gebhart/patrepeval huggingface dataset:
α-Galactosylceramide-Induced Liver Injury in Mice Is Mediated by TNF-α but Independent of Kupffer Cells (2005)

NKT cells expressing phenotypic markers of both T and NK cells seem to be pivotal in murine models of immune-mediated liver injury, e.g., in Con A-induced hepatitis. Also alpha-galactosylceramide (alpha-GalCer), a specific ligand for invariant Valpha14 NKT cells, induces hepatic injury. To improve the comprehension of NKT-cell mediated liver injury, we investigated concomitants and prerequisites of alpha-GalCer-induced hepatitis in mice. Liver injury induced by alpha-GalCer injection into C57BL/6 mice was accompanied by intrahepatic caspase-3 activity but appeared independent thereof. alpha-GalCer injection also induces pronounced cytokine responses, including TNF-alpha, IFN-gamma, IL-2, IL-4, and IL-6. We provide a detailed time course for the expression of these cytokines, both in liver and plasma. Cytokine neutralization revealed that, unlike Con A-induced hepatitis, IFN-gamma is not only dispensable for alpha-GalCer-induced hepatotoxicity but even appears to exert protective effects. In contrast, TNF-alpha was clearly identified as an important mediator for hepatic injury in this model that increased Fas ligand expression on NKT cells. Whereas intrahepatic Kupffer cells are known as a pivotal source for TNF-alpha in Con A-induced hepatitis, they were nonessential for alpha-GalCer-mediated hepatotoxicity. In alpha-GalCer-treated mice, TNF-alpha was produced by intrahepatic lymphocytes, in particular NKT cells. BALB/c mice were significantly less susceptible to alpha-GalCer-induced liver injury than C57BL/6 mice, in particular upon pretreatment with d-galactosamine, a hepatocyte-specific sensitizer to TNF-alpha-mediated injury. Finally, we demonstrate resemblance of murine alpha-GalCer-induced hepatitis to human autoimmune-like liver disorders. The particular features of this model compared with other immune-mediated hepatitis models may enhance comprehension of basic mechanisms in the etiopathogenesis of NKT cell-comprising liver disorders.
Specific binding of the Akt-1 protein kinase to phosphatidylinositol 3,4,5-trisphosphate without subsequent activation (1996)

Recent evidence has suggested that activation of phosphoinositide 3-kinase (PI 3-kinase) is required for the activation of Akt-1 by growth factors and insulin. Here we demonstrate by two independent methods that Akt-1 from L6 myotubes binds to PtdIns(3,4,5)P3, PtdIns(3,4)P2 and PtdIns(4,5)P2 when presented against a background of phosphatidylserine (PtdSer) or a 1:1 mixture of PtdSer and phosphatidylcholine (PtdCho). No binding was observed with the lipids PtdIns(3,5)P2, PtdIns4P and PtdIns3P or background lipids. Activated, hyperphosphorylated forms of Akt-1 from insulin-stimulated L6 myotubes bound to PtdIns(3,4,5)P3 in a similar manner as inactive Akt-1. Quantitative analysis using surface plasmon resonance showed that the equilibrium association constant for the binding of Akt-1 to PtdIns(3,4,5)P3 was submicromolar and that PtdIns(3,4)P2 and PtdIns(4,5)P2 bound to Akt-1 with 3- and 6-fold lower affinities respectively. Interaction of Akt-1 with PtdIns(3,4,5)P3 did not activate the protein kinase activity, either before or after incubation with MgATP. A model is presented in which PtdIns(3,4,5)P3 may prime Akt-1 for activation by another protein kinase, perhaps by recruiting it to the plasma membrane.
Subtractive Hybridization Strategy Using Paramagnetic Oligo(dT) Beads and PCR (1996)

Subtractive hybridization has been widely used for the identification of differentially expressed genes. Here we describe a simple, sensitive strategy of subtractive hybridization that involves binding the driver poly(A)+ RNA pool to paramagnetic Dynabeads Oligo (dT)25. After hybridization with target cDNA, the molecules common to both pools are removed. The subtracted cDNA is then amplified with PCR and used for library screening. Using this method, we have identified four cDNA clones that represent developmentally regulated transcripts in the central nervous system of the tobacco hornworm Manduca sexta. All four transcripts are of low abundance, comprising only 0.001%-0.5% of the poly(A)+ RNA pool.
Recent advances in microfluidic technologies for cell-to-cell interaction studies (2017)

Microfluidic cell cultures are ideally positioned to become the next generation of in vitro diagnostic tools for biomedical research, where key biological processes such as cell signalling and dynamic cell-to-cell interactions can be reliably analysed under reproducible physiological cell culture conditions. In the last decade, a large number of microfluidic cell analysis systems have been developed for a variety of applications including drug target optimization, drug screening and toxicological testing. More recently, advanced in vitro microfluidic cell culture systems have emerged that are capable of replicating the complex three-dimensional architectures of tissues and organs and thus represent valid biological models for investigating the mechanism and function of human tissue structures, as well as studying the onset and progression of diseases such as cancer. In this review, we present the most important developments in single-cell, 2D and 3D microfluidic cell culture systems for studying cell-to-cell interactions published over the last 6 years, with a focus on cancer research and immunotherapy, vascular models and neuroscience. In addition, the current technological development of microdevices with more advanced physiological cell microenvironments that integrate multiple organ models, namely, the so-called body-, human- and multi-organ-on-a-chip, is reviewed.
Implantation of cryopreserved allograft pulmonary monocusp patch to treat nonthrombotic femoral vein incompetence. (2002)

We implanted cryopreserved allograft monocusp patches made from cadaveric pulmonary arteries to correct nonthrombotic valvular insufficiency of the common femoral vein in patients with chronic venous ulcers. Thirty-eight patients with 40 ulcers of longer than 3 years' duration underwent valvular repair of the common femoral vein from September 1995 through November 2001. We studied ulcer healing and competence of the monocusp patches using duplex ultrasonography Three patients with a total of 4 ulcers were lost to follow-up; therefore, 35 patients with 36 ulcers were available for examination. Twenty-four ulcers healed, and 12 did not. Of the 24 healed ulcers, 5 recurred. Four of the 5 ulcers were treated, 3 by monocusp patch replacement and 1 by iliac vein dilation and stenting. All such recurrent ulcers healed. The 5th recurrent ulcer was not treated, because the patient refused therapy Therefore, of the 24 ulcers that healed initially, 23 were healed at the end of the study Of the 12 unhealed ulcers, 4 were treated: 2 by ligation of incompetent perforating veins, 1 by saphenous vein ligation and partial stripping, and 1 by monocusp replacement. All 4 ulcers healed. The other 8 patients, all of whom had severe monocusp insufficiency, refused therapy. Therefore, of the 12 ulcers that did not heal initially, 4 were healed after additional treatment. No implanted monocusp patch developed clots. The ulcers remained healed when the prostheses remained competent. We conclude that monocusp patches can restore valvular competence to the femoral vein in patients who have primary valve insufficiency. In such patients, venous ulcers heal rapidly after prosthesis implantation if the monocusp remains competent and if there is no severe incompetence of the superficial venous system or of perforating veins.
Cross-contamination: HS-Sultan is not a myeloma but a Burkitt lymphoma cell line (2001)

Continuous hematopoietic cell lines have become important research tools, contributing significantly to a better understanding of the pathophysiology of hematopoietic tumors.[1][1] [2][2] A relatively large number of cell lines have also been derived from patients with multiple myeloma and related
Survey of Texture Mapping (1986)

Texture mapping is one of the most successful new techniques in high-quality image synthesis. It can enchance the visual richness of raster-scan images immensely while entailing only a relatively smann increase in computation. The technique has been applied to a number of surface attributes: surface color, surface normal, specularity, transparency, illumination, and surface displacement-to name a few. Although the list is potentially endless, the techniques of texture mapping are essentially the same in all cases. This article surveys the fundamentals of texture mapping, which can be spilt into two topics: the geometric mapping that warps a texture onto a surface, and the filtering necessary to avoid aliasing. An extensive bibliography is included.
Genomes of replicatively senescent cells undergo global epigenetic changes leading to gene silencing and activation of transposable elements (2013)

Replicative cellular senescence is an important tumor suppression mechanism and also contributes to aging. Progression of both cancer and aging include significant epigenetic components, but the chromatin changes that take place during cellular senescence are not known. We used formaldehyde assisted isolation of regulatory elements (FAIRE) to map genome-wide chromatin conformations. In contrast to growing cells, whose genomes are rich with features of both open and closed chromatin, FAIRE profiles of senescent cells are significantly smoothened. This is due to FAIRE signal loss in promoters and enhancers of active genes, and FAIRE signal gain in heterochromatic gene-poor regions. Chromatin of major retrotransposon classes, Alu, SVA and L1, becomes relatively more open in senescent cells, affecting most strongly the evolutionarily recent elements, and leads to an increase in their transcription and ultimately transposition. Constitutive heterochromatin in centromeric and peri-centromeric regions also becomes relatively more open, and the transcription of satellite sequences increases. The peripheral heterochromatic compartment (PHC) becomes less prominent, and centromere structure becomes notably enlarged. These epigenetic changes progress slowly after the onset of senescence, with some, such as mobilization of retrotransposable elements becoming prominent only at late times. Many of these changes have also been noted in cancer cells.
Securing media for adaptive streaming (2003)

This paper describes the ARMS system which enables secure and adaptive rich media streaming to a large-scale, heterogeneous client population. The secure streaming algorithms ensure end-to-end security while the content is adapted and streamed via intermediate, potentially untrusted servers. ARMS streaming is completely standards compliant and to our knowledge is the first such end-to-end MPEG-4-based system.
Complete analysis of cellular nucleotides by two-dimensional thin layer chromatography. (1982)

We describe methods for the complete analysis of cellular nucleotides from as few as 10(6) 32Pi-labeled cells in a simple 2-day experiment. Nucleotides are extracted with acid, neutralized, and resolved by two-dimensional thin layer chromatography on polyethyleneimine cellulose. In the first dimension the nucleotides are separated based on the negative charge of their phosphate groups (i.e. cyclic, mono-, di, and triphosphates) and in the second dimension on their content of nucleobases (i.e. Ura, Cyt, Thy, Gua, and Ade). Because the separation is logical, one can predict the chromatographic migration of most nucleotides. By running standards we have determined the chromatographic location of over 90 biologically important nucleotides, nucleotide derivatives, and modified nucleotides from tRNA. We also developed a set of enzymatic and chemical methods to be used in conjunction with the chromatographic separations for verifying the identity of nucleotides and characterizing novel nucleotides. In this paper we use these methods to analyze and inventory the nucleotide content of Salmonella typhimurium in balanced log phase growth. Other potential uses of the method are also described.
Genetic relatedness among strains of the Mycobacterium tuberculosis complex. Analysis of restriction fragment heterogeneity using cloned DNA probes. (1986)

Chromosomal DNA isolated from 3 reference and 2 clinical isolates of Mycobacterium tuberculosis, 2 reference strains each of M. bovis and M. bovis BCG, and 1 reference strain of M. kansasii, was digested with 9 restriction endonucleases. The restriction fragments were analyzed by agarose gel electrophoresis. With each enzyme tested the patterns of the strains of M. tuberculosis, M. bovis, and M. bovis BCG were indistinguishable but clearly distinct from those of M. kansasii. A library of M. tuberculosis H37Rv DNA was prepared by cloning Bam HI digest fragments into lambda 1059. Eight randomly selected clones, having multiple Bam HI sites, were used to probe restriction digests of DNA from the strains of the tuberculosis complex. Two of the cloned segments hybridized with homologous fragments in 4 different enzyme digests of all strains. With 2 clones, hybridization differed among the strains; however, some homologous sequences were detected. With 4 clones, efficient hybridization occurred only with M. tuberculosis H37Rv DNA. These hybridization results indicate that some regions of the chromosome are highly conserved among members of the tuberculosis complex, whereas others are diverged. Selected DNA probes were useful in detecting differences among strains of the tuberculosis complex.
Networks and epidemic models (2005)

Networks and the epidemiology of directly transmitted infectious diseases are fundamentally linked. The foundations of epidemiology and early epidemiological models were based on population wide random-mixing, but in practice each individual has a finite set of contacts to whom they can pass infection; the ensemble of all such contacts forms a 'mixing network'. Knowledge of the structure of the network allows models to compute the epidemic dynamics at the population scale from the individual-level behaviour of infections. Therefore, characteristics of mixing networks-and how these deviate from the random-mixing norm-have become important applied concerns that may enhance the understanding and prediction of epidemic patterns and intervention measures. Here, we review the basis of epidemiological theory (based on random-mixing models) and network theory (based on work from the social sciences and graph theory). We then describe a variety of methods that allow the mixing network, or an approximation to the network, to be ascertained. It is often the case that time and resources limit our ability to accurately find all connections within a network, and hence a generic understanding of the relationship between network structure and disease dynamics is needed. Therefore, we review some of the variety of idealized network types and approximation techniques that have been utilized to elucidate this link. Finally, we look to the future to suggest how the two fields of network theory and epidemiological modelling can deliver an improved understanding of disease dynamics and better public health through effective disease control.
Prolonged proliferative response of smooth muscle cells after experimental intravascular stenting (1995)

The purpose of this experimental in vivo study was to determine the time course of smooth muscle cell proliferation early and late after intravascular stenting compared to conventional balloon angioplasty in normal vessels. A balloon expandable 2.0 mm tantalum Strecker stent was placed in the right carotid artery of 33 male New Zealand White rabbits after they had been fed a 0.5% cholesterol diet for 28 days. In addition, balloon angioplasty was performed in 27 of the animals; 19 contralateral vessels served as controls without treatment. The vessels were excised at 7, 14, 28, 42 or 90 days after treatment. During the final 18 h before the rabbits were killed, bromodeoxyuridine (BrdU) was applied and proliferating cells were detected by using a monoclonal antibody against BrdU. In histological cross sections the proportion of cells undergoing DNA synthesis was determined. Analysis was performed separately in the intimal and medial layers. Additionally, the area adjacent to the stent wire was compared with the intermediate area. Smooth muscle cells were identified by alpha-actin staining. Intimal wall thickness increased from 23 +/- 28 microns (control group without intervention) to 323 +/- 84 microns within 42 days after stenting (P < 0.01), and to 81 +/- 82 microns at day 42 after balloon angioplasty (P < 0.05). However, between 42 and 90 days following stent implantation a significant (P < 0.05) decrease in neointimal thickness was observed (90 days: 215 +/- 15 microns).(ABSTRACT TRUNCATED AT 250 WORDS)
INVESTIGATION OF THE MECHANISM OF DRUG-INDUCED AUTOIMMUNE HEMOLYTIC ANEMIA IN CYNOMOLGUS MONKEYS ELICITED BY A REPEATED-DOSE OF A HUMANIZED MONOCLONAL ANTIBODY DRUG (2003)

We investigated the mechanism of hemolytic anemia detected in a repeated-dose toxicity study using cynomolgus monkeys that were treated with a humanized antibody drug. This drug was an IgG1 monoclonal antibody (MoAb) that binds to the human HM1.24 antigen named anti-HM1.24 MoAb. The presence of the HM1.24 antigen on the erythrocyte membranes and the erythrocyte agglutination following the addition of anti-HM1.24 MoAb was examined. In addition, an indirect Coombs' test, a hemolysis assay and the measurement of anti-single stranded-DNA antibodies were performed using test animal serum or plasma. The specific binding of FITC- and 125I-labeled anti-HM1.24 MoAb to the erythrocyte membrane was not observed. HM1.24 antigen was not identified on the erythrocyte membranes. However, a high concentration (more than 713 microg/mL) of anti-HM1.24 MoAb hemagglutinated the erythrocyte suspensions. The cause of this agglutination was unclear, but it is assumed that the non-specific binding and/or adhesion caused the direct agglutination. In the examination using test serum from the anemic monkeys, a positive reaction in the indirect Coombs' test was noted. Moreover, in these Coombs' test-positive animals, the production of anti-single stranded-DNA antibodies was sequentially increased. In the female monkey sacrificed in extremis due to severe anemia, an in vitro hemolytic reaction was detected attributable to complement activation. From these results, the hemolytic anemia detected in the repeated-dose toxicity study was diagnosed as a drug-induced autoimmune hemolytic anemia (AIHA) and the primary cause was assumed to be production of IgG class anti-erythrocyte autoantibodies.
Increased F-18 FDG Accumulation in an Acute Fracture (1994)

Markedly increased FDG uptake was noted in a 2-week-old fracture of the clavicle and scapula in a 24-year-old man. This finding emphasizes the need to consider benign etiologies such as trauma for focally increased FDG accumulation in bone.
The Requirement of Membrane Lymphotoxin for the Presence of Dendritic Cells in Lymphoid Tissues (1999)

Although several cytokines, including tumor necrosis factor (TNF), can promote the growth of dendritic cells (DCs) in vitro, the cytokines that naturally regulate DC development and function in vivo have not been well defined. Here, we report that membrane lymphotoxin (LT), instead of TNF, regulates the migration of DCs in the spleen. LTalpha(-/-) mice, lacking membrane LTalpha/beta and LTalpha(3), show markedly reduced numbers of DCs in the spleen. Unlike wild-type mice and TNF(-/-) mice that have densely clustered DCs in the T cell zone and around the marginal zone, splenic DCs in LTalpha(-/-) mice are randomly distributed. The reduced number of DCs in lymphoid tissues of LTalpha(-/-) mice is associated with an increased number of DCs in nonlymphoid tissues. The number of splenic DCs in LTalpha(-/-) mice is restored when additional LT-expressing cells are provided. Blocking membrane LTalpha/beta in wild-type mice markedly diminishes the accumulation of DCs in lymphoid tissues. These data suggest that membrane LT is an essential ligand for the presence of DCs in the spleen. Mice deficient in TNF receptor, which is the receptor for both soluble LTalpha(3) and TNF-alpha(3) trimers, have normal numbers of DCs. However, LTbetaR(-/-) mice show reduced numbers of DCs, similar to the mice lacking membrane LT alpha/beta. Taken together, these results support the notion that the signaling via LTbetaR by membrane LTalpha/beta is required for the presence of DCs in lymphoid tissues.
Toxicological and Pharmacokinetic Properties of Chemically Modified siRNAs Targeting p53 RNA Following Intravenous Administration (2012)

We report the toxicological and pharmacokinetic properties of the synthetic, small interfering RNA I5NP following intravenous administration in rodents and nonhuman primates. I5NP is designed to act via the RNA interference (RNAi) pathway to temporarily inhibit expression of the pro-apoptotic protein p53 and is being developed to protect cells from acute ischemia/reperfusion injuries such as acute kidney injury that can occur during major cardiac surgery and delayed graft function that can occur following renal transplantation. Following intravenous administration, I5NP was very rapidly cleared from plasma was distributed predominantly to the kidney, with very low levels in liver and other tissues. Doses of 800 mg/kg I5NP in rodents, and 1,000 mg/kg I5NP in nonhuman primates, were required to elicit adverse effects, which in the monkey were isolated to direct effects on the blood that included a sub-clinical activation of complement and slightly increased clotting times. In the rat, no additional adverse effects were observed with a rat analogue of I5NP, indicating that the effects likely represent class effects of synthetic RNA duplexes rather than toxicity related to the intended pharmacologic activity of I5NP. Taken together, these data support clinical testing of intravenous administration of I5NP for the preservation of renal function following acute ischemia/reperfusion injury.
Random lasing in bone tissue (2010)

Owing to the low-loss and high refractive index variations derived from the basic building block of bone structure, we, for the first time to our knowledge, demonstrate coherent random lasing action originated from the bone structure infiltrated with laser dye, revealing that bone tissue is an ideal biological material for random lasing. Our numerical simulation shows that random lasers are extremely sensitive to subtle structural changes even at nanoscales and can potentially be an excellent tool for probing nanoscale structural alterations in real time as a novel spectroscopic modality.
On the optimization criteria used in two-view motion analysis (1998)

The three best-known criteria in two-view motion analysis are based, respectively, on the distances between points and their corresponding epipolar lines, on the gradient-weighted epipolar errors, and on the distances between points and the re-projections of their reconstructed points. The last one has a better statistical interpretation, but is significantly slower than the first two. The author shows that, given a reasonable initial guess of the epipolar geometry, the last two criteria are equivalent when the epipoles are at infinity, and differ from each other only a little even when the epipoles are in the image, as shown experimentally. The first two criteria are equivalent only when the epipoles are at infinity and when the observed object/scene has the same scale in the two images. This suggests that the second criterion is sufficient in practice because of its computational efficiency. Experiments with several thousand computer simulations and four sets of real data confirm the analysis.