gebhart/patrepeval huggingface dataset:
Multi-Resolution Sensitivity Analysis of Model of Immune Response to Helicobacter pylori Infection via Spatio-Temporal Metamodeling (2019)

Computational immunology studies the interactions between the components of the immune system that includes the interplay between regulatory and inflammatory elements. It provides a solid framework that aids the conversion of pre-clinical and clinical data into mathematical equations to enable modeling and in silico experimentation. The modeling-driven insights shed lights on some of the most pressing immunological questions and aid the design of fruitful validation experiments. A typical system of equations, mapping the interaction among various immunological entities and a pathogen, consists of a high-dimensional input parameter space that could drive the stochastic system outputs in unpredictable directions. In this paper, we perform spatio-temporal metamodel-based sensitivity analysis of immune response to Helicobacter pylori infection using the computational model developed by the ENteric Immune SImulator. We propose a two-stage procedure to obtain the estimates of the Sobol’ total and first-order indices for each input parameter, for quantifying their time-varying impacts on each output of interest. In particular, we fully reuse and exploit information from an existing simulated dataset, develop a novel sampling design for constructing the two-stage metamodels, and perform metamodel-based sensitivity analysis. The proposed procedure is scalable, easily interpretable, and adaptable to any multi-input multi-output complex systems of equations with a high-dimensional input parameter space.
Process Variations and Process-Tolerant Design (2007)

While CMOS technology has served semiconductor industry marvelously (by allowing nearly exponential increase in performance and device integration density), it faces some major roadblocks at sub-90nm process nodes due to the intrinsic physical limitations of the devices. One of the major barriers that the CMOS devices face at nanometer scale is increasing process parameter variations. Due to limitations of the fabrication process (e.g. sub-wavelength lithography and etching) and variations in the number of dopants in the channel of short channel devices, device parameters such as length (L), width (W), oxide thickness (T <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">ox</sub> ), threshold voltage (V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">th</sub> ) etc. suffer large variations. Variations in the device parameters, both systematic and random, translate into variations in circuit parameters like delay and leakage power, leading to loss in parametric yield. To deal with increasing parameter variations, it is important to accurately model the impact of device parameter variations at circuit level and develop process-tolerant design techniques for both logic and memory. This article analyzes the impact of process parameter variations on logic circuits and memory and focuses on some major works in the area of process-tolerant design methodology at circuit/architecture level
Clinical significance of left ventricular hypertrophy and changes in left ventricular mass in high-risk hypertensive patients: a subanalysis of the Candesartan Antihypertensive Survival Evaluation in Japan trial (2009)

Protection against LVH is associated with a reduced risk of cardiovascular events and may be related to the preservation of renal function in high-risk hypertensive patients.
Relaxing constraints in stateful network data plane design (2017)

Supporting programmable states in the data plane of a forwarding element, e.g., a switch or a NIC, has recently attracted the interest of the research community, which is now looking for the right abstraction to enable the programming of stateful network functions in hardware at line rate. We challenge the conservative assumptions of state-of-the-art abstractions in this field, e.g. always assuming minimum size packets arriving back-to-back. Using trace-based simulations we show that by making more realistic assumptions on the traffic characteristics, e.g. larger average packet size, we can relax the design constraints that currently limit the set of functions that can be implemented at line rate, allowing for more complex functions, with no harm for performance.
Enhancing the Light Extraction Efficiency of Blue Semipolar (1011) Nitride-Based Light Emitting Diodes through Surface Patterning (2009)

To enhance light extraction from a blue semipolar (1011) multiple-quantum-well light emitting diode (LED), surface patterning was performed on the backside of a GaN substrate on which LED epitaxial layers had previously been grown. After circular photoresist etching masks were defined, the surface was patterned with conical features by inductively-coupled plasma (ICP) etching. A substantial increase (100% before packaging and 33% after) in output power was observed in comparison with a reference sample which had a smooth backside at a drive current of 20 mA. Since ICP etching is a non-equilibrium process, this technique can potentially be applied to LEDs grown on nonpolar m- or a-plane GaN substrates.
Preclinical evaluation of multiple species of PEGylated recombinant phenylalanine ammonia lyase for the treatment of phenylketonuria (2008)

Phenylketonuria (PKU) is a metabolic disorder, in which loss of phenylalanine hydroxylase activity results in neurotoxic levels of phenylalanine. We used the Pah(enu2/enu2) PKU mouse model in short- and long-term studies of enzyme substitution therapy with PEGylated phenylalanine ammonia lyase (PEG-PAL conjugates) from 4 different species. The most therapeutically effective PAL (Av, Anabaena variabilis) species was one without the highest specific activity, but with the highest stability; indicating the importance of protein stability in the development of effective protein therapeutics. A PEG-Av-p.C503S/p.C565S-PAL effectively lowered phenylalanine levels in both vascular space and brain tissue over a >90 day trial period, resulting in reduced manifestations associated with PKU, including reversal of PKU-associated hypopigmentation and enhanced animal health. Phenylalanine reduction occurred in a dose- and loading-dependent manner, and PEGylation reduced the neutralizing immune response to the enzyme. Human clinical trials with PEG-Av-p.C503S/p.C565S-PAL as a treatment for PKU are underway.
Arabinogalactan in Clinical Use (2011)

This chapter contains sections titled: Introduction Natural Killer (NK) Cytotoxicity Arabinogalactan Proteins (AGPs) Medicinal Applications Side Effects and Toxicity Conclusions References
Compact Dual-Band Dual-Mode Antenna With Omni-/Unidirectional Radiation Characteristics (2019)

A novel dual-band dual-mode antenna that operates at 2.45/5.8 GHz is proposed in this letter. The antenna exhibits linearly polarized omnidirectional radiation in the low band, and circularly polarized broadside radiation in the high band. To improve the 3 dB axial-ratio (AR) bandwidth, both truncated patches and a sequential rotation technique are combined together in the antenna design. The omnidirectional radiation in the low band is achieved by exciting four open-ended slots etched in the ground plane for the first time. The four slots form a magnetic-dipole-like current distribution along the edge of the ground plane, resulting in omnidirectional radiation. The low- and high-band operations are seamlessly integrated into a common design, sharing the same structure. This work provides a novel approach for improving the versatility of a radio frequency front-end subsystem without increasing footprint. The proposed antenna is prototyped and measured, showing good results in terms of impedance/AR bandwidths, isolation, radiation, and polarization.
Loudness Differences for Voice-Over-Voice Audio in TV and Streaming (2020)

Despite the many articles about activated carbon with different precursors in adsorption process, no in-depth research has been carried out to understand the causes of the difference in surface adsorption characteristics of activated carbon with different precursors and different activation processes. In this work, the ability of two active carbon adsorbents made of walnut shell and peach kernel by two chemical and physical methods (totally 4 different types of activated carbon) in treatment of oily wastewater including diesel, gasoline, used oil or engine lubricant has been compared. The results show that the chemical activated peach carbon active with 97% hardness has provided the highest hardness and physical activated walnut carbon active has obtained the lowest hardness value (87%). It is also found that peach activated carbon has a higher iodine number than walnut activated carbon, and this amount can be increased using chemical methods; Therefore, the highest amount of Iodine Number is related to Peach activated carbon that is made by chemical method (1230 mg/g), and the lowest amount of iodine number is seen in walnut activated carbon that is made by physical method (1020 mg/g). moreover, the pore diameter of physical activated carbon is lower than chemical activated carbon in all cases. So that the pore diameter of chemical activated peach carbon active is equal to 22.08 m and the measured pore diameter of physical activated peach carbon active is equal to 20.42 m. These values for walnut are obtained as 22.74 m and 21.86 m, respectively. Furthermore, the temperature and pH effects on the adsorption of different synthesized oily wastewater was studied and it was found that a
Distance constraints between microRNA target sites dictate efficacy and cooperativity (2007)

MicroRNAs (miRNAs) have the potential to regulate the expression of thousands of genes, but the mechanisms that determine whether a gene is targeted or not are poorly understood. We studied the genomic distribution of distances between pairs of identical miRNA seeds and found a propensity for moderate distances greater than about 13 nt between seed starts. Experimental data show that optimal down-regulation is obtained when two seed sites are separated by between 13 and 35 nt. By analyzing the distance between seed sites of endogenous miRNAs and transfected small interfering RNAs (siRNAs), we also find that cooperative targeting of sites with a separation in the optimal range can explain some of the siRNA off-target effects that have been reported in the literature.
Cardiovascular Responses after Ionic and Nonionic Magnetic Resonance Contrast Media in Rats with Acute Myocardial Infarction (1993)

RATIONALE AND OBJECTIVES. Contrast media may have quantitatively or even qualitatively different effects in the presence of underlying pathologic states compared with normal states. This study was designed to examine and compare the hemodynamic effects of bolus administration of ionic (gadopentetate dimeglumine) and nonionic (gadodiamide) magnetic resonance (MR) contrast media in rats subjected to acute myocardial infarction. METHODS. Acute myocardial infarction was induced in two groups of rats (n=20) by ligating the left coronary artery. Each animal received four bolus injections, iso-osmolar glucose followed by three incremental doses of either an ionic or a nonionic MR contrast agent (0.1, 0.3, and 0.5 mmol/kg). The effects of iso-osmolar glucose and each dose of MR contrast agent on the cardiovascular system were monitored for 15 minutes. RESULTS. Iso-osmolar glucose injection did not cause hemodynamic parameters to significantly differ from baseline values. Nonionic gadodiamide produced no significant hemodynamic effects at all injected doses compared with iso-osmolar glucose. However, ionic gadopentetate dimeglumine caused significant deleterious hemodynamic effects in a dosedependent fashion. Gadopentetate dimeglumine caused depression in left ventricular (LV) systolic pressure and systemic arterial pressure at the lowest dose (0.1 mmol/kg). At the maximum dose (0.5 mmol/kg), gadopentetate dimeglumine decreased systolic arterial pressure by 48%, rate-pressure product by 55%, LV end systolic pressure by 48%, rate of rise of LV pressure (dP/dt) by 55%, and heart rate by 10%. LV end diastolic pressure increased by 46%. Arrhythmias were observed in 20% (2/10) of the animals after injection of gadopentetate dimeglumine, but not after gadodiamide. CONCLUSIONS. Compared with ionic gadopentetate dimeglumine, nonionic gadodiamide is a hemodynamically safe MR contrast agent in this experimental model when it is injected as a rapid bolus at high doses and in the presence of acute myocardial infarction.
Surface Chemistry and Electrical Properties of Germanium Nanowires (2004)

Germanium nanowires with p- and n-dopants were synthesized by chemical vapor deposition and used to construct complementary field effect transistors . Electrical transport and x-ray photoelectron spectroscopy data are correlated to glean the effects of Ge surface chemistry to the electrical characteristics of GeNWs. Large hysteresis due to water molecules strongly bound to GeO2 on GeNWs is revealed. Different oxidation behavior and hysteresis characteristics and opposite band bending due to Fermi level pinning by interface states between Ge and surface oxides are observed for p- and n-type GeNWs. Vacuum annealing above 400C is used to remove surface oxides and eliminate hysteresis in GeNW FETs. High-k dielectric HfO2 films grown on clean GeNW surfaces by atomic layer deposition (ALD) using an alkylamide precursor is effective serving as the first layer of surface passivation. Lastly, the depletion length along the radial direction of nanowires is evaluated. The result suggests that surface effects could be dominant over the bulk properties of small diameter wires.
High-throughput imaging of Caenorhabditis elegans aging using collective activity monitoring (2021)

ABSTRACT The genetic manipulability and short lifespan of C. elegans make it an important model for aging research. Widely applied methods for measurements of worm aging based on manual observation are labor intensive and low-throughput. Here, we describe the Worm Collective Activity Monitoring Platform (WormCamp), a system for assaying aging in C. elegans by monitoring activity of populations of worms in standard 24-well plates. We show that metrics based on the rate of decline in collective activity can be used to estimate the average lifespan and locomotor healthspan in the population. Using the WormCamp, we assay a panel of highly divergent natural isolates of C. elegans and show that both lifespan and locomotor healthspan display substantial heritability. To facilitate analysis of large numbers of worms, we developed a robotic imaging system capable of simultaneous automated monitoring of activity, lifespan, and locomotor healthspan in up to 2,304 populations containing a total of ~90,000 animals. We applied the automated system to conduct a large-scale RNA interference screen for genes that affect lifespan and locomotor healthspan. The WormCamp system is complementary to other current automated methods for assessing C. elegans aging and is well suited for efficiently screening large numbers of conditions.
Cell Trafficking Interference in Inflammatory Bowel Disease: Therapeutic Interventions Based on Basic Pathogenesis Concepts (2018)

After 20 years of successful targeting of pro-inflammatory cytokines for the treatment of IBD, an alternative therapeutic strategy has emerged, based on several decades of advances in understanding the pathogenesis of IBD. The targeting of molecules involved in leukocyte traffic has recently become a safe and effective alternative. With 2 currently approved drugs (ie, natalizumab, vedolizumab) and several others in phase 3 trials (eg, etrolizumab, ozanimod, anti-MAdCAM-1), the blockade of trafficking molecules has firmly emerged as a new therapeutic era for IBD. We discuss the targets that have been explored in clinical trials: chemokines and its receptors (eg, IP10, CCR9), integrins (eg, natalizumab, AJM300, vedolizumab, and etrolizumab), and its endothelial ligands (MAdCAM-1, ICAM-1). We also discuss a distinct strategy that interferes with lymphocyte recirculation by blocking lymphocyte egress from lymph nodes (small molecule sphingosine-phosphate receptor [S1PR] agonists: fingolimod, ozanimod, etrasimod, amiselimod). Strategies on the horizon include additional small molecules, allosteric inhibitors that specifically bind to the active integrin form and nanovectors that allow for the use of RNA interference in the quest to modulate pro-inflammatory leukocyte trafficking in IBD.
Retro-reflective evanescent field sensors based on Bragg gratings made in biconical tapered fiber with femtosecond IR radiation (2005)

Retro-reflective Bragg gratings were made with femtosecond radiation from a Ti: sapphire IR laser in the cladding region of a tapered single mode fiber. The evanescent field in the taper interacts with the ambient environment and the intensity of the reflected signal is used to evaluate the ambient refractive index changes as low as 2.5×10-
Molecular Epidemiology of Carbapenem-Nonsusceptible Acinetobacter baumannii in the United States (2011)

Acinetobacter baumannii is emerging as an important nosocomial pathogen worldwide. We report molecular epidemiology of 65 carbapenem-nonsusceptible A. baumannii isolates identified from hospitals in New York, Pennsylvania, Florida, Missouri, Nevada, and California between 2008 and 2009. All isolates were subjected to pulsed-field gel electrophoresis (PFGE). Select isolates then underwent multilocus sequence typing (MLST). While the PFGE patterns tended to cluster within each hospital, sequence types (STs) belonging to the clonal complex 92 (CC92) and the pan-European clonal lineage II (EUII; worldwide clonal lineage 2) were predominant in all hospitals. Of them, ST122 and ST208 were the most common and were found in four of the six hospitals. Isolates belonging to the pan-European clonal lineages I and III were identified in one hospital each. Carbapenemase-encoding genes bla(OXA-23) and/or ISAba1-bla(OXA-51-like) were present among the majority of isolates. These findings suggest that carbapenem-nonsusceptible A. baumannii isolates found in U.S. hospitals constitute part of the global epidemic driven by CC92, but have unique STs other than ST92, which may be spreading by means of patient transfer between health care facilities within the United States.
ChemInform Abstract: Schotten‐Baumann Acylation of N‐Debenzoyltaxol; An Efficient Route to N‐Acyl Taxol Analogues and Their Biological Evaluation. (1994)

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.
Deep Learning Based Resource Allocation Method to Control System Capacity and Fairness for MU-MIMO THP (2021)

This paper proposes a deep-learning-based resource allocation method to adaptively control system capacity and fairness for multi-user multiple-input and multiple-output (MU-MIMO). In the proposed method, Tomlinson-Harashima precoding (THP) is used to enhance the transmission rate. Additionally, channel resources are appropriately allocated based on user scheduling techniques, i.e., semiorthogonal user selection (SUS) for throughput maximization and proportional fairness (PF) for fairness among users. The primary feature of the proposed method is that it appropriately allocates channel resources by utilizing the user position information and target fairness index (FI) through deep learning. This makes it possible to meet various service requirements. Numerical simulations are used to demonstrate the effectiveness of the proposed method in terms of system capacity and fairness under different MIMO configurations and user distributions.
Amorphous Iron(III) OxideA Review (2007)

The syntheses of amorphous Fe(2)O(3) nanoparticles of varying size and morphology, their magnetic properties, crystallization mechanism, and applications are reviewed herein. The synthetic routes are classified according to the nature of the sample (powders, nanocomposites, films, coated particles). The contributions of various experimental techniques to the characterization of an amorphous Fe(2)O(3) phase are considered in this review, including some key experimental markers, allowing its distinction from nanocrystalline "X-ray amorphous" polymorphs (maghemite, hematite). We discuss the thermally induced crystallization mechanisms depending on transformation temperature, atmosphere, and the size of the amorphous particles that predetermine the structure of the primarily formed crystalline polymorph. The controversial description of the magnetic behavior, including an interpretation of the low-temperature and in-field Mössbauer spectra, is analyzed.
Oxygen Transfer from Mother to Fetus During Cesarean Section Under Epidural Anesthesia (1983)

Ramanathan, S.; Gandhi, S.; Arismendy, J.; Chalon, J.; Turndorf, H.; Rolbin, Stephen H. M.D. Author Information
The histological analysis of the coronary medial thickness: Implications for percutaneous coronary intervention (2023)

The human coronary arteries demonstrate variation in medial thickness which tends to vary depending upon an epicardial coronary artery itself, as well as its segments and branches. Understanding these variations in medial thickness can be useful for both the interventionalists and interventional product development teams.
Multimodal single-cell/nucleus RNA sequencing data analysis uncovers molecular networks between disease-associated microglia and astrocytes with implications for drug repurposing in Alzheimer's disease (2021)

Because disease-associated microglia (DAM) and disease-associated astrocytes (DAA) are involved in the pathophysiology of Alzheimer's disease (AD), we systematically identified molecular networks between DAM and DAA to uncover novel therapeutic targets for AD. Specifically, we develop a network-based methodology that leverages single-cell/nucleus RNA sequencing data from both transgenic mouse models and AD patient brains, as well as drug-target network, metabolite-enzyme associations, the human protein-protein interactome, and large-scale longitudinal patient data. Through this approach, we find both common and unique gene network regulators between DAM (i.e., <i>PAK1</i>, <i>MAPK14</i>, and <i>CSF1R</i>) and DAA (i.e., <i>NFKB1</i>, <i>FOS</i>, and <i>JUN</i>) that are significantly enriched by neuro-inflammatory pathways and well-known genetic variants (i.e., <i>BIN1</i>). We identify shared immune pathways between DAM and DAA, including Th17 cell differentiation and chemokine signaling. Last, integrative metabolite-enzyme network analyses suggest that fatty acids and amino acids may trigger molecular alterations in DAM and DAA. Combining network-based prediction and retrospective case-control observations with 7.2 million individuals, we identify that usage of fluticasone (an approved glucocorticoid receptor agonist) is significantly associated with a reduced incidence of AD (hazard ratio [HR] = 0.86, 95% confidence interval [CI] 0.83-0.89, <i>P</i> < 1.0 × 10<sup>-8</sup>). Propensity score-stratified cohort studies reveal that usage of mometasone (a stronger glucocorticoid receptor agonist) is significantly associated with a decreased risk of AD (HR = 0.74, 95% CI 0.68-0.81, <i>P</i> < 1.0 × 10<sup>-8</sup>) compared to fluticasone after adjusting age, gender, and disease comorbidities. In summary, we present a network-based, multimodal methodology for single-cell/nucleus genomics-informed drug discovery and have identified fluticasone and mometasone as potential treatments in AD.