gebhart/patrepeval huggingface dataset:
Novel Methods of Species and Product Authenticity and Traceability Testing Using DNA Analysis for Food and Agricultural Applications (2014)

Categorization and identification of biodiversity is key to global food security and integrity. Accurate species identification is relevant to many sectors involved in food production and processing, including for pest identification and management and for food authenticity testing. The usual methods of visual identification of species are often not applicable to food products as morphological characters are often removed during processing. However, methods using DNA analysis enable identifications from immature life stages, or fragmentary remains, and are therefore may be of particular use in the food and agriculture industries. Food fraud is a serious socioeconomic issue that continues to grow due to increasing global trade, and technological innovation for detection as well as perpetrating fraud. Incorrect species labeling of food products is one example of food adulteration that has broad impacts including economic, health, conservation and religious consequences. Molecular techniques, like DNA barcoding, have become part of routine methods for species identification and their implementation in the regulation of market products has begun. Although DNA barcoding provides several advantages over other methods, the ~650 base pair target required for analysis is often too long for recovery from degraded samples, for example in cooked or canned products. In these cases real-time PCR provides an alternative. Design of real-time PCR assays requires particular attention to the haplotype coverage and sequence quality. DNA barcode sequences from the Barcode of Life Data System (BOLD), an online DNA barcode sequence library, are a source of quality sequences available for a wide range of species, particularly those of commercial importance. Therefore, BOLD is a useful resource in the design of successful real-time PCR assays for identification of species in food products as well as other species of interest to the food industry, such as agricultural pests. When endogenous DNA is not available, or provides limited information, synthetic oligonucleotide “barcodes” can be employed for traceability and authenticity testing. This thesis explores the linkages between species identification and product authenticity in the agriculture and food industries and provides a proof of concept for the use and detection of an oligonucleotide tag for traceability of apple juice.
Advanced Mini Array Antenna Design Using High Fidelity Computer Modeling and Simulation (2000)

NAVSYS has developed a miniaturized GPS antenna 
array technology that reduces the size of the antenna 
elements and the array dimensions. This is an enabling 
technology, which allows GPS controlled reception 
pattern antenna arrays (CRPA) with anti-jamming 
capability to be installed on vehicles where their size has 
previously prohibited their use. This includes aircraft 
where size and weight constraints resulted in fixed 
reception pattern antenna (FRPA) installations instead of 
CRPAs and in munitions applications where space and 
surface area are at a premium. 

NAVSYS has developed a six-inch L1 four element 
phased array antenna. However, there is still a need for 
even smaller mini-array antenna with more elements and 
both L1/L2 capability. NAVSYS and SPAWAR have 
teamed to use the NAVSYS antenna design and the 
Department of Defense’s supercomputer power along 
with Electromagnetic Interactions GEneRalized (EIGER) 
code which is an advanced Method of Moment/Hybrid 
Finite Element Method to model the antenna and compare 
the results to test data. This paper will present the results 
of the modeling data versus test data and the results of a 
potential design modification.
Spotting Culprits in Epidemics: How Many and Which Ones? (2012)

Given a snapshot of a large graph, in which an infection has been spreading for some time, can we identify those nodes from which the infection started to spread? In other words, can we reliably tell who the culprits are? In this paper we answer this question affirmatively, and give an efficient method called NETSLEUTH for the well-known Susceptible-Infected virus propagation model. Essentially, we are after that set of seed nodes that best explain the given snapshot. We propose to employ the Minimum Description Length principle to identify the best set of seed nodes and virus propagation ripple, as the one by which we can most succinctly describe the infected graph. We give an highly efficient algorithm to identify likely sets of seed nodes given a snapshot. Then, given these seed nodes, we show we can optimize the virus propagation ripple in a principled way by maximizing likelihood. With all three combined, NETSLEUTH can automatically identify the correct number of seed nodes, as well as which nodes are the culprits. Experimentation on our method shows high accuracy in the detection of seed nodes, in addition to the correct automatic identification of their number. Moreover, we show NETSLEUTH scales linearly in the number of nodes of the graph.
Genome Evolution of Wolbachia Strain wPip from the Culex pipiens Group (2008)

The obligate intracellular bacterium Wolbachia pipientis strain wPip induces cytoplasmic incompatibility (CI), patterns of crossing sterility, in the Culex pipiens group of mosquitoes. The complete sequence is presented of the 1.48-Mbp genome of wPip which encodes 1386 coding sequences (CDSs), representing the first genome sequence of a B-supergroup Wolbachia. Comparisons were made with the smaller genomes of Wolbachia strains wMel of Drosophila melanogaster, an A-supergroup Wolbachia that is also a CI inducer, and wBm, a mutualist of Brugia malayi nematodes that belongs to the D-supergroup of Wolbachia. Despite extensive gene order rearrangement, a core set of Wolbachia genes shared between the 3 genomes can be identified and contrasts with a flexible gene pool where rapid evolution has taken place. There are much more extensive prophage and ankyrin repeat encoding (ANK) gene components of the wPip genome compared with wMel and wBm, and both are likely to be of considerable importance in wPip biology. Five WO-B-like prophage regions are present and contain some genes that are identical or highly similar in multiple prophage copies, whereas other genes are unique, and it is likely that extensive recombination, duplication, and insertion have occurred between copies. A much larger number of genes encode ankyrin repeat (ANK) proteins in wPip, with 60 present compared with 23 in wMel, many of which are within or close to the prophage regions. It is likely that this pattern is partly a result of expansions in the wPip lineage, due for example to gene duplication, but their presence is in some cases more ancient. The wPip genome underlines the considerable evolutionary flexibility of Wolbachia, providing clear evidence for the rapid evolution of ANK-encoding genes and of prophage regions. This host-Wolbachia system, with its complex patterns of sterility induced between populations, now provides an excellent model for unraveling the molecular systems underlying host reproductive manipulation.
A New Method for Preparing Mesenchymal Stem Cells and Labeling with Ferumoxytol for Cell Tracking by MRI (2016)

Mesenchymal stem cells (MSCs) are among the major stem cells used for cell therapy and regenerative medicine. In-vivo cell-tracking by magnetic resonance imaging (MRI) is crucial for regenerative medicine, allowing verification that the transplanted cells reach the targeted sites. Cellular MRI combined with superparamagnetic iron-oxide (SPIO) contrast agents is an effective cell-tracking method. Here, we are reporting a new "bio-mimicry" method by making use of the "in-vivo environment" of MSCs to prepare native MSCs, so that (i) the phagocytic activity of cultured MSCs can be recovered and expanded MSCs can be ex-vivo labeled with Ferumoxytol, which is currently the only FDA approved SPIO nanoparticles for human use. Using our new method, 7-day cultured MSCs regain the capability to take up Ferumoxytol and exhibit an intracellular iron concentration of 2.50 ± 0.50 pg/MSC, comparable to that obtained by using Ferumoxytol-heparin-protamine nanocomplex; and (ii) cells can be re-sized to more native size, reducing from 32.0 ± 7.2 μm to 19.5 ± 5.2 μm. Our method can be very useful for expanding MSCs and labeling with Ferumoxytol, without the need for transfection agents and/or electroporation, allowing cell-tracking by MRI in both pre-clinical and clinical studies.
Optical properties of nanoscale, one-dimensional silicon grating structures (1996)

We report a detailed study of nanostructure fabrication and optical characterization of sub-μm-period, one-dimensional, Si grating structures. Nanoscale wall width structures were fabricated by combining laser interferometric lithography with anisotropic wet-chemical etching (KOH) and thermal oxidation. Structure wall widths were characterized by Raman scattering (RS) and scanning electron microscopy. Salient features of the RS measurements as a function of wall widths from ∼100 to 10 nm were: (a) large cross-section enhancements, ∼100×, for linewidths ∼50 nm; (b) asymmetric line shapes with tails extending to smaller Raman shifts for linewidths ∼20 nm; and (c) splitting of the bulk Raman mode, again to lower Raman shifts, for linewidths ∼10 nm. For room temperature photoluminescence (PL) measurements, the grating structures were excited at 257 nm. PL measurements are reported for oxidized and unoxidized grating structures with peaks varying between 380 and 700 nm. PL was only observed for Si structures with dimensions less than about 10 nm. PL intensities and spectral line shapes varied significantly as a result of surface modification treatments such as high temperature anneal in a N2 atmosphere, immersion in boiling H2O, and long-term exposure to ambient air. The measurements indicate a strong correlation of the visible PL with crystal size (∼5–10 nm); however, it remains unclear if the mechanism responsible is quantum confinement, passivation of the surface by Si:Hx complexes, or optically active surface states.
A 16-bit microprocessor (1975)

The architecture of PACE (Processing and Control Element) microprocessor, organized to minimize external components, and provide a powerful instruction set, will be discussed. A parallel 16-bit, single-chip CPU, implemented in P-channel, silicon-gate technology. It features four general-purpose accumulators, a 10-word stack, interrupt logic, control and status flags, a 16-bit ALU, requires single-phase, true and complement clocks, and a typical execution time of 10μs.
Hydrate formation using water spraying onto a cooled solid surface in a guest gas (2006)

Abstract An experimental study has been performed involving water spraying onto a cooled metal‐block surface exposed to a hydrate‐forming gas as a means of high‐rate hydrate formation for the purpose of, for example, natural‐gas storage. Special attention has been paid to the effectiveness of conductive cooling through the metal block for directly removing the heat released by the hydrate formation from its site, that is, the surface of the metal block, and, thereby, increasing the rate of hydrate formation. HFC‐32 (CH 2 F 2 ) that forms a structure‐I hydrate at moderate pressures was used as a model gas to enable visual observations of the hydrate formation inside a large‐windowed spray chamber. The experiments revealed that the cooling by the metal block effectively increases the rate of hydrate formation while water is sprayed at a given volumetric rate and at a given degree of subcooling from the guest‐gas/water/hydrate equilibrium temperature. © 2006 American Institute of Chemical Engineers AIChE J, 2006
Bcl-2 is expressed in human natural killer cells and is regulated by interleukin-2. (1998)

Bcl-2 is a major anti-apoptotic protein expressed in many normal and malignant cells. Recently, low to absent expression was reported in human natural killer (NK) cells cultured in serum-free media which could be induced with stem cell factor. We investigated the expression of bcl-2 protein of NK cells in normal blood donors and compared the bcl-2 expression in CD56+ NK cells with CD3+ T cells. To determine bcl-2 reactivity, a three-color flow-cytometric technique was used. CD56+ CD3- NK cells had an average bcl-2 expression of 83% compared with CD3+ T cells. CD56 and CD3 double positive T cells had an average content of 111% compared with all peripheral CD3+ T lymphocytes. When peripheral mononuclear cells were cultured with interleukin-2 (IL-2), bcl-2 could be upregulated by IL-2 in all cell populations studied. The induction of bcl-2 in these cell populations paralleled the induction in CD56- T lymphocytes cultured under identical conditions. The induction of bcl-2 by IL-2 was confirmed by Western blotting. The maximum induction of bcl-2 by IL-2 was observed at an IL-2 dose of 100-1,000 U/ml. Our data confirm the anti-apoptotic protein bcl-2 as an activation- or proliferation-associated marker of normal NK cells which can be induced by IL-2.
General decomposition of sequential machines: relationships to state assignment (1989)

In this paper, we present new techniques for state assignment of finite state machines based on state machine decomposition algorithms.
Clinical Impact and Reliability of Pleural Fluid Mesothelin in Undiagnosed Pleural Effusions (2009)

Pleural fluid mesothelin provides additional diagnostic value relative to cytological examination. Mesothelin measurements are reproducible and not affected by inflammatory pleural processes.
Novel single-mode, grating WDM device based network (1988)

Experiments on a commercial grating WDM device show that it can be used as the core element in a passive, complete routing network, allowing secure communication between all system users. A system is configured to demonstrate this potential use.
Prostate Cancer Stem Cells: Research Advances (2015)

Cancer stem cells have been defined as cells within a tumor that possesses the capacity to self-renew and to cause the heterogeneous lineages of cancer cells that comprise the tumor. Experimental evidence showed that these highly tumorigenic cells might be responsible for initiation and progression of cancer into invasive and metastatic disease. Eradicating prostate cancer stem cells, the root of the problem, has been considered as a promising target in prostate cancer treatment to improve the prognosis for patients with advanced stages of the disease.
Polymerization of α-Olefins with Pyridylamidohafnium Catalysts:  Living Behavior and Unexpected Isoselectivity from a <i>C</i><i><sub>s</sub></i>-Symmetric Catalyst Precursor (2007)

ADVERTISEMENT RETURN TO ISSUEPREVNoteNEXTPolymerization of α-Olefins with Pyridylamidohafnium Catalysts: Living Behavior and Unexpected Isoselectivity from a Cs-Symmetric Catalyst PrecursorGregory J. Domski, Emil B. Lobkovsky, and Geoffrey W. CoatesView Author Information Department of Chemistry and Chemical Biology, Baker Laboratory, Cornell University, Ithaca, New York 14853-1301 Cite this: Macromolecules 2007, 40, 9, 3510–3513Publication Date (Web):April 7, 2007Publication History Received9 December 2006Revised12 February 2007Published online7 April 2007Published inissue 1 May 2007https://pubs.acs.org/doi/10.1021/ma062824shttps://doi.org/10.1021/ma062824sbrief-reportACS PublicationsCopyright © 2007 American Chemical SocietyRequest reuse permissionsArticle Views2471Altmetric-Citations110LEARN 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 (4)»Supporting Information Supporting Information SUBJECTS:Catalysts,Ligands,Olefin polymerization,Polymerization,Thermoresponsive polymers Get e-Alerts
Sonication-Dependent Electroporation of the Erythromycin-Producing Bacterium <i>Saccharopolyspora erythraea</i> (1998)

We report the development of an electrotransformation method applicable to all strains of Saccharopolyspora erythraea examined to date. Vegetatively grown mycelia were rendered electrocompetent by subjecting mycelial suspensions to ultrasound pulses. The protocol provides an alternative route for the introduction of DNA into filamentous microorganisms otherwise recalcitrant to transformation techniques.
The atypical anxiolytic drug, tofisopam, selectively blocks phosphodiesterase isoenzymes and is active in the mouse model of negative symptoms of psychosis (2010)

Tofisopam is a member of the 2,3-benzodiazepine compound family which is marketed for the treatment of anxiety in some European countries. In contrast to classical 1,4-benzodiazepines, the compound does not bind to the benzodiazepine binding site of the γ-aminobutyric acid receptor and its psychopharmacological profile differs from such compounds. In addition to anxiolytic properties, antipsychotic effects are reported. We now show that tofisopam, 50 mg/kg intraperitoneally (i.p.), administered in parallel to repeated doses of dizocilpine 0.2 mg/kg i.p. can ameliorate dizocilpine-induced prolongation of immobility, which is considered to be a model of negative symptoms of psychosis. We further show that tofisopam acts as an isoenzyme-selective inhibitor of phosphodiesterases (PDEs) with highest affinity to PDE-4A1 (0.42 μM) followed by PDE-10A1 (0.92 μM), PDE-3 (1.98 μM) and PDE-2A3 (2.11 μM). The data indicate that tofisopam is an interesting candidate for the adjuvant treatment of psychosis with focus on negative symptoms. Combined partial inhibition of PDE-4 and PDE-10 as well as PDE-2 may be the underlying mechanism to this activity. Due to the good safety profile of tofisopam as evident from long-term use of this agent in patients, it may be concluded that dual or triple inhibition of PDE isoenzymes with additive or synergistic effects may be an interesting approach to pharmacological activity, resulting in active compounds with beneficial safety profile. Dose-limiting side effects such as emesis induced by selective inhibition of PDE-4 may be prevented by such strategies.
Automatic car model classification (1991)

An application is described of dynamic-programming-based matching to car model classification. An edge map is first extracted, and a sequence of pre-processing stages is carried out, culminating in the use of a 2-dimensional circle Hough transform to generate a cued region containing a putative car. Within the cued area a dynamic programming search (edge-based classification) is carried out to classify the model or type of car. Experimental results are given.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Therapy for Cryptococcal Meningitis in Patients with AIDS (1992)

Treatment of cryptococcal meningitis in patients with AIDS with amphotericin B plus flucytosine is associated with a failure rate of 20%-30%. In the absence of chronic suppressive therapy, 40%-60% of patients develop recurrent disease. Recent comparative studies have evaluated fluconazole, a new triazole antifungal agent. In primary therapy, fluconazole is associated with response rates of 35%-60%, which are equivalent to those seen with amphotericin B alone. However, a smaller study suggested that amphotericin B plus flucytosine was superior to fluconazole alone. Both studies identified risk factors associated with a poor outcome; these factors include lethargy or obtundation at presentation, a high titer of cryptococcal antigen titer in the cerebrospinal fluid, and a low leukocyte count in the cerebrospinal fluid. Fluconazole is highly effective in suppressing relapses of cryptococcal meningitis. Itraconazole has been investigated less extensively in the treatment of cryptococcosis but offers promise. Future studies need to address alternative approaches to the management of acute cryptococcal disease and primary prophylaxis for cryptococcal infection in patients with AIDS.
<i>NUBPL</i> mutations in patients with complex I deficiency and a distinct MRI pattern (2013)

Our data show that NUBPL mutations are associated with a unique, consistent, and recognizable MRI pattern, which facilitates fast diagnosis and obviates the need for other tests, including assessment of mitochondrial complex activities in muscle or fibroblasts.
A single dose of pegfilgrastim compared with daily filgrastim for supporting neutrophil recovery in patients treated for low-to-intermediate risk acute myeloid leukemia: results from a randomized, double-blind, phase 2 trial (2008)

Clinicaltrials.gov NCT00114764.
Lithium in the brines of Fish Lake Valley and Columbus Salt Marsh, Nevada (1977)

Analyses of waters from springs in Nevada have led to the identification of an area containing anomalous amounts of lithium northwest of the Clayton Valley area. Fish Lake Valley and Columbus Salt Marsh contain waters having relatively high lithium and potassium concentrations. At least a part of these waters is 3 probably derived from the leaching of Tertiary rocks containing saline minerals. The high-lithium waters at Columbus Salt Marsh could be derived not only by the leaching of rocks with a high f soluble lithium anci potassium content but also by subsurface outflow from Fish Lake Valley.