gebhart/patrepeval huggingface dataset:
Application of ESMACS binding free energy protocols to diverse datasets: Bromodomain-containing protein 4 (2019)

As the application of computational methods in drug discovery pipelines becomes more widespread it is increasingly important to understand how reproducible their results are and how sensitive they are to choices made in simulation setup and analysis. Here we use ensemble simulation protocols, termed ESMACS (enhanced sampling of molecular dynamics with approximation of continuum solvent), to investigate the sensitivity of the popular molecular mechanics Poisson-Boltzmann surface area (MMPBSA) methodology. Using the bromodomain-containing protein 4 (BRD4) system bound to a diverse set of ligands as our target, we show that robust rankings can be produced only through combining ensemble sampling with multiple trajectories and enhanced solvation via an explicit ligand hydration shell.
Severe Influenza Is Characterized by Prolonged Immune Activation: Results From the SHIVERS Cohort Study (2017)

Severe influenza cases showed a delay in the peripheral immune activation that likely led prolonged inflammation, compared with mild influenza cases.
Flow Chemistry under Extreme Conditions: Synthesis of Macrocycles with Musklike Olfactoric Properties (2021)

Starting from small cyclic ketones, continuous flow synthesis is used to produce medium-sized rings and macrocycles that are relevant for the fragrance industry. Triperoxides are important intermediates in this process and are pyrolyzed at temperatures above 250 °C. The synthesis is carried out in two continuously operated flow reactors connected by a membrane-operated separator. The practicality of flow chemistry is impressively demonstrated in this work by the use of hazardous reagent mixtures (30% H<sub>2</sub>O<sub>2</sub>, 65% HNO<sub>3</sub>) and the pyrolysis of no less problematic peroxides. All new macrocycles were tested for their olfactory properties in relation to musk.
Secreted and Transmembrane Mucins Inhibit Gene Transfer with AAV4 More Efficiently than AAV5 (2002)

Adeno-associated virus (AAV) is a promising vector for gene transfer in cystic fibrosis. AAV4 and AAV5 both bind to the apical surface of differentiated human airway epithelia, but only AAV5 infects. Both AAV4 and AAV5 require 2,3-linked sialic acid for binding. However, AAV5 interacts with sialic acid on N-linked carbohydrates, whereas AAV4 interacts with sialic acid on O-linked carbohydrates. Because mucin is decorated with O-linked carbohydrates, we hypothesized that mucin binds AAV4 and inhibits gene transfer. To evaluate the effect of secreted mucin, we studied mucin binding and gene transfer to COS cells and the basolateral membrane of well differentiated human airway epithelia. AAV4 bound mucin more efficiently than AAV5, and mucin inhibited gene transfer with AAV4. Moreover, O-glycosidase-pretreated mucin did not block gene transfer with AAV4. Similar to secreted mucin, the transmembrane mucin MUC1 inhibited gene transfer with AAV4 but not AAV5. MUC1 inhibited AAV4 by blocking internalization of the virus. Thus, O-linked carbohydrates of mucin are potent inhibitors of AAV4. Furthermore, whereas mucin plays an important role in innate host defense, its activity is specific; some vectors or pathogens are more resistant to its effects.
New Trends in Reaction and Resistance to Fire of Fire-retardant Epoxies (2010)

This paper focuses on current trends in the flame retardancy of epoxy-based thermosets. This review examines the incorporation of additives in these polymers, including synergism effects. Reactive flame-retardants-which are incorporated in the polymer backbone-are reported and the use of fire-retardant epoxy coatings for materials protection is also considered.
First Results from a 3 Year Study in Sports Concussion In Varsity Athletes at Lehigh University Using a Novel Biosensor Based Assessment Platform (I13.010) (2016)

Objective: Evaluate the predictive accuracy of the Borealis neurodiagnostic platform in its ability to detect sports concussion in collegiate athletes. Background: Non-invasive biomarkers are emerging as essential tools as diagnostic aids to primary care physicians and neurologists. Static imaging (MRI/PET/SPECT) and fluid based (blood and CSF) biomarkers are limited in their ability to capture the inherent dynamics of brain physiology. The present study evaluates a telemetric EEG during a series of cognitive tasks to assess test-retest reliability of this approach, classify injured athletes, and collect longitudinal data during recovery. Methods: Recent advances in wireless EEG hardware have enabled Cerora to develop a novel activated EEG system (Cerora BorealisTM) to focus the physiological assessment of brain health while activating various neural circuits during cognitive tasks. In a 3 year study, baselines scans consisting of 16 tasks were conducted on N=274 varsity athletes. Longitudinal data was collected from N=49 concussed athletes (and N=48 non-injured comparator subjects) during the symptomatic and asymptomatic phase at 6-10 time points per subject. Results: Retest reliability analyses indicated that spectral values were not statistically different across 10 separate recording scans. Additionally, we observed that performance on components of the task battery were similar across scans (e.g. SAC Immediate Memory rmANOVA F(3,6) = 0.25, p = 0.93). In contrast, performance on the cognitive test battery was significantly different following concussion (e.g. Wilcoxon p=0.001). Conclusions: A physiologically focused battery of activated EEG tasks is able to probe elements of brain circuits not presently assessed with standard resting state (Eyes Open or Eyes Closed) quantitative EEG. These measures can be stable and reliable across multiple testing sessions occurring over months. Concussion alters these measures that can be followed longitudinally during recovery.
Acute Hypoxic Hypoxia and Isocapnic Hypoxia Effects on Oculometric Features (2014)

These results suggest that oculometric changes are indicators of hypoxia, which can be monitored using compact, portable, noninvasive eye-tracking devices in a cockpit analogous environment to detect hypoxia-induced physiological changes in aircrew. Comparative results between HH and IH support the potential role of carbon dioxide in augmenting cerebral perfusion and hence improved tissue oxygen delivery.
Elastic Cellulose Derivatives for Novel Mechanical Stress Sensing (2018)

This review article highlights an overview of cellulose derivatives for novel mechanical stress sensing. Natural polymers such as cellulose are known to form cholesteric liquid crystal (CLC) phase typically over 100 °C after chemical modification of their side chains. Bragg reflection is one of the most unique and important optical properties of the CLC helical structures. When hydroxypropyl cellulose (HPC) was esterified with both propionyl and another groups, we serendipitously found the continuous changes of Bragg reflection peak throughout the full visible-wavelength range between 400 nm and 800 nm at relatively low CLC mesophase temperatures below 100 °C. Furthermore, full-color imaging could be realized by crosslinkable HPC derivatives tethering acryloyl side chains. More interestingly, we succeeded in the demonstration of novel mechanical stress sensing by the elastic CLC films of crosslinked HPC derivatives, leading to the visualization of external mechanical stress as the changes in Bragg reflection color. In this way, the elastic cellulose CLC films are available as the social infrastructure sensors for deterioration or damage of concretes, wearable sensors for human medical care, and so forth.
Re-building the Underfill: Performance of percolating fillers at package scale (2016)

This paper addresses both, the thermal and the thermo-mechanical performance of percolating thermal underfill applied flip-chip packages. We present a thermal test platform in flip-chip package design allowing the thermal conductivity of any underfill to be measured at package scale. We give details about design technology and current fabrication status. We benchmarked the thermal performance of the platform with percolated thermal underfill against the capillary thermal underfill case. In a layout with peripheral solder bumps the performance benefit related to heat dissipation of an overall system with percolating thermal underfill can be over 50% for liquid cooling and over 25% for enforced convection. The improvement for natural convection, typical in mobile environment, is 5% in the best considered case. We also present a study of the thermomechanical performance of the flip chip test platform during thermo-shock cycling by the aid of finite element (FE) tools at the critical regions of interest. We benchmarked the percolating thermal underfill against capillary mechanical underfill and capillary thermal underfill. For that investigation we used an effective material merging a visco-elastic polymer and a viscoplastic solder for saving computation time. In the percolating thermal underfill applied package, we've found slightly higher risk of delamination at the die underfill interface but very low fillet loads compared to conventional underfill. The risk of solder fatigue is significantly lower and the risk of die cracking is 25% higher for percolating than for the capillary underfills.
The I.R. Spectra of Matrix‐isolated SiBr2 and SiCl2 (1972)

Abstract The divalent silicon species SiBr 2 and SiCl 2 were produced by the reaction of the corresponding silicon tetrahalides with elemental silicon at temperatures between 900 and 1150°. The I.R. spectra of these molecules trapped in different matrices (Ne, Ar, N 2 ) were observed, and the fundamentals assigned. A set of valence force constants and the bond angles were obtained from accurate measurements of chlorine and silicon isotopic splittings.
Seeded emulsion polymerization of styrene: Incorporation of acrylic acid in latex products (2000)

Seeded batch emulsion polymerization of styrene and acrylic acid was studied. The influence of pH and acrylic acid content on the polymerization rate and the amount of carboxylic acid groups incorporated in the final latex products was investigated. The distribution of the functional groups over the aqueous phase, the latex particle surface, and the interior of the latex particle was determined using aqueous conductometric titration and nonaqueous potentiometric titration at intermediate and complete overall conversions. Combined with kinetic results, the carboxylic acid group distribution history provided valuable information about the process of incorporation of acrylic acid in latex products. Two-step processes in which a shot of acrylic acid was performed in the last stage of the emulsion polymerization reaction were investigated as a strategy to increase the surface incorporation efficiency. © 2000 John Wiley & Sons, Inc. J Appl Polym Sci 78: 875–885, 2000
A high-speed CMOS comparator for use in an ADC (1988)

A dynamic latch preceded by an offset-cancelled amplifier is used in the 3- mu m CMOS comparator to obtain a response time of 43 ns. The offset-cancelled amplifier reduces the input-referred offset so that medium-resolution analog-to-digital converters (ADCs) can be built with this comparator. The use of pipelining within the comparator enables the offset cancellation to be done as the dynamic latch is enabled. Power and area are optimally distributed within the amplifier to minimize response time.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Experimental and Computational Investigations on Highly Syndioselective Styrene–Ethylene Copolymerization Catalyzed by Allyl ansa-Lanthanidocenes (2017)

The syndioselective copolymerization of styrene with ethylene (in bulk or in aliphatic hydrocarbon solutions, (nBu)2Mg as scavenger, Tpolym = 60–140 °C) was achieved in the presence of a series of ansa-lanthanidocenes of the type {R2C(C5H4)(R′R′Flu)}Ln(1,3-C3H3(SiMe3)2)(THF)x (1-Nd-K-allyl, 2–7-Nd, and 2-Sc,La,Sm,Pr). While precursors based on small ionic radius metals (2-Sc) or bearing bulky substituents in 3,6-positions of the fluorenyl moieties (3-Nd and 5-Nd) were poorly or not active under standard polymerization conditions (60 °C), 2-La,Pr,Nd,Sm which bear 2,7-tBu2 substituents on the Flu ligand produced efficiently sPSE materials (productivity 300–400+ kg mol(Ln)−1 h–1, [r]5 = 71%; controlled amount of ethylene inserted in the range 1–15 mol %). Under harsher conditions (Tpolym = 100–140 °C, [St]0/[Nd]0 = 40 000–147 000 equiv), 2-Nd produced similar sPSE materials with a productivity increased by 1 order of magnitude (up to 5430 kg mol(Nd)−1 h–1). Theoretical DFT investigations including the solvent model, performed on the first three insertion steps for the benchmark catalysts {(Me2C(C5H4)(Flu)}Nd(C3H5)(THF) (I), the putative 1-Nd, and the most effective 2-Nd, allowed to corroborate the nature of the obtained copolymers, with ethylene units randomly distributed within long sPS sequences. These studies established also that the presence of bulky substituents on the fluorenyl ligands is crucial in the activity, but the nature of the substituents on the allyl group has no effect on the chemistry and the nature of the resulting styrene–ethylene copolymer but only influences the initiation step in which the first ethylene insertion will be more or less favored with respect to the styrene insertion.
Object position and orientation tracking for manipulators considering nonnegligible sensor physics (2016)

Real-time object tracking for manipulators has been applied to industrial automation such as assembly and human robot collaboration. During the tracking process, the vision sensor is used as a feedback means to the robot controller. It means that the imperfect sensing and stability issues must be carefully considered. This paper deals with the modeling of sensor physics (e.g. limited sampling rate, irregular sampling time, packet loss, noise, and latency), and realizes a globally asymptotically stable tracking controller. First, an varying rate Kalman filter is applied to estimate the markers' positions and the corresponding error co-variances. Then, a maximum likelihood estimation problem is solved to estimate the transformation between the target frame and the world frame. In addition, a dynamic tracking controller is implemented to realize object tracking. The stability of the tracking controller under model uncertainties is also discussed. The proposed tracking algorithm is experimentally verified on an industrial robot.
Absolute quantum yield for the photochemical activation of methane by excited-state copper atoms in solid methane (1988)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAbsolute quantum yield for the photochemical activation of methane by excited-state copper atoms in solid methaneJ. Mark Parnis and Geoffrey A. OzinCite this: J. Phys. Chem. 1988, 92, 13, 3959–3960Publication Date (Print):June 1, 1988Publication History Published online1 May 2002Published inissue 1 June 1988https://pubs.acs.org/doi/10.1021/j100324a053https://doi.org/10.1021/j100324a053research-articleACS PublicationsRequest reuse permissionsArticle Views60Altmetric-Citations3LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access options Get e-Alerts
Wood Rot Fungi in the Advanced Biofuel Production (2022)

The second-generation biofuel production process is focusing on the utilization of abundant lignocellulose. In this production, the pretreatment step is essential to degrade lignin and modify the chemical structure in raw lignocellulose. Subsequently, polysaccharide content in pre-treated lignocellulose is enzymatically hydrolyzed to monosaccharides in the saccharification step. Finally, these monosaccharides are utilized to produce biofuel in the ethanol fermentation step. White-rot fungi are efficient in 1) degradation of lignin; 2) enzymatic hydrolysis of polysaccharides; 3) ethanol fermentation of monosaccharides. Thus, it is possible to directly produce ethanol from various lignocellulosic substrates using white-rot fungi. The advanced biofuel production is targeting genetic/metabolic engineering to enhance the enzymatic activities of white-rot fungal enzymes that participate in all of pretreatment, saccharification and fermentation, finally resulting in higher efficient conversion from lignocellulose to ethanol. Recently, biofuel production is targeted in butanol fermentation. Among the biofuels, butanol is a high-value compound that is produced by the acetone-butanol-ethanol (ABE) fermentation process using the bacteria Clostridium. However, these bacteria without saccharification are unable to utilize lignocellulosic materials. To implement a reasonable butanol production, it is designed to use the co-culture of white-rot fungus and Clostridium to convert lignocelluloses economically into biofuels. In this co-culture, white-rot fungus plays a role in lignin degradation and saccharification, while Clostridium simultaneously ferments monosaccharides into butanol. To actualize second-generation biofuel production on a large industrial scale in near future, it is still in need of advancement on not only the efficient fermentation process but also suitable characteristics of lignocellulosic materials.
Lifespan decrease in a Caenorhabditis elegans mutant lacking TRX‐1, a thioredoxin expressed in ASJ sensory neurons (2005)

Thioredoxins are a class of small proteins that play a key role in regulating many cellular redox processes. We report here the characterization of the first member of the thioredoxin family in metazoans that is mainly associated with neurons. The Caenorhabditis elegans gene B0228.5 encodes a thioredoxin (TRX-1) that is expressed in ASJ ciliated sensory neurons, and to some extent also in the posterior-most intestinal cells. TRX-1 is active at reducing protein disulfides in the presence of a heterologous thioredoxin reductase. A mutant worm strain carrying a null allele of the trx-1 gene displays a reproducible decrease in both mean and maximum lifespan when compared to wild-type. The identification and characterization of TRX-1 paves the way to use C. elegans as an in vivo model to study the role of thioredoxins in lifespan and nervous system physiology and pathology.
Mechanistic Insights into the Formation of InP Quantum Dots (2009)

Auf Molekülebene wurde der Bildungsmechanismus kolloidaler InP-Quantenpunkte (QDs) mithilfe von NMR-Spektroskopie untersucht. Anders als bei der Bildung von monodispersem PbSe und CdSe werden bei InP-Synthesen üblicherweise die molekularen Phosphorspezies nach der Keimbildung vollständig verbraucht, sodass die QDs ausschließlich durch Reifungsprozesse wachsen. Amine verhindern den Verbrauch der Vorstufen durch Solvatisierung (siehe Bild).
Peritoneal tuberculosis with negative polymerase chain reaction results: report of two cases. (2003)

Peritoneal tuberculosis is rarely observed in European countries. We report on peritoneal tuberculosis in two female immigrants from Somalia and Columbia who presented with diffuse abdominal pain, fever, weight loss and exudative, lymphocytic ascites. Laboratory investigations showed an increase in C-reactive protein and carcinoma antigen 125 serum levels. Nodular peritoneal lesions and adhesions were detected by ultrasound and computed tomography. In both patients, peritoneal biopsy from laparoscopy revealed epitheloid granulomas with central necrosis and multinucleate giant cells. Microscopy and PCR analysis were, however, negative for Mycobacterium tuberculosis in both patients. Despite repeated testing, ascites culture became positive for M. tuberculosis in only one patient. Shortly after starting antituberculous drug treatment, both patients improved, ascitic fluid disappeared and C-reactive protein and carcinoma antigen 125 serum levels returned to normal. Even in Western countries, peritoneal tuberculosis should be considered in any febrile patient with abdominal signs and symptoms, particularly if ascites is present. Empirical antituberculous treatment is justified in patients with clinical and histological features highly suggestive of peritoneal tuberculosis, even in cases with negative results from microscopy, culture and PCR analysis.
Combination of half doses of angiotensin type 1 receptor antagonist and angiotensin-converting enzyme inhibitor in diabetic nephropathy (2005)

In patients with type 2 diabetes and nephropathy, dual blockade of the renin system with an angiotensin-converting enzyme inhibitor and angiotensin receptor blocker significantly reduces albuminuria and, thus, may be renoprotective even when the doses of the agents are reduced by one half.
Designing Co-Creative AI for Virtual Environments (2021)

Co-creative AI tools provide a method of creative collaboration between a user and machine. One form of co-creative AI called generative design requires the user to input design parameters and wait substantial periods of time while the system computes design solutions. We explore this interaction dynamic by providing an embodied experience in VR. Calliope is a virtual reality (VR) system that enables users to explore and manipulate generative design solutions in real time. Calliope accounts for the typical idle times in the generative design process by using a virtual environment to encourage parallelized and embodied data-exploration and synthesis, while maintaining a tight human-in-the-loop collaboration with the underlying algorithms. In this paper we discuss design considerations informed by formative studies with generative designers and artists and provide design guidelines to aid others in the development of co-creative AI systems in virtual environments.
Five Performance Enhancements for Hybrid Hash Join (1992)

In this paper, we focus on set matching algorithms such as intersection, difference, union, and relational join, using join as a representative for all these matching problems. We discuss five performance enhancements for hybrid hash join algorithms, namely data compression, large cluster sizes and multi-level recursion, role reversal of build and probe inputs, histogram methods to exploit non-uniform data and hash value distributions (skew), and join algorithms for multiple inputs. While each of the enhancements is fairly simple, the most surprising result is that hash value skew can be exploited and improve performance rather than being a danger to hybrid hash join performance as conventionally thought. Our design for hash-based N-way matching algorithms is a dual to pipelining data without intermediate sorting between multiple merge-joins on the same attribute (interesting orderings), and exceeds its performance advantages. Each of the performance enhancements can be used by itself or they can be combined with each other as well as with parallel query execution techniques. The cumulative effect of the optimizations is that hybrid hash join will almost always be the set matching algorithm of choice, even in situations for which earlier research had recommended sorting and merge-join. DATABASE QUERY PROCESSING, SET MATCHING, HYBRID HASH JOIN, TUNING, DATA COMPRESSION, I/O SPEED, FAN-OUT, RECURSION DEPTH, ROLE REVERSAL, NON-UNIFORMITY, HISTOGRAMS, INTERESTING ORDERINGS, N-WAY PARTITIONING,