gebhart/patrepeval huggingface dataset:
Generation of Backbone-Free, Low Transgene Copy Plants by Launching T-DNA from the<i>Agrobacterium</i>Chromosome (2009)

Abstract In both applied and basic research, Agrobacterium-mediated transformation is commonly used to introduce genes into plants. We investigated the effect of three Agrobacterium tumefaciens strains and five transferred (T)-DNA origins of replication on transformation frequency, transgene copy number, and the frequency of integration of non-T-DNA portions of the T-DNA-containing vector (backbone) into the genome of Arabidopsis (Arabidopsis thaliana) and maize (Zea mays). Launching T-DNA from the picA locus of the Agrobacterium chromosome increases the frequency of single transgene integration events and almost eliminates the presence of vector backbone sequences in transgenic plants. Along with novel Agrobacterium strains we have developed, our findings are useful for improving the quality of T-DNA integration events.
ALIMENTARY TRACT Use of Direct, Endoscopic-Guided Measurements of Mucosal Impedance in Diagnosis of Gastroesophageal Reflux Disease (2012)

BACKGROUND & AIMS: Diagnostic tests for gastroesophageal reflux disease (GERD) are constrained because measurements are made at a single time point, so the long-term effects on the mucosa cannot be determined. We developed a minimally invasive system to assess changes in esophageal mucosal impedance (MI), a marker of reflux. We measured the extent of changes in MI along the esophagus and show that the device to assess MI can be used to diagnose patients with GERD. METHODS: A single-channel MI catheter composed of a unique sensor array was designed to easily traverse the working channel of an upper endoscope. We performed a prospective longitudinal study of patients with erosive esophagitis (n 19), nonerosive but pH-positive GERD (n 23), and those without GERD (n 27). MI was measured at the site of esophagitis as well as 2, 5, and 10 cm above the squamocolumnar junction. The MI values were compared among groups, at different levels along the esophageal axis. RESULTS: Median MI values were significantly lower at the site of erosive mucosa (811 ; range, 621‐1272 ) than other nonerosive regions (3723 ; range, 2421‐4671 ; P .001), and were significantly lower at 2 cm above the squamocolumnar junction in patients with GERD (2096 ; range, 1415‐2808 ), compared with those without GERD (3607 ; range, 1973‐4238 ; P .008). There was a significant and graded increase in MI along the axis of the distal to proximal esophagus in patients with GERD that was not observed in individuals without reflux (P .004). CONCLUSIONS: Measurements of MI along the esophagus can be used to identify patients with GERD. ClinicalTrials.gov, number NCT01194323.
Tube‐wave monitoring of oil fields (2006)

Tube‐wave monitoring is a fit‐for‐purpose downhole imaging and monitoring technique. It aims to detect and characterize time‐lapse changes in a cross‐well space. In contrast to conventional cross‐well seismic it does not require production interruption or reduces it to a minimum. Monitoring relies on tube waves in a well fluid column to carry the seismic signals to and from the reservoir. We present a simple modeling to support the concept and validate experimental data acquired at Stratton and Mallik fields.
Toward a better understanding of preeclampsia: Comparative proteomic analysis of preeclamptic placentas (2007)

Preeclampsia (PE), a pregnancy-specific syndrome of hypertension, proteinuria, and other systemic disturbances, is a state of widespread endothelial dysfunction secondary to defective placentation. Morphologically, the current data displayed degenerative and apoptotic changes in the mitochondria and villous trophoblasts of preeclamptic placenta. To reveal the superimposing alterations in placental proteins that might explain the pathophysiology of PE, we performed 2-DE MALDI-TOF MS/MS proteomics analysis of differentially expressed placental proteins with placenta from eight normal and eight preeclamptic pregnancies. The identified proteins were confirmed by Western blot analysis. We also performed morphologic evaluation of preeclamptic placentas under both electron and light microscopy. The results disclosed the marked overexpression of chaperonin 60, GST, VDAC, ERp29, and cathepsin D in PE. These proteomics findings clearly suggest the possible cellular battle against mitochondria-originated oxidative stress during PE that either end up with recovery or apoptosis. These results provide a better understanding of proteomic alterations and may help in clarification of stress-related changes in preeclamptic placentas.
Detecting controversial events from twitter (2010)

Social media provides researchers with continuously updated information about developments of interest to large audiences. This paper addresses the task of identifying controversial events using Twitter as a starting point: we propose 3 models for this task and report encouraging initial results.
Recommendation System Based on Complete Personalization (2016)

Current recommender systems are very inefficient. There are many metrics that are used to measure the effectiveness of recommender systems. These metrics often include "conversion rate" and "click through rate". Recently, these rates are in low single digit (less than 10%). In other words, for more than 90% of times, the model that the targeting system is based on, produces noise. The belief in this work is that the main problem leading to getting such unsatisfactory outcomes is the modeling problem. Much of the modeling problem could be represented and exemplified in treating users and items as member of clusters(segments). In this work, we consider full personalization of recommendation systems. We aim at personalization of users and contents simultaneously. Recommendations using baseline approach are inaccurate and targeting based on similarity-based recommendation (collaborative filtering) suffer from many disadvantages such as the neglect of interactive correlation. In this work, similarity based targeting has been combined with baseline approach and latent factor models and has been treated with adaptive regularization allowing complete personalization with respect to both users and items.
Polyphenol‐enriched apple extract attenuates food allergy in mice (2010)

Polyphenol-enriched apple extract can attenuate food allergy symptoms in sensitized mice via two distinct possible mechanisms.
Diode pumped laser action and self-frequency doubling in Nd/sup 3+/:YCOB (2002)

Development of the oxyborate materials has brought about the realization of single crystal elements under diode pumped operation for compact, simple, solid state lasers producing visible laser emission. YCa/sub 4/B/sub 3/O/sub 10/ (YCOB) doped with Nd/sup 3+/ has the distinct advantage of combining both an active laser medium with a modest nonlinear coefficient without associated photorefractive damage and self-absorption as with other self-frequency doubling (SFD) lasers. By beam shaping high brightness diodes and proper mode matching of the cavity mode with the laser mode, SFD output powers as high as those achieved by Ti:sapphire pumping can be obtained in a simple compact air cooled laser system ready for the market. We report efficient laser action and SFD generation in Nd/sup 3+/:YCOB under diode pumping.
New High Temperature Polymer Electrolyte Membranes. Influence of the Chemical Structure on their Properties (2008)

Abstract New polymer electrolytes based on aromatic polyethers bearing main chain pyridine groups have been synthesised. They possess good mechanical properties, high thermal and oxidative stability and can be used as electrolytes for high temperature PEM fuel cells. A study of the influence of the chemical structure on the properties of these materials with respect to their ability to be used in high temperature PEM fuel cells was made, while a blend of the current reported polymers is tested in single cell giving encouraging preliminary results.
Electrochemiluminescence from Tunicate, Tunichrome–Metal Complexes and Other Biological Samples (1996)

Low level intrinsic electrochemiluminescence (ECL) was induced from body fluids and homogenized tissues of oysters and several species of tunicates. No significant ECL was detected in human blood cell lysates, or bovine haematin, but minor ECL was observed in avian blood cell lysates. Both terrestrial grass and seagrass exhibited ECL, which is probably attributable to chlorophyll, since dead (brown) grass did not demonstrate ECL. It was postulated that organic–metal complexes in marine invertebrates were, at least in part, responsible for the intrinsic ECL, since such animals are known to be rich in organically bound metals. However, alternative biochemical mechanisms for the observed ECL, which do not involve metal chelates, are possible. Various metal ions were added to the invertebrate preparations to determine whether exogenous metals could enhance or inhibit the ECL reactions. Strongly oxidizing metal ions such as Ag+, Au+, Cu2+, Hg2+ and Sb2+ at ≥100 ppm severely inhibited the intrinsic ECL response. No statistically significant ECL enhancement due to addition of metal ions was noted. ECL ‘profiles’ were generated which demonstrated differences in the ECL responses of individual tunicate preparations to the presence of various exogenous metal ions. Differences in ECL profiles may represent differences in types or levels of endogenous metal chelates or other biochemical constituents. In addition, synthetic tunichromes (tunicate pigments) were analysed for ECL in the presence and absence of various added metal ions. One synthetic tunichrome isomer demonstrated a specific ECL interaction with Hg2+, while the other demonstrated broader ECL activity with several metal ions.
Widely tunable normal dispersion fiber optical parametric oscillator (2014)

We demonstrate a very wide tuning range normal dispersion fiber optical parametric oscillator (FOPO) using a femtosecond, fixed wavelength fiber laser as the pump source. A tuning range from 1360nm to 1835nm with pulse energy up to 1.3 nJ was achieved by operating the FOPO in the normal dispersion regime. We believe that the proposed laser design will be useful for developing widely tunable and high energy ultrafast fiber laser sources.
Trap and track: designing self-reporting porous Si photonic crystals for rapid bacteria detection (2014)

The task of rapid detection and identification of bacteria remains a major challenge in both medicine and industry. This work introduces a new concept for the design of self-reporting optical structures that can detect and quantify bacteria in real-time. The sensor is based on a two-dimensional periodic structure of porous Si photonic crystals in which the pore size is adjusted to fit the target bacteria cells (Escherichia coli). Spontaneous bacteria capture within the pores induces measurable changes in the zero-order reflectivity spectrum collected from the periodic structure. Confocal laser microscopy and electron microscopy confirm that the Escherichia coli cells are individually imprisoned within the porous array. A simple model is suggested to correlate the optical readout and the bacteria concentration and its predictions are found to be in good agreement with experimental results. In addition, we demonstrate that sensing scheme can be easily modified to potentially allow monitoring of concentration, growth and physiological state of bacteria cells. This generic platform can be tailored to target different microorganisms by tuning the array periodicity and its surface chemistry for rapid and label-free detection outside the laboratory environment.
Emerging Strategies to Access Peptide Macrocycles from Genetically Encoded Polypeptides (2013)

Macrocyclic peptides have emerged as attractive molecular scaffolds for the development of chemical probes and therapeutics. In this synopsis, we highlight contemporary strategies to access peptide macrocycles from ribosomally produced polypeptides. Challenges that have been tackled in this area involve orchestrating the desired macrocyclization process in the presence of unprotected polypeptide precursors and expanding the functional space encompassed by these molecules beyond that of canonical amino acid structures. Applications of these methodologies for the discovery of bioactive molecules are also discussed.
Introduction to Eye and Gaze Trackers (2012)

In the previous chapters of the book, you will have seen multiple applications for using (and the benefits of using) a gaze tracker. In this chapter, you will be given more insight into how an eye tracker operates. Not only can this aid in understanding the eye tracker better, it also gives important information about how future applications might improve on current ones, by using more of the information available from the eye tracker: as we shall see, an eye tracker can often provide you with more information than just coordinates on a screen. This chapter gives an overview of the components of an eye tracker and introduces basics of gaze modelling. It helps in understanding the following chapters which each provide some details of how to build an eye tracker. This section has technical content, but it is our hope that also readers not particularly interested in the details of eye and gaze trackers will gain some useful insights.
Selecting electrode configurations for image-guided cochlear implant programming using template matching (2017)

Cochlear implants (CIs) are neural prostheses that restore hearing using an electrode array implanted in the cochlea. After implantation, the CI processor is programmed by an audiologist. One factor that negatively impacts outcomes and can be addressed by programming is cross-electrode neural stimulation overlap (NSO). We have proposed a system to assist the audiologist in programming the CI that we call image-guided CI programming (IGCIP). IGCIP permits using CT images to detect NSO and recommend deactivation of a subset of electrodes to avoid NSO. We have shown that IGCIP significantly improves hearing outcomes. Most of the IGCIP steps are robustly automated but electrode configuration selection still sometimes requires manual intervention. With expertise, distance-versus-frequency curves, which are a way to visualize the spatial relationship learned from CT between the electrodes and the nerves they stimulate, can be used to select the electrode configuration. We propose an automated technique for electrode configuration selection. A comparison between this approach and one we have previously proposed shows that our method produces results that are as good as those obtained with our previous method while being generic and requiring fewer parameters.
Beyond Soundness: On the Semantic Consistency of Executable Process Models (2008)

Executable business process models build on the specification of process activities, their implemented business functions (e.g., Web services) and the control flow between these activities. Before deploying such a model, it is important to verify control-flow correctness. A process is sound if its control-flow guarantees proper completion and there are no deadlocks. However, a sound control flow is not sufficient to ensure that an executable process model indeed behaves as expected. This is due to business functions requiring certain preconditions to be fulfilled for execution and having an effect on the process (postconditions). Semantic annotations provide a means for taking such further aspects into account. Inspired by OWL-S and WSMO, we consider process models in which the individual activities are annotated with logical preconditions and postconditions specified relative to an ontology that axiomatizes the underlying business domain. Verification then means to determine whether the interaction of control flow and logical states of the process is correct. To this end, we formalize the semantics of annotated processes and point out which kinds of flaws may arise. We then identify a class of processes with restricted semantic annotations where correctness can be verified in polynomial time; and we prove that the semantic annotations cannot be generalized without losing computational efficiency. The paper is written at a semi-formal level using an illustrative example, details can be looked up in a longer technical report.
Fibromodulin promoted in vitro and in vivo angiogenesis (2013)

Fibromodulin (FMOD) is an extracellular matrix (ECM) small leucine-rich proteoglycan (SLRP) that plays an important role in cell fate determination. Previous studies revealed that not only is FMOD critical in fetal-type scarless wound healing, but it also promotes adult wound closure and reduces scar formation. In addition, FMOD-deficient mice exhibit significantly reduced blood vessel regeneration in granulation tissues during wound healing. In this study, we investigated the effects of FMOD on angiogenesis, which is an important event in wound healing as well as embryonic development and tumorigenesis. We found that FMOD accelerated human umbilical vein endothelial HUVEC-CS cell adhesion, spreading, actin stress fiber formation, and eventually tube-like structure (TLS) network establishment in vitro. On a molecular level, by increasing expression of collagen I and III, angiopoietin (Ang)-2, and vascular endothelial growth factor (VEGF), as well as reducing the ratio of Ang-1/Ang-2, FMOD provided a favorable network to mobilize quiescent endothelial cells to an angiogenic phenotype. Moreover, we also confirmed that FMOD enhanced angiogenesis in vivo by using an in ovo chick embryo chorioallantoic membrane (CAM) assay. Therefore, our data demonstrate that FMOD is a pro-angiogenic and suggest a potential therapeutic role of FMOD in the treatment of conditions related to impaired angiogenesis.
Interaction of human papillomavirus (HPV) type 16 capsid proteins with HPV DNA requires an intact L2 N-terminal sequence (1994)

Encapsidation of papillomavirus DNA involves DNA-protein and protein-protein interactions. We sought to define the role of each human papillomavirus (HPV) capsid protein in HPV DNA encapsidation. HPV16 major (L1) and minor (L2) capsid proteins purified from recombinant vaccinia virus-infected cells were compared for their ability to bind nucleic acids. L2 protein, but not L1 protein, could bind HPV DNA. To map the DNA-binding region of L2, a series of truncated or point-mutated L2 protein open reading frames were used to show that only the N terminal of L2 was required for L2-DNA binding. This interaction depends critically on charged amino acids (Lys or Arg) in the first 12 amino acids of the N terminal of the protein. Several techniques were used to show that L2 interaction with DNA did not require specific DNA sequences. We propose that HPV L2 protein may play a major role in papillomavirus capsid assembly by introducing HPV DNA to the virus particles formed by the self assembly of the L1 major structural protein.
Aggravated Endoplasmic Reticulum Stress as a Basis for Enhanced Glioblastoma Cell Killing by Bortezomib in Combination with Celecoxib or Its Non-Coxib Analogue, 2,5-Dimethyl-Celecoxib (2008)

The proteasome inhibitor bortezomib (Velcade) is known to trigger endoplasmic reticulum (ER) stress via the accumulation of obsolete and damaged proteins. The selective cyclooxygenase-2 (COX-2) inhibitor celecoxib (Celebrex) causes ER stress through a different mechanism (i.e., by causing leakage of calcium from the ER into the cytosol). Each of these two mechanisms has been implicated in the anticancer effects of the respective drug. We therefore investigated whether the combination of these two drugs would lead to further increased ER stress and would enhance their antitumor efficacy. With the use of human glioblastoma cell lines, we show that this is indeed the case. When combined, bortezomib and celecoxib triggered elevated expression of the ER stress markers GRP78/BiP and CHOP/GADD153, caused activation of c-Jun NH(2)-terminal kinase and ER stress-associated caspase-4, and greatly increased apoptotic cell death. Small interfering RNA-mediated knockdown of the protective ER chaperone GRP78/BiP further sensitized the tumor cells to killing by the drug combination. The contribution of celecoxib was independent of the inhibition of COX-2 because a non-coxib analogue of this drug, 2,5-dimethyl-celecoxib (DMC), faithfully and more potently mimicked these combination effects in vitro and in vivo. Taken together, our results show that combining bortezomib with celecoxib or DMC very potently triggers the ER stress response and results in greatly increased glioblastoma cytotoxicity. We propose that this novel drug combination should receive further evaluation as a potentially effective anticancer therapy.
Canine Coronavirus Highly Pathogenic for Dogs (2006)

Canine coronavirus (CCoV) is usually responsible for mild, self-limiting infections restricted to the enteric tract. We report an outbreak of fatal disease in puppies caused by a pathogenic variant of CCoV that was isolated from organs with severe lesions.
A critical GxxxA motif in the γ<sub>6</sub> calcium channel subunit mediates its inhibitory effect on Cav3.1 calcium current (2008)

The eight members of the calcium channel gamma subunit family are integral membrane proteins that regulate the expression and behaviour of voltage and ligand gated ion channels. While a subgroup consisting of gamma(2), gamma(3), gamma(4) and gamma(8) (the TARPs) modulate AMPA receptor localization and function, the gamma(1) and gamma(6) subunits conform to the original description of these proteins as regulators of voltage gated calcium channels. We have previously shown that the gamma(6) subunit is highly expressed in atrial myocytes and that it is capable of acting as a negative modulator of low voltage activated calcium current. In this study we extend our understanding of gamma(6) subunit modulation of low voltage activated calcium current. Using engineered chimeric constructs, we demonstrate that the first transmembrane domain (TM1) of gamma(6) is necessary for its inhibitory effect on Cav3.1 current. Mutational analysis is then used to identify a unique GxxxA motif within TM1 that is required for the function of the subunit strongly suggesting the involvement of helix-helix interactions in its effects. Results from co-immunoprecipitation experiments confirm a physical association of gamma(6) with the Cav3.1 channel in both HEK cells and atrial myocytes. Single channel analysis reveals that binding of gamma(6) reduces channel availability for activation. Taken together, the results of this study provide both a molecular and a mechanistic framework for understanding the unique ability of the gamma(6) calcium channel subunit to modulate low voltage activated (Cav3.1) calcium current density.
Development, Evaluation, and Standardization of a Real-Time TaqMan Reverse Transcription-PCR Assay for Quantification of Hepatitis A Virus in Clinical and Shellfish Samples (2006)

A standardized real-time reverse transcription-PCR (RT-PCR) assay has been developed for an accurate estimation of the number of genome copies of hepatitis A virus (HAV) in clinical and shellfish samples. Real-time procedures were based on the amplification of a fragment of the highly conserved 5' noncoding region and detection through an internal fluorescent probe, including TaqMan and beacon chemistries, in one- and two-step RT-PCR formats. The best performance in terms of sensitivity and reproducibility was achieved by a one-step TaqMan RT-PCR, with a sensitivity enabling the detection of 0.05 infectious unit and 10 copies of a single-stranded RNA (ssRNA) synthetic transcript. Standard reagents, such as a mengovirus strain and an ssRNA transcript, were employed as controls of nucleic acid extraction and RT-PCR, respectively. The test proved to be highly specific after a broad panel of enteric viruses was tested. Sequence alignment of target regions of the primers and probe proved them to be adequate for the quantification of all HAV genotypes. In addition, a quasispecies analysis of the mutant spectrum indicated that these regions are not prone to variability, thus confirming their robustness.