gebhart/patrepeval huggingface dataset:
Evaluation of hypermethylated tumor suppressor genes as tumor markers in mouth and throat rinsing fluid, nasopharyngeal swab and peripheral blood of nasopharygeal carcinoma patient (2003)

The purpose of our study was to evaluate the frequency of hypermethylated tumor suppressor genes (TSGs) in peripheral blood, mouth and throat (M&T) rinsing fluid and nasopharyngeal (NP) swabs of nasopharyngeal carcinoma (NPC) patients. Six normal NP tissues, 43 M&T rinsing fluid, 37 NP swabs and 43 peripheral blood from healthy non-smokers and non-drinkers without a family history of NPC, and 30 NPC tumors and their matched body fluid were analyzed for the presence of hypermethylated p15, p16, Ras association domain family 1 (RASSF1A), E-cadherin, and death-associated protein kinase (DAPK) by methylation-specific PCR. Sequencing analysis was carried out on selected NPC tumors and body fluid samples. Twenty-nine (97%) tumors displayed methylation in at least 1 of the 5 genes. The methylation frequencies were 80% for p15, 77% for DAPK, 67% for RASSF1A, 53% for E-cadherin and 33% for p16. The frequency range of aberrant methylated genes in the body fluids were NP swabs (17-63%) and M&T rinsing fluid (17-50%). Methylation was found in <20% of peripheral blood for each respective gene. Methylation was, however, detected in 1 M&T rinsing fluid in which the primary tumor showed methylation free for RASSF1A. Five healthy individuals exhibited methylation for DAPK, or RASSF1A, or p15 in their body fluid samples. All body fluid samples of healthy controls showed methylation free for E-cadherin and p16. Epigenetic change is found frequently in NPC and the high detection rate in body fluids suggest its potential application in non-invasive screening of NPC or detection of residual carcinoma after treatment.
Contracting Wide-area Network Topologies to Solve Flow Problems Quickly (2021)

Many enterprises today manage traffic on their wide-area networks using software-defined traffic engineering schemes, which scale poorly with network size; the solver runtimes and number of forwarding entries needed at switches increase to untenable levels. We describe a novel method, which, instead of solving a multi-commodity flow problem on the network, solves (1) a simpler problem on a contraction of the network, and (2) a set of sub-problems in parallel on disjoint clusters within the network. Our results on the topology and demands from a large enterprise, as well as on publicly available topologies, show that, in the median case, our method nearly matches the solution quality of currently deployed solutions, but is 8x faster and requires 6x fewer FIB entries. We also show the value-add from using a faster solver to track changing demands and to react to faults.
A Low-Jitter Ring-Oscillator Phase-Locked Loop Using Feedforward Noise Cancellation With a Sub-Sampling Phase Detector (2018)

Ring-oscillator (RO)-based phase-locked loops (PLLs) are very attractive for system-on-chip applications for their compactness and tuning range, but suffer from high jitter and supply noise sensitivity. This paper presents a sub-sampling phase detector (SSPD)-based feedforward noise cancellation (FFNC) technique to improve these drawbacks of the RO PLL. The FFNC scheme utilizes the already available SSPD output to perform cancellation with high sensitivity while utilizing low power and area overhead. The 2- to 2.8-GHz RO PLL proof-of-principle prototype occupies 0.022 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> active area in 65 nm CMOS; it achieves a 633 fs rms jitter at 2.36 GHz with 5.86 mW power consumption and an figure of merit (FOM <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">jitter</sub> ) of -236.3 dB. The cancellation reduces the jitter by 1.4×, the phase noise by 10.2 dB to -123.5 dBc/Hz at 300-kHz offset, and the RO supply sensitivity by 19.5 dB for a 1 mVpp 100-kHz noise tone on the RO supply.
Cloning and characterization of the genes encoding the malolactic enzyme and the malate permease of Leuconostoc oenos (1996)

Using degenerated primers from conserved regions of the protein sequences of malic enzymes, we amplified a 324-bp DNA fragment by PCR from Leuconostoc oenos and used this fragment as a probe for screening a Leuconostoc oenos genomic bank. Of the 2,990 clones in the genomic bank examined, 7 with overlapping fragments were isolated by performing colony hybridization experiments. Sequencing 3,453 bp from overlapping fragments revealed two open reading frames that were 1,623 and 942 nucleotides long and were followed by a putative terminator structure. The first deduced protein (molecular weight, 59,118) is very similar (level of similarity, 66%) to the malolactic enzyme of Lactococcus lactis; as in several malic enzymes, highly conserved protein regions are present. The synthesis of a protein with an apparent molecular mass of 60 kDa was highlighted by the results of labelling experiments performed with Escherichia coli minicells. The gene was expressed in E. coli and Saccharomyces cerevisiae and conferred "malolactic activity" to these species. The second open reading frame encodes a putative 34,190-Da protein which has the characteristics of a carrier protein and may have 10 membrane-spanning segments organized around a central hydrophilic core. Energy-dependent L-[14C]malate transport was observed with E. coli dicarboxylic acid transport-deficient mutants carrying the malate permease-expressing vector. Our results suggest that in Leuconostoc oenos the genes that encode the malolactic enzyme and a malate carrier protein are organized in a cluster.
The Third Extracellular Loop of the μ Opioid Receptor Is Important for Agonist Selectivity (1995)

To investigate the interaction between the mu opioid receptor and its ligands, we compared the binding of mu-selective ligands to two mu/kappa chimeric opioid receptors and to mu and kappa receptors. The two chimeras were constructed from cloned rat mu and kappa receptors in which a segment from the middle of the third intracellular loop to the C terminus was exchanged. When this portion of the kappa receptor was replaced by that of the mu receptor, affinities of mu selective agonists, DAMGO (Tyr-D-Ala-Gly-NMePhe-Gly-ol), PL017 (Tyr-Pro-NMePhe-D-Pro-NH2), sufentanil, and morphine, were greatly increased as compared to those for the kappa receptor. Conversely, when this region of the mu receptor was substituted by that of the kappa receptor, affinities for these agonists were substantially decreased as compared with those of the mu receptor. Unlike selective agonists, the mu-selective antagonist, CTAP (D-Phe-Cys-Tyr-D-Trp-Arg-Thr-penicillamine-Thr-NH2), displayed a low affinity for both chimeric receptors, similar to that of the kappa receptor. Thus, the region from the middle of the third intracellular loop to the C terminus of the mu receptor is important for the binding of selective agonists. Conversely, the determinants for selective binding of the antagonist CTAP reside in a more extended region of the receptor.
Molecular-beam epitaxial growth of uniform Ga0.47In0.53As with a rotating sample holder (1981)

Ga0.47In0.53As and Al0.48In0.52As were grown lattice matched to InP substrates with a rotating substrate holder. The Ga, In, and Al beams were supplied by separate effusion cells and the uniformity of the resulting layers was evaluated with x-ray rocking curves for different rotation speeds. Lateral variation of the lattice constant as small as 10−5 per cm may be achieved with a rotation speed of 3 rpm. The full width at half-maximum of the x-ray spectrum from the epitaxial layer is comparable to that of the substrate indicating that there is practically no compositional grading.
Whole-body cooperative force control for a two-armed and two-wheeled mobile robot using Generalized Inverse Dynamics and Idealized Joint Units (2010)

This paper proposes a control framework for a two-armed and two-wheeled mobile robot that can coordinate all the joint forces to achieve diverse motion objectives such as position, velocity, acceleration, force and impedance at any part of the body. The framework comprises two components: 1) Generalized Inverse Dynamics (GID) that determines joint forces satisfying multiple objectives considering task priorities and various constraints and 2) the Idealized Joint Unit (IJU) that generates accurate torque with assigned apparent inertia and viscosity. GID treats the robot as a single manipulator with multiple branches using a joint model with 2-DOF motion subspace equivalent to two opposing wheels. A 21-DOF mobile robot equipped with IJUs is set up and GID is applied to it. The result shows that GID works well in the examples of physical human-robot interaction and object manipulation where motion objectives are attained coordinating the whole body while keeping passivity due to the redundancy and the assigned impedance property.
The Inhibition of Foaming. VI. The Transmission of Light by Unstable Foams (1954)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThe Inhibition of Foaming. VI. The Transmission of Light by Unstable FoamsSydney Ross, Bruce Barth, and J. F. TerenziCite this: J. Phys. Chem. 1954, 58, 3, 247–250Publication Date (Print):March 1, 1954Publication History Published online1 May 2002Published inissue 1 March 1954https://pubs.acs.org/doi/10.1021/j150513a015https://doi.org/10.1021/j150513a015research-articleACS PublicationsRequest reuse permissionsArticle Views39Altmetric-Citations4LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access options Get e-Alerts
On methods for improving performance of PI-type fuzzy logic controllers (1993)

To improve limitations of fuzzy PI controller especially when applied to high order systems, we propose two types of fuzzy logic controllers that take out appropriate amounts of accumulated control input according to fuzzily described situations in addition to the incremental control input calculated by conventional fuzzy PI controllers. The structures of the proposed controller were motivated by the problems of fuzzy PI controllers that they generally give inevitable overshoot when one tries to reduce rise time of response especially when a system of order higher than one is under consideration. Since the undesirable characteristics of the fuzzy PI controller are caused by integrating operation of the controller, even though the integrator itself is introduced to to overcome steady state error in response, we propose two fuzzy controllers that fuzzily clear out integrated quantities according to situation. The first controller determines the fuzzy resetting rate by situations described fuzzily by error and error rate, and the second one by error and control input. The two structures both give reduced rise time as well as small overshoot.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Quantitative Analysis of Gene Suppression in Integrated Retrovirus Vectors (1986)

Previously, we described a retrovirus vector that contained two genes: a 5' gene under transcriptional control of the viral long terminal repeat and a 3' gene under transcriptional control of the herpes simplex virus thymidine kinase promoter. By using a biological assay, we found that expression of the 5' gene is suppressed when there was selection for the 3' gene and expression of the 3' gene is suppressed when there is selection for the 5' gene (M. Emerman and H. M. Temin, Cell 39:459-467, 1984). In the present study, we replaced the thymidine kinase promoter with stronger promoters, and we measured expression of the genes in the retrovirus vectors by enzyme activity and RNA analysis. We found that all of the vectors displayed gene suppression when analyzed biochemically, although not when analyzed biologically. The suppressed genes produced about 10 to 50% as much product as when they were selected. The amount of suppression depended on whether the suppressed gene was 5' or 3' to the selected gene and from which promoter the suppressed gene was transcribed. The amount of suppression correlated with a decrease in the amount of steady-state RNA transcribed from the suppressed gene's promoter.
A New Race of <i>Fusarium oxysporum</i> f. sp. <i>melonis</i> Causing Fusarium Wilt of Muskmelon in the Central Valley of California (1997)

In 1996, cantaloupe (Cucumis melo L. cv. Durango) vines in two fields exhibited wilt, vascular discoloration, and necrotic streaks on the stems. Fusarium oxysporum Schlechtend.:Fr. was isolated from the stems of vines from both fields. One isolate from each field was compared with known isolates of F. oxysporum f. sp. melonis (Leach & Currence) W.C. Snyder & H.N. Hansen races 1 and 2 in a differential host range experiment in the greenhouse. Three-week-old seedlings were root-dip inoculated with monoconidial isolates at a concentration of 5 × 10 5 spores per ml. Control plants were dipped in water. In two experiments, the test isolates killed the susceptible varieties Top Mark and Magnum .45 and the race 2 resistant varieties Durango, Gold Mine, and Perlita FR. Seedlings of variety Charentais with the Fom2 gene conferring resistance to race 1 were resistant to both test isolates. It was determined that both of these isolates are associated with vegetative compatibility group (VCG) 0134 (1). This is the first report of race 1 and VCG 0134 of F. oxysporum f. sp. melonis causing Fusarium wilt of muskmelon in the Central Valley of California, and the first reported occurrence of race 1 in California since 1973 (2). Cantaloupe varieties currently grown in California are susceptible to race 1 of F. oxysporum f. sp. melonis References: (1) D. J. Jacobson and T. R. Gordon. Phytopathology 78:668, 1988. (2) J. V. Leary and W. D. Wilbur. Phytopathology 66:15, 1976.
Can Music Foster Learning – Effects of Different Text Modalities on Learning and Information Retrieval (2018)

This study investigates the possibilities of fostering learning based on differences in recall and comprehension after learning with texts which were presented in one of three modalities: either in a spoken, written, or sung version. All three texts differ regarding their processing, especially when considering working memory. Overall, we assume the best recall performance after learning with the written text and the best comprehension performance after learning with the sung text, respectively, compared to both other text modalities. We also analyzed whether the melody of the sung material functions as a mnemonic aid for the learners in the sung text condition. If melody and text of the sung version are closely linked, presentation of the melody during the post-test phase could foster text retrieval. 108 students either learned from a sung text performed by a professional singer, a printed text, or the same text read out loud. Half of the participants worked on the post-test while listening to the melody used for the musical learning material and the other half did not listen to a melody. The written learning modality led to significantly better recall than with the spoken (<i>d</i> = 0.97) or sung text (<i>d</i> = 0.78). However, comprehension after learning with the sung modality was significantly superior compared to when learning with the written learning modality (<i>d</i> = 0.40). Reading leads to more focus on details, which is required to answer recall questions, while listening fosters a general understanding of the text, leading to higher levels of comprehension. Listening to the melody during the post-test phase negatively affected comprehension, irrespective of the modality during the learning phase. This can be explained by the seductive detail effect, as listening to the melody during the post-test phase may distract learners from their main task. In closing, theoretical and practical implications are discussed.
ON THE PROBLEM OF PLACING NAMES IN A GEOGRAPHIC MAP (1987)

The automatic placement of names on a geographic map, a seemingly straightforward computer task, is, in fact, remarkably complex. This paper describes the results of a research study which has led to the development of AUTONAP, an expert system for automatic name placement. The system attempts to emulate the manner in which an expert cartographer would place names. It utilizes heuristic knowledge about map placement and visual perception, embeds this in a set of explicit rules that form the knowledge base of the system, and draws on techniques from machine pattern analysis to achieve fully automatic placement of all the names in a map.
A Qualitative Comparison of CoQA, SQuAD 2.0 and QuAC (2018)

We compare three new datasets for question answering: SQuAD 2.0, QuAC, and CoQA, along several of their new features: (1) unanswerable questions, (2) multi-turn interactions, and (3) abstractive answers. We show that the datasets provide complementary coverage of the first two aspects, but weak coverage of the third. Because of the datasets' structural similarity, a single extractive model can be easily adapted to any of the datasets and we show improved baseline results on both SQuAD 2.0 and CoQA. Despite the similarity, models trained on one dataset are ineffective on another dataset, but we find moderate performance improvement through pretraining. To encourage cross-evaluation, we release code for conversion between datasets at https://github.com/my89/co-squac .
The selective tyrosine kinase inhibitor STI571 inhibits small cell lung cancer growth. (2000)

At least 70% of small cell lung cancers express the Kit receptor tyrosine kinase and its ligand, stem cell factor (SCF). Numerous lines of evidence have demonstrated that this coexpression constitutes a functional autocrine loop, suggesting that inhibitors of Kit tyrosine kinase activity could have therapeutic efficacy in this disease. STI571, formerly known as CGP 57148B, is a p.o. bioavailable 2-phenylaminopyrimide derivative that was designed as an Abl tyrosine kinase inhibitor, but also has efficacy against the platelet-derived growth factor receptor and Kit in vitro. Pretreatment of the H526 small cell lung cancer (SCLC) cell line with STI571 inhibited SCF-mediated Kit activation with an IC50 of 0.1 microM as measured by inhibition of receptor tyrosine phosphorylation and 0.2 microM as measured by immune complex kinase assay. This paralleled the inhibition of SCF-mediated growth by STI571, which had an IC50 of approximately 0.3 microM. Growth inhibition in SCF-containing medium was accompanied by induction of apoptosis. STI571 efficiently blocked SCF-mediated activation of mitogen-activated protein kinase and Akt, but did not affect insulin-like growth factor-1 or serum-mediated mitogen-activated protein kinase or Akt activation. Growth of five of six SCLC cell lines in medium containing 10% FCS was inhibited by STI571 with an IC50 of approximately 5 microM. Growth inhibition in serum-containing medium appeared to be cytostatic in nature because no increase in apoptosis was observed. Despite this growth inhibition, STI571 failed to enhance the cytotoxicity of either carboplatinum or etoposide when coadministered. However, taken together with the minimal toxicity that this compound has shown in preclinical studies, these data suggest that STI571 could have a role in the treatment of SCLC, possibly to block or slow recurrence after chemotherapy-induced remissions.
<i>Pseudomonas</i> Exotoxin A-Mediated Apoptosis Is Bak Dependent and Preceded by the Degradation of Mcl-1 (2010)

Pseudomonas exotoxin A (PE) is a bacterial toxin that arrests protein synthesis and induces apoptosis. Here, we utilized mouse embryo fibroblasts (MEFs) deficient in Bak and Bax to determine the roles of these proteins in cell death induced by PE. PE induced a rapid and dose-dependent induction of apoptosis in wild-type (WT) and Bax knockout (Bax(-/-)) MEFs but failed in Bak knockout (Bak(-/-)) and Bax/Bak double-knockout (DKO) MEFs. Also a loss of mitochondrial membrane potential was observed in WT and Bax(-/-) MEFs, but not in Bak(-/-) or in DKO MEFs, indicating an effect of PE on mitochondrial permeability. PE-mediated inhibition of protein synthesis was identical in all 4 cell lines, indicating that differences in killing were due to steps after the ADP-ribosylation of EF2. Mcl-1, but not Bcl-x(L), was rapidly degraded after PE treatment, consistent with a role for Mcl-1 in the PE death pathway. Bak was associated with Mcl-1 and Bcl-x(L) in MEFs and uncoupled from suppressed complexes after PE treatment. Overexpression of Mcl-1 and Bcl-x(L) inhibited PE-induced MEF death. Our data suggest that Bak is the preferential mediator of PE-mediated apoptosis and that the rapid degradation of Mcl-1 unleashes Bak to activate apoptosis.
Privacy-preserving experimentation with sensibility testbed (2015)

Recent privacy breaches and security break-ins of mobile systems have raised concerns about using mobile devices like smartphones and tablets [1]. As a result, many users are aware that running apps on their smartphones can increase privacy risks. On the other hand, the data from the enormous number of smartphones, if used properly, can be of tremendous value to the research community. Is there a way to safely do research on these devices without rendering them vulnerable? We explain about how our project may help both researchers and volunteers.
PmSUC3: Characterization of a SUT2/SUC3-Type Sucrose Transporter from <i>Plantago major</i> (2003)

Higher plants possess medium-sized gene families that encode plasma membrane-localized sucrose transporters. For several plant species, it has been shown that at least one of these genes (e.g., AtSUC3 in Arabidopsis and LeSUT2 in tomato) differs from all other family members in several features, such as the length of the open reading frame, the number of introns, and the codon usage bias. For these reasons, and because two of these proteins did not rescue a yeast mutant defective in sucrose utilization, it had been speculated that this subgroup of transporters might have sensor functions. Here, we describe the detailed functional characterization and cellular localization of PmSUC3, the orthologous transporter from the Plantago major transporter family. The PmSUC3 protein is localized in the sieve elements of the Plantago phloem and mediates the energy-dependent transport of sucrose and maltose. In contrast to the situation in solanaceous plants, PmSUC3 is not colocalized with PmSUC2, the source-specific, phloem-loading sucrose transporter of Plantago. Moreover, PmSUC3 also was identified in sieve elements of sink leaves and in several nonphloem cells and tissues. Arguments for and against a potential sensor function for this type of sucrose transporter are presented, and the role of this type of transporter in the regulation of sucrose fluxes is discussed.