gebhart/patrepeval huggingface dataset:
Marine phytoplankton: how many species in the world ocean? (1991)

Towards the end of the 1980s, living plankton flora of the world ocean amounted to 474-504 genera and 3444–4375 species if one neglects the increase rate of taxa during the latest years In the above figures, the lower estimate is that of the ‘reliable’ taxa (of practical value for identification tasks), whereas the higher estimate includes the insufficiently known or doubtful organisms, and synonyms are excluded. The frequency distribution of the numbers of species per genus confirms the general hyperbolic law, which implies that a relatively large number of genera are uni- or paucispecific.
Herpes simplex virus type 1 dUTPase mutants are attenuated for neurovirulence, neuroinvasiveness, and reactivation from latency (1992)

Herpes simplex virus type 1 (HSV-1) encodes a dUTPase which has been shown to be dispensable for normal viral replication in cultured cells (S. J. Caradonna and Y. Cheng, J. Biol. Chem. 256:9834-9837, 1981; F. B. Fisher and V. G. Preston, Virology 148:190-197, 1986). However, the importance of this enzyme in vivo has not been determined. In this report, HSV-1 strain 17 syn+ and two isogenic engineered dUTPase-negative mutants were characterized in the mouse model. Both mutants replicated with wild-type kinetics and achieved wild-type titers in cultured cells. The mutants were 10-fold less neurovirulent than 17 syn+ following intracranial inoculation and more than 1,000-fold less virulent following footpad inoculation. The dUTPase- mutants replicated with wild-type kinetics in the footpad and entered and replicated efficiently in the peripheral nervous system of the mouse. However, their replication in the central nervous system was significantly reduced. The dUTPase- strains established latent infections but displayed a greatly reduced reactivation frequency in vivo. Neurovirulence, neuroinvasiveness, and reactivation frequency were all restored by recombination with wild-type dUTPase sequences. These results have important implications with regard to anti-herpesvirus therapeutic strategies.
Pulmonary Immunity to Viral Infection: Adenovirus Infection of Lung Dendritic Cells Renders T Cells Nonresponsive to Interleukin-2 (2006)

Adenovirus (Ad) infection has been identified as predisposing hosts to the development of pulmonary disease through unknown mechanisms. Lung dendritic cells (DCs) are vital for initiating pulmonary immune responses; however, the effects of Ad infection on primary lung DC have not been studied. In contrast to the effects on bone marrow- and monocyte-derived DCs, the current study shows that Ad infection of murine BALB/c lung DCs in vitro and in vivo suppresses DC-induced T-cell proliferation. The effect of Ad on DCs was not due to a downregulation of major histocompatibility complex or costimulatory molecules. Analysis of the production of interleukin-12 (IL-12), alpha interferon (IFN-alpha), and IFN-gamma by the Ad-infected DCs shows no significant differences over noninfected control lung DCs. Ad-induced suppression was not due to a deficiency of IL-2 or other DC-secreted factors and was dependent on viral protein synthesis, as UV irradiation of Ad abrogated the suppressive effect. Results suggest that Ad-infected DCs induce T cells to be nonresponsive to IL-2 during primary coculture, as the addition of IL-2 in secondary cultures recovered T-cell proliferation. In vivo studies supported in vitro results showing that Ad infection resulted in lung T cells with decreased proliferative ability. This study demonstrates that Ad infection induces local immunoincompetence by altering DC-T-cell interactions.
A Single-Batch Fermentation System to Simulate Human Colonic Microbiota for High-Throughput Evaluation of Prebiotics (2016)

We devised a single-batch fermentation system to simulate human colonic microbiota from fecal samples, enabling the complex mixture of microorganisms to achieve densities of up to 1011 cells/mL in 24 h. 16S rRNA gene sequence analysis of bacteria grown in the system revealed that representatives of the major phyla, including Bacteroidetes, Firmicutes, and Actinobacteria, as well as overall species diversity, were consistent with those of the original feces. On the earlier stages of fermentation (up to 9 h), trace mixtures of acetate, lactate, and succinate were detectable; on the later stages (after 24 h), larger amounts of acetate accumulated along with some of propionate and butyrate. These patterns were similar to those observed in the original feces. Thus, this system could serve as a simple model to simulate the diversity as well as the metabolism of human colonic microbiota. Supplementation of the system with several prebiotic oligosaccharides (including fructo-, galacto-, isomalto-, and xylo-oligosaccharides; lactulose; and lactosucrose) resulted in an increased population in genus Bifidobacterium, concomitant with significant increases in acetate production. The results suggested that this fermentation system may be useful for in vitro, pre-clinical evaluation of the effects of prebiotics prior to testing in humans.
CD47 mediates post-adhesive events required for neutrophil migration across polarized intestinal epithelia. (1996)

Transepithelial migration of neutrophils (PMN) is a defining characteristic of active inflammatory states of mucosal surfaces. The process of PMN transepithelial migration, while dependent on the neutrophil beta 2 integrin CD11b/CD18, remains poorly understood. In these studies, we define a monoclonal antibody, C5/D5, raised against epithelial membrane preparations, which markedly inhibits PMN migration across polarized monolayers of the human intestinal epithelial cell line T84 in a bidirectional fashion. In T84 cells, the antigen defined by C5/D5 is upregulated by epithelial exposure to IFN-gamma, and represents a membrane glycoprotein of approximately 60 kD that is expressed on the basolateral membrane. While transepithelial migration of PMN was markedly inhibited by either C5/D5 IgG or C5/D5 Fab fragments, the antibody failed to inhibit both adhesion of PMN to T84 monolayers and adhesion of isolated T84 cells to the purified PMN integrin, CD11b/CD18. Thus, epithelial-PMN interactions blocked by C5/D5 appear to be downstream from initial CD11b/CD18-mediated adhesion of PMN to epithelial cells. Purification, microsequence analysis, and cross-blotting experiments indicate that the C5/D5 antigen represents CD47, a previously cloned integral membrane glycoprotein with homology to the immunoglobulin superfamily. Expression of the CD47 epitope was confirmed on PMN and was also localized to the basolateral membrane of normal human colonic epithelial cells. While C5/D5 IgG inhibited PMN migration even in the absence of epithelial, preincubation of T84 monolayers with C5/D5 IgG followed by antibody washout also resulted in inhibition of transmigration. These results suggest the presence of both neutrophil and epithelial components to CD47-mediated transepithelial migration. Thus, CD47 represents a potential new therapeutic target for downregulating active inflammatory disease of mucosal surfaces.
Ubiquitin-Fusion Protein System: A Powerful Tool for Ectopic Protein Expression in Mammalian Cells (2009)

Clonal cell lines stably expressing a protein of interest are frequently used in the characterization of the potential physiological functions of mammalian proteins, but the generation of such cell lines is laborious and time-consuming. Here, we made use of the fact that fusion proteins consisting of ubiquitin linked to the N terminus of a protein of interest are efficiently processed by ubiquitin-specific proteases into their respective free proteins within eukaryotic cells, and designed an expression system that allows easy and highly efficient selection of mammalian cells ectopically expressing a protein of interest.
Immune responses to Mycoplasma bovis vaccination and experimental infection in the bovine mammary gland. (1988)

This study characterized the immune responses in four vaccinated and four control cows in response to vaccination and experimental intramammary inoculation with Mycoplasma bovis. Specific antibody responses occurred in serum and milk in response to vaccination and experimental infection. Lymphocytes from peripheral blood, but not from the mammary gland of vaccinated cows had increased responsiveness to mitogens. No lymphocytes tested were responsive to M. bovis antigen. Both vaccination and experimental infection resulted in skin test reactivity. These results imply that vaccination results in immune responses which may alter the course of experimental M. bovis mastitis, but may contribute to cellular inflammation.
Cloned stromal cell lines derived from human Whitlock/Witte-type long-term bone marrow cultures. (1990)

We report a human bone marrow culture technique that initially parallels the murine Whitlock/Witte culture system. As in the murine system, B cells predominate over other cell types, and all differentiation stages from pre-B to plasma cell are observed. Although these human long-term cultures pass through stages resembling phases I to III of murine Whitlock/Witte cultures, no outgrowth of nonadherent cells was seen after cultures had reached the "crisis" phase unless Epstein-Barr virus (EBV)-transformants appeared. The stromal cells persisted well beyond crisis, but they could not be maintained and passaged as cell lines, limiting their use in molecular analysis. Transfection of these stromal cells with plasmid DNA containing the simian virus 40 (SV40) early region yielded 124 cloned cell lines. Analysis of these lines showed that all expressed SV40 large T antigen, but they retained most phenotypic markers found on non-transformed stromal cells. When adherent and T-cell-depleted bone marrow cells were cultured on either nontransformed stromal layers or transformed cell lines they proliferated actively and soon yielded predominantly lymphoid nonadherent populations. Moreover, prolonged survival of acute lymphoblastic leukemia cells of pre-B phenotype was regularly achieved on both normal and transformed adherent cell layers. Although the liquid culture system favored lymphocytes, transformed stroma supported colony formation by both human and murine hemopoietic progenitors when marrow was added in agar medium. This was not explained by colony-stimulating factor (CSF) production, because striking heterogeneity in the levels of granulocyte CSF (G-CSF) and granulocyte-macrophage CSF (GM-CSF) secretion by the lines was noted. Some lines that did not produce detectable CSF demonstrated good support of fresh bone marrow growth and acute lymphoblastic leukemia (ALL) cell survival. The heterogeneity of these cell lines and their capacity to support hemopoiesis suggest that they will be useful in studying the molecular basis of in vitro lymphohemopoiesis in man.
Disruption of the immune-checkpoint VISTA gene imparts a proinflammatory phenotype with predisposition to the development of autoimmunity (2014)

V domain-containing Ig suppressor of T-cell activation (VISTA) is a negative checkpoint regulator that suppresses T cell-mediated immune responses. Previous studies using a VISTA-neutralizing monoclonal antibody show that VISTA blockade enhances T-cell activation. The current study describes a comprehensive characterization of mice in which the gene for VISTA has been deleted. Despite the apparent normal hematopoietic development in young mice, VISTA genetic deficiency leads to a gradual accumulation of spontaneously activated T cells, accompanied by the production of a spectrum of inflammatory cytokines and chemokines. Enhanced T-cell responsiveness was also observed upon immunization with neoantigen. Despite the presence of multiorgan chronic inflammation, aged VISTA-deficient mice did not develop systemic or organ-specific autoimmune disease. Interbreeding of the VISTA-deficient mice with 2D2 T-cell receptor transgenic mice, which are predisposed to the development of experimental autoimmune encephalomyelitis, drastically enhanced disease incidence and intensity. Disease development is correlated with the increase in the activation of encephalitogenic T cells in the periphery and enhanced infiltration into the CNS. Taken together, our data suggest that VISTA is a negative checkpoint regulator whose loss of function lowers the threshold for T-cell activation, allowing for an enhanced proinflammatory phenotype and an increase in the frequency and intensity of autoimmunity under susceptible conditions.
The Free Radical Theory of Aging (2003)

Aging is the accumulation of changes that increase the risk of death. Aging changes can be attributed to development, genetic defects, the environment, disease, and an inborn process: the aging process. The latter is the major risk factor for disease and death after age 28 in the developed countries. In these countries, average life expectancies at birth (ALE-B) now range from 76 to 79 years, 6-9 years less than the limit of approximately 85 years imposed by aging. Aging changes may be caused by free radical reactions. The extensive studies based on this possibility hold promise that the ALE-B can be extended to >85 years and the maximum life span increased.
Recent developments in neuronal nicotinic acetylcholine receptor antagonists (2000)

Neuronal nicotinic acetylcholine receptors (nAChRs) belong to a superfamily of ligand-gated ion channel receptors and are distributed extensively throughout the central and peripheral nervous systems. The structural and functional diversity of these receptors has stimulated interest in the development of subtype-selective agonists, as a result of a greater understanding of the role of these receptors in neuropathology and disease, including Alzheimer’s and Parkinson’s disease, Tourette’s syndrome, drug addiction and pain. Surprisingly, much less attention has been focused on the development of subtype-selective antagonists, which may also be useful as therapeutic agents. This article reviews the published patent literature on neuronal nicotinic receptor antagonists, with particular attention to receptor subtype selectivity of novel compounds that have been recently disclosed in the patent literature.
(S)‐norlaudanosoline synthase: The first enzyme in the benzylisoquinoline biosynthetic pathway (1981)

1. introduction Isoquinoline alkaloids form the largest group of alkaloids in the plant kingdom. Numerous publications deal with aspects of the biosynthesis of these compounds in vivo [ 11, while isoquinoline biosynthesis at the cell-free level had hardly been touched [Z]. The initial reaction in isoquinoline biosynthesis has long [3] been assumed to be a condensation of two aromatic units, both derived from tyrosine, namely dopamine and 3,4-d~ydroxyphenylacet~dehyde [4]. This scheme was later modified [5] where it was reported that condensation of dopamine with 3,4-dihydroxyphenylpyruvate would lead to an amino acid, norlaudanosoline-l-carboxylic acid, which in turn, by decarboxylation, would yield norlaudanosoline,
Compact video signatures for near-duplicate detection on mobile devices (2014)

In this paper, we focus on generating compact but efficient video signatures on mobile devices so that users quickly know whether there are near-duplicates in the social network systems when they upload a video. For this, the proposed method employs the idea of inverted index that is one of the most popular text retrieval methods. Experimental results show that our method can achieve similar results compared with state-of-the-art method whereas it requires low memory and computation cost.
Selective infection of human CD4+ cells by simian immunodeficiency virus: productive infection associated with envelope glycoprotein-induced fusion. (1989)

Simian immunodeficiency virus (SIV) and human immunodeficiency virus share the property of tropism for CD4-bearing cells. Infection is initiated by a high-affinity interaction between CD4 and conserved domains on the viral envelope glycoprotein. In this report, we demonstrated that SIV had a restricted host range among human CD4+ cells when compared with human immunodeficiency virus type 1 or type 2. This restricted tropism was associated with the inability of the SIV envelope glycoprotein to induce membrane fusion in cells not susceptible to productive exogenous infection by SIV. We conclude that the major route of SIV entry into CD4+ cells is by envelope-mediated direct fusion with the cell and that additional envelope-cell interactions after CD4 binding are required for productive infection.
Voltage gating of ion channels (1994)

Voltage-gated ion channels are membrane proteins that play a central role in the propagation and transduction of cellular signals (Hille, 1992). Calcium ions entering cells through voltage-gated calcium channels serve as the trigger for neurotransmitter release, muscle contraction, and the release of hormones. Voltage-gated sodium channels initiate the nerve action potential and provide for its rapid propagation because the ion fluxes through these channels regeneratively cause more channels to open.
Note on optimal tile partition for space region of integrated-circuit geometry (1996)

An OTP algorithm for solving the optimal tile-partitioning problem has recently been published. The OTP algorithm makes use of an elimination algorithm to find a maximum set of nonintersecting critical partition edges. It is shown that this elimination algorithm is flawed.
New facial rejuvenation techniques (2000)

The popularity of cutaneous laser resurfacing has soared in recent years. For optimal clinical improvement, patients have been limited to the carbon dioxide and erbium:yttrium aluminum garnet lasers. With these systems, tissue can effectively be ablated to induce collagen shrinkage and remodeling that result in an improved clinical appearance. The prolonged recovery periods associated with traditional cutaneous laser resurfacing have sparked an immense interest in devices that rejuvenate the skin while minimizing adverse effects. Both physicians and patients seem willing to accept more gradual improvement if it is associated with fewer complications such as prolonged erythema or delayed-onset hypopigmentation. The following review discusses the newest devices in development or currently available for skin rejuvenation.
Correlations between polyamine analogue-induced increases in spermidine/spermine N1-acetyltransferase activity, polyamine pool depletion, and growth inhibition in human melanoma cell lines. (1991)

The polyamine analogue, N1,N12-bis(ethyl(-spermine (BESPM), is known to suppress ornithine and S-adenosylmethionine decarboxylase levels, deplete intracellular polyamine pools, and inhibit cell growth. Among human melanoma cell lines, MALME-3 cells were found to be typically sensitive to the antiproliferative activity of the BESPM, whereas LOX cells were atypically insensitive to the analogue. A comparison of polyamine-related parameters revealed that the most differentially altered activity between the 2 BESPM-treated cell lines was that of spermidine/spermine N1-acetyltransferase (SSAT), which increased from 50 pmol/min/mg to greater than 10,000 pmol/min/mg in MALME-3 cells and from 16 pmol/min/mg to only 120 pmol/min/mg in LOX cells over 48 h. The basis for the large difference seems to be related to increased enzyme synthesis in both cell lines coupled with differences in prolongation of SSAT half-life (greater than 12 h in MALME-3 cells versus 1.6 h in LOX cells) after BESPM treatment. In MALME-3 cells, SSAT accumulation was found to be differentially modulated by the BESPM homologues, N1,N11-bis-(ethyl)norspermine and N1,N14-bis-(ethyl)homospermine, which were 5-fold more and 9-fold less effective, respectively, than BESPM in increasing SSAT but similar in analogue uptake and effects on polyamine biosynthesis and cell growth inhibition. Treatment of MALME-3 cells with BESPM resulted in an accumulation of N-acetylspermidine in cells and the enhanced excretion of putrescine, spermidine, and N-acetylspermidine into the medium. The relationship between SSAT induction and growth sensitivity was deduced to be a possible function of increased excretion of acetylated polyamines leading to enhanced polyamine pool depletion. The data suggest that, in cell types in which it occurs, unusually high increases in SSAT activity may serve as a determinant of growth sensitivity to bis-ethyl spermine analogues or, alternatively, as a target for appropriately designed chemotherapeutic strategies.
Livestock 2.0 – genome editing for fitter, healthier, and more productive farmed animals (2018)

The human population is growing, and as a result we need to produce more food whilst reducing the impact of farming on the environment. Selective breeding and genomic selection have had a transformational impact on livestock productivity, and now transgenic and genome-editing technologies offer exciting opportunities for the production of fitter, healthier and more-productive livestock. Here, we review recent progress in the application of genome editing to farmed animal species and discuss the potential impact on our ability to produce food.
Sex-Dependent Gene Expression in Human Pluripotent Stem Cells (2014)

Males and females have a variety of sexually dimorphic traits, most of which result from hormonal differences. However, differences between male and female embryos initiate very early in development, before hormonal influence begins, suggesting the presence of genetically driven sexual dimorphisms. By comparing the gene expression profiles of male and X-inactivated female human pluripotent stem cells, we detected Y-chromosome-driven effects. We discovered that the sex-determining gene SRY is expressed in human male pluripotent stem cells and is induced by reprogramming. In addition, we detected more than 200 differentially expressed autosomal genes in male and female embryonic stem cells. Some of these genes are involved in steroid metabolism pathways and lead to sex-dependent differentiation in response to the estrogen precursor estrone. Thus, we propose that the presence of the Y chromosome and specifically SRY may drive sex-specific differences in the growth and differentiation of pluripotent stem cells.
Antimicrobials and Non-Healing Wounds. Evidence, controversies and suggestions—key messages (2014)

This article constitutes an extraction of key messages originally presented in the Document: Antimicrobials and Non-Healing Wounds. Evidence, controversies and suggestions written by the European Wound Management Association (EWMA), and originally published by the Journal of Wound Care in 2013. All sections are shortened and some not included. For further details please refer to in the original document which can be downloaded via www.ewma.org .