gebhart/patrepeval huggingface dataset:
Downhole acoustic surveillance of deepwater wells (2008)

Deepwater production increasingly relies on a few precious wells that are complex and expensive. Success is critically dependent on our ability to understand and manage these wells, particularly at the sandface. These wells are filled with expensive “jewelry” like sand control and production allocation systems that aim at maximizing production and minimizing risk. While this smart equipment can mitigate many anticipated dangers, it can easily fail when something unexpected happens. For example, repairing a sand control system that failed due to plugging can cost US $30–40 million, while the costs of lost production due to long-term well impairment can be even higher. Lower-than-expected production is often referred to as “well underperformance” (Wong et al., 2003) and can be caused by various impairments: a plugged sand screen, contaminated gravel sand, clogged perforations, damaged formation around the wellbore or larger-scale compartmentalization. While 4D seismic can address large-scale compartmentalization, it has insufficient resolution to address near-well issues. Scarce downhole data from pressure and temperature gauges also cannot unambiguously characterize the impairment. This limits mitigation opportunities and prevents us from finding more effective drawdown strategies for high-rate, high ultimate-recovery deepwater wells. We strongly believe that geophysical surveillance in boreholes has a big role to play in identifying sources of well impairment and optimizing production. Here we describe one possible avenue—real-time completion monitoring (RTCM)—that utilizes acoustic signals in the fluid column to monitor changes in permeability along the completion. In essence, this is a miniaturized 4D seismic survey in a well. We illustrate the capabilities of acoustic surveillance through a series of full-scale laboratory tests with realistic completion and discuss opportunities for deployment in deepwater wells.
Antimicrobial resistance in Enterobacteriaceae from healthy broilers in Egypt: emergence of colistin-resistant and extended-spectrum β-lactamase-producing Escherichia coli (2018)

This is the first study reporting colistin resistance and emergence of multidrug resistance in <i>Enterobacteriaceae</i> isolated from healthy broilers in the Nile Delta region, Egypt. Colistin-resistant <i>E. coli</i> in poultry is of public health significance. The global rise of ESBL- and carbapenemase-producing Gram-negative bacteria demands intensified surveillance. ESBL-producing <i>E. coli</i> in poultry farms in Egypt are of major concern that emphasizes the possibility of spread of such strains to humans. The results also reinforce the need to develop strategies and to implement specific control procedures to reduce the use of antibiotics.
Recursive Multi-Tensor Contraction for XEB Verification of Quantum Circuits (2021)

The computational advantage of noisy quantum computers have been demonstrated by sampling the bitstrings of quantum random circuits. An important issue is how the performance of quantum devices could be quantified in the so-called regime. The standard approach is through the linear cross entropy (XEB), where the theoretical value of the probability is required for each bitstring. However, the computational cost of XEB grows exponentially. So far, random circuits of the 53-qubit Sycamore chip was verified up to 10 cycles of gates only; the XEB fidelities of deeper circuits were approximated with simplified circuits instead. Here we present a multi-tensor contraction algorithm for speeding up the calculations of XEB of quantum circuits, where the computational cost can be significantly reduced through a recursive manner with some form of memoization. As a demonstration, we analyzed the experimental data of the 53-qubit Sycamore chip and obtained the exact values of the corresponding XEB fidelities up to 16 cycles using only moderate computing resources (few GPUs). If the algorithm was implemented on the Summit supercomputer, we estimate that for the 20-cycles supremacy circuits, it would only cost 7.5 days, which is several orders of magnitudes lower than previously estimated in the literature.
Cooperative Jamming and Power Allocation for Wireless Relay Networks in Presence of Eavesdropper (2011)

Relying on physical layer security is an attractive alternative of utilizing cryptographic algorithms at upper layers of protocol stack for secure communications. In this paper, we consider a two-hop wireless relay network in the presence of an eavesdropper. Our scenario of interest spans over a four-node network model including a source, a destination, a trusted relay, and an untrusted eavesdropper in which the relay forwards the source message in a decode-and-forward (DF) fashion. The source and relay are allowed to use some of their available power to transmit jamming signals in order to create interference at the eavesdropper. The relay and destination are assumed to have the knowledge of the jamming signals. An important question is how to allocate the transmission power of the message signal and that of the jamming signal. First, we propose an optimal power allocation solution in which the knowledge of global channel state information (CSI) is required. To facilitate practical system design, two simple yet sub-optimal power allocation solutions are proposed which do not rely on eavesdropper's channels. For the purpose of performance comparisons, power allocation problems for two benchmark schemes without jamming are also analyzed.
Tube wave to shear wave conversion at borehole plugs (2014)

ABSTRACT In hydraulic fracturing experiments, perforation shots excite body and tube waves that sample, and thus can be used to characterize, the surrounding medium. While these waves are routinely employed in borehole operations, their resolving power is limited by the experiment geometry, the signal‐to‐noise ratio, and their frequency content. It is therefore useful to look for additional, complementary signals that could increase this resolving power. Tube‐to‐body‐wave conversions (scattering of tube to compressional or shear waves at borehole discontinuities) are one such signal. These waves are not frequently considered in hydraulic fracture settings, yet they possess geometrical and spectral attributes that greatly complement the resolution afforded by body and tube waves alone. Here, we analyze data from the Jonah gas field (Wyoming, USA) to demonstrate that tube‐to‐shear‐wave conversions can be clearly observed in the context of hydraulic fracturing experiments. These waves are identified primarily on the vertical and radial components of geophones installed in monitoring wells surrounding a treatment well. They exhibit a significantly lower frequency content (10–100 Hz) than the primary compressional waves (100–1000 Hz). Tapping into such lower frequencies could help to better constrain velocity in the formation, thus allowing better estimates of fracture density, porosity and permeability. Moreover, the signals of tube‐to‐shear‐wave conversion observed in this particular study provide independent estimates of the shear wave velocity in the formation and of the tube wave velocity in the treatment well.
Is Rhinorrhea an Under-Recognized Intrinsic Symptom of Parkinson Disease? A Prospective Pilot Study (2010)

Rhinorrhea is more prevalent in PD patients compared to controls and it does not significantly impact performance on a smell test.
Efficient production of bispecific IgG of different isotypes and species of origin in single mammalian cells (2016)

Bispecific IgG production in single host cells has been a much sought-after goal to support the clinical development of these complex molecules. Current routes to single cell production of bispecific IgG include engineering heavy chains for heterodimerization and redesign of Fab arms for selective pairing of cognate heavy and light chains. Here, we describe novel designs to facilitate selective Fab arm assembly in conjunction with previously described knobs-into-holes mutations for preferential heavy chain heterodimerization. The top Fab designs for selective pairing, namely variants v10 and v11, support near quantitative assembly of bispecific IgG in single cells for multiple different antibody pairs as judged by high-resolution mass spectrometry. Single-cell and in vitro-assembled bispecific IgG have comparable physical, in vitro biological and in vivo pharmacokinetics properties. Efficient single-cell production of bispecific IgG was demonstrated for human IgG<sub>1</sub>, IgG<sub>2</sub> and IgG<sub>4</sub> thereby allowing the heavy chain isotype to be tailored for specific therapeutic applications. Additionally, a reverse chimeric bispecific IgG<sub>2a</sub> with humanized variable domains and mouse constant domains was generated for preclinical proof-of-concept studies in mice. Efficient production of a bispecific IgG in stably transfected mammalian (CHO) cells was shown. Individual clones with stable titer and bispecific IgG composition for >120 days were readily identified. Such long-term cell line stability is needed for commercial manufacture of bispecific IgG. The single-cell bispecific IgG designs developed here may be broadly applicable to biotechnology research, including screening bispecific IgG panels, and to support clinical development.
Classification of platelet aggregates by agonist type (2019)

SUMMARY Platelets are anucleate cells in blood whose principal function is to stop bleeding by forming aggregates for hemostatic reactions. In addition to their participation in physiological hemostasis, platelet aggregates are also involved in pathological thrombosis and play an important role in inflammation, atherosclerosis, and cancer metastasis. The aggregation of platelets is elicited by various agonists, but these platelet aggregates have long been considered indistinguishable and impossible to classify. Here we present an intelligent method for classifying them by agonist type. It is based on a convolutional neural network trained by high-throughput imaging flow cytometry of blood cells to identify and differentiate subtle yet appreciable morphological features of platelet aggregates activated by different types of agonists. The method is a powerful tool for studying the underlying mechanism of platelet aggregation and is expected to open a window on an entirely new class of clinical diagnostics, pharmacometrics, and therapeutics.
Supplementary Table 5 from Patterns of Known and Novel Small RNAs in Human Cervical Cancer (2023)

Supplementary Table 5 from Patterns of Known and Novel Small RNAs in Human Cervical Cancer
SGX523 is an exquisitely selective, ATP-competitive inhibitor of the MET receptor tyrosine kinase with antitumor activity in vivo (2009)

The MET receptor tyrosine kinase has emerged as an important target for the development of novel cancer therapeutics. Activation of MET by mutation or gene amplification has been linked to kidney, gastric, and lung cancers. In other cancers, such as glioblastoma, autocrine activation of MET has been demonstrated. Several classes of ATP-competitive inhibitor have been described, which inhibit MET but also other kinases. Here, we describe SGX523, a novel, ATP-competitive kinase inhibitor remarkable for its exquisite selectivity for MET. SGX523 potently inhibited MET with an IC50 of 4 nmol/L and is >1,000-fold selective versus the >200-fold selectivity of other protein kinases tested in biochemical assays. Crystallographic study revealed that SGX523 stabilizes MET in a unique inactive conformation that is inaccessible to other protein kinases, suggesting an explanation for the selectivity. SGX523 inhibited MET-mediated signaling, cell proliferation, and cell migration at nanomolar concentrations but had no effect on signaling dependent on other protein kinases, including the closely related RON, even at micromolar concentrations. SGX523 inhibition of MET in vivo was associated with the dose-dependent inhibition of growth of tumor xenografts derived from human glioblastoma and lung and gastric cancers, confirming the dependence of these tumors on MET catalytic activity. Our results show that SGX523 is the most selective inhibitor of MET catalytic activity described to date and is thus a useful tool to investigate the role of MET kinase in cancer without the confounding effects of promiscuous protein kinase inhibition.
Acetylthiostearates – mass spectroscopy and NMR characterization (2019)

Oleic and linoleic acids are common fatty acids in commodity vegetable oils. Their modification into sulfur-containing molecules can be a route for producing biobased lubricants. We investigated modification of methyl oleate and methyl linoleate with thioacetic acid using UV-initiated thio-ene reaction to obtain methyl (acetylthio)stearates and methyl bis(acetylthio)stearates, respectively. Small amounts of acetyldithio derivatives were also detected. The products were characterized by Electron Impact Mass Spectrometry, High Resolution Mass Spectrometry, and 1- and 2-D NMR. The MS confirmed the anticipated molecular formulas. The fragmentation patterns can be explained with predominant breakage of carbon–sulfur bonds. The isomers of methyl bis(acetylthio)stearates were partially separated by chromatography, and some characteristic NMR peaks were identified and compared with the ones predicted by software. NMR showed distinct patterns of the quasi-meso- and quasi-rac- forms of the isomers. Most often thioacetates are used as protecting groups or intermediary of thiol groups.
Efficient halogen photoelimination from dibromo, dichloro and difluoro tellurophenes (2014)

We present the reactivity and photochemistry of 2,5-diphenyltellurophene. A change in oxidation state from Te(ii) to Te(iv) occurs by oxidative addition of bromine, chlorine, and fluorine from appropriate halogen sources. Photoreductive halogen elimination is demonstrated using optical absorption spectroscopy and NMR spectroscopy. The photodebromination reaction occurs with 16.9% quantum yield, the highest value for any Te compound. Photoreductive elimination of chlorine and fluorine occurs with quantum yields of 1.6% and 2.3%, respectively, albeit with less efficient halogen trapping when an organic trap is used. Improved fluorine trapping was achieved using water, allowing for much cleaner photodefluorination. This is the first example of photodefluorination from a tellurium compound.
Temperature instability comparison of micro- and mesoscale Joule-Thomson cryocoolers employing mixed refrigerants (2012)

Previously we demonstrated cryogenic cooling in a Joule-Thomson (JT) microcryocooler (MCC) with mixed refrigerants operating at pressure ratios of 16:1 that achieved stable temperatures of 140 K, with transient temperatures down to 76 K, with precooling of the refrigerant to 240 K. Pre-cooling improves the minimum enthalpy difference, (ΔhhT)min compared with that of pure fluids. Micro-scale compressors have been unavailable to meet 16:1 ratios. By reducing the ratio to 4:1, mini-compressors become viable in the near term. Utilizing mixed refrigerants optimized for 4:1 pressure ratios we compare the performance stability of this micro-JT employing a 25 mm long multichannel glass fiber heat exchanger (outer low-pressure capillary ID/OD=536 μm/617 μm, inner high-pressure channels ID/OD=75 μm/125 μm) with a scaled up (meso-scopic) version employing a 20 cm long single channel stainless steel heat exchanger (outer low pressure channel ID/OD=580 μm/760 μm, inner high pressure channel ID/OD=150 μm/266 μm). This easy to fabricate and modify meso-scale version was fabricated to investigate the temperature instabilities of mixed refrigerants for similar operating conditions but for proportionally higher flows of ~ 30 cm3/min compared with ~ 10 cm3/min. We compare measured pressures, flow rates, temperatures, and stabilities for both micro- and meso-JT cryocoolers to better understand the causes for the temperature instabilities within the micro-JT cryocooler. KEYWORDS: Cryocooler, Joule-Thomson, microcryocooler, micro-JT, mixed
Using Language to Learn Structured Appearance Models for Image Annotation (2008)

Given an unstructured collection of captioned images of cluttered scenes featuring a variety of objects, our goal is to simultaneously learn the names and appearances of the objects. Only a small fraction of local features within any given image are associated with a particular caption word, and captions may contain irrelevant words not associated with any image object. We propose a novel algorithm that uses the repetition of feature neighborhoods across training images and a measure of correspondence with caption words to learn meaningful feature configurations (representing named objects). We also introduce a graph-based appearance model that captures some of the structure of an object by encoding the spatial relationships among the local visual features. In an iterative procedure, we use language (the words) to drive a perceptual grouping process that assembles an appearance model for a named object. Results of applying our method to three data sets in a variety of conditions demonstrate that, from complex, cluttered, real-world scenes with noisy captions, we can learn both the names and appearances of objects, resulting in a set of models invariant to translation, scale, orientation, occlusion, and minor changes in viewpoint or articulation. These named models, in turn, are used to automatically annotate new, uncaptioned images, thereby facilitating keyword-based image retrieval.
Posttransplant Outcome of Lean Compared With Obese Nonalcoholic Steatohepatitis in the United States: The Obesity Paradox (2019)

Morbid obesity is considered a relative contraindication for liver transplantation (LT). We investigated if body mass index (BMI; lean versus obese) is a risk factor for post-LT graft and overall survival in nonalcoholic steatohepatitis (NASH) and non-NASH patients. Using the United Network for Organ Sharing (UNOS) database, LT recipients from January 2002 to June 2013 (age ≥18 years) with follow-up until 2017 were included. The association of BMI categories calculated at LT with graft and overall survival after LT were examined. After adjusting for confounders, all obesity cohorts (overweight and class 1, class 2, and class 3 obesity) among LT recipients for NASH had significantly reduced risk of graft and patient loss at 10 years of follow-up compared with the lean BMI cohort. In contrast, the non-NASH group of LT recipients had no increased risk for graft and patient loss for overweight, class 1, and class 2 obesity groups but had significantly increased risk for graft (P < 0.001) and patient loss (P = 0.005) in the class 3 obesity group. In this retrospective analysis of the UNOS database, adult recipients selected for first LT and NASH patients with the lowest BMI have the worse longterm graft and patient survival as opposed to non-NASH patients where the survival was worse with higher BMI.
Atomic ordering, magnetic properties, and electronic structure of Mn 2 CoGa Heusler alloy (2018)

The magnetic properties and atomic arrangement of Mn<sub>2</sub>CoGa Heusler alloy were investigated experimentally and by theoretical calculations. The magnetic moment derived from spontaneous magnetization at 5 K was 2.06 μ <sub>B</sub>/f.u. and was close to the integer number of the expected value from theoretical calculation and the Slater-Pauling rule predicted by Galanakis et al. The Curie temperature and L2<sub>1</sub>-B2 order-disorder phase transition temperature were 741 and 1047 K, respectively. Powder neutron diffraction experiment results suggested that the atomic arrangement prefers an L2<sub>1b</sub>-type structure rather than that of Hg<sub>2</sub>CuTi, being consistent with our previous results of high-angle annular dark-field-scanning transmission electron microscopic observations. The magnetic moments obtained were in good agreement with the theoretical values in the model of the L2<sub>1b</sub>-type structure. The density of states obtained by the first-principles calculation combined with the coherent potential approximation in Mn<sub>2</sub>CoGa with the L2<sub>1b</sub>-type crystal structure maintained the half-metallic character, even though disordering by Mn and Co atoms was introduced.
ChemInform Abstract: UNFUSED HETEROBICYCLES AS AMPLIFIERS OF PHLEOMYCIN. VII. SOME TRIAZOLYL‐, THIADIAZOLYL‐ AND OXADIAZOLYLPYRIDINES AND RELATED PYRIMIDINES (1984)

Abstract Die Synthese einiger Triazolyl‐, Thiadiazolyl‐ und Oxadiazolylpyridine bzw. ‐pyrimidine wird beschrieben.
Interactions Between Bromine and Natural Organic Matter (1996)

Bromine reacts quickly with natural organic matter (NOM) to form bromide and organo-bromine species. Bromine consumption by NOM occurs rapidly and the pseudo first order rate constants for bromine decomposition are on the order of 0.12 to 1.3x10-3 s-1 (DOC = 3 mg/L, pH = 7.5, and bromine dose = 5 μm); values decrease for preozonated NOM (0.11 to 0.24x10-3 s-1). Based on multiple pH experiments, both hypobromous acid (HOBr) and hypobromite (OBr-) appear to react with equally with NOM under experimental conditions in this study. Bromine reduction by NOM appears to contribute to 80% of the reaction, while bromine incorporation into NOM accounts for the remaining 20%. The formation of organo-bromine species was noted to be extremely rapid (< 5 minutes) for DOC = 3 mg/L, pH = 7.5, and bromine dose = 5 μm. Overall, reactions between bromine and NOM may significantly influence the formation of disinfection by-products (DBPs) such as bromate during ozonation of bromide containing waters.
Boosting BOLD fMRI by K-Space Density Weighted Echo Planar Imaging (2013)

Functional magnetic resonance imaging (fMRI) has become a powerful and influential method to non-invasively study neuronal brain activity. For this purpose, the blood oxygenation level-dependent (BOLD) effect is most widely used. T2* weighted echo planar imaging (EPI) is BOLD sensitive and the prevailing fMRI acquisition technique. Here, we present an alternative to its standard Cartesian recordings, i.e. k-space density weighted EPI, which is expected to increase the signal-to-noise ratio in fMRI data. Based on in vitro and in vivo pilot measurements, we show that fMRI by k-space density weighted EPI is feasible and that this new acquisition technique in fact boosted spatial and temporal SNR as well as the detection of local fMRI activations. Spatial resolution, spatial response function and echo time were identical for density weighted and conventional Cartesian EPI. The signal-to-noise ratio gain of density weighting can improve activation detection and has the potential to further increase the sensitivity of fMRI investigations.
The Determination of the J-Integral on Precracked Charpy Specimens by Instrumented Impact Testing and Slow-Bend Testing (1978)

The fracture criterion JIC is determined on SA-516-70 steel using precracked CVN specimens. The addition of an appropriate side-groove results in a better plane-strain condition at the crack tip and removes a major part of the absorbed energy due to lateral deformation. The value of JIC static is calculated from a single three-point-bend experiment. The displacement of the cracked front is followed by the measurement of the electrical resistance. We have shown that a single specimen is sufficient for determining JIC. Experiments on an instrumented Charpy machine were used for the calculation of the value of JICD. We assumed, for elasto-plastic behavior, that the maximum point of the load-displacement curve corresponds to the instability threshold of the crack. The values of JIC and JICD obtained by these two methods are compared and discussed.