gebhart/patrepeval huggingface dataset:
α-Fetoprotein gene sequences mediating <i>Afr2</i> regulation during liver regeneration (1998)

alpha-fetoprotein (AFP) gene expression occurs in the yolk sac, in the fetal liver and gut, and in the adult liver during regeneration and tumorigenesis. Two unlinked genes determine the level of AFP gene expression in adult mice: Afr1 regulates the basal level of expression in the normal adult liver, and Afr2 regulates the increase in expression during liver regeneration. It has been shown that AFP-derived transgenes, including the sequences between -1,010 and -838 bp and between -118 bp and the transcriptional start site were induced appropriately during liver regeneration and were Afr2-regulated. To assess the role of the distal sequence in gene expression during liver regeneration, a new transgene with 7.6 kilobases of 5'-flanking sequence deleted between -1,010 and -838 bp was designed. We show that this transgene was subject to characteristic AFP tissue-specific and developmental regulation, in that it was highly expressed in the yolk sac and the fetal liver and gut but not in normal adult tissues. Expression was induced in response to liver regeneration as observed for the endogenous gene. The genetic regulation of the basal level of AFP gene expression in adult liver by the Afr1 gene was undisturbed. However, transgene expression was not regulated by Afr2 during liver regeneration. Our data suggest that Afr2 regulation of AFP gene expression during liver regeneration requires the sequence between -1,010 and -838 bp and is independent of other regulatory mechanisms.
Chemical congress convnes in Cancun (1997)

RETURN TO ISSUEPREVNewsNEXTChemical congress convnes in CancunPAMELA ZURERCite this: Chem. Eng. News 1997, 75, 46, 7Publication Date (Print):November 17, 1997Publication History Published online12 November 2010Published inissue 17 November 1997https://pubs.acs.org/doi/10.1021/cen-v075n046.p007https://doi.org/10.1021/cen-v075n046.p007newsACS PublicationsCopyright © 1997 AMERICAN CHEMICAL SOCIETYArticle Views6Altmetric-Citations-LEARN 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 SUBJECTS:Petrochemicals Get e-Alerts
Plasma-Treated Superhydrophobic Polyethylene Surfaces: Fabrication, Wetting and Dewetting Properties (2009)

Superhydrophobic surfaces correspond to hydrophobic surfaces whose water contact angle is higher than 150°. Two new routes involving plasma technique are proposed to prepare such surfaces: the first one is a one-step process (CF4 plasma modification of low density polyethylene), and the second involves two steps (O2 plasma treatment followed by CF4 plasma treatment). The plasma parameters are defined to optimize the degradation and/or the functionalization. The O2 plasma allows to create a variable roughness while CF4 plasma accentuates this roughness and creates a non-polar layer. With the two-step treatment, plasma parameters were found which produced superhydrophobic surfaces with a controlled roughness and whose chemical structure was close to a Teflon-like structure. The wetting and dewetting of these superhydrophobic surfaces are compared to those of only hydrophobic polyethylene. The behavior of surfaces, whether dry or prewetted with water vapor, is found to be different. The dewetting of the dried surface previously prewetted is found to be discontinuous, and slower than that of the dry one. This specific behavior is interpreted as a roughness effect on trapped water. However, its dewetting is still faster than that of the corresponding hydrophobic surface such as PTFE.
Evaluation of a novel approach to circulating tumor cell isolation for cancer gene panel analysis in patients with breast cancer (2017)

Liquid biopsy isolation of circulating tumor cells (CTCs) allows the genomic analysis of CTCs, which is useful in the determination of personalized cancer therapy. In the present study, CTCs from patients with breast cancer were enriched and successfully analyzed using cancer gene panel analysis. Blood samples from 11 patients with breast cancer were collected and CTCs enriched for using size-based filtration. The enriched CTCs were analyzed using immunofluorescence staining with antibodies directed against epithelial cell adhesion molecule (EpCAM) and cluster of differentiation 45. The genomic DNA of CTCs was extracted, amplified and 50 genes screened for mutations using the Ion AmpliSeq™ Cancer Hotspot Panel v2. EpCAM staining detected CTCs in 10/11 patients and the average CTC count was 3.9 in 5 ml blood. The average purity of enriched CTCs was 14.2±29.4% and the average amount of amplified DNA was 28.6±11.9 µg. Catalogue Of Somatic Mutations In Cancer mutations were detected in the CTCs and included IDH2, TP53, NRAS, IDH1, PDGFRA, HRAS, STK11, EGFR, PTEN, MLH1, PIK3CA, CDKN2A, KIT and SMARCB1. In conclusion, a novel size-based filtration approach for the isolation of CTCs was evaluated and successfully applied for the genomic analysis of CTCs from patients with breast cancer.
Microscopic structure of interfaces in<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mrow><mml:msub><mml:mrow><mml:mi mathvariant="normal">Si</mml:mi></mml:mrow><mml:mrow><mml:mn>1</mml:mn><mml:mi mathvariant="normal">−</mml:mi><mml:mi mathvariant="italic">x</mml:mi></mml:mrow></mml:msub></mml:mrow></mml:math><mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mrow><mml:msub><mml:mrow><mml:mi mathvariant="normal">Ge</mml:mi></mml:mrow><mml:mrow><mml:mi mathvariant="italic">x</mml:mi></mml:mrow></mml:msub></mml:mrow></mml:math>/Si heterostructures and superlattices studied by x-ray scattering and fluorescence yield (1993)

The angular dependences of grazing-incidence x-ray scattering and Ge K\ensuremath{\alpha} fluorescence yield were measured for ${\mathrm{Si}}_{1\mathrm{\ensuremath{-}}\mathit{x}}$${\mathrm{Ge}}_{\mathit{x}}$/Si and its inverted Si/${\mathrm{Si}}_{1\mathrm{\ensuremath{-}}\mathit{x}}$${\mathrm{Ge}}_{\mathit{x}}$ heterostructures. The results reveal useful information on microstructures in these layered materials and show similar interfacial structures in terms of the rms interfacial roughness, correlation length of height fluctuations, and Ge density profile. Two ten-period superlattices with different thickness and Ge concentration were also investigated; correlation between height fluctuations of different interfaces is clearly demonstrated in the data of x-ray-diffuse scattering. These results show that x-ray scattering and fluorescence techniques can be employed as convenient tools for nondestructive characterization of epilayer thickness, interfacial roughness, density profile of selected atomic species, and correlations between microstructures of different interfaces in layered materials.
A Genetic Screen in Drosophila for Identifying Novel Components of the Hedgehog Signaling Pathway (2005)

The Hedgehog signaling pathway plays an essential role in the pattern formation and development of metazoan animals. Misregulation of Hedgehog signaling has also been associated with the formation of multiple types of cancer. For these reasons, the Hedgehog pathway has attracted considerable interest. Many proteins required in the Hedgehog pathway have been identified, and while much has been learned about their function in signal transduction, it is clear that this complement of proteins does not comprise the full set necessary for Hedgehog signal transduction. Because significant gaps remain in our knowledge of the molecules required for Hedgehog signaling, we performed an enhancer/suppressor screen in Drosophila melanogaster to identify novel components of the pathway. In addition to the isolation of new alleles of the known pathway components patched and smoothened, this screen identified 14 novel complementation groups and a larger number of loci represented by single alleles. These groups include mutations in the genes encoding the translation factors eRF1 and eIF1A and the kinesin-like protein Pavarotti. It also identified mutations in a gene whose product is necessary for the movement of Hedgehog protein through tissues.
Quantum mechanical/quantum mechanical methods. I. A divide and conquer strategy for solving the Schrödinger equation for large molecular systems using a composite density functional–semiempirical Hamiltonian (2000)

Herein we describe a new combined quantum mechanical/quantum mechanical (QM/QM) method for solving the Schrödinger equation for large molecular systems. The new method uses the divide and conquer (D&C) strategy to partition a large molecular system into subsystems and a composite density functional theory (DFT)–semiempirical (SEM) Hamiltonian to describe the molecular interactions. The DFT and SEM subsystems are coupled through the chemical potential and are equilibrated by exchanging electronic charge. Calculations performed with the DFT, SEM, and composite (DFT/SEM) methods on diatomic, triatomic, and polyatomic molecules show that as one moves away from the QM/QM boundary region the Mulliken charges converge to the values that would be obtained using the “pure” Hamiltonian. In other words, we find that the quality of each SEM and DFT wave function is largely conserved, which strongly suggests that this type of approach could be applied to study chemical reactivity much in the same way combined quantum mechanical/molecular mechanical (QM/MM) methods are presently utilized.
Quantum Gaussian filter for exploring ground-state properties (2022)

Filter methods realize a projection from a superposed quantum state onto a target state, which can be efficient if two states have sufficient overlap. Here we propose a quantum Gaussian filter (QGF) with the filter operator being a Gaussian function of the system Hamiltonian. A hybrid quantum-classical algorithm feasible on near-term quantum computers is developed, which implements the quantum Gaussian filter as a linear combination of Hamiltonian evolution at various times. Remarkably, the linear combination coefficients are determined classically and can be optimized in the postprocessing procedure. Compared to the existing filter algorithms whose coefficients are given in advance, our method is more flexible in practice under given quantum resources with the help of postprocessing on classical computers. We demonstrate the quantum Gaussian filter algorithm for the quantum Ising model with numeral simulations under noises. We also propose an alternative full quantum approach that implements a QGF with an ancillary continuous-variable mode.
A computationally efficient channel estimation with signal detection for MIMO-OFDM systems (2004)

In this paper, a computationally efficient adaptive channel estimation scheme is proposed for a space-time block coded (STBC) multiple-input multiple-output orthogonal frequency division multiplexing (MIMO-OFDM) system. This adaptive channel estimation scheme is based on recursive least square (RLS) algorithm. The proposed channel estimation scheme is less complex and bandwidth efficient than the conventional channel estimation schemes for MIMO-OFDM systems. Simulation results show that the proposed channel estimator performs quite close to the system where ideal channel state information is available. At the receiver, signals from different co-channel users are detected using minimum mean squared error (MMSK) interference cancellation (IC) method. It is shown that the signal detection with the proposed channel estimator could be used to increase the system capacity. Simulation results are compared with theoretical error bounds.
Controlled solvent vapor annealing of a high χ block copolymer thin film (2017)

Molecular self-assembling block copolymers (BCPs) have shown promise as a next generation bottom-up lithography technology. However, a critical step in advancing this approach is the elimination of polymer dewetting due to bulk solvent nucleation and thermodynamically driven film rupture that can occur during the solvent vapor annealing process. We report on the pattern formation via phase segregation of spin coated diblock copolymer films through the investigation of annealing parameters in the limit of high solvent vapor saturation conditions that results in wafer-scale patterning without observing polymer dewetting defects. Specifically, the work addresses polymer dewetting in diblock copolymer nanodot templates through the use of a "neutral" functionalization layer and the development of a custom-built solvent vapor annealing chamber to precisely control saturation conditions. Furthermore, the long anneal times (4 h) using a standard static solvent vapor annealing procedure were reduced to ∼15-30 minutes with our dynamic solvent vapor annealing system for the high χ, cylindrical forming poly(styrene)-block-poly(4-vinyl-pyridine) [PS-b-P4VP] diblock copolymer system. We discuss the kinetic mechanism governing the phase segregation process that highlights the small processing window bounded by long phase segregation timescales (≳1 min) on one side and the initiation of polymer film dewetting on the other. These results demonstrate a key step towards realizing a high fidelity, low cost BCP patterning technique for large-scale "bottom-up" feature definition at nanometer length scales.
A Simple Printed Circuit Board–Based Ion Funnel for Focusing Low<i>m/z</i>Ratio Ions with High Kinetic Energies at Elevated Pressure (2019)

Ion funnels are one of the key components for transferring ions from higher pressure into the vacuum. Typically, ion funnels are constructed of several different plate ring electrodes with a decreasing inner diameter where radio frequency (RF) voltages and electric DC fields are applied to the electrodes to focus and transport ion clouds. In this work, we developed and investigated a simple and low-cost ion funnel design that is based on standard printed circuit boards (PCB) with integrated planar electrodes including the signal distribution network. This ion funnel is capable of withstanding high electric fields with superimposed RF voltages due to its buried capacitors. To evaluate the ion focusing efficiency of the ion funnel, we simulated the movement of ions inside this funnel and experimentally evaluated the ion transfer. Our simulations show that a rectangular ion funnel like the PCB ion funnel has similar performance compared with conventional stacked ring funnels. Due to the hundredfold lower parasitic capacitance between the planar electrodes compared with conventional ion funnels, high RF voltage amplitudes up to 195 V and reduced electric DC field strengths up to 100 Td can be reached at a frequency of about 5 MHz. Thus, the funnel is appropriate to focus light ions at elevated pressures up to 20 mbar. Graphical Abstract .
Studies on heart. XXI. Amino acid sequence of antiarrhythmic peptide (AAP) isolated from atria. (1982)

The amino acid sequence of an atrial peptide, AAP, that improves the rhythmicity of cultured myocardial cell clusters, was established as Gly-Pro-4Hyp-Gly-Ala-Gly. This was accomplished by the sequence analyses with dansyl-Edman degradation and carboxypeptidase Y digestion on the isolated native peptide. The hexapeptide and its several constituent peptides were synthesized by using dicyclohexylcarbodiimide as a condensing agent. Synthetic AAP was found to be chemically and biologically indistinguishable from the native one. In a structure-activity correlation of AAP, it was recognized that the whole molecule of this peptide was essential for its antiarrhythmic activity and its promoting effect on spreading phenomenon of myocardial cells in culture.
Between the Sheets: Why Do Protein Strands Line Up? (1996)

To understand how protein chains fold into their complex structures and mimic them in new drugs and materials, protein chemists want to know how their basic structural elements--coils, bends, and sheets--take shape. The toughest to understand are the so-called beta sheets, in which two or more segments of the protein chain lie parallel to each other, like pencils placed side by side. But by making their own small beta sheets or disrupting natural ones, biochemists are learning the key factors that hold them together.
Implementing malleability on MPI jobs (2004)

Parallel jobs are characterized for having processes that communicate and synchronize with each other frequently. A processor allocation strategy widely used in parallel supercomputers is space-sharing, that is assigning a processors partition to each job for its exclusive use. We present a global solution to offer virtual malleability on message-passing parallel jobs, by applying a processor allocation strategy, the Folding by JobType (FJT). This technique is based on folding and moldability concepts and tries to decide the optimal initial number of processes, when to fold jobs and the number of folding times by analyzing the current and past system information. At processor level, we apply co-scheduling. We implement and evaluate the FJT under several workloads with different job sizes, classes and machine utilization. Results show that the FJT adapts easily to load changes, and can obtain better performance than the rest evaluated, on workloads with high coefficient variation and especially with burst arrivals.
A label-free electrochemical immunosensor for beta-amyloid detection (2016)

A label-free detection of beta-amyloid (βA) proteins using an electrochemical immunosensor fabricated <italic>via</italic> immobilizing specific anti-beta-amyloid antibodies (An-βA-Abs) onto an interdigitated electrode of gold (IDE-Au) modified using a self-assembled monolayer (SAM) of dithiobis(succinimidyl propionate) [DTSP] is presented here.
Techniques of fracture reduction: The Ilizarov method (1990)

This article summarizes basic techniques of fracture reduction and the general principles of frame construction using the Ilizarov method. Radiologic evaluation of the fracture, soft tissue injury assessment, operating room table arrangement, and extremity supports as pertinent to the fracture treatment with the Ilizarov method are considered. The sequence of fracture reduction for diaphyseal, intraarticular, and segmental fractures as well as the basic frame constructs for correcting angulation, translation, and rotation of the fracture fragments are discussed.
The Emb proteins of mycobacteria direct arabinosylation of lipoarabinomannan and arabinogalactan via an N‐terminal recognition region and a C‐terminal synthetic region (2003)

The arabinans of the mycobacterial cell wall are key structural and immunological polymers in the context of arabinogalactan (AG) and lipoarabinomannan (LAM) respectively. The three homologous membrane proteins EmbA, EmbB and EmbC are known to be involved in the synthesis of arabinan but their biochemical functions are not understood. Herein we show, that synthesis of LAM, but not AG, ceases after inactivation of embC in Mycobacterium smegmatis by insertional mutagenesis. LAM synthesis is restored upon complementation with the embC wild-type gene. Previously we have shown that the synthesis of the arabinan of AG is affected by embA or embB disruption. Thus the Emb proteins are capable of differential recognition of the galactan or mannan acceptors prior to appropriate arabinosylation. In addition, a combination of genetic and biochemical approaches have allowed us to assign some specific functions to the regions of emb gene products. Complementation of the embCmacr; mutant with a hybrid gene encoding the N-terminus of EmbC and the C-terminus of EmbB resulted in LAM with a lower molecular weight than the wild-type LAM. Structural studies involving enzyme digestion, chromatography and mass spectrometry analyses revealed that the arabinan of the 'LAM' formed in the hybrid was of AG kind rather than LAM type of arabinan.
FFT interpolation for arbitrary factors: a comparison to cubic spline interpolation and linear interpolation (2002)

The authors applied FFT interpolation (FTI) for arbitrary factors to a common image task: 1D zoom, and compared it to cubic splines interpolation and linear interpolation. The authors also determined the relative error of the arbitrary factors FFT and the conventional FFT (integral powers of 2) for computing the Fourier transforms of trigonometric eigenfunctions. In the interpolation study, FTI proved to be satisfactory. If the data was band-limited, or nearly so, FTI was as effective as conventional interpolation. If the data was not band-limited, an anti-oscillation filter provided better results. The test data was a curve consisting of a rectangle, gaussian function and a 4th degree polynomial. The authors used interpolation to zoom the image by a factor of 3.1:1, and determined the rms (root mean square) errors by comparing the result to the known image values. To determine the relative error for computing eigenfunctions, the authors FFT'd trigonometric eigenfunctions. For an FFT of dimension 120, the relative error was less than 10/sup -10/ over a wide range of eigenvalues and compared favorably with an FFT of dimension 128, which had a relative error of less than 10/sup -13/ over the same range. The advantage of this approach is that the arbitrary factors algorithm is quite simple in design, and replaces an entire suite of FFT's based upon different prime factorizations. The authors also show that FTI is exact if the Fourier transform of the function is absolutely band-limited.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
MHT Approach to Ubiquitous Monitoring of Spatio-Temporal Phenomena (2018)

This paper describes a multiple-hypothesis tracking (MHT) formulation of a particular set of situational awareness problems that involve monitoring of spatio-temporal phenomena using ubiquitous sensing. In particular, the focus is on large-scale monitoring (or tracking) applications utilizing volunteer mobile ubiquitous sensors to track the evolution of spatio-temporal `targets' of interest (e.g., tracking snow-fall or ride-quality at a certain stretch of a roadway using vehicles). An efficient framework is developed utilizing MHT as the basis to carry out detection and tracking of evolutionary behavior. The framework is described via an illustrative example on ride-quality monitoring as applied to autonomous driving environments, where vibration and GPS data recorded by voluntarily participating vehicles are utilized for threat detection and tracking.
Design of Wireless Power Transfer System for Railway Application (2012)

As wireless power transfer (WPT) technologies emerge in a wide range of applications including public transportation, many expect that applying the technology to the current railway systems will bring positive effects to current railway systems. In this paper, we introduce design methodology of a WPT system for railway application. Fundamental principles of magnetic fields and a WPT circuit are first analyzed, and advantages and efficiency of a possible train system are discussed. It then examines other significant factors such as performance requirements and EMC criteria to design a wireless train system.