gebhart/patrepeval huggingface dataset:
Unexpected Effect of Matrix Metalloproteinase Down-Regulation on Vascular Intravasation and Metastasis of Human Fibrosarcoma Cells Selected In vivo for High Rates of Dissemination (2005)

The human tumor/chick embryo model involving grafting of human HT-1080 fibrosarcoma cells on the chorioallantoic membrane was used in conjunction with quantitative real-time Alu PCR to select in vivo a pair of isogenic cell lines (HT-hi/diss and HT-lo/diss), dramatically differing in their ability to disseminate from the primary tumor (i.e., intravasate into the chorioallantoic membrane vasculature and metastasize to the lungs). During an immunohistochemical time course study, HT-hi/diss cells were sequentially visualized having escaped from the primary tumors, engaged with the blood vessels, and eventually observed inside the chorioallantoic membrane capillaries, thus reflecting early intravasating events. In contrast, HT-lo/diss cells seemed restricted to their primary tumor. Importantly, after i.v. inoculation, both variants arrested, extravasated, and proliferated in host tissues with similar efficiencies, highlighting that the observed earlier events at the periphery of the primary tumor could account for their differential dissemination. In a mechanistic probing of these events, we determined that HT-hi/diss intravasation was sensitive to a broad-range matrix metalloproteinase (MMP) inhibitor. To analyze the possible role of individual MMPs, membrane-bound MMP-14 and secreted MMP-9 were individually down-regulated in HT-hi/diss cells with their corresponding small interfering RNAs. Despite efficient down-regulation of MMP-14, neither intravasation nor metastasis of HT-hi/diss cells was affected significantly. However, a substantial down-regulation of MMP-9 was accompanied by a surprising 3-fold increase in intravasation and metastasis. The results emphasize a rising awareness that targeting certain MMPs might result in an enhanced malignancy, exemplified herein at the intravasation level as this step of the metastatic cascade is dissected and quantified.
Exposure to Acute Stress Induces Brain Interleukin-1β Protein in the Rat (1998)

Peripheral immune stimulation such as that provided by lipopolysaccharide (LPS) has been reported to increase brain levels of IL-1beta mRNA, immunoreactivity, and bioactivity. Stressors produce many of the same neural and endocrine responses as those that follow LPS, but the impact of stressors on brain interleukin-1beta (IL-1beta) has not been systematically explored. An ELISA designed to detect IL-1beta was used to measure levels of IL-1beta protein in rat brain. Brain IL-1beta was explored after exposure to inescapable shock (IS; 100 1.6 mA tail shocks for 5 sec each) and LPS (1 mg/kg) as a positive control. Rats were killed either immediately or 2, 7, 24, or 48 hr after IS. Brains were dissected into hypothalamus, hippocampus, cerebellum, posterior cortex, and nucleus tractus solitarius regions. LPS produced widespread increases in brain IL-1beta, but IS did not. Adrenal glucocorticoids are known to suppress IL-1beta production in both the periphery and brain. Thus, it was possible that the stressor did provide stimulus input to the brain IL-1beta system(s), but that the production of IL-1beta protein was suppressed by the rapid and prolonged high levels of glucocorticoids produced by IS. To test this possibility rats were adrenalectomized or given sham surgery, with half of the adrenalectomized rats receiving corticosterone replacement to maintain basal corticosterone levels. IS produced large increases in brain IL-1beta protein in the adrenalectomized subjects 2 hr after stress, whether basal corticosterone levels had been maintained. Thus elimination of the stress-induced rise in corticosterone unmasked a robust and widespread increase in brain IL-1beta.
Distributed Robust Receding Horizon Control for Multivehicle Guidance (2007)

This paper presents a new distributed robust model predictive control algorithm for multivehicle trajectory optimization and demonstrates the approach with numerical simulations and multivehicle experiments. The technique builds on the robust-safe-but-knowledgeable (RSBK) algorithm, which is developed in this paper for the multivehicle case. RSBK uses constraint tightening to achieve robustness to external disturbances, an invariant set to ensure safety in the presence of changes to the environment, and a cost-to-go function to generate an intelligent trajectory around known obstacles. The key advantage of this RSBK algorithm is that it enables the use of much shorter planning horizons while still preserving the robust feasibility guarantees of previously proposed approaches. The second contribution of this paper is a distributed version of the RSBK algorithm, which is more suitable for real-time execution. In the distributed RSBK (DRSBK) algorithm, each vehicle only optimizes for its own decisions by solving a subproblem of reduced size, which results in shorter computation times. Furthermore, the algorithm retains the robust feasibility guarantees of the centralized approach while requiring that each agent only have local knowledge of the environment and neighbor vehicles' plans. This new approach also facilitates the use of a significantly more general implementation architecture for the distributed trajectory optimization, which further decreases the delay due to computation time.
Localization of sucrose synthase activity in developing maize kernels by in situ enzyme histochemistry (1998)

Sucrose synthase is usually localized by immunocytochemistry, but this method does not show the actual activity of the localized enzyme. A histochemical assay is presented here showing the activity of sucrose synthase by tetrazolium salt precipitation on sections of developing maize kernels. The advantages of the assay are a high sensitivity for low amounts of active sucrose synthase and the independence of specific antibodies. In this study the activity of endosperm sucrose synthase is shown to move gradually from the apical part of the endosperm to the basal endosperm during kernel development. This shift in sucrose synthase activity correlates well with the localization of starch synthesis during kernel development. The assay also shows the early loss of activity in the aleurone layer bordering the embryo, and a loss of activity in the apical aleurone during the final stage of kernel development while the enzyme was still found by immunocytochemistry. This is in contrast to a high sucrose synthase activity in the epithelium of the scutellum, where hardly any labelling was found with antibodies against maize sucrose synthase. Low sucrose synthase activities were found in the pericarp and pedicel parenchyma. Possible functions of the high and low activity patterns in the developing maize kernels and differences between the enzyme assay and immunocytochemistry are discussed.
How I treat refractory CLL (2005)

Therapy for patients with chronic lymphocytic leukemia (CLL) has greatly changed over the past few years. After years of stagnation, with treatment revolving around the use of rather ineffective drugs such as alkylators, many patients are now being treated with more effective agents such as purine analogs either alone or combined with other drugs and/or monoclonal antibodies. Treatment of patients refractory to these treatments is particularly challenging and should be decided only upon a careful evaluation of the disease, patient characteristics, and prognostic factors. Refractory disease should be clearly separated from relapsing disease. The only curative therapy for patients with CLL, including those with refractory disease, is allogeneic stem cell transplantation. However, the use of allogeneic transplantation is limited because of the advanced age of most patients and the high transplant-related mortality (TRM). Transplants with nonmyeloablative regimens may reduce TRM and allow more patients to receive transplants more safely. For patients in whom an allogeneic transplantation is not feasible or in whom it is deemed inappropriate, participation in phase 2 trials should be encouraged. Finally, to investigate mechanisms to overcome resistance to therapy in CLL and to identify patients that might gain benefit from early, intensive therapies (eg, based on biologic markers) constitute a challenge that needs active investigation.
Distinct Clonal Ig Diversification Patterns in Young Appendix Compared to Antigen-Specific Splenic Clones (2002)

The young rabbit appendix is a dynamic site for primary B cell repertoire development. To study diversification patterns during clonal expansion, we collected single appendix B cells from 3- to 9-wk-old rabbits and sequenced rearranged H and L chain genes. Single cells obtained by hydraulic micromanipulation or laser capture microdissection were lysed, PCR amplified, and products directly sequenced. Gene conversion-like changes occurred in rearranged H and L chain sequences by 3-4 wk of age. Somatic mutations were found in the D regions that lack known conversion donors and probably also occurred in the V genes. A few small sets of clonally related appendix B cells were found at 3-5 wk; by 5.5 wk, some larger clones were recovered. The diversification patterns in the clones from appendix were strikingly different from those found previously in splenic germinal centers where an immunizing Ag was driving the expansion and selection process toward high affinity. Clonally related appendix B cells developed different amino acid sequences in each complementarity-determining region (CDR) including CDR3, whereas dominant clones from spleen underwent few changes in CDR3. The variety of combining sites generated by diversification within individual clones suggests that at least some clonal expansion and selection, known to require normal gut flora, may be driven through indirect effects of microbial components rather than solely by their recognition as specific foreign Ags. This diversity of combining sites within B cell clones supports the proposed role of appendix in generating the preimmune repertoire.
A novel 5′-iodonucleoside allows efficient nonenzymatic ligation of single-stranded and duplex DNAs (1997)

A new iodothymidine phosphoramidite enables the placement of a 5'-iodide into oligonucleotides; the iodide is stable to ammonia deprotection and allows nonenzymatic ligations of DNA.
Quantification of high-density-lipoprotein cholesterol by precipitation with phosphotungstic acid/MgCl2. (1983)

We evaluated the use of a modified phosphotungstic acid/MgCl2 precipitation procedure for the precipitation of apolipoprotein B-containing lipoproteins. Precipitation of these lipoproteins [very-low- and low-density lipoproteins, and lipoprotein (a)] is complete, with negligible coprecipitation of high-density lipoprotein subfractions (HDL1, HDL2, HDL3), even in hypertriglyceridemic sera. In comparison with ultracentrifugation, the precipitation method yields, on the average, values that are 0.17 mmol/L lower for cholesterol values but almost identical for apolipoprotein A-I and phosphatidylcholine. Looking for delta 3,5-cholestadiene formed from cholesterol in the precipitation residue, we used "high-performance" liquid chromatography and "high-performance" thin-layer chromatography and found none.
MicroRNA-375 inhibits tumour growth and metastasis in oesophageal squamous cell carcinoma through repressing insulin-like growth factor 1 receptor (2011)

This study demonstrates that miR-375 has a strong tumour-suppressive effect through inhibiting the expression of IGF1R. The downregulation of miR-375, which is mainly caused by promoter methylation, is one of the molecular mechanisms involved in the development and progression of ESCC.
Affinity purification of the opioid receptor in NG 108‐15 cells using an avidin‐biotin system with a novel elution method (1986)

Affinity purification of the opioid receptor in NG 108-15 cells was carried out using an affinity resin based on the avidin-biotin interactions, but a new elution method was employed with a radioligand of sub-micromolar concentration. A synthesized biotinyl derivative of leucine-enkephalin has a high affinity for the delta-receptor, but the affinity was lowered 10-fold in the presence of avidin. The new elution method is based on this affinity decrease and resulted in a 100-fold purification over the initial crude materials in the single step. SDS-polyacrylamide gel electrophoresis of the purified receptor revealed three polypeptides of 58, 65 and 71 kDa as possible components of the delta-receptor.
Vasculae Reactions of Normal and Malignant Tissues in Vivo. I. Vascular Reactions of Mice to Wounds and to Normal and Neoplastic Transplants (1945)

Journal Article Vasculae Reactions of Normal and Malignant Tissues in Vivo. I. Vascular Reactions of Mice to Wounds and to Normal and Neoplastic Transplants Get access Glenn H. Algire, Glenn H. Algire Search for other works by this author on: Oxford Academic PubMed Google Scholar Harold W. Chalkley, Harold W. Chalkley Search for other works by this author on: Oxford Academic PubMed Google Scholar Frances Y. Legallais, Frances Y. Legallais Search for other works by this author on: Oxford Academic PubMed Google Scholar Helen D. Park Helen D. Park Search for other works by this author on: Oxford Academic PubMed Google Scholar JNCI: Journal of the National Cancer Institute, Volume 6, Issue 1, August 1945, Pages 73–85, https://doi.org/10.1093/jnci/6.1.73 Published: 01 August 1945
Electropore diameters, lifetimes, numbers, and locations in individual erythrocyte ghosts (1986)

Low light level video microscopy was used to study the diameter, lifetime, number, and location characteristics of electric field-induced pores (electropores) in erythrocyte ghosts. The diameter of electropores was probed by following the efflux of soluble fluorescent-tagged molecules out of the resealed ghost cytoplasmic compartments. After reaching a peak radius of at least 8.4 nm the electropores resealed within 200 ms to a radius of about 0.5 nm and stayed at that radius thereafter. Video sequences clearly show that pores are induced preferentially in the cathodal hemisphere. Pores induced in the hemisphere facing the positive electrode were either never greater than 0.5 nm in radius, much smaller in number if they were greater than 0.5 nm in radius, or shorter lived. Calculations indicated that an upper limit of 700 electropores were induced per membrane.
EXTRACTION OF SNAKEHEAD FISH [Ophiocephalus striatus (Bloch, 1793)] INTO FISH PROTEIN CONCENTRATE AS ALBUMIN SOURCE USING VARIOUS SOLVENT (2016)

Study aimed to determine the optimum solvent for extraction of soluble protein (albumin) and identify the chemical composition of snakehead fish protein concentrate. The method was experimental while the treatments were the variation of solvents: distilled water, HCl 0.1 M, and NaCl 0.9 %. Soluble protein (albumin) and yield parameters analyzed by using completely randomized design (CRD) which consist three treatments and four replications, the other parameters were described descriptively. The result showed that the highest soluble protein (albumin) (7.65 %) was produced by HCl 0.1 M solvent with 2.55 % yield, 10.76 % dry basis moisture content, 63.78 % total protein content, and 2.54 % fat content.
Development of a soup powder enriched with microencapsulated linseed oil as a source of omega‐3 fatty acids (2012)

Abstract The main objective of this study was to develop an optimized formulation of soup powder enriched with omega‐3 fatty acids. For this purpose, the process conditions for optimizing the microencapsulation efficiency (ME) of linseed oil by spray drying were determined using the Taguchi methodology with an orthogonal array L 4 (2 3 ). The effect of the variables on the ME, such as wall material concentration (25 and 30%), linseed oil concentration (14 and 20%), and wall material type (gum arabic GA; and a mixture maltodextrin/GA), was evaluated. The oxidative stability of the microcapsules obtained were determined by the Rancimat method, and a morphological and size characterization of microcapsules was performed by scanning electronic microscopy, confocal microscopy, and laser diffraction. The optimization of the soup formulation was reached by means of RSM, using the central composite design, two control factors (salty taste and consistency), and 11 design points. The hedonic test was applied to measure the acceptability of the optimized formulation. Chemical characterization of optimized soup and its oxidative stability were also evaluated. This study resulted in a healthy soup enriched with omega‐3 which was highly acceptable to consumers. Practical applications: Linseed oil is a healthy and nutritive oil, very rich in unsaturated fatty acids such as omega‐3. In addition to protecting the oil against oxidative damage, the microencapsulation of oils in a polymeric matrix (mainly polysaccharides and proteins) also offers the possibility of controlled release of the lipophilic functional ingredient and can be useful for the supplementation of foods with PUFA. The soup powder enriched with microencapsulated linseed oil as a source of omega‐3 formulated in this study will contribute to the development of foods according to the functionality requirements of current consumers and markets.
Current Overview of Allergens of Plant Pathogenesis Related Protein Families (2014)

Pathogenesis related (PR) proteins are one of the major sources of plant derived allergens. These proteins are induced by the plants as a defense response system in stress conditions like microbial and insect infections, wounding, exposure to harsh chemicals, and atmospheric conditions. However, some plant tissues that are more exposed to environmental conditions like UV irradiation and insect or fungal attacks express these proteins constitutively. These proteins are mostly resistant to proteases and most of them show considerable stability at low pH. Many of these plant pathogenesis related proteins are found to act as food allergens, latex allergens, and pollen allergens. Proteins having similar amino acid sequences among the members of PR proteins may be responsible for cross-reactivity among allergens from diverse plants. This review analyzes the different pathogenesis related protein families that have been reported as allergens. Proteins of these families have been characterized in regard to their biological functions, amino acid sequence, and cross-reactivity. The three-dimensional structures of some of these allergens have also been evaluated to elucidate the antigenic determinants of these molecules and to explain the cross-reactivity among the various allergens.
DNA bending by negative regulatory proteins: Gal and Lac repressors. (1989)

The ability of two negative regulatory proteins, Gal and Lac repressors, to induce DNA bending was tested by the respective cloning of gal and lac operator DNA sequences into a sensitive vector, pBend2. pBend2 can generate a large number of DNA fragments in each of which a cloned operator is present in circularly permuted positions along the length of the DNA. Gel electrophoresis of these DNA fragments individually complexed to a repressor shows that the Gal repressor bends both of the gal operators, OE and OI. Similarly, the Lac repressor induces a bend to a lac operator DNA. In each case, the center of the average bent segment is located at or close to the dyad symmetry axis of the operator sequence. In view of these findings, we discuss how these negative regulatory proteins may function by a more dynamic mechanism than was perceived previously.
Online but Accurate Inference for Latent Variable Models with Local Gibbs Sampling (2016)

We study parameter inference in large-scale latent variable models. We first propose an unified treatment of online inference for latent variable models from a non-canonical exponential family, and draw explicit links between several previously proposed frequentist or Bayesian methods. We then propose a novel inference method for the frequentist estimation of parameters, that adapts MCMC methods to online inference of latent variable models with the proper use of local Gibbs sampling. Then, for latent Dirich-let allocation,we provide an extensive set of experiments and comparisons with existing work, where our new approach outperforms all previously proposed methods. In particular, using Gibbs sampling for latent variable inference is superior to variational inference in terms of test log-likelihoods. Moreover, Bayesian inference through variational methods perform poorly, sometimes leading to worse fits with latent variables of higher dimensionality.
Multiwavelength DFB laser array transmitters for ONTC reconfigurable optical network testbed (1996)

We discuss the design, fabrication, and performance of experimental multiwavelength laser array transmitters that have been used in the reconfigurable optical network testbed for the Optical Network Technology Consortium (ONTC). The experimental four-node multiwavelength network testbed is SONET/ATM compatible. It has employed multiwavelength DFB laser arrays with 4 nm wavelength spacing for the first time. The testbed has demonstrated that multiwavelength DFB laser arrays are indeed practical and reproducible. For the DFB laser arrays used in such a network the precise wavelength spacing in the array and the absolute wavelength control are the most challenging tasks. We have obtained wavelength accuracy better than /spl plusmn/0.35 nm for all lasers, with some registered to better than /spl plusmn/0.2 nm. We have also studied the array yield of our devices and used wavelength redundancy to improve the array yield. Coupling efficiencies between -2.1 to -4.5 dB for each wavelength channel have been obtained. It is achieved by using specially designed lensed fiber arrays placed on a silicon V-grooved substrate to exactly match the laser spacing. The transmitter consisted of a multichip module containing a DFB laser array, an eight-channel driver array based on GaAs IC's, and associated RF circuitry.
Molecular Dynamics Simulation of the Ligand Binding Domain of Farnesoid X Receptor. Insights into Helix-12 Stability and Coactivator Peptide Stabilization in Response to Agonist Binding (2005)

The dynamic changes which take place in the ligand binding domain (LBD) of farneosid X receptor (FXR) in response to agonist binding and in the presence of coactivator peptides were studied with nanosecond time-scale molecular dynamics. Four different systems were analyzed, including the holo-LBD complexed with 6ECDCA, the holo-LBD in the presence of two coactivator peptides, and two artificial apo forms, with and without coactivator peptides. Our results revealed a detailed picture of the differential micro- and macromodifications occurring in the LBD in the presence or not of the agonist molecule and the coactivator peptides. In the apo simulation a major conformational change took place in the crucial helix 12, while the holo-LBD was globally stabilized by the ligand. When the coactivator peptides were included in the simulation, a clear agonist-induced stabilization was observed for the canonical peptide. Interestingly, the second peptide was released from the holo-LBD while it was kept bound in the apo simulation. The present results provide a molecular basis for the understanding the role played by the bile acid agonist in receptor stabilization and enhanced cofactor recruitments.