gebhart/patrepeval huggingface dataset:
Transfer of information from mRNA to chromosomes by reverse transcription in early development of goldfish eggs. (1989)

In earlier publications, we have recorded evidence that micro-injection of globin mRNA from rabbit into goldfish eggs leads to the production of rabbit globin in mature red blood cells of goldfish. This paper is concerned with the mechanism of that apparent transfer of genetic information from the cytoplasm to the nucleus. We investigate the possibility that the injected mRNA is reverse transcribed to create a corresponding cDNA in goldfish eggs. By using purified mRNA from rabbit reticulocytes and micro-injection into enucleated and nucleated goldfish eggs, we show that the production of a DNA sequence hybridizes to cloned cDNA of rabbit globin mRNA and appears to become incorporated into the chromosomes of the developing eggs.
The protein phosphatase 2C (PP2C) superfamily: Detection of bacterial homologues (1996)

A thorough sequence analysis of the various members of the eukaryotic protein serine/threonine phosphatase 2C (PP2C) family revealed the conservation of 11 motifs. These motifs could be identified in numerous other sequences, including fungal adenylate cyclases that are predicted to contain a functionally active PP2C domain, and a family of prokaryotic serine/threonine phosphatases including SpoIIE. Phylogenetic analysis of all the proteins indicates a widespread sequence family for which a considerable number of isoenzymes can be inferred.
The development, benefits and disadvantages of serum-free media. (1999)

Serum-free culture is used routinely for many cell types, especially if transformed, e.g. CHO, hybridoma and recombinant myeloma cell lines. Serum-free medium reduces operating costs and process variability, and removes a potential source of infectious agents. The removal of the components of serum and the elimination of other animal-derived raw materials are proving more challenging. Nevertheless, careful risk/benefit analyses to target R&D toward critical materials is presenting several solutions in this area. A risk/benefit analysis is required for each component replacing serum or serum derivatives. Specific serum proteins used in serum-free media can be eliminated. At present large scale protein-free processes are not routine.
An evolutionary history of the FGF superfamily (2005)

Fibroblast growth factors (FGF) are associated with multiple developmental and metabolic processes in triploblasts, and perhaps also in diploblasts. The evolution of the FGF superfamily has accompanied the major morphological and functional innovations of metazoan species. The study of FGFs throughout species shows that the FGF superfamily can be subdivided in eight families in present-day organisms and has evolved through phases of gene duplications and gene losses. At least two major expansions of the superfamily can be recognized: a first expansion increased the number of FGFs from one or few archeo-FGFs to eight proto-FGFs, prototypic of the eight families. A second expansion, which took place during euchordate evolution, is associated with genome duplications. It increased the number of members in the families. Subsequent losses reduced that number to the present-day figures.
Specific nutritional problems in acute kidney injury, treated with non-dialysis and dialytic modalities (2009)

Patients who develop AKI, especially in the intensive care unit (ICU), are at risk of protein-energy malnutrition, which is a major negative prognostic factor in this clinical condition. Despite the lack of evidence from controlled trials of its effect on outcome, nutritional support by the enteral (preferentially) and/or parenteral route appears clinically indicated in most cases of ICU-acquired AKI, independently of the actual nutritional status of the patient, in order to prevent deterioration in the nutritional state with all its known complications. Extrapolating from data in other conditions, it seems intrinsically unlikely that starvation of a catabolic patient is more beneficial than appropriate nutritional support by an expert team with the skills to avoid the potential complications of the enteral and parenteral nutrition methodologies. By the same token, it is ethically impossible to conduct a trial in which the control group undergoes prolonged starvation. The primary goals of nutritional support in AKI, which represents a well-known inflammatory and pro-oxidative condition, are the same as those for other critically ill patients with normal renal function, i.e. to ensure the delivery of adequate nutrition, to prevent protein-energy wasting with its attendant metabolic complications, to promote wound healing and tissue repair, to support immune system function, to accelerate recovery and to reduce mortality. Patients with AKI on RRT should receive a basic intake of at least 1.5 g/kg/day of protein with an additional 0.2 g/kg/day to compensate for amino acid/protein loss during RRT, especially when daily treatments and/or high efficiecy modalities are used. Energy intake should consist of no more than 30 kcal non-protein calories or 1.3 × BEE (Basal Energy Expenditure) calculated by the Harris-Benedict equation, with ∼30-35% from lipid, as lipid emulsions. For nutritional support, the enteral route is preferred, although it often needs to be supplemented through the parenteral route in order to meet nutritional requirements.
Implant of Autologous Mesothelial Cells in Animals and a Peritoneal Dialysis Patient (1989)

Success in culturing human and animal peritoneal mesothelial cells for the purpose of study, led us to determine whether these cells could be autoimplanted in animals and man during peritoneal dialysis in cases of acute and extensive loss of mesothelial surface area. Using an original biopsy technique, we were able to cultivate and characterize from the structural and caryological point of view, human and rabbit peritoneal mesothelial cells. Staphylococcal peritonitis was provoked in 12 rabbits with in-dwelling peritoneal catheters and after 4 days of antibiotic therapy, 6 of them were autoimplanted with cultured mesothelial cells. In the animals sacrificed on the third and sixth days, direct morphological observation and autoradiographic techniques showed that the transplanted cells had taken and revealed a different picture from that in the non-transplanted rabbits. In a 56 year old female diabetic patient, upon insertion of the first peritoneal catheter, a specimen of mesothelial cells was cultured and then frozen. Seven months later after an episode of peritonitis from candida which dictated removal of the peritoneal catheter, since there was a sufficient number of cultured mesothelial cells and the patient consented, the implant was performed. Peritoneal biopsy by laparoscopy three and six days later showed that the cells had taken. The purpose of the study was merely to show that autoimplant of mesothelium in man and animals is possible.
The Campylobacter jejuni general glycosylation system is important for attachment to human epithelial cells and in the colonization of chicks (2004)

It has recently been shown that the enteropathogen Campylobacter jejuni has an N-linked general protein glycosylation pathway (Pgl) that modifies many of the organism's proteins. To determine the role of the N-linked general glycosylation in C jejuni, the authors studied the pglH gene, which shows high similarity to a family of sugar transferases. pglH mutants were constructed in strains 81116 and 11168H. Both mutants were shown to be deficient in their ability to glycosylate a number of C. jejuni proteins, but their lipooligosaccharide and capsule were unaffected. The pglH mutants had significantly reduced ability to adhere to and invade human epithelial Caco-2 cells. Additionally, the 81116 pglH mutant was severely affected in its ability to colonize chicks. These results suggest that glycosylation is important for the attachment of C. jejuni to human and chicken host cells and imply a role for glycoproteins in the pathogenesis of C. jejuni.
The Role of Protein Tyrosine Kinases and Protein Tyrosine Phosphatases in T Cell Antigen Receptor Signal Transduction (1994)

Engagement of the T cell antigen receptor (TCR) by peptide antigen bound to the major histocompatibility complex (MHC) molecules initiates a biochemical cascade involving protein tyrosine kinases (PTKs) and protein tyrosine phosphatases (PTPases). Recent biochemical and genetic evidence has implicated at least three cytoplasmic protein tyrosine kinases (PTKs), Lck, Fyn, and ZAP-70, that are involved in the initiation of TCR signal transduction. In addition, genetic evidence has demonstrated the requirement of the transmembrane PTPase, CD45, for TCR function. Activation of T cells through the TCR represents an alteration in the dynamic equilibrium between PTKs and PTPases. The TCR is a multi-subunit complex composed of at least six different gene products. Dissection of the TCR utilizing chimeric receptors and TCR mutants has demonstrated that the multi-subunit receptor is composed of at least two signal transducing modules, the CD3 and the zeta chain subunits. These two modules have in common peptide sequences within their cytoplasmic domains termed antigen recognition activation motifs (ARAMs) that are responsible for transducing signaling events. Moreover, the ARAM sequence is also found in subunits associated with a variety of other hematopoietic cell antigen receptors and is likely to form the basis for interactions with effector molecules within the signaling cascades of these receptors. Here we review the mechanism by which the ARAM sequences interact with PTKs and the cascades of PTKs and PTPases that are involved in mediating TCR function.
Telomeres, telomerase and senescence (1990)

Eukaryotic chromosomes end with tandem repeats of simple sequences. These GC rich repeats allow telomere replication and stabilize chromosome ends. Telomere replication involves an equilibrium of sequence loss and addition at the ends of chromosomes. Repeats are added de novo by telomerase, an unusual DNA polymerase. Telomerase is an RNP in which an essential RNA component provides the template for the added telomere repeats. Telomere length maintenance plays an essential role in cell viability.
A hsp70-2 Mutation Recognized by CTL on a Human Renal Cell Carcinoma (1999)

Abstract We performed T cell cloning experiments with a tumor-infiltrating lymphocyte subpopulation derived from a renal cell carcinoma tumor site (RCC-7) in which the TCR clonotypic repertoire had been analyzed in terms of TCRBV complementarity-determining region 3 size distribution. We report in this work the characterization of one of the five RCC-specific MHC class I-restricted CTL clones isolated in RCC-7. This TCRBV6J1S1 CTL recognized only the autologous RCC-7 tumor cell line in the context of HLA-A*0201, and the Ag is encoded by a mutated form of the hsp70-2 gene found in the tumor cells, but not in autologous PBLs nor in 47 other tumors. The identification of this gene was achieved by cotransfecting into COS cells a cDNA library of RCC-7 together with HLA-A*0201. Transfectants expressing the Ag were identified by their ability to stimulate TNF release by the CTL clone. The antigenic peptide is a decamer with a mutated residue at position 8. Half-maximal lysis was obtained with only 5 × 10−11 M of decapeptide in target sensitization assays compared with 5 × 10−8 M for the wild-type decapeptide. This difference in recognition was not related to difference in binding HLA-A*0201-presenting molecules, as assessed in an immunofluorescence-based peptide-binding assay using T2 cells. Constitutive hsp70 expression in various tumors suggests that this stress-induced protein may be recognized in situ by tumor-infiltrating lymphocytes. The finding in the tumor of a mutated form of the stress-induced hsp70-2 gene whose product is specifically recognized by TILs with high avidity is discussed in view of the present use of mycobacteria or heterologous heat-shock proteins as immunomodulators or as subunit vaccine candidates.
Light Suppresses Melatonin Secretion in Humans (1980)

Bright artificial light suppressed nocturnal secretion of melatonin in six normal human subjects. Room light of less intensity, which is sufficient to suppress melatonin secretion in other mammals, failed to do so in humans. In contrast to the results of previous experiments in which ordinary room light was used, these findings establish that the human response to light is qualitatively similar to that of other mammals.
Seizures After Stroke (2000)

Seizures occur more commonly with hemorrhagic stroke than with ischemic stroke. Only a small minority later develop epilepsy. Patients with a disabling cortical infarct or a cortical hemorrhage are more likely to have seizures after stroke; those with late-onset seizures are at greater risk of epilepsy.
Validation and Calibration of an Accelerometer in Preschool Children (2006)

Accelerometer counts were highly correlated with Vo(2) in young children. Accelerometers can be appropriately used as a measure of physical activity in this population.
Hotring advertising model for broadband hotspots (2004)

The market for broadband hotspots is expected to grow with the deployment of WiFi technology becoming the standard to access the Internet in a range of mobile settings. Many businesses are entering into the market, looking at the promising prospects and opportunities offered by hotspots. Some companies are investing to become a hotspot venue like Starbucks and McDonalds, while T-Mobile, the telecommunication carrier, is providing WiFi service to hotspot venues. Toshiba and Hewlett Packard are competing to develop inexpensive and deploy systems to be used in hotspots. Despite the rapid development, some analysts are concerned about operation models of hotspots that might affect hotspot businesses in the long term and consequently, limit the growth in this area. The existing models such as the pay-per-use model are not user-friendly in terms of the cost imposed to users. Therefore, we are proposing a new hotspot model developed for local community. This model will be able to drive the deployment of hotspots in favour of the users. This paper discusses the concept of Webring used by the Internet to link Websites that have common interests and applies the framework to create a new hotspot model for local communities called a 'hotring'. The feature and structure of the proposed model enable information sharing, enabling local advertisement and announcement to be displayed on a user machine accessing the hotspots are also presented.
Polyunsaturated fatty acid biosynthesis in Saccharomyces cerevisiae: expression of ethanol tolerance and the FAD2 gene from Arabidopsis thaliana (1996)

The Arabidopsis thaliana delta-12 fatty acid desaturase gene (FAD2) was overexpressed in Saccharomyces cerevisiae by using the GAL1 promoter. S. cerevisiae harboring the FAD2 gene was capable of forming hexadecadienoyl (16:2) and linoleoyl (18:2) residues in the membrane lipid when cultured in medium containing galactose. Gas-liquid chromatography analysis of total lipids indicated that the transformed S. cerevisiae accumulated these dienoic fatty acyl residues and that they accounted for approximately 50% of the total fatty acyl residues. Phospholipid analysis of this strain indicated that the oleoyl (18:1) residue binding phosphatidylcholine (PC) was mostly converted to the 18:2 residue binding PC, whereas 50% of the palmitoleoyl (16:1) residue binding PC was converted to the 16:2 residue binding PC. A marked effect on the unsaturation of 16:1 and 18:1 was observed when S. cerevisiae harboring the FAD2 gene was cultured at 8 degrees C. To assess the ethanol tolerance of S. cerevisiae producing polyunsaturated fatty acids, the cell viability of this strain in the presence of ethanol was examined. The results indicated that S. cerevisiae cells overexpressing the FAD2 gene had greater resistance to 15% (vol/vol) ethanol than did the control cells.
Assessment of automatic ligand building inARP/wARP (2006)

The efficiency of the ligand-building module of ARP/wARP version 6.1 has been assessed through extensive tests on a large variety of protein-ligand complexes from the PDB, as available from the Uppsala Electron Density Server. Ligand building in ARP/wARP involves two main steps: automatic identification of the location of the ligand and the actual construction of its atomic model. The first step is most successful for large ligands. The second step, ligand construction, is more powerful with X-ray data at high resolution and ligands of small to medium size. Both steps are successful for ligands with low to moderate atomic displacement parameters. The results highlight the strengths and weaknesses of both the method of ligand building and the large-scale validation procedure and help to identify means of further improvement.
Further observations on the folate-binding factor in some leukemic cells (1971)

The lysates of peripheral cells as well as the serum from some patients with chronic myelogenous leukemia, contained a macromolecular factor which bound tritiated folic acid. Bound tracer folate filtered through Sephadex G-75 and G-100 columns with the early effluent and appeared with the inner volume through a Sephadex G-200 column. Bound tracer could not be extracted from solution by coated charcoal or the anion exchange resin Dowex 2-X8 and could not be reduced to tetrahydrofolate by folate reductase. The velocity of the binding reaction was very rapid and dissociation of bound tracer extremely slow. Binding decreased sharply below pH 5.0 and the binding factor as well as the folate-binder complex, resisted 56 degrees C for 30 min. The binding factor in the leukemic lysate could be separated from endogenous folate reductase by filtration through a G-75 Sephadex column. Competitive inhibition studies demonstrated little or no inhibition of binding of tritiated folic acid by formyltetrahydrofolate and methyltetrahydrofolate. Diopterin (pteroyldiglutamate), pteropterin (pteroyltriglutamate), methotrexate, and dihydrofolate inhibited binding of tracer folate but not as effectively as unlabeled folic acid. The function of this folate binder is unknown. However, that it reacts with dihydrofolate suggests some relationship (physiologic or pathologic) to DNA synthesis since this folate cofactor is essential for the de novo synthesis of thymidylate from deoxyuridylate. In addition, these findings also suggest that the binding of methotrexate may, like folate, inhibit its reaction with folate reductase, and thus be a mechanism by which leukemic cells become resistant to this drug.
Clonal analysis of cytolytic T lymphocyte specificity. I. Phenotypically distinct sets of clones as the cellular basis of cross-reactivity to alloantigens. (1980)

The cellular basis of the cytolytic cross-reactivity observed in primary allogeneic (C56BL/6 anti-DBA/2 and C57BL/6 anti-C3H/He) mixed-leukocyte cultures (MLC) was investigated by analysis of the specificity of clonal progeny derived from individual cytolytic T lymphocyte (CTL) precursor cells (CTL-P) contained within these populations. A sensitive mixed-leukocyte microculture (micro-MLC) technique was used with limiting dilution analysis by Poisson statistics to determine the frequency of CTL-P reactive against both specific and third-party (P815 and AKRA) target cells, to calculate the probability that each micro-MLC was a clone derived from a single CTL-P, and to examine the specificity of each micro-MLC assayed separately against both target cells. A total of 287 phenotypically specific, heteroclitic, and cross-reactive micro-MLC from the 2 different strain combinations were observed with a relative frequency of 81, 11, and 8%, respectively, and were calculated to have mean clone probability of 90 and 99% when based, respectively, upon the frequencies of CTL-P reactive against the specific and third-party target cells. These clones were estimated to have an approximate size of 6 X 10(4) cells, which corresponded to roughly 16 cell doublings during the 7 d of culture. 22 clones were successfully subcloned and in virtually every case, the subclones retained the specificity phenotype of the original clone from which they were derived. These results provide direct evidence for three phenotypically distinct sets of CTL as the cellular basis of cross-reactivity in MLC populations assayed against two different target cells.
The gadd and MyD genes define a novel set of mammalian genes encoding acidic proteins that synergistically suppress cell growth. (1994)

A remarkable overlap was observed between the gadd genes, a group of often coordinately expressed genes that are induced by genotoxic stress and certain other growth arrest signals, and the MyD genes, a set of myeloid differentiation primary response genes. The MyD116 gene was found to be the murine homolog of the hamster gadd34 gene, whereas MyD118 and gadd45 were found to represent two separate but closely related genes. Furthermore, gadd34/MyD116, gadd45, MyD118, and gadd153 encode acidic proteins with very similar and unusual charge characteristics; both this property and a similar pattern of induction are shared with mdm2, whic, like gadd45, has been shown previously to be regulated by the tumor suppressor p53. Expression analysis revealed that they are distinguished from other growth arrest genes in that they are DNA damage inducible and suggest a role for these genes in growth arrest and apoptosis either coupled with or uncoupled from terminal differentiation. Evidence is also presented for coordinate induction in vivo by stress. The use of a short-term transfection assay, in which expression vectors for one or a combination of these gadd/MyD genes were transfected with a selectable marker into several different human tumor cell lines, provided direct evidence for the growth-inhibitory functions of the products of these genes and their ability to synergistically suppress growth. Taken together, these observations indicate that these genes define a novel class of mammalian genes encoding acidic proteins involved in the control of cellular growth.
Arabidopsis requires polyunsaturated lipids for low-temperature survival. (1993)

Mutants of Arabidopsis that contain reduced levels of polyunsaturated fatty acids showed growth characteristics at 22 degrees C that were very similar to wild type. By contrast, at 12 degrees C, the mutants failed to undergo stem elongation during reproductive growth although they produced normal flowers and fertile seeds. After transfer to 6 degrees C, rosette leaves of the mutants gradually died, and the plants were inviable. These different responses of the mutant plants at 12 degrees C and 6 degrees C suggest that distinct functions may be affected at these two temperatures. The gradual development of symptoms at 6 degrees C and other lines of evidence argue against a general collapse of membrane integrity as the cause of the lethal phenotype. Rather, they indicate that the decrease in polyunsaturated membrane lipids may initially have relatively limited effects in disrupting cellular function.
Sequencing by ligation variation with endonuclease V digestion and deoxyinosine-containing query oligonucleotides (2011)

Combining this read length with sequencing in the 5' - 3' direction would allow a read length of over twenty bases on a single tage. Implementing mate-paired tags and this SBL variation could enable > 95% coverage of the genome.