gebhart/patrepeval huggingface dataset:
The use of upward gradients to arrest downward dense, nonaqueous phase liquid (DNAPL) migration in the presence of solubilizing surfactants (1995)

This paper presents a mathematical analysis and the results of a series of laboratory experiments investigating in situ dissolution of dense, nonaqueous phase liquid (DNAPL) pools from porous media using solubilizing surfactants under upward-flowing conditions. Surfactant flood experiments were conducted in a one-dimensional glass column packed with natural sand. Perchloroethylene (PCE) was emplaced in the column as a pool perched above a coarse–fine sand interface to reproduce conditions occurring when DNAPL pools on a low permeability layer in the subsurface. Aqueous surfactant solution was directed vertically upward to counteract downward pool mobilization resulting from reduction of the PCE-water interfacial tension in the presence of surfactant. Experiments were conducted at overall hydraulic gradients across the sand pack of 0.0, 0.1, 0.2, 0.3, and 0.5. The surfactant flood solution consisted of a 1:1 blend of two commercial surfactants, Witconol NP-100 and Rexophos 25/97, in a 2% aqueous solution. Surfactant flooding was conducted until all visible traces of PCE were removed from the column. Subsequent water flooding was continued until effluent PCE concentrations exiting the column dropped below 5 ppm. In the zero gradient experiment, the PCE pool invaded the fine sand layer immediately upon contact with the surfactant because of a lowering of interfacial tension. PCE entry into the fine sand did not occur in the 0.3 and 0.5 gradient runs. Minor amounts of PCE mobilization occurred in the late stages of the 0.1 and 0.2 gradient runs and is attributed to a lowering of interfacial tension with time upon exposure to surfactant. Key words : solubilizing surfactant, groundwater remediation, DNAPL, tetrachloroethylene.
A 0.18¿m CMOS Dual-Band UWB Transceiver (2007)

A dual-band transceiver able to work on both UWB low band (3 to 5GHz) and high band (7 to 9GHz) is presented. A method of DSB upconversion in TX, and SSB downconversion and detection in RX is proposed to achieve high data rate non-coherent communication. Realized in 0.18 μm CMOS, the RX achieves an NF of 9.4dB, an IIP3 of -10.3dBm, and a sensitivity of -76dBm. It can attain a transmission rate up to 800Mb/s and draw 55mA and 76mA from a 1.8V supply in TX and RX, respectively.
An Improved General Amino Acid Replacement Matrix (2008)

Amino acid replacement matrices are an essential basis of protein phylogenetics. They are used to compute substitution probabilities along phylogeny branches and thus the likelihood of the data. They are also essential in protein alignment. A number of replacement matrices and methods to estimate these matrices from protein alignments have been proposed since the seminal work of Dayhoff et al. (1972). An important advance was achieved by Whelan and Goldman (2001) and their WAG matrix, thanks to an efficient maximum likelihood estimation approach that accounts for the phylogenies of sequences within each training alignment. We further refine this method by incorporating the variability of evolutionary rates across sites in the matrix estimation and using a much larger and diverse database than BRKALN, which was used to estimate WAG. To estimate our new matrix (called LG after the authors), we use an adaptation of the XRATE software and 3,912 alignments from Pfam, comprising approximately 50,000 sequences and approximately 6.5 million residues overall. To evaluate the LG performance, we use an independent sample consisting of 59 alignments from TreeBase and randomly divide Pfam alignments into 3,412 training and 500 test alignments. The comparison with WAG and JTT shows a clear likelihood improvement. With TreeBase, we find that 1) the average Akaike information criterion gain per site is 0.25 and 0.42, when compared with WAG and JTT, respectively; 2) LG is significantly better than WAG for 38 alignments (among 59), and significantly worse with 2 alignments only; and 3) tree topologies inferred with LG, WAG, and JTT frequently differ, indicating that using LG impacts not only the likelihood value but also the output tree. Results with the test alignments from Pfam are analogous. LG and a PHYML implementation can be downloaded from http://atgc.lirmm.fr/LG.
Utility-Aware Anonymization of Diagnosis Codes (2012)

The growing need for performing large-scale and low-cost biomedical studies has led organizations to promote the reuse of patient data. For instance, the National Institutes of Health in the U.S. requires patient-specific data collected and analyzed in the context of Genome-wide Association Studies (GWAS) to be deposited into a biorepository and broadly disseminated. While essential to comply with regulations, disseminating such data risks privacy breaches because patients' genomic sequences can be linked to their identities through diagnosis codes. This paper proposes a novel approach that prevents this type of data linkage by modifying diagnosis codes to limit the probability of associating a patient's identity to their genomic sequence. Our approach employs an effective algorithm that uses generalization and suppression of diagnosis codes to preserve privacy and takes into account the intended uses of the disseminated data to guarantee utility. We also present extensive experiments using several datasets derived from the electronic medical record (EMR) system of the Vanderbilt University Medical Center, as well as a large-scale case study using the EMRs of 79K patients, which are linked to DNA contained in the Vanderbilt University biobank. Our results verify that our approach generates anonymized data that permit accurate biomedical analysis in tasks including case count studies and GWAS.
Marriage: Sacrament of Love or Sacrament of Bond? (2000)

Devant les faillites nombreuses des couples, meme chretiens, d'une part, et la constante rigueur de l'Eglise, d'autre part, plusieurs peuvent se demander si le mariage doit etre avant tout considere comme un signe ou un sacrement de l'amour ou bien plutot comme le sacrement d'un lien a maintenir a tout prix. Comment l'Eglise s'est-elle autorisee a legiferer exclusivement sur le mariage de ses fideles, alors que c'est une institution qui appartient a la nature meme des humains ? L'A. s'est pose ces questions et, dans le present article, il cherche a demontrer que ce n'est pas par un coup d'etat que l'Eglise s'est emparee du mariage de ses fideles, mais graduellement, sous l'effet de circonstances historiques. Il concede d'abord que le mariage est une institution naturelle, mais tout de meme sacree car la Parole de Dieu l'a toujours considere comme l'image de son alliance avec le peuple juif et avec l'humanite entiere. Dans une deuxieme section, l'A. trace l'historique des interventions de l'Eglise qui, d'abord pastorales, morales, liturgiques et juridiques, sont devenues theologiques et dogmatiques. Dans une section a part, il souligne trois grandes interventions qui ont marque cette marche : l'interdiction du mariage des pretres, l'introduction d'une forme pour eviter les mariages clandestins et l'acceptation d'une identite du contrat avec le sacrement. Pour terminer son expose, l'A. fait six reflexions, dont les unes resument l'article et les autres posent de nouvelles questions, par ex. sur les ministres du sacrement, sur la facon de voir le divorce un peu comme les Eglises orientales, sur la necessite d'une forme canonique et enfin sur le pardon a accorder a ceux qui ne sont pas toujours fideles a leurs engagements.
The GENCODE pseudogene resource (2012)

At one extreme, some pseudogenes possess conventional characteristics of functionality; these may represent genes that have recently died. On the other hand, we find interesting patterns of partial activity, which may suggest that dead genes are being resurrected as functioning non-coding RNAs. The activity data of each pseudogene are stored in an associated resource, psiDR, which will be useful for the initial identification of potentially functional pseudogenes.
Resource bound certification (2000)

Various code certification systems allow the certification and static verification of important safety properties such as memory and control-flow safety. These systems are valuable tools for verifying that untrusted and potentially malicious code is safe before execution. However, one important safety property that is not usually included is that programs adhere to specific bounds on resource consumption, such as running time.
Repetitively pulsed mode-locked Nd:phosphate glass laser oscillator-amplifier system (1982)

Performance of a repetitively pulsed mode-locked Nd:glass laser system employing athermal phosphate glass in the oscillator and amplifier stages is described. Improved passive mode-locking characteristics of the oscillator are achieved through use of a l00-microm thick intracavity etalon, enabling reliable generation of transform-limited pulses typically of 5-psec duration. The system produces 1054-nm pulses of high beam quality and ~25-mJ energy at a pulse repetition rate of ~0.2 Hz. Subsequent frequency-doubling steps give conversion efficiencies of ~50% and 25%, respectively.
MPLS Transport Profile (MPLS-TP) Linear Protection to Match the Operational Expectations of Synchronous Digital Hierarchy, Optical Transport Network, and Ethernet Transport Network Operators (2014)

This document describes alternate mechanisms to perform some of the
functions of MPLS Transport Profile (MPLS-TP) linear protection
defined in RFC 6378, and also defines additional mechanisms. The
purpose of these alternate and additional mechanisms is to provide
operator control and experience that more closely models the behavior
of linear protection seen in other transport networks. This document
also introduces capabilities and modes for linear protection. A
capability is an individual behavior, and a mode is a particular
combination of capabilities. Two modes are defined in this document:
Protection State Coordination (PSC) mode and Automatic Protection
Switching (APS) mode. This document describes the behavior of the PSC
protocol including priority logic and state machine when all the
capabilities associated with the APS mode are enabled. This document
updates RFC 6378 in that the capability advertisement method defined
here is an addition to that document.
A novel MCM package enabling proximity communication I-O (2011)

A novel packaging approach is described that is based on micro-machined features integrated into CMOS chips. Our solution combines two key self-alignment mechanisms for the first time: solder reflow self-alignment and a novel micro-ball and pyramidal pit for passive self-alignment. We report on the demonstration of a MCM package with large footprint semiconductor CMOS chips interconnected by Proximity Communication (PxC), characterization of their high accuracy assembly process, and metrology of the resulting chip misalignment. Our goal is to develop a scalable, lead-free packaging approach by which large NxN PxC-enabled chip arrays are assembled with high precision on organic substrates in a cost effective manner while using industry standard parts and tooling.
PINK1-linked parkinsonism is associated with Lewy body pathology (2010)

Phosphatase and tensin homolog-induced putative kinase 1 gene mutations have been associated with autosomal recessive early-onset Parkinson's disease. To date, no neuropathological reports have been published from patients with Parkinson's disease with both phosphatase and tensin homolog-induced putative kinase 1 gene copies mutated. We analysed the coding region of phosphatase and tensin homolog-induced putative kinase 1 gene in a large Spanish family with six members with parkinsonism. The phenotype was characterized by an early-onset (mean: 31.6, standard deviation: 9.6 years, range: 14-45 years), slowly progressive levodopa-responsive parkinsonism, initial gait impairment and psychiatric symptoms. We identified two segregating pathogenic phosphatase and tensin homolog-induced putative kinase 1 mutations that were either in homozygous or heterozygous compound state in all affected family members. We found an exon 7 deletion (g.16089_16383del293; c.1252_1488del) and a novel+1U1-dependent 5' splice-site mutation in exon 7 (g.16378G>A; c.1488+1G>A). Leukocyte-derived messenger RNA analysis showed that both mutations caused exon 7 skipping and c.1488+1G>A also lead to an in-frame transcript with a 33 base-pair deletion (p.L485_R497del) resulting from activation of a 5' cryptic exon 7 splice site. Single photon emission computed tomography quantification of striatal dopamine transporter binding (123I-Ioflupane) revealed a posterior-anterior gradient similar to that of idiopathic Parkinson's disease, but there was no correlation between striatal reduced uptake and disease duration. Post-mortem neuropathological examination of an early-onset Parkinson's disease carrier of two heterozygous compound phosphatase and tensin homolog-induced putative kinase 1 mutations showed neuronal loss in the substantia nigra pars compacta, Lewy bodies and aberrant neurites in the reticular nuclei of the brainstem, substantia nigra pars compacta and Meynert nucleus, but the locus ceruleus and the amygdala were spared. This is the first neuropathological report of the brain from an early-onset phosphatase and tensin homolog-induced putative kinase 1-linked parkinsonism showing that mutated phosphatase and tensin homolog-induced putative kinase 1 protein induces Lewy body pathology. Unbalanced preservation of the locus ceruleus may well play a role in the slow evolution of motor symptoms and, probably, in the psychiatric symptoms often encountered in Parkinson's disease associated with phosphatase and tensin homolog-induced putative kinase 1 mutation.
FERRIC CITRATE: AN IRON-BASED ORAL PHOSPHATE BINDER (2012)

Patients with end-stage renal disease (ESRD) often experience secondary bone and mineral disorder requiring treatment with phosphate-binder (PB) medications, vitamin D sterols, and calcimimetics. Ferric citrate is an oral, iron-based PB in clinical development that has been shown to reduce serum phosphorus while increasing serum ferritin and transferrin saturation (TSAT) in ESRD patients. In a Phase 2 study, patients receiving ferric citrate experienced significant increases in serum ferritin (+10%) and TSAT (+18%) after 4 weeks of treatment. We analyzed electronic medical records of patients with concurrent rises in TSAT (≥ 10%) and ferritin (15% to 25%) between 6/1/08 and 12/31/10, excluding patients with significant change in iron or erythropoiesis-stimulating agent (ESA) dose, hemoglobin, or change in PB during the prior month. We assessed changes in epoetin alfa and iron dosing when physicians observed these increases in lab values. We constructed a cost offset model from a per patient per month (PPPM) considering average sales price of epoetin and iron that assumed equivalent phosphorus outcomes and pricing across all PB. The analysis included 2,037 concurrent, non-treatment related rises in ferritin and TSAT. Decreases in dose/dialysis session in mean epoetin and iron use 2 months following the index date represented an average combined savings of $90.51 to $181.01 PPPM. The model was most sensitive to baseline drug doses: patients at highest baseline epoetin doses (> 9,000U/session) showed savings of $471.80 to $943.61 PPPM. Based on actual physician behavior in response to ferritin and TSAT increases and ferric citrate clinical trial results, and assuming equivalent pricing to other PBs, there would be cost savings with ferric citrate use through reduced ESA and iron use.
Abstract C270: In vitro and in vivo antitumor activity of DCBCI0901, a potent PI3K/mTORC1/mTORC2 inhibitor. (2013)

Abstract The mammalian target of rapamycin (mTOR) is a highly conserved Ser/Thr protein kinase and a central controller of cell growth, proliferation, and survival. Studies have linked the hyperactive PI3K-AKT-mTOR signaling pathway in a variety of human cancers. Drugs targeting to PI3K and mTOR are likely to be an effective treatment for human malignancies that rely on these targets for their growth. Institute of Pharmaceutics at Development Center for Biotechnology in Taiwan has developed a novel and potent small molecule DCBCI0901 as PI3K/mTORC1/mTORC2 inhibitor. DCBCI0901 attenuated cell survival and proliferation in both in vitro and in vivo models. DCBCI0901 possessed IC50 of 8.4 nM against mTOR kinase and IC50 of 78 nM against PI3Kα (p110α/p85α) while exerting high selectivity against a panel of 20 other serine/ threonine and tyrosine kinases. In addition, DCBCI0901 is highly active in cellular assays. It causes a significant reduction in phospho-p70S6K (mTORC1 substrate), phospho-AKT (S473) (mTORC2 substrate), and phospho-AKT (T308) (PI3K substrate) levels. The antitumor efficacy of DCBCI0901 was evaluated in diverse human tumor cell lines. DCBCI0901 effectively inhibits cell proliferation of five well-established cell lines (one NSCLC, A549; two prostate cancers, PC-3 and LNCap; two breast cancers, HCC1954 and BT474), with IC50 values ranging from 6 to 48 nM. Notably, DCBCI0901 is effective against a panel of nine lung cancer cell lines (one cell line is EGFR-TKI sensitive model and eight cell lines are EGFR-TKI resistant model), with IC50 in the ten of nanomolar range. DCBCI0901 showed significant antitumor efficacy in mouse xenograft models including lung cancer, prostate cancer, and leukemia with tumor growth inhibition greater than 65%. DCBCI0901 also demonstrated effective suppression of tumor growth in advanced-stage xenograft models (lung cancer (A549), mean tumor volume &gt; 350mm3 at the start of treatment). Furthermore, in an EGFR-TKI resistant lung cancer H1975 xenograft model, DCBCI0901 effectively suppressed tumor growth. Based on the in vitro/in vivo pharmacology data, DCBCI0901 was selected as a drug candidate for further development as anticancer agent. This publication is dedicated to the memory of Dr. Paonien Chen. Citation Information: Mol Cancer Ther 2013;12(11 Suppl):C270. Citation Format: Ying-Shuan E. Lee, Mann-Yan Kuo, Yi-Ting Huang, Yu-Wen Tseng, Yu Jie Lin, Yen His Liu, Shian-Yi Chiou, Li Jung Chen, Y.-Y. Lu, Chih-Hsin Yang, Pan-Chyr Yang. In vitro and in vivo antitumor activity of DCBCI0901, a potent PI3K/mTORC1/mTORC2 inhibitor. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2013 Oct 19-23; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2013;12(11 Suppl):Abstract nr C270.
A Development of Information Management Model and System for Systematic Infrastructure Maintenance Management (2004)

The increase of social concern with the infrastructure maintenance and management makes it necessary to develop various types of information systems to support the management of social infrastructure in Korea. However most of the existing systems have decreased the practical usability, not because undue values were given to develop the functions of computistical aggregation on maintenance data, but because little consideration is given to present working conditions in practice. The purpose of this study is to develop Road Maintenance Business Support System(RMBSS), an information system, which is based on information management model for infrastructure management. This research is implemented to highway infrastructure which is being executed under the Korea MOCT. Business process of Local Highway Maintenance & Construction Service(LHMCS), as a authority of highway, was analyzed for user requirements focused on the core business process. An information management model was developed based on the result of these analysis. In turn an infrastructure maintenance & management system was developed for administrative business and technical affairs. The system will provide capabilities of maintenance work such as various reports, the state of affairs, statistical data without special efforts.
Cycloheximide-resistant temperature-sensitive lethal mutations of Saccharomyces cerevisiae. (1988)

We describe the isolation and preliminary characterization of a set of pleiotropic mutations resistant to the minimum inhibitory concentration of cycloheximide and screened for ts (temperature-sensitive) growth. These mutations fall into 22 complementation groups of cycloheximide resistant ts lethal mutations (crl). None of the crl mutations appears to be allelic with previously isolated mutations. Fifteen of the CRL loci have been mapped. At the nonpermissive temperature (37 degrees), these mutants arrest late in the cell cycle after several cell divisions. Half of these mutants are also unable to grow at very low temperatures (5 degrees). Although mutants from all of the 22 complementation groups exhibit similar temperature-sensitive phenotypes, an extragenic suppressor of the ts lethality of crl3 does not relieve the ts lethality of most other crl mutants. A second suppressor mutation allows crl10, crl12, and crl14 to grow at 37 degrees but does not suppress the ts lethality of the remaining crl mutants. We also describe two new methods for the enrichment of auxotrophic mutations from a wild-type yeast strain.
The Phosphatase MKP1 Is a Transcriptional Target of p53 Involved in Cell Cycle Regulation (2003)

The tumor suppressor p53 protein suppresses cell growth by inducing cell cycle arrest or apoptosis. Despite the fact that p53-dependent p21-mediated G1 arrest induced by DNA damage is well defined, the role of p53 in the cell cycle in response to the MAKP signaling remains to be determined. Here we show that MKP1, a member of the dual specificity protein phosphatase family capable of inactivating MAPKs, is a transcriptional target of p53. MKP1 mRNA and protein levels were increased upon p53 activation in several well defined p53-regulated cell systems. p53 bound to a consensus p53 binding site located in the second intron of the MKP1 gene and transactivated MKP1 in reporter gene assays. Inhibition of phosphatase activity impaired p53-mediated G1 arrest in arrested human glioblastoma GM cells in response to growth factor stimuli. Importantly conditional expression of MKP1 prevented arrested human cancer cells from entering into the cell cycle. Thus, these results provide a novel mechanism by which p53 controls the cell cycle in response to the MAPK signaling in the absence of DNA damage and suggest that p53 may negatively control the MAKP pathway via MKP1.
Photoemission study of the effect of annealing temperature on a<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mrow><mml:msub><mml:mrow><mml:mi mathvariant="normal">K</mml:mi></mml:mrow><mml:mrow><mml:mn>2</mml:mn></mml:mrow></mml:msub></mml:mrow><mml:mrow><mml:msub><mml:mrow><mml:mi mathvariant="normal">O</mml:mi></mml:mrow><mml:mrow><mml:mn>2</mml:mn></mml:mrow></mml:msub></mml:mrow><mml:mo>/</mml:mo><mml:mi mathvariant="normal">S</mml:mi><mml:mi mathvariant="normal">i</mml:mi><mml:mo>(</mml:mo><mml:mn>100</mml:mn><mml:mo>)</mml:mo><mml:mn/></mml:math>surface (1999)

Photoelectron spectroscopy and work-function measurements have been used to study a ${\mathrm{K}}_{2}{\mathrm{O}}_{2}/\mathrm{S}\mathrm{i}(100)$ surface as a function of annealing temperature. The results show that the features for ${\mathrm{K}}_{2}{\mathrm{O}}_{2}$ gradually move to high binding energy, and the work function decreases with increasing temperature up to 460 K. As the species of ${\mathrm{K}}_{2}{\mathrm{O}}_{2}$ decomposes at 540 K, there exist two kinds of oxygen bonding states. A thin K-O layer is formed on the top surface, while oxygen bonded to silicon is located at subsurface, leading to an extremely low value (0.3 eV) of the work function. For further annealing, the oxygen bonded to potassium gradually transfers to Si due to the desorption of potassium, and Si-O bonds appear on the top layer, which is related to increases of the work function.