gebhart/patrepeval huggingface dataset:
The Arabidopsis Mitogen-Activated Protein Kinase Kinase MKK3 Is Upstream of Group C Mitogen-Activated Protein Kinases and Participates in Pathogen Signaling (2007)

Although the Arabidopsis thaliana genome contains genes encoding 20 mitogen-activated protein kinases (MAPKs) and 10 MAPK kinases (MAPKKs), most of them are still functionally uncharacterized. In this work, we analyzed the function of the group B MAPK kinase, MKK3. Transgenic ProMKK3:GUS lines showed basal expression in vascular tissues that was strongly induced by Pseudomonas syringae pv tomato strain DC3000 (Pst DC3000) infection but not by abiotic stresses. The growth of virulent Pst DC3000 was increased in mkk3 knockout plants and decreased in MKK3-overexpressing plants. Moreover, MKK3 overexpression lines showed increased expression of several PR genes. By yeast two-hybrid analysis, coimmunoprecipitation, and protein kinase assays, MKK3 was revealed to be an upstream activator of the group C MAPKs MPK1, MPK2, MPK7, and MPK14. Flagellin-derived flg22 peptide strongly activated MPK6 but resulted in poor activation of MPK7. By contrast, MPK6 and MPK7 were both activated by H(2)O(2), but only MPK7 activation was enhanced by MKK3. In agreement with the notion that MKK3 regulates the expression of PR genes, ProPR1:GUS expression was strongly enhanced by coexpression of MKK3-MPK7. Our results reveal that the MKK3 pathway plays a role in pathogen defense and further underscore the importance and complexity of MAPK signaling in plant stress responses.
Clinical translation of an ultrasmall inorganic optical-PET imaging nanoparticle probe (2014)

A first-in-human clinical trial of ultrasmall inorganic hybrid nanoparticles, "C dots" (Cornell dots), in patients with metastatic melanoma is described for the imaging of cancer. These renally excreted silica particles were labeled with (124)I for positron emission tomography (PET) imaging and modified with cRGDY peptides for molecular targeting. (124)I-cRGDY-PEG-C dot particles are inherently fluorescent, containing the dye, Cy5, so they may be used as hybrid PET-optical imaging agents for lesion detection, cancer staging, and treatment management in humans. However, the clinical translation of nanoparticle probes, including quantum dots, has not kept pace with the accelerated growth in minimally invasive surgical tools that rely on optical imaging agents. The safety, pharmacokinetics, clearance properties, and radiation dosimetry of (124)I-cRGDY-PEG-C dots were assessed by serial PET and computerized tomography after intravenous administration in patients. Metabolic profiles and laboratory tests of blood and urine specimens, obtained before and after particle injection, were monitored over a 2-week interval. Findings are consistent with a well-tolerated inorganic particle tracer exhibiting in vivo stability and distinct, reproducible pharmacokinetic signatures defined by renal excretion. No toxic or adverse events attributable to the particles were observed. Coupled with preferential uptake and localization of the probe at sites of disease, these first-in-human results suggest safe use of these particles in human cancer diagnostics.
Inhaled, dual release liposomal ciprofloxacin in non-cystic fibrosis bronchiectasis (ORBIT-2): a randomised, double-blind, placebo-controlled trial (2013)

Once-daily inhaled DRCFI demonstrated potent antipseudomonal microbiological efficacy in adults with non-CF bronchiectasis and ciprofloxacin-sensitive P aeruginosa. In this modest-sized phase II study, DRCFI was also well tolerated and delayed time to first pulmonary exacerbation in the per protocol population.
Recovery Assessment of Open-heart Cardiac Surgery Patients Using Heart Rate Variability Parameters (2022)

Surgical operation causes short-term stress changing the balance of the autonomic nervous system (ANS). The ANS activity can be assessed through heart rate variability (HRV). This work aims to evaluate the recovery process of open-heart cardiac surgery patients under two postsurgery physiotherapy interventions using HRV parameters. Ten-minute ECG recordings were performed on 17 open-heart cardiac surgery patients pre-operatively (PREOP) and during three consecutive post-operative days (POD1, POD2 and POD3).The recovery process was promoted using two different physiotherapy techniques: positive expiratory pressure (PEP, N = 9) and inspiratory training (IMT, N = 8).Common HRV parameters (SDNN, LF power and SD1) were calculated for each patient and statistical analyses were performed.The results show significant differences between HRV parameters pre-and post-operatively, and there was a reduction of all three investigated HRV parameters in the POD1 for both groups.HRV parameters average values increased between POD1 to POD3 for both intervention groups indicating that patients were eventually starting to recover from the surgery.Statistically significant difference between PEP and IMT interventions was not discovered (e.g., p = 0.54 for SDNN, PREOP vs. POD3).Based on the results, all studied HRV parameters are potential indicators of the short-term recovery after cardiac surgery.
Wide Range Vacuum Pumps for the SAM Instrument on the MSL Curiosity Rover (2014)

Creare Incorporated and NASA Goddard Space Flight Center developed and space qualified two wide range pumps (WRPs) that were included in the Sample Analysis at Mars (SAM) instrument. This instrument was subsequently integrated into the Mars Science Laboratory (MSL) Curiosity Rover, launched aboard an Atlas V rocket in 2011, and landed on August 6, 2012, in the Gale Crater on Mars. The pumps have now operated for more than 18 months in the Gale Crater and have been evacuating the key components of the SAM instrument: a quadrupole mass spectrometer, a tunable laser spectrometer, and six gas chromatograph columns. In this paper, we describe the main design challenges and the ways in which they were solved. This includes the custom design of a miniaturized, high-speed motor to drive the turbo drag pump rotor, analysis of rotor dynamics for super critical operation, and bearing/lubricant design/selection.
In vivo neurometabolic profiling in orthostatic tremor (2016)

The pathogenesis of orthostatic tremor (OT) remains unclear, although some evidence points to dysfunction in the brainstem or cerebellum. We used single voxel proton magnetic resonance spectroscopy (1H-MRS) (3 T) to investigate whether neurochemical changes underlie abnormal cerebellar or cortical function in OT. Fourteen OT patients and 14 healthy controls underwent 1H-MRS studies with voxels placed in midparietal gray matter and cerebellum (vermis and central white matter). Spectral analysis was analyzed using the software package LCModel (version 6.3). The absolute metabolite concentrations and ratios of total N-acetylaspartate + N-acetylaspartyl glutamate (NAA), choline-containing compounds, myoinositol, and glutamate + glutamine to creatine were calculated. In midparietal gray matter spectra, we found a significant decrease in the absolute concentration of NAA in OT patients versus healthy controls (7.76 ± 0.25 vs 8.11 ± 0.45, P = 0.017). A similar decrease in NAA was seen in the cerebellar vermis (7.33 ± 0.61 vs 8.55 ± 1.54, P = 0.014) and cerebellar white matter (8.54 ± 0.79 vs 9.95 ± 1.57, P = 0.010). No differences in the other metabolites or their ratios were observed. Reductions in both cerebral cortical and cerebellar NAA suggest that there is neuronal damage or loss in OT, raising the intriguing question as to whether OT is a neurodegenerative disease. Along with clinical history and electrophysio0logical examination, 1H-MRS could serve as a useful diagnostic aid for OT.
Analytical framework for MANET learning and routing (2016)

This paper presents an analytical model of a multi-layer (social-communication) network supported with on-the-fly learned and prior social-cognitive features. In this model, routing is formulated in a distributed setting where each node operating with local information only finds the next-hop node, among all social and mobile ad hoc network (MANET) communication link neighbors, whose normalized delay is the smallest. This approach minimizes the end-to-end delay and readily extends to optimize other metrics, e.g., success probability. Delay performance is analytically evaluated as a function of distance to the destination node, which is estimated in social-cognitive learning under two social-cognitive features, frequency of encounters and social pressure metric. Different mobility models (random waypoint and group) are considered for the communication topology and different graph models (uniform random or scale-free) are considered for the underlying social network. Analysis is provided for both infinite and finite node models with different levels of granularity. In addition, real social network data is used to evaluate the analysis. Results show that online learning can closely track the actual distances to the destination and the expected delay with learning is close to that with perfect knowledge of network dynamics, while it saturates with hop distance, implying that the small-world phenomenon is captured.
A two-layered wavelet-based algorithm for efficient lossless and lossy image compression (2000)

In this paper, we propose a wavelet-based image-coding scheme allowing lossless and lossy compression, simultaneously. Our two-layered approach utilizes the best of two worlds: it uses a highly performing wavelet-based or wavelet packet-based coding technique for lossy compression in the low bit range as a first stage. For the second (optional) stage, we extend the concept of reversible integer wavelet transforms to the more flexible class of adaptive reversible integer wavelet packet transforms which are based on the generation of a whole library of bases, from which the best representation for a given residue between the reconstructed lossy compressed image and the original image is chosen using a fast-search algorithm. We present experimental results demonstrating that our compression algorithm yields a rate-distortion performance similar or superior to the best currently published pure lossy still image-coding methods. At the same time, the lossless compression performance of our two-layered scheme is comparable to that of state-of-the-art pure lossless image-coding schemes. Compared to other combined lossy/lossless coding schemes such as the emerging JPEG-2000 still image-coding standard PSNR improvements up to 3 dB are achieved for a set of standard test images.
Immunopathogenesis of Pulmonary Granulomas in the Guinea Pig after Infection withMycobacterium tuberculosis (2003)

Pulmonary tuberculosis in guinea pigs is similar to the disease in humans and is accordingly widely used as a model to test tuberculosis vaccines. The primary site of expression of acquired immunity and the hallmark of tuberculosis is the granuloma. Granuloma morphology is well described, but there is limited information regarding T-cell subset influx. We monitored the course of pulmonary tuberculosis in guinea pigs and observed four distinct immunohistopathological stages. In all stages there were similar numbers and arrangement of CD4 and CD8 T cells. There were only small numbers of apoptotic lymphocytes, scattered around and within the necrotic core, and acid-fast bacilli were visible both within macrophages and free within airway debris. A key finding of the study was the observation that the development of the necrotic core was an early event and almost certainly preceded the emergence of the acquired immune response. This in turn suggests that innate mechanisms are the basis of the early lesions and that subsequent acquired responses are unable to moderate them. This hypothesis differs from the current dogma that excessive activity of T cells mediates delayed-type hypersensitivity and that cellular cytolysis is the root cause of the necrosis.
Src promotes delta opioid receptor (DOR) desensitization by interfering with receptor recycling (2008)

Abstract An important limitation in the clinical use of opiates is progressive loss of analgesic efficacy over time. Development of analgesic tolerance is tightly linked to receptor desensitization. In the case of delta opioid receptors (DOR), desensitization is especially swift because receptors are rapidly internalized and are poorly recycled to the membrane. In the present study, we investigated whether Src activity contributed to this sorting pattern and to functional desensitization of DORs. A first series of experiments demonstrated that agonist binding activates Src and destabilizes a constitutive complex formed by the spontaneous association of DORs with the kinase. Src contribution to DOR desensitization was then established by showing that pre-treatment with Src inhibitor PP2 (20 microM; 1 hr) or transfection of a dominant negative Src mutant preserved DOR signalling following sustained exposure to an agonist. This protection was afforded without interfering with endocytosis, but suboptimal internalization interfered with PP2 ability to preserve DOR signalling, suggesting a post-endocytic site of action for the kinase. This assumption was confirmed by demonstrating that Src inhibition by PP2 or its silencing by siRNA increased membrane recovery of internalized DORs and was further corroborated by showing that inhibition of recycling by monensin or dominant negative Rab11 (Rab11S25N) abolished the ability of Src blockers to prevent desensitization. Finally, Src inhibitors accelerated recovery of DOR-Galphal3 coupling after desensitization. Taken together, these results indicate that Src dynamically regulates DOR recycling and by doing so contributes to desensitization of these receptors.
Development of a Deterministic Total Organic Carbon (TOC) Predictor for Shale Reservoirs (2023)

Abstract Unconventional reservoirs like shale oil/gas are expected to play a major role in many unexplored regions, globally. Shale resource evaluation involves the estimation of Total Organic Carbon (TOC) which correlates to the prospective capability of generating and containing hydrocarbons. Direct measurement of TOC through geochemical analysis is often not feasible, and hence researchers have focused on indirect methods to estimate TOC using analytical and statistical techniques. Accordingly, this work proposes the application of artificial intelligence (AI) techniques to leverage routinely available well logs for the prediction of TOC. Multiple algorithms are developed and compared to rank the most optimum solution based on efficiency analysis. Support Vector Regression (SVR), Random Forest (RF), and XGBoost algorithms are utilized to analyze the well-log data and develop intelligent models for shale TOC. A process-based approach is followed starting with systematic data analysis, which includes the selection of the most relevant input parameters, data cleaning, filtering, and data-dressing, to ensure optimized inputs into the AI models. The data utilized in this work is from major shale basins in Asia and North America. The AI models are then used to develop TOC predictor as a function of fundamental open-hole logs including sonic, gamma-ray, resistivity, and density. Furthermore, to strengthen AI input-output correlation mapping, a k-fold cross-validation methodology integrating with the exhaustive-grid search approach is adopted. This ensures the optimized hyperparameters of the intelligent algorithms developed in this work are selected. Finally, developed models are compared to geochemically derived TOC using a comprehensive error analysis schema. The proposed models are teted for veracity by applying them on blind dataset. An error metrics schema composed of root-mean-squared-error, and coefficient of determination, is developed. This analysis ranks the respective AI models based on the highest performance efficiency and lowest prediction error. Consequently, it is concluded that the XGBoost and SVR-based TOC predictions are inaccurate yielding high deviations from the actual measured values in predictive mode. On the other hand, Random Forest TOC predictor optimized using k-fold validation produces high R2 values of more than 0.85 and reasonably low errors when compared to true values. The RF method overpowers other models by mapping complex non-linear interactions between TOC and various well logs.
New thiazolidinones reduce iron overload in mouse models of hereditary hemochromatosis and β-thalassemia (2019)

Genetic iron-overload disorders, mainly hereditary hemochromatosis and untransfused β-thalassemia, affect a large population worldwide. The primary etiology of iron overload in these diseases is insufficient production of hepcidin by the liver, leading to excessive intestinal iron absorption and iron efflux from macrophages. Hepcidin agonists would therefore be expected to ameliorate iron overload in hereditary hemochromatosis and β-thalassemia. In the current study, we screened our synthetic library of 210 thiazolidinone compounds and identified three thiazolidinone compounds, 93, 156 and 165, which stimulated hepatic hepcidin production. In a hemochromatosis mouse model with hemochromatosis deficiency, the three compounds prevented the development of iron overload and elicited iron redistribution from the liver to the spleen. Moreover, these compounds also greatly ameliorated iron overload and mitigated ineffective erythropoiesis in β-thalassemic mice. Compounds 93, 156 and 165 acted by promoting SMAD1/5/8 signaling through differentially repressing ERK1/2 phosphorylation and decreasing transmembrane protease serine 6 activity. Additionally, compounds 93, 156 and 165 targeted erythroid regulators to strengthen hepcidin expression. Therefore, our hepcidin agonists induced hepcidin expression synergistically through a direct action on hepatocytes via SMAD1/5/8 signaling and an indirect action via eythroid cells. By increasing hepcidin production, thiazolidinone compounds may provide a useful alternative for the treatment of iron-overload disorders.
ChemInform Abstract: 2‐(Triphenylphosphonio)‐4,5‐bis(benzoylthio)‐1,3‐dithiole Tetrafluoroborate: A Versatile Wittig Reagent for the Synthesis of Unsymmetrical Tetrathiafulvalenes and 1,3‐Dithiol‐2‐ylidene Derivatives. (1995)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Maximizing Aggregate Recommendation Diversity: A Graph-Theoretic Approach (2011)

Recommender systems are being used to help users find relevant items from a large set of alternatives in many online applications. Most existing recommendation techniques have focused on improving recommendation accuracy; however, diversity of recommendations has also been increasingly recognized in research literature as an important aspect of recommendation quality. This paper proposes a graph-theoretic approach for maximizing aggregate recommendation diversity based on maximum flow or maximum bipartite matching computations. The proposed approach is evaluated using real-world movie rating datasets and demonstrates substantial improvements in both diversity and accuracy, as compared to the recommendation re-ranking approaches, which have been introduced in prior literature for the purpose of diversity improvement.
A Placebo-Controlled Trial of Prazosin vs. Paroxetine in Combat Stress-Induced PTSD Nightmares and Sleep Disturbance (2007)

Abstract : The primary goal of this proposal is to evaluate the efficacy and tolerability of the alpha-1 adrenergic antagonist prazosin compared to placebo for combat trauma-related nightmares, sleep disturbance and overall function in recently combat-exposed returnees from OIF and OEF. A secondary goal is to evaluate the effects of the SSRI paroxetine on behavioral symptoms and overall function in this population. Specific hypotheses (described below) will be tested in a three parallel arm 12-week randomized controlled trial of prazosin, paroxetine and placebo in combat-exposed troops recently returned from OIF and OEF with combat trauma-related persistent nightmares and sleep disturbance. This will be a two-site study performed in the Seattle/Tacoma area at Madigan AMC and in the Washington DC area at Walter Reed AMC.
ChemInform Abstract: HETEROGENEOUS CATALYSIS IN ORGANIC CHEMISTRY. 3. COMPETITIVE ADSORPTION OF SOLVENTS DURING ALKENE HYDROGENATIONS (1985)

Abstract Der Einfluß verschiedener Lösungsmittel auf die katalytische Hydrierung von Alkenen wie I‐Buten wird ausführlich untersucht.
Sunlight Oxidation of Alkyl Aryl Tellurides to the Corresponding Carbonyl Compounds: A New Carbonyl Precursor (2009)

Alkyl aryl tellurides were efficiently transformed to the corresponding carbonyl compounds by photo-oxidation with sunlight without affecting various functional groups in the alkyl moiety. The tellurides can be used as a new carbonyl precursor, and the photolysis can be conducted without special equipment for light sources.
Evaluation of Conventional Blood Glucose Monitoring as an Indicator of Integrated Glucose Values Using a Continuous Subcutaneous Sensor (2002)

-The breakfast and dinnertime SMBG values are good indicators of integrated glucose values in the time period preceding them, while the bedtime test correlates well with the integrated values both preceding and following it. This information should aid in the meaningful use of SMBG to evaluate glycemic control and make insulin dose adjustments.
Cobalt-Catalyzed Regio- and Enantioselective Allylic Amination (2019)

The first earth-abundant cobalt-catalyzed highly branched- and enantioselective allylic amination of racemic branched allylic carbonates bearing alkyl groups with both aromatic and aliphatic amines has been developed. The process allows rapid access of allylic amines in high yields with exclusively branched selectivity and excellent enantioselectivities (normally 99% <i>ee</i>) under mild reaction conditions.
Iridium‐Catalyzed Asymmetric Hydrogenation of Imines (2010)

We have evaluated a wide range of iridium complexes derived from chiral oxazoline-based N,P ligands for the asymmetric hydrogenation of imines and identified three efficient catalysts. These catalysts are readily synthesized by straightforward convenient routes and are air and moisture stable. In the reduction of acetophenone N-arylimines and related acyclic substrates, excellent enantioselectivities (up to 96 % ee) were obtained by using 0.1-0.5 mol % of catalyst at -20 degrees C and 5-50 bar hydrogen pressure.