gebhart/patrepeval huggingface dataset:
Enhanced Colloidal Stability of Various Gold Nanostructures Using a Multicoordinating Polymer Coating (2017)

We describe the effectiveness of a multicoordinating polymer coating to surface functionalize gold nanospheres, nanoshells, and nanorods and promote their steric stabilization in biological media. The polymer ligand synthesized via one-step nucleophilic addition reaction starting with poly(isobutylene-alt-maleic anhydride) precursor presents multiple lipoic acid groups for strong coordination on metal-rich surfaces and several hydrophilic motifs (e.g., zwitterion groups or short poly(ethylene glycol) (PEG) chains) to promote water solubilization. We show that nanocrystals ligated with this polymer are compact in size and exhibit excellent long-term colloidal stability over broad conditions. We compare the ability of zwitterion- and PEG-modified polymer ligands to shield the metal surfaces from sodium cyanide digestion, or resist the competitive removal by dithiothreitol (DTT). We find that polymers appended with either hydrophilic motif essentially eliminate DTT competition for surface binding, while nanocrystals capped with the PEGylated coating exhibits substantially better resistance to sodium cyanide digestion compared with zwitterionic coating. Furthermore, we probe the differences between the two coatings in terms of endowing surface charge to the nanocrystals and affecting their Brownian diffusion properties. Additionally, we show that zwitterionic coating is very effective in preventing the formation of protein corona on such nanostructures, a highly valuable result with direct implications in biotechnology.
Glucose effectiveness and insulin sensitivity from the minimal models: consequences of undermodeling assessed by Monte Carlo simulation (1999)

The unlabeled (cold) minimal model (MM) and the labeled (hot) minimal model (HMM) are a powerful tool to investigate in vivo metabolism from a standard intravenous glucose tolerance test (IVGTT) or hot IVGTT (HIVGTT). They allow to estimate metabolic indexes of the glucose-insulin system, namely glucose effectiveness (GE) and insulin sensitivity (IS) (of uptake and production those of MM, and of uptake only those of HMM). Here, the consequences of the single-compartment glucose kinetics approximation used in the MM's are investigated via Monte Carlo simulation, using a physiologic reference model (RM) of the system. RM allows to generate noisy synthetic plasma concentrations of glucose, tracer glucose, and insulin during IVGTT and HIVGTT, which are then analyzed with MM and HMM. The MM and HMM GE and IS are then compared with the RM ones. Results of 400 runs show that: 1) correlation of MM GE with the RM index is weak; 2) MM IS is well correlated with the RM index, but severely underestimates it; 3) HMM clearance rate is correlated with RM clearance; and 4) HMM IS is well correlated and only slightly overestimates the RM index. These results demonstrate that GE of MM is most affected by the single-compartment approximation and the indexes of HMM are more robust than those of MM.
Indoor tracking of multiple persons with a 77 GHz MIMO FMCW radar (2017)

In this paper, we tackle the task of multi-target tracking of humans in an indoor setting using a low power 77 GHz MIMO CMOS radar. A drawback of such a highresolution and low-power device is the higher sensitivity to noise, which makes the analysis of signals more challenging. Therefore, a pipeline is proposed to address both pre-processing of the radar signal and multi-target tracking. In the pre-processing phase, we focus on handling the low Signal-to-Noise Ratio (SNR) and eliminating so-called ghost targets. The tracking method we propose is based on Markov Chain Monte Carlo Data Association (MCMCDA), thus taking a combinatorial approach towards the task of tracking. The pipeline is tested on a number of real-world scenarios and shows promising results, overcoming the significant amount of noise associated with embedded radar devices.
Stochastic Reassembly for Managing the Information Complexity in Multilevel Analysis of Heterogeneous Materials (2012)

Efficient and accurate analysis of materials behavior across multiple scales is critically important in designing complex materials systems with exceptional performance. For heterogeneous materials, apparent properties are typically computed by averaging stress-strain behavior in a statistically representative cell. To be statistically representative, such cells must be larger and are often computationally intractable, especially with standard computing resources. In this research, a stochastic reassembly approach is proposed for managing the information complexity and reducing the computational burden, while maintaining accuracy, of apparent property prediction of heterogeneous materials. The approach relies on a hierarchical decomposition strategy that carries the materials analyses at two levels, the RVE (representative volume element) level and the SVE (statistical volume element) level. The hierarchical decomposition process uses clustering methods to group SVEs with similar microstructure features. The stochastic reassembly process then uses t-testing to minimize the number of SVEs to garner their own apparent properties and fits a random field model to high-dimensional properties to be put back into the RVE. The RVE thus becomes a coarse representation, or “mosaic,” of itself. Such a mosaic approach maintains sufficient microstructure detail to accurately predict the macro-property but becomes far cheaper from a computational standpoint. A nice feature of the approach is that the stochastic reassembly process naturally creates an apparent-SVE property database. Thus, material design studies may be undertaken with SVE-apparent properties as the building blocks of a new material’s mosaic. Some simple examples of possible designs are shown. The approach is demonstrated on polymer nanocomposites.
Effects of Probiotics on Gut Microbiomes of Extremely Preterm Infants in the Neonatal Intensive Care Unit: A Prospective Cohort Study (2022)

<b>Background:</b> Probiotics have been previously reported to reduce the incidence of necrotizing enterocolitis (NEC) in extremely preterm infants, but the mechanisms by which the probiotics work remain unknown. We aimed to investigate the effects of probiotics on the gut microbiota of extremely preterm infants. <b>Methods:</b> A prospective cohort study was conducted on 120 extremely preterm neonates (gestational age ≤ 28 weeks) between August 2019 and December 2021. All neonates were divided into the study (receiving probiotics) and the control (no probiotics) groups. Multivariate logistic regression analysis was performed to investigate the significantly different compositions of gut microbiota between these two groups. The effects of probiotics on the occurrence of NEC and late-onset sepsis were also investigated. <b>Results:</b> An increased abundance of <i>Lactobacillus</i> was noted in neonates who received the probiotics (AOR 4.33; 95% CI, 1.89-9.96, <i>p</i> = 0.009) when compared with the control group. Subjects in the probiotic group had significantly fewer days of total parenteral nutrition (median [interquartile range, IQR]) 29.0 (26.8-35.0) versus 35.5 (27.8-45.0), <i>p</i> = 0.004) than those in the control group. The probiotic group had a significantly lower rate of late-onset sepsis than the control group (47.1% versus 70.0%, <i>p</i> = 0.015), but the rate of NEC, duration of hospitalization and the final in-hospital mortality rates were comparable between these two groups. <b>Conclusions:</b> Probiotic supplementation of extremely preterm infants soon after the initiation of feeding increased the abundance of <i>Lactobacillus</i>. Probiotics may reduce the risk of late-onset sepsis, but further randomized controlled trials are warranted in the future.
Sucrose Diffusion in Decellularized Heart Valves for Freeze-Drying (2015)

Decellularized heart valves can be used as starter matrix implants for heart valve replacement therapies in terms of guided tissue regeneration. Decellularized matrices ideally need to be long-term storable to assure off-the-shelf availability. Freeze-drying is an attractive preservation method, allowing storage at room temperature in a dried state. However, the two inherent processing steps, freezing and drying, can cause severe damage to extracellular matrix (ECM) proteins and the overall tissue histoarchitecture and thus impair biomechanical characteristics of resulting matrices. Freeze-drying therefore requires a lyoprotective agent that stabilizes endogenous structural proteins during both substeps and that forms a protective glassy state at room temperature. To estimate incubation times needed to infiltrate decellularized heart valves with the lyoprotectant sucrose, temperature-dependent diffusion studies were done using Fourier transform infrared spectroscopy. Glycerol, a cryoprotective agent, was studied for comparison. Diffusion of both protectants was found to exhibit Arrhenius behavior. The activation energies of sucrose and glycerol diffusion were found to be 15.9 and 37.7 kJ·mol(-1), respectively. It was estimated that 4 h of incubation at 37°C is sufficient to infiltrate heart valves with sucrose before freeze-drying. Application of a 5% sucrose solution was shown to stabilize acellular valve scaffolds during freeze-drying. Such freeze-dried tissues, however, displayed pores, which were attributed to ice crystal damage, whereas vacuum-dried scaffolds in comparison revealed no pores after drying and rehydration. Exposure to a hygroscopic sucrose solution (80%) before freeze-drying was shown to be an effective method to diminish pore formation in freeze-dried ECMs: matrix structures closely resembled those of control samples that were not freeze-dried. Heart valve matrices were shown to be in a glassy state after drying, suggesting that they can be stored at room temperature.
Characterization of Amorphous Systems Using Local Configurations (1974)

We present a new method to study the electronic density of states of an amorphous system of atoms with four‐fold coordination in terms of the local density of states of an atom in a small cluster of this system. Our results show unequivocally that the number and type of rings of bonds in the vicinity of and passing through a certain atom are intimately related to the position and number of peaks in the local density of states of this atom. The method involves choosing a small cluster of atoms and using the Bethe lattice as a boundary condition.
Abstract 2929: Predictors of survival in never-smokers with non-small cell lung cancer: A large-scale, two-phase genetic study (2012)

Abstract Lung cancer in never-smokers is increasingly recognized as distinct from that in ever-smokers owing to substantial differences in etiology, clinical characteristics, and prognosis. Therefore, we aimed to identify prognostic markers specific for lung cancer in never-smokers in a two-stage study. First, 11,930 single-nucleotide polymorphisms (SNPs) in 904 inflammation-related genes were genotyped, and their associations with overall survival in 411 never-smokers with lung cancer at The University of Texas MD Anderson Cancer Center were analyzed. Next, fast-track validation of the top 37 SNPs in 311 never-smokers with lung cancer at Mayo Clinic was performed. Three SNPs (interleukin 17 receptor A:rs879576, bone morphogenetic protein 8A:rs698141, and spleen tyrosine kinase:rs290229) were validated (p&amp;lt;0.05), and two more SNPs (CD74:rs1056400 and CD38:rs10805347) were borderline significant (p=0.08) in the Mayo Clinic population. In combined analysis of the MD Anderson and Mayo Clinic patients, IL17RA:rs879576 resulted in a 40% reduction in the risk of death (p=4.1 × 10−5 [p=0.61, heterogeneity test]). We successfully validated a survival tree created in MD Anderson population based on gene-gene interactions in the Mayo Clinic population. This survival tree stratified patients into subsets with significantly different risks of death: patients at MD Anderson with the rs1056400_GG/rs698141_GA+AA genotype had a 2.32-fold higher risk of death (p=1.72 × 10−5) and 9-month shorter median survival time (MST) (p=4.5 × 10−4, log-rank test) than did those with the rs1056400_GG/rs698141_GG or rs1056400_GA+AA genotype in the discovery phase. Also, the patients at Mayo Clinic with the former genotype had an approximately twofold higher risk of death (p=0.02) and a strikingly shorter (by 26 months) MST (p=0.029, log-rank test) than did those with the latter genotype in the validation phase. We evaluated these five SNPs in 996 ever-smokers and found no significant associations. To our knowledge, this is the first study to systematically evaluate the associations of genetic variations in major inflammation-related genes with outcome of lung cancer in never-smokers. It provides strong evidence that inflammation-related genetic variations can affect clinical outcomes in these patients, which may lead to significant biological insight into these outcomes. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 2929. doi:1538-7445.AM2012-2929
Verticalization of bacterial biofilms (2018)

Biofilms are communities of bacteria adhered to surfaces. Recently, biofilms of rod-shaped bacteria were observed at single-cell resolution and shown to develop from a disordered, two-dimensional layer of founder cells into a three-dimensional structure with a vertically-aligned core. Here, we elucidate the physical mechanism underpinning this transition using a combination of agent-based and continuum modeling. We find that verticalization proceeds through a series of localized mechanical instabilities on the cellular scale. For short cells, these instabilities are primarily triggered by cell division, whereas long cells are more likely to be peeled off the surface by nearby vertical cells, creating an "inverse domino effect". The interplay between cell growth and cell verticalization gives rise to an exotic mechanical state in which the effective surface pressure becomes constant throughout the growing core of the biofilm surface layer. This dynamical isobaricity determines the expansion speed of a biofilm cluster and thereby governs how cells access the third dimension. In particular, theory predicts that a longer average cell length yields more rapidly expanding, flatter biofilms. We experimentally show that such changes in biofilm development occur by exploiting chemicals that modulate cell length.
Fragment-Based Discovery of a Regulatory Site in Thioredoxin Glutathione Reductase Acting as “Doorstop” for NADPH Entry (2018)

Members of the FAD/NAD-linked reductase family are recognized as crucial targets in drug development for cancers, inflammatory disorders, and infectious diseases. However, individual FAD/NAD reductases are difficult to inhibit in a selective manner with off-target inhibition reducing usefulness of identified compounds. Thioredoxin glutathione reductase (TGR), a high molecular weight thioredoxin reductase-like enzyme, has emerged as a promising drug target for the treatment of schistosomiasis, a parasitosis afflicting more than 200 million people. Taking advantage of small molecules selected from a high-throughput screen and using X-ray crystallography, functional assays, and docking studies, we identify a critical secondary site of the enzyme. Compounds binding at this site interfere with well-known and conserved conformational changes associated with NADPH reduction, acting as a doorstop for cofactor entry. They selectively inhibit TGR from Schistosoma mansoni and are active against parasites in culture. Since many members of the FAD/NAD-linked reductase family have similar catalytic mechanisms, the unique mechanism of inhibition identified in this study for TGR broadly opens new routes to selectively inhibit homologous enzymes of central importance in numerous diseases.
ChemInform Abstract: Spherical Molecular Assemblies: A Class of Hosts for the Next Millennium (2001)

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.
A high efficiency Chireix out-phasing power amplifier for 5GHz WLAN applications (2004)

This paper describes the design methodology and presents measured results for a 5GHz Chireix out-phasing power amplifier. The outputs of two high efficiency amplifiers operating in class F are combined using a lossless combiner. A novel implementation of the class F output tuning networks and combiner using bond wires is also described. To our knowledge, this is the most efficient 802.11a amplifier ever reported.
MaxSynBio: Avenues Towards Creating Cells from the Bottom Up (2018)

A large German research consortium mainly within the Max Planck Society ("MaxSynBio") was formed to investigate living systems from a fundamental perspective. The research program of MaxSynBio relies solely on the bottom-up approach to synthetic biology. MaxSynBio focuses on the detailed analysis and understanding of essential processes of life through modular reconstitution in minimal synthetic systems. The ultimate goal is to construct a basic living unit entirely from non-living components. The fundamental insights gained from the activities in MaxSynBio could eventually be utilized for establishing a new generation of biotechnological processes, which would be based on synthetic cell constructs that replace the natural cells currently used in conventional biotechnology.
Fuel Efficient Control Algorithms for Connected and Automated Line-Haul Trucks (2019)

In this paper, an optimal and predictive multilevel control solution is developed to utilize data and capabilities provided by the Connected and Automated Vehicle (CAV) technologies to reduce fuel consumption for line-haul class 8 trucks. The longer horizon road grade and speed limit data combined with shorter horizon and time-varying traffic data on real-world driving scenarios is utilized in the developed integrated optimal control algorithms to further reduce fuel consumption with respect to a production baseline control with state-of-art Advanced Driver-Assistance Systems (ADAS) control features. Furthermore, integration of the developed control algorithms for the front vehicle automation in platoon with a rear truck is also studied. The results indicate that with the application of the developed control solutions for powertrain efficiency in both single truck automation or the automation of the front truck in platoon with a rear truck, the fuel consumption is significantly reduced over real-world driving scenarios with road grade, speed limit and traffic data. The proposed solution is implementable in real-time with the utilization of CAV technologies with the proposed multilevel control architecture.
Improving virtual-grid compaction through grouping (1987)

In the past, Virtual-Grid Compactors have not been well received because they generated sparse layouts. In analyzing this problem, we found three major areas where improvements could be made: breaking the virtual-grid lines into segments; decoupling the placement of non-interacting layers; and eliminating the centered nature of elements. The result is a compactor with substantially better mask generation.
Localized Triggering of the Insulator-Metal Transition in VO2 Using a Single Carbon Nanotube (2019)

Vanadium dioxide (VO<sub>2</sub>) has been widely studied for its rich physics and potential applications, undergoing a prominent insulator-metal transition (IMT) near room temperature. The transition mechanism remains highly debated, and little is known about the IMT at nanoscale dimensions. To shed light on this problem, here we use ∼1 nm-wide carbon nanotube (CNT) heaters to trigger the IMT in VO<sub>2</sub>. Single metallic CNTs switch the adjacent VO<sub>2</sub> at less than half the voltage and power required by control devices without a CNT, with switching power as low as ∼85 μW at 300 nm device lengths. We also obtain potential and temperature maps of devices during operation using Kelvin probe microscopy and scanning thermal microscopy. Comparing these with three-dimensional electrothermal simulations, we find that the local heating of the VO<sub>2</sub> by the CNT plays a key role in the IMT. These results demonstrate the ability to trigger IMT in VO<sub>2</sub> using nanoscale heaters and highlight the significance of thermal engineering to improve device behavior.
Effects of aromatic compounds on hemicellulose‐degrading enzymes in Aspergillus japonicus (1985)

Aspergillus japonicus was grown in the presence of various aromatic compounds at 0.1 and 1 mg/mL, and extracellular xylanase and arabanase activities were measured. Some of the aromatic compounds tested, especially at the higher concentration, suppressed the appearance of hemicellulase activities, expressed as xylanase or arabanase. Vanillin at 1 mg/mL in the presence of either xylan or araban completely suppressed growth, and guaiacol and p-coumaric acid markedly inhibited the growth of A. japonicus. The effects of the aromatic compounds on the activity of crude enzyme preparations were also ascertained. In vitro arabanase activity was affected more than xylanase activity.
Silica‐Supported Molybdenum Oxo Alkylidenes: Bridging the Gap between Internal and Terminal Olefin Metathesis (2019)

Grafting a molybdenum oxo alkylidene on silica (partially dehydroxylated at 700 °C) affords the first example of a well-defined silica-supported Mo oxo alkylidene, which is an analogue of the putative active sites in heterogeneous Mo-based metathesis catalysts. In contrast to its tungsten analogue, which shows poor activity towards terminal olefins because of the formation of a stable off-cycle metallacyclobutane intermediate, the Mo catalyst shows high metathesis activity for both terminal and internal olefins that is consistent with the lower stability of Mo metallacyclobutane intermediates. This Mo oxo metathesis catalyst also outperforms its corresponding neutral silica-supported Mo and W imido analogues.
Reflections on the origins of the National Center for Physical Acoustics (2017)

The National Center for Physical Acoustics arose from a group of faculty within the Physics Department at the University of Mississippi that had a strong interest in the general area of physical acoustics. With Hank Bass’s leadership, and support of the University of Mississippi’s central administration, this group constantly sought to expand their interest and their expertise in this area. Financial support from ONR permitted the expansion of their research space and the establishment of the Institute for Technology Development in the State of Mississippi led to eventual support from Congress. In October of 1986, by an act of the Congress of the United States of America, the National Center for Physical Acoustics was established. This presentation will provide some of the history concerning this event.