gebhart/patrepeval huggingface dataset:
Data from Genome-Wide Somatic Copy Number Alterations in Low-Grade PanINs and IPMNs from Individuals with a Family History of Pancreatic Cancer (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; Characterizing the earliest chromosomal alterations of pancreatic precursor neoplasms from individuals with a familial aggregation of pancreatic cancer may provide clues as to the loci of pancreatic cancer susceptibility genes.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental Design:&lt;/b&gt; We used Illumina 370/660K SNP arrays to conduct genome-wide copy number analysis in 60 benign neoplasms [58 mostly low-grade pancreatic intraepithelial neoplasias (PanIN) and intraductal papillary mucinous neoplasms (IPMN) and two pancreatic neuroendocrine tumors (PNET)] and matched normal tissues from 16 individuals with a family history of pancreatic cancer. PanINs and IPMNs were analyzed for &lt;i&gt;KRAS&lt;/i&gt; codon 12/13 mutations.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; Of 40 benign neoplasms with adequate SNP calls and allele ratios, somatic chromosomal copy number changes were identifiable in only nine lesions, including eight of the 38 PanIN/IPMNs (two of which had identical alterations) and one of the two PNETs. Only two precursor lesions had more than one somatic copy number alteration. In contrast, the overwhelming majority (∼95%) of PanINs harbored &lt;i&gt;KRAS&lt;/i&gt; mutations. The chromosomal alterations identified included nine chromosomal arms affected by chromosomal loss and two by chromosomal gain. Copy number loss spanning 9p21.3 was identified in three precursor lesions; two precursors had chromosomal losses affecting 6q and 17p.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusions:&lt;/b&gt; Low- and intermediate-grade PanINs and IPMNs from patients with a family history of pancreatic cancer harbor few if any somatic chromosomal alterations. The absence of a locus of recurrent chromosomal loss in most low-grade pancreatic cancer precursor lesions supports the hypothesis that there is no one tumor suppressor gene locus consistently involved in initiating familial pancreatic neoplasia. &lt;i&gt;Clin Cancer Res; 18(16); 4303–12. ©2012 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
Luminescent and Magnetoresponsive Multifunctional Chalcogenide/Polymer Hybrid Nanoparticles (2013)

Cadmium sulfide/magnetite/polymer multifunctional hybrid nanoparticles are prepared by crystallizing CdS in a controlled manner on the surface of phosphonate-functionalized polystyrene particles with a magnetic core. The supporting polymer magnetoresponsive nanoparticles are produced by a modified miniemulsion polymerization process: a first miniemulsion containing the core monomer (styrene) and a phosphonate-functionalized surface-active monomer is mixed with a second miniemulsion containing magnetite nanoparticles capped with oleic acid and the same surface-active monomer. The chalcogenide formation occurs in situ at the surface of the polymer particles by adding a precipitating agent (sodium sulfide) at a controlled rate. The phosphonate groups on the surface of the polymer particles have the ability to bind the cadmium ions and act as nucleating centers from which the controlled crystallization of CdS takes place. The resulting hybrid particles show a “raspberry-like” structure, with CdS nanocrystals surrounding the polymeric core. The superparamagnetic behavior of the initial iron oxide nanoparticles, without a recognizable blocking temperature, is retained in the final hybrids particles. The obtained hybrids show luminescence in the visible light with a maximum at 620 nm (2.00 eV).
Identification of a novel Xenopus laevis poly (A) binding protein (2004)

Poly (A) binding proteins are intimately implicated in controlling a number of events in mRNA metabolism from nuclear polyadenylation to cytoplasmic translation and stability. The known poly(A) binding proteins can be divided into three distinct structural groups (prototypes PABP1, PABPN1/PABP2 and Nab2p) and two functional families, showing that similar functions can be accomplished by differing structural units. This has prompted us to perform a screen for novel poly(A) binding proteins using Xenopus laevis. A novel poly(A) binding protein of 32 kDa (p32) was identified. Sequence analysis showed that p32 has about 50% identity to the known nuclear poly(A) binding proteins (PABPN1) but is more closely related to a group of mammalian proteins of unknown function. The expression of Xenopus laevis ePABP2 is restricted to early embryos. Accordingly, we propose that p32 is the founder member of a novel class of poly(A) binding proteins named ePABP2.
Large-Scale Turbulence Effects Simulations for Piston Phase Retrieval (2012)

In the conventional atmospheric turbulence numerical simulation techniques based on the “split”-operator method, the turbulence-induced refractive index inhomogeneities are represented by a set of infinitely narrow (2D) phase distorting layers (phase screens). These conventional phase screens cannot represent large-scale refractive index inhomogeneities due to limitations imposed by computational grid size. For this reason, this commonly used model cannot be applied for computer analysis of atmospheric optical systems that are affected by the presence of large-scale turbulence eddies. Among these systems are coherent imaging ladars, optical vibrometers and interferometers. In the classical Kolmogorov turbulence theory, the impact of the large-scale turbulence eddies are associated with the turbulence outer scale. Contrary to the conventional approach, in the computer simulation technique introduced here the turbulence-induced refractive index inhomogeneities are represented by a set of large-scale phase distorting screens that account for refractive index inhomogeneities which extend beyond the numerical grid correlation length. The results are applied to the analysis of piston phase fluctuations for the cases when the turbulence outer scale significantly exceeds the receiver aperture size. We also analyze the piston phase fluctuations in deep turbulence conditions in presence of phase singularities (phase cuts and branch points), and show that the conventional definition of piston phase cannot be applied for this case. We introduce a more general definition of piston phase which is useful for analysis in deep turbulence conditions. 1.
Evolutionary feature design for object recognition with hierarchical networks (2003)

A major problem in designing neural vision models is the large dimensionality of the search space for defining the needed networks. By using hierarchical vision models inspired by biology we narrow the space of possible architectures. We perform evolutionary optimization of remaining critical network parts e.g. the combination features, which are up to now mostly subject to manually determination. We show that the evolutionary approach leads to an optimized recognition system with respect to speed and performance, which is highly competitive with other state of the art systems.
The IA-64 architecture at work (1998)

Two key architectural features: predication and control speculation, will enable IA-64 compilers to extract instruction level parallelism. To show how compilers will use IA-64 instructions, the author uses code fragments from the pointer chasing problem, an inherently serial code, and from a nested loop with difficult to predict branches.
What Genomics Has Taught Us about Gram-Positive Protein Secretion and Targeting (2014)

This chapter briefly reviews the Sec pathway and its modification in gram-positive bacteria and discusses second independent protein targeting pathways. Some gram-positive bacteria have evolved protein secretion machines dedicated to the assembly of macro-molecular structures such as flagella, type 4 pili, or Flp pili, all of which can be viewed by light or electron microscopy as elongated organelles that protrude from the cell surface. The chapter describes the general principles of protein secretion in gram-positive bacteria along with a few examples. The factors that catalyze protein secretion can be predicted in silico and identified in genomes of all gram-positive bacteria. Sec-mediated protein secretion has been best studied in Escherichia coli and, more recently, in Bacillus subtilis. S-layer proteins are deposited on the surface of gram-positive bacteria to establish specific interactions with cell wall polymers. Many other proteins decorate the cell wall envelope of gram-positive bacteria but are not covalently attached to the envelope. The major subunit of flagella, flagellin, is exported through the hollow conduct made by the basal body across the membrane and hook. Rational vaccine design was achieved by interrogating conserved antigens (secreted or surface displayed) for protective immunity, which led to the identification of multiple surface proteins of group B streptococci as candidates.
A market for gastric NOTES closure: which path should we take? (2009)

The new approach of natural-orifice transluminal endoscopic surgery (NOTES) has excited surgeons and gastroenterologists alike. Not only is the method of passing through the gut into the peritoneal cavity with a flexible endoscope exciting, but the development of the devices necessary to work in the newly conquered space is stimulating likewise. A NOTES incision closure device is one of the most important new developments to look forward to. It needs to be a very reliable tool since as soon as a potential iatrogenic complication has been created, a robust solution to fix it should be the first requirement. Some variations of many novel devices and techniques are described in this issue of Endoscopy [1].
Tuning magnetic frustration of nanomagnets in triangular-lattice geometry (2008)

We study the configuration of magnetic moments on triangular lattices of single-domain ferromagnetic islands, examining the consequences of magnetostatic interactions in this frustrated geometry. By varying the island-island distance along one direction, we are able to tune the ratio of different interactions between neighboring islands, resulting in a corresponding variation in the local correlations between the island moments. Unlike other artificial frustrated magnets, this lattice geometry displays regions of ordered moment orientation, possibly resulting from a higher degree of anisotropy leading to a reduced level of frustration.
Circulating MicroRNAs as biomarkers for disease staging in multiple sclerosis (2013)

Our results establish circulating miRNAs as a readily accessible blood biomarker to monitor disease in MS.
Regression analysis of residential air-conditioning energy consumption at Dhahran, Saudi Arabia (1990)

The energy consumption of a house air conditioner located at Dhahran, Saudi Arabia, is modeled as a function of weather parameters and total (global) solar radiation on a horizontal surface. The selection of effective parameters that significantly influence energy consumption is carried out using general stepping regression methods. The problem of collinearity between the regressors is also investigated. The final model involves parameters of total solar radiation on a horizontal surface, wind speed, and temperature difference between the indoor and outdoor condition. However, the model coefficients are functions of relative humidity and/or temperature difference between the indoor and outdoor condition. Model adequacy is examined by the residual analysis technique. Model validation is carried out by the data-splitting technique. The sensitivity of the model indicates that relative humidity and temperature difference strongly influence the cooling energy consumption. It was found that an increase in relative humidity from 20% to 100% can cause a 100% increase in cooling energy consumption during the high cooling season.
Synthesis of a Stereoblock Polyketone through Ancillary Ligand Exchange (1996)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTSynthesis of a Stereoblock Polyketone through Ancillary Ligand ExchangeM. Brookhart and Mark I. WagnerView Author Information Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3290 Cite this: J. Am. Chem. Soc. 1996, 118, 30, 7219–7220Publication Date (Web):July 31, 1996Publication History Received27 March 1996Published online31 July 1996Published inissue 1 January 1996https://pubs.acs.org/doi/10.1021/ja9610141https://doi.org/10.1021/ja9610141rapid-communicationACS PublicationsCopyright © 1996 American Chemical SocietyRequest reuse permissionsArticle Views826Altmetric-Citations123LEARN 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 (2)»Supporting Information Supporting Information SUBJECTS:Copolymerization,Ligand exchange,Ligands,Microstructures,Polymers Get e-Alerts
Compact S Band Antenna for CubeSat (2018)

In this work, a compact antenna design that can be used in space communication is presented. This antenna element has a height of less than 6 mm and can be used for space application due to its excellent axial ratio in a half-sphere radiation space and good bandwidth performance. The element is compact occupying just 28 × 28 mm and has a dual band operation for the duplex S band satellite to earth communications. Each band has 80–90 Mhz matching bandwidth and covers the communications channels allocated for the low earth orbit satellites in S band. The antenna has an efficiency of around −1 dB across the two bands and it is easy to manufacture with lightweight materials. In addition, this design simplifies the front end architecture and minimizes loses. Compared with literature is the most compact element for the given bandwidth.
Size-Dependent Multiple Twinning in Nanocrystal Superlattices (2009)

We report a size-dependent change in the morphology of superlattices self-assembled from monodisperse colloidal PbS nanocrystals. Superlattices of large (>7 nm) PbS nanocrystals showed a strong tendency to form multiply twinned face-centered cubic superlattices with decahedral and icosahedral symmetry, exhibiting crystallographically forbidden five-fold symmetry elements. On the other hand, superlattices of small (<4 nm) PbS nanocrystals exhibited no twinning. To explain such a dramatic difference in the twinning probability, we showed that twinning energy in a nanocrystal superlattice is strongly size-dependent. In addition, the interparticle potentials acting during the self-assembly process are "softer" in the case of larger PbS nanocrystals, thus favoring the formation of multiply twinned superlattices. Our work introduces a new class of materials exhibiting multiple twinning, while offering flexibility in designing interparticle potentials.
Using Transcriptomes as Mutant Phenotypes Reveals Functional Regions of a Mediator Subunit in Caenorhabditis elegans (2018)

Although transcriptomes have recently been used as phenotypes with which to perform epistasis analyses, they are not yet used to study intragenic function/structure relationships. We developed a theoretical framework to study allelic series using transcriptomic phenotypes. As a proof-of-concept, we apply our methods to an allelic series of <i>dpy-22</i>, a highly pleiotropic <i>Caenorhabditis elegans</i> gene orthologous to the human gene <i>MED12</i>, which encodes a subunit of the Mediator complex. Our methods identify functional units within <i>dpy-22</i> that modulate Mediator activity upon various genetic programs, including the Wnt and Ras modules.
An Organ Culture System for the Study of Programmed Cell Death in the Rat Ventral Prostate* (1990)

Glandular epithelial cells of the rat ventral prostate undergo programmed cell death in vivo following androgen ablation. Fragmentation of the prostatic DNA is an irreversible commitment step in this programmed cell death process. The amount of prostatic DNA fragmentation thus is a quantitative measure of the number of androgen-dependent prostatic glandular cells undergoing programmed death. An in vitro organ culture system was devised for determining rates of prostatic programmed cell death based upon the daily percentage of prostatic DNA fragmentation. To do this, rats were castrated and 2 weeks later treated in vivo for 3 days with exogenous androgen replacement to maximally stimulate DNA synthesis (i.e. proliferation) of the ventral prostatic glandular cells. In vitro organ cultures were established from these ventral prostates and the DNA of these explants was 125I-labeled by incubation in media containing [125I]iododeoxyuridine [( 125I]IDU). Using this in vivo-in vitro DNA labeling technique, greater than 85% of the [125I]IDU radioactivity was incorporated into DNA of the prostatic explants glandular cells. The decrease in 125I-radioactivity from prostatic explants was determined for over a 10-day period of organ culture. Using regression analysis of these data, the daily rate of programmed cell death of the glandular cells was determined. To test the validity of the method, organ cultures were maintained in media capable of inducing either necrotic (i.e. HgCl2-containing media) or programmed cell death (i.e. media lacking testosterone) and the daily decrease in the percentage of [125I]IDU retained in the tissue determined. In addition, the morphologic appearance of necrotic vs apoptotic cell death (i.e. programmed) was quantitated and compared to the [125I]IDU data. These studies demonstrated that this [125I]IDU labeled rat prostatic organ culture system can be used as an in vitro screen to quantitate the ability of various test agents to activate the programmed cell death pathway in prostatic glandular cells.
Cheminfomatic-based Drug Discovery of Human Tyrosine Kinase Inhibitors (2016)

Receptor Tyrosine Kinases (RTKs) are essential components for regulating cell-cell signaling and communication events in cell growth, proliferation, differentiation, survival and metabolism. Deregulation of RTKs and their associated signaling pathways can lead to a wide variety of human diseases such as immunodeficiency, diabetes, arterosclerosis, psoriasis and cancer. Thus RTKs have become one of the most important drug targets families in recent decade. Pharmaceutical companies have dedicated their research efforts towards the discovery of small-molecule inhibitors of RTKs, many of which had been approved by the U.S. Food and Drug Administration (US FDA) or are currently in clinical trials. The great successes in the development of small-molecule inhibitors of RTKs are largely attributed to the use of modern cheminformatic approaches to identifying lead scaffolds. Those include the quantitative structure-activity relationship (QSAR) modeling, as well as the structure-, and ligand-based pharmacophore modeling techniques in this case. Herein we inspected the literature thoroughly in an effort to conduct a comparative analysis of major findings regarding the essential structure-activity relationships (SARs)/pharmacophore features of known active RTK inhibitors, most of which were collected from cheminformatic modeling approaches.
An achievable measurement rate-MSE tradeoff in compressive sensing through partial support recovery (2013)

For compressive sensing, we derive achievable performance guarantees for recovering partial support sets of sparse vectors. The guarantees are determined in terms of the fraction of signal power to be detected and the measurement rate, defined as a relation between the dimensions of the measurement matrix. Based on this result we derive a tradeoff between the measurement rate and the mean square error, and illustrate it by a numerical example.
Signal-apparition simultaneous source acquisition: Results from a penta-source towed marine test (2021)

We present results from a recent field test where an apparitionencoded penta-source towed marine configuration was used to acquire a densely sampled data set. The decoded data are compared against the production partially-overlapping triplesource acquired data. Although the two data sets do not exactly overlap, a qualitative comparison of signal-to-noise ratio (SNR), signal fidelity and resolution can be made.
Ontogenesis of 3β-Hydroxysteroid DehydrogenaseΔ5-Δ4 Isomerase in the Rat Adrenal as Revealed by Immunocytochemistry andin SituHybridization (1991)

The enzyme 3 beta-hydroxy-5-ene-steroid dehydrogenase/5-ene-4-ene isomerase (3 beta-HSD) catalyzes an essential step in the biosynthesis of all classes of active steroids, namely glucocorticoids, mineralocorticoids, progesterone, and sex steroids. To obtain further information on the expression and localization of 3 beta-HSD during development in the rat adrenal, two complementary cytochemical techniques were used: immunocytochemical localization with antibodies against purified human placental 3 beta-HSD, and 3 beta-HSD messenger RNA localization achieved by in situ hybridization with a rat 3 beta-HSD complementary DNA probe. During foetal development, the first detection of 3 beta-HSD messenger RNA was achieved on day 16 by in situ hybridization, the silver grains being located on the cortical cells. Between days 17 and 20, on the other hand, immunostaining became positive in the cytoplasm of the same cortical cells, the capsule being negative by both immunostaining and in situ hybridization. Interestingly, two distinct zones of intensity of 3 beta-HSD localization could be distinguished, namely the highly labeled reticular and fascicular zones and the less positive glomerular zone. This observation coincides with the onset of fetal ACTH secretion on days 17-18 and with accelerated adrenocortical growth and differentiation. After birth and until day 25, strong immunolabeling was observed in the cytoplasm of adrenocortical cells, the glomerular zone being labeled at a lower degree than the remaining cortex. The same localization was obtained by in situ hybridization. This low labeling of the glomerular zone might be related to the low plasma levels of angiotensin II observed in the immature rat. From day 25 after birth, the three zones of the cortex were uniformly labeled and no immunostaining was seen in the medulla or capsule. Similarly, by in situ hybridization, silver grains were located exclusively in the adrenal cortex. The present data suggest that 3 beta-HSD expression could well play a major role in regulating adrenal function during foetal and postnatal development.