gebhart/patrepeval huggingface dataset:
Petrosaspongiolides M−R:  New Potent and Selective Phospholipase A2 Inhibitors from the New Caledonian Marine Sponge Petrosaspongia nigra (1998)

Five new bioactive sesterterpenes (1-5) have been isolated from the New Caledonian marine sponge Petrosaspongia nigra Bergquist and named petrosaspongiolides M-R. Their chemical structures were determined from 1D and 2D NMR studies and MS data. All compounds inhibited different preparations of phospholipase A2 (PLA2) by irreversibly blocking these enzymes (particularly human synovial and bee venom, see Table 3), with IC50 values in the micromolar range. Interestingly, these compounds displayed a much lower activity (or no activity at all) toward porcine pancreas and Naja naja venom PLA2 enzymes. The most potent compound, 1 (IC50 1.6 and 0.6 microM for human synovial and bee venom PLA2 enzymes, respectively), was slightly more active than manoalide (6) (IC50 3.9 and 7.5 microM) under our experimental conditions. Compound 3 is more selective, inhibiting human synovial PLA2 to a greater extent than bee venom PLA2.
Association of Angiotensin Modulators With the Course of Idiopathic Pulmonary Fibrosis (2019)

ClinicalTrials.gov; Nos.: NCT01366209, NCT00287716, NCT00287729, NCT00075998; URL: www.clinicaltrials.gov).
Comparison of Frailty Measures as Predictors of Outcomes After Orthopedic Surgery (2016)

FP and FI predict postoperative outcomes after major elective orthopedic surgery and should be considered for preoperative risk stratification.
Automatic synthesis of a multi-bus architecture for DSP (2003)

An architectural synthesis methodology for a multibus multifunctional unit processor is presented. It is implemented as part of a design aid tool called SPAID. The input to SPAID is a DSP flow graph algorithm description with the required throughput and latency. The synthesized processor is a self-timed element externally, while it is internally synchronous and suitable for a systolic multiprocessor implementation for large DSP applications. For a benchmark elliptic filter algorithm SPAID synthesizes architectures with a linear topology that use fewer interconnects and multiplexers than other systems synthesizing random-topology architectures for the same throughput.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Pseudomonas aeruginosa modulates neutrophil granule exocytosis in an in vitro model of airway infection (2022)

A population of neutrophils recruited into cystic fibrosis (CF) airways is associated with proteolytic lung damage, exhibiting high expression of primary granule exocytosis marker CD63 and reduced phagocytic receptor CD16. Causative factors for this population are unknown, limiting intervention. Here we present a laboratory model to characterize responses of differentiated airway epithelium and neutrophils following respiratory infection. Pediatric primary airway epithelial cells were cultured at the air-liquid interface, challenged individually or in combination with rhinovirus (RV) and Pseudomonas aeruginosa, then apically washed with medical saline to sample epithelial infection milieus. Cytokine multiplex analysis revealed epithelial antiviral signals, including IP-10 and RANTES, increased with exclusive RV infection but were diminished if P. aeruginosa was also present. Proinflammatory signals interleukin-1α and β were dominant in P. aeruginosa infection milieus. Infection washes were also applied to a published model of neutrophil transmigration into the airways. Neutrophils migrating into bacterial and viral-bacterial co-infection milieus exhibited the in vivo CF phenotype of increased CD63 expression and reduced CD16 expression, while neutrophils migrating into milieus of RV-infected or uninfected cultures did not. Individually, bacterial products lipopolysaccharide and N-formylmethionyl-leucyl-phenylalanine and isolated cytokine signals only partially activated this phenotype, suggesting that additional soluble factors in the infection microenvironment trigger primary granule release. Findings identify P. aeruginosa as a trigger of acute airway inflammation and neutrophil primary granule exocytosis, underscoring potential roles of airway microbes in prompting this neutrophil subset. Further studies are required to characterize microbes implicated in primary granule release, and identify potential therapeutic targets.
Induced Systemic Resistance and Plant Responses to Fungal Biocontrol Agents (2010)

Biocontrol fungi (BCF) are agents that control plant diseases. These include the well-known Trichoderma spp. and the recently described Sebacinales spp. They have the ability to control numerous foliar, root, and fruit pathogens and even invertebrates such as nematodes. However, this is only a subset of their abilities. We now know that they also have the ability to ameliorate a wide range of abiotic stresses, and some of them can also alleviate physiological stresses such as seed aging. They can also enhance nutrient uptake in plants and can substantially increase nitrogen use efficiency in crops. These abilities may be more important to agriculture than disease control. Some strains also have abilities to improve photosynthetic efficiency and probably respiratory activities of plants. All of these capabilities are a consequence of their abilities to reprogram plant gene expression, probably through activation of a limited number of general plant pathways.
Low level light in combination with metabolic modulators for effective therapy (2015)

Vascular damage occurs frequently at the injured brain causing hypoxia and is associated with poor outcomes in the clinics. We found high levels of glycolysis, reduced ATP generation, and increased formation of reactive oxygen species (ROS) and apoptosis in neurons under hypoxia. Strikingly, these adverse events were reversed significantly by noninvasive exposure of injured brain to low-level light (LLL). LLL illumination sustained the mitochondrial membrane potential, constrained cytochrome C leakage in hypoxic cells, and protected them from apoptosis, underscoring a unique property of LLL. The effect of LLL was further bolstered by combination with metabolic substrates such as pyruvate or lactate both <i>in</i> <i>vivo</i> and <i>in</i> <i>vitro</i>. The combinational treatment retained memory and learning activities of injured mice to a normal level, whereas those treated with LLL or pyruvate alone, or sham light displayed partial or severe deficiency in these cognitive functions. In accordance with well-protected learning and memory function, the hippocampal region primarily responsible for learning and memory was completely protected by a combination of LLL and pyruvate, in marked contrast to the severe loss of hippocampal tissue due to secondary damage in control mice. These data clearly suggest that energy metabolic modulators can additively or synergistically enhance the therapeutic effect of LLL in energy-producing insufficient tissues like injured brain. Keywords:
Northstar enables automatic classification of known and novel cell types from tumor samples (2020)

Single cell transcriptomics is revolutionising our understanding of tissue and disease heterogeneity, yet cell type identification remains a partially manual task. Published algorithms for automatic cell annotation are limited to known cell types and fail to capture novel populations, especially cancer cells. We developed northstar, a computational approach to classify thousands of cells based on published data within seconds while simultaneously identifying and highlighting new cell states such as malignancies. We tested northstar on data from glioblastoma, melanoma, and seven different healthy tissues and obtained high accuracy and robustness. We collected eleven pancreatic tumors and identified three shared and five private neoplastic cell populations, offering insight into the origins of neuroendocrine and exocrine tumors. Northstar is a useful tool to assign known and novel cell type and states in the age of cell atlases.
Landslide observation and volume estimation in central Georgia based on L-band InSAR (2014)

Abstract. The republic of Georgia is a mountainous and tectonically active area that is vulnerable to landslides. Because landslides are one of the most devastating natural hazards, their detection and monitoring is of great importance. In this study we report on a previously unknown landslide in central Georgia near the town of Sachkhere. We used a set of Advanced Land Observation Satellite (ALOS) Phased Array type L-band Synthetic Aperture Radar (PALSAR) data to generate displacement maps using interferometric synthetic aperture radar (InSAR). We detected a sliding zone of dimensions 2 km north–south by 0.6 km east–west that threatens four villages. We estimated surface displacement of up to ∼30 cm/yr over the sliding body in the satellite line-of-sight (LOS) direction, with the largest displacement occurring after a local tectonic earthquake. We mapped the morphology of the landslide mass by aerial photography and field surveying. We found a complex set of interacting processes, including surface fracturing, shear and normal faults at both the headwall and the sides of the landslide, local landslide velocity changes, earthquake-induced velocity peaks, and loss in toe support due to mining activity. Important implications that are applicable elsewhere can be drawn from this study of coupled processes. We used inverse dislocation modelling to find a possible dislocation plane resembling the landslide basal décollement, and we used that plane to calculate the volume of the landslide. The results suggest a décollement at ∼120 m depth, dipping at ∼10° sub-parallel to the surface, which is indicative of a translational-type landslide.
High-dimensional time-energy entanglement-based quantum key distribution using dispersive optics (2014)

We implement a high-dimensional quantum key distribution protocol secure against collective attacks. We transform between conjugate measurement bases using group velocity dispersion. We obtain &gt; 3 secure bits per photon coincidence.
Microscopic Rearrangement of Bound Minor Groove Binders Detected by NMR (2012)

Thermodynamic and structural studies are commonly utilized to optimize small molecules for specific DNA interactions, and, thus, a significant amount of binding data is available. However, the dynamic processes that are involved in minor groove complex formation and maintenance are not fully understood. To help define the processes involved, we have conducted 1D and 2D NMR in conjunction with biosensor-SPR experiments with a variety of compounds and symmetric, as well as asymmetric, AT tract DNA sequences. Surprisingly, the NMR data clearly show exchange between equivalent binding sites for strongly binding compounds like netropsin and DB921 (Ka > 10(8) M(-1)) that does not involve dissociation off the DNA. A quantitative analysis of the data revealed that these bound exchange rates are indeed much faster than the macroscopic dissociation rates which were independently determined by biosensor-SPR. Additionally, we could show the existence of at least two 1:1 compound DNA complexes at the same site for the interaction of these compounds with an asymmetric DNA sequence. To explain this behavior we introduced a model in which the ligand is rapidly flipping between two orientations while in close association with the DNA. The ligand reorientation will contribute favorably to the binding entropy. As the potential of minor groove binders to form more than a single complex with asymmetric, as well as symmetric, duplexes is widely unknown, the consequences for binding thermodynamics and compound design are discussed.
Learning-based Physical Layer Communications for Multiagent Collaboration (2019)

Consider a collaborative task carried out by two autonomous agents that can communicate over a noisy channel. Each agent is only aware of its own state, while the accomplishment of the task depends on the value of the joint state of both agents. As an example, both agents must simultaneously reach a certain location of the environment, while only being aware of their own positions. Assuming the presence of feedback in the form of a common reward to the agents, a conventional approach would apply separately: (i) an off-the-shelf coding and decoding scheme in order to enhance the reliability of the communication of the state of one agent to the other; and (ii) a standard multiagent reinforcement learning strategy to learn how to act in the resulting environment. In this work, it is argued that the performance of the collaborative task can be improved if the agents learn how to jointly communicate and act. In particular, numerical results for a baseline grid world example demonstrate that the jointly learned policy carries out compression and unequal error protection by leveraging information about the action policy.
Crossed-beam study of the reaction H$sub 3$$sup +$(D$sub 2$,H$sub 2$)D$sub 2$H$sup +$ (1976)

A new crossed-beam apparatus has been applied to a study of the dynamics of simple proton and deuteron transfer reactions M. L. Vestal, Ph. D. Dissertation, University of Utah, Salt Lake City, Utah (1975). The results of detailed studies of the reactions H$sup +$$sub 3$(D$sub 2$,H$sub 2$)D$sub 2$H$sup +$ and D$sup +$$sub 3$(H$sub 2$D$sub 2$)H$sub 2$D$sup +$ are presented. Results are also reported on the reactions H$sup +$$sub 3$(Ar,H$sub 2$)ArH$sup +$ and H$sup +$$sub 3$(N$sub 2$,H$sub 2$)N$sub 2$H$sup +$. The experimental results are presented as contour maps of relative intensity normalized for Cartesian velocity coordinates plotted superimposed on the Newton diagram as described by Cross and Wolfgang J. Phys. Chem. 73, 743 (1969). The data are also presented in an intensity contour plot using the relative translational energy and center-of-mass scattering angle as rectangular coordinates. This method for plotting data from crossed-beam experiments, which was developed in this work, has the advantage that the relative differential cross sections as functions of relative translational energy of the products and center-of-mass scattering angle are directly displayed. Product angular distributions obtained by integrating the contour diagrams over the relative translational energy distributions are also given. (AIP)
Bur1 Kinase Is Required for Efficient Transcription Elongation by RNA Polymerase II (2003)

The Saccharomyces cerevisiae cyclin-dependent kinase (CDK) Bur1 (Sgv1) may be homologous to mammalian Cdk9, which functions in transcriptional elongation. Although Bur1 can phosphorylate the Rpb1 carboxy-terminal domain (CTD) kinase in vitro, it has no strong specificity within the consensus heptapeptide YSPTSPS for Ser2 or Ser5. BUR1 mutants are sensitive to the drugs 6-azauracil and mycophenolic acid and interact genetically with the elongation factors Ctk1 and Spt5. Chromatin immunoprecipitation experiments show that Bur1 and its cyclin partner Bur2 are recruited to transcription elongation complexes, cross-linking to actively transcribing genes. Interestingly, Bur1 shows reduced cross-linking to transcribed regions downstream of polyadenylation sites. In addition, bur1 mutant strains have a reduced cross-linking ratio of RNA polymerase II at the 3' end of genes relative to promoter regions. Phosphorylation of CTD serines 2 and 5 appears normal in mutant cells, suggesting that Bur1 is not a significant source of cotranscriptional Rpb1 phosphorylation. These results show that Bur1 functions in transcription elongation but may phosphorylate a substrate other than the CTD.
Gravity and Surface Tension Effects on the Shape Change of Soft Materials (2013)

Surface tension and gravity, whose influence on the deformation of conventional engineering materials is negligible, become important for soft materials that are typically used in the microfabrication of devices such as microfluidic channels. Although for soft materials the shape change due to these forces can be large, it is often neglected in the design processes. To capture conditions under which the influence of these forces is important, we propose a deformation map in which the shape change is captured by two dimensionless material parameters. Our idea is demonstrated by simulating the large deformation of a short circular cylinder made of a neo-Hookean material in frictionless contact with a rigid substrate. These simulations are carried out using a finite element model that accounts for surface tension and gravity. Our model integrates the two different approaches typically used to determine the shape change of solids and liquid drops in contact with a substrate.
Dendritic Bipyridine Ligands and Their Tris(Bipyridine)Ruthenium(II) Chelates—Syntheses, Absorption Spectra, and Photophysical Properties (1997)

Abstract Several synthetic strategies have been explored to prepare dendrimers having the [Ru(bpy) 3 ] 2+ complex as their core (bpy = 2,2′‐bipyridine). Dendritic ligands have been synthesized by attaching branches in the 4,4′‐positions of bpy. The largest dendritic bipyridine ligand contains 54 peripherical methylester units. Four Ru II dendritic complexes have been prepared. Their absorption and emission spectra are very similar to those of the unsubstituted parent Ru II –bipyridine complexes. The large dendritic complexes, however, exhibit a more intense emission and a longer excited‐state lifetime than [Ru(bpy) 3 ] 2+ in aerated solutions. This is due to the shielding effect of the dendrimer branches on the Ru–bipyridine core, which limits the quenching effect of molecular oxygen. For the largest dendritic complex, which contains 54 peripherical methylester units, the excited‐state lifetime in aerated acetonitrile solution is longer than 1 μs, and the rate constant for dioxygen quenching is twelve times smaller than for [Ru(bpy) 3 ] 2+ .
Optimal System Design for an Implantable CW Doppler Ultrasonic Flowmeter (1978)

A totally implantable telemetry system utilizing custom micropower monolithic integrated circuits has been developed to measure instantaneous pulsatile blood flow in the major arteries of animals. The device utilizes the Doppler effect at ultrasonic frequencies to achieve a flowmeter possessing small size and weight, low power consumption, inherent accuracy, and long-term stability. The integrated circuit electronics package occupies a volume of 3.8 cc and requires a power consumption of 10 mW from a single 135 volt mercury cell. The volume of the entire implantable flowmeter package is less than 36 cc. As a micro-miniature radio-telemetry system, the flow-meter can be totally implanted within the body, thereby eliminating the need for wires penetrating the skin, a serious problem with "back-pack" flowmeters due to danger of infection. The implantable flow-meter system provides a new and necessary tool for accurate quantitative measurements in the study of cardiovascular disease. It has been used in the study of transplanted heart rejection to monitor blood velocity in the major arteries of doB
Fracture Energy of Strain Hardening Cementitious Composites (1998)

Peer Reviewed
Chondroinductive factor-free chondrogenic differentiation of human mesenchymal stem cells in graphene oxide-incorporated hydrogels (2018)

Graphene-based nanomaterials have been applied as biomaterials to enhance stem cell adhesion, growth and differentiation by serving as nanocarriers for growth factors or other small molecules. However, the direct effect of graphene oxide (GO) itself on stem cells, in the absence of exogenous differentiation inductive factors, has not been tested. In this study, we loaded GO nanosheets and human bone marrow-derived mesenchymal stem cells (hBMSC) into a photopolymerizable poly-d,l-lactic acid/polyethylene glycol (PDLLA) hydrogel, a robust chondrosupportive scaffold recently developed in our laboratory, and assessed hBMSC differentiation along the chondrogenic lineage without supplemental chondroinductive factors. We first examined the effect of GO incorporation on the mechanical properties of constructs, and observed that the GO-containing constructs (GO/PDLLA) exhibited enhanced compressive modulus in a GO concentration dependent manner. hBMSCs cultured in GO/PDLLA maintained high cell viability (>95%), indicating minimal cytotoxicity of GO. Importantly, compared to those encapsulated in PDLLA hydrogel, hBMSCs within GO/PDLLA showed significantly higher level of gene expression of the cartilage matrix genes, aggrecan and collagen type II, and produced more cartilage matrix. In addition, the pro-chondrogenesis effect of GO increased with increasing GO concentration. Immunohistochemical results suggested that GO-enhanced hBMSC chondrogenesis was correlated with enriched sequestration of insulin, a necessary supplement known to have pro-chondrogenesis effects on hBMSC. Taken together, these findings demonstrate the utility of using GO to improve the mechanical properties and chondrogenic differentiation state of MSC-laden, engineered hydrogel constructs, without the use of exogenous growth factors, thus representing a potentially promising, biologics-free approach for cartilage tissue engineering.
ChemInform Abstract: A New Class of Room Temperature Luminescent Organometallic Complexes: Luminescence and Photophysical Properties of Permethylscandocene Chloride in Fluid Solution. (1990)

Abstract With the view to searching for organometallic complexes that emit in fluid solution at room temp., photophysics of the d° first row transition‐metal complex (I) are investigated.
MIMO Receiver Design in the Presence of Radio Frequency Interference (2008)

Multi-input multi-output (MIMO) receivers have been designed and their communication performance analyzed under the assumption of additive Gaussian noise. Wireless transceivers, however, may be affected by radio frequency interference (RFI) that is well modeled using non-Gaussian impulsive statistics. In this paper, we consider the problem of receiver design for a two transmit, two receive antenna MIMO system in the presence of RFI. First, we show that RFI is well modeled using a bivariate Middleton Class A model and validate the model with measured data. Using this RFI model, we demonstrate that conventional MIMO receivers experience significant degradation in communication performance. Then we derive the maximum likelihood (ML) receiver assuming bivariate Middleton Class A noise. Furthermore, we develop a parameter estimation method for this noise model and propose two sub-optimal ML receivers with reduced computational complexity. Simulations show significant improvement in symbol error rate performance of the proposed techniques over receivers designed assuming additive Gaussian noise.
Design of high voltage 4H-SiC superjunction schottky rectiers (2005)

This paper presents a novel Schottky rectifier structure based on the superjunction approach, which is utilizes 2- and 3D field shaping to increase the avalanche breakdown voltage. Device forward and blocking characteristics are analyzed with numerical simulations and compared with conventional 4H-SiC Schottky rectifiers. Optimal design tradeoffs between breakdown voltage and specific on-resistance are obtained for high voltage 4H-SiC superjunction Schottky rectifiers. The results show that the new structure can provide a 20 /spl times/ lower R/sub on,sp/ than conventional Schottky rectifier for 6kV device. In addition, device termination and possible fabrication steps for the superjunction devices are also presented.