gebhart/patrepeval huggingface dataset:
Next-generation polymeric photonic devices (1997)

A versatile polymeric waveguide technology is proposed for low-cost high-performance photonic devices that address the needs of both the telecom and the datacom industries. We have developed advanced organic polymeric materials that can be readily made into both multimode and single-mode optical waveguide structures of controlled numerical aperture (NA) and geometry. These materials are formed from highly-crosslinked acrylate monomers with specific linkages that determine properties such as flexibility, toughness, loss, and stability with temperature and humidity. These monomers are intermiscible, providing for precise adjustment of the refractive index from 1.3 to 1.6. Waveguides are formed photolithographically, with the liquid monomer mixture polymerizing upon illumination in the UV via either mask exposure or laser direct-writing. A wide range of rigid and flexible substrates can be used, including glass, quartz, oxidized silicon, glassfilled epoxy printed circuit board substrate, and flexible polyimide film. We discuss the use of these materials on chips, on multi-chip modules (MCM’s), on boards, and on backplanes. Light coupling from and to chips is achieved by cutting 45&deg; mirrors using Excimer laser ablation. Fabrication of the planar polymeric structures directly on the modules provides for stability, ruggedness, and hermeticity in packaging.
Modeling Passive Safety in the Westinghouse Small Modular Reactor: Assessment of Wall Condensation and CMT Natural Circulation (2013)

Passive safety design that utilizes gravity, natural circulation, heat sink and stored potential energy for reactor safety functions is being increasingly adopted in advanced reactors, especially in the small modular reactor (SMR) designs. The passive safety design of the Westinghouse SMR is described in details and compared with the AP1000® passive safety design. The natural circulation loops and heat transfer mechanism in a postulated Westinghouse SMR loss of coolant accident (LOCA) are discussed. The key thermal hydraulic phenomena pertinent to the passive safety design of the Westinghouse SMR have been identified in the small break LOCA Phenomena Identification and Rank Table (PIRT). Among the identified phenomena, condensation on the containment wall and natural circulation in core makeup tank (CMT) loop are highly ranked. Those passive safety phenomena are expected to be assessed using the WCOBRA/TRAC-TF2 LOCA thermal hydraulic code, which will provide the design basis LOCA analysis in the SMR design control documentation. In this paper, the progress on the assessing two key phenomena in passive safety of Westinghouse SMR is reported. The preliminary assessments against UCB tube condensation tests and Westinghouse core makeup tank tests reveals the capability of WCOBRA/TRAC-TF2 code to reasonably predict the condensation on the containment wall and natural circulation in the core makeup tank (CMT) loop.
Toll‐like receptor 9 binds single‐stranded CpG‐DNA in a sequence‐ and pH‐dependent manner (2004)

Abstract Toll‐like receptors (TLR) recognize bacterial and viral components, but direct interaction of receptor and ligand is unclear. Here, we demonstrate that TLR9 binds directly and sequence‐specifically to single‐stranded unmethylated CpG‐DNA containing a phosphodiester backbone. TLR9‐CpG‐DNA interaction occurs at the acidic pH (6.5–5.0) found in endosomes and lysosomes. By sequence comparison we identified a potential CpG‐DNA binding domain homologous to that described for methyl‐CpG‐DNA binding proteins. Amino acid substitutions in this region abrogated CpG‐DNA binding and led to loss of NF‐κB activation. Furthermore, chloroquine and quinacrine, therapeutic agents for autoimmune diseases like rheumatoid arthritis and systemic lupus erythematosus, directly blocked TLR9‐CpG‐DNA interaction but not TLR2‐Pam3Cys binding. Our results demonstrate direct binding of TLR9 to CpG‐DNA and suggest that the therapeutic activity of chloroquine and quinacrine in autoimmune diseases may be due to its activity as a TLR9 antagonist and inhibitor of endosomal acidification.
Leveraging virtualization to optimize high-availability system configurations (2008)

Leveraging redundant resources is a common means of addressing availability requirements, but it often implies redundant costs as well. At the same time, virtualization technologies promise cost reduction through resource consolidation. Virtualization and high-availability (HA) technologies can be combined to optimize availability while minimizing costs, but merging them properly introduces new challenges. This paper looks at how virtualization technologies and techniques can augment and amplify traditional HA approaches while avoiding potential pitfalls. Special attention is paid to applying HA configurations (such as active/active and active/passive) to virtualized environments, stretching virtual environments across physical machine boundaries, resource-sharing approaches, field experiences, and avoiding potential hazards.
Genome-Wide Association Study on Plasma Levels of Midregional-Proadrenomedullin and C-Terminal-Pro-Endothelin-1 (2013)

Endothelin-1 (ET-1) and adrenomedullin (ADM) are circulating vasoactive peptides involved in vascular homeostasis and endothelial function. Elevated levels of plasma ET-1 and ADM, and their biologically stable surrogates, C-terminal-pro-endothelin-1 (CT-pro-ET-1) and midregional proadrenomedullin (MR-pro-ADM), are predictors of cardiac death and heart failure. We studied the association of common genetic variation with MR-pro-ADM and CT-pro-ET-1 by genome-wide association analyses in 3444 participants of European ancestry. We performed follow-up genotyping of single nucleotide polymorphisms (SNPs) that showed suggestive or significant association in the discovery stage in additional 3230 participants. The minor variants in KLKB1 (rs4253238) and F12 (rs2731672), both part of the kallikrein-kinin system, were associated with higher MR-pro-ADM (P=4.46E-52 and P=5.90E-24, respectively) and higher CT-pro-ET-1 levels (P=1.23E-122 and P=1.26E-67, respectively). Epistasis analyses showed a significant interaction between the sentinel SNP of F12 and KLKB1 for both traits. In addition, a variant near the ADM gene (rs2957692) was associated with MR-pro-ADM (P=1.05E-12) and a variant in EDN-1 (rs5370) was associated with CT-pro-ET-1 (P=1.49E-27). The total phenotypic variation explained by the genetic variants was 7.2% for MR-pro-ADM and 14.6% for CT-pro-ET-1. KLKB1 encodes plasma kallikrein, a proteolytic enzyme known to cleave high-molecular-weight kininogen to bradykinin and prorenin to renin. We cloned the precursors of ADM and ET-1 and demonstrated that purified plasma kallikrein can cleave these recombinant proteins into multiple smaller peptides. The discovery of genetic variants in the kallikrein-kinin system and in the genes encoding pre-pro-ET-1 and pre-pro-ADM provides novel insights into the (co-)regulation of these vasoactive peptides in the vascular system.
Attribution of genetic engineering: A practical and accurate machine-learning toolkit for biosecurity (2020)

Abstract The promise of biotechnology is tempered by its potential for accidental or deliberate misuse. Reliably identifying telltale signatures characteristic to different genetic designers, termed genetic engineering attribution , would deter misuse, yet is still considered unsolved. Here, we show that recurrent neural networks trained on DNA motifs and basic phenotype can reach 70% attribution accuracy distinguishing between over 1,300 labs. To make these models usable in practice, we introduce a framework for weighing predictions against other investigative evidence using calibration, and bring our model to within 1.6% of perfect calibration. Additionally, we demonstrate that simple models can accurately predict both the nation-state-of-origin and ancestor labs, forming the foundation of an integrated attribution toolkit which should promote responsible innovation and international security alike.
Leptospiral extracellular matrix adhesins as mediators of pathogen-host interactions (2013)

Leptospirosis is been considered an important infectious disease that affects humans and animals worldwide. This review summarizes our current knowledge of bacterial attachment to extracellular matrix (ECM) components and discusses the possible role of these interactions for leptospiral pathogenesis. Leptospiral proteins show different binding specificity for ECM molecules: some are exclusive laminin-binding proteins (Lsa24/LfhA/LenA, Lsa27), while others have broader spectrum binding profiles (LigB, Lsa21, LipL53). These proteins may play a primary role in the colonization of host tissues. Moreover, there are multifunctional proteins that exhibit binding activities toward a number of target proteins including plasminogen/plasmin and regulators of the complement system, and as such, might also act in bacterial dissemination and immune evasion processes. Many ECM-interacting proteins are recognized by human leptospirosis serum samples indicating their expression during infection. This compilation of data should enhance our understanding of the molecular mechanisms of leptospiral pathogenesis.
PAX6-positive microglia evolve locally in hiPSC-derived ocular organoids (2022)

Microglia are the resident immune cells of the central nervous system (CNS). They govern the immunogenicity of the retina, which is considered to be part of the CNS; however, it is not known how microglia develop in the eye. Here, we studied human-induced pluripotent stem cells (hiPSCs) that had been expanded into a self-formed ectodermal autonomous multi-zone (SEAM) of cells that partially mimics human eye development. Our results indicated that microglia-like cells, which have characteristics of yolk-sac-like linage cells, naturally develop in 2D eye-like SEAM organoids, which lack any vascular components. These cells are unique in that they are paired box protein 6 (PAX6)-positive, yet they possess some characteristics of mesoderm. Collectively, the data support the notion of the existence of an isolated, locally developing immune system in the eye, which is independent of the body's vasculature and general immune system.
Sliding-frequency figure-eight optical fibrelaser (1995)

Operation of an optical fibre solitary pulse laser with control elements in both time and frequency domains is demonstrated. The laser combines the advantages of both sliding-frequency and fast saturable absorber action to provide a tunable picosecond optical fibre laser with a relatively low self-starting threshold.
Localized Surface Plasmons Shed Light on Nanoscale Metal Hydrides (2010)

Nanometer-sized hydrides are attractive for hydrogen storage. Nanofabricated model systems can be studied by a novel localized surface plasmon resonance (LSPR) based direct sensing approach and by quartz crystal microbalance. The role of nanoparticle size, shape and microstructure on the storage thermodynamics can be scrutinized. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
REVIEW: ENDOTHIOPEPTIDES ALIAS PEPTIDE THIOAMIDES (1996)

Abstract Modifications of biologically active peptides are often undertaken in order to improve the properties of these peptides for more efficient use in medicine and biochemistry.1 An important class of compounds in this field is the so-called backbone modified peptides or pseudopeptides. These are peptides or peptide-like molecules, which contain one or more non-peptide linkages between the a-amino acids or a-amino acid-like residues. Pseudopeptides are generally written with a ψ followed by the unnatural linkage in a square bracket,1 e.g. Gly-ψ[CSNH]-Gly. Resistance towards enzymatic degradation was an early goal with pseudopeptides, but additionally their altered conformational properties can lead to powerful effects, such as enhanced activity andor selectivity between receptors.
Shape-selective zeolite catalysis for bioplastics production (2015)

Biodegradable and renewable polymers, such as polylactic acid, are benign alternatives for petrochemical-based plastics. Current production of polylactic acid via its key building block lactide, the cyclic dimer of lactic acid, is inefficient in terms of energy, time, and feedstock use. We present a direct zeolite-based catalytic process, which converts lactic acid into lactide. The shape-selective properties of zeolites are essential to attain record lactide yields, outperforming those of the current multistep process by avoiding both racemization and side-product formation. The highly productive process is strengthened by facile recovery and practical reactivation of the catalyst, which remains structurally fit during at least six consecutive reactions, and by the ease of solvent and side-product recycling.
Complex network prediction using deep learning (2021)

Systematic relations between multiple objects that occur in various fields can be represented as networks. Real-world networks typically exhibit complex topologies whose structural properties are key factors in characterizing and further exploring the networks themselves. Uncertainty, modelling procedures and measurement difficulties raise often insurmountable challenges in fully characterizing most of the known real-world networks; hence, the necessity to predict their unknown elements from the limited data currently available in order to estimate possible future relations and/or to unveil unmeasurable relations. In this work, we propose a deep learning approach to this problem based on Graph Convolutional Networks for predicting networks while preserving their original structural properties. The study reveals that this method can preserve scale-free and small-world properties of complex networks when predicting their unknown parts, a feature lacked by the up-to-date conventional methods. An external validation realized by testing the approach on biological networks confirms the results, initially obtained on artificial data. Moreover, this process provides new insights into the retainability of network structure properties in network prediction. We anticipate that our work could inspire similar approaches in other research fields as well, where unknown mechanisms behind complex systems need to be revealed by combining machine-based and experiment-based methods.
Numerical Comparisons of Linear Power Flow Approximations: Optimality, Feasibility, and Computation Time (2022)

Linear approximations of the AC power flow equations are of great significance for the computational efficiency of large-scale optimal power flow (OPF) problems. Put differently, the feasibility of the obtained solution is essential for practical use cases of OPF. However, most studies focus on approximation error and come short of comprehensively studying the AC feasibility of different linear approximations of power flow. This paper discusses the merits of widely-used linear approximations of active power in OPF problems. The advantages and disadvantages of the linearized models are discussed with respect to four criteria; accuracy of the linear approximation, optimality, feasibility, and computation time. Each method is tested on five different systems.
Enhanced frequency response in buried ridge quantum well intermixed SGDBR laser modulators (2004)

We have studied the effects of various proton implant profiles on the performance of buried-ridge-stripe electro-absorption modulators monolithically integrated with SG-DBR lasers. Two implant profiles weie performed adjacent to the buried ridge, enhancing the bandwidth. 0 2003 Optic,d Society of Amenca
Photoinduced Processes of Supramolecular Nanoarrays Composed of Porphyrin and Benzo[ghi]perylenetriimide Units through Triple Hydrogen Bonds with One‐Dimensional Columnar Phases (2016)

One-dimensional supramolecular columnar phases composed of porphyrins (electron donor: D) and benzo[ghi]perylenetriimides (electron acceptor: A) through triple hydrogen bonds have been successfully constructed to perform sequential light-harvesting and electron-transfer processes. A series of benzo[ghi]peryleneimide derivatives have been synthesized to examine the substituent effects such as imide and nitrile groups on the spectroscopic and electrochemical properties. Then, formation of the 1:1 supramolecular complex between zinc porphyrin and benzo[ghi]perylenetriimide derivatives through triple hydrogen bonds was confirmed by Job's plot of (1) H NMR titration. Next, the one-dimensional supramolecular nanoarrays were successfully prepared in a mixed solvent. X-ray diffraction (XRD) measurement suggested that these nanoarrays contained one-dimensional columnar phases composed of stacked donor and acceptor layers. Finally, femtosecond transient absorption and electron spin resonance (ESR) measurements clearly indicated that photoinduced electron transfer occurred via the singlet excited states in the supramolecular columns.
Extracellular magnesium and potassium concentrations interact to modulate tone and reactivity of isolated canine cerebral vascular muscle. (1990)

In vitro studies were undertaken to investigate the effects of external potassium [K+]o, 0-7.1 mM, and magnesium [Mg2+]o, 0-4.8 mM, concentration on canine middle cerebral and basilar arterial basal tone and on 5-hydroxytryptamine (5-HT)-induced contractions. The lower the [K+]o, the greater the degree of spontaneous contraction upon acute withdrawal of [Mg2+]o. An inverse linear relationship between the concentration of [K+]o and the degree of cerebrovasospasm upon acute withdrawal of [Mg2+]o was observed over the range of 1-6 mM [K+]o. As [K+]o was increased, stepwise, the slow phase of the contractions became attenuated, while the magnitude of the fast phase became progressively smaller. Acute withdrawal of [K+]o produced contraction of middle cerebral and basilar arteries which could be modulated by the concentration of [Mg2+]o. The higher the [Mg2+]o, the less the tension developed upon acute withdrawal of [K+]o. Contractility to 5-HT was depressed when [K+]o was lowered. This attenuation was reversed completely when [Mg2+]o was acutely withdrawn. Sensitivity (EC50) of canine middle cerebral and basilar arteries to 5-HT was inversely related to the [K+]o/[Mg2+]o ratio. These actions took place over pathophysiological ranges of [K+]o and [Mg2+]o. Maintenance of a constant [K+]o/[Mg2+]o ratio, irrespective of the exact [K+]o and [Mg2+]o, produced similar degrees of maximum tension and sensitivity (EC50) to 5-HT. Use of intact ring preparations and helically cut vascular strips produced similar results with varying [K+]o/[Mg2+]o. A variety of pharmacological receptor antagonists (phentolamine, propranolol, atropine, diphenhydramine, cimetidine), as well as a prostaglandin cyclo-oxygenase inhibitor, did not modify the altered contractile responses or basal tone evoked by varying the [K+]o/[Mg2+]o ratios. These experiments suggest: (1) that basal tone and contractility of canine cerebral vascular smooth muscle cells appear to be exquisitely sensitive to alterations in extracellular K+ and Mg2+ and (2) that 5-HT receptor-operated Ca2+ channels, as well as those Ca2+ channels involved in the generation of cerebral arterial basal tone, are modulated and controlled by the precise concentrations of [K+]o and [Mg2+]o.
An Immune Response Network Associated with Blood Lipid Levels (2010)

While recent scans for genetic variation associated with human disease have been immensely successful in uncovering large numbers of loci, far fewer studies have focused on the underlying pathways of disease pathogenesis. Many loci which are associated with disease and complex phenotypes map to non-coding, regulatory regions of the genome, indicating that modulation of gene transcription plays a key role. Thus, this study generated genome-wide profiles of both genetic and transcriptional variation from the total blood extracts of over 500 randomly-selected, unrelated individuals. Using measurements of blood lipids, key players in the progression of atherosclerosis, three levels of biological information are integrated in order to investigate the interactions between circulating leukocytes and proximal lipid compounds. Pair-wise correlations between gene expression and lipid concentration indicate a prominent role for basophil granulocytes and mast cells, cell types central to powerful allergic and inflammatory responses. Network analysis of gene co-expression showed that the top associations function as part of a single, previously unknown gene module, the Lipid Leukocyte (LL) module. This module replicated in T cells from an independent cohort while also displaying potential tissue specificity. Further, genetic variation driving LL module expression included the single nucleotide polymorphism (SNP) most strongly associated with serum immunoglobulin E (IgE) levels, a key antibody in allergy. Structural Equation Modeling (SEM) indicated that LL module is at least partially reactive to blood lipid levels. Taken together, this study uncovers a gene network linking blood lipids and circulating cell types and offers insight into the hypothesis that the inflammatory response plays a prominent role in metabolism and the potential control of atherogenesis.
Design and Implementation of Time-Sensitive Wireless IoT Networks on Software-Defined Radio (2020)

Time-sensitive wireless networks are an important enabling building block for many emerging industrial Internet of Things (IoT) applications. Quick prototyping and evaluation of time-sensitive wireless technologies are desirable for R&amp;D efforts. Software-defined radio (SDR), by allowing wireless signal processing on a personal computer (PC), has been widely used for such quick prototyping efforts. Unfortunately, because of the \textit{uncontrollable delay} between the PC and the radio board, SDR is generally deemed not suitable for time-sensitive wireless applications that demand communication with low and deterministic latency. For a rigorous evaluation of its suitability for industrial IoT applications, this paper conducts a quantitative investigation of the synchronization accuracy and end-to-end latency achievable by an SDR wireless system. To this end, we designed and implemented a time-slotted wireless system on the Universal Software Radio Peripheral (USRP) SDR platform. We developed a time synchronization mechanism to maintain synchrony among nodes in the system. To reduce the delays and delay jitters between the USRP board and its PC, we devised a {\textit{Just-in-time}} algorithm to ensure that packets sent by the PC to the USRP can reach the USRP just before the time slots they are to be transmitted. Our experiments demonstrate that $90\%$ ($100\%$) of the time slots of different nodes can be synchronized and aligned to within $ \pm 0.5$ samples or $ \pm 0.05μs$ ($ \pm 1.5$ samples or $ \pm 0.15μs$), and that the end-to-end packet delivery latency can be down to $3.75ms$. This means that SDR-based solutions can be applied in a range of IIoT applications that require tight synchrony and moderately low latency, e.g., sensor data collection, automated guided vehicle (AGV) control, and Human-Machine-Interaction (HMI).