gebhart/patrepeval huggingface dataset:
Rational Design of Amphiphilic Fluorinated Peptides: Evaluation of Self-Assembly Properties and Hydrogel Formation (2022)

Advanced peptide-based nanomaterials composed of self-assembling peptides (SAPs) gain an emerging interest in pharmaceutical and biomedical applications. The introduction of fluorine into peptides, in fact, offers unique opportunities to tune their biophysical properties and intermolecular interactions. In particular, the degree of fluorination plays a crucial role in peptide engineering as it can be used to control the intensity of fluorine-specific interactions. Here, we designed and explored a series of amphipathic self-assembling peptides by incorporating the fluorinated amino acids (2S)-4-monofluoroethylglycine (MfeGly), (2S)-4,4-difluoroethylglycine (DfeGly) and (2S)-4,4,4-trifluoroethylglycine (TfeGly) as main components. This approach enabled studying the impact of fluorination on secondary structure formation and peptide self-assembly on a structural basis. We show that the interplay between polarity and hydrophobicity, both induced by varying degrees of side chain fluorination, affects peptide folding and leads to the generation of peptide hydrogels composed of fluorinated aliphatic amino acids. Molecular simulations revealed the formation of electrostatically driven intra-chain and inter-chain contact pairs caused by side chain fluorination. Our study provides a systematic report about the distinct features of fluorinated oligomeric peptides with potential applications as peptide-based biomaterials.
Scheduling Inference Workloads on Distributed Edge Clusters with Reinforcement Learning (2023)

Many real-time applications (e.g., Augmented/Virtual Reality, cognitive assistance) rely on Deep Neural Networks (DNNs) to process inference tasks. Edge computing is considered a key infrastructure to deploy such applications, as moving computation close to the data sources enables us to meet stringent latency and throughput requirements. However, the constrained nature of edge networks poses several additional challenges to the management of inference workloads: edge clusters can not provide unlimited processing power to DNN models, and often a trade-off between network and processing time should be considered when it comes to end-to-end delay requirements. In this paper, we focus on the problem of scheduling inference queries on DNN models in edge networks at short timescales (i.e., few milliseconds). By means of simulations, we analyze several policies in the realistic network settings and workloads of a large ISP, highlighting the need for a dynamic scheduling policy that can adapt to network conditions and workloads. We therefore design ASET, a Reinforcement Learning based scheduling algorithm able to adapt its decisions according to the system conditions. Our results show that ASET effectively provides the best performance compared to static policies when scheduling over a distributed pool of edge resources.
<title>Quasi-VBR model for packet video</title> (1990)

The variable bit rate concept has been converted in one of the mean topics in the study of coding algorithms for packet video. These algorithms are strongly dependent on the characteristics of the ATM network. In that sense, a quasi-variable bit rate coding scheme for packet video, based on some modifications of the codec in CCITT Rec.H.261 is presented in this paper. The proposed solution consists in giving the codec the possibility of switching the p value for each case, adequating it to the minimum value, with the condition that the quality of the coded sequence is maintained. After a full description of the introduced modifications, the results of the simulations obtained with the proposed model and several standard sequences will be done.
Substrates and Products of Purified Rat Liver Bilirubin Udp – Glucuronosyltransferase (1986)

To determine whether the isoform of UDP-glucuronosyltransferase which catalyzes the formation of bilirubin monoglucuronide also mediates the formation of bilirubin diglucuronide and other specific sugar conjugates of bilirubin, Wistar rats were treated with clofibrate (300 mg per kg i.p. X 7 days); this resulted in a 200% increase in hepatic transferase specific activity for bilirubin. Proteins from hepatic microsomal fractions were solubilized, and the transferase isoform with activity toward bilirubin was purified by a combination of chromatofocusing, affinity chromatography and hydrophobic chromatography, to apparent homogeneity as judged by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The purified isoform catalyzed the formation of monoglucuronide and diglucuronide (with UDP-glucuronic acid as a cosubstrate), and glucoside and xyloside (with UDP-glucose and UDP-xylose as respective cosubstrates) of bilirubin and glucuronidation of the carcinogen metabolite 4'-hydroxydimethylaminoazobenzene. It also catalyzed the conversion of bilirubin monoglucuronide to diglucuronide (with UDP-glucuronic acid as cosubstrate, pH optimum 7.8), to mixed glucuronide-glucoside conjugate (with UDP-glucose as a cosubstrate) and to unconjugated bilirubin (with UDP as a cosubstrate, pH optimum 5.5). Each transferase activity was copurified at each purification step. Results of enzyme kinetic studies suggest that UDP-glucuronic acid, UDP-glucose and UDP-xylose recognize a common site. Transferase activities toward bilirubin were not detectable in homozygous Gunn rats liver microsomal fractions; in heterozygous Gunn rats, these activities were reduced by 40 to 60%. The results suggest that conjugation of bilirubin with glucuronic acid, glucose or xylose is catalyzed by a single transferase isoform.
Single-Shot Ultrafast Pulse Reconstruction with Deep Learning (2020)

We propose a simple all-in-line single-shot scheme for diagnostics of ultrashort laser pulses. consisting of a multi-mode fiber and a x (2) nonlinear crystal. Complete pulse characterization is done from the measurements using Deep Learning methods.
Direct Dry Cooling System Spreadsheet Model for sCO<sub>2</sub> (2020)

The attached cost and performance spreadsheet model is for a direct dry cooling system, one of four cooling system models developed for use in optimizing indirectly-heated supercritical CO2 (sCO2) power cycles. Running the model requires that the user has REFPROP version 9 or below installed, as well as the Microsoft Excel REFPROP Add-In. Upon opening, use Excel’s Edit Links feature to link to the user’s installed REFPROP.xla or REFPROP.xlam file. For the spreadsheet model compatible with REFPROP version 10 and above, contact Nathan Weiland at nathan.weiland@netl.doe.gov. Technical documentation for the model can be found here: https://www.netl.doe.gov/energy-analysis/details?id=3199.
Foundations of Language (2002)

Abstract This book surveys the last thirty-five years of research in generative linguistics and related fields and offers a new understanding of how language, the brain, and perception intermesh. The book renews the conclusions of early generative linguistics: that language can be a valuable entrée into understanding the human mind and brain. The approach is interdisciplinary. The book proposes that the creativity of language derives from multiple parallel generative systems linked by interface components. This shift in basic architecture allows for a reconception of mental grammar and how it is learned. The book aims to reintegrate linguistics with philosophy of mind, cognitive and developmental psychology, evolutionary biology, neuroscience, and computational linguistics. Among the major topics treated are language processing, the relation of language to perception, the innateness of language, and the evolution of the language capacity, as well as more standard issues in linguistic theory such as the roles of syntax and the lexicon. In addition, this book offers a sophisticated theory of semantics that incorporates insights from philosophy of language, logic and formal semantics, lexical semantics of various stripes, cognitive grammar, psycholinguistic and neurolinguistic approaches, and the author's own conceptual semantics.
Distributed laser Doppler velocimeter (1991)

A monobeam laser Doppler velocimeter that permits continuous recovery of the flow velocity profile along the beam is described. The scheme applies the coherence-multiplexing concept to backscattering Doppler detection. A theoretical analysis of the distributed velocimeter is given, along with a description of an experiment with a superluminescent diode source inserted in an all-fiber-optic scheme. The velocity profile of water flow in a duct is reported. The results confirm the exceptional capabilities offered by this velocimeter in experimental fluid mechanics.
E-Entrepreneurship (2005)

E-business is being heralded as the new economy. However, developments in the area of new online business-to-consumer (B2C) venture creation has been accompanied by varying degrees of success, and it is increasingly recognized that online venture creation does not materialize overnight. E-business development typically follows an evolutionary cycle of initial experimentation with Internet technologies and the transformation of consumer propositions toward the creation of a commercially viable online presence. To enable entrepreneurs to negotiate this new business landscape, Netrepreneur simulates the initial startup phases of e-business creation in the online economy. Through the modeling and electronic simulation of the e-commerce environment, Netrepreneur aims to create a holistic understanding of the entrepreneurial process as well as encourage participants to learn by doing in the simulated virtual world instead of trial and error in the real e-economy. This paper reviews the underpinning entrepreneurial pedagogic requirements for design conceptualization and the integration of the real and virtual business worlds within the Netrepreneur system development. It documents the key factors that academia should consider when designing learning programs and activities for would-be e-entrepreneurs. It is our hope that by showing the background to the development of this product, we will facilitate more of this type of innovation in education.
Expansion and Diversification of thePopulusR2R3-MYB Family of Transcription Factors (2008)

The R2R3-MYB proteins comprise one of the largest families of transcription factors in plants. R2R3-MYB family members regulate plant-specific processes, such as the elaboration of specialized cell types, including xylem, guard cells, trichomes, and root hairs, and the biosynthesis of specialized branches of metabolism, including phenylpropanoid biosynthesis. As such, R2R3-MYB family members are hypothesized to contribute to the emergence of evolutionary innovations that have arisen in specific plant lineages. As a first step in determining the role played by R2R3-MYB family members in the emergence of lineage-specific innovations in the genus Populus, the entire Populus trichocarpa R2R3-MYB family was characterized. The Populus R2R3-MYB complement is much larger than that found in other angiosperms with fully sequenced genomes. Phylogenetic analyses, together with chromosome placement, showed that the expansion of the Populus R2R3-MYB family was not only attributable to whole genome duplication but also involved selective expansion of specific R2R3-MYB clades. Expansion of the Populus R2R3-MYB family prominently involved members with expression patterns that suggested a role in specific components of Populus life history, including wood formation and reproductive development. An expandable compendium of microarray-based expression data (PopGenExpress) and associated Web-based tools were developed to better enable within- and between-species comparisons of Populus R2R3-MYB gene expression. This resource, which includes intuitive graphic visualization of gene expression data across multiple tissues, organs, and treatments, is freely available to, and expandable by, scientists wishing to better understand the genome biology of Populus, an ecologically dominant and economically important forest tree genus.
A Multicriteria Optimization Approach to the Synthesis of Shale Gas Monetization Supply Chains (2018)

The aim of this chapter is to provide an optimization approach to the design of shale gas monetization networks. Various feedstocks, conversion technologies, and candidate products are simultaneously considered. A superstructure representation is developed to embed alternate configurations and interconnections of the supply chains. A mixed-integer nonlinear programming formulation is devised to synthesize, screen, and select the monetization network. An economic objective function is used subject to safety and environmental constraints. Other constraints include technical, economic, safety, and environmental performance of the monetization technologies and mass balances for the interconnection among the feedstocks, conversion plants, and products while accounting for feedstock availability, plant capacity limitations, and market demands. A case study is solved for the Barnett and Eagle Ford shale formations. Sensitivity analysis is used to assess the impact of several parameters on the optimal solution.
Identification and Designing of the S3 Site of Aqualysin I, a Thermophilic Subtilisin-Related Serine Protease (1999)

Aqualysin I is a bacterial subtilisin-related alkaline serine protease, originating in Thermus aquaticus YT-1. Based on computational analysis, we predicted that two residues, Ser102 and Gly131, form the S3 site of aqualysin I, and we proved that this prediction by site-directed mutagenesis. To alter the P3-specificity of the enzyme, we built a "wall" on the S3 site edge by introducing a bulky side chain at target sites. Six mutant proteins were prepared: S102H, S102K, S102E, G131H, G131K, and G131D. The mutant enzymes were examined with two kinetically typical peptides for aqualysin I, suc-X-Ala-Ala-pNA, where X is Ala or Phe. All mutations reduced the efficiency for the Phe-containing peptide, while they raised the k(cat) values for the Ala-containing peptide. Especially, the S102K mutant protein hydrolyzed the polyalanine peptide efficiently. The strategies we have adopted in this paper are applicable to all subtilisin-related enzymes.
HAWAII: a domain-based approach for supporting mobility in wide-area wireless networks (2002)

Mobile IP is the current standard for supporting macromobility of mobile hosts. However, in the case of micromobility support, there are several competing proposals. We present the design, implementation and performance evaluation of HAWAII (handoff-aware wireless access Internet infrastructure), a domain-based approach for supporting mobility. HAWAII uses specialized path setup schemes which install host-based forwarding entries in specific routers to support intra-domain micromobility. These path setup schemes deliver excellent performance by reducing mobility related disruption to user applications. Also, mobile hosts retain their network address while moving within the domain, simplifying quality-of-service (QoS) support. Furthermore, reliability is achieved through maintaining soft-state forwarding entries for the mobile hosts and leveraging fault detection mechanisms built in existing intra-domain routing protocols. HAWAII defaults to using Mobile IP for macromobility, thus providing a comprehensive solution for mobility support in wide-area wireless networks.
Regulation of SIRT3 signal related metabolic reprogramming in gastric cancer byHelicobacter pylorioncoprotein CagA (2017)

Injection of the <i>Helicobacter pylori</i> cytotoxin-associated gene A (CagA) is closely associated with the development of chronic gastritis and gastric cancer. Individuals infected with <i>H. pylori</i> possessing the CagA protein produce more reactive oxygen species (ROS) and show an increased risk of developing gastric cancer. Sirtuins (SIRTs) are nicotinamide adenine dinucleotide (NAD<sup>+</sup>)-dependent deacetylases and mitochondrial SIRT3 is known to be a tumor suppressor via its ability to suppress ROS and hypoxia inducible factor 1α (HIF-1α). However, it is unclear whether increased ROS production by <i>H. pylori</i> is regulated by SIRT3 followed by HIF-1α regulation and whether intracellular CagA acts as a regulator thereof. In this study, we investigated correlations among SIRT3, ROS, and HIF-1α in <i>H. pylori</i>-infected gastric epithelial cells. We observed that SIRT3-deficient AGS cells induce HIF-1α protein stabilization and augmented transcriptional activity under hypoxic conditions. In CagA <sup><i>+</i></sup><i>H. pylori</i> infected cells, CagA protein localized to mitochondria where it subsequently suppressed SIRT3 proteins. CagA <sup><i>+</i></sup><i>H. pylori</i> infection also increased HIF-1α activity through the ROS production induced by the downregulated SIRT3 activity, which is similar to the hypoxic condition in gastric epithelial cells. In contrast, overexpression of SIRT3 inhibited the HIF-1α protein stabilization and attenuated the increase in HIF-1α transcriptional activity under hypoxic conditions. Moreover, CagA <sup><i>+</i></sup><i>H. pylori</i> attenuated HIF-1α stability and decreased transcriptional activity in SIRT3-overexpressing gastric epithelial cells. Taken together, these findings provide valuable insights into the potential role of SIRT3 in CagA <sup><i>+</i></sup><i>H. pylori</i>-mediated gastric carcinogenesis and a possible target for cancer prevention via inhibition of HIF-1α.
THE IMPACT OF ANALOGUE AND BANG-BANG STEERING GEAR CONTROL ON SHIP'S FUEL ECONOMY (1982)

This paper presents a comprehensive survey of steering gear principles commonly used, inlcuding relevant details of three analogue steering gear servo principles, which have shown better performance than conventional designs. Control system performance is evaluated from direct measurements of speed and fuel consumption, and results from several ships are given. The analysis should be of value to ship owners and steering gear manufacturers in the design of safe and economic rudder control systems.
Jewish Bridges: East to West (1996)

Illustrations Preface Acknowledgments The Eastern Setting Pressures on Eastern European Jewry The Migration of Ideas The Fur Business Cloth and Clothing The Music Makers From Badkhen to Hollywood Images of the Ghetto Glossary Selected Bibliography Index
Inhibition of endotoxin or lipid A-induced tumor necrosis factor production by synthetic lipid A partial structures in human peripheral blood mononuclear cells. (1992)

Most of the toxic reactions during Gram-negative infections are mediated by inflammatory cytokines induced by endotoxin, also termed lipopolysaccharide (LPS). To evaluate the possibility of synthetic derivatives of LPS to antagonize endotoxin-mediated activities, we have examined the effect of synthetic lipid A partial structures, precursor Ia (compound 406 or LA-14-PP) and lipid X (compound 401) on in vitro LPS or lipid A-induced release of tumor necrosis factor (TNF) by human peripheral blood mononuclear cells. In agreement with previous reports it was shown that LPS of Salmonella abortus equi and synthetic Escherichia coli-type lipid A (compound 506 or LA-15-PP) have potent TNF-inducing capacity. The maximum release of TNF was found after stimulation with 1 to 10 ng/ml of LPS or 10 to 1000 ng/ml of lipid A. Synthetic precursor Ia and lipid X failed to induce TNF release, but could inhibit LPS or lipid A-induced TNF release in a dose-dependent manner. Inhibition was not due to a shift of the kinetic of cytokine release, and was observed in the early stage of TNF production. Moreover, we found that the synergistic effect of interferon-gamma with LPS in induction of TNF release could also be counteracted by the addition of synthetic precursor Ia. The observation that precursor Ia failed to inhibit the induction of TNF by Bacillus Calmette-Guérin, Staphylococcus aureus cowan I or lipopeptide indicated that specific mechanisms are involved in suppression by lipid A partial structures on LPS-induced cytokine production.(ABSTRACT TRUNCATED AT 250 WORDS)
Extraction and high-throughput sequencing of oak heartwood DNA: Assessing the feasibility of genome-wide DNA methylation profiling (2021)

Tree ring features are affected by environmental factors and therefore are the basis for dendrochronological studies to reconstruct past environmental conditions. Oak wood often provides the data for these studies because of the durability of oak heartwood and hence the availability of samples spanning long time periods of the distant past. Wood formation is regulated in part by epigenetic mechanisms such as DNA methylation. Studies of the methylation state of DNA preserved in oak heartwood thus could identify epigenetic tree ring features informing on past environmental conditions. In this study, we aimed to establish protocols for the extraction of DNA, the high-throughput sequencing of whole-genome DNA libraries (WGS) and the profiling of DNA methylation by whole-genome bisulfite sequencing (WGBS) for oak (Quercus robur) heartwood drill cores taken from the trunks of living standing trees spanning the AD 1776-2014 time period. Heartwood contains little DNA, and large amounts of phenolic compounds known to hinder the preparation of high-throughput sequencing libraries. Whole-genome and DNA methylome library preparation and sequencing consistently failed for oak heartwood samples more than 100 and 50 years of age, respectively. DNA fragmentation increased with sample age and was exacerbated by the additional bisulfite treatment step during methylome library preparation. Relative coverage of the non-repetitive portion of the oak genome was sparse. These results suggest that quantitative methylome studies of oak hardwood will likely be limited to relatively recent samples and will require a high sequencing depth to achieve sufficient genome coverage.
Electrophysiological properties of neuroendocrine cells of the intact rat pars intermedia: multiple calcium currents (1990)

Intracellular recordings for current and voltage clamping were obtained from 130 neuroendocrine cells of the pars intermedia (PI) in intact pituitaries maintained in vitro. Spontaneous and evoked action potentials were blocked by TTX or by intracellular injection of a local anesthetic, QX-222. After potassium (K+) currents were blocked by tetraethylammonium (TEA), 4-aminopyridine, and intracellular cesium (Cs+), 2 distinct calcium (Ca2+) spikes were observed which were differentiated by characteristic thresholds, durations, and amplitudes. Both Ca2+ spikes were blocked by cobalt (Co2+) but were unaffected by TTX or QX-222. The low-threshold spike (LTS) had a smaller amplitude and inactivated when membrane potential was depolarized past -40 mV or when evoked at a fast rate (greater than 0.5 Hz). The high-threshold spike (HTS) typically had a larger amplitude and longer duration, was not inactivated at potentials which inactivated the LTS, and could be evoked at rates of up to 10 Hz. Single-electrode voltage-clamp analysis revealed that 3 distinct components of the Ca2+ current were present in most cells. From a negative holding potential (-90 mV), 2 separate peak inward currents were observed; a low-threshold transient current, similar to a T-type Ca2+ current, activated at -40 mV, whereas a large-amplitude inactivating current activated above -20 mV. This large inactivating Ca2+ current was significantly inactivated at a holding potential of -40 mV or by brief prepulses to positive potentials, and was similar to an N-type Ca2+ current. A sustained Ca2+ current (L-type) was observed which was not altered by different holding potentials.(ABSTRACT TRUNCATED AT 250 WORDS)