gebhart/patrepeval huggingface dataset:
Analysis and improvement of Brinkman lattice Boltzmann schemes: Bulk, boundary, interface. Similarity and distinctness with finite elements in heterogeneous porous media (2015)

This work focuses on the numerical solution of the Stokes-Brinkman equation for a voxel-type porous-media grid, resolved by one to eight spacings per permeability contrast of 1 to 10 orders in magnitude. It is first analytically demonstrated that the lattice Boltzmann method (LBM) and the linear-finite-element method (FEM) both suffer from the viscosity correction induced by the linear variation of the resistance with the velocity. This numerical artefact may lead to an apparent negative viscosity in low-permeable blocks, inducing spurious velocity oscillations. The two-relaxation-times (TRT) LBM may control this effect thanks to free-tunable two-rates combination Λ. Moreover, the Brinkman-force-based BF-TRT schemes may maintain the nondimensional Darcy group and produce viscosity-independent permeability provided that the spatial distribution of Λ is fixed independently of the kinematic viscosity. Such a property is lost not only in the BF-BGK scheme but also by "partial bounce-back" TRT gray models, as shown in this work. Further, we propose a consistent and improved IBF-TRT model which vanishes viscosity correction via simple specific adjusting of the viscous-mode relaxation rate to local permeability value. This prevents the model from velocity fluctuations and, in parallel, improves for effective permeability measurements, from porous channel to multidimensions. The framework of our exact analysis employs a symbolic approach developed for both LBM and FEM in single and stratified, unconfined, and bounded channels. It shows that even with similar bulk discretization, BF, IBF, and FEM may manifest quite different velocity profiles on the coarse grids due to their intrinsic contrasts in the setting of interface continuity and no-slip conditions. While FEM enforces them on the grid vertexes, the LBM prescribes them implicitly. We derive effective LBM continuity conditions and show that the heterogeneous viscosity correction impacts them, a property also shared by FEM for shear stress. But, in contrast with FEM, effective velocity conditions in LBM give rise to slip velocity jumps which depend on (i) neighbor permeability values, (ii) resolution, and (iii) control parameter Λ, ranging its reliable values from Poiseuille bounce-back solution in open flow to zero in Darcy's limit. We suggest an "upscaling" algorithm for Λ, from multilayers to multidimensions in random extremely dispersive samples. Finally, on the positive side for LBM besides its overall versatility, the implicit boundary layers allow for smooth accommodation of the flat discontinuous Darcy profiles, quite deficient in FEM.
C‐reactive protein, cardiovascular risk factors and the association with myocardial infarction in men (2000)

Our findings confirm previous reports that C-reactive protein predicts the risk of myocardial infarction. However, this association does not appear to be causal, since the increase in risk can to a large extent be explained by the presence of other cardiovascular risk factors.
Differential regulation of two thiolase genes from Clostridium acetobutylicum DSM 792. (2000)

Thiolase of Clostridium acetobutylicum is an important enzyme involved in both, acid and solvent fermentation. Two thiolase genes (thlA and thIB) have been cloned and sequenced from Clostridium acetobutylicum DSM 792, showing high homology to each other and to thiolases of PHA-synthesizing bacteria. The thlA gene is identical to the gene already cloned and sequenced from strain ATCC 824 (Stim-Herndon et al., 1995, Gene 154: 81-85). Using primer extension and S1 nuclease analysis a transcriptional start site was identified 102 bp upstream of the thlA start codon. This site was preceded by a region that exhibits high similarity to the sigma70 consensus promoter sequences of Gram-positive and -negative bacteria. Regulation of thlA and thlB was studied at the transcriptional level to elucidate the specific function of each gene. Non-radioactive primer extension analysis using fluorescein-labelled oligonucleotides and Northern blot analysis revealed high levels of thlA transcripts in acid- and solvent-producing cells. During an induced shift of a continuous culture from acid to solvent formation, the transcript level transiently decreased to a minimum, 3 to 7 h after induction. The thlA transcript length is about 1.4 kb, indicating a monocistronic organisation, whereas genetic organization and reverse transcription (RT)-PCR analysis indicated that thlB forms an operon with two other adjacent genes, thlR and thlC. Transcription and regulation of the thlB operon was studied using RTPCR and showed a very low expression in acid- and solvent-producing cells. Heterologously expressed clostridial ThlB showed high thiolase activity in Escherichia coli. The N-terminal part of ThlR possesses a potential helix-turn-helix motif and shows significant homology to regulatory proteins belonging to the TetR/AcrR family of transcriptional regulators. ThlR possibly acts as a transcriptional repressor of thlB operon expression. The data provide strong evidence that ThlA is involved in the metabolism of both acid and solvent formation, whereas the physiological function of ThlB has yet to be elucidated.
ChemInform Abstract: Spin Control in Organic Molecules (1991)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Under-constrained execution (2007)

Article Share on Under-constrained execution: making automatic code destruction easy and scalable Authors: Dawson Engler Stanford University Stanford UniversityView Profile , Daniel Dunbar Stanford University Stanford UniversityView Profile Authors Info & Claims ISSTA '07: Proceedings of the 2007 international symposium on Software testing and analysisJuly 2007 Pages 1–4https://doi.org/10.1145/1273463.1273464Online:09 July 2007Publication History 43citation404DownloadsMetricsTotal Citations43Total Downloads404Last 12 Months27Last 6 weeks4 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteGet Access
Global Efforts in Structural Genomics (2001)

A worldwide initiative in structural genomics aims to capitalize on the recent successes of the genome projects. Substantial new investments in structural genomics in the past 2 years indicate the high level of support for these international efforts. Already, enormous progress has been made on high-throughput methodologies and technologies that will speed up macromolecular structure determinations. Recent international meetings have resulted in the formation of an International Structural Genomics Organization to formulate policy and foster cooperation between the public and private efforts.
Efficient decomposition of single-qubit gates intoVbasis circuits (2013)

We develop efficient algorithms for compiling single-qubit unitary gates into circuits over the universal $V$ basis. The $V$ basis is an alternative universal basis to the more commonly studied basis consisting of Hadamard and $\ensuremath{\pi}/8$ gates. We propose two classical algorithms for quantum circuit compilation: the first algorithm has expected polynomial time [in precision $\mathrm{log}(1/\ensuremath{\epsilon})$] and produces an $\ensuremath{\epsilon}$ approximation to a single-qubit unitary with a circuit depth $\ensuremath{\le}12\phantom{\rule{0.16em}{0ex}}{\mathrm{log}}_{5}(2/\ensuremath{\epsilon})$. The second algorithm performs optimized direct search and yields circuits a factor of 3 to 4 times shorter than our first algorithm, but requires time exponential in $\mathrm{log}(1/\ensuremath{\epsilon})$; however, we show that in practice the runtime is reasonable for an important range of target precisions. Decomposing into the $V$ basis may offer advantages when considering the fault-tolerant implementation of quantum circuits.
[Evaluation of six rapid tests for screening of cannabis in sweat, saliva and tears]. (1999)

In order to demonstrate an intake of cannabis, there are a number of rapid tests, all of them being focused on urine. In this study, we evaluated the results of six tests when applied to sweat (DrugWipe), saliva and urine (Syva Rapidtest, Biomedix, Frontline, DrugWipe, Cortez Dako). Fifty regular users of cannabis and fifty persons who denied consuming it were studied. The results obtained with DrugWipe in sweat were compared with anamnesis data, whereas results obtained in saliva and urine were compared with those of gas chromatography--mass spectrometry. The results indicate that DrugWipe may be useful for screening cannabis in sweat when the intake took place less than two hours before. The results obtained in saliva showed that none of the tests studied are reliable to be used with this medium, because of the great number of false positive and false negative results. With urine, four tests (Syva Rapidtest, Biomedix, Cortez, Dako) led to very good results and may be recommended when an immediate presumptive test result is required.
Frequency trimming and Q-factor enhancement of micromechanical resonators via localized filament annealing (2002)

A batch-compatible, post-fabrication annealing technique based upon filament-like heating of microstructures is demonstrated as an effective means for trimming the resonance frequencies (f/sub 0/'s) and increasing the quality factors (Q's) of surface-micromachined, polysilicon, mechanical resonators. Although the technique is straightforward, involving the mere application of a suitable voltage between the anchors of a micromechanical resonator, it provides a substantial range of adjustment, with frequency trims of over 2.7% and Q increases of up to 600%, depending upon resonator fabrication history. By pulsing the anneal voltage waveforms, controlled frequency trims of less than 16 ppm per trial are achievable.
Liquid Chromatography-Mass Spectrometry (2006)

A constructive evaluation of the most significant developments in liquid chromatography-mass spectrometry (LC-MS) and its uses for quantitative bioanalysis and characterization for a diverse range of disciplines, Liquid Chromatography-Mass Spectrometry, Third Edition offers a well-rounded coverage of the latest technological developments and
The amino acid sequence of Escherichia coli cyanase. (1983)

The amino acid sequence of the enzyme cyanase (cyanate hydrolase) from Escherichia coli has been determined by automatic Edman degradation of the intact protein and of its component peptides. The primary peptides used in the sequencing were produced by cyanogen bromide cleavage at the methionine residues, yielding 4 peptides plus free homoserine from the NH2-terminal methionine, and by trypsin cleavage at the 7 arginine residues after acetylation of the lysines. Secondary peptides required for overlaps and COOH-terminal sequences were produced by chymotrypsin or clostripain cleavage of some of the larger peptides. The complete sequence of the cyanase subunit consists of 156 amino acid residues (Mr 16,350). Based on the observation that the cysteine-containing peptide is obtained as a disulfide-linked dimer, it is proposed that the covalent structure of cyanase is made up of two subunits linked by a disulfide bond between the single cystine residue in each subunit. The native enzyme (Mr 150,000) then appears to be a complex of four or five such subunit dimers.
The Rh blood group system: a review (2000)

The Rh blood group system is one of the most polymorphic and immunogenic systems known in humans. In the past decade, intense investigation has yielded considerable knowledge of the molecular background of this system. The genes encoding 2 distinct Rh proteins that carry C or c together with either E or e antigens, and the D antigen, have been cloned, and the molecular bases of many of the antigens and of the phenotypes have been determined. A related protein, the Rh glycoprotein is essential for assembly of the Rh protein complex in the erythrocyte membrane and for expression of Rh antigens. The purpose of this review is to provide an overview of several aspects of the Rh blood group system, including the confusing terminology, progress in molecular understanding, and how this developing knowledge can be used in the clinical setting. Extensive documentation is provided to enable the interested reader to obtain further information. (Blood. 2000;95:375-387)
Clustering Schemes for D2D Communications under Partial/No Network Coverage (2014)

Device-to-device (D2D) communications as an underlay to cellular networks can not only increase the system capacity and energy efficiency, but it can also enable national security and public safety (NSPS) services. A key requirement is to provide access to cellular services when the network is available and maintain local communication in the (partial) absence of the infrastructure. In this paper we propose and compare clustering schemes that are applicable for integrating D2D communications into cellular networks such that communication services can be maintained when the cellular infrastructure becomes partially dysfunctional. Our results show that there is a trade-off between coverage, energy efficiency and cluster formation delay and this trade-off can be handled by our proposed threshold-based clustering scheme.
Downregulation of Foxc2 enhances apoptosis induced by 5-fluorouracil through activation of MAPK and AKT pathways in colorectal cancer (2016)

The chemotherapy drug 5-fluorouracil (5-FU) is fundamental for the treatment of colorectal cancer (CRC); however, drug resistance to 5-FU may occasionally occur. Abnormal expression of Forkhead box C2 gene (Foxc2) has been identified in several human cancers, but the role of Foxc2 in the progression of CRC remains unclear. The present study established a stable Foxc2-short hairpin (sh)RNA cell line, which was confirmed by western blot analysis and quantitative polymerase chain reaction. The Foxc2-shRNA cells were treated with 5-FU and the cell viability was determined by an MTT assay. Western blot analysis was performed to investigate the signaling pathway involved in 5-FU treatment. The present study identified that 5-FU increased the percentage of apoptotic CRC cells among the Foxc2/RNA interference-transfected cells compared with cells transfected with an empty vector. Therefore, the downregulation of Foxc2, induced by 5-FU, may enhance apoptosis by the downregulation of apoptotic factors, including B cell lymphoma-2 and pro-caspase-3, in Foxc2-shRNA CRC cells. Furthermore, the mitogen-activated protein kinase (MAPK) and phosphatidylinositide 3-kinases/protein kinase B (PI3K/AKT) pathways were essential for the sensitization effect of Foxc2 to 5-FU treatment. Overall, these findings reveal the mechanisms behind Foxc2 depletion and 5-FU treatment of CRC and suggest that Foxc2 enhances resistance to apoptosis, induced by 5-FU, through the activation of MAPK and P13K/AKT pathways, and may serve as a valuable clinical prognostic marker for CRC.
High serum YKL‐40 level after surgery for colorectal carcinoma is related to short survival (2002)

These results suggest that determination of serum YKL-40 during followup of patients operated on for colorectal carcinoma might be useful for monitoring curatively resected patients.
Synthetic low-toxicity muramyl dipeptide and monophosphoryl lipid A replace Freund complete adjuvant in inducing growth-inhibitory antibodies to the Plasmodium falciparum major merozoite surface protein, gp195 (1991)

The Plasmodium falciparum major merozoite surface protein (gp195) is a protective antigen against lethal malaria. However, increasing evidence indicates that the efficacy of a malaria vaccine will require a strong adjuvant that is safe for human use. We compared the efficacies of two low-toxicity synthetic immunomodulators, B30-MDP (a lipophilic muramyl dipeptide derivative) and LA-15-PH (a synthetic equivalent of monophosphoryl lipid A), with that of Freund complete adjuvant (FCA) in eliciting an antibody response to gp195. Rabbits were immunized with native gp195 and B30-MDP, LA-15-PH, or the two in combination, with liposomes as the vehicle. Aluminum hydroxide and FCA were used as reference adjuvants. Results showed that adjuvant formulations based on B30-MDP alone or in combination with LA-15-PH induced high antibody titers to gp195, as compared with FCA. LA-15-PH alone was less effective. Aluminum hydroxide induced significantly lower antibody titers. The functional activity of the rabbit anti-gp195 antibodies induced by different adjuvants was evaluated in an in vitro parasite growth inhibition assay previously shown to correlate with anti-gp195 immunity in the Aotus monkey model. All rabbits immunized with B30-MDP-LA-15-PH and two of three rabbits immunized with B30-MDP alone produced sera that strongly inhibited parasite growth. The degree of growth inhibition was similar to that with FCA. The antibody titers of the rabbits receiving B30-MDP-LA-15-PH strongly correlated with the degree of in vitro growth inhibition. Our findings provided strong evidence that adjuvant formulations based on synthetic B30-MDP and LA-15-PH can replace FCA as adjuvants in stimulating protective immunity specific for gp195.
Oral Synthetic Phospholipid (DMPC) Raises High-Density Lipoprotein Cholesterol Levels, Improves High-Density Lipoprotein Function, and Markedly Reduces Atherosclerosis in Apolipoprotein E–Null Mice (2003)

DMPC (but not lecithin) raises HDL cholesterol and apoA-I, improves HDL function, and prevents lesions or causes their regression in apoE-null mice.
Higher Education and Graduate Employment in the Netherlands (2000)

Higher education in the Netherlands comprises the university sector and the sector for higher vocational education (Hoger Beroepsonderwijs or HBO). They developed under very different historical circumstances and are based on different rationales. There are 13 universities, nine of which provide teaching and conduct research in a wide range of disciplines in arts and sciences. Three (technical) universities offer courses mainly in science and engineering subjects and one is specialised in agricultural sciences. The HBO sector was established in the late 1960s when colleges for higher vocational training were upgraded. Major reforms in this sector resulted in the amalgamation of more than 400 smaller institutions oriented towards specific professional fields into large institutions providing a wide range of vocationally-oriented courses, with a standard period of study of four years. Today, there are some 65 HBO institutions providing theoretical and practical training with a clear vocational orientation. They have an important societal task of transferring and developing knowledge for the benefit of the professions in both the industrial and service sectors.
Interleukin 13 Mediates Signal Transduction through Interleukin 13 Receptor α2 in Pancreatic Ductal Adenocarcinoma: Role of IL-13 Pseudomonas Exotoxin in Pancreatic Cancer Therapy (2010)

These results indicate that IL-13Ralpha2 is a functional receptor as IL-13 mediates signaling in human pancreatic cancer cell lines. IL-13 causes transforming growth factor-beta activation via AP-1 pathway, which may cause tumor induced immunosuppression in the host. In addition, IL13-PE cytotoxin may be an effective therapeutic agent for the treatment of pancreatic cancer.
Surgery with cooperative robots (2008)

Advances in endoscopic techniques for abdominal procedures continue to reduce the invasiveness of surgery. Gaining access to the peritoneal cavity through small incisions prompted the first significant shift in general surgery. The complete elimination of external incisions through natural orifice access is potentially the next step in reducing patient trauma. While minimally invasive techniques offer significant patient advantages, the procedures are surgically challenging. Robotic surgical systems are being developed that address the visualization and manipulation limitations, but many of these systems remain constrained by the entry incisions. Alternatively, miniature in vivo robots are being developed that are completely inserted into the peritoneal cavity for laparoscopic and natural orifice procedures. These robots can provide vision and task assistance without the constraints of the entry incision, and can reduce the number of incisions required for laparoscopic procedures. In this study, a series of minimally invasive animal-model surgeries were performed using multiple miniature in vivo robots in cooperation with existing laparoscopy and endoscopy tools as well as the da Vinci Surgical System. These procedures demonstrate that miniature in vivo robots can address the visualization constraints of minimally invasive surgery by providing video feedback and task assistance from arbitrary orientations within the peritoneal cavity.
Epithelium formation in the Drosophila midgut depends on the interaction of endoderm and mesoderm (1994)

The reorganization of mesenchymal cells into an epithelial sheet is a widely used morphogenetic process in metazoans. An example of such a process is the formation of the Drosophila larval midgut epithelium that develops through a mesenchymal-epithelial transition from endodermal midgut precursors. We have studied this process in wild type and a number of mutants that show defects in midgut epithelium formation. Our results indicate that the visceral mesoderm serves as a basal substratum to which endodermal cells have to establish direct contact in order to form an epithelium. Furthermore, we have analyzed the midgut phenotype of embryos mutant for the gene shotgun, and the results suggest that shotgun directs adhesion between midgut epithelial cells, which is independent from the adhesion between endoderm and visceral mesoderm.
What are "ecogenomic sensors?" A review and thoughts for the future (2010)

Abstract. The OceanSensors08 workshop held 31 March–4 April 2008 in Warnemünde, Germany, brought together an international group of marine scientists, sensor developers and technologists with a common interest in shaping the future of ocean sensing. In preparation for that meeting a series of review papers was commissioned, one of which was meant to cover Sensors for Ocean-omics. The "ocean-omics" topic was cast very broadly. The notion was to review use of genetic techniques for assessing presence and diversity of organisms, their genomic capacity and gene expression, and to provide a prospectus of how such methods could be applied in an autonomous capacity. I chose "ecogenomic sensor" as a descriptor to convey the essence of such a system – a device that integrates genetic level sensing with larger scale environmental characterization. This phrase is derived from workshops refining the US's Ocean Observatories Initiative (OOI) and visions for instrument systems that could be deployed on such a network. But what exactly are ecogenomic sensors? A clear definition is lacking and conceptualizations far outweigh actual hardware that can be deployed in the ocean. This prospectus builds from that point. I advance a definition of "ecogenomic sensor" and outline the opportunities and challenges associated with developing such instruments. Suggestions as to how this technology may be further refined and applied are offered against the backdrop of the Autonomous Microbial Genosensor (AMG) and Environmental Sample Processor (ESP). Applications that center on detection of DNA and RNA are emphasized. The word "review" appears in the title at the request of the editors.