gebhart/patrepeval huggingface dataset:
Restriction-ligation-free (RLF) cloning: a high-throughput cloning method by in vivo homologous recombination of PCR products (2015)

In this study, we optimized a restriction-ligation-free (RLF) method to save time and cost of constructing multiple plasmids with the same gene insert, and examined the efficacy of RLF on high-throughput multi-plasmid cloning. This method utilizes the precise DNA repair and recombination systems within Escherichia coli, which allows to bypass the in vitro restriction and ligation enzyme reactions commonly included in routine cloning procedures. A homologous arm is linked to the 5'-end of the forward primer used to amplify both the target gene and vector. A different homologous arm is linked to the 5'-end of the reverse primer. Therefore, genes can be cloned into the vectors by homologous recombination after co-transformation of the amplified target gene and the linearized vector, which bear the same homologous arm on either end. More than twenty-four different plasmids were generated by this method, which uses two simple polymerase chain reaction steps. This method is highly efficient in cloning any gene of interest into any vector at any site without sequence constraints, as no restriction and ligation reactions are required.
Natural killer cell depletion enhances virus synthesis and virus-induced hepatitis in vivo. (1983)

The role of natural killer (NK) cells in the natural resistance of mice to infections by several viruses was examined. Mice were specifically depleted of NK cells by i.v. injection of rabbit antiserum to asialo GM1, a neutral glycosphingolipid present at high concentrations on the surface of NK cells. Control mice were left untreated or were injected with normal rabbit serum. Four to 6 hr later, these mice were infected with lymphocytic choriomeningitis virus (LCMV), mouse hepatitis virus (MHV), murine cytomegalovirus (MCMV), or vaccinia virus. The mice were sacrificed 3 days post-infection and assayed for virus in liver and spleen, spleen NK cell activity, and plasma interferon (IFN). All mice treated with anti-asialo GM1 antibody had drastically reduced NK cell-mediated lysis. Correlating with NK cell depletion, these mice had significantly higher (up to 500-fold) titers of MCMV, MHV, or vaccinia virus in their livers and spleens as compared to control mice. NK cell-depleted MCMV and MHV-infected mice had higher levels of plasma IFN than controls, correlating with the higher virus titers. These NK cell-depleted, virus-infected mice had more extensive hepatitis, assayed by the number of inflammatory foci in their livers, as compared to control virus-infected mice; these foci were also larger and contained more degenerating liver cells than those in control mice. In contrast to the results obtained with MHV, MCMV, and vaccinia virus, NK cell depletion had no effect on virus titers in the early stages of acute LCMV infection or during persistent LCMV infection. Mice depleted of NK cells had similar amounts of LCMV in their spleens and similar plasma IFN levels. Because this antibody to asialo GM1 does not impair other detectable immunologic mechanisms, these data support the hypothesis that NK cells act as a natural resistance mechanism to a number of virus infections, but suggest that their relative importance may vary from virus to virus.
Multiview Intrinsic Images of Outdoors Scenes with an Application to Relighting (2015)

We introduce a method to compute intrinsic images for a multiview set of outdoor photos with cast shadows, taken under the same lighting. We use an automatic 3D reconstruction from these photos and the sun direction as input and decompose each image into reflectance and shading layers, despite the inaccuracies and missing data of the 3D model. Our approach is based on two key ideas. First, we progressively improve the accuracy of the parameters of our image formation model by performing iterative estimation and combining 3D lighting simulation with 2D image optimization methods. Second, we use the image formation model to express reflectance as a function of discrete visibility values for shadow and light, which allows to introduce a robust visibility classifier for pairs of points in a scene. This classifier is used for shadow labeling, allowing to compute high-quality reflectance and shading layers. Our multiview intrinsic decomposition is of sufficient quality to allow relighting of the input images. We create shadow-caster geometry which preserves shadow silhouettes and, using the intrinsic layers, we can perform multiview relighting with moving cast shadows. We present results on several multiview datasets, and show how it is now possible to perform image-based rendering with changing illumination conditions.
Endotoxin-induced serum factor that stimulates gamma interferon production (1989)

Serum from Mycobacterium bovis BCG-infected mice that had been challenged with lipopolysaccharide (LPS) exhibited a marked ability to induce gamma interferon (IFN-gamma) in cultures of spleen cells of normal mice in the presence of interleukin-2 (IL-2). The inducing activity became detectable in the circulatory system about 90 min after LPS challenge, disappeared at around 5 h, and was observable upon 640x dilution of the serum. Addition of monoclonal anti-IL-2 receptor antibody to the culture inhibited the induction by the serum. The activity induced high levels of IFN-gamma even in nylon wool-nonadherent cells, while concanavalin A failed to do so. Serum from uninfected mice challenged with LPS contained no such activity. The molecular weight of the active substance, estimated by gel filtration, was about 70,000. There were pronounced differences among mouse strains in the activities of the sera prepared, which paralleled the amounts of IFN-gamma produced in vivo. However, the levels of IFN-gamma produced in whole spleen cells and in nylon wool-nonadherent cells from mice of various strains were the same when stimulated with competent serum. These results indicate the existence of an unidentified factor that induces IFN-gamma in cooperation with IL-2 in macrophage-depleted splenocytes. They also suggest that IFN-gamma production in vivo is not genetically controlled at the lymphocyte level but, rather, at the level of synthesis of the unknown factor.
HLA-A*3101 and Carbamazepine-Induced Hypersensitivity Reactions in Europeans (2011)

The presence of the HLA-A*3101 allele was associated with carbamazepine-induced hypersensitivity reactions among subjects of Northern European ancestry. The presence of the allele increased the risk from 5.0% to 26.0%, whereas its absence reduced the risk from 5.0% to 3.8%. (Funded by the U.K. Department of Health and others.).
Acidic Residues Important for Substrate Binding and Cofactor Reactivity in Eukaryotic Ornithine Decarboxylase Identified by Alanine Scanning Mutagenesis (1995)

Ornithine decarboxylases from Trypanosoma brucei, mouse, and Leishmania donovani share strict specificity for three basic amino acids, ornithine, lysine, and arginine. To identify residues involved in this substrate specificity and/or in the reaction chemistry, six conserved acidic resides (Asp-88, Glu-94, Asp-233, Glu-274, Asp-361, and Asp-364) were mutated to alanine in the T. brucei enzyme. Each mutation causes a substantial loss in enzyme efficiency. Most notably, mutation of Asp-361 increases the Km for ornithine by 2000-fold, with little effect on kcat, suggesting that this residue is an important substrate binding determinant. Mutation of the only strictly conserved acidic residue, Glu-274, decreases kcat 50-fold; however, substitution of N-methylpyridoxal-5'-phosphate for pyridoxal-5'-phosphate as the cofactor in the reaction restores the kcat of E274A to wild-type levels. These data demonstrate that Glu-274 interacts with the protonated pyridine nitrogen of the cofactor to enhance the electron withdrawing capability of the ring, analogous to Asp-222 in aspartate aminotransferase (Onuffer, J. J., and Kirsch, J. F. (1994) Protein Eng. 7, 413-424). Eukaryotic ornithine decarboxylase is a homodimer with two shared active sites. Residues 88, 94, 233, and 274 are contributed to each active site from the same subunit as Lys-69, while residues 361 and 364 are part of the Cys-360 subunit.
Biology of the RANKLâ€“RANKâ€“OPG System in Immunity, Bone, and Beyond (2014)

Discovery and characterization of the cytokine receptor-cytokine-decoy receptor triad formed by receptor activator of nuclear factor kappa-B ligand (RANKL)-receptor activator of NF-κB (RANK)-osteoprotegerin (OPG) have led not only to immense advances in understanding the biology of bone homeostasis, but have also crystalized appreciation of the critical regulatory relationship that exists between bone and immunity, resulting in the emergence of the burgeoning field of osteoimmunology. RANKL-RANK-OPG are members of the tumor necrosis factor (TNF) and TNF receptor superfamilies, and share signaling characteristics common to many members of each. Developmentally regulated and cell-type specific expression patterns of each of these factors have revealed key regulatory functions for RANKL-RANK-OPG in bone homeostasis, organogenesis, immune tolerance, and cancer. Successful efforts at designing and developing therapeutic agents targeting RANKL-RANK-OPG have been undertaken for osteoporosis, and additional efforts are underway for other conditions. In this review, we will summarize the basic biology of the RANKL-RANK-OPG system, relate its cell-type specific functions to system-wide mechanisms of development and homeostasis, and highlight emerging areas of interest for this cytokine group.
Two-fluid flow in sedimentary rock: simulation, transport and complexity (1997)

The macroscopic properties and structure of the flow of two immiscible fluids through Fontainebleau sandstone are studied by numerical simulation. The pore space geometry was obtained by X-ray microtomography (Kinney et al . 1993) and the numerical simulations were performed by a new lattice-gas cellular automaton method (Olson &amp; Rothman 1995). We first validate the numerical method by showing that the drag on a cubic array of spherical drops matches theoretical predictions. As a further test, we present a comparison between computed relative permeability and experimental measurements on the same rock. We then present a study of fluid–fluid coupling; we find that it is significant, and that it appears to be reciprocal: the flux of one fluid due to forcing on the other is the same, regardless of which fluid is forced. Lastly, we characterize the complexity and organization of the flow by means of a statistical parameter, the skewness of the distribution of local velocities.
A Novel Polymorphism at Codon 333 of Human Immunodeficiency Virus Type 1 Reverse Transcriptase Can Facilitate Dual Resistance to Zidovudine and l -2′,3′-Dideoxy-3′-Thiacytidine (1998)

ABSTRACT Recent clinical trials examining 3′-azido-3′-deoxythymidine (AZT, zidovudine, or Retrovir) combined with l -2′,3′-dideoxy-3′-thiacytidine (3TC or lamivudine) have shown that combination therapy with these nucleoside analogs affords significant virological and clinical benefits. The addition of 3TC to AZT delays AZT resistance in therapy-naive patients and can restore viral AZT susceptibility in patients who previously received AZT alone. In some AZT-experienced patients, the virological response to AZT-3TC therapy is not sustained and virus resistant to both drugs can be identified. To gain insight into the possible mechanism of dual resistance, we studied a recently described variant resistant to both AZT and 3TC and obtained by simultaneous passage of an AZT-resistant clinical isolate in cell culture with AZT and 3TC. Genetic mapping and site-directed mutagenesis experiments demonstrated that a polymorphism at codon 333 (Gly to Glu) of human immunodeficiency virus type 1 reverse transcriptase (RT) was critical in facilitating dual resistance in a complex background of AZT and 3TC resistance mutations. To assess the potential clinical relevance of RT codon 333 changes, we studied dually resistant viruses from patients taking AZT and 3TC. Genetic mapping of RT molecular clones derived from patients’ plasma samples demonstrated that in some cases polymorphism at codon 333 was responsible for facilitating dual resistance.
Circulating Palmitoleate Strongly and Independently Predicts Insulin Sensitivity in Humans (2009)

Circulating palmitoleate strongly and independently predicts insulin sensitivity, suggesting that it plays an important role in the pathophysiology of insulin resistance in humans.
Prostate-Specific Antigen as a Serum Marker for Adenocarcinoma of the Prostate (1987)

To compare the clinical usefulness of the serum markers prostate-specific antigen (PSA) and prostatic acid phosphatase (PAP), we measured them by radioimmunoassay in 2200 serum samples from 699 patients, 378 of whom had prostatic cancer. PSA was elevated in 122 of 127 patients with newly diagnosed, untreated prostatic cancer, including 7 of 12 patients with unsuspected early disease and all of 115 with more advanced disease. The PSA level increased with advancing clinical stage and was proportional to the estimated volume of the tumor. The PAP concentration was elevated in only 57 of the patients with cancer and correlated less closely with tumor volume. PSA was increased in 86 percent and PAP in 14 percent of the patients with benign prostatic hyperplasia. After radical prostatectomy for cancer, PSA routinely fell to undetectable levels, with a half-life of 2.2 days. If initially elevated, PAP fell to normal levels within 24 hours but always remained detectable. In six patients followed postoperatively by means of repeated measurements, PSA--but not PAP--appeared to be useful in detecting residual and early recurrence of tumor and in monitoring responses to radiation therapy. Prostate massage increased the levels of both PSA and PAP approximately 1.5 to 2 times. Needle biopsy and transurethral resection increased both considerably. We conclude that PSA is more sensitive than PAP in the detection of prostatic cancer and will probably be more useful in monitoring responses and recurrence after therapy. However, since both PSA and PAP may be elevated in benign prostatic hyperplasia, neither marker is specific.
Analysis of 3D Motion Recognition using Meta-analysis for Interaction (2010)

Most of the research on three-dimensional interaction field have showed different accuracy in terms of sensing, mode and method. Furthermore, implementation of interaction has been a lack of consistency in application field. Therefore, this study is to suggest research trends of three-dimensional interaction using meta-analysis. Searching relative keyword in database provided with 153 domestic papers and 188 international papers covering three-dimensional interaction. Analytical coding tables determined 18 domestic papers and 28 international papers for analysis. Frequency analysis was carried out on method of action, element, number, accuracy and then verified accuracy by effect size of the meta-analysis. As the results, the effect size of sensor-based was higher than vision-based, but the effect size was extracted to small as 0.02. The effect size of vision-based using hand motion was higher than sensor-based using band motion. Therefore, implementation of three-dimensional sensor-based interaction and vision-based using hand motions more efficient. This study was significant to comprehensive analysis of three-dimensional motion recognition for interaction and suggest to application directions of three-dimensional interaction.
v-Src-induced degradation of focal adhesion kinase during morphological transformation of chicken embryo fibroblasts. (1995)

Morphological transformation of cells by the v-Src tyrosine kinase is incompletely understood. However, it is independent of nuclear functions and probably involves phosphorylation of targets associated with the cytoskeleton and focal adhesions, structures which tether the cytoskeleton to the points of cell attachment. v-Src activity both stimulates tyrosine phosphorylation of a tyrosine kinase present in focal adhesions (focal adhesion kinase or pp125FAK) and disrupts focal adhesions, leading to cell rounding and detachment. However, pp125FAK is also phosphorylated on tyrosine as a result of integrin stimulation which induces quite different biological consequences including the organisation of focal adhesions when cells spread on fibronectin (reviewed in Schaller and Parsons, 1993). To address this paradox, we examined changes in pp125FAK during activation and shut-off of temperature sensitive mutant v-Src proteins that induce varying degrees of transformation in chick embryo fibroblasts. An efficiently transforming v-Src mutant initially stimulated pp125FAK tyrosine phosphorylation, but induced subsequent pp125FAK degradation prior to the onset of cell rounding and detachment. v-Src mutants which are impaired in their ability to induce morphological transformation were much less efficient at inducing degradation of pp125FAK. Moreover, cell spreading during restitution of normal morphology did not require detectable tyrosine phosphorylation of pp125FAK, or its potential substrate paxillin, suggesting that pp125FAK may function more in the turnover of focal adhesions than in their assembly.
Extraction of visual features for lipreading (2002)

The multimodal nature of speech is often ignored in human-computer interaction, but lip deformations and other body motion, such as those of the head, convey additional information. We integrate speech cues from many sources and this improves intelligibility, especially when the acoustic signal is degraded. The paper shows how this additional, often complementary, visual speech information can be used for speech recognition. Three methods for parameterizing lip image sequences for recognition using hidden Markov models are compared. Two of these are top-down approaches that fit a model of the inner and outer lip contours and derive lipreading features from a principal component analysis of shape or shape and appearance, respectively. The third, bottom-up, method uses a nonlinear scale-space analysis to form features directly from the pixel intensity. All methods are compared on a multitalker visual speech recognition task of isolated letters.
Clinical and Laboratory Studies of KMcC Strain Live Attenuated Varicella Virus (1981)

Small-scale studies were carried out to test the KMcC strain varicella virus at various passage levels for clinical and serologic responses in order to find an optimal level of attenuation for vaccine purpose. Virus at passage 50 induced antibody responses, caused only minimal clinical reactions, and will be studied further. The clinical reactions to vaccine virus were very mild at all virus passage levels and were limited to mild transient fever and papular rash that became vesicular in a small proportion of individuals. The immune response to vaccination was accompanied by protection against natural challenge and antibody induced by vaccine virus persisted for at least 3.5 years, the longest period observed. Attenuation of virus appeared to be accompanied by alteration in the proportion of incomplete virus particles formed and by the degree of spontaneous release of virus from infected cells.
A short sequence in the p60src N terminus is required for p60src myristylation and membrane association and for cell transformation. (1984)

We have constructed mutants by using linker insertion followed by deletion in the region of cloned Rous sarcoma virus DNA coding for the N-terminal 9 kilodaltons of the src protein. Previous work implicated this region in the membrane association of the protein. The mutations had little effect on src tyrosine kinase activity. Substitution of a tri- or tetrapeptide for amino acids 15 to 27, 15 to 49, or 15 to 81 had little effect on the in vitro transforming capacity of the virus. Like wild-type p60src, the src proteins of these mutants associated with plasma membranes and were labeled with [3H]myristic acid. In contrast, a mutant whose src protein had the dipeptide Asp-Leu substituted for amino acids 2 to 81 and a mutant with the tripeptide Asp-Leu-Gly substituted for amino acids 2 to 15 were transformation defective, and the mutant proteins did not associate with membranes and were not labeled with [3H]myristic acid. These results suggest that amino acids 2 to 15 serve as an attachment site for myristic acid and as a membrane anchor. Since deletions including this region prevent transformation, and since tyrosine kinase activity is not diminished by the deletions, these results imply that target recognition is impaired by mutations altering the very N terminus, perhaps through their effect on membrane association.
The International Workshop on Meibomian Gland Dysfunction: Report of the Subcommittee on the Epidemiology of, and Associated Risk Factors for, MGD (2011)

Scientists have been interested in studying the secretions of the meibomian glands for many years, 1– 8 and diseases associated with the meibomian glands (e.g., cancers, posterior blepharitis) have been noted in the medical literature since at least the early part of the 20th Century. 9 –13 However, the term “meibomian gland dysfunction” (MGD) was only introduced by Korb and Henriquez in 1980. 14 The terminology “meibomian gland disease” was later introduced by Bron et al. 15 as an umbrella term to indicate any disease affecting the meibomian glands (see Definition and Classification). Although the etiology of MGD may differ from that of aqueous-deficient dry eye disease (which is due to insufficient lacrimal gland production), the two conditions share many clinical features, including symptoms of ocular surface irritation and visual fluctuation, altered tear film stability, and potential ocular surface compromise. When MGD is of sufficient degree, it may give rise to the second major subtype of dry eye disease, evaporative dry eye. 16 These subtypes are not mutually exclusive, as has been acknowledged. 16
Computational Validation of a 3-D Microwave Imaging System for Breast-Cancer Screening (2009)

The microwave imaging system currently being developed at the Technical University of Denmark is described and its performance tested on simulated data. The system uses an iterative Newton-based imaging algorithm for reconstructing the images in conjunction with an efficient method-of-moments solution of the associated forward scattering problem. A cylindrical multistatic antenna setup with 32 horizontally oriented antennas is used for collecting the data. It has been found that formulating the imaging algorithm in terms of the logarithm of the amplitude and the unwrapped phase of the measured signals improves its performance when compared to the more commonly used complex phasor formulation. This improvement is illustrated by imaging a simulated hemispherical breast model using both formulations. In addition to this, the importance of using the correct position and orientation of the antennas in the measurement system is shown by imaging the same breast model using a measurement setup in which the antennas are vertically oriented.