gebhart/patrepeval huggingface dataset:
Comparing Pili Producing Gene (mtp-flp) in Susceptible and Resistant Dormant Mycobacterium Tuberculosis Strains with Active Clinical Isolates (2022)

Background: Pili producing genes in different life cycles of Mycobacterium tuberculosis ( M. tuberculosis ) were assessed. M. tuberculosis has two life cycles: dormant and active states. We aimed to assess the pili producing genes such as curli pili of M. tuberculosis (mtp) encoded by the mtp gene (Rv3312A) and fimbrial low-molecular-weight protein encoded by flp gene (Rv3656c) which were compared and analyzed. Methods: Two hundred M. tuberculosis isolates were investigated both at active and dormant states for production and expression of pili. The dormant M. tuberculosis was achieved by incubation in a sealed tube (modified Wayne method). The susceptibility of M. tuberculosis was evaluated on genes, rpob, inh, katg, and gyra by using multiplex polymerase chain reaction (PCR) and single-strand conformational polymorphism methods. The PCR–restriction fragment length polymorphism was used to express pili genes mtp and flp and then the PCR products was digested using restriction enzyme Fnu4HI, XmaI, and MspJI and AciI, TagII, and HaeII, respectively. The transmission electron microscopy was also used to detect pili in different isolates. The result was compared and analyzed using H37RV as a gold standard. Results: The mtp and flp PCR products were 263 and 122 bp in the studied strains irrespective of M. tuberculosis different life cycles, respectively. The PCR products were analyzed on 8% Polyacrylamide gel electrophoresis (PAGE), and in the 180/200 (20%), producing five fragments of 25,40,45,63,90 bp with the Fun4HI and two fragments of 126,138 bp with the XmaI and uncut with the MspJI for mtp gen were obtained at the dormant and active states of M. tuberculosis ( P &lt; 0.05). Similarly in flp gene producing three fragments of 22,35,65 bp with AciI and two fragments of 35.87 bp with TagII and two fragments of 38.84 bp with HaeII were obtained (P &lt; 0.05). In contrast to genotyping analysis, the electron microscopy examination showed protruding of pili from M. tuberculosis , especially in dormant mycobacterium (15/100; 15%), that was multidrug resistance and extensive drug resistance isolates ( P &gt; 0.05). Conclusion: Pili were shown by electron microscopy, although at the gene expression, the insignificant difference was observed at the dormant strains in comparison to active states. Therefore, we may conclude that other genes might be involved in pili production of M. tuberculosis that needs further investigation. Although, the resistance phenomena might influence the pili producing gene expression that showed in our results.
Enhancement of Friction against a Rough Surface by a Ridge–Channel Surface Microstructure (2014)

We report on a study of the sliding friction of elastomeric surfaces patterned with ridges and channels (and unstructured flat controls), against both smooth and roughened spherical indenters. Against the smooth spherical indenter, all of the structured surfaces have highly reduced sliding friction due to the reduction in actual area of contact. Against roughened spherical indenters, however, the sliding force for structured samples can be up to 50% greater than that of an unstructured flat control. The mechanism of enhanced friction against a rough surface is due to a combination of increased actual area of contact, interlocking between roughness and the surface structure, and attendant dynamic instabilities that dissipate energy.
Expression of Estrogen Sulfotransferase 1E1 and Steroid Sulfatase in Breast Cancer: A Immunohistochemical Study (2009)

It is known that the steroid sulfatase (STS) and the estrogen sulfotransferase (EST1E1) are commonly expressed in human breast carcinomas. STS and EST1E1 combined action could maintain the equilibrium between sulfated (inactive) and unconjugated (active) estrogens, which might have effects on development of hormone dependent breast cancer.We studied the expression of the STS and EST1E1 in 88 breast carcinomas and 57 adjacent non-malignant tissues by immunohistochemistry. The results were correlated with the tumor expression of estrogen receptor α (ER-α) and β (ER-β), progesterone receptor A (PR-A) and B (PR-B) and the proliferation marker CDC47, the tumoral type and stage and the age at surgery.STS expression was higher in carcinoma specimens than in adjacent normal tissues, although not to a significant level (p = 0.064) and it was positively associated with CDC47 expression (p < 0.05). These observations support the hypothesis that STS is overexpressed in breast cancer and associated with a worse prognosis.EST1E1 was observed for the first time in the nuclei of epithelial and tumoral cells. Tumor expression of EST1E1 was positively correlated with ER-β (p < 0.01) and PR-B (p < 0.05), two steroid receptors already associated with an improve prognosis for breast cancer.Controlling the STS overexpression in carcinomas could be a way to inhibit cancer growth. The significance of the association between EST1E1 and ER-β or PR-B should be further studied since these two receptors are transcription activators and may regulate the expression of protective enzymes like EST1E1.
Improved/Enhanced Oil Recovery from Carbonate Reservoirs by Tuning Injection Water Salinity and Ionic Content (2012)

Abstract Improved/enhanced oil recovery by tuning the ionic composition of the injection water is currently deemed as new emerging recovery method. In the recent years, extensive research on oil/brine/rock systems has shown that injecting low salinity brines has a significant impact on oil recovery from sandstone reservoirs. Although, the potential for carbonates has not been carefully investigated, some reported studies have excluded carbonates from this effect. In view of research results for the last three years, we demonstrated in previous reports (SPE 137634; SPEREE Journal, vol. 14(5), pp. 578-593, SPE 143550, SPE 141082) that substantial oil recovery beyond conventional waterflooding from carbonates can be achieved by optimizing ionic composition of field injection brine. Also, research confirmed that the driving mechanism is wettability alteration. In this paper, we present the results of new reservoir condition laboratory coreflooding studies, conducted using composite rock samples from different carbonate reservoir, to investigate the impact of ionic content on oil recovery at both secondary and tertiary recovery modes. Also, we report a broad range of laboratory studies addressing role of water ions. In addition, we briefly disclose the results of first-ever field application conducted in a carbonate reservoir to demonstrate the SmartWater Flood potential. The experimental results revealed that substantial tertiary oil recovery beyond conventional waterflooding can be achieved by altering the ionic content of field injection water. Similar potential has been confirmed also in the secondary recovery mode. For recovery mechanisms, the new results confirmed that wettability alteration is the main cause for the substantial increase in oil recovery. Compared to previous reported work, the variation in oil recovery from two different carbonate reservoirs is attributed to the variations in reservoir temperature and also the chemistry of initial formation water. For field application, two field trials confirmed that injection of SmartWater achieved ∼7 saturation units reductions in residual oil beyond conventional seawater flooding. Considering these field trials are the first-ever applications in carbonate reservoirs, they further provided another confirmation that SmartWater Flood is emerging recovery method targeting carbonate reservoirs.
High Strength Polymer-Modified Repair Cementitious Composite for Fire Protection (2007)

The purpose of this study was to evaluate the mechanical performance and fire resistance of a high strength polymer-modified cementitious composite, to test its ability to repair concrete tunnel structures that are in danger of collapse due to cracks or deterioration. In particular, because existing repair materials are not fire-resistant and commercial fire-resistant materials have low strength, this study was aimed at increasing the water tightness and strength of a repair material and also making it resistant to fire. In addition, this study evaluated changes in internal temperature depending on the cover thickness of repair materials to determine the optimal cover thickness at which a high strength polymer-modified cementitious composite could protect existing concrete tunnel structures from fire. Results indicated that the high strength polymer-modified cementitious composite had superior strength and water tightness than commercial fire-resistant materials and it also provided good fire resistance. The high strength polymer-modified cementitious composite required to be applied in an optimal layer thickness of at least 40 mm to protect existing structures from fire.
A Hypergraph-Based Blockchain Model and Application in Internet of Things-Enabled Smart Homes (2018)

With the fast development and expansion of the Internet of Things (IoT), billions of smart devices are being continuously connected, and smart homes, as a typical IoT application, are providing people with various convenient applications, but face security and privacy issues. The idea of Blockchain (BC) theory has brought about a potential solution to the IoT security problem. The emergence of blockchain technology has brought about a change of decentralized management, providing an effective solution for the protection of network security and privacy. On the other hand, the smart devices in IoT are always lightweight and have less energy and memory. This makes the application of blockchain difficult. Against this background, this paper proposes a blockchain model based on hypergraphs. The aims of this model are to reduce the storage consumption and to solve the additional security issues. In the model, we use the hyperedge as the organization of storage nodes and convert the entire networked data storage into part network storage. We discuss the design of the model and security strategy in detail, introducing some use cases in a smart home network and evaluating the storage performance of the model through simulation experiments and an evaluation of the network.
Feasibility of Optical Transition Radiation Imaging for Laser-driven Plasma Accelerator Electron-Beam Diagnostics (2017)

We report the initial considerations of using linearly polarized optical transition radiation (OTR) to characterize the electron beams of laser plasma accelerators (LPAs) such as at the Univ. of Texas at Austin. The two LPAs operate at 100 MeV and 2-GeV, and they currently have estimated normalized emittances at ~ 1-mm mrad regime with beam divergences less than 1/γ and beam sizes to be determined at the micron level. Analytical modeling results indicate the feasibility of using these OTR techniques for the LPA applications.
An Alternative Lagrange-Dual Based Algorithm for Sparse Signal Reconstruction (2011)

In this correspondence, we propose a new Lagrange-dual reformulation associated with an <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">l</i> <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1</sub> -norm minimization problem for sparse signal reconstruction. There are two main advantages of our proposed approach. First, the number of the variables in the reformulated optimization problem is much smaller than that in the original problem when the dimension of measurement vector is much less than the size of the original signals; Second, the new problem is smooth and convex, and hence it can be solved by many state of the art gradient-type algorithms efficiently. The efficiency and performance of the proposed algorithm are validated via theoretical analysis as well as some illustrative numerical examples.
Polyether ionophore antibiotics target drug-resistant clinical isolates, persister cells, and biofilms (2023)

ABSTRACT Polyether ionophores are complex natural products known to transport various cations across biological membranes. While several members of this family are used in agriculture, e.g. as anti-coccidiostats, and have potent antibacterial activity, they are not currently pursued as antibiotics for human use. Polyether ionophores are typically grouped as having similar functions, despite the fact that they differ significantly in structure, and for this reason, it remains unclear how structure and activity are related. To triage whether certain members of the family constitute particularly interesting springboards for in-depth investigations, and future synthetic optimization, we here conduct a systematic comparative study of nine different polyether ionophores for their potential as antibiotics. This includes clinical isolates from bloodstream infections and studies of the compounds’ effects on bacterial biofilms and persister cells. We uncover distinct differences within the compound class and identify the compounds lasalocid, calcimycin, and nanchangmycin as having particularly interesting activity profiles for further development.
Measurement of myocardial blood flow by cardiovascular magnetic resonance perfusion: comparison of distributed parameter and Fermi models with single and dual bolus (2015)

Comparison of single bolus versus dual bolus values suggests that distributed parameter modeling is less dependent on arterial input function saturation than Fermi modeling. Distributed parameter modeling showed excellent accuracy in detecting reduced myocardial blood flow in all stenotic vessels.
A global bus power optimization methodology for physical design of memory dominated systems by coupling bus segmentation and activity driven block placement (2004)

This paper presents a methodology which can substantially reduce the bus power consumption in memory dominated systems. It systematically combines an activity driven placement of the memories and a bus segmentation approach for the interconnect to localize the wire switching activity and minimize the associated wire capacitive load of the memory bus. A factor of 2.8 in bus power reduction is achieved for a real life design while maintaining the same performance.
Ruthenium-Catalyzed Azide Alkyne Cycloaddition Reaction: Scope, Mechanism, and Applications (2016)

The ruthenium-catalyzed azide alkyne cycloaddition (RuAAC) affords 1,5-disubstituted 1,2,3-triazoles in one step and complements the more established copper-catalyzed reaction providing the 1,4-isomer. The RuAAC reaction has quickly found its way into the organic chemistry toolbox and found applications in many different areas, such as medicinal chemistry, polymer synthesis, organocatalysis, supramolecular chemistry, and the construction of electronic devices. This Review discusses the mechanism, scope, and applications of the RuAAC reaction, covering the literature from the last 10 years.
Creation of ordered structures in a classical thermal plasma containing macroparticles: Experiment and computer simulation (1997)

We have compared experimental measurements of ordered structures in a thermal plasma containing macroparticles of CeO2 at atmospheric pressure and a temperature around 1700 K with the results of numerical Monte Carlo calculations for the Yukawa model. We describe several distinctive features of the way the experiments were done, including how the ordered macroparticle structures were detected. We discuss a theoretical model of the behavior of an equilibrium system of charged macroparticles in a plasma and the effective interaction potential between them. Good agreement between the experimental and numerical results is noted, and possible reasons for the observed discrepancies are discussed.
X-ray and extreme ultraviolet emission induced by variable pulse-width irradiation of Ar and Kr clusters and droplets (2000)

Measurements are presented of x-ray (>1.5 keV) and extreme ultraviolet (EUV, lambda=2-44 nm) emission from argon and krypton supersonic gas jets at room (T=300 K) and cryogenic (T=173 K) temperatures irradiated with constant energy (50 mJ), variable width laser pulses ranging from 100 fs to 10 ns. Two regimes of jet operation are explored: cluster formation (radius<100 nm) and droplet formation (radius>1 &mgr;m). The results for both clusters and droplets can be understood in terms of two time scales: a short time scale for optimal resonant absorption at the critical density layer in the expanding plasma, and a longer time scale for the plasma to drop below critical density.
Efficient Synthesis/Sintering Routes To Obtain Fully Dense Ultra-High-Temperature Ceramics (UHTCs) (2007)

Two different synthesis/sintering routes are proposed in this work for the preparation of fully dense 2ZrB2−SiC ultra-high-temperature ceramic (UHTC) composites. Both processes start from commercial powders of zirconium, boron carbide (B4C), and silicon, and both take advantage of the spark plasma sintering (SPS) apparatus. In the first synthesis route, reactive spark plasma sintering (RSPS), it is possible to gradually synthesize and fully consolidate the UHTC material in a single step. This result is achieved within a total time (tT) of 20 min and with a maximum temperature (TD) of 1900 °C. The second proposed synthesis method (i.e., SHS−SPS) consists in first synthesizing the composite powders, via self-propagating high-temperature synthesis (SHS), and subsequently consolidating them via SPS. In this case, the optimal operating conditions that are able to guarantee the obtainment of a fully dense material are TD = 1600 °C and tT = 30 min or TD = 1800 °C and tT = 20 min. Based on the results reported in this work, it can be stated that the two proposed methods represent particularly rapid and convenient preparation routes, in comparison to the techniques that are available in the literature for the preparation of analogous materials.
Quantification of Extracellular and Intracellular Adenosine Production (1999)

We rejected the hypothesis that the cytosolic adenosine concentration exceeds the interstitial. Rather, there is significant extracellular production, and the parenchymal cell represents a sink, not a source, for adenosine under well-oxygenated conditions.
A Study of Temperature-Created Shadow Zones in the Atmosphere (1954)

The sound field around a spherical source located above ground in an atmosphere with a vertical temperature gradient has been studied experimentally and theoretically. The ground is assumed to be described by a normal impedance, and the temperature to fall off with height over ground so as to give rise to the formation of a shadow zone. Experimental results obtained in a model weather chamber will be presented and compared with theory.
CO‐OPERATION BETWEEN ENDOTHELIN AND NITRIC OXIDE IN PROMOTING ENDOTHELIAL CELL MIGRATION AND ANGIOGENESIS (1999)

1. Among the diverse functions of endothelins (ET), their role in the remodelling of blood vessels remains poorly examined. In the present review, we summarize findings obtained in our laboratory and present four independent lines of evidence to support this novel function. We also demonstrate that the motogenic and angiogenic effects of ET are mediated via the ETB receptor and that the functional endothelial nitric oxide synthase (NOS) is requisite for this action. 2. We demonstrated that ET stimulates transmigration of endothelial cells in a modified Boyden chamber and accelerates endothelial wound healing acting via ETB receptors. 3. In genetically engineered Chinese hamster ovary cells expressing either ETB receptor or endothelial NOS or both, application of ET results in accelerated cell migration only when the receptor and the enzyme are coexpressed. Application of antisense oligonucleotides producing a specific knockdown of the endothelial NOS results in the loss of ET ability to stimulate endothelial cell migration in response to ET. 4. Finally, using a novel model of in vivo angiogenesis, we were able to demonstrate that ET enhances formation of new vessels, but this effect requires functional endothelial NOS. 5. The described phenomenon of NO production, serving as a prerequisite for endothelial cell locomotion in response to activation of ETB receptor may explain a host of pathophysiological observations on inadequate angiogenesis despite enhanced generation of ET-1. 6. Based on the contribution of endothelial cell migration to angiogenesis, these data may implicate insufficient NO production in pathological states (e.g. atherosclerosis, heart failure and hypertension) in the inappropriate response to angiogenic stimuli.
Mapping photonic entanglement into and out of a quantum memory (2008)

We demonstrate reversible mapping of photonic entanglement into and out of two atomic memories. We achieve input-output transfer efficiency of entanglement approaching 20%. Our protocol helps to enable “push-button” capabilities for entanglement in quantum networks.
Bandwidth-variable tunable optical filter unit for illumination and spectral imaging systems using thin-film optical band-pass filters (2013)

An optical filter unit is demonstrated, which uses two successively arranged tunable thin-film optical band-pass filters and allows for simultaneous adjustment of the central wavelength in the spectral range 522-555 nm and of the spectral bandwidth in the range 3-16 nm with a wavelength switching time of 8 ms∕nm. Different spectral filter combinations can cover the complete visible spectral range. The transmitted intensity was found to decrease only linearly with the spectral bandwidth for bandwidths >6 nm, allowing a high maximum transmission efficiency of >75%. The image of a fiber bundle was spectrally filtered and analyzed in terms of position-dependency of the transmitted bandwidth and central wavelength.
Bone regeneration in the presence of a synthetic hydroxyapatite/silica oxide-based and a xenogenic hydroxyapatite-based bone substitute material (2010)

There is evidence that the synthetic hydroxyapatite/silica oxide granules provide comparable results with a standard xenogenic bovine mineral in terms of bone formation and defect bridging in non-critical size defects.
The DNA repair protein ALKBH2 mediates temozolomide resistance in human glioblastoma cells (2012)

Our findings identify ALKBH2 as a novel mediator of temozolomide resistance in human GBM cells. Furthermore, we place ALKBH2 into a new cellular context by showing its regulation by the p53 pathway.