gebhart/patrepeval huggingface dataset:
Evolution of intrastratal karst within evaporitic sequences (2015)

The presented study simulates the evolution of an intrastratal halite karst, which is embedded in a sequence of carbonates, marls, anhydrites and gypsum. A numerical model is developed to simulate laminar flow in a subhorizontal void similar to a developing intrastratal karst. The numerical model is based on the laminar steady state Stokes flow equation, and the advection dispersion transport equation coupled with the dissolution equation. The flow equation is solved using the nonconforming Crouzeix-Raviart (CR) finite element approximation for the Stokes equation. For the transport equation, a combination between Discontinuous Galerkin Method and Multipoint Flux Approximation Method is proposed. The numerical effect of the dissolution is considered by using a dynamic mesh variation that increases the size of the mesh based on the amount of dissolved salt. The numerical method is applied to a 2D geological cross section representing Horst and Graben structures bound by normal faults in the Tabular Jura of north-western Switzerland. The model simulates salt dissolution within the geological section and, therefore, also predicts the amount of vertical displacement of the halite−intrastratal karst interface. The interface displacement serves as an indicator of potential subsidence that could occur at the surface above. Simulation results showed that the highest dissolution amount is observed near the hydraulically higher conductive normal fault zones. Therefore, the highest surface subsidence rates are expected above normal fault zones. The temporal and spatial distribution of the simulated dissolution along the 2D cross sections can be qualitatively compared to the shape and subsidence rate of the observed subsidence areas in the same area of the Tabular Jura.
Uncalibrated View Synthesis with Homography Interpolation (2012)

This paper presents a novel approach to uncalibrated view synthesis that overcomes the sensitivity to the epipole of existing methods. The approach follows a interpolate-then-derectify scheme, as opposed to the previous derectify-then-interpolate strategy. Both approaches generate a trajectory in an uncalibrated framework that is related to a specific Euclidean counterpart, but our method yields a warping map that is more resilient to errors in the estimate of the epipole, as it is confirmed by synthetic experiments.
Abstract #4416: 2-arylthiazolidine-4-carboxylic acid amides (ATCAA) target dual pathways: Effects on the 5\#8217;-AMP-activated protein kinase (AMPK) and Akt pathways. (2009)

The 5\#8217;-AMP-Activated Protein Kinase (AMPK) and phosphatidylinositol-3-kinase (PI3-K)/AKT signaling pathways are attractive targets for cancer research. Activation of AMPK or inhibition of AKT has shown to be cytotoxic to human cancer cells in vitro and in vivo . In a previous contribution from our laboratory, we developed 2-Arylthiazolidine-4-carboxylic acid amides (ATCAA) as effective cytotoxic agents in prostate cancer cell lines, with IC 50 values in the low/sub micromolar range. In LNCaP cells, we found that a potent compound in this class, ATCAA-10 activated AMPK, and greatly reduced phospho-PDK1, phospho-AKT and glycogen synthase kinase-3b (GSK-3b). In cell-free enzyme experiments, we found that ATCAA-10 did not directly affect PI3K, PDK1 or AKT, suggesting that its molecular target was located upstream of PDK1/PI3K/AKT. An inhibitor of AMPK, Compound C, blocked de-phosphorylation of AKT, suggesting cross-talk between the AMPK and AKT pathways. Flow cytometric analyses showed that cells accumulated in the sub-G1 phase when treated with 5 \#956;M of ATCAA-10, while the G1 phase fraction decreased, suggesting that LY-I-10 also induced apoptosis in LNCaP cells. Taken together; these results suggest that ATCAA-10 may act as a potential anticancer drug via effects on AMPK and AKT, resulting in the inhibition of prostate cancer cell growth. Citation Information: In: Proc Am Assoc Cancer Res; 2009 Apr 18-22; Denver, CO. Philadelphia (PA): AACR; 2009. Abstract nr 4416.
Vancomycin conjugated iron oxide nanoparticles for magnetic targeting and efficient capture of Gram-positive and Gram-negative bacteria (2021)

Drug conjugated iron oxide magnetite (Fe<sub>3</sub>O<sub>4</sub>) nanoparticles are of great interest in the field of biomedicine. In this study, vancomycin (Van) conjugated magnetite (Fe<sub>3</sub>O<sub>4</sub>) nanoparticles were envisioned to capture and inhibit the growth of bacteria. Hydrophobic Fe<sub>3</sub>O<sub>4</sub> nanoparticles were synthesized by using co-precipitation of ferrous (Fe<sup>2+</sup>) and ferric (Fe<sup>3+</sup>) ions following a surface modification step with oleic acid as stabilizers. Thereafter, a ligand exchange technique was employed to displace oleic acid with hydrophilic dopamine (DOPA) molecules which have a catechol group for anchoring to the iron oxide surface to prepare water dispersible nanoparticles. The surface of the resulting Fe<sub>3</sub>O<sub>4</sub>/DOPA nanoparticles contains amino (-NH<sub>2</sub>) groups that are conjugated with vancomycin <i>via</i> a coupling reaction between the -NH<sub>2</sub> group of dopamine and the -COOH group of vancomycin. The prepared vancomycin conjugated Fe<sub>3</sub>O<sub>4</sub>/DOPA nanoparticles were named Fe<sub>3</sub>O<sub>4</sub>/DOPA/Van and exhibited a magnetic response to an external magnetic field due to the presence of magnetite Fe<sub>3</sub>O<sub>4</sub> in the core. The Fe<sub>3</sub>O<sub>4</sub>/DOPA/Van nanoparticles showed bactericidal activity against both Gram positive <i>Bacillus subtilis</i> (<i>B. subtilis</i>) and <i>Streptococcus</i> and Gram-negative bacteria <i>Escherichia coli</i> (<i>E</i>. <i>coli</i>). Maximum inhibition zones of 22 mm, 19 mm and 18 mm were found against <i>B. subtilis</i>, <i>Streptococcus</i> and <i>E. coli</i> respectively. Most importantly, the vancomycin conjugated nanoparticles were effectively bound to the cell wall of the bacteria, promoting bacterial separation and growth inhibition. Therefore, the prepared Fe<sub>3</sub>O<sub>4</sub>/DOPA/Van nanoparticles can be promising for effective bacterial separation and killing in the dispersion media.
Get with the guidelines: management of chronic obstructive pulmonary disease in emergency departments in Europe and Australasia is sub‐optimal (2019)

Abstract Background Exacerbations of chronic obstructive pulmonary disease (COPD) are common in emergency departments (ED). Guidelines recommend administration of inhaled bronchodilators, systemic corticosteroids and antibiotics along with non‐invasive ventilation (NIV) for patients with respiratory acidosis. Aim To determine compliance with guideline recommendations for patients treated for COPD in ED in Europe (EUR) and South East Asia/Australasia (SEA) and to compare management and outcomes. Methods In each region, an observational prospective cohort study was performed that included patients presenting to ED with the main complaint of dyspnoea during three 72‐h periods. This planned sub‐study included those with an ED primary discharge diagnosis of COPD. Data were collected on demographics, clinical features, treatment, disposition and in‐hospital mortality. We determined overall compliance with guideline recommendations and compared treatments and outcome between regions. Results A total of 801 patients was included from 122 ED (66 EUR and 46 SEA). Inhaled bronchodilators were administered to 80.3% of patients, systemic corticosteroids to 59.5%, antibiotics to 44 and 60.6% of patients with pH &lt;7.3 received NIV. The proportion administered systemic corticosteroids was higher in SEA (EUR vs SEA for all comparisons; 52 vs 66%, P &lt; 0.001) as was administration of antibiotics (40 vs 49%, P = 0.02). Rates of NIV and mechanical ventilation were similar. Overall in‐hospital mortality was 4.2% (SEA 3.9% vs EUR 4.5%, P = 0.77). Conclusion Compliance with guideline recommended treatments, in particular administration of corticosteroids and NIV, was sub‐optimal in both regions. Improved compliance has the potential to improve patient outcome.
Design and Properties of Intermediate-Sized Narrow Band-Gap Conjugated Molecules Relevant to Solution-Processed Organic Solar Cells (2014)

Increases in the molecular length of narrow band gap conjugated chromophores reveal potentially beneficial optical and electronic properties, thermal stabilities, and high power conversion efficiencies when integrated into optoelectronic devices, such as bulk heterojunction organic solar cells. With the objective of providing useful information for understanding the transition from small-sized molecules to polymers, as well as providing a general chemical design platform for extracting relationships between molecular structure and bulk properties, we set out to vary the electron affinity of the molecular backbone. Therefore, a series of donor (D)-acceptor (A) alternating narrow band gap conjugated chromophores were synthesized based on the general molecular frameworks: D(1)-A(1)-D(2)-A(2)-D(2)-A(1)-D(1) and D(1)-A(1)-D(2)-A(2)-D(2)-A(2)-D(2)-A(1)-D(1). When the central electron-accepting moiety (A(2)) was varied or modified, two classes of molecules could be compared. First, we showed that the alteration of one single electron-accepting group, while maintaining the shape of the molecular framework, can effectively impact the optical properties and energy levels of the molecules. DFT ground state structure optimizations show similar "U" shape conformations among these molecules. Second, we examined how the site-specific introduction of fluorine atom(s) modifies the thermal properties in the solid state, while maintaining relatively similar optical and electrochemical features of interest. Structure-property relationship of such molecular systems could be rationally evaluated in the aspects of thermal-responsive molecular organizations in the solid state and dipole moments both in the ground and excited states. The impact of molecular structure on charge carrier mobilities in field effect transistors and the performance of photovoltaic devices were also studied.
A Nuclear Tyrosine Kinase Becomes a Cytoplasmic Oncogenea (1995)

It is a great pleasure to be here at this celebration. My whole scientific career has, of course, been shaped by the discovery in 1953 of the structure of DNA. At that time I was in high school, and hardly aware of it. But I do remember an incident in the late 1950s when, as a college student, I had the rare opportunity to drive Jim Watson from Cold Spring Harbor to a nearby airport on Long Island. At that time he said to me “There’s a virus that’s just been discovered that has only a small amount of DNA in it.” It had to be SV40 or polyoma virus. “That such a virus is able to cause cancer means that a very small amount of genetic information is all that’s required to cause cancer and we should be able to decipher that very quickly,” he observed. Well, as usual, his insight was remarkable, because those viruses have played a central role in developing the notions of oncogenes; his time line, however, was a little short.
Cadaver Computed Tomography: Virtual dissection as a tool for teaching anatomy (2009)

Traditionally, cadaver dissection has been the mainstay of anatomy instruction. However, as clinical medicine becomes more image driven, familiarity with cross‐sectional anatomy is crucial. Additionally, introducing clinical correlates in the preclinical years of medical education is essential in generating student enthusiasm. In order to facilitate these goals high resolution computed tomography was performed on all cadavers used in the first year anatomy class. Axial, sagittal, coronal and 3D volume rendered reconstructions were performed. Specific reconstructions of bony structures, aerodigestive tract, and vascular system were also done. All of the CT scans were read by a radiologist and findings recorded. Students were then given access to all of the studies and instructed on how to use a DICOM viewer. Images from reconstructions were included on their examinations, and part of the students' final grade came from a team building exercise using the CT images. The applicability of this tool to clinical medicine is twofold: 1) it introduces students to cross sectional imaging; and 2) it allows students to identify variant anatomy, post‐surgical changes, and pathology prior to dissection. Unlike other anatomy correlates such as the Visible Human, these reconstructions are of the students' own cadaver, and provide a permanent resource to the student long after the dissection is completed. Grant Funding Source n/a
Real time streaming of 8K 360 degree video to mobile VR headsets (2019)

In this demo, we showcase how to stream 8K 360° video to commodity mobile devices without pre-processing or viewpoint prediction using our MEC-VR system. Users can freely select 360° video from YouTube and immediately become immersed in the video of 8K resolution using a Samsung GearVR compatible smartphone. Our system can support zoom in and zoom out while saving up to 80% bandwidth.
Requirement for Geranylgeranyl Transferase I and Acyl Transferase in the TGF-β-Stimulated Pathway Leading to Elastin mRNA Stabilization (1998)

The TGF-betas are multipotent in their biological activity, modulating cell growth and differentiation as well as extracellular matrix deposition and degradation. Most of these activities involve modulation of gene transcription. However, TGF-beta1 has been shown previously to substantially increase the expression of elastin by stabilization of tropoelastin mRNA through a signaling pathway which involves a phosphatidylcholine-specific phospholipase and a protein kinase C. The present results, through the use of specific inhibitors of geranylgeranyl transferase I, farnesyl transferase, and acyl transferase, demonstrate that geranylgeranylated and acylated, but not farnesyslated protein(s) is required for this TGF-beta1 effect. In addition, the general tyrosine kinase inhibitor genistein completely blocked this TGF-beta1 effect. The results suggest that the TGF-beta1 signaling pathway requires not only receptor ser/thr kinase activity, but also tyrosine kinase and small GTPase activities.
Pertussis and cholera toxins modulate κ-opioid receptor agonists-induced hypothermia and gut inhibition (1995)

In mice pretreated intracerebroventricularly (i.c.v.) with either saline (10 microliters/mouse), pertussis (1 microgram/mouse) or cholera (2.5 micrograms/mouse) toxins, effect of kappa-opioid receptor agonists on the colonic temperature and charcoal meal transit time were assessed. The kappa-opioid receptor agonist, trans-(+)-3,4-dichloro-N-methyl-[2-(1- pyrrolidinyl)cyclohexyl]-benzeneacetamide methane sulfonate hydrate (U-50488H, 50, 100 and 200 micrograms/mouse, i.c.v.) produced dose dependent hypothermia. Pertussis toxin pretreatment (72 and/or 144 h before) antagonized (P < 0.05) the hypothermic effect of U-50488H (100 micrograms/mouse) and (+)-trans-N-methyl-N-[2-(1- pyrrolidinyl)cyclohexyl[benz[b]-thio-phene-4-acetamide (PD 117302, 30 micrograms/mouse). In contrast, cholera toxin pretreatment (48 and/or 96 h before) did not antagonize the hypothermic effect of the kappa-opioid receptor agonists. Moreover, both i.c.v. and intrathecal (i.t.) administration of kappa-opioid receptor agonists, U-50488H, }[5R-(5 alpha,7 alpha,8 beta)]-(+/-)-N-methyl-N-[7-(1- pyrrolidinyl)-1-oxaspiro[4,5]dec-8-yl]-benzeneacetamide¿ (U-69593) and PD 117302, produced dose dependent inhibition of the charcoal meal transit. Cholera toxin pretreatment (48 and 96 h before) augmented (P < 0.05) the antitransit effect of i.c.v. administered U-50488H (100 micrograms/mouse), U-69593 (100 micrograms/mouse) and PD 117302 (50 micrograms/mouse). However, pertussis toxin pretreatment did not affect the gastrointestinal inhibitory effect of the kappa-opioid receptor agonists. The present results extend our previous results on the effect of kappa-selective agonists on gastrointestinal motility and indicate, like the prototype opiate agonist morphine, kappa-opioid receptor agonists are effective in inhibiting the gastrointestinal motility when administered either by intrathecal or intracerebroventricular routes.(ABSTRACT TRUNCATED AT 250 WORDS)
A First Investigation of Truck Drivers’ Preferences and Behaviors using a Prototype Cooperative Adaptive Cruise Control System (2018)

Cooperative adaptive cruise control (CACC) is a driver-assist technology that uses vehicle-to-vehicle wireless communication to realize faster braking responses in following vehicles and shorter headways compared with adaptive cruise control. This technology not only enhances road safety, but also offers fuel savings benefits as a result of reduced aerodynamic drag. The amount of fuel savings is dictated by the following distances and the driving speeds. So, the overarching goal of this work is to explore driving preferences and behaviors when following in “CACC mode,” an area that remains largely unexplored. While in CACC mode, the brake and throttle actions are automated. A human factors study was conducted to investigate truck drivers’ experiences and performance using CACC at shorter-than-normal vehicle following time gaps. “On-the-road” experiments were conducted by recruiting drivers from commercial fleets to operate the second and third trucks in a three-truck CACC string. The driving route spanned 160 miles on freeways in Northern California and five different time gaps between 0.6 and 1.8 seconds were tested. Factors such as cut-ins by other vehicles, road grades, and traffic conditions were found to influence the drivers’ opinions about use of CACC. The findings presented in this paper provide insights into the factors that will influence driver reactions to the deployment of CACC in their truck fleets.
Role of the spoT gene product and manganese ion in the metabolism of guanosine 5‘-diphosphate 3‘-diphosphate in Escherichia coli. (1979)

Addition of divalent ion chelating agents picolinic acid, 1,10-phenanthroline, or quinoline-2-carboxylic acid to wild type, relA, or relX, but not spoT strains of Escherichia coli increases the levels of guanosine 5'-diphosphate 3'-diphosphate (ppGpp). Poorly chelating analogs of these agents and a larger and more highly charged chelating agent, ethylene glycol bis(beta-amino-ethyl ether) N,N,N',N'-tetraacetic acid are ineffective. Mn2+ reverses the increase in ppGpp. The increase in ppGpp in wild type cells can be explained by an inhibition of degradation. In spoT cells the response is more complex; ppGpp does not increase although degradation is completely inhibited. The lack of increase in spoT cells suggests a role for spoT in synthesis of ppGpp in addition to its known role in degradation. Growth of both spoT+ and spoT cells is inhibited following chelator addition. This suggests that growth inhibition is through a mechanism not directly involving ppGpp. The results of this study provide evidence in intact cells for a role for Mn2+ and the spoT gene product in ppGpp degradation, and provide further evidence for an involvement of spoT and possibly divalent ions in ppGpp synthesis.
The cumulative effect of inflammation and infection on structural lung disease in early cystic fibrosis (2019)

Introduction Pulmonary inflammation and infection are important clinical and prognostic markers of lung disease in cystic fibrosis (CF). However, whether in young children they are transient findings or have cumulative, long-term impacts on respiratory health is largely unknown. We aimed to determine whether their repeated detection has a deleterious effect on structural lung disease. Methods All patients aged &lt;6 years with annual computed tomography (CT) and bronchoalveolar lavage (BAL) were included. Structural lung disease on CT (%Disease) was determined using the PRAGMA-CF (Perth–Rotterdam Annotated Grid Morphometric Analysis for CF) method. The number of times free neutrophil elastase (NE) and infection were detected in BAL were counted, to determine cumulative BAL history. Linear mixed model analysis, accounting for repeat visits and adjusted for age, was used to determine associations. Results 265 children (683 scans) were included for analysis, with BAL history comprising 1161 visits. %Disease was significantly associated with the number of prior NE (0.31, 95% CI 0.09–0.54; p=0.007) but not infection (0.23, 95% CI −0.01–0.47; p=0.060) detections. Reference equations were determined. Conclusions Pulmonary inflammation in surveillance BAL has a cumulative effect on structural lung disease extent, more so than infection. This provides a strong rationale for therapies aimed at reducing inflammation in young children.
Discovery of Novel Oral Protein Synthesis Inhibitors of Mycobacterium tuberculosis That Target Leucyl-tRNA Synthetase (2016)

The recent development and spread of extensively drug-resistant and totally drug-resistant resistant (TDR) strains of Mycobacterium tuberculosis highlight the need for new antitubercular drugs. Protein synthesis inhibitors have played an important role in the treatment of tuberculosis (TB) starting with the inclusion of streptomycin in the first combination therapies. Although parenteral aminoglycosides are a key component of therapy for multidrug-resistant TB, the oxazolidinone linezolid is the only orally available protein synthesis inhibitor that is effective against TB. Here, we show that small-molecule inhibitors of aminoacyl-tRNA synthetases (AARSs), which are known to be excellent antibacterial protein synthesis targets, are orally bioavailable and effective against M. tuberculosis in TB mouse infection models. We applied the oxaborole tRNA-trapping (OBORT) mechanism, which was first developed to target fungal cytoplasmic leucyl-tRNA synthetase (LeuRS), to M. tuberculosis LeuRS. X-ray crystallography was used to guide the design of LeuRS inhibitors that have good biochemical potency and excellent whole-cell activity against M. tuberculosis Importantly, their good oral bioavailability translates into in vivo efficacy in both the acute and chronic mouse models of TB with potency comparable to that of the frontline drug isoniazid.
Snow-Fence Experiments in Alpine Areas (1973)

Abstract Snow fences built up-wind of natural snowdrifts at four alpine sites in the Colorado Rocky Mountains changed snow accumulation appreciably. The 3 m tall fences increased the amount of snow at three sites but decreased it at the fourth. At two of the three sites where snow was increased, there was no change in melt rate, so the additional snow prolonged the melt period 1–3 weeks. Fences most successfully augmented natural snow accumulation at sites with level or gently sloping terrain down-wind from the accumulation site. Between 15 and 30 m of fence was needed to produce an extra 1000 m 3 of water equivalent in the snowfields at the beginning of the melt season. Fences of the type described here, if properly located, are a means of increasing summer stream flow from alpine areas.
Carbon Nanotube Thin-Film Antennas (2016)

Multiwalled carbon nanotube (MWCNT) and single-walled carbon nanotube (SWCNT) dipole antennas have been successfully designed, fabricated, and tested. Antennas of varying lengths were fabricated using flexible bulk MWCNT sheet material and evaluated to confirm the validity of a full-wave antenna design equation. The ∼20× improvement in electrical conductivity provided by chemically doped SWCNT thin films over MWCNT sheets presents an opportunity for the fabrication of thin-film antennas, leading to potentially simplified system integration and optical transparency. The resonance characteristics of a fabricated chlorosulfonic acid-doped SWCNT thin-film antenna demonstrate the feasibility of the technology and indicate that when the sheet resistance of the thin film is >40 ohm/sq no power is absorbed by the antenna and that a sheet resistance of <10 ohm/sq is needed to achieve a 10 dB return loss in the unbalanced antenna. The dependence of the return loss performance on the SWCNT sheet resistance is consistent with unbalanced metal, metal oxide, and other CNT-based thin-film antennas, and it provides a framework for which other thin-film antennas can be designed.