gebhart/patrepeval huggingface dataset:
Reversal of Azole Resistance in Candida albicans by Sulfa Antibacterial Drugs (2017)

Invasive candidiasis presents an emerging global public health challenge due to the emergence of resistance to the frontline treatment options, such as fluconazole. Hence, the identification of other compounds capable of pairing with fluconazole and averting azole resistance would potentially prolong the clinical utility of this important group. In an effort to repurpose drugs in the field of antifungal drug discovery, we explored sulfa antibacterial drugs for the purpose of reversing azole resistance in <i>Candida</i> In this study, we assembled and investigated a library of 21 sulfa antibacterial drugs for their ability to restore fluconazole sensitivity in <i>Candida albicans</i> Surprisingly, the majority of assayed sulfa drugs (15 of 21) were found to exhibit synergistic relationships with fluconazole by checkerboard assay with fractional inhibitory concentration index (ΣFIC) values ranging from <0.0312 to 0.25. Remarkably, five sulfa drugs were able to reverse azole resistance in a clinically achievable range. The structure-activity relationships (SARs) of the amino benzene sulfonamide scaffold as antifungal agents were studied. We also identified the possible mechanism of the synergistic interaction of sulfa antibacterial drugs with azole antifungal drugs. Furthermore, the ability of sulfa antibacterial drugs to inhibit <i>Candida</i> biofilm by 40% <i>in vitro</i> was confirmed. In addition, the effects of sulfa-fluconazole combinations on <i>Candida</i> growth kinetics and efflux machinery were explored. Finally, using a <i>Caenorhabditis elegans</i> infection model, we demonstrated that the sulfa-fluconazole combination does possess potent antifungal activity <i>in vivo</i>, reducing <i>Candida</i> in infected worms by ∼50% compared to the control.
Increasing the Coulombic Efficiency of Glucose Biofuel Cell Anodes by Combination of Redox Enzymes (2009)

Abstract not Available.
Enhancing user fairness in non-orthogonal access with successive interference cancellation for cellular downlink (2012)

Aiming at a better tradeoff between the system frequency efficiency measured by the mean user throughput and the user fairness measured by the cell-edge user throughput, we propose applying fractional frequency reuse (FFR) and weighted proportional fair (PF)-based multiuser scheduling to non-orthogonal access with a successive interference canceller (SIC) in the cellular downlink. We also propose a frequency block access policy for cell-interior and cell-edge user groups in FFR, which are appropriate for non-orthogonal access with the SIC. The optimum power is allocated to the non-orthogonally multiplexed users in conjunction with the weighted multiuser PF scheduler. Extensive simulation results show that the proposed non-orthogonal access scheme with the SIC significantly enhances the system frequency efficiency and user fairness at the same time compared to orthogonal access, which is widely used in 3.9 and 4G mobile communication systems.
Systematic Error in Gas Chromatography-Mass Spectrometry–Based Quantification of Hydrolyzed Urinary Steroids (2010)

Gas chromatography-mass spectrometry-based metabolite profiling can lead to an understanding of various disease mechanisms as well as to identifying new diagnostic biomarkers by comparing the metabolites related in quantification. However, the unexpected transformation of urinary steroids during enzymatic hydrolysis with Helix pomatia could result in an underestimation or overestimation of their concentrations. A comparison of beta-glucuronidase extracted from Escherichia coli revealed 18 conversions of 84 steroids tested as an unexpected transformation under hydrolysis with beta-glucuronidase/arylsulfatase extracted from Helix pomatia. In addition to the conversion of 3beta-hydroxy-5-ene steroids into 3-oxo-4-ene steroids, which has been reported, the transformation of 3beta-hydroxy-5alpha-reduced and 3beta-hydroxy-5beta-reduced steroids to 3-oxo-5alpha-reduced and 3-oxo-5beta-reduced steroids, respectively, was newly observed. The formation of by-products was in proportion to the concentration of substrates becoming saturated against the enzyme. The substances belonging to these three steroid groups were undetectable at low concentrations, whereas the corresponding by-products were overestimated. These results indicate that the systematic error in the quantification of urinary steroids hydrolyzed with Helix pomatia can lead to a misreading of the clinical implications. All these hydrolysis procedures are suitable for study purposes, and the information can help prevent false evaluations of urinary steroids in clinical studies.
Caching Strategies in Transcoding-Enabled Proxy Systems for Streaming Media Distribution Networks (2004)

With the wide availability of high-speed network access, we are experiencing high quality streaming media delivery over the Internet. The emergence of ubiquitous computing enables mobile users to access the Internet with their laptops, PDAs, or even cell phones. When nomadic users connect to the network via wireless links or phone lines, high quality video transfer can be problematic due to long delay or size mismatch between the application display and the screen. Our proposed solution to this problem is to enable network proxies with the transcoding capability, and hence provide different, appropriate video quality to different network environment. The proxies in our transcoding-enabled caching (TeC) system perform transcoding as well as caching for efficient rich media delivery to heterogeneous network users. This design choice allows us to perform content adaptation at the network edges. We propose three different TeC caching strategies. We describe each algorithm and discuss its merits and shortcomings. We also study how the user access pattern affects the performance of TeC caching algorithms and compare them with other approaches. We evaluate TeC performance by conducting two types of simulation. Our first experiment uses synthesized traces while the other uses real traces derived from an enterprise media server logs. The results indicate that compared with the traditional network caches, with marginal transcoding load, TeC improves the cache effectiveness, decreases the user-perceived latency, and reduces the traffic between the proxy and the content origin server.
The Decision To Publish Gutierrez-Alvarez et al., “Middle East Respiratory Syndrome Coronavirus Gene 5 Modulates Pathogenesis in Mice” (2020)

The paper “Middle East respiratory syndrome coronavirus gene 5 modulates pathogenesis in mice” by Gutierrez-Alvarez et al., in this issue of the Journal of Virology (1), demonstrates that the Middle East respiratory syndrome coronavirus (MERS-CoV) accessory protein encoded by gene 5, also known as ORF5, plays a major role in MERS-CoV pathogenesis. While constructing and characterizing a cDNA clone of a mouse-adapted strain of MERS-CoV, the investigators noted that their mouse-adapted virus (MERS-MA) contained an early stop codon and deletions within viral gene 5. Gene 5 is a viral accessory gene that is dispensable for viral replication, and while prior studies indicated that gene 5 modulates host inflammatory responses (2), the function of gene 5 in MERS-CoV pathogenesis is incompletely understood. Therefore, Gutierrez-Alvarez et al. constructed a cDNA clone of MERS-MA carrying a complete deletion of the gene 5 (MERS-MA-Δ5) and characterized this virus for the capacity to cause disease in mice. Somewhat surprisingly, they discovered that the MERS-MA-Δ5 virus displayed enhanced virulence in mice, including increased respiratory pathology at late times postinoculation, as well as mortality higher than that seen with the parental MERS-MA virus. Further analysis indicated that the MERS-MA-Δ5 virus-infected mice exhibited delayed type I interferon (IFN) and inflammatory responses in the lung, suggesting that gene 5 modulates the host type I IFN response and suppresses MERS-CoV-induced pathology in the lungs.
Selected Contribution: Effects of spaceflight on immunity in the C57BL/6 mouse. I. Immune population distributions (2003)

There are several aspects of the spaceflight environment that may lead to changes in immunity: mission-related psychological stress, radiation, and changes in gravity. On December 5, 2001, the space shuttle Endeavor launched for a 12-day mission to examine these effects on C57BL/6 mice for the first time. On their return, assays were performed on the spleen, blood, and bone marrow. In response to flight, there were no significant differences in the general circulating leukocyte proportions. In contrast, there was an increase in splenic lymphocyte percentages, with a corresponding decrease in granulocytes. There was an overall shift in splenic lymphocytes away from T cells toward B cells, and a decrease in the CD4-to-CD8 ratios due to a decrease in T helpers. In contrast, there were proportional increases in bone marrow T cells, with decreases in B cells. Although the blast percentage and count were decreased in flight mice, the CD34(+) population was increased. The data were more consistent with a shift in bone marrow populations rather than a response to changes in the periphery. Many of the results are similar to those using other models. Clearly, spaceflight can influence immune parameters ranging from hematopoiesis to mature leukocyte mechanisms.
Supplementary Movie 12 from Ovarian Cancer Spheroids Use Myosin-Generated Force to Clear the Mesothelium (2023)

&lt;p&gt;File Type: .mov; File Size: 6 MB.&lt;/p&gt;
Image Stereo Matching Based on Multi-Scale Plane Set (2013)

The disparity map of dynamic programming method is poor. To overcome it, a stereo matching method based on multi-scale plane set is proposed in this paper. This method converts the structural model into the plane set. Define the key plane. Then the key planes are in a high-scale. The other planes are in the low scale. Stereo matching the multi-scale plane set using dynamic programming method. The experimental results show that: this method can solve the dynamic programming algorithm`s problem that disparity map has low matching accuracy and a lot of stripes error.
Amplification in "few-mode" Er3+-doped fiber amplifiers (1993)

High-gain (G > 20 dB) multimode erbium-doped amplifiers pumped at 980-nm using a Ti:Sapphire laser and at 1485-nm using a laser+amplifier photonic integrated circuit have been demonstrated. Low amplifier noise power is achieved by coupling pump light into a limited number of fiber modes.
3D PHOVIS: 3D photoacoustic visualization studio (2020)

Photoacoustic (PA) imaging (or optoacoustic imaging) is a novel biomedical imaging method in biological and medical research. This modality performs morphological, functional, and molecular imaging with and without labels in both microscopic and deep tissue imaging domains. A variety of innovations have enhanced 3D PA imaging performance and thus has opened new opportunities in preclinical and clinical imaging. However, the 3D visualization tools for PA images remains a challenge. There are several commercially available software packages to visualize the generated 3D PA images. They are generally expensive, and their features are not optimized for 3D visualization of PA images. Here, we demonstrate a specialized 3D visualization software package, namely 3D Photoacoustic Visualization Studio (3D PHOVIS), specifically targeting photoacoustic data, image, and visualization processes. To support the research environment for visualization and fast processing, we incorporated 3D PHOVIS onto the MATLAB with graphical user interface and developed multi-core graphics processing unit modules for fast processing. The 3D PHOVIS includes following modules: (1) a mosaic volume generator, (2) a scan converter for optical scanning photoacoustic microscopy, (3) a skin profile estimator and depth encoder, (4) a multiplanar viewer with a navigation map, and (5) a volume renderer with a movie maker. This paper discusses the algorithms present in the software package and demonstrates their functions. In addition, the applicability of this software to ultrasound imaging and optical coherence tomography is also investigated. User manuals and application files for 3D PHOVIS are available for free on the website (www.boa-lab.com). Core functions of 3D PHOVIS are developed as a result of a summer class at POSTECH, "High-Performance Algorithm in CPU/GPU/DSP, and Computer Architecture." We believe our 3D PHOVIS provides a unique tool to PA imaging researchers, expedites its growth, and attracts broad interests in a wide range of studies.
Micromechanical Models of Mechanical Response of HPFRCC (1996)

Peer Reviewed
THE CONVERSION OF SYNTHESIS GAS TO HIGHER OXYGENATED FUEL ON Rh-BASED CATALYSTS: EFFECT OF CHEMICAL ADDITIVES (1991)

ABSTRACT In light of environmental concerns and the global economy, higher oxygenated fuel, such as ethanol, is a viable and attractive alternative to conventional gasoline. Presently, the major process to produce ethanol, the fermentation of corn, is economically inefficient. A more direct route, the reaction of synthesis gas (CO/H2) to produce higher oxygenates (aldehydes and alcohols), appears to be a better method. Rhodium catalysts have been known to exhibit higher oxygenate activity and selectivity from synthesis gas. The mechanism involves CO dissociation followed by hydrogenation to form an adsorbed CHX species. The CHX intermediate can undergo either hydrogenation to form methane, chain propagation to form higher hydrocarbons, or CO insertion to form C2 oxygenates. Experiments were performed to study the effects on the synthesis of higher alcohols from syngas of S, P, Cu, and Ag as additives to Rhodium supported on a silica support (Rh/Si02). The additive S was found to suppress the CO dissociation step, therefore lowering the overall product rate. The addition of P or Cu to the Rh catalyst enhance the CHX intermediate hydrogenation, resulting in the increase of methane formation. The addition of Ag to Rh/SiO2 promotes the CO insertion activity, therefore increasing the oxvtfenate selectivity.
Optical properties of neodymium ions in nanoscale regions of gallium nitride (2020)

Wide bandgap semiconductors are increasingly important for bioimaging applications, as they can possess good biocompatibility and host a large range of fluorescent defects spanning the visible to infrared. Gallium nitride is one promising host for photostable fluorophores. In particular, neodymium (Nd)-doped gallium nitride (GaN) shows bright near-infrared fluorescence and narrow room temperature linewidth and is therefore a candidate material for fluorescent probes for bioimaging. To explore the conditions necessary to generate biomarkers based on Nd:GaN, this paper reports the room temperature photoluminescence (PL) properties of small ensembles of Nd ions implanted into the nanoscale regions of GaN epilayers. The minimum volume of Nd-implanted GaN that can be optically detected in this study is about 8×10 4 nm 3 and the minimum detected ensemble of Nd ions is about 4×10 3 , although not all of implanted Nd ions activate as luminescence centers. We show from the PL excitation spectra that the strongest resonant excitation appears at 619 nm, attributed to the 4 I 9/2 → 4 G 5/2 ( 4 G 7/2 ) transition in the 4 f -shell. We measure the luminescence lifetime to be several tens of microseconds. We also identify the presence of a different excitation mechanism from the resonant excitation when excited below 510 nm (above 2.43 eV).
Liquid Chromatography-Mass Spectrometry (LC-MS) (2016)

This document contains recommendations for terminology in mass spectrometry. Development of standard terms dates back to 1974 when the IUPAC Commission on Analytical Nomenclature issued recommendations on mass spectrometry terms and definitions. In 1978, the IUPAC Commission on Molecular Structure and Spectroscopy updated and extended the recommendations and made further recommendations regarding symbols, acronyms, and abbreviations. The IUPAC Physical Chemistry Division Commission on Molecular Structure and Spectroscopy’s Subcommittee on Mass Spectroscopy revised the recommended terms in 1991 and appended terms relating to vacuum technology. Some additional terms related to tandem mass spectrometry were added in 1993 and accelerator mass spectrometry in 1994. Owing to the rapid expansion of the field in the intervening years, particularly in mass spectrometry of biomolecules, a further revision of the recommendations has become necessary. This document contains a comprehensive revision of mass spectrometry terminology that represents the current consensus of the mass spectrometry community.
Synthesis of heteroepitaxial BP and related Al-B-Sb-As-P films via CVD of Al(BH 4 ) 3 and MH 3 (M=P, As, Sb) at temperatures below 600 °C (2020)

Abstract Low temperature chemical vapor deposition using the Al(BH 4 ) 3 and PH 3 precursors at ∼600 °C produces pure and crystalline BP films directly on Si and on ZrB 2 buffer layers with no sign of Al incorporation. The BP films on ZrB 2 are epitaxial despite the structural difference between the hexagonal buffer and the cubic epilayer. Density functional theory calculations of the interface energies revealed strong bonding interactions at the heterojunction due to compliant lattice matching behavior, corroborating the favorable assembly of BP on ZrB 2 . A systematic study of the growth method is carried out by substituting As and Sb for P in the group-V carrier gas. Reactions of Al(BH 4 ) 3 with AsH 3 at 320 °C yielded the expected BAs films with small amounts of Al. In this case the samples are amorphous and efforts to crystallize them by increasing the growth temperature yielded boron-rich analogues. Analogous reactions of Al(BH 4 ) 3 with SbD 3 on Si at 300 °C produce AlSb epitaxial crystals doped with B instead of the BSb phase. This indicates that the process favors formation of Al-Sb bonds over the weaker B-Sb bonds. The results of this study indicate that the Al(BH 4 ) 3 approach represents a viable low-temperature route that may be advantageous in producing useful BP coatings with applications in thermal and optical technologies. The compound also represents an intriguing low-temperature route to BP, BAs, and AlSb type materials when reacted with corresponding P, As, and Sb hydrides, yielding in each case the thermodynamically driven products.
Rubber–Filler Interactions and Network Structure in Relation to Stress–Strain Behavior of Vulcanized, Carbon Black Filled EPDM (2011)

Immobilization of EPDM chains on the surface of carbon black and network structure in the rubber matrix of filled EPDM rubbers were studied by low-field proton NMR experiments. Advanced NMR experiments unambiguously show strong immobilization of EPDM chain fragments on the surface of carbon black. The thickness of the immobilized EPDM–carbon black interfacial layer is estimated to be ≥0.6 nm. The average number of monomer units per adsorption site is approximately nine, which suggests preferential chain adsorption at the crystal boundaries of carbon-black particles. The adsorbed chain fragments form physical (adsorption) junctions restricting chain mobility in the rubbery matrix outside of the interface. The cross-link density in filled EPDM is determined as a function of the filler type and its amount. The contribution of adsorption junctions to the total cross-link density is moderate as compared to the density of chemical cross-links and entanglement density. The mechanically effective network density in carbon-black-filled vulcanizates is determined by analysis of the stress–strain curves on the basis of the dynamic flocculation model. Comparison of the network density as measured by NMR and mechanical experiments shows significant differences which helps in better understanding of the reinforcement mechanism of filled rubbers. The study demonstrates that a relatively small amount of strongly adsorbed chains impacts the stress–strain properties of filled elastomers significantly.
Multi-Investigator Letter on Reproducibility of Neonatal Heart Regeneration following Apical Resection (2014)

(Stem Cell Reports 3, 1, July 8, 2014) Yu Nie’s name was spelled incorrectly in the original letter. It appears correctly in the author list printed above. Multi-Investigator Letter on Reproducibility of Neonatal Heart Regeneration following Apical ResectionSadek et al.Stem Cell ReportsJuly 08, 2014In BriefWe appreciate the interest that Andersen et al. (2014) have shown in our work on neonatal cardiac regeneration. Their recent paper relates directly to resection methodology first presented by Porrello et al. (2011) and describes a failure to reproduce the observations made in that study regarding regeneration after resection. We are puzzled by the results and conclusion because in the hands of the seven different groups who authored this letter, this methodology has proved robust and reproducible and has been used in several ongoing studies across our different laboratories that are in various stages of completion (Heallen et al., [2013], as well as studies by the Lee, Takeuchi, and Nei groups that are currently under review). Full-Text PDF Open Access
Current nonclinical approaches for immune assessments of immuno-oncology biotherapeutics (2022)

Harnessing the immune system to kill tumors has been revolutionary and, as a result, has had an enormous benefit for patients in extending life and resulting in effective cures in some. However, activation of the immune system can come at the cost of undesirable adverse events such as cytokine release syndrome, immune-related adverse events, on-target/off-tumor toxicity, neurotoxicity and tumor lysis syndrome, which are safety risks that can be challenging to assess non-clinically. This article provides a review of the biology and mechanisms that can result in immune-mediated adverse effects and describes industry approaches using in vitro and in vivo models to aid in the nonclinical safety risk assessments for immune-oncology modalities. Challenges and limitations of knowledge and models are also discussed.
Un même paradigme pour la réponse immunitaire au virus de l'hépatite C et au VIH ? (2000)

Un même paradigme pour la réponse immunitaire au virus de l'hépatite C et au VIH ?
Intravitreal Chemotactic and Mitogenic Activity (1986)

We produced breakdown of the blood-retinal barrier (BRB) in pigmented rabbits by several different mechanisms: retinal cryopexy, retinal laser, intravenous sodium iodate (30 mg/kg), or intravitreal injection of epinephrine (0.1 mL, 10(-3) M). The degree of BRB breakdown was monitored by computerized vitreous fluorophotometry. At 72 hours after treatment, rabbits were killed, and eyes were quickly removed, washed, and placed in liquid nitrogen. The vitreous was then carefully isolated free of contamination from other ocular tissues, homogenized, and aliquotted. For each sample we measured protein content, retinal pigment epithelial (RPE) cell chemotactic activity, and RPE mitogenic activity. Each of the above modalities produced significant breakdown of the BRB as measured by vitreous fluorophotometry and intravitreal protein concentration, while a pars plana intravitreal injection of saline (0.1 mL) did not. Vitreous from eyes treated with each of the above modalities caused significant stimulation of RPE migration (cryopexy, 684%; laser, 211%; sodium iodate, 480%; intravitreal epinephrine, 546%), while control vitreous and saline-injected vitreous caused only 89% and 77% stimulations, respectively. Similarly, vitreous from eyes treated with the above modalities caused significant stimulation of RPE proliferation (116% to 159%), while control vitreous caused only a 56% increase above baseline. Proliferative vitreoretinopathy, a disease process in which cellular migration and proliferation play important roles, occurs most commonly after surgical intervention. Breakdown of the BRB at the time of surgery may be a critical event due to intravitreal accumulation of serum-derived chemoattractants and mitogens.