gebhart/patrepeval huggingface dataset:
Cell Wall Composition and Candidate Biosynthesis Gene Expression During Rice Development (2016)

Cell walls of grasses, including cereal crops and biofuel grasses, comprise the majority of plant biomass and intimately influence plant growth, development and physiology. However, the functions of many cell wall synthesis genes, and the relationships among and the functions of cell wall components remain obscure. To better understand the patterns of cell wall accumulation and identify genes that act in grass cell wall biosynthesis, we characterized 30 samples from aerial organs of rice (Oryza sativa cv. Kitaake) at 10 developmental time points, 3-100 d post-germination. Within these samples, we measured 15 cell wall chemical components, enzymatic digestibility and 18 cell wall polysaccharide epitopes/ligands. We also used quantitative reverse transcription-PCR to measure expression of 50 glycosyltransferases, 15 acyltransferases and eight phenylpropanoid genes, many of which had previously been identified as being highly expressed in rice. Most cell wall components vary significantly during development, and correlations among them support current understanding of cell walls. We identified 92 significant correlations between cell wall components and gene expression and establish nine strong hypotheses for genes that synthesize xylans, mixed linkage glucan and pectin components. This work provides an extensive analysis of cell wall composition throughout rice development, identifies genes likely to synthesize grass cell walls, and provides a framework for development of genetically improved grasses for use in lignocellulosic biofuel production and agriculture.
The Breadcrumb Forwarding Service and the Digital Fountain Rainbow: Toward a TCP-Friendly Reliable Multicast (1999)

If ubiquitously deployed, IP Multicast promises to provide an efficient datagram service for an arbitrary sending host to reach an arbitrary and dynamic set of destination hosts anywhere in the Internet. Unfortunately, two very difficult problems -- interdomain multicast routing and viable end-to-end multicast transport -- have yet to be solved and deployed satisfactorily. &lt;p&gt;This paper proposes a new multicast service model called the "Breadcrumb Forwarding Service" (BCFS) synthesized from the EXPRESS service model and the network component of the Pragmatic Multicast protocol (PGM). Like EXPRESS, BCFS utilizes explicit-source group join and like PGM, enhances the network forwarding architecture with finer-granularity group control. To demonstrate the flexibility and efficacy of BCFS, we developed a novel reliable multicast transport protocol, Rainbow, for bulk data transfer built on top of BCFS. In this approach, each receiver runs an independent, window-based congestion control algorithm modeled after TCP, thereby affording "TCP friendliness" while retaining the efficiency of IP Multicast. To enhance scalability and support asynchronous receiver behavior, we employ a Digital Fountain at the source. In this paper, we detail BCFS service model, describe how Rainbow builds on this service model and on the Digital Fountain abstraction, and evaluate the resulting system. Our simulation results show that Rainbow/BCFS performs well in a variety of configurations and is "TCP friendly"
Development of a web-based molecular dynamics virtual flow laboratory (2007)

We performed a quasiclassical trajectory dynamics study on a model analytical 21-dimensional (7 active atoms) potential energy surface (PES) to examine in detail the mechanism of the hydrogen absorption in a simple (NaAlH(4))(2)Ti model system. The reaction involves a capture of H(2) by the Ti centre and formation of the (η(2)-H(2))Ti(NaAlH(3))(2) coordination complex containing the side-on bonded dihydrogen ligand. The calculated rate constant corresponds to a very fast capture of H(2) by the Ti coordination sphere without a demonstrable barrier. This implies that this step is not the rate-determining step in the complex multi-step process of the NaAlH(4) recovery. The model analytical PES captures the essence of this reaction well and the corresponding energy contours compare favourably to those based on the all-atom hybrid density functional theory calculations.
Probabilistic model for sensor fault detection and identification (2003)

Abstract A new Bayesian belief network (BBN) model with discretized nodes is proposed for fault detection and identification in a single sensor. The single‐sensor model is used as a building block to develop a BBN model for all sensors in the process considered. A new fault detection index, a fault identification index, and a threshold setting procedure for the multisensor model are introduced. The fault detection index exploits the probabilistic information of the multisensor model, which, along with the proposed threshold setting procedure, leads to effective detection of faulty sensors. The fault identification index uses only the probabilistic information of the faulty sensor to determine in a discretized fashion the size of faults that should be analyzed within a moving time window to identify the fault type. Single‐sensor model design parameters (prior and conditional probability data) are optimized to achieve maximum effectiveness in detection and identification of sensor faults. The single‐sensor model and optimal values of design parameters are used to develop a multisensor BBN model for a polymerization reactor at steady‐state conditions. Its capabilities to detect and identify bias, drift, and noise in sensor readings are illustrated for single and simultaneous multiple faults by several case studies.
Topological superconductivity in nanowires proximate to a diffusive superconductor–magnetic-insulator bilayer (2021)

We study semiconductor nanowires coupled to a bilayer of a disordered superconductor and a magnetic insulator, motivated by recent experiments reporting possible Majorana-zero-mode signatures in related architectures. Specifically, we pursue a quasiclassical Usadel equation approach that treats superconductivity in the bilayer self-consistently in the presence of spin-orbit scattering, magnetic-impurity scattering, and Zeeman splitting induced by both the magnetic insulator and a supplemental applied field. Within this framework we explore prospects for engineering topological superconductivity in a nanowire proximate to the bilayer. We find that a magnetic-insulator-induced Zeeman splitting, mediated through the superconductor alone, cannot induce a topological phase since the destruction of superconductivity (i.e., Clogston limit) preempts the required regime in which the nanowire's Zeeman energy exceeds the induced pairing strength. However, this Zeeman splitting does reduce the critical applied field needed to access the topological phase transition, with fields antiparallel to the magnetization of the magnetic insulator having an optimal effect. Finally, we show that magnetic-impurity scattering degrades the topological phase, and spin-orbit scattering, if present in the superconductor, pushes the Clogston limit to higher fields yet simultaneously increases the critical applied field strength.
Hardware Design and Optimization of Multimode Pipeline Based FFT for IEEE 802.11ax WLAN Devices (2018)

In this paper, a new architecture of a multi-mode Fast Fourier Transform hardware for IEEE 802.11ax WLAN standard is presented. The proposed architecture is based on Radix-2 Multipath Delay Commutator (MDC), Radix-2 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> and Radix 2 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">4</sup> Single-path Delay Feedback(SDF) stages. To optimize the throughput and area of the FFT hardware, we applied two design techniques such as compression of redundant twiddle factors, and optimization of twiddle factor multiplication. In FPGA implementation using Altera Stratix IV EP4SGX530KH40C3, the proposed FFT achieved 1.2 GSamples/s throughput and met the requirements of the 802.11ax standard. The synthesis results show that the proposed circuit is 6.19% lower latency and 30.2% lower area compared to a recently presented work while maintaining higher working frequency.
Semiochemical (Patent US 2003/0109586 A1) (2003)

cis-Jasmone has been discovered to be useful as a semiochemical that changes the behaviour of insects and/or the physiology of plants. It has direct signalling roles with plant-feeding aphids, in attraction of aphid predators and parasitoids, and may act as an airborne signal inducing production of volatile plant semiochemicals, including the monoterpene (E)-beta-ocimene, that stimulate foraging by parasitoids. It is an extremely benign compound having, to human beings, a pleasant aroma and gives a long-lasting effect after removal of the stimulus.
The putative human stem cell marker,Rex-1 (Zfp42): Structural classification and expression in normal human epithelial and carcinoma cell cultures (2006)

Human Rex-1 (hRex-1) (also referred to as zinc-finger protein-42, Zfp42) encodes a zinc finger protein expression of which is believed to be characteristic of pluripotent stem cells. We have applied bioinformatics to classify the relationship of human, rat, and mouse REX1 proteins in the C2H2 family of zinc finger proteins and demonstrate that REX1 is a member of the YY1 sub-family of transcription factors, which includes the Drosophila pleiohomeotic (Pho) protein. We have generated a molecular model of the human REX1 zinc finger domains based on the crystal structure of the YY1 transcription factor. To date, expression of hRex-1 and its extensively studied mouse homolog mRex-1, has been reported only in embryonic and adult stem cells and in differentiated spermatocytes. In this study, reverse transcription-PCR and Western analysis were employed to assay for hRex-1 expression in cultured normal human epithelial cells and human carcinoma cell lines. Expression of hRex-1 mRNA was detected in normal human epidermal keratinocytes, normal prostate epithelial cells (PrEC), bronchial, and small airway lung epithelial cells. Other stem cell markers, such as Oct 4, DAB2, and cMyc were also detected in normal human epidermal keratinocyte cultures. Expression of hRex-1 was also detected in some human tumor cell lines including MDA-MB-468 mammary carcinoma, SCC-15 head and neck squamous cell carcinoma, and N-TERA2 human teratocarcinoma cells. Western analyses confirmed expression of the human REX1 (ZFP42) protein in MDA-MB-468 cells and normal human keratinocytes. This research has identified model human cell culture systems, in addition to embryonic stem (ES) cells, in which Rex-1 is expressed, and this should enable the characterization of REX1 functions in normal adult epithelial cells and tumorigenic stem cells.
Proton and Li+ Cation Interactions with H2O3 and H2O/O2:  Ab Initio Molecular Orbital Study (1997)

Ab initio molecular orbital calculations at the QCISD(FULL)/DZ+P level of theory were carried out on the hydrogen trioxides H2O3 and H2O/O2 (O2 is 3Σg-) and their Li+ ion and proton adducts to determine the binding energies (Li+ affinity and proton affinity) for H2O3−Li+ and H2O−Li+−O2. Calculations include the thermochemistry at 298 K and enthalpy corrections for comparison with experimental values. Our prediction for the binding energy of Li+ to H2O3 is 33.0 kcal/mol, which closely resembles that between Li+ and homologous molecules of water and H2O2. In the case of the H2O−Li+−O2 system, the process may be that a primary product of H2OLi+ would then bind to oxygen (or O2Li+ to water). Binding energies of H2OLi+ or Li+ to O2 are 8.6 or 5.2 kcal/mol, respectively, which are smaller than those required for adduct formation under conventional experimental conditions. The overall results suggest the validity of our recent experimental detections of Li+ ion attachment to hydrogen trioxide. But the detection of the H2O−Li+−O2 complex may not be possible.
ChemInform Abstract: TOTAL SYNTHESIS OF (.+‐.) VARIOTIN AND ITS ANALOGS (1978)

Abstract Ausgehend von den Butenaldehyden (I) werden nach angegebenem Schema die für die Synthese von (i)‐Variotin (XIa) und seinen Analogen (XIb) und (XIc) benötigten Schlüsselverbindungen (VIII) dargestellt.
The clinical, immunological and microbiological impact of the 10-valent pneumococcal-Protein D conjugate vaccine in children with recurrent protracted bacterial bronchitis, chronic suppurative lung disease and bronchiectasis: a multi-centre, double-b (2018)

We aimed to determine the efficacy of the 10-valent pneumococcal-Haemophilus influenzae protein D conjugate vaccine (PHiD-CV) in children aged 18-months to &lt;18-years with recurrent protracted bacterial bronchitis (rPBB), chronic suppurative lung disease (CSLD) or bronchiectasis. In a multi-centre, double-blind randomised controlled trial, children received two doses, 2-months apart of the 10vPHiD-CV or quadrivalent meningococcal-ACYW135 conjugate vaccine. Active surveillance for acute exacerbations, respiratory symptoms and antibiotic use was undertaken through to 12-months after the second vaccine dose (clinical cohort only). Serum, saliva and nasopharyngeal swabs were collected to measure immunological and microbiological effects (immunology cohort). Between December 2012 and August 2015, 62 children were enrolled onto the clinical protocol (1 excluded from clinical analyses due to unblinding), while 74 contributed to the immunology cohort (overall mean age=6.8-years (standard deviation=3.7), 42 (56.8%) male). The absolute risk difference comparing the 10vPHiD-CV group (n=31 children) to the MenACYW135 group (n=30 children) for acute exacerbations was -0.5 exacerbations/100-weeks at risk (95% confidence interval (CI) -2.0, 0.9). Compared to the MenACYW135 group, children who received the 10vPHiD-CV were less likely to have respiratory symptoms in each fortnight of surveillance (incidence density ratio (IDR) 0.82, 95%CI 0.61, 1.10) and required fewer short-course (&lt;14-days duration) antibiotics (IDR 0.81, 95%CI 0.61, 1.09). The vaccine was immunogenic and no serious adverse events related to the vaccine were reported. In conclusion, 10vPHiD-CV might have a future role in managing children with rPBB, CSLD and bronchiectasis, but larger multicentre trials are needed to confirm or refute findings from this preliminary study.
Reasons for failure of MOPP to cure Hodgkinʼs disease The importance of dose and schedule (1982)

Thirty-six patients with advanced Hodgkin's disease who were treated primarily with MOPP were evaluated to determine the reasons for MOPP failure. Complete remission was achieved in 22 (61%) of the patients, and the predicted 5-year survival rate for all patients is 60%. Reasons for the failure of MOPP to cure patients in this series included: 1) Idiosyncratic drug reactions in 2 patients (6%). MOPP was discontinued after one cycle because of drug-related hepatitis or skin rash; 2) Resistant disease in 8 patients (22%). Primary treatment failure was significantly associated with the presence of B symptoms (p = .005) and age greater than 40 years (p = .02); 3) Death from complicating infection in 5 patients (14%). Four patients died without evidence of Hodgkin's disease while responding to MOPP from pneumocystis pneumonia, viral pneumonia, bacterial pneumonia, or bacterial septicemia. One patient died in complete remission from sudden, overwhelming sepsis; 4) Relapse from complete remission in 4 patients (11%). All patients who relapsed had deviations from the planned dose or timing of MOPP. Remission duration was shorter (p = .06) in patients with documented deviations in MOPP administration than in patients without such changes. It appears that new treatment approaches are needed for patients with B symptoms, and that failure to deliver MOPP on schedule in the planned dose increases the risk of relapse.
Controlled reversal of Co/Pt Dots for nanomagnetic logic applications (2012)

Domain reversal in perpendicular multilayer films is governed by an intrinsic distribution of anisotropy. However, control of the switching field distribution (SFD) of field-coupled, single domain Co/Pt dots is the key to building large integrated systems for nanomagnetic logic applications. In this work, partial Ga+ focused ion beam (FIB) irradiation of single-domain Co/Pt dots is employed which locally reduces the anisotropy and renders the film-inherent SFD ineffective. Controlled reduction in the switching field compared to non-irradiated dots is achieved, depending on size and dose of irradiation. TEM images of an as-grown and irradiated Co/Pt stack show a change in morphology from distinct Co/Pt interfaces to intermixed and randomly oriented grains due to the Ga+ ion impact. The presented method is highly suitable to control the switching behavior in field-coupled logic devices. Experimental results are used to demonstrate a nanomagnetic fanout operation.
Catalytic Olefin Epoxidation and Dihydroxylation with Hydrogen Peroxide in Common Ionic Liquids: Comparative Kinetics and Mechanistic Study (2004)

Abstract For Abstract see ChemInform Abstract in Full Text.
An AM1 computational study of the cationic polymerization mechanism of cyclic acetals (1990)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAn AM1 computational study of the cationic polymerization mechanism of cyclic acetalsPaul M. Lahti, C. Peter Lillya, and James C. W. ChienCite this: Macromolecules 1990, 23, 4, 1214–1218Publication Date (Print):February 1, 1990Publication History Published online1 May 2002Published inissue 1 February 1990https://pubs.acs.org/doi/10.1021/ma00206a048https://doi.org/10.1021/ma00206a048research-articleACS PublicationsRequest reuse permissionsArticle Views56Altmetric-Citations2LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Toward software-defined middlebox networking (2012)

Current middlebox (MB) management mechanisms are clumsy and unsuitable for taking full advantage of new MB deployment models and diverse MB functionality. Instead, we advocate for mechanisms that help exercise unified control over the key factors influencing MB operations. Our goal is to realize a software-defined MB networking framework to simplify management of complex, diverse functionalities and engender rich deployments. We discuss the major challenges that arise---representing, manipulating, and knowledgeably controlling MB state---and we present initial thoughts on the appropriate abstractions and interfaces to address them.
Duplications and de novo deletions of the SMNt gene demonstrated by fluorescence‐based carrier testing for spinal muscular atrophy (1999)

Approximately 95% of individuals with spinal muscular atrophy (SMA) lack both copies of the SMNt gene at 5q13. The presence of a nearly identical centromeric homolog of the SMNt gene, SMNc, necessitates a quantitative polymerase chain reaction approach to direct carrier testing. Adapting a radioactivity-based method described previously, multiplex polymerase chain reaction was performed using fluorescently labeled primers followed by analysis on an ABI 373a DNA sequencer. The SMNt copy number was calculated from ratios of peak areas using both internal and genomic standards. Samples from 60 presumed carriers (50 parents of affected individuals and 10 relatives implicated by linkage analysis) and 40 normal control individuals were tested. Normalized results (to the mean of five or more control samples harboring two copies of the SMNt gene) were consistently within the ranges of 0.4 to 0.6 for carriers (one copy) and 0.8 to 1.2 for normal controls (two copies), without overlap. Combining linkage analyses with direct carrier test results demonstrated de novo deletions associated with crossovers, unaffected individuals carrying two SMNt gene copies on one chromosome and zero SMNt gene copies on the other chromosome, and unaffected individuals with three copies of the SMNt gene. This report demonstrates that fluorescence-based carrier testing for SMA is accurate, reproducible, and useful for genetic risk assessment, and that carrier testing may need to be combined with linkage analysis in certain circumstances. Am. J. Med. Genet. 85:463–469, 1999. © 1999 Wiley-Liss, Inc.
NMR methods for studying the structure and dynamics of oncogenic and antihistaminic peptides in biomembranes (2004)

We present several applications of both wide-line and magic angle spinning (MAS) solid-state NMR of bicelles in which are embedded fragments of a tyrosine kinase receptor or enkephalins. The magnetically orientable bicelle membranes are shown to be of particular interest for studying the functional properties of lipids and proteins in a state that is very close to their natural environment. Quadrupolar, dipolar and chemical shielding interactions can be used to determine minute alterations of internal membrane dynamics and the orientation of peptides with respect to the membrane plane. MAS of bicelles can in turn lead to high-resolution proton spectra of hydrated membranes. Using deuterium-proton contrast methods one can then obtain pseudo-high-resolution proton spectra of peptides or proteins embedded in deuterated membranes and determine their atomic 3D structure using quasi-conventional liquid-state NMR methods.
Chromatin Immunoprecipitation (ChIP) (2009)

INTRODUCTION Chromatin immunoprecipitation (ChIP) is an invaluable method for studying interactions between specific proteins or modified forms of proteins and a genomic DNA region. ChIP can be used to determine whether a transcription factor interacts with a candidate target gene and is used with equal frequency to monitor the presence of histones with post-translational modifications at specific genomic locations. In early ChIP studies, UV light from a transilluminator was used to cross-link proteins to DNA irreversibly. The cross-linked chromatin was then either sonicated or cleaved with restriction enzymes to generate smaller DNA fragments, followed by immunoprecipitation with the desired antibodies. The precipitated protein-DNA adducts were then purified, treated with a protease, and analyzed by dot blot or Southern blot using a radiolabeled probe derived from the cloned DNA fragment of interest. The use of formaldehyde as a reversible protein-DNA and protein-protein cross-linking agent for ChIP and the use of polymerase chain reaction (PCR) to detect precipitated DNA fragments were later added as components of the modern ChIP procedure. The protocol below represents a standard ChIP procedure for use in mammalian cells. Cross-linking is performed by adding formaldehyde to growing cells, and chromatin is prepared, sheared by sonication, and precleared to reduce nonspecific immunoprecipitation. Immunoprecipitation is performed with a specific antibody. After elution of the protein-DNA complexes from protein A- or protein G-agarose resin, the samples are heated to reverse the covalent cross-links. The DNA fragments are purified and analyzed by PCR or real-time PCR.