gebhart/patrepeval huggingface dataset:
MYC oncogene involved in a t(8;22) chromosome translocation is not altered in its putative regulatory regions. (1987)

We have cloned the translocation-associated MYC gene from the Burkitt lymphoma cell line (BL2) with a t(8;22) chromosomal translocation and have determined the nucleotide sequence of the first exon and of the 3' and 5' flanking regions, where sequences with putative regulatory functions have been identified. The nucleotide sequence of the 5' flanking region, which contains regions of DNase hypersensitivity and binding sites for putative regulatory proteins, is the same as that of the normal MYC. Accordingly, mutations in these regulatory regions are not required for the transcriptional deregulation of MYC in the BL2 cell line. The nucleotide sequence of the first exon is similar to that of the normal MYC [Gazin, C., Dupont de Direchin, S., Hampe, A., Masson, J. M., Martin, P., Stehelin, D. & Galibert, F. (1984) EMBO J. 3, 383-387] and has the coding capacity for a 188-residue polypeptide. However, six nucleotide changes that occur in the middle of this reading frame could result in amino acid substitutions. We also have cloned and sequenced the t(8;22) chromosomal breakpoint that is located 10 kilobases 3' of the MYC exon 3 and near the C lambda 3 gene on chromosome 22. Sequences with homology to immunoglobulin joining signals occur close to the breakpoint both on chromosome 8 and 22, providing further evidence that the immunoglobulin joining enzymes may be involved in the recombinations associated with a variety of chromosomal translocations in B and T cells.
Induction of peptide‐specific primary cytotoxic T lymphocyte responses from human peripheral blood (1995)

Various protocols were developed and compared for eliciting specific cytotoxic T lymphocyte (CTL) cell lines from the unselected human peripheral blood mononuclear cells of naive donors. Interleukin-7 and CD4+ T cells primed in vitro by keyhole limpet hemocyanin were shown to act together in the generation of these responses. Primary responses were consistently induced with a variety of different HLA class I-binding malarial peptides. Primary CTL responses could be induced from unselected CD8+ and from CD45RA+CD8+ T cells. The CTL lines derived from these naive donors were CD8+ and demonstrated a high level of HLA class I-restricted killing for > 3 months after priming in vitro. They were also able to recognize and kill targets infected with a recombinant vaccinia virus containing the full-length antigen. In addition, this same protocol enhanced up to fourfold the levels of secondary CTL responses induced. The optimal method presented for naive cytotoxic T cell stimulation is simple, rapid and generally applicable and should provide a useful tool for both basic research and human therapy.
Lazy task creation: a technique for increasing the granularity of parallel programs (1990)

Many parallel algorithms are naturally expressed at a fine level of granularity, often finer than a MIMD parallel system can exploit efficiently. Most builders of parallel systems have looked to either the programmer or a parallelizing compiler to increase the granularity of such algorithms. In this paper we explore a third approach to the granularity problem by analyzing two strategies for combining parallel tasks dynamically at run-time. We reject the simpler load-based inlining method, where tasks are combined based on dynamic load level, in favor of the safer and more robust lazy task creation method, where tasks are created only retroactively as processing resources become available.
Distortion viewing techniques for 3-dimensional data (2002)

As the use of 3D information presentation becomes more prevalent, the need for effective viewing tools grows accordingly. Much work has been done in developing tools for 2D spaces which allow for detail in context views. We examine the extension of such 2D methods to 3D and explore the limitations encountered in accessing internal regions of the data with these methods. We then describe a novel solution to this problem of internal access with the introduction of a distortion function which creates a clear line of sight to the focus revealing sections previously obscured. The distortion is symmetric about the line of sight and is smoothly integrated back into the original 3D layout.
Identification of a regulatory domain of the interleukin-6 receptor. (1994)

IL-6 signal transduction occurs when the liganded interleukin-6 receptor (IL-6R) interacts with glycoprotein (gp) 130. We hypothesized that synthetic peptides modeled from the extramembranous domain of the IL-6R may interfere with the IL-6-induced reaction between IL-6R and gp130 and may serve to elucidate the initial steps in IL-6 signal transduction. The capacity of such peptides to modulate two different IL-6 functions was evaluated: 1) IL-6-dependent B9 cell mitogenesis, and 2) IL-6-induced acute phase protein synthesis in HepG2 cells. A synthetic peptide, 249Y16T264, corresponding to residues 249-264, inhibited IL-6-dependent B9 proliferation and IL-6-induced acute phase protein up-regulation in HepG2 cells. Other peptides modeled from different regions of the IL-6R were not inhibitory. 249Y16T264 did not inhibit IL-6-independent HepG2 cell proliferation or total cellular protein synthesis. The inhibitory effect was reversible, indicating that the peptide was not cytotoxic. 249Y16T264 did not inhibit 125I-IL-6 binding in U266 cells. Delineation of this domain identified 249Y10R258 as the minimum effective sequence capable of inhibiting fibrinogen synthesis. Amino acid substitutions in 249Y10R258 obliterated the inhibitory effect on fibrinogen synthesis. In conclusion, a region of the extramembranous domain of the IL-6R has been identified that is involved in the regulation of IL-6 signal transmission. A synthetic peptide representing this region inhibits IL-6-dependent B9 cell mitogenesis and IL-6-stimulated acute phase response in HepG2 cells without affecting ligand binding.
Antiviral Effect of 6-diazo-5-oxo-L-Norleucine, Antagonist of -glutamyl Transpeptidase, on Replication of Human Parainfluenza Virus Type 2 (1990)

The antiviral effects of 6-diazo-5-oxo-L-norleucine (L-DON) on the replication of human parainfluenza virus type 2 (HPIV-2), mumps and vesicular stomatitis viruses were studied. L-DON suppressed growth of these viruses and, in particular, HPIV-2 in four cell types. L-DON was not toxic to the cells at the active dose and did not significantly inhibit cellular macromolecular synthesis. The L-DON-sensitive step of HPIV-2 replication was considered to be relatively early. The NP, P and M proteins were, although at a low level, clearly detectable in HPIV-2-infected Vero cells treated with L-DON, whereas the HN and F proteins were scarcely detected by either immunostaining or immunoprecipitation, indicating that L-DON mainly decreased the amounts of viral glycoproteins. Furthermore, Northern blot hybridization showed that secondary transcription of virus RNA was also inhibited.
Allergic conjunctivitis: a comprehensive review of the literature (2013)

Ocular allergy represents one of the most common conditions encountered by allergists and ophthalmologists. Allergic conjunctivitis is often underdiagnosed and consequently undertreated. Basic and clinical research has provided a better understanding of the cells, mediators, and immunologic events, which occur in ocular allergy. New pharmacological agents have improved the efficacy and safety of ocular allergy treatment. An understanding of the immunologic mechanisms, clinical features, differential diagnosis, and treatment of ocular allergy may be useful to all specialists who deal with these patients. The purpose of this review is to systematically review literature underlining all the forms classified as ocular allergy: seasonal allergic conjunctivitis, perennial allergic conjunctivitis, vernal keratoconjunctivitis, atopic keratocongiuntivitis, contact allergy, and giant papillary conjunctivitis.
Oligosaccharide structures present on asparagine-289 of recombinant human plasminogen expressed in a Chinese hamster ovary cell line (1991)

The oligosaccharide structures linked to Asn289 of a recombinant (r) variant (R561S) human plasminogen (HPg) expressed in Chinese hamster ovary (CHO) cells, after transfection of these cells with a plasmid containing the cDNA coding for the variant HPg, have been determined. Employing high-performance anion-exchange liquid chromatography mapping of the oligosaccharide units cleaved from the protein by glycopeptidase F, compared with elution positions of standard oligosaccharides, coupled with monosaccharide compositional determinations and analyses of sequential exoglycosidase digestions and specific lectin binding, we find that considerable microheterogeneity in oligosaccharide structure exists at this sole potential N-linked glycosylation site on HPg. A variety of high-mannose structures, as well as bi-, tri-, and tetraantennary complex-type carbohydrate, has been found, in relative amounts of 1-25% of the total oligosaccharides. The complex-type structures contain variable amounts of sialic acid (Sia), ranging from 0 to 5 mol/mol of oligosaccharide in the different glycan structures. Neither hybrid-type molecules, N-acetylglucosamine bisecting oligosaccharides, nor N-acetyllactosaminyl-repeat structures were found to be present in the complex-type carbohydrate pool in observable amounts. Of interest, a significant portion of the Sia exists an outer arm structures in an (alpha 2,6) linkage to the penultimate galactose, a novel finding in CHO cell-directed glycosylation.(ABSTRACT TRUNCATED AT 250 WORDS)
Theoretical Design and Analysis of Multivolume Digital Assays with Wide Dynamic Range Validated Experimentally with Microfluidic Digital PCR (2011)

This paper presents a protocol using theoretical methods and free software to design and analyze multivolume digital PCR (MV digital PCR) devices; the theory and software are also applicable to design and analysis of dilution series in digital PCR. MV digital PCR minimizes the total number of wells required for "digital" (single molecule) measurements while maintaining high dynamic range and high resolution. In some examples, multivolume designs with fewer than 200 total wells are predicted to provide dynamic range with 5-fold resolution similar to that of single-volume designs requiring 12,000 wells. Mathematical techniques were utilized and expanded to maximize the information obtained from each experiment and to quantify performance of devices and were experimentally validated using the SlipChip platform. MV digital PCR was demonstrated to perform reliably, and results from wells of different volumes agreed with one another. No artifacts due to different surface-to-volume ratios were observed, and single molecule amplification in volumes ranging from 1 to 125 nL was self-consistent. The device presented here was designed to meet the testing requirements for measuring clinically relevant levels of HIV viral load at the point-of-care (in plasma, <500 molecules/mL to >1,000,000 molecules/mL), and the predicted resolution and dynamic range was experimentally validated using a control sequence of DNA. This approach simplifies digital PCR experiments, saves space, and thus enables multiplexing using separate areas for each sample on one chip, and facilitates the development of new high-performance diagnostic tools for resource-limited applications. The theory and software presented here are general and are applicable to designing and analyzing other digital analytical platforms including digital immunoassays and digital bacterial analysis. It is not limited to SlipChip and could also be useful for the design of systems on platforms including valve-based and droplet-based platforms. In a separate publication by Shen et al. (J. Am. Chem. Soc., 2011, DOI: 10.1021/ja2060116), this approach is used to design and test digital RT-PCR devices for quantifying RNA.
Autologous confrontation of brain tumor derived spheroids with human dermal spheroids. (1998)

An in vitro model is presented to test the invasiveness of human brain tumour derived cells. Spheroids of brain tumours are confronted with autologous spheroids of human dermal fibroblasts. Aggregates of seven tested brain tumours, respectively 5 benign and 2 malignant ones are confronted for 7 days in vitro. The aggregates of the malignant tumours do invade into the dermal spheroids and progressive replacement of the dermal aggregate is observed. The aggregates of the benign tumours do not invade, a clearcut border between the tumour compartment and the dermal one is seen. This model will be applied for clinical testing of the invasiveness of selected tumours and will offer a good model to study mechanisms of invasion.
DEVELOPMENT OF POWER ASSISTING SUIT : Miniaturization of supply system to realize wearable suit (2002)

In order to realize a wearable power assisting suit for assisting a nurse caring a patient in her arm, the power supply and control systems have been miniaturized. The new suit consists of shoulders, arms, waist and legs units and is fitted on her body. The arms, waist and legs have pneumatic rotary actuators driven directly with micro air pumps. The muscle forces are sensed with a new muscle hardness sensor utilizing a sensing tip mounted on a polymer thick film device. This paper gives the design and characteristics of the new power assisting suit verifying its practicability.
A membrane antigen common to human cancer and fetal brain tissues. (1976)

Membrane antigens of a cultured human melanoma line, UCLASO-M14, were studied using immune adherence techniques. Allogeneic sera from melanoma patients that were reactive with the M14 but nonreactive with lymphoid cells of the M14 donor were used as antibodies. The antigen responsible for the reaction between M14 and the antibodies was searched for in other cancer, normal, and fetal tissues using antibody absorption techniques. The antigen was found in a variety of different histological types of biopsied and cultured cancer cells as well as in melanomas. The antigen did not exist in biopsied normal tissues, but it appeared in cultured normal skin and muscle. Neither normal lymphocytes nor cultured lymphoid cells showed any antigenicity. The antigen was present in human fetal tissues and was the strongest in fetal brain tissues at 22 weeks of development. Liver, spleen, thymus, and small intestine from the same fetus were negative for antigen.
Intratracheal Pulmonary Ventilation (ITPV) (1994)

A new mode of pulmonary ventilation called intratracheal pulmonary ventilation (ITPV) was studied. Briefly, a continuous flow of air/oxygen is introduced through a small catheter, the tip of which is positioned at the carina, with a diffuser mounted at its distal end. A timed expiration valve, when closed, provides for inspiration; when open, it provides for expiration. The system as first described had a potential for significant back pressure at the level of the carina, which was more at rapid gas flows and with smaller endotracheal tubes. We have now mounted a venturi on the tip of the catheter (reverse thrust catheter [RTC]) that avoids back pressure, and which facilitates expiration. At respiratory rates from 10 to 120/min, the ITPV system with the RTC maintained end-expiratory pressure at the level of the carina at, or near 0 cm H2O. Compared to conventional mechanical ventilation, at identical respiratory rates, this system reduced tidal volume by one half at the lowest respiratory rates, and by as much as two thirds at the highest respiratory rates, with a proportional decrease in peak inspiratory pressure. ITPV has the smallest minute volume ventilation of any conventional or nonconventional mode of pulmonary ventilation.
Chimeric antigen receptors that trigger phagocytosis (2018)

Chimeric antigen receptors (CARs) are synthetic receptors that reprogram T cells to kill cancer. The success of CAR-T cell therapies highlights the promise of programmed immunity and suggests that applying CAR strategies to other immune cell lineages may be beneficial. Here, we engineered a family of Chimeric Antigen Receptors for Phagocytosis (CAR-Ps) that direct macrophages to engulf specific targets, including cancer cells. CAR-Ps consist of an extracellular antibody fragment, which can be modified to direct CAR-P activity towards specific antigens. By screening a panel of engulfment receptor intracellular domains, we found that the cytosolic domains from Megf10 and FcRɣ robustly triggered engulfment independently of their native extracellular domain. We show that CAR-Ps drive specific engulfment of antigen-coated synthetic particles and whole human cancer cells. Addition of a tandem PI3K recruitment domain increased cancer cell engulfment. Finally, we show that CAR-P expressing murine macrophages reduce cancer cell number in co-culture by over 40%.
Herd Immunity to GII.4 Noroviruses Is Supported by Outbreak Patient Sera (2009)

Noroviruses (NoVs) of genogroup II, cluster 4 (GII.4), are the most common cause of outbreaks of acute gastroenteritis worldwide. During the past 13 years, GII.4 NoVs caused four seasons of widespread activity globally, each associated with the emergence of a new strain. In this report, we characterized the most recent epidemic strain, GII.4-2006 Minerva, by comparing virus-like particle (VLP) antigenic relationships and histo-blood group antigen (HBGA) binding profiles with strains isolated earlier. We also investigated the seroprevalence and specificity of GII.4 antibody in the years prior to, during, and following the GII.4 pandemic of 1995 and 1996 using a large collection of acute- and convalescent-phase serum pairs (n = 298) collected from 34 outbreaks. In a surrogate neutralization assay, we measured the blockade of HBGA binding using a panel of GII.4 VLPs representing strains isolated in 1987, 1997, 2002, and 2006 and a GII.3 VLP representing a strain isolated in the mid-1990s. Serum titers required for 50% HBGA blockade were compared between populations. In general, blockade of GII.4 VLP-HBGA binding was greater with convalescent-phase outbreak sera collected near the time of origin of the VLP strain. Heterotypic genotypes did not contribute to herd immunity against GII.4 NoVs based on their inability to block GII.4 VLP binding to HBGA. However, previous exposure to GII.4 NoV followed by infection by GII.3 NoV appeared to evoke an immune response to GII.4 NoV. These results support the hypothesis that herd immunity is a driving force for GII.4 evolution in the U.S. population. The data also suggest that complex patterns of cross-protection may exist across NoV genotypes in humans.
Quantitative aspects of passive immunity to respiratory syncytial virus infection in infant cotton rats (1985)

The amount of passively acquired serum respiratory syncytial virus (RSV)-neutralizing antibodies required to protect the respiratory tract of cotton rats against infection was studied. Infant cotton rats were inoculated intraperitoneally with various dilutions of a single pool of sera derived from cotton rats convalescent from RSV infection. After 24 h, these animals were inoculated with RSV intranasally. Virus replication in the respiratory tract was suppressed in cotton rats which had a serum neutralizing antibody titer of 1:100 or greater. Resistance was greater in the lungs than in the nose. Complete or almost complete resistance in the lungs was observed in cotton rats with a serum neutralizing antibody titer of 1:380 or greater. The level of serum RSV-neutralizing antibodies required to confer significant resistance to infection in the cotton rat was similar to the level of maternally derived serum antibodies possessed by human infants less than 2 months of age, who as a group exhibit relative resistance to RSV disease compared with infants 2 to 6 months of age.
Does yohimbine act as a slimming drug? (1991)

Yohimbine, an alpha 2-receptor antagonist, was examined for its suitability in the treatment of obesity. Twenty female obese outpatients were subjected to a 3-week low-energy diet (1,000 kcal/day), after which they were randomly allocated according to a double-blind study protocol to two treatments: 10 subjects received 5 mg yohimbine per os 4 times a day and 10 received a placebo for 3 weeks, in addition to a low-energy diet of 1,000 kcal/day. Before inclusion in the study, as well as the end of each of the 3-week treatment periods, thermogenesis (resting and exercise energy expenditure) was assessed by indirect calorimetry; serum noradrenaline concentration was taken as an index of sympathetic system activity and serum glycerol level as an index of lipolysis. Yohimbine significantly increased the mean weight loss in patients on a low-energy diet: 3.55 +/- 0.24 kg (yohimbine) vs. 2.21 +/- 0.37 kg (placebo), P less than 0.005. With yohimbine, a steady level of effort-induced energy expenditure and sympathetic system activity was maintained. No significant effect of yohimbine on lipolysis was observed under the experimental conditions of this study. In another group of 15 obese inpatients (11 women and 4 men) the influence of 15 mg yohimbine per os vs. placebo on gastric emptying of a radiolabelled solid meal was examined in a double-blind manner with the use of a gamma camera. No significant effect of yohimbine on gastric emptying was revealed--the mean gastric transit time was 42.0 +/- 0.4 min after placebo and 41.8 +/- 0.5 min after yohimbine. The results obtained warrant further research on the applicability of alpha 2-receptor inhibitory drugs as a supplementary management in the treatment of obesity.
Mutation of the PIK3CA Gene in Anaplastic Thyroid Cancer (2005)

The phosphatidylinositol 3'-kinase (PI3K) pathway is frequently activated in thyroid carcinomas through the constitutive activation of stimulatory molecules (e.g., Ras) and/or the loss of expression and/or function of the inhibitory PTEN protein that results in Akt activation. Recently, it has been reported that somatic mutations within the PI3K catalytic subunit, PIK3CA, are common (25-40%) among colorectal, gastric, breast, ovarian cancers, and high-grade brain tumors. Moreover, PIK3CA mutations have a tendency to cluster within the helical (exon 9) and the kinase (exon 20) domains. In this study, 13 thyroid cancer cell lines, 80 well-differentiated thyroid carcinomas of follicular (WDFC) and papillary (WDPC) type, and 70 anaplastic thyroid carcinomas (ATC) were investigated, by PCR-direct sequencing, for activating PIK3CA mutations at exons 9 and 20. Nonsynonymous somatic mutations were found in 16 ATC (23%), two WDFC (8%), and one WDPC (2%). In 18 of the 20 ATC cases showing coexisting differentiated carcinoma, mutations, when present, were restricted to the ATC component and located primarily within the kinase domain. Three cell lines of papillary and follicular lineage (K1, K2, and K5) were also found mutated. In addition, activation of Akt was observed in most of the ATC harboring PIK3CA mutations. These findings indicate that mutant PIK3CA is likely to function as an oncogene among ATC and less frequently well-differentiated thyroid carcinomas. The data also argue for a role of PIK3CA targeting in the treatment of ATC patients.
Field emission from nanotube bundle emitters at low fields (1997)

The fabrication of nanotube field emitters with an onset field as low as 0.8 V/μm is described and the low-field electron emission mechanism is discussed. These emitters are made using nanotube cathode deposit with the addition of epoxy resin. The preferred orientation of nanotubes in nanotube bundles of the deposit is preserved. The nanotube tips are sharpened by exposing the nanotube bundle surface to a microwave oxygen plasma. The local-field enhancement factor is estimated to be 8000 by using the Fowler–Nordheim equation. The low onset field is attributed to the well-distributed, highly orientated sharp tips at the sample surface.