gebhart/patrepeval huggingface dataset:
A High Density Integrated Genetic Linkage Map of Soybean and the Development of a 1536 Universal Soy Linkage Panel for Quantitative Trait Locus Mapping (2010)

Single nucleotide polymorphisms (SNPs) are the marker of choice for many researchers due to their abundance and the high‐throughput methods available for their multiplex analysis. Only recently have SNP markers been available to researchers in soybean [ Glycine max (L.) Merr.] with the release of the third version of the consensus genetic linkage map that added 1141 SNP markers to the map. Our objectives were to add 2500 additional SNP markers to the soybean integrated map and select a set of 1536 SNPs to create a universal linkage panel for high‐throughput soybean quantitative trait locus (QTL) mapping. The GoldenGate assay is one high‐throughput analysis method capable of genotyping 1536 SNPs in 192 DNA samples over a 3‐d period. We designed GoldenGate assays for 3456 SNPs (2956 new plus 500 previously mapped) which were used to screen three recombinant inbred line populations and diverse germplasm. A total of 3000 workable assays were obtained which added about 2500 new SNP markers to create a fourth version of the soybean integrated linkage map. To create a “Universal Soy Linkage Panel” (USLP 1.0) of 1536 SNP loci, SNPs were selected based on even distribution throughout each of the 20 consensus linkage groups and to have a broad range of allele frequencies in diverse germplasm. The 1536 USLP 1.0 will be able to quickly create a comprehensive genetic map in most QTL mapping populations and thus will serve as a useful tool for high‐throughput QTL mapping.
Reactive glia as rivals in regulating neuronal survival (1993)

Reactive gliosis is a response noted after nearly every type of CNS injury and involves both activated microglia and astroglia. Although many investigators believe that reactive glia in some way regulate the survival of injured neurons, the influence of glial elements upon damaged neural tissues remains uncertain. To examine relationships between reactive glia and neurons, secretion products from both microglia and astroglia are tested for their effects upon the survival of cultured neurons. Microglia are found to secrete neurotoxic agents, while astroglia are a source of neuronotrophic factors. Similar patterns of soluble factor production are noted for astroglia-rich or microglia-rich regions of rat neocortex damaged by ischemia. These observations suggest that microglia and astroglia compete for control of neuronal survival. Importantly, microglial neurotoxins might hinder the recovery of neurologic function at sites of inflammation.
Optical tweezers and manipulation of PMMA beads in various conditions (2009)

Laser optical trapping and micromanipulation of microparticles or cells and subcellular structures have gained remarkable interest in biomedical research and applications. Several laser sources are employed for the combination of a laser scalpel with an optical tweezers device, under microscopic control. However, although the principles and the mechanisms of pulsed laser ablation have been well described for macroscopic interventions, the microbeam operation, under microscopic guidance, necessitates further experiments and investigations. We present experimental results of controlled micro-ablation of PMMA beads of 3-8 &mu;m diameters, trapped by laser tweezers in various media e.g. solutes of different index of refraction. An optical tweezers system, based on a continuous wave He-Ne laser emitting at 632.8 nm, was tested on beads and, despite the low power of the He-Ne laser, the optical trap was stable. Another optical system, based on a cw Nd:YAG laser emitting at 1.06 &mu;m, was tested on microspheres too. Successful beads ablation was carried out by irradiation with multiple, or even a single nitrogen laser pulse of 7 ns pulse duration at a wavelength of 337 nm. The ablative perforation of the microspheres was estimated by controlling the laser fluence. Moreover, shape deformations of PMMA microspheres were observed. The experimentally obtained results are theoretically explained via the spatial intensity distribution based on Mie light scattering theory. Furthermore, the appearance of laser ablation holes in the back side of microspheres is explained by the ablation triggered shock waves propagation. The role of the stretching forces action is also discussed. Additionally, we report experimental results on measuring the optical trap force of PMMA beads. A powerful optical tweezers system based on a continuous wave Nd:YAG laser was used in order to estimate the trapping efficiency for several beads diameter.
Most Acute Myeloid Leukemia Progenitor Cells With Long-Term Proliferative Ability In Vitro and In Vivo Have the Phenotype CD34+/CD71−/HLA-DR− (1998)

Acute myeloid leukemia (AML) occurs as the result of malignant transformation in a hematopoietic progenitor cell, which proliferates to form an accumulation of AML blasts. Only a minority of these AML cells are capable of proliferation in vitro, suggesting that AML cells may be organized in a hierarchy, with only the most primitive of these cells capable of maintaining the leukemic clone. To further investigate this hypothesis, we have evaluated a strategy for purifying these primitive cells based on surface antigen expression. As an in vitro endpoint, we have determined the phenotype of AML progenitor cells which are capable of producing AML colony-forming cells (CFU) for up to 8 weeks in suspension culture (SC) and compared the phenotype with that of cells which reproduce AML in nonobese diabetic/severe combined immunodeficiency (NOD/SCID) mice. AML cells were fluorescence-activated cell sorted (FACS) for coexpression of CD34 and CD71, CD38, and/or HLA-DR and the subfractions were assayed in vitro and in vivo at various cell doses to estimate purification. While the majority of primary AML CFU lacked expression of CD34, most cells capable of producing CFU after 2 to 8 weeks in SC were CD34(+)/CD71(-). HLA-DR expression was heterogeneous on cells producing CFU after 2 to 4 weeks. However, after 6 to 8 weeks in SC, the majority of CFU were derived from CD34(+)/HLA-DR- cells. Similarly, the majority of cells capable of long-term CFU production from SC were CD34(+)/CD38(-). Most cells that were capable of engrafting NOD/SCID mice were also CD34(+)/CD71(-) and CD34(+)/HLA-DR-. Engraftment was not achieved with CD34(+)/CD71(+) or HLA-DR+ subfractions, however, in two patients, both the CD34(+) and CD34(-) subfractions were capable of engrafting the NOD/SCID mice. A three-color sorting strategy combining these antigens allowed approximately a 2-log purification of these NOD/SCID leukemia initiating cells, with engraftment achieved using as few as 400 cells in one experiment. Phenotyping studies suggest even higher purification could be achieved by combining lack of CD38 expression with the CD34(+)/CD71(-) or CD34(+)/HLA DR- phenotype. These results suggest that most AML cells capable of long-term proliferation in vitro and in vivo share the CD34(+)/CD71(-)/HLA-DR- phenotype with normal stem cells. Our data suggests that in this group of patients the leukemic transformation has occurred in a primitive progenitor, as defined by phenotype, with some degree of subsequent differentiation as defined by functional assays.
Étude cinétique de la polycondensation thermique d’α-amino acides (1971)

On a étudié la cinétique de réaction de polycondensation d’acides α aminés entre 140 et 220 °C par détermination de la quantité d’eau éliminée; on a considéré celle-ci comme représentative du nombre de liaisons [math] formées sans chercher à faire la distinction entre les divers types de produits possibles.
Induction of alpha-N-acetylgalactosamine-O-serine/threonine (Tn) antigen-mediated cellular immune response for active immunotherapy in mice. (1991)

A block in carbohydrate chain elongation of O-glycosylated mucins results in accumulation of alpha-GalNAc O linked to serine or threonine (Tn antigen) in a large percentage of human adenocarcinomas. Immunization of mice with desialylated ovine submaxillary mucin (A-OSM), which contains a large concentration of Tn antigen, provided protection against challenge of a highly invasive Tn expressing syngeneic mouse mammary tumor, TA3-Ha. A similar protective effect was not observed in mice immunized with the deglycosylated mucin or irradiated TA3-Ha cells. Immunization with A-OSM but not with deglycosylated mucin resulted in high anti-Tn antibody response in mice. A-OSM induced in vitro proliferation of T-lymphocytes obtained from mice preimmunized with A-OSM or irradiated TA3-Ha cells. This antigen-specific T-cell response was significantly lower if lymphocytes were stimulated with either the deglycosylated or sialylated form of mucin. A-OSM stimulation induced primarily a CD4+ T-cell population, and these cells secreted interleukin 2 in a dose-dependent fashion. A-OSM was also able to induce delayed-type hypersensitivity in mice in response to footpad injections with irradiated TA3-Ha cells. These studies indicate that Tn antigen presented on a protein backbone is capable of providing cellular immunity and protection against tumor in mice.
Gastrin-releasing peptide immunoreactivity in medullary thyroid carcinoma (1984)

Two cases of gastrin releasing peptide (GRP)-producing medullary thyroid carcinoma are presented. Immunohistochemical examination revealed the presence of GRP-like immunoreactivity (IR-GRP) in the primary tumor tissues. High concentration of IR-GRP was also demonstrated in extracts of the primary tumors by radioimmunologic means with use of a GRP-specific antiserum. Chromatographic analysis showed that the immunoreactivity was composed of at least two molecular forms: one behaved as synthetic porcine GRP on Sephadex G-50 gel filtration and the other as porcine GRP (14-27), a C-terminal active fragment of GRP. The IR-GRP was shown not to be attributed to bombesin-like immunoreactivity. Substance P-like immunoreactivity was not detected in the tumor tissues by either immunohistochemical or radioimmunologic means. This is, as far as the authors are aware, the first finding of IR-GRP as an ectopic product in medullary carcinoma.
The Human Glycine Receptor Subunit α3 (1998)

The neuronal glycine receptor is a ligand-gated chloride channel composed of ligand binding alpha and structural beta polypeptides. Homology screening of a human fetal brain cDNA library resulted in the identification of two alternative splice variants of the glycine receptor alpha3 subunit. The amino acid sequence predicted for the alpha3L variant was largely identical to the corresponding rat subunit. In contrast, the novel splice variant alpha3K lacked the coding sequence for 15 amino acids located within the cytoplasmic loop connecting transmembrane spanning region 3 (TM3) and TM4. Using P1 artificial chromosome (PAC) clones, the structure of the GLRA3 gene was elucidated and its locus assigned to human chromosomal bands 4q33-q34 by fluorescence in situ hybridization. Two transcripts of 2.4 and 9 kilobases, corresponding to alpha3L and alpha3K, respectively, were identified and found to be widely distributed throughout the human central nervous system. Structural analysis of the GLRA3 gene revealed that the alpha3K transcript resulted from a complex splice event where excision of the novel exon 8A comprising the alternative sequence of 45 base pairs coincides with the persistence of a large intronic sequence in the 3'-untranslated region. Functional expression in HEK 293 cells of alpha3L and alpha3K subunits resulted in the formation of glycine-gated chloride channels that differed significantly in desensitization behavior, thus defining the cytoplasmic loop as an important determinant of channel inactivation kinetics.
The architecture of a vector digital signal processor for video coding (1992)

Develops a high-performance vector digital signal processor (VDSP) for video coding that can execute instructions at 60 MHz. The VDSP employs a vector pipeline (VP) architecture, which is very well suited for image processing. In the VDSP, a DCT/IDCT circuit (CCITT standard), a two-dimensional space address generator (SAG), and an enhanced ALU to the VP architecture are included, and, as a result, a performance of 2.0 GOPS (giga operation per second) was achieved. The encoder and the decoder specified in CCITT H.261 (Full-CIF mode at 15 frame/s, 64 kb/s) can be realized with two VDSP chips, and one VDSP chip, respectively.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Acid‐catalyzed hydrolysis of triacylglycerols obeys monoexponential kinetics (1992)

Abstract The acid‐catalyzed hydrolyses of triacetyl‐glycerol and of tributyryl‐glycerol take place following a simple monoexponential kinetic scheme. The result can be interpreted as all three ester groups reacting with approximately the same specific rate. This observation reported in 1920 is unusual, because the intrinsic reactivities of primary and secondary esters are different, and because as far as the reaction proceeds, the remaining ester groups have neighboring hydroxyl groups, which undoubtly alter the reactivity of the reaction centers, relative to the situation in the initial reactant structure. The phenomenom can be explained by considering that local solvation effects due to neighboring hydrophylic groups remain unchanged as the transition‐state complex is formed in all three stages of the reaction. © John Wiley &amp; Sons, Inc.
The Influence of Fuel Composition on Emissions of Carbon Monoxide and Oxides of Nitrogen (1970)

&lt;div class="htmlview paragraph"&gt;A theoretical and experimental investigation has been carried out in an attempt to determine the effect of fuel composition on the exhaust emission levels of carbon monoxide and nitric oxide from a reciprocating spark ignition engine. Fuels considered in the investigation were representative of the aromatic, paraffin, cycloparaffin, and olefin families.&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;Results show that both energy content and hydrogen/carbon ratio of the fuel are instrumental in predicting the carbon monoxide and nitric oxide concentrations present in the exhaust. In addition, it has been shown that a progressive change from paraffinicity to aromaticity is accompanied by an increase in nitric oxide and, to a lesser extent, an increase in carbon monoxide exhaust concentrations.&lt;/div&gt;
Gene Transfer into Skeletal Muscles by Isogenic Myoblasts (1994)

The best way to overcome immunorejection in heterologous myoblast transfer (HMT) is by the use of immunodeficient and/or highly immunosuppressed mice as hosts. The same may be attained by autologous myoblast transfer (AMT). In this paper, we describe myoblast transfer in mdx and normal mice where the donor myogenic cells originated from highly inbred litter mates that are considered to be isogenic and thus the procedure is analogous to AMT. The myoblasts were marked in vitro with Rous Sarcoma Virus (RSV)-luciferase (Lux) or RSV-beta-galactosidase (LacZ) reporter genes through transduction mediated by an autonomously replication-defective recombinant human adenovirus. This permitted us to follow their fate after transplantation. mdx and normal mice were irradiated with 20 Gray gamma rays; necrosis and regeneration were induced by intramuscular notexin prior to myoblast injection. In both mdx and normal mice, the expression of luciferase rapidly declined after the injection implying that a large portion of the injected myoblasts were lost by 48 hr, due to undetermined cause(s). The surviving, injected myoblasts well-mosaicized large groups of host fibers but only in the immediate vicinity of the injection. Substantial expression of the reporter gene continued up to 1 month post-transplantation in normal mice, but there was a gradual decline and eventual disappearance of the reporter gene expression in mdx mice. This latter phenomenon was due to the ongoing intense necrosis of muscle fibers in mdx. There was no evidence of immunorejection. These experiments indicate that even in the absence of immunorejection, myoblast transfer suffers from important negative features: major loss of myoblasts within 48 hr after the injection and lack of significant spread of the injected cells from the injection site in the host muscle. These factors, plus the limited proliferative and fusion capacity of Duchenne muscular dystrophy (DMD) myoblasts, make them less than an ideal vector for the dystrophin cDNA for dystrophin gene replacement therapy in DMD.
BayGenomics: a resource of insertional mutations in mouse embryonic stem cells (2003)

The BayGenomics gene-trap resource (http://baygenomics.ucsf.edu) provides researchers with access to thousands of mouse embryonic stem (ES) cell lines harboring characterized insertional mutations in both known and novel genes. Each cell line contains an insertional mutation in a specific gene. The identity of the gene that has been interrupted can be determined from a DNA sequence tag. Approximately 75% of our cell lines contain insertional mutations in known mouse genes or genes that share strong sequence similarities with genes that have been identified in other organisms. These cell lines readily transmit the mutation to the germline of mice and many mutant lines of mice have already been generated from this resource. BayGenomics provides facile access to our entire database, including sequence tags for each mutant ES cell line, through the World Wide Web. Investigators can browse our resource, search for specific entries, download any portion of our database and BLAST sequences of interest against our entire set of cell line sequence tags. They can then obtain the mutant ES cell line for the purpose of generating knockout mice.
The NeuroD1/BETA2 Sequences Essential for Insulin Gene Transcription Colocalize with Those Necessary for Neurogenesis and p300/CREB Binding Protein Binding (1999)

NeuroD1/BETA2 is a key regulator of pancreatic islet morphogenesis and insulin hormone gene transcription in islet beta cells. This factor also appears to be involved in neurogenic differentiation, because NeuroD1/BETA2 is able to induce premature differentiation of neuronal precursors and convert ectoderm into fully differentiated neurons upon ectopic expression in Xenopus embryos. We have identified amino acid sequences in mammalian and Xenopus NeuroD1/BETA2 that are necessary for insulin gene expression and ectopic neurogenesis. Our results indicate that evolutionarily conserved sequences spanning the basic helix-loop-helix (amino acids [aa] 100 to 155) and C-terminal (aa 156 to 355) regions are important for both of these processes. The transactivation domains (AD1, aa 189 to 299; AD2, aa 300 to 355) were within the carboxy-terminal region, as analyzed by using GAL4:NeuroD1/BETA2 chimeras. Selective activation of mammalian insulin gene enhancer-driven expression and ectopic neurogenesis in Xenopus embryos was regulated by two independent and separable domains of NeuroD1/BETA2, located between aa 156 to 251 and aa 252 to 355. GAL4:NeuroD1/BETA2 constructs spanning these sequences demonstrated that only aa 252 to 355 contained activation domain function, although both aa 156 to 251 and 300 to 355 were found to interact with the p300/CREB binding protein (CBP) coactivator. These results implicate p300/CBP in NeuroD1/BETA2 function and further suggest that comparable mechanisms are utilized to direct target gene transcription during differentiation and in adult islet beta cells.
Autologous versus allogeneic bone marrow transplantation for non-Hodgkin's lymphoma: a case-controlled analysis of the European Bone Marrow Transplant Group Registry data. (1992)

This study suggests that ABMT and alloBMT for non-Hodgkin's lymphoma are comparable, with the exception of lymphoblastic lymphoma in which a graft-versus-lymphoma effect may account for the lower relapse rate for patients who underwent alloBMT.
Evaluation of rhBMP-2 With an OPLA Carrier in a Canine Posterolateral (Transverse Process) Spinal Fusion Model (1995)

Recombinant bone morphogenetic protein-2 carried by open-cell polyactic acid polymer is superior to autogenous iliac bone for producing radiographically and mechanically solid transverse process fusions in canines by 3 months. Spontaneous transverse process fusion does not occur in canines after decortication and open-cell polylactic acid polymer implantation.
Rapid, sensitive analysis of protein mixtures by mass spectrometry. (1990)

We have developed a method for determining the molecular masses of proteins in complex mixtures by mass spectrometry. The method has the capacity to examine the components of mixtures without using any chromatographic separation steps and will tolerate relatively large amounts of buffers and inorganic contaminants. It allows the simultaneous determination of protein molecular masses from 1 to 40 kDa with an accuracy of +/- 0.01% and above 40 kDa with reduced accuracy. The lower limit for practical detection of a protein is a concentration of approximately 0.1 microM, and less than 1 microliter of such a solution is consumed. The analysis is very fast: less than 15 min is necessary to perform the complete analysis, including sample preparation, introduction into the mass spectrometer, mass spectrum collection, and data reduction. The mass spectrum that is obtained does not require elaborate interpretation because there is no fragmentation of the ionized protein (or protein subunit) molecule. Therefore, there is a one-to-one correspondence between the peaks in the mass spectrum and the proteins present in the original mixture. The spectra assume the appearance of chromatograms, with the abscissa being mass-to-charge ratio rather than chromatographic retention time.
Malaria ookinetes exhibit multiple markers for apoptosis-like programmed cell death in vitro (2009)

We have confirmed previous reports that Plasmodium ookinetes display multiple signs that suggest they die by a mechanism resembling apoptosis. This occurs in vivo and in vitro without experimental application of triggers. Our findings support the hypothesis that non-necrotic mechanisms of cell death evolved before the advent of multicellular organisms.
The Transcription Factor E2F-1 Is a Downstream Target of RB Action (1995)

Reintroduction of RB into SAOS2 (RB-/-) cells causes a G1 arrest and characteristic cellular swelling. Coexpression of the cellular transcription factor E2F-1 could overcome these effects. The ability of E2F-1 to bind to RB was neither necessary nor sufficient for this effect, and S-phase entry was not accompanied by RB hyperphosphorylation under these conditions. Furthermore, E2F-1 could overcome the actions of a nonphosphorylatable but otherwise intact RB mutant. These data, together with the fact that RB binds to E2F-1 in vivo, suggest that E2F-1 is a downstream target of RB action. Mutational analysis showed that the ability of E2F-1 to bind to DNA was necessary and sufficient to block the formation of large cells by RB, whereas the ability to induce S-phase entry required a functional transactivation domain as well. Thus, the induction of a G1 arrest and the formation of large cells by RB in these cells can be genetically dissociated. Furthermore, the ability of the E2F-1 DNA-binding domain alone to block one manifestation of RB action is consistent with the notion that RB-E2F complexes actively repress transcription upon binding to certain E2F-responsive promoters. In keeping with this view, we show here that coproduction of an E2F1 mutant capable of binding to DNA, yet unable to transactivate, is sufficient to block RB-mediated transcriptional repression.