gebhart/patrepeval huggingface dataset:
Ovalbumin injected with complete Freund's adjuvant stimulates cytolytic responses (1995)

CD8+ cytotoxic T lymphocytes (CTL) recognize antigens (Ag) associated with class I major histocompatibility complex (MHC) molecules. Endogenously synthesized protein Ag are processed into peptides in the cytoplasm and transported to the endoplasmic reticulum where they are bound by class I proteins. Exogenous Ag do not enter the class I processing pathway of most cells and thus do not activate CD8+ CTL. Nevertheless, several investigators have reported that immunization with exogenous Ag can activate CD8+ T cells that have immunoregulatory activity. To determine how exogenous Ag entered the class I pathway in vivo and whether immunosuppressive CD8+ T cells were cytolytic, we have shown in this report that injection with OVA emulsified in the complete Freund's adjuvant (CFA) primed CD8+, class I MHC-restricted, OVA-specific CTL in mice. These CTL recognize the OVA257-264 epitope, produce tumor necrosis factor-alpha and interferon-gamma upon activation. Both oil and mycobacteria components in CFA were required for inducing CTL responses. Priming was not attributed to direct sensitization of class I-bearing cells by contaminating peptides. Rather, phagocytic cells, but not CD4+ helper T cells, were required for priming CD8+ CTL by OVA-CFA. Thus, OVA in CFA is taken up by antigen-presenting cells and processed into the class I pathway by phagocytic cells in vivo. In addition, CTL induced by OVA-CFA suppressed the antibody response to OVA in adoptive recipients. These results suggest that CD8+ CTL specific for exogenous proteins might be routinely stimulated by injecting proteins in conventional adjuvants and that such cells have the potential to regulate immune responses in vivo.
Autocrine production and TGF-beta 1-mediated effects on metabolism and viability in renal cells (1996)

Transforming growth factor-beta 1 (TGF-beta 1) treatment (0.2-2.0 ng/ml, 8-80 M) of confluent primary cultures of rabbit renal proximal bular cells (RPTC) for 6 consecutive days resulted in both a benotypic transformation of the monolayer into solid clus- rs of cells and apoptosis. TGF-beta 1 treatment stimulated glycolysis before any effect on monolayer DNA content or morphology. TGF-beta 1 treatment also resulted in a 35% decrease in oxygen consumption, 50% inhibition of Na(+)-K(+)- ATPase activity, and a 57% decrease in gluconeogenesis. A concentration of 0.06 ng/ml TGF-beta 1 decreased oxygen consumption and induced glycolysis but had no effect on morphology and viability of RPTC. Endogenous production of TGF-beta 1 by RPTC increased 2.6-fold during 10 days of culture. Control RPTC treated with anti-TGF-beta antibodies exhibited decreased glycolysis, and lactate metabolism shifted from net production to net consumption. These results show that TGF-beta 1 stimulates glycolysis, decreases respiration, and, at higher concentrations, induces RPTC apoptosis and phenopic changes. Inhibition of net lactate production in cells grown in the presence of anti-TGF-beta antibodies suggests that increased endogenous production of TGF-beta is responsible for the stimulation of glycolysis in long-term cultures of RPTC.
Transformation of Rice via PEG-Mediated DNA Uptake into Protoplasts (2003)

For stable transformation of cereals through PEG-mediated DNA uptake into protoplasts, the two most critical requisites are the ability to isolate and culture protoplasts in large numbers, and the development of an efficient and reliable system for routine plant regeneration from protoplasts (1–3). Based on early success with mesophyll protoplasts of some dicotyledonous species, extensive efforts were made to induce sustained division in protoplasts isolated from leaves or young shoots of different cereal plants. However, there is still no convincing evidence of sustained divisions in protoplasts isolated from leaves or shoots of any cereal In contrast, protoplasts isolated from embryogenic suspension cultures could be induced to divide in culture (4). Obtaining a fast-growing and highly embryogenic suspension culture is the most important factor for cereal plant regeneration from protoplasts (4–8). Microspore cultures, and immature or mature embryos may be used to obtain embryogenic calh which can eventually be used to establish embryogenic cell suspensions ECS (2,7).
Origin of Multiple Melting Endotherms in a High Hard Block Content Polyurethane. 2. Structural Investigation (2004)

The structure and morphology of a set of high hard block content (50% to 100% hard segment by weight) linear thermoplastic polyurethanes has been investigated mainly via small angle X-ray scattering (SAXS) and transmission electron microscopy (TEM). All the results obtained in this investigation have been correlated to our previous work on the thermodynamic properties of the same set of samples (Saiani et al. Macromolecules 2001, 34, 9059). The soft segment was based on a poly(propylene oxide) polyol end-capped with ethylene oxide and the hard segment on a 4,4‘-methylenediphenyleneisocyanate (MDI) chain extended by 2-methyl-1,3-propanediol (MP−Diol). Samples with a hard segment volume fraction higher than 65% are shown to have a morphology consisting in soft phase domains embedded in a hard phase matrix. Alignment of the soft phase domains could be observed under specific preparation conditions. From our SAXS results, the same average interdomain distance was found for all the samples (di ≈ 15 nm). These results confirm our DSC results and suggest a two-phase structure for the melt-quenched samples: “pure” hard segment phase + mixed phase (soft + hard segments) with a hard segment content of 65 wt %. The mixed phase then undergoes phase separation during the annealing at 120 °C. The dynamics of the phase separation was also investigated showing a strong correlation between the peak observed in the scattering curves and the so-called TMMT melting endotherm. The results confirm the assignment of this endotherm to the microphase mixing of the soft and hard segments. The rate of phase separation was found to be a function of the hard segment content of the samples, and a delay time was found before the start of the phase separation process for the high hard block content samples. The degree of phase separation was calculated and found to be the same for all the samples except the PU-50%HS sample, which showed a higher degree of phase separation. The interface thickness is found to increase with increasing hard segment content.
Detection of anti-human immunodeficiency virus type 1 (HIV-1) immunoglobulin G in urine by an ultrasensitive enzyme immunoassay (immune complex transfer enzyme immunoassay) with recombinant reverse transcriptase as an antigen (1994)

Anti-human immunodeficiency virus type 1 immunoglobulin G in urine was detected by an immunoassay with reverse transcriptase as the antigen and beta-D-galactosidase as the label; this immunoassay was 30-fold more sensitive than the previous immunoassay with peroxidase as the label. The sensitivity and specificity were both 100%. The lowest signal for asymptomatic carriers was 20-fold higher than the highest signal for seronegative subjects.
A pattern matching and clustering based approach for supporting requirements transformation (2002)

One problem in requirements transformation from informal prose requirements to formal specifications is natural language processing. Although natural language understanding is still not practical for general requirements processing, syntactical information is useful for concept extraction. This paper discusses the correspondence between requirements sentence structure patterns and the events/transition concepts. It addresses how this correspondence might be utilized to extract events and transitions from conditional sentences. A pattern matching and clustering based approach is proposed to support event and transition extraction. The approach first selects requirements that are likely to contain event/transition information and then groups similar requirements to extract events. Once events are identified, the original requirements are clustered based on events to identify, related transition information. The approach is simple and does not require a parser.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Encapsulation of pyrene within self-assembled peptide amphiphile nanofibers (2005)

Certain peptide amphiphiles (PAs) in aqueous media are known to form high-aspect-ratio cylindrical nanofibers with hydrophobic cores. Using cholesterol or palmitic acid as the hydrophobe and the biological adhesion epitope RGDS as the hydrophilic segment, we studied the encapsulation of pyrene, a small hydrophobic molecule, within the cores of the self-assembling PA nanofibers. Circular dichroism (CD), transmission electron microscopy (TEM) and fluorescence were used to characterize formation of the supramolecular structures. Pyrene excimer formation observed by fluorescence demonstrated the encapsulation and aggregation of pyrene within the hydrophobic cores. In addition, peptide amphiphiles covalently functionalized with pyrene linked to the hydrophobic portion of the molecule exhibited excimer formation upon self-assembly into nanofibers. Interestingly excimer formation was not observed in similar molecules that formed spherical aggregates rather than cylindrical nanofibers.
Transfer of skills between human operators through haptic training with robot coordination (2010)

In this paper, we discuss a coordinated haptic training architecture useful for transferring expertise in teleoperation-based manipulation between two human users. The objective is to construct a reality-based haptic interaction system for knowledge transfer by linking an expert's skill with robotic movement in real time. The benefits from this approach include 1) a representation of an expert's knowledge into a more compact and general form by learning from a minimized set of training samples, and 2) an increase in the capability of a novice user by coupling learned skills absorbed by a robotic system with haptic feedback. In order to evaluate our ideas and present the effectiveness of our paradigm, human handwriting is selected as our experiment of interest. For the learning algorithms, artificial neural network (ANN) and support vector machine (SVM) are utilized and their performances are compared. For the evaluation of the performance of the output of the learning modules, a modified Longest Common Subsequence (LCSS) algorithm is implemented. Results show that one or two experts' samples are sufficient for the generation of haptic training knowledge, which can successfully recreate manipulation motion with a robotic system and transfer haptic forces to an untrained user with a haptic device. Also in the case of handwriting comparison, the similarity measures result in up to an 88% match even with a minimized set of training samples.
Rabbit muscle creatine kinase: genomic cloning, sequencing, and analysis of upstream sequences important for expression in myocytes (1991)

Muscle creatine kinase (MCK) is a major enzyme of cellular energy metabolism that is expressed upon differentiation of myoblasts into myotubes. Previously we cloned and sequenced the entire rabbit enzyme cDNA which was used as a probe in these studies to obtain a genomic clone from a rabbit library. The transcription start site was identified by primer extension analysis and over 800 bp of 5' flanking DNA was sequenced. Comparison of this sequence with the published sequences from the upstream regions of the mouse MCK gene and the human MCK gene showed two conserved regions and a large intervening block of non-conserved sequence. The conserved regions are separated by about 800 bp in the mouse and by about 400 bp in the human, but are much closer (200 bp) in the rabbit. The upstream conserved region of the mouse gene encompasses a region possessing the properties of an enhancer and containing two MyoD binding sites; the downstream element is adjacent to the start of transcription. A set of of overlapping deletions of the 5' upstream DNA was fused to the CAT gene and transfected into mouse C2 myocytes, chick primary myocytes, and chick primary liver cells. Constructs which contained both conserved 5' regions were strongly expressed in C2 and chick myocytes, but were not expressed (above background) in primary liver cells. Surprisingly, while the upstream enhancer element was required for strong expression in C2 myocytes, it was less important for expression in chick myocytes. This suggests that there are important muscle-specific transcriptional signals in the proximal promoter region of mammalian MCK genes.
Expression and Regulation of Bcl-2, Bcl-xl, and Bax Correlate With p53 Status and Sensitivity to Apoptosis in Childhood Acute Lymphoblastic Leukemia (1997)

Bcl-2 and its homologue, Bcl-x1, encode membrane-associated proteins that protect neoplastic cells from DNA damage-induced apoptosis, whereas Bax is a Bcl-2 antagonist that promotes cell death. In the present study, we examined the expression and regulation of these genes at both the mRNA and protein level in 22 pediatric acute lymphoblastic leukemia (ALL) cell lines, as well as their sensitivity to apoptosis after exposure to ionizing radiation (IR). Eleven of 22 lines expressed wild-type (wt) p53, 4 expressed mutant p53, and 7 did not express p53 (p53-null). Nine of 22 (41%) lines expressed Bcl-2; of these, 8 were wt-p53+ and 1 expressed mutant p53. Bcl-2 was not expressed in any p53-null lines. In contrast, all 22 lines were positive for Bcl-x1 and Bax, although expression level varied. Treatment with IR (10 Gy) induced both downregulation of Bcl-2 and upregulation of Bax at 2 to 5 hours post-IR in 5 of 8 (63%) wt-p53+ lines, leading to apoptosis. Conversely, lines that failed to both downregulate Bcl-2 and upregulate Bax after IR were resistant to apoptosis. Although levels of Bcl-x1 expression varied among the 22 lines, high levels of Bcl-x1 were observed in 5 of 7 (71%) p53- lines. There were no obvious changes in the expression of Bcl-x1 in these lines after IR. However, among the p53-null lines, resistance to IR was observed only in those expressing high levels of Bcl-x1. These results suggest that expression of Bcl-2 but not Bcl-x1 is p53-dependent and that IR-induced downregulation of Bcl-2 and upregulation of Bax occur in most wt-p53+ lines and are associated with radiosensitivity. Furthermore, high-level expression of Bcl-x1 occurs predominantly in p53-null lines and is associated with resistance to IR-induced apoptosis in these lines, indicating differential expression and regulation of Bcl-2 and Bcl-x1 in pediatric ALL.
Interleukin 6 plays a key role in the development of antigen-induced arthritis (1998)

To investigate the direct role of interleukin (IL) 6 in the development of rheumatoid arthritis, IL-6-deficient (IL-6 -/-) mice were backcrossed for eight generations into C57BL/6 mice, a strain of mice with a genetic background of susceptibility for antigen-induced arthritis (AIA). Both histological and immunological comparisons were made between IL-6-deficient (IL-6 -/-) mice and wild-type (IL-6 +/+) littermates after the induction of AIA. Although all IL-6 +/+ mice developed severe arthritis, only mild arthritis was observed in IL-6 -/- mice. Safranin O staining demonstrated that articular cartilage was well preserved in IL-6 -/- mice, whereas it was destroyed completely in IL-6 +/+ mice. In addition, comparable mRNA expression for both IL-1beta and tumor necrosis factor alpha, but not for IL-6, was detected in the inflamed joints of IL-6 -/- mice, suggesting that IL-6 may play a more crucial role in cartilage destruction than either IL-1beta or tumor necrosis factor alpha. In immunological comparisons, both antigen-specific in vitro proliferative response in lymph node cells and in vivo antibody production were elicited in IL-6 -/- mice, but they were reduced to less than half of that found in IL-6 +/+ mice. Lymph node cells of IL-6 -/- mice produced many more Th2 cytokines than did IL-6 +/+ mice with either antigen-specific or nonspecific stimulation in in vitro culture. Taken together, these results indicate that IL-6 may play a key role in the development of AIA at the inductive as well as the effector phase, and the blockade of IL-6 is possibly beneficial in the treatment of rheumatoid arthritis.
Lattice vector quantization of generalized Gaussian sources (1997)

Many important sources of data including sub-band image and speech coefficients are highly peaked and can be well-modeled by the family of generalized Gaussian (GG) PDFs parameterized by a shape parameter /spl nu/. We present here algorithms for defining and quantizing to a Z lattice in which the boundary is optimized to the characteristics of GG sources, and show that these techniques lead to high performance and low complexity for bit rates and dimensions that are of interest in a number of practical coding applications. We derive an analytical description of the granular and overload distortion valid for low and moderate bit rates, and also provide a description of quantizer performance in the limit of high rate and dimension.
Evolution of theRhodococcus equi vapPathogenicity Island Seen through Comparison of Host-AssociatedvapAandvapBVirulence Plasmids (2008)

The pathogenic actinomycete Rhodococcus equi harbors different types of virulence plasmids associated with specific nonhuman hosts. We determined the complete DNA sequence of a vapB(+) plasmid, typically associated with pig isolates, and compared it with that of the horse-specific vapA(+) plasmid type. pVAPB1593, a circular 79,251-bp element, had the same housekeeping backbone as the vapA(+) plasmid but differed over an approximately 22-kb region. This variable region encompassed the vap pathogenicity island (PAI), was clearly subject to selective pressures different from those affecting the backbone, and showed major genetic rearrangements involving the vap genes. The pVAPB1593 PAI harbored five different vap genes (vapB and vapJ to -M, with vapK present in two copies), which encoded products differing by 24 to 84% in amino acid sequence from the six full-length vapA(+) plasmid-encoded Vap proteins, consistent with a role for the specific vap gene complement in R. equi host tropism. Sequence analyses, including interpolated variable-order motifs for detection of alien DNA and reconstruction of Vap family phylogenetic relationships, suggested that the vap PAI was acquired by an ancestor plasmid via lateral gene transfer, subsequently evolving by vap gene duplication and sequence diversification to give different (host-adapted) plasmids. The R. equi virulence plasmids belong to a new family of actinobacterial circular replicons characterized by an ancient conjugative backbone and a horizontally acquired niche-adaptive plasticity region.
Gene Therapy for Genetic Diseases (1989)

(1989). Gene Therapy for Genetic Diseases. Cancer Investigation: Vol. 7, No. 2, pp. 179-192.
A Fifth Allelomorph in the Agouti Series of the House Mouse (1928)

Experiments with a strain of black-and-tan mice obtained from an English fancier* 'have shown that these mice contain a hi-therto unde- scribed gene which is allelomorphic to yellow, agouti, and non-agouti (black}, and: consequently forms a fifth member of this series of multiple allelomorphs.The black-and-tans used are jet black dorsally with a bright yellow belly and retain this coloration throughout life.They breed true and produce
Genes encoding the β1 subunit of voltage‐dependent Na+ channel in rat, mouse and human contain conserved introns (1995)

We provide evidence in this study that the 86-bp insert in the beta 1.2 mRNA isoform of the voltage gated sodium channel is an intron. Transcripts still retaining this intron were detected in all tissues where the beta 1 gene expression was investigated. We also show that the exon/intron boundaries of the last two introns are conserved among rat, mouse and human beta 1 gene. Unlike the highly conserved cDNAs, introns in only the rat and mouse genes are highly related. The last intron is very short (86-90 bp) and is located in the 3' untranslated sequence, both uncommon properties of mammalian pre-mRNA introns.
Efficient Saturation Mutagenesis of a Pentapeptide Coding Sequence Using Mixed Oligonucleotides (1987)

Site-directed mutagenesis using oligonucleotides that are degenerate at a specific codon was employed to construct a set of mutations in a pentapeptide sequence targeting cytosolic proteins to lysosomes during serum withdrawal. Low-temperature annealing of the mixed oligonucleotides to single-stranded phage DNA and a genetic selection for the DNA strand carrying the mutations were utilized. The use of mixed oligonucleotides by this technique provides an economical means of generating a large set of substitution mutations. A single codon can be changed to codons for most other amino acids in one step. This approach eliminates the need for restriction enzyme cleavage sites flanking the target for mutagenesis and, therefore, is useful for targeting mutations to any DNA fragment cloned into an appropriate single-stranded bacteriophage.
An Asymmetrical Offset Source/Drain Structure For Virtual Ground Array Flash Memory With DINOR Operation (1993)

We proposed previously [1] a novel flash memory cell structure named DINOR (Divided bit-line NOR ) utilizing Fowler-Nordheim erase/write operation, which has realized low power dissipation and high performance with low cost. In this paper, a new application of this DINOR operation ( F-N erase/write ) to a virtual ground array flash memory is described. By using a novel asymmetrical offset source/drain structure, small cell size of 1.0/spl mu/m/sup 2/ based on 0.5/spl mu/m CMOS process will be realized and which makes it possible to realize high speed 3V only 64M bit flash memory.
Porous Hydroxyapatite and Tricalcium Phosphate Cylinders with Two Different Pore Size Ranges Implanted in the Cancellous Bone of Rabbits (1988)

To investigate the histophysiology of implant degradation, hydroxyapatite and tricalcium phosphate cylinders with a diameter of 3 mm were implanted in the cancellous bone of the distal femur and the proximal tibia of 15 New Zealand White rabbits for up to six months. All implants had a homogeneous pore distribution and a porosity of 60%. Ceramics with a pore size range of 50-100 micron and 200-400 micron were compared. Morphometric analysis showed that up to 85.4% of the originally implanted tricalcium phosphate was degraded after six months, whereas the volume reduction of the hydroxyapatite was only 5.4% after the same period. Within the first months bone and tissue ingrowth and implant resorption occurred at a higher rate in the smaller-pored tricalcium phosphate than in the larger-pored material. Hydroxyapatite cylinders with small pores were totally infiltrated by bone or bone marrow after four months, whereas in the larger-pored hydroxyapatite implants tissue did not penetrate all pores after six months and the amount of bone within the implant was small. Scanning electron microscopy of the material before implantation revealed the existence of numerous pore interconnections with diameters of about 20 micron in the smaller-pored ceramics. Such interconnections were rare in the larger-pored implants. The pore interconnections seem to promote vascular and tissue ingrowth and consequently the initial rate of implant resorption. Implant resorption is an active process and involves two different cell types. Acid phosphatase-positive osteoclast-like cells suggesting active resorption adhere directly to the surface, especially in tricalcium phosphate implants. Clusters of macrophages tightly packed with granular material are found in the pores and along the perimeter of all implant cylinders. They may play an active role in the intracellular degradation of small detached ceramic particles.