gebhart/patrepeval huggingface dataset:
Cystamine potently suppresses in vitro HIV replication in acutely and chronically infected human cells. (1994)

We have investigated the effects of cystamine on the replication of human immunodeficiency virus (HIV) in human lymphocytes and macrophages, the natural targets of HIV in vivo. Treatment of chronically infected macrophages with cystamine, at a concentration (500 microM) that did not show any cytotoxic or cytostatic effects, strongly decreased (> 80%) HIV-p24 antigen production and completely abolished the production of infectious viral particles. Cystamine does not affect viral transcription, translation or protein processing; indeed, all HIV proteins are present in a pattern similar to that of nontreated cells. Instead, cystamine interferes with the orderly assembly of HIV virions, as shown by electron microscopy analysis, that reveals only defective viral particles in treated cells. Moreover, suppression of HIV replication, due to the inhibition of proviral DNA formation was observed in acutely infected lymphocytes and macrophages pretreated with cystamine. These results show that cystamine potently suppresses HIV replication in human cells by contemporaneously blocking at least two independent steps of the viral life cycle, without affecting cell viability, suggesting that this compound may represent a new possibility towards the treatment of HIV-1 infection.
Smooth muscle cells in human coronary atherosclerosis can originate from cells administered at marrow transplantation (2003)

Atherosclerosis is the major cause of adult mortality in the developed world, and a significant contributor to atherosclerotic plaque progression involves smooth muscle cell recruitment to the intima of the vessel wall. Controversy currently exists on the exact origin of these recruited cells. Here we use sex-mismatched bone marrow transplant subjects to show that smooth muscle cells throughout the atherosclerotic vessel wall can derive from donor bone marrow. We demonstrate extensive recruitment of these cells in diseased compared with undiseased segments and exclude cell–cell fusion events as a cause for this enrichment. These data have broad implications for our understanding of the cellular components of human atherosclerotic plaque and provide a potentially novel target for future diagnostic and therapeutic strategies.
NMR and biochemical characterization of recombinant human tRNA3 Lys expressed in Escherichia coli: Identification of posttranscriptional nucleotide modifications required for efficient initiation of HIV-1 reverse transcription (2000)

Reverse transcription of HIV-1 viral RNA uses human tRNA(Lys)3 as a primer. Some of the modified nucleotides carried by this tRNA must play a key role in the initiation of this process, because unmodified tRNA produced in vitro is only marginally active as primer. To provide a better understanding of the contribution of base modifications in the initiation complex, we have designed a recombinant system that allows tRNA(Lys)3 expression in Escherichia coli. Because of their high level of overexpression, some modifications are incorporated at substoichiometric levels. We have purified the two major recombinant tRNA(Lys)3 subspecies, and their modified nucleotide contents have been characterized by a combination of NMR and biochemical techniques. Both species carry psis, Ds, T, t6A, and m7G. Differences are observed at position 34, within the anticodon. One fraction lacks the 5-methylaminomethyl group, whereas the other lacks the 2-thio group. Although the s2U34-containing recombinant tRNA is a less efficient primer, it presents most of the characteristics of the mammalian tRNA. On the other hand, the mnm5U34-containing tRNA has a strongly reduced activity. Our results demonstrate that the modifications that are absent in E. coli (m2G10, psi27, m5C48, m5C49, and m1A58) as well as the mnm5 group at position 34 are dispensable for initiation of reverse transcription. In contrast, the 2-thio group at position 34 seems to play an important part in this process.
Examination of Ionic Liquids and Their Interaction with Molecules, When Used as Stationary Phases in Gas Chromatography (1999)

Stable room-temperature ionic liquids (RTILs) have been used as novel reaction solvents. They can solubilize complex polar molecules such as cyclodextrins and glycopeptides. Their wetting ability and viscosity allow them to be coated onto fused silica capillaries. Thus, 1-butyl-3-methylimidazolium hexafluorophosphate and the analogous chloride salt can be used as stationary phases for gas chromatography (GC). Using inverse GC, one can examine the nature of these ionic liquids via their interactions with a variety of compounds. The Rohrschneider-McReynolds constants were determined for both ionic liquids and a popular commercial polysiloxane stationary phase. Ionic liquid stationary phases seem to have a dual nature. They appear to act as a low-polarity stationary phase to nonpolar compounds. However, molecules with strong proton donor groups, in particular, are tenaciously retained. The nature of the anion can have a significant effect on both the solubilizing ability and the selectivity of ionic liquid stationary phases. It appears that the unusual properties of ionic liquids could make them beneficial in many areas of separation science.
Use of High Specific Activity StarFire™ Oligonucleotide Probes to Visualize Low-Abundance Pre-mRNA Splicing Intermediates in S. pombe (2000)

An oligonucleotide labeling system was developed that can produce radiolabeled hybridization probes with tenfold or more higher specific activity than is obtained by traditional 5'-end-labeling with polynucleotide kinase. Yet the system is as rapid and simple as kinase labeling. The reaction uses the Klenow fragment of E. coli DNA polymerase to add alpha-32P-dA residues to the 3'-end of an oligonucleotide in a primer-extension reaction. Unlike other methods of radioactive tailing (e.g., terminal transferase), a single species is produced of both known length and known specific activity. The reaction is efficient, and over 90% of probe molecules are routinely labeled. Using this method of labeling, an oligonucleotide was shown to be tenfold more sensitive in detecting target DNA sequences in a dot blot hybridization assay, compared to the same oligonucleotide labeled using polynucleotide kinase. Northern blots of Schizosaccharomyces pombe RNA were probed with an oligonucleotide specific for intron 1 of the tf2d gene, a TATA-box binding transcription factor. Kinase-labeled tf2d probe detected only unspliced RNA, while the same oligonucleotide labeled using the new method detected both unspliced tf2d RNA and rare pre-mRNA splicing intermediates.
Common human melanoma-associated antigen(s) detected by monoclonal antibodies. (1980)

Hybridoma cells have been derived from a fusion between mouse myeloma cells (P3-NSI/1Ag4) and spleen cells from a mouse immunized with membrane-enriched fractions from the human melanoma cell line Me-43. Of the 26 hybrids obtained, seven secreted antibodies which reacted with the melanoma cell line used for immunoassay. The specificity of the antibodies produced by the seven positive hybrids was further investigated on 16 melanoma cell lines, 15 other tumors, and 14 lymphoblastoid cell lines. The antibodies from four positive hybrids showed a broad reactivity, whereas those from three hybrids reacted exclusively with melanoma cells. The antibodies from two of these three hybrids, alpha-Mel/5 and alpha-Mel/14, seem to be directed against common melanoma antigen(s) since they reacted with all (with one exception) of the 16 melanoma cell lines tested only with five of the 16 melanoma lines. Reciprocal binding inhibition tests using [3H]leeucine-labeled antibodies showed that alpha-Mel/5 and alpha-Mel/14 antibodies were directed against different antigenic determinants.
CHARACTERIZATION OF INTRA‐TUMORAL PORPHYRIN FOLLOWING INJECTION OF HEMATOPORPHYRIN DERIVATIVE OR ITS PURIFIED COMPONENT* (1987)

Photodynamic therapy (PDT) utilizes either hematoporphyrin derivative (Hpd) or a purified form of Hpd termed DHE, as photosensitizers for treatment of a variety of solid tumors in man. The reasons for long retention of these porphyrins in a wide range of histologically diverse tumors remain obscure. We have found that the RIF fibrosarcoma and SMT-F mammary carcinoma in mice, a intrapancreatic tumor in the hamster and a tumor removed from a patient with a myxoid sarcoma, make take up Hpd or DHE by endocytosis. On the other hand the RIF tumor cells in vitro show a tendency for selective uptake and retention of the more hydrophobic components of the mixture.
Targeting One Carbon Metabolism with an Antimetabolite Disrupts Pyrimidine Homeostasis and Induces Nucleotide Overflow (2016)

Antimetabolites that affect nucleotide metabolism are frontline chemotherapy agents in several cancers and often successfully target one carbon metabolism. However, the precise mechanisms and resulting determinants of their therapeutic value are unknown. We show that 5-fluorouracil (5-FU), a commonly used antimetabolite therapeutic with varying efficacy, induces specific alterations to nucleotide metabolism by disrupting pyrimidine homeostasis. An integrative metabolomics analysis of the cellular response to 5-FU reveals intracellular uracil accumulation, whereas deoxyuridine levels exhibited increased flux into the extracellular space, resulting in an induction of overflow metabolism. Subsequent analysis from mice bearing colorectal tumors treated with 5-FU show specific secretion of metabolites in tumor-bearing mice into serum that results from alterations in nucleotide flux and reduction in overflow metabolism. Together, these findings identify a determinant of an antimetabolite response that may be exploited to more precisely define the tumors that could respond to targeting cancer metabolism.
Paper-Based Archiving of Mammalian and Plant Samples for RNA Analysis (2000)

The ability to archive biological samples for subsequent nucleic acid analysis is essential for tissue specimens and forensic samples. FTA Card is a chemically treated filter paper designed for the collection and room temperature storage of biological samples for subsequent DNA analysis. Its usefulness for the preservation of biological samples for subsequent RNA analysis was tested. Here, we demonstrate that RNA in biological samples stored on FTA Cards is stable and can be used successfully for RT-PCR and northern blot analysis. RNA stability depends on the storage temperature and the type of biological specimen. RNA in mammalian cells stored on FTA Cards is stable for over one year at temperatures at or below -20 degrees C and for two to three months in samples stored at room temperature. For plant leaf, longer storage times (> 5 days) require temperatures at or below -70 degrees C following sample application. FTA Cards may constitute a method not only for convenient collection and storage of biological samples but also for rapid RT-PCR analysis of tissue and cell samples.
Temporal Vegetation Modelling Using Long Short-Term Memory Networks for Crop Identification from Medium-Resolution Multi-spectral Satellite Images (2017)

Land-cover classification (LCC) is one of the central problems in earth observation and was extensively investigated over recent decades. In many cases, existing approaches concentrate on single-time and multi- or hyper-spectral reflectance measurements observed by spaceborne and airborne sensors. However, land-cover classes, such as crops, change their reflective characteristics over time, thus complicating a classification at one particular observation time. Opposed to that, these characteristics change in a systematic and predictive manner, which should be utilized in a multi-temporal approach.,,,,,,We employ long short-term memory (LSTM) networks to extract temporal characteristics from a sequence of SENTINEL 2A observations. We compared the performance of LSTM networks with other architectures and a support vector machine (SVM) baseline and show the effectiveness of dynamic temporal feature extraction. For our experiments, a large study area together with rich ground truth annotations provided by public authorities was used for training and evaluation. Our rather straightforward LSTM variant achieved state-of-the art classification performance, thus opening promising potential for further research.
Phidgets (2001)

Physical widgets or phidgets are to physical user interfaces what widgets are to graphical user interfaces. Similar to widgets, phidgets abstract and package input and output devices: they hide implementation and construction details, they expose functionality through a well-defined API, and they have an (optional) on-screen interactive interface for displaying and controlling device state. Unlike widgets, phidgets also require: a connection manager to track how devices appear on-line; a way to link a software phidget with its physical counterpart; and a simulation mode to allow the programmer to develop, debug and test a physical interface even when no physical device is present. Our evaluation shows that everyday programmers using phidgets can rapidly develop physical interfaces.
The bacterial species definition in the genomic era (2006)

The bacterial species definition, despite its eminent practical significance for identification, diagnosis, quarantine and diversity surveys, remains a very difficult issue to advance. Genomics now offers novel insights into intra-species diversity and the potential for emergence of a more soundly based system. Although we share the excitement, we argue that it is premature for a universal change to the definition because current knowledge is based on too few phylogenetic groups and too few samples of natural populations. Our analysis of five important bacterial groups suggests, however, that more stringent standards for species may be justifiable when a solid understanding of gene content and ecological distinctiveness becomes available. Our analysis also reveals what is actually encompassed in a species according to the current standards, in terms of whole-genome sequence and gene-content diversity, and shows that this does not correspond to coherent clusters for the environmental Burkholderia and Shewanella genera examined. In contrast, the obligatory pathogens, which have a very restricted ecological niche, do exhibit clusters. Therefore, the idea of biologically meaningful clusters of diversity that applies to most eukaryotes may not be universally applicable in the microbial world, or if such clusters exist, they may be found at different levels of distinction.
The role of lexico-semantic feedback in open-domain textual question-answering (2001)

This paper presents an open-domain textual Question-Answering system that uses several feedback loops to enhance its performance. These feedback loops combine in a new way statistical results with syntactic, semantic or pragmatic information derived from texts and lexical databases. The paper presents the contribution of each feedback loop to the overall performance of 76% human-assessed precise answers.
Growth regulation by p27Kip1 is abrogated by multiple mechanisms in aggressive malignant lymphomas (2003)

The cyclin-dependent kinase inhibitor p27Kip1 is a key regulator of the G1/S transition, and an inverse relationship between p27Kip1 protein expression and proliferation index has been reported in malignant lymphomas. However, a subset of aggressive B-cell lymphomas demonstrates high p27Kip1 expression despite a high proliferation index. The aim of this study was to determine potential mechanisms by which lymphoma cells abrogate the growth inhibitory effect of high p27Kip1. The effect of transforming growth factor-beta (TGF-beta) and serum stimulation on p27Kip1 expression and cyclin E/cdk2 activity was investigated in four lymphoma cell lines, Jurkat, CEM-6, OCI-Ly1 and Nalm-6. Reactive lymphocytes responded to growth inhibitory TGF-beta by inducing p27Kip1 expression, with subsequent accumulation of cells in G0/G1. In contrast, TGF-beta did not alter the level of p27Kip1 in Jurkat, CEM-6 and OCI-Ly1 cells with no change in cyclin E/cdk2-kinase activity. Serum stimulation also did not result in a significant change in p27Kip1 expression. Western blot analysis of subcellular fractions demonstrated cytoplasmic p27Kip1, corroborated by immunocytochemistry in a subset of the lymphoma cells. Sequestration of p27Kip1 by cyclin D3 was observed in the nuclear and cytoplasmic fractions of Nalm-6, OCI-Ly-1 and NCEB cells. These results indicate that multiple mechanisms contribute to the abrogation of growth regulation by unscheduled high p27Kip1 protein expression including deficient response to TGF-beta and serum, sequestration by cyclin D3 and cytoplasmic displacement.
Vasoactive intestinal peptide and pituitary adenylate cyclase‐activating polypeptide promote in vivo generation of memory Th2 cells (2002)

Functionally active effector T cells are generated through clonal expansion. Most effector T cells are later eliminated, whereas a small number survive and differentiate into memory T cells. The mechanisms by which some effector T cells escape apoptosis and become memory T cells are not understood. Neuropeptides such as the vasoactive intestinal peptide (VIP) and pituitary adenylate cyclase-activating polypeptide (PACAP) inhibit antigen-induced apoptosis of CD4 T cells. By using an in vivo long-term experimental model, in which CD4 T cells from TRC-transgenic mice were transferred into hosts, we demonstrate that VIP and PACAP induce the survival and/or generation of antigen-specific CD4 T cells with a memory Th2 phenotype. This was confirmed by the fact that transgenic CD4 T cells were recovered only from mice that received Th2, but not Th1 effector cells, in the presence of VIP or PACAP. In vitro, VIP/PACAP support the survival of Th2, but not Th1, cell lines through an inhibition of antigen-induced apoptosis. The role of neuropeptides in the biased development of Th2 memory cells is particularly relevant in view of the immune deviation existing in immune-privileged sites such as the brain and eye, where Th2, but not Th1, responses occur in nonpathological conditions.
Iterative Divergent/Convergent Approach to Linear Conjugated Oligomers by Successive Doubling of the Molecular Length: A Rapid Route to a 128Å‐Long Potential Molecular Wire (1994)

An iodination, a protodesilylation, and a Pd/Cu-catalyzed cross coupling are the three reactions needed to successively double the length of molecular units to form 1, a 128 Å long linear 16-mer, in a doubling sequence with only four iterations. Compound 1 could possibly serve as a molecular wire in molecular electronics studies.
RETRACTED: Segregation of atrial-specific and inducible expression of an atrial natriuretic factor transgene in an in vivo murine model of cardiac hypertrophy. (1991)

To study the mechanisms that activate expression of the atrial natriuretic factor (ANF) gene during pressure-induced hypertrophy, we have developed and characterized an in vivo murine model of myocardial cell hypertrophy. We employed microsurgical techniques to produce a stable 35- to 45-mmHg pressure gradient across the thoracic aorta of the mouse that is associated with rapid and transient expression of an immediate-early gene program (c-fos/c-jun/junB/Egr-1/nur-77), an increase in heart weight/body weight ratio, and up-regulation of the endogenous ANF gene. These responses that are identical to those in cultured cell and other in vivo models of hypertrophy. To determine whether tissue-specific and inducible expression of the ANF gene can be segregated, we used a transgenic mouse line in which 500 base pairs of the human ANF promoter region directs atrial-specific expression of the simian virus 40 large tumor antigen (T antigen), with no detectable expression in the ventricles. Thoracic aortic banding of these mice led to a 20-fold increase in the endogenous ANF mRNA in the ventricle but no detectable expression of the T-antigen marker gene. This result provides evidence that atrial-specific and inducible expression of the ANF gene can be segregated, suggesting that a distinct set of regulatory cis sequences may mediate the up-regulation of the ANF gene during in vivo pressure overload hypertrophy. This murine model demonstrates the utility of microsurgical techniques to study in vivo cardiac physiology in transgenic mice and should allow the application of genetic approaches to identify the mechanisms that activate ventricular expression of the ANF gene during in vivo hypertrophy.
Effect of Semen Dilution on Bovine Sperm Viability as Determined by Dual‐DNA Staining and Flow Cytometry (1997)

Living and dead spermatozoa were examined for the effects of sperm concentration level on sperm viability. Semen was collected from two different bulls on each of four collection dates. A ninth bull was collected on all four collection dates as a control for effects of collection date. The ejaculates from these nine bulls were diluted to 30 x 10(6) spermatozoa/0.5 ml and then serially diluted to 20, 10, 5, or 1 x 10(6) spermatozoa/0.5 ml French straw. One-half of the straws for each dilution series was stored 24 hours at 5 degrees C, while the other half was cryopreserved. Spermatozoa were stained with SYBR-14 and propidium iodide (PI) to assess viability. Flow cytometry yielded dot plots showing three distinct sperm populations: dead red-stained spermatozoa (PI), viable green-stained spermatozoa (SYBR-14), and moribund spermatozoa that stained both red and green (doubly-stained). Populations were expressed and analyzed in terms of mean percentage of viable spermatozoa and by actual numbers of viable spermatozoa per insemination dose. The mean percentage of living spermatozoa decreased linearly with decreasing sperm concentration; whereas the decrease was parabolic when those same samples were expressed as the mean number of living spermatozoa per insemination dose. The percentage of SYBR-14-stained spermatozoa differed among concentration levels and among bulls (P < 0.01). There were no differences among straws from the same ejaculate. The total volume of ejaculated semen and the concentration of spermatozoa in that ejaculate were both significantly positively correlated with the percentage of SYBR-14-stained spermatozoa in that semen when it was cryopreserved and diluted to < 10 x 10(6) spermatozoa/0.5 ml. In contrast, there were no significant correlations between the initial ejaculate characteristics and the proportion of SYBR-14-stained spermatozoa in the 24-hour-stored samples at any concentration. In conclusion, the percentage of viable spermatozoa in an ejaculate significantly decreased with increasing dilution. Further, in cryopreserved samples, the percentage of living spermatozoa < 10 x 10(6) spermatozoa/0.5 ml depended on the original volume and the sperm concentration of that particular ejaculate.