gebhart/patrepeval huggingface dataset:
Multimodal Meta-Analysis of 1,494 Hepatocellular Carcinoma Samples Reveals Significant Impact of Consensus Driver Genes on Phenotypes (2018)

Although driver genes in hepatocellular carcinoma (HCC) have been investigated in various previous genetic studies, prevalence of key driver genes among heterogeneous populations is unknown. Moreover, the phenotypic associations of these driver genes are poorly understood. This report aims to reveal the phenotypic impacts of a group of consensus driver genes in HCC. We used MutSigCV and OncodriveFM modules implemented in the IntOGen pipeline to identify consensus driver genes across six HCC cohorts comprising 1,494 samples in total. To access their global impacts, we used The Cancer Genome Atlas (TCGA) mutations and copy-number variations to predict the transcriptomics data, under generalized linear models. We further investigated the associations of the consensus driver genes to patient survival, age, gender, race, and risk factors. We identify 10 consensus driver genes across six HCC cohorts in total. Integrative analysis of driver mutations, copy-number variations, and transcriptomic data reveals that these consensus driver mutations and their copy-number variations are associated with a majority (62.5%) of the mRNA transcriptome but only a small fraction (8.9%) of miRNAs. Genes associated with <i>TP53, CTNNB1</i>, and <i>ARID1A</i> mutations contribute to the tripod of most densely connected pathway clusters. These driver genes are significantly associated with patients' overall survival. Some driver genes are significantly linked to HCC gender (<i>CTNNB1, ALB, TP53</i>, and <i>AXIN1</i>), race (<i>TP53</i> and <i>CDKN2A</i>), and age (<i>RB1</i>) disparities. This study prioritizes a group of consensus drivers in HCC, which collectively show vast impacts on the phenotypes. These driver genes may warrant as valuable therapeutic targets of HCC.
Gene signatures of tumor inflammation and epithelial-to-mesenchymal transition (EMT) predict responses to immune checkpoint blockade in lung cancer with high accuracy (2019)

The EMT/Inflammation signature score may be useful in directing checkpoint inhibitor therapy in lung cancer and suggests that reversal of EMT might augment efficacy of ICB.
Systems modeling based on Legendre polynomials (2009)

A new method for obtaining models of continuous systems, based on Legendre orthogonal filters, is proposed in this paper. Recent results in the field of orthogonal functions were used to improve accuracy of modeling. First, Legendre orthogonal filters were designed on the basis of orthogonal functions. Then, adjustable models were formed. Models parameters were optimized using genetic algorithm. As a case study, an experimental simple DC drive was considered and described in details. Simulations were performed out to approve theoretical results and demonstrate that the method described in the paper is very suitable for modeling continuous systems. It achieves excellent results in the sense of model accuracy and modeling algorithm speed.
Functional importance of cystic fibrosis immunoglobulin G fragments generated by Pseudomonas aeruginosa elastase. (1989)

We examined the functional importance of immunoglobulin polypeptide fragments generated by Pseudomonas aeruginosa elastase (Pseudomonas elastase). The purpose of this study was to determine whether the elastase produced by Pseudomonas aeruginosa cleaves human IgG into immune fragments that functionally inhibit opsonophagocytosis. Our results confirm that IgG isolated from patients with cystic fibrosis (CF) incubated with purified pseudomonas elastase results in the generation of two major polypeptide fragments and that, furthermore, these fragments significantly inhibit bacterial uptake by human neutrophils. After 75 minutes bacterial uptake was six times greater when intact IgG was used as an opsonin (uptake 90.2% +/- 18.6% SEM) compared with a IgG was used as an opsonin (uptake 90.2% +/- 18.6% SEM) compared with a mixture of pseudomonas-lipopolysaccharide-reactive Fab and F(ab')2 fragments generated by pseudomonas elastase (uptake 15.4% +/- 0.8% SEM, p less than 0.001). Hydrolyzed CF IgG antibodies consistently resulted in a level of bacterial uptake less than that of normal saline negative controls (NS): (at 10 minutes, NS 26.6% vs CF 16.8%, p less than 0.05; at 75 minutes, NS 28.2% vs CF 15.4%, p less than 0.01. This suggests that the immune polypeptides are active inhibitors of the essential neutrophil phagocyte-bacterial cell interaction. Intact immune IgG reversed the defect in opsonophagocytosis. When intact IgG was mixed with IgG fragments the phagocytic rates increased directly with increasing amounts of intact IgG. We conclude that the elastase exoproduct secreted by Pseudomonas aeruginosa is capable of cleaving IgG into functionally important fragments that inhibit bacterial uptake. Furthermore, this inhibition can be overcome by increasing amounts of a commercially available preparation of intact immune IgG.(ABSTRACT TRUNCATED AT 250 WORDS)
Prediction of protein interdomain linker regions by a hidden Markov model (2005)

We applied our method to a dataset of protein sequences in which domains and interdomain linkers had been delineated using the Pfam-A database. The prediction results are superior to a simpler method that also uses linker index.
SENLEX: sensor layout expert system (1986)

An expert system is under development to carry out intrusion detection sensor placement for physical security systems. Expert systems are computer programs that use symbolic programming techniques to duplicate the reasoning processes of human experts. Because sensitive facilities often require complex, multi-sensor intrusion detection systems, the design rules for achieving high levels of detection performance are not easily transferred to novices. Since these design rules reside in the minds of the individual experts performing the tasks, the need to consolidate this knowledge in a form that is available to others was a driving force in this project. The first phase of this project is described in this paper. It consists of an expert system for sensor placement in a graded clear zone. The program has the capability of handling several different sensor types and of coordinating the placement of multiple sensor types. The designs produced by the program in comparison with the designs produced by human experts are discussed.
Role of ERK and JNK pathways in regulating cell motility and matrix metalloproteinase 9 production in growth factor-stimulated human epidermal keratinocytes (1999)

Invasion is an essential cellular response that plays an important role in a number of physiological and pathological processes. Matrix metalloproteinase (MMP) production and cell movement are diverse cellular responses integral to the process of invasion. The complexity of the invasive process suggests the necessity of coordinate activation of more than one signaling pathway in order to activate specific factors responsible for regulating these cellular responses. In this report, we demonstrate that cell movement and MMP-9 production are both directly dependent on the activation of endogenous ERK signaling in hepatocyte growth factor (HGF)-or epidermal growth factor (EGF)-stimulated human epidermal keratinocytes. The kinetic profiles of endogenous MEK and ERK activity suggest that prolonged activation of these signal transducers is an underlying mechanism involved in stimulating cell motility and MMP-9 production. In support of this finding, a transient MEK/ERK signal elicited by keratinocyte growth factor (KGF) or insulin-like growth factor-1 (IGF-1) fails to stimulate these invasion-related responses. Specific inhibition of MEK leads to suppression of ERK activation, marked reduction in steady-state levels of c-Fos, and inhibition of cell movement and MMP-9 production. This occurs despite continued activation of JNK and c-Jun signaling in the presence of MEK-specific inhibition. In contrast, when JNK activity is specifically inhibited in HGF-stimulated cells, AP-1 activity is suppressed but cell motility is not affected. This evidence suggests that while ERK and JNK activity are necessary for AP-1 activation, ERK but not JNK is sufficient in stimulating cell motility.
Efficacy of Typical and Atypical Antipsychotics for Primary and Comorbid Anxiety Symptoms or Disorders (2006)

Except for trifluoperazine, there is no large, well-designed study of antipsychotics in the treatment of primary or comorbid anxiety symptoms or disorders. The efficacy of these agents in various anxiety conditions needs to be further investigated with large, well-designed comparison studies.
Complementary and Alternative Medicine Use Among Adults and Children: United States, 2007 (2008)

In 2007, almost 4 out of 10 adults had used CAM therapy in the past 12 months, with the most commonly used therapies being nonvitamin, nonmineral, natural products (17.7%) and deep breathing exercises (12.7%). American Indian or Alaska Native adults (50.3%) and white adults (43.1%) were more likely to use CAM than Asian adults (39.9%) or black adults (25.5%). Results from the 2007 NHIS found that approximately one in nine children (11.8%) used CAM therapy in the past 12 months, with the most commonly used therapies being nonvitamin, nonmineral, natural products (3.9%) and chiropractic or osteopathic manipulation (2.8%). Children whose parent used CAM were almost five times as likely (23.9%) to use CAM as children whose parent did not use CAM (5.1%). For both adults and children in 2007, when worry about cost delayed receipt of conventional care, individuals were more likely to use CAM than when the cost of conventional care was not a worry. Between 2002 and 2007 increased use was seen among adults for acupuncture, deep breathing exercises, massage therapy, meditation, naturopathy, and yoga. CAM use for head or chest colds showed a marked decrease from 2002 to 2007 (9.5% to 2.0%).
<i>Pseudomonas aeruginosa</i> killing of <i>Caenorhabditis elegans</i> used to identify <i>P. aeruginosa</i> virulence factors (1999)

We reported recently that the human opportunistic pathogen Pseudomonas aeruginosa strain PA14 kills Caenorhabditis elegans and that many P. aeruginosa virulence factors (genes) required for maximum virulence in mouse pathogenicity are also required for maximum killing of C. elegans. Here we report that among eight P. aeruginosa PA14 TnphoA mutants isolated that exhibited reduced killing of C. elegans, at least five also exhibited reduced virulence in mice. Three of the TnphoA mutants corresponded to the known virulence-related genes lasR, gacA, and lemA. Three of the mutants corresponded to known genes (aefA from Escherichia coli, pstP from Azotobacter vinelandii, and mtrR from Neisseria gonorrhoeae) that had not been shown previously to play a role in pathogenesis, and two of the mutants contained TnphoA inserted into novel sequences. These data indicate that the killing of C. elegans by P. aeruginosa can be exploited to identify novel P. aeruginosa virulence factors important for mammalian pathogenesis.
Hydrochloric Acid (2000)

Abstract The article contains sections titled: 1. Introduction 2. Properties 2.1. Physical Properties 2.2. Chemical Properties 2.3. The HCl‐H 2 O System 3. Production 3.1. Methods of Preparation 3.2. Industrial Production 3.2.1. From Hydrogen and Chlorine 3.2.2. Reaction of Metal Chlorides with Sulfuric Acid 3.2.3. Recovery as a Chlorination Byproduct 3.2.4. Recovery from Waste Incineration 3.3. Purification 4. Quality Specifications 5. Storage and Transportation 6. Uses and Economic Aspects 7. Toxicology and Occupational Health
An analysis of Internet content delivery systems (2002)

In the span of only a few years, the Internet has experienced an astronomical increase in the use of specialized content delivery systems, such as content delivery networks and peer-to-peer file sharing systems. Therefore, an understanding of content delivery on the lnternet now requires a detailed understanding of how these systems are used in practice.This paper examines content delivery from the point of view of four content delivery systems: HTTP web traffic, the Akamai content delivery network, and Kazaa and Gnutella peer-to-peer file sharing traffic. We collected a trace of all incoming and outgoing network traffic at the University of Washington, a large university with over 60,000 students, faculty, and staff. From this trace, we isolated and characterized traffic belonging to each of these four delivery classes. Our results (1) quantify, the rapidly increasing importance of new content delivery systems, particularly peer-to-peer networks, (2) characterize the behavior of these systems from the perspectives of clients, objects, and servers, and (3) derive implications for caching in these systems.
The future of treatment for systemic lupus erythematosus. (2001)

The future promises good news for the treatment of systemic lupus erythematosus, some of which can already be foreseen. Increased knowledge on genes that participate in the predisposition, pathogenesis, pharmacogenetics of, and protection against this disease may permit intervention at this level. Also, better understanding about the role of sex hormones has allowed trials of weak androgens or prolactin inhibitors. New immunomodulators or immunosuppressors may enable more precise treatment at the immunoregulatory level, and greater knowledge on the disturbance of circuits has already provided hints and even allowed trials of anti-interleukin-10 antibodies, an IL-10 decreasing agent, tolerance-induction strategies or intervention at the level of T cell co-stimulation, as well as immune ablation with subsequent stem cell transplantation. Autoantibodies can be removed, controlled by means of anti-idiotypes, which are blocked from reaching their target antigen or uncoupled from the tissues they have reached. All these treatment strategies will gradually become decanted in order to achieve the optimal treatment of SLE, which may tum out to be its cure.
Removal of Dilute Nitrogen Oxide by the Absorption in Mn–Zr Oxide (1995)

Abstract The removal of NO by absorption in manganese zirconium oxide (Mn–Zr oxide) was investigated in both the presence and absence of gaseous O2. The Mn–Zr oxide at Mn/Zr = 1 exhibited a high NO absorption rate and capacity at 200 °C. The absorption was promoted in the presence of O2. The absorption capacity was not strongly affected by the NO concentration (75—900 ppm) and W/F (0.125—1 g s cm−3). An infrared analysis of the absorbed species indicated that the absorption proceeds as the formation of nitrate in the bulk solid. The absorption and desorption were reversible, and the oxide solid was recovered upon heating a preabsorbed sample at 400 °C. Although the amorphous phase of the Mn–Zr oxide which is formed after heating at 450 °C is effective for NO absorption, due to good mixing of manganese oxide and zirconium oxide, heating at higher temperatures (≥550 °C), leading to a decrease in the surface area and crystallization of single oxides, resulted in a decrease in the absorption capacity. NO removal appears to proceed by the oxidation of NO on the Mn sites, and a subsequent absorption at the Zr sites as (NO3)− species.
Microwave assisted preparation of binary oxide nanoparticles (2000)

A group of binary oxide nanophase materials were prepared using a microwave assisted soft-chemical route. BaTiO3, Ba6Ti17O40, BaZrO3 and PbTiO3 were prepared from BaCl2 hydrate, Pb(Ac)2, Ti(OPri)4 and ZrOCl2. All reactions were performed in ethylene glycol, which acted as both a solvent and a growth regulating agent, under atmospheric pressure in a microwave reactor. The products that were obtained were analyzed by using XRD, TEM, XPS, EDX and FT-IR.
Influence of <i>in situ</i> ultrasound treatment during ion implantation on amorphization and junction formation in silicon (2002)

We report the first study of the effect of in situ ultrasound treatment during ion implantation on amorphization and transient enhanced diffusion (TED) in silicon. Rutherford backscattering spectroscopy, ion channeling, and Raman spectroscopy measurements show that amorphization of Si during Ar ion implantation is increased by ultrasound treatment, especially at ultrasound frequencies around 2 MHz. By secondary ion mass spectroscopy we investigate the influence of ultrasound treatment on TED of B atoms. Our data show that TED is reduced due to the influence of ultrasound treatment. The results are discussed in terms of the interaction of ultrasound waves with point defects and the ultrasound stimulated enhanced diffusion of interstitials.
Finite element methods on composite meshes for tuning plasma equilibria in tokamaks (2018)

The fundamental concept of magnetically confined nuclear fusion devices is the magnetohydrodynamic (MHD) equilibrium: the pressure gradient due to highly energetic charged particles is balanced by the Lorenz force due to strong magnetic fields. Hence, numerical methods for MHD equilibria are also fundamental for fusion engineering applications. We rely here on a finite element method on composite meshes for the simulation of axisymmetric equilibria in tokamaks, torus-shaped nuclear fusion devices. One mesh with Cartesian quadrilaterals covers the domain accessible by the plasma and one mesh with triangles discretizes the region outside the chamber. The two meshes overlap in a narrow region. This approach gives the flexibility to achieve easily and at low cost higher order regularity for the approximation of the principal unknown, the poloidal magnetic flux, while preserving accurate meshing of the geometric details in the exterior. We show that higher order regularity allows to formulate appropriate optimal control problems that help to find a special type of equilibria, called snowflake equilibria, that are a very promising concept to mitigate high heat loads due to plasma escaping particles.
Thermal Performance Testing of Cryogenic Insulation Systems (2007)

Efficient methods for characterizing thermal performance of materials under cryogenic and vacuum conditions have been developed. These methods provide thermal conductivity data on materials under actual-use conditions and are complementary to established methods. The actual-use environment of full temperature difference in combination with vacuum-pressure is essential for understanding insulation system performance. Test articles include solids, foams, powders, layered blankets, composite panels, and other materials. Test methodology and apparatus design for several insulation test cryostats are discussed. The measurement principle is liquid nitrogen boil-off calorimetry. Heat flux capability ranges from approximately 0.5 to 500 watts per square meter; corresponding apparent thermal conductivity values range from below 0.01 up to about 60 mW/m- K. Example data for different insulation materials are also presented. Upon further standardization work, these patented insulation test cryostats can be available to industry for a wide range of practical applications.
DksA and ppGpp directly regulate transcription of the <i>Escherichia coli</i> flagellar cascade (2009)

The components of the Escherichia coli flagella apparatus are synthesized in a three-level transcriptional cascade activated by the master regulator FlhDC. The cascade co-ordinates the synthesis rates of a large number of gene products with each other and with nutritional conditions. Recent genome-wide studies have reported that flagellar transcription is altered in cells lacking the transcription regulators DksA or ppGpp, but some or all reported effects could be indirect, and some are contradictory. We report here that the activities of promoters at all three levels of the cascade are much higher in strains lacking dksA, resulting in overproduction of flagellin and hyperflagellated cells. In vitro, DksA/ppGpp inhibits the flhDC promoter and the sigma(70)-dependent fliA promoter transcribing the gene for sigma(28). However, DksA and ppGpp do not affect the sigma(28)-dependent fliA promoter or the sigma(28)-dependent fliC promoter in vitro, suggesting that the dramatic effects on expression of those genes in vivo are mediated indirectly through direct effects of DksA/ppGpp on FlhDC and sigma(28) expression. We conclude that DksA/ppGpp inhibits expression of the flagellar cascade during stationary phase and following starvation, thereby co-ordinating flagella and ribosome assembly and preventing expenditure of scarce energy resources on synthesis of two of the cell's largest macromolecular complexes.
The effect of various recovery modalities on subsequent performance, in consecutive supramaximal exercise. (1993)

Different recovery strategies from maximal exercise seem to induce different lactate utilization patterns without significantly affecting performance on one subsequent maximal exercise. It remains unclear however, how varying recovery modalities affects repeated maximal exercise. To study this, we examined in 16 subjects, the influence of passive (P), active leg (L) and active arm (A) twenty minutes recovery periods separating a series of four exhaustive exercises, up to two minutes duration. Significant decreases in performance between the first and fourth exercise were observed in all recovery series but a significant decrease in performance in the second exercise was observed during passive recovery alone (p < 0.01). When the different types of recovery are compared, a more pronounced decrement in performance was found during passive recovery when first and last exercises are compared (p < 0.04). Pedaling duration in each successive exercise was unaffected in A or L but was significantly shorter in P (p < 0.03). Highly significant differences in mean blood lactate kinetics were found for the three recovery patterns used, with more elevated peak and nadir levels in passive recovery, intermediate values in active arm and lowest concentrations in active leg recovery. However, no correlation was found between performance and lactate concentration at the onset of exercise (r = -0.15; p = NS). Mean heart rates were similar throughout the experimental protocol except for a lower cardiac frequency during the last 5 minutes of passive recovery (p < 0.01). Blood hematocrits showed higher hemoconcentrations in repeated exercise during passive recovery (p < 0.01) despite significantly lower total fluid losses in this group. A significant correlation between peak hematocrit and blood lactate was also found (r = 0.67; p < 0.001). We conclude that the type of recovery has a significant effect on blood lactate elimination kinetics, and active recovery is beneficial in the preservation of performance during repeated maximal exercise. Furthermore, plasma shifts across the extra and intravascular spaces are induced by maximal exercise, and appear to closely follow blood lactate kinetics.
Influence of C-terminal Modifications of oX174 Lysis Gene E on its Lysis-inducing Properties (1985)

The phi X174 gene E product (gpE) causes lysis of Escherichia coli by inducing the host autolytic system. Experiments were carried out to ascertain which part of the 91 amino acid polypeptide carries the functional site for this process. For this purpose fusion genes were created comprising the first 51 codons of gene E and unrelated sequences coding for 102 or 33 amino acids respectively. The chimeric protein of 153 amino acids consisting of the N-terminal part of gpE and a fragment of beta-galactosidase, was neither able to lyse E. coli nor to restore beta-galactosidase activity by alpha-complementation. Expression of the 84 amino acid polypeptide, however, was able to induce lysis of E. coli. It is therefore concluded that the functional lysis-inducing site of gpE is located within the cloned N-terminal part of gene E. In the shorter chimeric protein the sequence following the functional site was tolerated or necessary for stabilization, but in the longer chimeric protein, the C-terminal sequence disturbed the lysis-inducing conformation.