hypusine is found in all eukaryotes examined as well as in archaebacteria; it does not occur in eubacteria. The protein containing hypusine from each species displays a high degree of amino acid identity; the sequence of amino acids surrounding the hypusine residue is strictly conserved, suggesting the importance of the hypusine modification throughout evolution. Expression of one of the two yeast eIF-5A genes is required for survival and the lysine codon at the site of hypusine synthesis is vital for yeast growth. The precise cellular function of eIF-5A remains to be elucidated; however, eIF-5A stimulates methionyl-puromycin synthesis in a model assay for translation initiation and eIF-5A precursors containing lysine in place of hypusine are inactive in this assay. This provides evidence that the hypusine modification is needed for eIF-5A activity. In view of the important role of hypusine in eIF-5A and because of the narrow specificities of the enzymes involved in formation of this unusual amino acid, the hypusine biosynthetic steps offer promising targets for intervention in cellular proliferation. Spermidine analogs that are inhibitors of deoxyhypusine synthase in vitro also cause inhibition of hypusine formation in cells, together with a reduction in protein synthesis and in cell growth. In addition, certain metal chelating inhibitors of deoxyhypusine hydroxylase exhibit anti-proliferative effects by arresting mammalian cells at the G1/S boundary of the cell cycle. These results lay the foundation for the potential regulation of cellular events through the application of specific and potent inhibitors of hypusine biosynthesis.
Electron Beam Solid Freeform Fabrication of Metal Parts (2018)

A novel method for near-net-shape fabrication of large, complex metal parts without the need&#13;\nfor specific tooling is described. Parts are built up in a layer-by-Iayer fashion by feeding raw&#13;\nmaterial in wire form into a melt pool which is maintained with an electron beam. Several different&#13;\nalloys have been successfully deposited using a low-energy electron beam. A model has been&#13;\ndeveloped which permits determination ofthe melt depth and vaporization-limited power input as&#13;\nfunctions of beam energy and travel velocity. Processing parameters obtained from experiments&#13;\nwith low-energy electron beams can be used to predict melting behavior under the influence of&#13;\nhigher energy beams. The process is being investigated as a possible means for manufacturing&#13;\ncompositionally-graded components.
Probing Surface Charge Fluctuations with Solid-State Nanopores (2009)

We identify a contribution to the ionic current noise spectrum in solid-state nanopores that exceeds all other noise sources in the frequency band 0.1-10 kHz. Experimental studies of the dependence of this excess noise on pH and electrolyte concentration indicate that the noise arises from surface charge fluctuations. A quantitative model based on surface functional group protonization predicts the observed behaviors and allows us to locally measure protonization reaction rates. This noise can be minimized by operating the nanopore at a deliberately chosen pH.
Adenovirus Early Region 3 Antiapoptotic 10.4K, 14.5K, and 14.7K Genes Decrease the Incidence of Autoimmune Diabetes in NOD Mice (2003)

Genes in the early region 3 (E3) of the adenovirus genome allow the virus to evade host immune responses by interfering with major histocompatibility (MHC) class I-mediated antigen presentation and tumor necrosis factor-alpha (TNF-alpha)- or Fas-induced apoptosis of infected cells. Autoimmune type 1 diabetes (T1D) is inhibited in NOD mice transgenically expressing all E3 genes under control of a rat insulin promoter (RIPE3/NOD). For dissecting the protective mechanisms afforded by various E3 genes, they were subdivided into RIP-driven transgene constructs. Strong T1D protection mediated at the beta-cell level characterized DL704/NOD mice lacking the E3 gp19K gene suppressing MHC class I expression but retaining the 10.4K, 14.5K, and 14.7K genes inhibiting Fas- or TNF-alpha-induced apoptosis and TNF-alpha-induced NF-kB activation. Much weaker protection characterized DL309/NOD mice expressing the gp19K but not the 10.4K, 14.5K, and 14.7K genes. While RIPE3/NOD splenocytes had an unexpected decrease in ability to adoptively transfer T1D, splenocytes from both the DL704 and DL309 stocks efficiently did so. These findings indicate that all E3 genes must be expressed to inhibit the diabetogenic potential of NOD immune cells. They also demonstrate that the antiapoptotic E3 genes most effectively protect pancreatic beta-cells from diabetogenic immune responses.
Expression of a Trk high affinity nerve growth factor receptor in the human prostate (1995)

Nerve growth factor-beta (NGF beta) and a NGF beta-immunoreactive protein derived from human prostatic stromal cell secretory protein (hPS) have been shown to stimulate the growth of prostate epithelial cells. An NGF beta-immunoreactive protein has been localized to the stroma of human prostate tissues, and a low affinity NGF receptor (gp75NGFR) has been localized to the adjacent epithelia, consistent with the paracrine regulation of prostate growth. Interestingly, gp75NGFR is progressively lost during neoplastic progression of the human prostate. In this report we have characterized the expression of the signal-transducing component of the NGF receptor, the Trk tyrosine receptor kinase, in prostate epithelial cells that bind exogenous NGF beta and an endogenous NGF beta-immunoreactive protein in hPS. In this context, a pan-Trk antibody that recognizes all of the members of the Trk receptor family (TrkA, TrkB, and TrkC) specifically localized expression of the Trk receptor to the epithelial component of normal prostate tissue, benign prostatic hyperplasia, and adenocarcinoma tissue. The binding of [125I]NGF beta to the surface of primary cultures of human prostate epithelia and the TSU-pr1 human metastatic prostate tumor cell line was displaced with either excess cold NGF beta or hPS, whereas binding was not displaced by epidermal growth factor or platelet-derived growth factor. Scatchard plot analysis of [125I]NGF beta binding to these cells identified a low affinity binding site (Kd = 1.9 x 10(-9) M) and a high affinity binding site (Kd = 1.8 x 10(-11) M) on the primary prostate epithelia, whereas only a high affinity binding site (Kd = 1.3 x 10(-11) M) was observed on the TSU-pr1 tumor cells. Stimulation of TSU-pr1 cells with either NGF beta or hPS induced tyrosine phosphorylation of Trk proteins, whereas no phosphorylation was evident in untreated cells, cells treated with hPS immunoprecipitated with anti-NGF beta antibody, or brain-derived neurotrophic factor- and neurotrophin-3-treated cells. The Trk protein was also observed in these cells by immunoblot analysis with pan-Trk antibody. These results demonstrate a functional Trk receptor in the epithelia of the human prostate that is responsive to exogenous NGF beta and an endogenous NGF beta-immunoreactive protein in hPS, thereby supporting the concept of the paracrine regulation of growth in the human prostate via a stromal neurotrophin-epithelial Trk receptor interaction.
Idiopathic Pulmonary Fibrosis: Prevailing and Evolving Hypotheses about Its Pathogenesis and Implications for Therapy (2001)

Idiopathic pulmonary fibrosis is a progressive and usually fatal lung disease characterized by fibroblast proliferation and extracellular matrix remodeling, which result in irreversible distortion of the lung's architecture. Although the pathogenetic mechanisms remain to be determined, the prevailing hypothesis holds that fibrosis is preceded and provoked by a chronic inflammatory process that injures the lung and modulates lung fibrogenesis, leading to the end-stage fibrotic scar. However, there is little evidence that inflammation is prominent in early disease, and it is unclear whether inflammation is relevant to the development of the fibrotic process. Evidence suggests that inflammation does not play a pivotal role. Inflammation is not a prominent histopathologic finding, and epithelial injury in the absence of ongoing inflammation is sufficient to stimulate the development of fibrosis. In addition, the inflammatory response to a lung fibrogenic insult is not necessarily related to the fibrotic response. Clinical measurements of inflammation fail to correlate with stage or outcome, and potent anti-inflammatory therapy does not improve outcome. This review presents a growing body of evidence suggesting that idiopathic pulmonary fibrosis involves abnormal wound healing in response to multiple, microscopic sites of ongoing alveolar epithelial injury and activation associated with the formation of patchy fibroblast-myofibroblast foci, which evolve to fibrosis. Progress in understanding the fibrogenic mechanisms in the lung is likely to yield more effective therapies.
Molecular Cloning of a Novel Murine Cell-surface Glycoprotein Homologous to Killer Cell Inhibitory Receptors (1997)

We have isolated a cDNA clone encoding a novel murine cell-surface glycoprotein. This polypeptide is predicted to be composed of a signal peptide of 23 amino acids, an extracellular region of 620 amino acids that contains six immunoglobulin-like domains with five potential N-glycosylation sites, a transmembrane sequence of 20 amino acids, and a cytoplasmic tail of 178 amino acids with four sets of sequences similar to the immunoreceptor tyrosine-based inhibition motif. The relative molecular mass of the mature polypeptide is calculated to be 90,520 Da. The polypeptide, designated as p91, shows striking homologies to human killer cell inhibitory receptors, a murine gp49B1 protein, a bovine Fcgamma2 receptor, and a human Fcalpha receptor. The mRNA of p91 was especially abundant in murine macrophages. Western blot analysis using p91-specific anti-peptide sera detected a 130-kDa polypeptide in macrophages. Surface biotinylation and immunoprecipitation analysis verified the surface expression of the translation products on COS-1 cells transfected with the p91 cDNA, but the cells failed to show any Fc binding activity.
Neurogenesis of Rhesus adipose stromal cells (2004)

In this study, we isolated and characterized a population of non-human primate adipose tissue stromal cells (pATSCs) containing multipotent progenitor cells. We show that these pATSCs can differentiate into several mesodermal lineages, as well as neural lineage cells. For neural induction of pATSCs and non-human primate bone marrow stromal cells (pBMSCs), the cells were cultured in Neurobasal (NB) media supplemented with B27, basic fibroblast growth factor (bFGF), brain-derived neurotrophic factor (BDNF) and epidermal growth factor (EGF). After 4 days in culture, the pATSCs form compact, spheroid bodies that ultimately become neurospheres (NS). Free-floating neurospheres undergo extensive differentiation when cultured on PDL-laminin. Our data suggest that the neurogenic potential of pATSCs is markedly higher than that of pBMSCs. We have also performed microarray analysis and characterized the gene expression patterns in undifferentiated pATSCs. The direct comparison of gene expression profiles in undifferentiated pATSCs and pATSC-NS, and delineated specific members of important growth factor, signaling, cell adhesion and transcription factors families. Our data indicate that adipose tissue may be an alternative source of stem cells for therapy of central nervous system (CNS) defects.