gebhart/patrepeval huggingface dataset:
Abstract 6609: Detection of rare mutations, copy number variation, and DNA methylation in the same template DNA molecules (2023)

Abstract The analysis of cell-free DNA (cfDNA) from plasma offers great promise for the earlier detection of cancer. At present, changes in DNA sequence, methylation, or copy number are the most sensitive ways to detect the presence of cancer. To increase the sensitivity of such assays, it would be useful to be able evaluate the same template molecules for all these changes. Here we report an approach, called MethylSaferSeqS, that achieves this goal, and can be applied to any standard library preparation method suitable for massively parallel sequencing. The innovative step was to copy both strands of each DNA-barcoded molecule with a primer that allows the subsequent separation of the original strands (retaining their 5-methylcytosine residues) from the copied strands (in which the 5-methylcytosine residues are replaced with unmodified cytosine residues). The original and copied strands are queried for epigenetic and genetic alterations, respectively. We applied this approach to plasma from 265 individuals, including 198 with cancers of the pancreas, ovary, lung or colon, and found the expected patterns of mutations, copy number alterations, and methylation. Furthermore, we could determine which original template DNA molecules were methylated and/or mutated. MethylSaferSeqS should be useful for addressing a variety of questions relating genetics and epigenetics in the future. Citation Format: Yuxuan Wang, Christopher Douville, Joshua Cohen, Chetan Bettegowda, Nick Papadopoulos, Ken Kinzler, Bert Vogelstein. Detection of rare mutations, copy number variation, and DNA methylation in the same template DNA molecules. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6609.
Eigenvalues of a Microwave Cavity Filled with a Plasma of Variable Radial Density (1970)

A solution to the eigenvalue problem of a cylindrical plasma of variable radial density placed coaxially within a cylindrical cavity has been obtained. The solution is based on a model constructed by dividing the plasma into a series of concentric shells, in each of which the plasma density is assumed to be constant but not necessarily equal to that of any other shell. Maxwell's equations are solved exactly for the electro-magnetic fields in each shell. The boundary relations at the inner and outer surface of each shell and at the cavity walls result in a set of simultaneous equations which may be solved numerically for the eigenfrequencies if the cavity dimensions, number of shells, and density in each shell are specified. For a given density profile, which may be obtained from experiments, the frequency shift of the system for a given mode may be determined as a function of the density of the central shell. A 10-shell model has been used to solve for the frequencies of the first 10 modes of a cylindrical cavity.
Alternative Input Devices for Efficient Navigation of Large CT Angiography Data Sets (2005)

The trackball may not be the optimal device for navigation of large CT angiography data sets; the use of other existing devices may improve the efficiency of interpretation of these sets.
Mixing and Turbulence in a Flooding Coastal River (2013)

An experimental study of turbulence and vertical mixing was carried out in the lower east Pearl River (Mississippi and Louisiana) during a high-discharge period in February and March of 2010. Direct estimates were made of the time-varying profile of turbulent Reynolds stresses (τx/ρ=−u′w′¯) through the water column. From this, both the vertical eddy viscosity (Km) and mean vertical mixing time were calculated, and the water column was shown to be vertically well mixed at all times. Segmenting the stresses into stresses due to river discharge and stresses due to tidal flows shows the coequal nature of each component and highlights the ways they vary in importance during different flow regimes. Two simple turbulence models are examined and compared to the measured mixing parameters.
2-(Triphenylphosphonio)-4,5-bis(thiobenzoyl)-1,3-dithiole Tetrafluoroborate: A Versatile Wittig Reagent for the Synthesis of Unsymmetrical Tetrathiafulvalenes and 1,3-Dithiol-2-ylidene Derivatives (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXT2-(Triphenylphosphonio)-4,5-bis(thiobenzoyl)-1,3-dithiole Tetrafluoroborate: A Versatile Wittig Reagent for the Synthesis of Unsymmetrical Tetrathiafulvalenes and 1,3-Dithiol-2-ylidene DerivativesThomas K. Hansen, Martin R. Bryce, Judith A. K. Howard, and Dimitri S. YufitCite this: J. Org. Chem. 1994, 59, 18, 5324–5327Publication Date (Print):September 1, 1994Publication History Published online1 May 2002Published inissue 1 September 1994https://pubs.acs.org/doi/10.1021/jo00097a038https://doi.org/10.1021/jo00097a038research-articleACS PublicationsRequest reuse permissionsArticle Views201Altmetric-Citations22LEARN 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 optionsGet e-Alertsclose Get e-Alerts
Review: Circulating microRNAs in Predicting the Prognosis of Gastrointestinal Cancers (2016)

Gastrointestinal cancers remain a significant health problem worldwide. Resistance to treatment in a subset of patients is a major problem and personalized treatment is expected to improve prognosis in these individuals. Assessment of biomarkers, which are generally genes, proteins, phosphoproteins and/or microRNAs (miRNAs), and their levels in tumor or blood, leads to a view of the molecular characteristics (signature) of a given patient’s tumor and thus provides information that will enable personalized treatment. miRNAs are short noncoding RNAs that regulate gene expression at the post-transcriptional level. Deregulation of miRNA expression has been demonstrated in various cancers, including gastrointestinal (GI) cancers. The high stability of miRNAs in the blood circulation offers enormous advantage for prognostic applications as blood samples can be easily procured noninvasively. Circulating miRNAs have been demonstrated to be valuable instruments in prognosis of GI cancers. Additionally, serial collection of blood samples is possible for monitoring the progress of cancer, something that cannot be done reasonably with tumor tissue. We review previous reports that used circulating miRNAs as biomarkers in the prognosis of GI cancers, and also highlight the fascinating possibility of using the gathered information to identify new therapeutic targets. Keywords: Circulating microRNA, colorectal cancer, esophageal cancer, gastric cancer, gastrointestinal cancers, hepatocellular carcinoma, pancreatic cancer.
Hierarchical decision processes that operate over distinct timescales underlie choice and changes in strategy (2016)

Decision-making in a natural environment depends on a hierarchy of interacting decision processes. A high-level strategy guides ongoing choices, and the outcomes of those choices determine whether or not the strategy should change. When the right decision strategy is uncertain, as in most natural settings, feedback becomes ambiguous because negative outcomes may be due to limited information or bad strategy. Disambiguating the cause of feedback requires active inference and is key to updating the strategy. We hypothesize that the expected accuracy of a choice plays a crucial rule in this inference, and setting the strategy depends on integration of outcome and expectations across choices. We test this hypothesis with a task in which subjects report the net direction of random dot kinematograms with varying difficulty while the correct stimulus-response association undergoes invisible and unpredictable switches every few trials. We show that subjects treat negative feedback as evidence for a switch but weigh it with their expected accuracy. Subjects accumulate switch evidence (in units of log-likelihood ratio) across trials and update their response strategy when accumulated evidence reaches a bound. A computational framework based on these principles quantitatively explains all aspects of the behavior, providing a plausible neural mechanism for the implementation of hierarchical multiscale decision processes. We suggest that a similar neural computation-bounded accumulation of evidence-underlies both the choice and switches in the strategy that govern the choice, and that expected accuracy of a choice represents a key link between the levels of the decision-making hierarchy.
Announcing the otolaryngology-head and neck surgery section of the Medscape Journal of Medicine. (2008)

I am proud to introduce the Otolaryngology-Head and Neck Surgery (OTO-HNS) section of The Medscape Journal of Medicine. This is the first exclusively online, open access, MEDLINE-indexed journal dedicated to otolaryngology-head and neck surgery. Not to be mislabeled as “just another Web site” or an “online textbook,” the OTO-HNS section of The Medscape Journal of Medicine is a fully peer-reviewed, MEDLINE-indexed journal.
Downlink MIMO Systems Using Cooperation Among Base Stations in a Slow Fading Channel (2007)

To increase the achievable sum rate of downlink MIMO (Multiple Input Multiple Output) systems, the cooperation among Base Stations (BS) is investigated in a slow fading channel. Three levels of BS coordination are considered: full coordination, partial coordination, and no coordination. This paper assumes that the downlink MIMO channel state information (CSI) is sent to the corresponding BS through a feedback link with some delay. In a fully coordinated system, the CSI at each BS needs to be collected at the central coordinator, and this process may result in significant additional delay. In this paper, the achievable throughput of each coordination level is evaluated and compared including the effects of the delay in CSI. A quasi-static fading is considered where the channel is static within one codeword, but it gradually changes over time based on the well-known Jake's model. Also, dirty paper coding (DPC) is applied, which is a transmission method shown to achieve the sum capacity of MIMO broadcast channels (BC). The results show that under certain delay conditions, the partially-coordinated system outperforms the fully-coordinated system. In addition, this paper presents a new partial-coordination method that provides higher throughput than the conventional partial-coordinated system.
Relationship of natural occlusal plane with different anatomical landmarks (2020)

Inter-pupillary line and retromolar pad area should be used as a guide in the determination of plane of occlusion. The ala-tragus line was not found to be a reliable guide.
Federated Control with Hierarchical Multi-Agent Deep Reinforcement\n Learning (2017)

We present a framework combining hierarchical and multi-agent deep\nreinforcement learning approaches to solve coordination problems among a\nmultitude of agents using a semi-decentralized model. The framework extends the\nmulti-agent learning setup by introducing a meta-controller that guides the\ncommunication between agent pairs, enabling agents to focus on communicating\nwith only one other agent at any step. This hierarchical decomposition of the\ntask allows for efficient exploration to learn policies that identify globally\noptimal solutions even as the number of collaborating agents increases. We show\npromising initial experimental results on a simulated distributed scheduling\nproblem.\n
Posttranslational modification of CENP-A influences the conformation of centromeric chromatin (2013)

Centromeres are chromosomal loci required for accurate segregation of sister chromatids during mitosis. The location of the centromere on the chromosome is not dependent on DNA sequence, but rather it is epigenetically specified by the histone H3 variant centromere protein A (CENP-A). The N-terminal tail of CENP-A is highly divergent from other H3 variants. Canonical histone N termini are hotspots of conserved posttranslational modification; however, no broadly conserved modifications of the vertebrate CENP-A tail have been previously observed. Here, we report three posttranslational modifications on human CENP-A N termini using high-resolution MS: trimethylation of Gly1 and phosphorylation of Ser16 and Ser18. Our results demonstrate that CENP-A is subjected to constitutive initiating methionine removal, similar to other H3 variants. The nascent N-terminal residue Gly1 becomes trimethylated on the α-amino group. We demonstrate that the N-terminal RCC1 methyltransferase is capable of modifying the CENP-A N terminus. Methylation occurs in the prenucleosomal form and marks the majority of CENP-A nucleosomes. Serine 16 and 18 become phosphorylated in prenucleosomal CENP-A and are phosphorylated on asynchronous and mitotic nucleosomal CENP-A and are important for chromosome segregation during mitosis. The double phosphorylation motif forms a salt-bridged secondary structure and causes CENP-A N-terminal tails to form intramolecular associations. Analytical ultracentrifugation of phospho-mimetic CENP-A nucleosome arrays demonstrates that phosphorylation results in greater intranucleosome associations and counteracts the hyperoligomerized state exhibited by unmodified CENP-A nucleosome arrays. Our studies have revealed that the major modifications on the N-terminal tail of CENP-A alter the physical properties of the chromatin fiber at the centromere.
Observations of the Boundary Current System at 26.5°N in the Subtropical North Atlantic Ocean* (1997)

Five current meter moorings and four horizontal electric field records spanning June 1990-February 1992 are used to describe the mean structure and variability of the vertically averaged velocity field and volume transport extending 425 km east of Abaco, The Bahamas, at 26.5N. Examination of zonal and meridional velocity sections shows that, while meandering may explain part of the variability, there is substantial evidence for pulsation of the core DWBC velocity in the record. Intermittently strong northward flow is observed 225 km east of Abaco that is significantly coherent and out of phase with the currents closer to the boundary at periods of 50-100 d and longer, suggesting recirculation. This is never observed 315 km offshore. At 380 km offshore and extending east at least 60 km, a strong, dominantly southward flow is observed that is coherent with both that near Abaco (in phase) and in the intervening recirculation zone (out of phase) at long periods. The net mean transport (over 17 months) from Abaco to 325 km offshore, spanning the recirculation region, is 17 Sv (Sv 10 6 m 3 s 1 ). The transport exhibits robust annual variability, and correction for the bias from the annual cycle in the 17-month dataset reduces the net mean transport at 325 km to 13.6 Sv. Allowing for a northward Antilles Current transport of 5.1 Sv yields a mean southward DWBC transport corrected for local recirculation of about 18.5 Sv, in approximate agreement with the thermohaline input from the northern North Atlantic. Comparison of transport time series from the Florida Current with that extending 125 km east of Abaco demonstrates significant and out of phase coherence over the period range 100-250 d. The coherence decreases as the Abaco transport is integrated farther to the east.
Low power coordination in wireless ad-hoc networks (2003)

Distributed wireless ad-hoc networks (DWANs) pose numerous technical challenges. Among them, two are widely considered as crucial: autonomous localized operation and minimization of energy consumption. We address the fundamental problem of how to maximize life-time of the network by using only local information while preserving network connectivity. We start by introducing the Care-Free Sleep (CS) Theorem that provides provably optimal necessary and sufficient conditions for a node to turn off its radio while ensuring that global connectivity is not affected.The CS theorem is the basis for an efficient localized algorithm that decides which node will turn its radio off, and for how long. The effectiveness of the approach is demonstrated using numerous simulations of the performance of the algorithm over a wide range of network parameters.
Anatomical View of Thoracodorsal Artery Variants Using Computed Tomography Angiography (2023)

While there is some diversity in the vascular anatomical structures of the LD flap, the dominant vessel can be found in a similar location in almost all cases and no flap had absence of a dominant vessel. Therefore, in surgical procedures using the thoracodorsal artery as the pedicle, preoperative radiological confirmation is not absolutely necessary; however, due to variants, performing the surgery with an understanding of this aspect should lead to good outcomes.
The Effects of Shell Composition in Core-Shell Structure Cathode Materials on Electrochemical Properties and Structural Stability (2010)

Abstract not Available.
Supplementary Figure Legend and Tables 1 - 5 from IGKV3 Proteins as Candidate “Off-the-Shelf” Vaccines for Kappa-Light Chain–Restricted B-Cell Non-Hodgkin Lymphomas (2023)

&lt;p&gt;PDF file, 157KB, Supplementary Table 1. Patient data Supplementary Table 2. HLA-A and-B genotypes of donors from whom IGKV3-specific CTL lines were induced and extent of specific cytotoxicity against IGKV3-15 or IGKV3-20 proteins Supplementary Table 3. Differentiation features of T cell cultures induced with recombinant IGKV3 proteins from PBMCs of healthy donors Supplementary Table 4: Relative affinity and complex stability data for IGKV3-20-derived peptides. Supplementary Table 5. "Variant" IGKV3-20 epitopes carried by different IGK chains broadly expressed by B cell lymphomas&lt;/p&gt;
FRED II Quasistatic Seat Testing Rearward: An Improved Method Based on the SAE H-point Manikin (2019)

&lt;div class="section abstract"&gt;&lt;div class="htmlview paragraph"&gt;Various methods have been used to load a seat in the rear direction, including FMVSS 207, assorted body blocks and QST (quasistatic seat test). However, each method lacks some critical aspect of occupant loading of the seat or is too complex for routine development work. A new method is presented to determine the strength and energy transfer of a seat to an occupant in rear impacts that reflects how an occupant interacts with the seat in a rear impact. A metal-cast H-point manikin, called FRED II, was modified to support a loading bar and was pulled rearward into the seatback by a hydraulic ram. The force and displacement of the loading and the inboard and outboard seatback angle were measured. The response of the seat was recorded by video. The moment about the recliner pivot at peak force was determined by aligning the center of the recliner in side views of the seat position initially and at peak load. The height of the cable above the center of the recliner was determined giving the moment arm at peak load. The force was integrated with displacement to determine energy transfer to the seat. Twelve tests were performed with FRED II and twelve with a traditional body block used by CRA. There were nine matched tests with identical seats. With FRED II, the average peak moment was 2,407 ± 460 Nm and the energy transfer was 2,046 ± 531 J. With the body block, the average peak moment was 2,534 ± 297 Nm using the same method to determine the moment at peak force and the energy transfer was 1,740 ± 379 J. FRED II loads the seatback as the Hybrid III dummy does in sled tests. It measures the energy transfer capability of the seat in a manner that is similar to occupant loading in a rear impact. FRED II is a simple and improved quasistatic method for seat testing. FRED II provides the H-point location and can be used to measure head restraint position.&lt;/div&gt;&lt;/div&gt;
Study on heavy matching layer transducer towards producing second harmonics (2016)

Abstract Cavitation bubbles are microbubbles which can be incepted by highly negative pressure. Producing such highly negative pressure exceeding the cavitation threshold is difficult to accomplish due to nonlinear propagation followed by focal phase shift. By superimposing the second harmonic to fundamental is a way to significantly reduce the problem. However, the conventional design for an air-backed transducer is not suitable to generate both the second harmonic and fundamental at the same time. In order to overcome this problem, we propose a high impedance matching layer approach. Furthermore, we also construct a study to foresee the impact by adjusting the thickness ratio towards fundamental and second harmonic. Numerical simulation and experimental measurement have shown that by using a high impedance matching layer, efficiently generation of both the second harmonic (2 MHz) and fundamental (1 MHz) at the same time is possible. Besides, by adjusting the thickness ratio between piezocomposite and heavy matching layer will influence the amplitude of acoustic power over squared of voltage of the fundamental and second harmonic.
Efficient and colour-stable hybrid white organic light-emitting diodes utilizing electron–hole balanced spacers (2010)

High-efficiency two-colour white organic light-emitting diodes (WOLEDs) comprising a newly synthesized iridium complex orange phosphor ((impy) 2 Ir(acac)) and a blue fluorophor (BD012) have been realized by placing several kinds of thin spacers between two emitters. Hybrid WOLEDs with a spacer composed of a hole-transporting N , N -dicarbazolyl-3,5-benzene (mCP) and an electron-transporting 4,7-diphenyl-1,10-phenanthroline (Bphen) exhibit a high external quantum efficiency (EQE) of up to 8.4% and a negligible colour change (the colour coordinate of (0.39, 0.41) at 1000 cd m −2 ) with increasing brightness, whereas the device using a hole-transporting mCP spacer shows a relatively low EQE of 6.2% and a large shift of emitting colour with increasing brightness. Device performance is further characterized based on the charge transport behaviour of the spacers inserted between the two emitters.
Message from the technical program chairs (2012)

Welcome to the 13th IEEE Conference on High-Performance Switching and Routing (HPSR 2012). This conference brings together researchers from around the world to present the latest advances in the fields of switching and routing. This year, we are proud to present a rich technical program comprising of 39 excellent technical paper presentations, one keynote presentation, two tutorials by world-renowned experts in the field, and an industrial panel discussion involving six experts from leading companies.
3D-RESURF SOI LDMOSFET for RF power amplifiers (2004)

There has been an on going effort to improve RF performance in LDMOSFETs for high voltage applications. This paper examines the suitability of a 3D-RESURF LDMOSFET on SOI technology for RF power applications using the 3D-device simulator, Davinci. For the same blocking voltage rating, the 3D-RESURF device has improved current handling capability at high gate voltages. This in turn causes the transconductance to be higher, leading to overall better RF performance.