gebhart/patrepeval huggingface dataset:
Repair of double-stranded DNA breaks by homologous DNA fragments during transfer of DNA into mouse L cells. (1990)

To test the validity of various models for recombination between extrachromosomal DNAs in mammalian cells, we measured recombination between a plasmid containing a herpesvirus thymidine kinase (tk) gene with an internal BamHI linker insertion mutation (ptkB8) and a tk gene deleted at both ends (tk delta 3' delta 5'). The two DNAs shared 885 base pairs of perfect tk homology except for the interruption at the linker insertion site. Recombination events that restored the mutated insertion site to wild type were monitored by the generation of hypoxanthine-aminopterine-thymidine-resistant colonies after cotransformation of Ltk- cells with the two DNAs. We found that cleavage of the ptkB8 DNA at the linker insertion site was essential for gene restoration. If the tk delta 3' delta 5' DNA was ligated into mp10 vector DNA, then recombination with the cleaved ptkB8 DNA was inefficient. In contrast, if it was excised from that vector by cleavage at flanking restriction sites, then recombination was stimulated about 150-fold. Using restriction site polymorphisms, we showed that most of the recombination events leading to restoration of the tk gene with the excised tk delta 3' delta 5' fragment involved three double-strand duplexes: two ptkB8 DNAs and one tk delta 3' delta 5' fragment. These results are much more readily explained by the single-strand annealing model of recombination than by the double-strand break repair model, and they suggest that the deficiency of the latter pathway for extrachromosomal mammalian recombination may be due, at least in part, to the obligate tripartite nature of the reaction. Finally, we measured the effect of DNA homology on the efficiency of the ptkB8-tk delta 3' delta 5' reaction. Our results showed a near-linear relationship between the efficiency of recombination and the amount of homology flanking either side of the linker insertion site. Moreover, we could detect thymidine kinase-positive transformants with as little as 10 base pairs of homology.
Materials investigation for thermally-assisted magnetic random access memory robust against 400 °C temperatures (2015)

Magnetic materials are investigated in order to enable a new type of Thermally Assisted Magnetic Random Access Memory (TAS-MRAM). A TAS-MRAM materials stack that is robust against the 400 °C process temperatures required for embedded integration with complementary metal oxide silicon processes is demonstrated. In unpatterned sheet film stacks, a stable resistance-area product, tunneling magnetoresistance (MR) &amp;gt; 100%, and temperature-dependent exchange bias of 1500 Oe after 400 °C anneal are shown for this stack. It is further shown that by doping the sense and storage layers with Ta using thin laminations of Ta/CoFeB, the moment of each layer can be reduced by more than 40% without a major reduction in MR. In patterned nanopillar devices, it is shown that by reducing the moment of the sense and storage layers with laminations of Ta, and by adding a second MgO barrier, the resistance versus applied field loop quality is maintained, while the read field is reduced by more than 40% and devices survive 108 write cycles without breakdown or significant degradation.
Novel Antibodies Reveal Inclusions Containing Non-Native SOD1 in Sporadic ALS Patients (2010)

Mutations in CuZn-superoxide dismutase (SOD1) cause amyotrophic lateral sclerosis (ALS) and are found in 6% of ALS patients. Non-native and aggregation-prone forms of mutant SOD1s are thought to trigger the disease. Two sets of novel antibodies, raised in rabbits and chicken, against peptides spaced along the human SOD1 sequence, were by enzyme-linked immunosorbent assay and an immunocapture method shown to be specific for denatured SOD1. These were used to examine SOD1 in spinal cords of ALS patients lacking mutations in the enzyme. Small granular SOD1-immunoreactive inclusions were found in spinal motoneurons of all 37 sporadic and familial ALS patients studied, but only sparsely in 3 of 28 neurodegenerative and 2 of 19 non-neurological control patients. The granular inclusions were by confocal microscopy found to partly colocalize with markers for lysosomes but not with inclusions containing TAR DNA binding protein-43, ubiquitin or markers for endoplasmic reticulum, autophagosomes or mitochondria. Granular inclusions were also found in carriers of SOD1 mutations and in spinobulbar muscular atrophy (SBMA) patients and they were the major type of inclusion detected in ALS patients homozygous for the wild type-like D90A mutation. The findings suggest that SOD1 may be involved in ALS pathogenesis in patients lacking mutations in the enzyme.
Proper levels of c-Myb are discretely defined at distinct steps of hematopoietic cell development (2006)

The definitive hematopoietic cell lineages have been proposed to originate from hemogenic endothelial cells during mouse embryogenesis. c-Myb is a transcription factor that is essential for the development of definitive hematopoiesis. To investigate the functional role of c-Myb in hematopoietic cell development from endothelial cells, we introduced a c-myb transgene expressed under the control of a tetracycline-regulated promoter into the c-myb(-/-) embryonic stem (ES) cell line, with the aim of inducing c-Myb expression at any stage and at any level. Induction of c-Myb expression after replating c-myb(-)(/)(-) endothelial cells rescued the generation and proliferation of definitive hematopoietic progenitor cells, suggesting that c-Myb expression in developing endothelial cells is not a prerequisite for their hematogenic potential. Overexpression of c-Myb, however, prevented the terminal differentiation of erythrocytes and megakaryocytes and completely abolished B-lymphocyte development. Our results indicate that c-Myb is a major factor that controls differentiation as well as proliferation of hematopoietic progenitor cells derived from hemogenic endothelial cells, and that appropriate levels of c-Myb protein are strictly defined at distinct differentiation steps of each hematopoietic cell lineage.
Modulation of lymphocyte migration by human lymphokines. I. Identification and characterization of chemoattractant activity for lymphocytes from mitogen-stimulated mononuclear cells. (1982)

Abstract Delayed-type hypersensitivity reactions are characterized by mononuclear cell infiltration consisting of macrophages and lymphocytes, the majority of which are not specifically sensitized for the antigen eliciting the reaction. Although the mechanisms for the accumulation of macrophages by chemotactic lymphokines has been extensively studied, little information is available describing chemotactic lymphokines for lymphocytes. Human peripheral blood mononuclear cells were studied for the secretion of chemoattractant activity for lymphocytes after antigen and mitogen stimulation in vitro. Lymphotactic activity for nonsensitized human peripheral blood lymphocytes and rat splenic lymphocytes could be identified in 48-hr supernatants of nonadherent peripheral blood mononuclear cells incubated with antigen, concanavalin A, or phytohemagglutinin. This activity is sensitive to degradation by trypsin and neuraminidase but stable when heated to 56°C for 30 min, suggesting it is a sialoprotein. Nonadherent lymphocytes are preferentially stimulated, whereas adherent cells, monocytes, neutrophils, and eosinophils are not. The activity is predominantly chemokinetic; that is, it is a more active stimulant of random rather than directed migration. It expresses its activity without high-dose inhibition. Because the crude supernatant of incubated mononuclear cells inhibited migration in high doses, whereas the purified lymphokine did not, simultaneous release of a distinct inhibitor of lymphocyte migration is suggested (see companion paper for description of purification). These studies show that human lymphocytes secrete chemoattractant and migration inhibitory factors for nonsensitized lymphocytes and present a mechanism for accumulation of these cells at sites of delayed-type hypersensitivity.
Conclusion (2013)

To people who grew up and came of age between the Famine and Independence/Partition, the past was always present. Seventy-two years is a very short time: someone born in the 1850s could be entering the grandparent generation when the Treaty was signed. Changing patterns of work, migration and emigration, new ways of dressing, eating, working, furnishing houses, happened within the comfortable memory-span of an adult. It was this apparently rapid pace of social change and nationalism which fostered self-consciousness. There were some success stories. Luck, skill or both enabled some people to make the vital step from chronic hardship to some kind of security; parental and elder-sibling struggle and sacrifice produced clerks, shop-workers, secretaries, administrators, teachers and uniformed workers of various kinds, in police barracks, hospitals, asylums, prisons and railways. However, the rise in the numbers convicted for homelessness and prostitution was part of this speeded-up way of life.
Expression of the beta-nerve growth factor gene correlates with the density of sympathetic innervation in effector organs. (1984)

Although beta-nerve growth factor (NGF), a protein necessary for survival and development of sympathetic neurons, is believed to be a trophic factor that is produced by sympathetic effector organs, its synthesis by these tissues has never been conclusively demonstrated. Using an assay capable of detecting 10 fg of mRNA, we measured the level of NGF mRNA in tissues innervated by sympathetic neurons. NGF mRNA was detected unambiguously in each tissue at a level that appeared to be more than enough to account for the low levels of NGF protein previously detected. Tissues that were densely innervated had comparatively high levels of NGF mRNA, while those with sparser innervation had lower levels. There was a strong positive correlation between the NGF mRNA level and norepinephrine content, a measure of the density of sympathetic innervation. NGF gene expression in one of these tissues, the iris, was shown to be induced by denervation. NGF mRNA was also found in other areas, including elements of the adult peripheral nervous system--the sciatic nerve and the sympathetic and sensory ganglia. In the central nervous system, levels of NGF mRNA were found that are too high to be attributed entirely to the vasculature, suggesting a role for NGF in adult central nervous system function.
Stem cell therapy in end-stage ischaemic heart failure: a catheter-based therapeutic strategy targeting myocardial viability (2006)

Recent evidence that the adult heart can repair itself through the proliferation of cardiac precursor cells and the recruitment and engraftment of bone marrow-derived precursor cells has stimulated interest in stem cell therapy for cardiac diseases. Although preclinical studies have shown the efficacy of stem cell treatment, numerous controversies exist, and many basic questions still await answers. Meanwhile, clinical trials of stem cell therapy continue to advance. Our group has focused on using stem cells to treat patients with end-stage ischaemic heart failure who are ineligible for surgical or percutaneous revascularization. The preliminary results of the phase I trial are encouraging but need to be reproduced before larger randomized trials can be attempted. This review covers some of the most important clinical developments in targeted, transendocardially delivered stem cell therapy for end-stage ischaemic heart failure.
The pseudorabies virus gII gene is closely related to the gB glycoprotein gene of herpes simplex virus (1987)

We have looked for conserved DNA sequences between four herpes simplex virus type 1 (HSV-1) glycoprotein genes encoding gB, gC, gD, and gE and pseudorabies virus (PRV) DNA, HSV-1 DNA fragments representing these four glycoprotein-coding sequences were hybridized to restriction enzyme fragments of PRV DNA by the Southern blot procedure. Specific hybridization was observed only when HSV-1 gB DNA was used as probe. This region of hybridization was localized to a 5.2-kilobase (kb) region mapping at approximately 0.15 map units on the PRV genome. Northern blot (RNA blot) analysis, with a 1.2-kb probe derived from this segment, revealed a predominant hybridizing RNA species of approximately 3 kb in PRV-infected PK15 cells. DNA sequence analysis of the region corresponding to this RNA revealed a single large open reading frame with significant nucleotide homology with the gB gene of HSV-1 KOS 321. In addition, the beginning of the sequenced PRV region also contained the end of an open reading frame with amino acid homology to HSV-1 ICP 18.5, a protein that may be involved in viral glycoprotein transport. This sequence partially overlaps the PRV gB homolog coding sequence. We have shown that the PRV gene with homology to HSV-1 gB encoded the gII glycoprotein gene by expressing a 765-base-pair segment of the PRV open reading frame in Escherichia coli as a protein fused to beta-galactosidase. Antiserum, raised in rabbits, against this fusion protein immunoprecipitated a specific family of PRV glycoproteins of apparent molecular mass 110, 68, and 55 kilodaltons that have been identified as the gII family of glycoproteins. Analysis of the predicted amino acid sequence indicated that the PRV gII protein shares 50% amino acid homology with the aligned HSV-1 gB protein. All 10 cysteine residues located outside of the signal sequence, as well as 4 of 6 potential N-linked glycosylation sites, were conserved between the two proteins. The primary protein sequence for HSV-1 gB regions known to be involved in the rate of virus entry into the cells and cell-cell fusion, as well as regions known to be associated with monoclonal antibody resistance, were highly homologous with the PRV protein sequence. Furthermore, monospecific antibody made against PRV gII immunoprecipitated HSV-1 gB from infected cells. Taken together, these findings suggest significant conservation of structure and function between the two proteins and may indicate a common evolutionary history.
An improved approach for predicting the distribution of rare and endangered species from occurrence and pseudo‐absence data (2004)

Summary Few examples of habitat‐modelling studies of rare and endangered species exist in the literature, although from a conservation perspective predicting their distribution would prove particularly useful. Paucity of data and lack of valid absences are the probable reasons for this shortcoming. Analytic solutions to accommodate the lack of absence include the ecological niche factor analysis (ENFA) and the use of generalized linear models (GLM) with simulated pseudo‐absences. In this study we tested a new approach to generating pseudo‐absences, based on a preliminary ENFA habitat suitability (HS) map, for the endangered species Eryngium alpinum . This method of generating pseudo‐absences was compared with two others: (i) use of a GLM with pseudo‐absences generated totally at random, and (ii) use of an ENFA only. The influence of two different spatial resolutions (i.e. grain) was also assessed for tackling the dilemma of quality (grain) vs. quantity (number of occurrences). Each combination of the three above‐mentioned methods with the two grains generated a distinct HS map. Four evaluation measures were used for comparing these HS maps: total deviance explained, best kappa, Gini coefficient and minimal predicted area (MPA). The last is a new evaluation criterion proposed in this study. Results showed that (i) GLM models using ENFA‐weighted pseudo‐absence provide better results, except for the MPA value, and that (ii) quality (spatial resolution and locational accuracy) of the data appears to be more important than quantity (number of occurrences). Furthermore, the proposed MPA value is suggested as a useful measure of model evaluation when used to complement classical statistical measures. Synthesis and applications. We suggest that the use of ENFA‐weighted pseudo‐absence is a possible way to enhance the quality of GLM‐based potential distribution maps and that data quality (i.e. spatial resolution) prevails over quantity (i.e. number of data). Increased accuracy of potential distribution maps could help to define better suitable areas for species protection and reintroduction.
Ethics summit I: assembling the ethical community. (1998)

Ethics Summit I was a unique gathering of organizations representing all of oral health care, convened by the American College of Dentists, for the purpose of seeking a common ethical ground. The background of the conference and its logistics are described here. Four themes were discussed: the role of ethics codes, conflicting values, responding to unethical behavior, and organizations as ethical agents. The conference was grounded in the unusual assumptions that the participants did not have to have a common profile of values to engage in ethical discussion and that individual behavior is not the only level at which ethical discussion must take place. Finally, we did not begin with an assumption that one group could define an ethical code that all others might subscribe to. One strong consensus that emerged was the desirability of creating an alliance of all concerned with oral health care to continue such conversations.
Expression of human stem cell factor in the baculovirus expression system. (1995)

A partial cDNA of human Stem Cell Factor (SCF) was isolated and transferred into the genome of Bombyx Mori Nuclear Polyhedrosis Virus adjacent to the polyhedrin promoter. The soluble form of the SCF protein was expressed in Bombyx Mori cells and silkworm larvae and was secreted into the medium in an active state. The recombinant SCF was similar to natural SCF with respect to its interaction with monoclonal antibody and its synergistic biological activity in conjunction with colony-stimulating factor.
A Core Paired-Type and POU Homeodomain-Containing Transcription Factor Program Drives Retinal Bipolar Cell Gene Expression (2008)

The diversity of cell types found within the vertebrate CNS arises in part from action of complex transcriptional programs. In the retina, the programs driving diversification of various cell types have not been completely elucidated. To investigate gene regulatory networks that underlie formation and function of one retinal circuit component, the bipolar cell, transcriptional regulation of three bipolar cell-enriched genes was analyzed. Using in vivo retinal DNA transfection and reporter gene constructs, a 200 bp Grm6 enhancer sequence, a 445 bp Cabp5 promoter sequence, and a 164 bp Chx10 enhancer sequence, were defined, each driving reporter expression specifically in distinct but overlapping bipolar cell subtypes. Bioinformatic analysis of sequences revealed the presence of potential paired-type and POU homeodomain-containing transcription factor binding sites, which were shown to be critical for reporter expression through deletion studies. The paired-type homeodomain transcription factors (TFs) Crx and Otx2 and the POU homeodomain factor Brn2 are expressed in bipolar cells and interacted with the predicted binding sequences as assessed by electrophoretic mobility shift assay. Grm6, Cabp5, and Chx10 reporter activity was reduced in Otx2 loss-of-function retinas. Endogenous gene expression of bipolar cell molecular markers was also dependent on paired-type homeodomain-containing TFs, as assessed by RNA in situ hybridization and reverse transcription-PCR in mutant retinas. Cabp5 and Chx10 reporter expression was reduced in dominant-negative Brn2-transfected retinas. The paired-type and POU homeodomain-containing TFs Otx2 and Brn2 together appear to play a common role in regulating gene expression in retinal bipolar cells.
Music emotion recognition: A state of the art review (2010)

This paper surveys the state of the art in automatic emotion recognition in music. Music is oftentimes referred to as a "language of emotion" [1], and it is natural for us to categorize music in terms of its emotional associations. Myriad features, such as harmony, timbre, interpretation, and lyrics affect emotion, and the mood of a piece may also change over its duration. But in developing automated systems to organize music in terms of emotional content, we are faced with a problem that oftentimes lacks a welldefined answer; there may be considerable disagreement regarding the perception and interpretation of the emotions of a song or ambiguity within the piece itself. When compared to other music information retrieval tasks (e.g., genre identification), the identification of musical mood is still in its early stages, though it has received increasing attention in recent years. In this paper we explore a wide range of research in music emotion recognition, particularly focusing on methods that use contextual text information (e.g., websites, tags, and lyrics) and content-based approaches, as well as systems combining multiple feature domains. © 2010 International Society for Music Information Retrieval.
IDTT therapy in cadaveric lumbar spine: temperature and thermal dose distributions (2001)

The purpose of this study was to perform extensive temperature mapping throughout human cadaveric disc (n=12) specimens during Intradiscal Thermal Therapy IDTT using the SpineCathTM applicator. Temperature distributions and accumulated thermal dose or thermal damage calculated from the temperature-time history are used to define probable regions of thermal necrosis (destruction of nerves) or thermal coagulation (induced structural changes). The IDTT procedure using SpineCath (5 cm resistive heating segment) and the current standard heating protocol (~17 min) produces intra-discal temperatures which are too low to generate appreciable regions of thermal coagulation and resultant changes in biomechanical properties. This finding was supported by temperature measurements which were mostly below the critical temperature of 60-65°C, except for regions within 1-2 mm of the SpineCath applicator. Furthermore, the analysis of the thermal dose profiles indicate that sufficient thermal doses (240-640 EM43°C) capable of generating complete thermal damage to the nociceptive nerves fibers infiltrating the disc are limited to within ~6 mm of the nucleus and IDTT probe heating segment.
In Vivo Expression of MHC Class I Genes Depends on the Presence of a Downstream Barrier Element (2009)

Regulation of MHC class I gene expression is critical to achieve proper immune surveillance. In this work, we identify elements downstream of the MHC class I promoter that are necessary for appropriate in vivo regulation: a novel barrier element that protects the MHC class I gene from silencing and elements within the first two introns that contribute to tissue specific transcription. The barrier element is located in intergenic sequences 3' to the polyA addition site. It is necessary for stable expression in vivo, but has no effect in transient transfection assays. Accordingly, in both transgenic mice and stably transfected cell lines, truncation of the barrier resulted in transcriptional gene silencing, increased nucleosomal density and decreased histone H3K9/K14 acetylation and H3K4 di-methylation across the gene. Significantly, distinct sequences within the barrier element govern anti-silencing and chromatin modifications. Thus, this novel barrier element functions to maintain transcriptionally permissive chromatin organization and prevent transcriptional silencing of the MHC class I gene, ensuring it is poised to respond to immune signaling.