gebhart/patrepeval huggingface dataset:
Reconstruction of the repetitive antifreeze glycoprotein genomic loci in the cold-water gadids Boreogadus saida and Microgadus tomcod (2018)

Antifreeze glycoproteins (AFGPs) are a novel evolutionary innovation in members of the northern cod fish family (Gadidae), crucial in preventing death from inoculative freezing by environmental ice in their frigid Arctic and sub-Arctic habitats. However, the genomic origin and molecular mechanism of evolution of this novel life-saving adaptive genetic trait remained to be definitively determined. To this end, we constructed large insert genomic DNA BAC (bacterial artificial chromosome) libraries for two AFGP-bearing gadids, the high-Arctic polar cod Boreogadus saida and the cold-temperate Atlantic tomcod Microgadus tomcod, to isolate and sequence their AFGP genomic regions for fine resolution evolutionary analyses. The BAC library construction encountered poor cloning efficiency initially, which we resolved by pretreating the agarose-embedded erythrocyte DNA with a cationic detergent, a method that may be of general use to BAC cloning for teleost species and/or where erythrocytes are the source of input DNA. The polar cod BAC library encompassed 92,160 clones with an average insert size of 94.7 kbp, and the Atlantic tomcod library contained 73,728 clones with an average insert size of 89.6 kbp. The genome sizes of B. saida and M. tomcod were estimated by cell flow cytometry to be 836 Mbp and 645 Mbp respectively, thus their BAC libraries have approximately 10- and 9.7-fold genome coverage respectively. The inclusiveness and depth of coverage were empirically confirmed by screening the libraries with three housekeeping genes. The BAC clones that mapped to the AFGP genomic loci of the two gadids were then isolated by screening the BAC libraries with gadid AFGP gene probes. Eight minimal tiling path (MTP) clones were identified for B. saida, sequenced, and assembled. The B. saida AFGP locus reconstruction produced both haplotypes, and the locus comprises three distinct AFGP gene clusters, containing a total of 16 AFGP genes and spanning a combined distance of 512 kbp. The M. tomcod AFGP locus is much smaller at approximately 80 kbp, and contains only three AFGP genes. Fluorescent in situ hybridization with an AFGP gene probe showed the AFGP locus in both species occupies a single chromosomal location. The large AFGP locus with its high gene dosage in B. saida is consistent with its chronically freezing high Arctic habitats, while the small gene family in M. tomcod correlates with its milder habitats in lower latitudes. The results from this study provided the data for fine resolution sequence analyses that would yield insight into the molecular mechanisms and history of gadid AFGP gene evolution driven by northern hemisphere glaciation.
Analysis of the Atomic Structure of the Si(111)√3×√3-Bi Surface by X-Ray Photoelectron Diffraction (1987)

It is found by X-ray photoelectron spectroscopy and LEED that the saturation coverage of Bi is one monolayer for the Si(111)√3×√3-Bi surface. Azimuthal dependence of Bi 4d photoelectron diffraction has been measured for the Si(111)√3×√3-Bi surface and analyzed kinematically. The results of the analysis have confirmed the presence of Bi-triplets with sides of 3.1 Å as proposed by X-ray diffraction. It is further found that the Bi-triplets form an overlayer on the substrate.
Web services and speech-based applications (2006)

VoiceXML applications are described by context-free grammars. Then, recognized vocabulary is limited. We show in this paper one possible approach in order to use VoiceXML applications and speech Web services, together. The idea is to use capabilities of speech-dictation systems when the input value is not recognized in an active grammar. A prototype of VoiceXML application using speech Web services is presented. A user can speak a free sentence, in English for instance, and receive a French translation, on the same modality (phone) or via another one (PC screen, for example)
Development of a field method for measuring manganese in welding fume (2007)

Workers who perform routine welding tasks are potentially exposed to fume that may contain manganese. Manganese may cause respiratory problems and is implicated in causing the occurrence of Parkinson-like symptoms. In this study, a field colorimetric method for extracting and measuring manganese in welding fume was developed. The method uses ultrasonic extraction with an acidic hydrogen peroxide solution to extract welding fume collected on polyvinyl chloride filters. Commercially available pre-packaged reagents are used to produce a colored solution, created by a reaction of manganese(ii) with 1-(2-pyridylazo)-2-naphthol. Absorbance measurements are then made using a portable spectrophotometer. The method detection limit and limit of quantification (LOQ) were 5.2 microg filter(-1) and 17 microg filter(-1), respectively, with a dynamic range up to 400 microg filter(-1). When the results are above the LOQ for the colorimetric method, the manganese masses are equivalent to those measured by the International Organization for Standardization Method 15202-2, which employs a strong acid digestion and analysis using inductively coupled plasma-optical emission spectrometry.
POI Semantic Model with a Deep Convolutional Structure (2019)

When using the electronic map, POI retrieval is the initial and important step, whose quality directly affects the user experience. Similarity between user query and POI information is the most critical feature in POI retrieval. An accurate similarity calculation is challenging since the mismatch between a query and a retrieval text may exist in the case of a mistyped query or an alias inquiry. In this paper, we propose a POI latent semantic model based on deep networks, which can effectively extract query features and POI information features for the similarity calculation. Our model describes the semantic information of complex texts at multiple layers, and achieves multi-field matches by modeling POI's name and detailed address respectively. Our model is evaluated by the POI retrieval ranking datasets, including the labeled data of relevance and real-world user click data in POI retrieval. Results show that our model significantly outperforms our competitors in POI retrieval ranking tasks. The proposed algorithm has become a critical component of an online system serving millions of people everyday.
Single-Chain Fv Antibodies Expressed in Plants (1998)

Methods of gene cloning and genetic engineering of immunoglobulins and transgenic plant techniques have given rise to new approaches in plant biotechnology (1). The high affinity and specificity of antibodies to different structures can be used to block regulation factors in plant cells by expression of specifically designed antibody constructs (2). Antibodies expressed in plants can also be used to influence and block plant pathogen development and action (3,4). Furthermore, plant cells, especially plant storage organs, can serve as factories for the production of antibodies of biotechnological interest (5).
KEAP1 inhibition is neuroprotective and suppresses the development of epilepsy (2018)

Hippocampal sclerosis is a common acquired disease that is a major cause of drug-resistant epilepsy. A mechanism that has been proposed to lead from brain insult to hippocampal sclerosis is the excessive generation of reactive oxygen species, and consequent mitochondrial failure. Here we use a novel strategy to increase endogenous antioxidant defences using RTA 408, which we show activates nuclear factor erythroid 2-related factor 2 (Nrf2, encoded by NFE2L2) through inhibition of kelch like ECH associated protein 1 (KEAP1) through its primary sensor C151. Activation of Nrf2 with RTA 408 inhibited reactive oxygen species production, mitochondrial depolarization and cell death in an in vitro model of seizure-like activity. RTA 408 given after status epilepticus in vivo increased ATP, prevented neuronal death, and dramatically reduced (by 94%) the frequency of late spontaneous seizures for at least 4 months following status epilepticus. Thus, acute KEAP1 inhibition following status epilepticus exerts a neuroprotective and disease-modifying effect, supporting the hypothesis that reactive oxygen species generation is a key event in the development of epilepsy.
Automatic classification of dual-modalilty, smartphone-based oral dysplasia and malignancy images using deep learning (2018)

With the goal to screen high-risk populations for oral cancer in low- and middle-income countries (LMICs), we have developed a low-cost, portable, easy to use smartphone-based intraoral dual-modality imaging platform. In this paper we present an image classification approach based on autofluorescence and white light images using deep learning methods. The information from the autofluorescence and white light image pair is extracted, calculated, and fused to feed the deep learning neural networks. We have investigated and compared the performance of different convolutional neural networks, transfer learning, and several regularization techniques for oral cancer classification. Our experimental results demonstrate the effectiveness of deep learning methods in classifying dual-modal images for oral cancer detection.
Biochemistry of DNA Lesions (1985)

Ionizing radiation produces a range of damage types in cellular DNA. All damage types do not have the same biological significance. Here arguments are presented supporting the view that lesions in which damage is present on both strands in a local region of the DNA (locally multiply damaged sites--LMDS) will present problems for cellular repair processes. We have previously shown that lesions produced in DNA by individual OH radicals, i.e., single OH species acting alone, are ineffective in mammalian cell killing [J.F. Ward, W.F. Blakely, and E.I. Joner, Radiat. Res. 103, 383-392 (1985)]. We have similar evidence in mutagenesis studies (Ward and Calabro-Jones, unpublished data). Thus the formation of such damage by individual OH radicals formed by ionizing radiation would be similarly ineffectual. Earlier [J.F. Ward, Radiat. Res. 86, 185-195 (1981)] we suggested that OH-radical scavenging studies were consistent with the scavenging of OH radicals in volumes of high radical density, spurs, etc., i.e., in volumes which, when they overlap the DNA, will cause the production of LMDS. The individual constituent lesions of LMDS will be formed as a result of direct ionization or as a result of an OH-radical attack. Both mechanisms can lead to base damage or strand breakage. It is clear that damage in both bases of a deoxyribonucleotide pair leads to loss of base sequence information and can be repaired correctly only by accident or in a recombinational process.(ABSTRACT TRUNCATED AT 250 WORDS)
Symptoms and Visceral Perception in Patients With Pain-Predominant Irritable Bowel Syndrome (1999)

In a tertiary referral population of IBS patients: 1) abdominal pain is reported by only one third of patients as their most bothersome viscerosensory symptoms; and 2) pain-predominance correlates with development of rectal hypersensitivity after a noxious sigmoid stimulus.
Activation of CYP3A4: Evidence for the Simultaneous Binding of Two Substrates in a Cytochrome P450 Active Site (1994)

A unique characteristic of the CYP3A subfamily of cytochrome P450 enzymes is their ability to be activated by certain compounds. It is reported that CYP3A4-catalyzed phenanthrene metabolism is activated by 7,8-benzoflavone and that 7,8-benzoflavone serves as a substrate for CYP3A4. Kinetic analyses of these two substrates show that 7,8-benzoflavone increases the Vmax of phenanthrene metabolism without changing the Km and that phenanthrene decreases the Vmax of 7,8-benzoflavone metabolism without increasing the Km. These results suggest that both substrates (or substrate and activator) are simultaneously present in the active site. Both compounds must have access to the active oxygen, since neither phenanthrene nor 7,8-benzoflavone can competitively inhibit the other substrate. These data provide the first evidence that two different molecules can be simultaneously bound to the same P450 active site. Additionally, structure-activity relationship studies were performed with derivatives of 7,8-benzoflavone structure. The effects of 13 different compounds on the regioselectivity of phenanthrene, chrysene, and benzo[a]pyrene metabolism were determined. Of the 13 compounds studied, 6 were activators, 2 were partial activators, and 5 were inhibitors. Analyses of the data suggest that (1) naphthalene substituted with a ketone in the 2-position can activate 3A4 and (2) the presence of an activator results in a narrower effective substrate binding site. Since the CYP3A enzymes are very important in drug metabolism, the possibility of activation, and autoactivation, must be considered when in vitro-in vivo correlations are made and when possible drug interactions are considered.
Tetrahydrocurcumin is more effective than curcumin in preventing azoxymethane‐induced colon carcinogenesis (2011)

Taken together, these results demonstrated for the first time the in vivo chemopreventive efficacy and molecular mechanisms of dietary THC against AOM-induced colonic tumorigenesis.
EFFECTS OF COMPLEX WIND REGIMES ON TURBINE PERFORMANCE (2009)

The frequency and magnitude of variation in the above wind flow parameters have been examined here using measurements from several sites across the Great Plains/Midwest region. The sensitivity of turbine power performance to each of these factors has been analyzed using measured power production and dynamic wind turbine models. Results suggest that while power performance variation due to some parameters, such as turbulence intensity, is generally well understood, further research is needed to clarify the wind shear profile throughout the turbine rotor and its time-varying effects on performance in this region. In addition, increasing numbers of turbine manufacturers are adding restrictions to their power curve warranties to filter out data for these meteorological conditions. Such filters, which are not included in a standard IEC 61400-12-1 test, increase the amount of time needed for testing and may eliminate data that reflect a site’s normal wind conditions. This study examines how power curve warranty restrictions affect guarantee levels and the period of data collection needed to complete power performance tests. 1.1 Great Plains/Midwest wind regime The interior of North America, particularly the Great Plains/Midwest region, supports one of the most robust wind regimes in the world. While the terrain in this region is generally flat and simple, the region’s wind regime can be considered complex. The Great Plains/Midwest region experiences a strongly stable nocturnal boundary layer, which is characterized by a large vertical wind speed gradient and low turbulence intensity. Stable conditions can be enhanced when high pressure aloft remains a dominant weather pattern. The daytime boundary layer can often be unstable, however. During unstable conditions, strong vertical mixing creates a generally homogeneous wind profile with relatively higher magnitudes of turbulence intensity and lower wind shear values. In addition, the Great Plains/Midwest region experiences a phenomenon known as the Low-Level Jet (LLJ). The LLJ is due to the meridional heating differences created by the slope of the terrain to the west. The resulting pressure gradient force pulls wind toward the west. The Coriolis force turns it to the right,
Ouabain stimulates endothelin release and expression in human endothelial cells without inhibiting the sodium pump (2004)

Ouabain, a sodium pump (Na+/ K+-ATPase) inhibitor, has been shown to act as a hormone and is possibly involved in the pathogenesis of hypertension. The mechanism by which ouabain may act was investigated using primary cultures of human umbilical artery endothelial cells (HUAECs), which are known to express and release the vasoconstrictive hormone endothelin (ET-1). Five minutes after application, low concentrations of ouabain induced Ca2+ oscillations and stimulated ET-1 release from endothelial cells into the medium. To investigate whether the observed effects were due to inhibition of the sodium pump, the effects of ouabain on the uptake of 86Rb+ by HUAECs were examined. Unexpectedly, ouabain concentrations below 10 nm stimulated 86Rb+ uptake by 15-20%, and in some experiments by 50%, results that are consistent with a stimulation of the pump. Within the concentration range 1-10 nm, ouabain induced a 2.5-fold stimulation (phosphorylation) of mitogen-activated protein kinase (MAP kinase). After incubation of HUAECs with ouabain for 12 h, the glycoside stimulated cell growth by 49 +/- 4%, as measured by cell number, with a maximum response at 5 nm. At similar concentrations, ouabain also increased ET-1 mRNA abundance by 19.5 +/- 3.1%. The results indicate that, by influencing ET-1 expression and release, ouabain may contribute to the regulation of vascular tone. The data also confirm that it is not a global inhibition of the sodium pump that is involved in the mechanism of action of this cardiac glycoside.
Use of Radar Chaff for Studying Circulations in and around Shallow Cumulus Clouds (2014)

Abstract Circulations in and around cumulus clouds are inferred by using a passive tracer (radar chaff) and an airborne cloud radar during the Barbados Aerosol Cloud Experiment (BACEX). The radar chaff elements used for this experiment are fibers that are cut to a length of about ½ of the radar wavelength to maximize radar returns by serving as dipole antennas. The fibers are packed in fiber tubes and are mounted in a dispenser beneath the wing of the aircraft. The chaff was released near the tops and edges of a growing small cumulus cloud. The aircraft then made penetrations of the cloud at lower levels to observe the chaff signals above the aircraft with the zenith-pointing cloud radar. This study shows that the environmental air above the cloud top descends along the downshear side of the cloud edge and is subsequently entrained back into the same cloud near the observation level. The in-cloud flow follows an inverted letter P pattern. The merits and limitations of the chaff method for tracking circulations in and around small cumuli are discussed.
Towards Understanding Text Factors in Oral Reading (2018)

Anastassia Loukina, Van Rynald T. Liceralde, Beata Beigman Klebanov. Proceedings of the 2018 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies, Volume 1 (Long Papers). 2018.
Modulation of the unitary exocytic event amplitude by cAMP in rat melanotrophs (1998)

1. Secretory responses were measured in single rat pituitary melanotrophs as the relative increase in membrane capacitance (Cm) 8 min after the start of dialysis with solutions containing 0.45 microM Ca2+. In the added presence of cAMP (0.2 mM) in the patch pipette solution, capacitance responses increased 2- to 3-fold in comparison with controls. 2. To study whether cAMP-dependent mechanisms affect cytosolic calcium activity ([Ca2+]i), dibutyryl cyclic AMP (dbcAMP, 10 mM) was added to intact melanotrophs and [Ca2+]i was measured using fura-2 AM. Addition of dbcAMP caused a transient reduction in [Ca2+]i to 82 +/- 21 nM from a resting value of 100 +/- 19 nM (mean +/- S.E.M., n = 32, P < 0.002), indicating that the cAMP-induced increase in secretory activity was not the result of cAMP acting to increase [Ca2+]i, which then increased secretory activity. 3. To investigate whether cAMP affects the secretory apparatus directly, the interaction of a single secretory granule with the plasmalemma was monitored by measuring discrete femtofarad steps in Cm. The signal-to-noise ratio of recordings was increased by pre-incubating the cells with a hydrophobic anion, dipicrylamine. 4. Recordings of unitary exocytic events (discrete 'on' steps in Cm) showed that the amplitude of 'on' steps - a parameter correlated to the size of exocytosing secretory granules - increased from 4.2 +/- 0.2 fF (n = 356) in controls to 7.9 +/- 0.2 fF in the presence of cAMP (n = 329, P < 0.001), while the frequency of unitary exocytic events was similar in controls and in the presence of cAMP. 5. The results suggest that a cAMP-dependent mechanism mediates the fusion of larger granules with the plasmalemma.
Molecular characterization of Mycobacterium paratuberculosis isolates from sheep, goats, and cattle by hybridization with a DNA probe to insertion element IS900 (1996)

Mycobactin J-dependent mycobacterial isolates from sheep, goat, and cattle herds with Johne's disease in Morocco, South Africa, the United States, and Germany were tested for the repetitive insertion sequence IS900 of Mycobacterium paratuberculosis by PCR. The IS900 PCR target sequence was detected in 90 of 93 fecal culture isolates tested (96.8%). Restriction fragment length polymorphisms (RFLPs) and in vitro growth characteristics were studied in 46 of the IS900-positive isolates and in two bovine vaccine strains of M. paratuberculosis. Five different RFLP types were identified in PvuII digests of genomic DNA by Southern hybridization with a DNA probe specific for IS900. All isolates of M. paratuberculosis could be classified into two major clusters by their growth rates as well as the relatedness of their PvuII-RFLP hybridization patterns. All of the sheep isolates were classified into cluster I (extremely slow growth), while all cattle and goat isolates were members of cluster II (moderately slow growth). Different PvuII-RFLP patterns were detected in different sheep flocks from Morocco and South Africa. Our results demonstrate that genetically and phenotypically different strains of M. paratuberculosis were present in ruminant populations. The strains from sheep in Morocco and South Africa tested in the study appeared to belong to a unique group of M. paratuberculosis strains that might have adapted to this host species. The presence of several genetically distinct strains in different sheep flocks suggested that analysis of IS900-specific RFLP patterns may provide a useful tool for the epidemiologic investigation of ovine paratuberculosis outbreaks.
Ten years at Tameside (1991)

Take a dingy ward, a core of staff with drive and vision and add ten years of sheer hard work. The result? Steve Wright celebrates a decade of achievement at Tameside’s Nursing Development Unit
Debugging optimized code without being misled (1994)

Correct optimization can change the behavior of an incorrect program; therefore at times it is necessary to debug optimized code. However, optimizing compilers produce code that impedes source-level debugging. Optimization can cause an inconsistency between where the user expects a breakpoint to be located and the breakpoint's actual location. This article describes a mapping between statements and breakpoint locations that ameliorates this problem. The mapping enables debugger behavior on optimized code that approximates debugger behavior on unoptimized code sufficiently closely for the user to use traditional debugging strategies. Optimization can also cause the value of a variable to be noncurrent —to differ from the value that would be predicted by a close reading of the source code. This article presents a method of determining when this has occurred, and shows how a debugger can describe the relevant effects of optimization. The determination method is more general than previously published methods; it handles global optimization and many flow graph transformations, and it is not tightly coupled to optimizations performed by a particular compiler. Necessary compiler support is also described.
Endothelium--Chicken Soup for the Endoderm (2001)

Endothelial cells in blood vessels are known to be important during the later stages of organ development in the embryo. However, their involvement at the induction stage of organ formation has not been previously documented. As Bahary and Zon explain in their Perspective, new work demonstrates that endothelial cells secrete factors early in development that induce embryonic endoderm to become liver or pancreas (Matsumoto et al., Lammert et al.).