gebhart/patrepeval huggingface dataset:
Intratumoral bacteria may elicit chemoresistance by metabolizing anticancer agents (2017)

We recently reported that bacteria can be found within pancreatic ductal adenocarcinoma (PDAC) tumors. Some of these bacteria can metabolize and thereby inactivate the nucleoside analog gemcitabine. We demonstrated that the long isoform of the bacterial enzyme cytidine deaminase (CDD) mediates the metabolism of gemcitabine. The clinical effect of overcoming this potential mechanism of drug resistance has yet to be studied.
The evolution of A‐, F‐, and V‐type ATP synthases and ATPases: reversals in function and changes in the H<sup>+</sup>/ATP coupling ratio (2004)

Members of the FoF1, AoA1 and VoV1 family of ATP synthases and ATPases have undergone at least two reversals in primary function. The first was from a progenitor proton-pumping ATPase to a proton-driven ATP synthase. The second involved transforming the synthase back into a proton-pumping ATPase. As proposed earlier [FEBS Lett. 259 (1990) 227], these reversals required changes in the H+/ATP coupling ratio from an optimal value of about 2 for an ATPase function to about 4 for an ATP synthase function. The doubling of the ratio that occurred at the ATPase-to-Synthase transition was accomplished by duplicating the gene that encodes the nucleotide-binding catalytic subunits followed by loss of function in one of the genes. The halving of the ratio that occurred at the Synthase-to-ATPase transition was achieved by a duplication/fusion of the gene that encodes the proton-binding transporter subunits, followed by a loss of function in one half of the double-sized protein. These events allowed conservation of quaternary structure, while maintaining a sufficient driving force to sustain an adequate phosphorylation potential or electrochemical gradient. Here, we describe intermediate evolutionary steps and a fine-tuning of the H+/ATP coupling ratio to optimize synthase function in response to different environments. In addition, we propose a third reversal of function, from an ATPase back to an ATP synthase. In contrast to the first two reversals which required a partial loss in function, the change in coupling ratio required for the third reversal is explained by a gain in function.
Visualization of coupling in time series by order recurrence plots (2005)

We introduce a method to visualize dependencies between two time series by applying the concept of cross recurrence plots to the local ordinal structure. We derive a measure of the coupling strength which is robust against observational noise, nonlinear distortion of the amplitude, and low-frequency trends. Connections to the instantaneous phase and the determination of phase coupling of two coupled Rössler systems in the standard and funnel regimes are shown. An application to electroencephalogram data demonstrates that the method is robust with respect to artifacts.
<title>Strain effects in multilayers</title> (1997)

High stress levels can cause problems for both electronics and micromechanics. It is therefore important to characterize the stress and strain of the different mechanical layers used for processing. In order to predict the properties of a multilayered structure it is not sufficient to know the mechanical properties of each independent layer. The deposited layers may have a considerable effect on the mechanical properties of the underlying layer. This paper discusses the importance of the effect of each layer on underlying layers and on the total structure, using poly-silicon and silicon- nitride as the mechanical layers. The measurements show that at an anneal of 850 degrees Celsius the influence of nitride on the underlying poly is considerable. At an anneal of 1000 degrees Celsius this effect disappears. We also examined the stress in poly-nitride-poly layers in order to find out the influence of annealing in between the deposition of the layers. Measurements show that the temperature of the anneal is the dominant factor.
Effects of susceptibility variations on NMR measurements of diffusion (1991)

A pulsed-gradient spin-echo method has been used to measure the water self-diffusion coefficient in various media containing susceptibility variations arising from the presence of superparamagnetic iron oxide particles. These include aqueous suspensions, polyacrylamide gels, and rat livers. The results for each medium indicate that, contrary to intuition, the apparent diffusion coefficient decreases as the iron particle concentration increases. A simple theoretical model has been developed to interpret the data. This model relates the changes in apparent diffusion to the variance of the internal gradient distribution generated by the iron particles. A computer simulation of nuclei undergoing a random walk in an inhomogeneous medium was performed and the results provide qualitative confirmation of the experimental observations. The relevance of these phenomena to measurements of molecular diffusion in heterogeneous systems and their use to estimate internal gradient strengths are discussed.
ANTIBLASTIC PHENOMENA IN ACTIVE ACQUIRED IMMUNITY AND IN NATURAL IMMUNITY TO PNEUMOCOCCUS (1919)

The paper gives the results of a series of experiments made with a special technique for the purpose of testing whether or not so called antiblastic phenomena or bactericidal phenomena play any part in immunity to pneumococcus. The technique employed is that devised by the writer and consists in the isolation of single bacteria and their growth in hanging drops where growth can be continuously observed. From these experiments it may be concluded that: (1) Whole fresh blood, coagulated plasma, or serum of the immunized horse added directly to pneumococci, has considerable inhibiting action on the growth of pneumococci. The inhibiting effect of the fresh blood, coagulated plasma, or serum of a normal horse, however, is as marked as that of a horse highly immunized to pneumococci of the same type. This property, therefore, does not seem to be of importance in acquired immunity in the horse. No such property has been demonstrated in whole fresh rabbit blood. (2) It has been impossible to demonstrate that antiblastic phenomena play any part in natural immunity to pneumococcus, at least as far as the immunity of the pigeon is concerned. The whole fresh blood of the pigeon under the conditions employed exhibits no inhibiting action on the growth rate of pneumococci.
IL‐1β induces COX2, MMP‐1, ‐3 and ‐13, ADAMTS‐4, IL‐1β and IL‐6 in human tendon cells (2003)

Overuse injuries and trauma in tendon often involve acute or chronic pain and eventual matrix destruction. Anti-inflammatory drugs have been used as a treatment, however, the cellular and molecular mechanisms of the destructive processes in tendon are not clearly understood. It is thought that an inflammatory event may be involved as an initiating factor. Mediators of the inflammatory response include cytokines released from macrophages and monocytes. Interleukin-1 beta (IL-1 beta) is a candidate proinflammatory cytokine that is active in connective tissues such as bone and cartilage. We hypothesized that tendon cells would express receptors and respond to IL-1 beta in an initial "molecular inflammation" cascade, that is, connective tissue cell expression of cytokines that induce matrix destructive enzymes. This cascade results in expression of matrix metalloproteinases (MMPs) and aggrecanases that may lead to matrix destruction. Normal human tendon cells from six patients were isolated, grown to quiescence and treated with human recombinant IL-1 beta in serum-free medium for 16 h. Total RNA was isolated and mRNA expression assessed by semiquantitative RT-PCR. IL-1 beta (1 nM) induced mRNAs for cyclooxygenase 2 (COX2), MMP-1, -3, -13 and aggrecanase-1 as well as IL-1 beta and IL-6, whereas mRNAs for COX1 and MMP-2 were expressed constitutively. The IL-1 beta-treated tendon cells released prostaglandin E(2) (PGE(2)) in the medium, suggesting that the inducible COX2 catalyzed this synthesis. Induction of PGE(2) was detectable at 10 pM IL-1 beta. IL-1 beta also stimulated MMP-1 and -3 protein secretion. Induction of MMP-1 and -3 was detectable at 10 pM IL-1 beta. Post-injury or after some other inciting events, exogenous IL-1 beta released upon bleeding or as leakage of local capillaries may drive a proinflammatory response at the connective tissue cell level. The resulting induction of COX2, MMP-1 and -3 may underscore a potential for nonlymphocyte-mediated cytokine production of MMPs that causes matrix destruction and a loss of tendon biomechanical properties. Endogenous IL-1 beta might contribute to the process through a positive feedback loop by stimulating expression and accumulation of MMPs in the tendon matrix.
Effects of the calcium influx inhibitor carboxyamido-triazole on the proliferation and invasiveness of human prostate tumor cell lines (1996)

Aberrant cellular signaling is a central feature of malignant cells and a potential target for anti-cancer therapy. Carboxyamido-triazole (CAI) is a calcium influx inhibitor that alters calcium-sensitive signal transduction pathways and suppresses the proliferative and metastatic potential of malignant cells. We have examined the effects of CAI on several tumor-associated parameters in human prostate cancer cell lines to evaluate the potential of CAI as a signal-transduction therapy agent for advanced-stage prostate cancer. Measuring anchorage-dependent cell growth, continuous application of CAI inhibited the growth of DU-145, PPC-1, PC3 and LNCaP tumor cells with 50% inhibitory concentrations ranging 10-30 microM. Direct cell enumeration assays revealed that the growth-suppressing activity of CAI toward DU-145 cells was reversible, indicating a cytostatic effect of the drug on tumor cells. The drug also inhibited the proliferation of several immortalized human prostatic epithelial cell lines. The proliferation of HaCaT- and RHEK-1-immortalized keratinocyte cell lines was relatively insensitive to CAI. Additionally, invasion by DU-145, PC3 and PPC-1 cells through Matrigel in vitro was reduced approximately 60-70% by 10 microM CAI. Other cellular effects of CAI included an attenuation of the elevation of intracellular free calcium in response to bombesin and carbachol in PC3 cells and a marked dose-dependent inhibition of prostate-specific antigen secretion in LNCaP cell cultures.
<i>Streptococcus mutans</i> Genes That Code for Extracellular Proteins in <i>Escherichia coli</i> K-12 (1982)

Chromosomal DNA from Streptococcus mutans 6715 (serotype g) was cloned into Escherichia coli K-12 by using the cosmid pJC74 cloning vector and a bacteriophage lambda in vitro packaging system. Rabbit antiserum against S. mutans extracellular proteins was used for immunological screening of the clone bank. Twenty-one clones produced weak to strong precipitin bands around the colonies, but only after the lambda c1857 prophage was induced by being heated to lyse the E. coli cells. None of the clones expressed enzyme activity for several known S. mutans extracellular enzymes. One of these clones contained a 45-kilobase recombinant plasmid designated pYA721. An 8.5-kilobase fragment of S. mutans DNA from pYA721 was isolated and recloned into the BamHI restriction site of the plasmid vector pACYC184 to construct pYA726. pYA726 contained all, or nearly all, of the gene for a surface protein antigen (the spaA protein) of S. mutans 6715. This was deduced from immunological studies in which extracts of cells harboring pYA726 reacted with antisera against both purified 6715 spaA protein (about 210,000 daltons) and the immunologically similar antigen I/II of serotype c strains of S. mutans. In addition, the S. mutans spaA protein was found to possess at least one antigenic determinant not present on the protein specified by pYA726. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis of E. coli clone extracts revealed that pYA726 produced a polypeptide with a molecular mass of about 180,000 daltons which was predominantly found in the periplasmic space of E. coli cells. Antisera to the spaA protein of S. mutans reacted with extracellular protein from representative strains of S. mutans serotypes a, c, d, e, f, and g, but not b.
A Novel Method of Cone Beam CT Projection Binning Based on Image Registration (2017)

Accurate sorting of beam projections is important in 4D cone beam computed tomography (4D CBCT) to improve the quality of the reconstructed 4D CBCT image by removing motion-induced artifacts. We propose image registration-based projection binning (IRPB), a novel marker-less binning method for 4D CBCT projections, which combines intensity-based feature point detection and trajectory tracking using random sample consensus. IRPB extracts breathing motion and phases by analyzing tissue feature point trajectories. We conducted experiments with two phantom and six patient datasets, including both regular and irregular respirations. In experiments, we compared the performance of the proposed IRPB, Amsterdam Shroud method (AS), Fourier transform-based method (FT), and local intensity feature tracking method (LIFT). The results showed that the average absolute phase shift of IRPB was 3.74 projections and 0.48 projections less than that of FT and LIFT, respectively. AS lost the most breathing cycles in the respiration extraction for the five patient datasets, so we could not compare the average absolute phase shift between IRPB and AS. Based on the peak signal-to-noise ratio (PSNR) of the reconstructed 4D CBCT images, IRPB had 5.08, 1.05, and 2.90 dB larger PSNR than AS, FT, and LIFT, respectively. The average Structure SIMilarity Index (SSIM) of the 4D CBCT image reconstructed by IRPB, AS, and LIFT were 0.87, 0.74, 0.84, and 0.70, respectively. These results demonstrated that IRPB has superior performance to the other standard methods.
The effective permeability of granular thin films (1993)

An extended effective medium theory for calculating the permeability spectra of 2-D, granular films is presented. In plane dipole lattice sites are summed to determine the proper relation between the applied and local fields. The Clausius-Mossotti relation is then combined with the exact scattering solution to permit calculation of the complex mu /sub eff/ spectra of polycrystalline or amorphous 2-D arrays of spherical grains excited by a magnetic field incident perpendicular or parallel to the basal plane. In calculating the effective permeability spectra it is found that there are notable differences between the bulk and thin film models. In agreement with the authors' theoretical predictions, it is found that as the granular film changes from 2-D to 3-D the magnitude of the permeability traces decreases while the resonance frequency increases. Comparison with experimental data shows the 2-D model to predict more accurately the frequency dependent permeability of thin films than the bulk model.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Replication and episomal maintenance of Epstein-Barr virus-based vectors in mouse embryonal fibroblasts enable synthetic lethality screens. (2003)

Recently, we demonstrated the establishment of chemical and genetic synthetic lethality screens in cultured human cells. Here, we report the establishment of this method in mouse embryonal fibroblasts (MEF). The method employs an immortalized mammalian cell line, deficient in a gene of interest, which is complemented by an episomal survival plasmid expressing the wild-type cDNA for the gene of interest and the use of a novel green fluorescent protein (GFP)-based double-label fluorescence system. The crucial part in this endeavor has been the identification of a DNA replicon that could stably replicate in MEFs while under selection for survival and gets spontaneously lost relatively fast in the absence of such a pressure. Here, we show for the first time that EBV-based replicons but not polyoma virus-based ones can replicate and be stably maintained in MEFs. In the chemical screen, selective pressure imposed by synthetic lethal drugs prevented the spontaneous loss of the GFP-marked episome, enabling drug identification. Retention or spontaneous loss over time of the episomal survival plasmid could be sensitively detected in a large-scale blind test in the presence or absence of synthetic lethal chemicals, respectively. Establishing the synthetic lethality screen should thus permit high throughput screening for chemicals, which are synthetically lethal with any mouse mutant/knockout gene of interest. Moreover, it forms the basis for a genetic synthetic lethality screen in MEFs, an important new tool for mouse functional genomics.
Recombinant protein production facility for fungal biomass-degrading enzymes using the yeast Pichia pastoris (2015)

Filamentous fungi are the predominant source of lignocellulolytic enzymes used in industry for the transformation of plant biomass into high-value molecules and biofuels. The rapidity with which new fungal genomic and post-genomic data are being produced is vastly outpacing functional studies. This underscores the critical need for developing platforms dedicated to the recombinant expression of enzymes lacking confident functional annotation, a prerequisite to their functional and structural study. In the last decade, the yeast Pichia pastoris has become increasingly popular as a host for the production of fungal biomass-degrading enzymes, and particularly carbohydrate-active enzymes (CAZymes). This study aimed at setting-up a platform to easily and quickly screen the extracellular expression of biomass-degrading enzymes in P. pastoris. We first used three fungal glycoside hydrolases (GHs) that we previously expressed using the protocol devised by Invitrogen to try different modifications of the original protocol. Considering the gain in time and convenience provided by the new protocol, we used it as basis to set-up the facility and produce a suite of fungal CAZymes (GHs, carbohydrate esterases and auxiliary activity enzyme families) out of which more than 70% were successfully expressed. The platform tasks range from gene cloning to automated protein purifications and activity tests, and is open to the CAZyme users' community.
FERTILIZATION IN THE PARASITIC COPEPOD, LERNÆOPODA EDWARDSII OLSSON (1914)

1. About two and a half or three weeks after the attachment of Lernæopoda edwardsii to the brook-trout, the parasite is mature for fertilization. 2. The mature male is about one third as long as the mature female. The reproductive organs of the male are paired, and are located in the posterior region of the body, between the intestine and the body wall. They consist of a testis, a coiled vas deferens, and a spermatophore. 3. The female reproductive apparatus is also paired in character and is located within the abdomen, between the intestine and the body wall. The ovaries give rise to slender oviducts, which open at the lower extremity of the abdomen. Slightly above their terminations, the oviducts combine to form the spermatheca, which opens to the exterior through the two genital pores. Within each oviduct a spiral gland can be seen, which later develops into the cement gland. 4. In order to effect fertilization, the male makes circling movements while still attached to the host, thereby meeting a female. Then the male releases his hold on the host, attaches himself to the female, and moves down posteriorly in the vicinity of the genital pores. 5. The male bends his abdomen upward towards the female, and extrudes the spermatophores from the reproductive organs. These he manipulates with his second maxillæ and soon attaches them about the genital pores of the female. 6. The spermatozoa wander from the spermatophores into the spermatheca of the female and are stored until the eggs are ripe enough to undergo fertilization. 7. The eggs pass down the oviducts when mature, and are fertilized by the stored spermatozoa as they pass the spermatheca. The embryos pass into the external egg-sacs, where they develop into larvæ.
Data feature oriented data partition and weighted data mining (2005)

It is comprehensible that to find as much interesting knowledge as possible is the initial and main aim to mine data, no matter which pattern (parallel or sequential) is utilized in data mining, though parallelism is practically important as well. We present a principle, called DFDP, for partitioning large dataset-the first step for parallelization. Data subsets after partitioning are treated tendentiously for possible parallel or distributed processing. One feasible logical structure for parallel processing is recommended in the paper. Also experimental comparisons are reported in the paper, which shows that weighted data mining will find more interesting rules from data.
ÌNDICE DE FLEXIBILIDAD EN DEPORTISTAS DE RENDIMIENTO DE LA CIUDAD DE BOGOTÀ (2009)

Resumen es: El objetivo de este estudio fue caracterizar la flexibilidad de deportistas de rendimiento; para ello se hizo la medicion de 20 movimientos articulares b...
From approximate to optimal solutions: constructing pruning and propagation rules (1997)

At the heart of many optimization procedures are powerful pruning and propagation rules. This paper presents a case study in the construction of such rules. We develop a new algorithm, Complete Decreasing Best Fit, that finds the optimal packing of objects into bins. The algorithm use a branching rule based on the well known Decreasing Best Fit approximation algorithm. In addition, it includes a powerful pruning rule derived from a bound on the solution to the remaining subproblem. The bound is constructed by using modular arithmetic to decompose the numerical constraints. We show that the pruning rule adds essentially a constant factor overhead to runtime, whilst reducing search significantly. On the hardest problems, runtime can be reduced by an order of magnitude. Finally we demonstrate how propagation rules can be built by adding lookahead to pruning rules. This general approach- optimization procedures built from branching rules based on good approximation algorithms, and pruning and propagation rules derived from bounds on the remaining subproblem- may be effective on other NP-complete problems. 1
A Fully Automated Method for Lung Nodule Detection From Postero-Anterior Chest Radiographs (2006)

In the past decades, a great deal of research work has been devoted to the development of systems that could improve radiologists' accuracy in detecting lung nodules. Despite the great efforts, the problem is still open. In this paper, we present a fully automated system processing digital postero-anterior (PA) chest radiographs, that starts by producing an accurate segmentation of the lung field area. The segmented lung area includes even those parts of the lungs hidden behind the heart, the spine, and the diaphragm, which are usually excluded from the methods presented in the literature. This decision is motivated by the fact that lung nodules may be found also in these areas. The segmented area is processed with a simple multiscale method that enhances the visibility of the nodules, and an extraction scheme is then applied to select potential nodules. To reduce the high number of false positives extracted, cost-sensitive support vector machines (SVMs) are trained to recognize the true nodules. Different learning experiments were performed on two different data sets, created by means of feature selection, and employing Gaussian and polynomial SVMs trained with different parameters; the results are reported and compared. With the best SVM models, we obtain about 1.5 false positives per image (fp/image) when sensitivity is approximately equal to 0.71; this number increases to about 2.5 and 4 fp/image when sensitivity is = 0.78 and = 0.85, respectively. For the highest sensitivity (= 0.92 and 1.0), we get 7 or 8 fp/image.