gebhart/patrepeval huggingface dataset:
[Improvement in the healing of colonic anastomoses by vitamin B5 and C supplements. Experimental study in the rabbit]. (1990)

To study the effects of vitamins B5 and C on the healing process of colonic anastomoses, 3 groups of 20 rabbits were given daily either placebo (group A), or vitamin B5 (100 mg/kg: group B) or vitamin C (100 mg/kg: group C). After 8 days of supplementation, via a midline incision and under general anaesthesia, 2 colonic segments were removed, and the continuity was restored. On the 3rd post-operative day, the rabbits were killed and the anastomoses were removed. Mechanical properties of both normal colon and anastomoses were determined by using bursting pressure tests, number of burst anastomoses, fibroblast count, hydroxyproline concentration and determination by microanalysis of trace element content: Mg, P, S, Ca, Fe, Cu, Zn and Mn. Vitamin B5 (p = 0.03) and vitamin C (p less than 0.01) both decreased the number of burst anastomoses. Furthermore the required bursting pressure values were higher with vitamin C (p = 0.01) than in controls. Both vitamins restored normal Zn levels at the anastomotic site, whereas these levels decreased on the 3rd post-operative day during the normal healing process of colonic anastomosis. Moreover, vitamins B5 and C increased Fe, Cu and Mn levels, which are intimately all involved in collagen synthesis. Vitamins B5 and C enhance the colonic wound healing process in the rabbit, acting together in synergy in vivo as well as in vitro, as previously demonstrated.
Elevation of intracellular calcium in smooth muscle causes endothelial cell generation of NO in arterioles (1997)

It is well known that vascular smooth muscle tone can be modulated by signals arising in the endothelium (e.g., endothelium-derived relaxing factor, endothelium-derived hyperpolarizing factor, and prostaglandins). Here we show that during vasoconstriction a signal can originate in smooth muscle cells and act on the endothelium to cause synthesis of endothelium-derived relaxing factor. We studied responses to two vasoconstrictors (phenylephrine and KCl) that act by initiating a rise in smooth muscle cell intracellular Ca2+ concentration ([Ca2+]i) and exert little or no direct effect on the endothelium. Fluo-3 was used as a Ca2+ indicator in either smooth muscle or endothelial cells of arterioles from the hamster cheek pouch. Phenylephrine and KCl caused the expected rise in smooth muscle cell [Ca2+]i that was accompanied by an elevation in endothelial cell [Ca2+]i. The rise in endothelial cell [Ca2+]i was followed by increased synthesis of NO, as evidenced by an enhancement of the vasoconstriction induced by both agents after blockade of NO synthesis. The molecule involved in signal transmission from smooth muscle to endothelium is as yet unknown. However, given that myoendothelial cell junctions are frequent in these vessels, we hypothesize that the rise in smooth muscle cell Ca2+ generates a diffusion gradient that drives Ca2+ through myoendothelial cell junctions and into the endothelial cells, thereby initiating the synthesis of NO.
Isolation of a Transformation-Defective Deletion Mutant of Moloney Murine Sarcoma Virus (1982)

A transformation-defective (td) deletion mutant of Moloney murine sarcoma virus (td Mo-MSV) and a transforming component termed Mo-MSV 3 were cloned from a stock of clone 3 Mo-MSV. To define the defect of the transforming function, the RNA of td Mo-MSV was compared with those of Mo-MSV 3 and of another transforming variant termed Mo-MSV 124 and with helper Moloney murine leukemia virus (Mo-MuLV). The RNA monomers of td Mo-MSV and Mo-MSV 3 comigrated on polyacrylamide gels and were estimated to be 4.8 kilobases (kb) in length. In agreement with previous analyses, the RNA of Mo-MSV 124 measured 5.5 kb and that of Mo-MuLV measured 8.5 kb. The interrelationships among the viral RNAs were studied by fingerprinting and mapping of RNase T(1)-resistant oligonucleotides (T(1)-oligonucleotides) and by identification of T(1)-oligonucleotides present in hybrids formed by a given viral RNA with cDNA's made from another virus. The nontransforming td Mo-MSV RNA lacked most of the Mo-MSV-specific sequence, i.e., the four 3'-proximal T(1)-oligonucleotides of the six T(1)-oligonucleotides that are shared by the Mo-MSV-specific sequences of Mo-MSV 3 and Mo-MSV 124. The remaining two Mo-MSV-specific oligonucleotides identified td Mo-MSV as a deletion mutant of MSV rather than a deletion mutant of Mo-MuLV. td Mo-MSV and Mo-MSV 124 exhibited similar deletions of gag, pol, and env sequences which were less extensive than those of Mo-MSV 3. Hence, td Mo-MSV is not simply a deletion mutant of Mo-MSV 3. In addition to their MSV-specific sequences, all three MSV variants, including td Mo-MSV, shared the terminal sequences probably encoding the proviral long terminal repeat, which differed from their counterpart in Mo-MuLV. This may indirectly contribute to the oncogenic potential of MSV. A comparison of td Mo-MSV sequences with either Mo-MSV 124 or Mo-MSV 3 indicated directly, in a fashion similar to the deletion analyses which defined the src gene of avian sarcoma viruses, that Mo-MuLV-unrelated sequences of Mo-MSV are necessary for transformation. A definition of transformation-specific sequences of Mo-MSV by deletion analysis confirmed and extended previous analyses which have identified Mo-MuLV-unrelated sequences in Mo-MSV RNA and other studies which have described transformation of mouse 3T3 fibroblasts upon transfection with DNAs containing the Mo-MSV-specific sequence.
Molecular and clinical determinants of response and resistance to rucaparib for recurrent ovarian cancer treatment in ARIEL2 (Parts 1 and 2) (2021)

ARIEL2 (NCT01891344) is a single-arm, open-label phase 2 study of the PARP inhibitor (PARPi) rucaparib in relapsed high-grade ovarian carcinoma. In this post hoc exploratory biomarker analysis of pre- and post-platinum ARIEL2 samples, RAD51C and RAD51D mutations and high-level BRCA1 promoter methylation predict response to rucaparib, similar to BRCA1/BRCA2 mutations. BRCA1 methylation loss may be a major cross-resistance mechanism to platinum and PARPi. Genomic scars associated with homologous recombination deficiency are irreversible, persisting even as platinum resistance develops, and therefore are predictive of rucaparib response only in platinum-sensitive disease. The RAS, AKT, and cell cycle pathways may be additional modulators of PARPi sensitivity.
Technologies of ETERNUS VS900 storage virtualization switch (2006)

This paper gives an outline of storage virtualization and then describes a new-generation storage virtualization system that is based on Fujitsu's ETERNUS VS900 storage virtualization switch. The VS900 provides a simplified, logical view of a complicated storage system and simplifies storage management. It adopts a network-based, out-of-band virtualization model. Among other advantages, the VS900 provides high performance, reliability, and availability. It is managed by Systemwalk-er Resource Coordinator, which not only manages a storage system but also manages other system resources such as servers and networks to enable unified system-wide management.
Information-Theoretic Data Discarding for Dynamic Trees on Data Streams (2013)

Ubiquitous automated data collection at an unprecedented scale is making available streaming, real-time information flows in a wide variety of settings, transforming both science and industry. Learning algorithms deployed in such contexts often rely on single-pass inference, where the data history is never revisited. Learning may also need to be temporally adaptive to remain up-to-date against unforeseen changes in the data generating mechanism. Online Bayesian inference remains challenged by such transient, evolving data streams. Nonparametric modeling techniques can prove particularly ill-suited, as the complexity of the model is allowed to increase with the sample size. In this work, we take steps to overcome these challenges by porting information theoretic heuristics, such as exponential forgetting and active learning, into a fully Bayesian framework. We showcase our methods by augmenting a modern non-parametric modeling framework, dynamic trees, and illustrate its performance on a number of practical examples. The end product is a powerful streaming regression and classification tool, whose performance compares favorably to the state-of-the-art.
The spatial orientation of <i>Helicobacter pylori</i> in the gastric mucus (2004)

The highly motile human pathogen Helicobacter pylori lives deep in the gastric mucus layer. To identify which chemical gradient guides the bacteria within the mucus layer, combinations of luminal perfusion, dialysis, and ventilation were used to modify or invert transmucus gradients in anaesthetized Helicobacter-infected mice and Mongolian gerbils. Neither changes in lumen or arterial pH nor inversion of bicarbonate/CO2 or urea/ammonium gradients disturbed Helicobacter orientation. However, elimination of the mucus pH gradient by simultaneous reduction of arterial pH and bicarbonate concentration perturbed orientation, causing the bacteria to spread over the entire mucus layer. H. pylori thus uses the gastric mucus pH gradient for chemotactic orientation.
A miniaturization technique for wideband tightly coupled phased arrays (2009)

Using an equivalent circuit, a new wideband array was examined using physically realizable tightly coupled dipoles. A miniaturized element using inductive and capacitive loading was used to suppress ground plane effects for a broadband conformal array. Serial inductance was demonstrated to effectively miniaturize the radiating element and lead to even greater bandwidth as compared to the CSA array in [3]. A 4.5:1 bandwidth was demonstrated with a dipole length of λ <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">o</inf> /10 and a total array thickness of λ <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">o</inf> /12.8 at the lowest operating frequency.
Control strategy optimization of a hybrid fuel cell vehicle with braking energy regeneration (2008)

This paper deals with the optimized control strategy within the vehicle which is driven by a fuel cell stack hybrid with a NiMH battery. The aim is the instantaneous energy management to optimize the hydrogen consumption. At first the powertrain was modeled using data on testbed. Then the optimization control problem basing on an equivalent hydrogen consumption strategy is defined, where the motor target torque and DC/DC target current should be calculated. According to the shift signals and pedal position signals, the vehicle operation can be divided into two modes, non-brake mode (idle, drive backward, drive forward, slide) and brake mode. The optimization problem was solved respectively. Results in ldquoChina typical city bus cyclerdquo testing show the robustness and effectiveness of the strategy in improving fuel economy while maintaining drivability. The fuel economy was improved from 9.6 kg/100 km to 7.9 kg/100 km and the battery SOC was kept around 47%.
An Optical Clock Based on a Single Trapped <sup>199</sup> Hg <sup>+</sup> Ion (2001)

Microwave atomic clocks have been the de facto standards for precision time and frequency metrology over the past 50 years, finding widespread use in basic scientific studies, communications, and navigation. However, with its higher operating frequency, an atomic clock based on an optical transition can be much more stable. We demonstrate an all-optical atomic clock referenced to the 1.064-petahertz transition of a single trapped 199Hg+ ion. A clockwork based on a mode-locked femtosecond laser provides output pulses at a 1-gigahertz rate that are phase-coherently locked to the optical frequency. By comparison to a laser-cooled calcium optical standard, an upper limit for the fractional frequency instability of 7 x 10(-15) is measured in 1 second of averaging-a value substantially better than that of the world's best microwave atomic clocks.
Fast-Gated Single-Photon Avalanche Diode for Wide Dynamic Range Near Infrared Spectroscopy (2009)

We present a novel technique for wide dynamic range optical investigations. It is based on a fast-gated silicon single-photon avalanche diode (SPAD) in time-correlated single-photon counting (TCSPC) setup. The SPAD is gated- <emphasis emphasistype="smcaps" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">on</emphasis> and <emphasis emphasistype="smcaps" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">off </emphasis> in 500 ps so as to detect photons only within a given time interval. This technique is particularly useful in applications where a large amount of unnecessary photons precede or follow the optical signal to be detected, such as in time-resolved near infrared (NIR) spectroscopy, optical mammography, and optical molecular imaging. In particular, in time-resolved reflectance spectroscopy, it is desirable to minimize the source–detector separation to improve system performance. This leads to the saturation of the detection electronics because of the huge amount of “early” photons back scattered by superficial layers. Our setup is able to reject these photons and detect only “late” photons from the sample, thus allowing an increase in the dynamic range and the injected power. We acquired diffusive curves of two phantoms with 95 ps time resolution and 10 <formula formulatype="inline" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex Notation="TeX">$^7$</tex></formula> dynamic range with a measurement time three orders of magnitude shorter than what is currently possible with a standard TCPSC setup.
Identification of two SNPs in the 5' flanking region of the ACP1 gene and evaluation of disequilibrium among polymorphic sites. (2002)

We have studied the 5' flanking region of the ACP1 gene looking for new polymorphisms. Two SNPs, DdeI and FokI restricted, have been found in this region. We determined the genotype of DdeI and FokI SNPs, as well as of three other known SNPs, codon 43 (CfoI restricted), codon 41 and codon 105 (TaqI restricted), located respectively in exons 3, 4 and 6 in 62 unrelated subjects from the Italian population. Haplotype distribution for the ten possible pairs of loci were determined by a maximum likelihood procedure. Overall, statistically significant deviations from expected frequencies assuming equilibrium have been observed for the following pairs: FokI/codon 41, FokI/TaqI, codon 41/TaqI (complete association), DdeI/FokI, DdeI/codon 41 and DdeI/TaqI. The data suggest that the FokI area could include sequences operating in strict functional association with sequences included in the codon 41/TaqI area, possibly in order to regulate the F/S isoforms ratio of the A* and *B alleles. Since the ratio between the concentration of the two F and S isoforms is different for the three ACP1 alleles, we suggest that the ACP1 locus has been subjected to strong selective pressure to obtain an optimal alternative splicing mechanism of the *A and *B alleles. The *C variant, on the other hand, seems completely independent from sequences in the FokI/codon 41/TaqI areas, resulting in an inverted F/S ratio compared to that found for *A and *B alleles.
Fabrication of three-dimensional microstructures by soft molding (2001)

We have developed soft molding as a method for meso-scale-area fabrication of three-dimensional structures. The soft molding, which is a form of soft lithography, involves placing an elastomeric mold on the surface of a spin-coated polymer film with a slight pressure (&lt;1 N/cm2), allowing the mold to absorb solvent, releasing the pressure, and then letting the mold and the substrate remain undisturbed for a period of time. The three-dimensional structure thus formed is robust in that the pattern fidelity is preserved without any distortion or defects. For the soft molding to be successful, the rate of solvent absorption by the mold should be larger than the rate of solvent evaporation. The method is demonstrated with several three-dimensional structures.
Two Lipoproteins Extracted from <i>Escherichia coli</i> K-12 LCD25 Lipopolysaccharide Are the Major Components Responsible for Toll-Like Receptor 2-Mediated Signaling (2002)

Toll-like receptor 2 (TLR2)-mediated cell activation induced by commercial preparations of LPS was recently shown to arise from impurities whose identities are not known. In this work, we determined the molecules responsible for TLR2-mediated cell activation in LPS derived from Escherichia coli K-12 strain LCD25. When LCD25 LPS was phenol extracted, two proteins capable of TLR2-mediated cell activation were purified and identified as E. coli lipoproteins. We cloned, expressed, and purified these two lipoproteins, Lip19 and Lip12. Lip19 or Lip12 activated TNF-alpha production from RAW264.7 and THP-1 cells in a TLR2-dependent manner. However, neither Lip19 nor Lip12 activated HUVECs, which lack endogenous TLR2. Additionally, IkappaB kinase beta and c-Jun N-terminal kinase 1 activation in THP-1 cells induced by Lip19 or Lip12 was observed. TLR2 activation by Lip19 and Lip12 in HEK293 cells was blocked by inhibitory anti-TLR2 mAbs. The unlipidated mutants, Lip19-C19S and Lip12-C21S, in which the NH(2)-terminal cysteine was substituted by serine, lost their ability to activate TLR2-transfected HEK 293 cells. Taken together, these results demonstrate that two lipoproteins constitute the major contaminants responsible for TLR2-mediated cell activation in E. coli LCD25 LPS.
Beta-catenin signaling in prostate cancer: an early perspective. (2003)

Further understanding of the molecular mechanisms responsible for prostate cancer (CaP) development and progression is paramount for overcoming the current diagnostic and therapeutic hurdles presented by this urologic disease. The beta-catenin nuclear signaling molecule has been widely implicated as an oncogene in human cancer, including CaP. Pooling together knowledge gathered on the contributions of beta-catenin and other factors to human neoplasia may assist in the development of better strategies for management and treatment of prostate tumors of all stages (early, advanced/androgen-dependent, advanced/androgen-independent). Although there is considerable lack of comprehension regarding the function of beta-catenin transcriptional activity in prostate tumors in vivo, recent evidence indicates the probability that beta-catenin contributes to multiple signaling pathways for which a causative role in CaP is already known. In this review, we will approach such pathway interactions, perhaps the most notable being androgen receptor (AR) signaling, in order to highlight those avenues through which beta-catenin may exert its cancer-related function. To the same end, we will draw attention to normal beta-catenin signaling in the prostate; however, as only very limited knowledge exists on this topic, much of the discussion will be correlative. Our final topic will concentrate on how, given realistic scenarios of androgen stimulation or absence in both normal and neoplastic prostate cells, nuclear beta-catenin may ultimately potentiate wnt cell-cell signaling and AR activities. Heightening our comprehension of beta-catenin signaling mechanisms and its phenotypic consequences in CaP - and in normal prostate - may contribute to that body of knowledge which will eventually prove useful for devising more effective therapies.
Learning to Navigate the Web (2018)

Learning in environments with large state and action spaces, and sparse rewards, can hinder a Reinforcement Learning (RL) agent's learning through trial-and-error. For instance, following natural language instructions on the Web (such as booking a flight ticket) leads to RL settings where input vocabulary and number of actionable elements on a page can grow very large. Even though recent approaches improve the success rate on relatively simple environments with the help of human demonstrations to guide the exploration, they still fail in environments where the set of possible instructions can reach millions. We approach the aforementioned problems from a different perspective and propose guided RL approaches that can generate unbounded amount of experience for an agent to learn from. Instead of learning from a complicated instruction with a large vocabulary, we decompose it into multiple sub-instructions and schedule a curriculum in which an agent is tasked with a gradually increasing subset of these relatively easier sub-instructions. In addition, when the expert demonstrations are not available, we propose a novel meta-learning framework that generates new instruction following tasks and trains the agent more effectively. We train DQN, deep reinforcement learning agent, with Q-value function approximated with a novel QWeb neural network architecture on these smaller, synthetic instructions. We evaluate the ability of our agent to generalize to new instructions on World of Bits benchmark, on forms with up to 100 elements, supporting 14 million possible instructions. The QWeb agent outperforms the baseline without using any human demonstration achieving 100% success rate on several difficult environments.
An indirect optimization method for biochemical systems: Description of method and application to the maximization of the rate of ethanol, glycerol, and carbohydrate production in Saccharomyces cerevisiae (1997)

Three metabolic models for the production of ethanol, glycerol, and carbohydrates in yeast are optimized with respect to different production rates. While originally nonlinear, all three optimization problems are reduced in such a way that methods of linear programming can be used. The optimizations lead to profiles of enzyme activities that are compatible with the physiology of the cells, which guarantees their viability and fitness, and yield higher rates of the desired final end products than the original systems. In order to increase ethanol rate production at least three times, six enzymes must be modulated. By contrast, when the production of glycerol or carbohydrates is optimized, modulation of just one enzyme (in the case of glycerol) or two enzymes (in the case of carbohydrates) is necessary to yield significant increases in product flux rate. Comparisons of our results with those obtained from other methods show great similarities and demonstrate that both are valid methods. The choice of one or the other method depends on the question of interest. © 1997 John Wiley & Sons, Inc. Biotechnol Bioeng 55: 758–772, 1997.
Flow cytometric identification of microorganisms by dual staining with FITC and PI (1990)

The identification of microorganisms by flow cytometry was evaluated by using a double staining technique with propidium iodide and fluorescein isothiocyanate and a two dimensional analysis. A diverse group of 19 different species and strains of microorganisms was tested to determine if they could be differentiated by flow cytometry. The organisms tested displayed characteristic and distinct two dimensional fluorescent patterns which allowed ready grouping and differentiation into subsets of organisms. The slopes and correlation coefficients of the histograms and the ratio of red to green signals expressed these differences quantitatively and allowed organisms to be placed into one of three groups based on these values. In some instances, as with Streptococcus pneumoniae and pyogenes and Staphylococcus aureus and epidermidis, it was possible to distinguish between species of bacteria from the same genus. The use of dual dye labeling and flow cytometry provided a rapid method of identifying selected microorganisms and may be broadly applicable for the detection and identification of many bacteria and fungi.