gebhart/patrepeval huggingface dataset:
Reference transcriptome data in silkworm <i>Bombyx mori</i> (2019)

Abstract Background The silkworm Bombyx mori is a lepidopteran model insect with biological and industrial importance. Its high-quality genome sequence has recently become available and the utilization of this information in combination with extensive transcriptomic analyses is expected to provide an elaborate gene model. It will also be possible to clarify gene expression in detail using this approach. Results We herein performed RNA-seq analysis of ten major tissues/subparts of silkworm larvae. Sequences were mapped onto the reference genome assembly and reference transcriptome data was successfully constructed. The reference data provided a nearly complete sequence for sericin - 1 , a major silk gene with a complex structure. We also markedly improved the gene model for other genes. Transcriptomic expression was investigated in each tissue and a number of transcripts were identified that were exclusively expressed in tissues such as the testis. Transcripts strongly expressed in the midgut formed tight genomic clusters, suggesting that they originated from tandem gene duplication. Transcriptional factor genes expressed in specific tissues or the silk gland subparts were also identified. Conclusions We successfully constructed reference transcriptome data in the silkworm and found that a number of transcripts showed unique expression profiles. These results will facilitate basic studies on the silkworm and accelerate its applications, which will contribute to further advances in lepidopteran and entomological research and the practical use of these insects.
Anti-inflammatory Potential of Saponins from <i>Aster tataricus</i> via NF-κB/MAPK Activation (2019)

Four new aster saponins (1-4) together with five known analogues (5-9) were isolated from Aster tataricus. The chemical structures of 1-4 were elucidated based on spectrometric and spectroscopic analysis and comparison with reported data. The potential anti-inflammatory activities of aster saponins 1-9 were evaluated subsequently by measuring lipopolysaccharide (LPS)-enhanced nitric oxide (NO) formation in murine macrophages. Among these, aster saponin B (6) exhibited the most potent inhibitory activity (IC<sub>50</sub>: 1.2 μM). Additionally, inducible nitric oxide synthase (iNOS) and cyclooxygenase-2 (COX-2) protein levels were dose-dependently suppressed by 6 in LPS-activated RAW 264.7 cells. Investigation of the anti-inflammatory mechanism indicated that 6 attenuated the phosphorylation and degradation of the inhibitor of NF-κB (IκB), which led to the blocking of NF-κB p65 translocation to the nucleus.
Monte Carlo POMDPs (1999)

We present a Monte Carlo algorithm for learning to act in partially observable Markov decision processes (POMDPs) with real-valued state and action spaces. Our approach uses importance sampling for representing beliefs, and Monte Carlo approximation for belief propagation. A reinforcement learning algorithm, value iteration, is employed to learn value functions over belief states. Finally, a sample-based version of nearest neighbor is used to generalize across states. Initial empirical results suggest that our approach works well in practical applications.
Embolic Cerebral Infarction Caused by Intraluminal Thrombus in the Carotid Siphon Successfully Treated With Combination of Anticoagulant and Antiplatelet Drugs (2005)

A 54-year-old-man experienced serial ischemic embolic strokes and retinal artery embolism in the left carotid territory. In the acute phase, intraluminal thrombus in the left carotid siphon and frequent microembolic signals (MES) in the left middle cerebral artery were detected with magnetic resonance angiography (MRA) and transcranial Doppler (TCD). The patient was initially treated with only heparin for 3 days; however, more than 30 MES per 30 min were still detected. After adding ticlopidine as an antiplatelet therapy, MES were suppressed completely. After starting combination therapy of heparin (later warfarin) and ticlopidine, repeated MRA confirmed resolution of carotid thrombus and ischemic stroke did not recur. For management of intraluminal thrombus in the carotid artery, MES with TCD was useful in evaluating the risk of distal embolism. Combination treatment with anticoagulants and ticlopidine can both resolve the thrombus and prevent distal embolism.
Approaches for Gene Discovery and Defining Novel Protein Interactions and Networks (2004)

Global or selective alterations in gene expression patterns and / or post-translational modifications in protein profiles underlie the genesis of potentially all physiological or pathological processes. Unraveling the complexities of these events requires in-depth analysis of intracellular changes at the molecular level. The present review describes some of the techniques employed to identify novel genes, to determine changes in global gene expression patterns and to evaluate qualitative and quantitative changes at the level of encoded proteins. The successful application of these approaches has revolutionized our knowledge and understanding of many fatal diseases and is also facilitating the development of novel and specific therapeutic modalities for improving treatment.
A Multi-Fidelity Approach to Quantification of Uncertainty in Stability and Control Databases for use in Stochastic Aircraft Simulations (2015)

Stability and control derivatives are of utmost importance in the design of new aircraft. Companies spend millions of dollars trying to certify aircraft that are designed with only basic estimates of these features. This paper outlines a methodology to combine multiple fidelity levels of analysis tools in a stochastic aerodynamic database using surrogate models to represent the aircraft configuration. The vehicle of interest is then simulated through certification maneuvers incorporating a deterministic instance of the database to calculate the probability of meeting the requirements. Deterministic instances of the database are built incorporating a multivariate Gaussian conditioned on previous analysis points necessary for the maneuver. The stochastic database is updated by adding samples found by either minimizing the computational cost for a specified uncertainty or minimizing the uncertainty for a fixed computational cost. This analysis capability is applied to the NASA CRM using a fixed number of trim points to simulate an emergency descent maneuver with a Vortex Lattice Method as the high fidelity information source and conceptual level handbook methods as the low fidelity information source. Output distributions characterized by the mean and variance are generated to estimate the certification probability. This analysis tool provides designers with information on likelihood of certification and the potential to identify areas of the design dominating uncertainty in meeting requirements.
[Perspective of development of vaccine against infectious diseases]. (2011)

It is really expected to develop vaccines which are based on newly developed technologies, since we are facing to various emerging infectious diseases such as new influenza epidemic. Various vaccines for infants or children have been developed to use, but vaccines for adolescent such as human papilloma vaccine, and those for adults such as zoster vaccine have been recently developed in USA and Europe. Vaccines based on new concept such as recombinant vaccine, DNA vaccine, polypeptide vaccine and mucosal vaccine will be on market in near future. Furthermore, development of new adjuvants inducing high immunity but having few side-reaction is urgently needed.
Analytical investigation on polishing pressure distribution by utilizing three-dimensional process simulation (2014)

This paper presents analytical investigation on polishing pressure distribution in Chemical Mechanical Polishing (CMP) process. In general, the polishing pressure is distributed unevenly around a wafer edge. This uneven distribution is essentially due to discontinuous contact of a wafer against a polishing pad. An edge profile of the wafer and nonlinear viscoelastic properties of the polishing pad affect the polishing pressure distribution significantly. The compression by a retainer ring against the polishing pad also has an indirect effect on the polishing pressure distribution. These phenomena are empirically known in industry. In order to quantify the influence of these factors, a series of analytical investigations on the polishing pressure distribution are conducted in the present study. The simulator developed by authors is utilized. Arbitrary Lagrangian-Eulerian (ALE) Finite Element Method (FEM) is employed in dynamic nonlinear analysis. In a series of process simulations, material properties, i.e., Young's modulus, Poisson's ratio and proportional damping factor, of the polishing pad and geometries of the wafer and the retainer ring are changed, respectively. The calculated results indicated that the polishing pressure distribution around the wafer edge varies considerably depending on the parameters.
Temperature-aware dynamic resource provisioning in a power-optimized datacenter (2010)

The current energy and environmental cost trends of datacenters are unsustainable. It is critically important to develop datacenter-wide power and thermal management (PTM) solutions that improve the energy efficiency of the datacenters. This paper describes one such approach where a PTM engine decides on the number and placement of ON servers while simultaneously adjusting the supplied cold air temperature. The goal is to minimize the total power consumption (for both servers and air conditioning units) while meeting an upper bound on the maximum temperature seen in any server chassis in the data center. To achieve this goal, it is important to be able to predict the incoming workload in terms of requests per second (which is done by using a short-term workload forecasting technique) and to have efficient runtime policies for bringing new servers online when the workload is high or shutting them off when the workload is low. Datacenter-wide power saving is thus achieved by a combination of chassis consolidation and efficient cooling. Experimental results demonstrate the effectiveness of the proposed dynamic resource provisioning method. 1
Bombesin Inhibits Growth of Pancreatic Ductal Adenocarcinoma (H2T) in Nude Mice (1994)

Bombesin (BBS), a tetradecapeptide, stimulates growth of various types of cells, including fibroblasts and human small cell lung cancer, and has been termed the universal "on-switch" due to its ability to stimulate the release of numerous hormones. In addition, BBS receptors have been identified in normal and neoplastic pancreatic tissue. A pancreatic ductal adenocarcinoma cell line (H2T), established in our laboratory, possesses specific binding sites for BBS. The purpose of this study was to examine the effect of BBS on the growth of H2T tumors transplanted into athymic nude mice. H2T cells (5 x 10(6) cells/mouse) were injected s.c. into the interscapular region of the nude mice and then the mice were randomized into two groups (n = 10/group). Mice received either 0.1 ml of saline with 0.1% bovine serum albumin (BSA) (control) or 0.1 ml BBS (5 micrograms/kg) intraperitoneally, three times/day. Tumor area was measured twice weekly until the mice were killed (day 32), when tumor and normal pancreas were removed, weighted, and assayed for DNA and protein content. Administration of BBS significantly inhibited H2T tumor area, weight, and DNA and protein content. Conversely, growth of normal pancreas, removed as an in vivo bioassay so as to ensure the efficacy of BBS, was stimulated. We conclude that BBS is a growth inhibitory factor for H2T tumors and that different mechanisms may be responsible for the differential growth effects elicited by normal and neoplastic pancreas in response to BBS.
(Invited) How Does Oxygen Open Up New Horizons at the Interface III-Vs/Liquid Ammonia? (2021)

In acidic pH, after a short period of illumination, a significant increase of the cathodic current in the dark is recorded onto p -GaAs until reaching a stationary current. This “final configuration” of the interface is unique since O 2 reduction mechanism proceeds then only by holes injections. Collapse straight lines of Mott-Schottky are recorded after O 2 reduction. A dissolution of the p -GaAs is observed. As a corrosive reactant, H 2 O 2 can be also suggested in acidic NH 3 Liq.
Visual Markers for Detecting Gene Conversion Directly in the Gametes of Arabidopsis thaliana (2009)

Measuring meiotic gene conversion is important both because of its role in the fundamental mechanisms of meiotic recombination and because of its influence on linkage relationships and allelic diversity in the genome. Historically, gene conversion has been most thoroughly examined in fungal organisms through the use of tetrad analysis. Here we describe a method for using tetrad analysis in the model plant Arabidopsis thaliana to detect and quantify gene conversion events - a resource unavailable in most other higher eukaryotic model systems.
ChemInform Abstract: SYNTHESIS OF C‐NUCLEOSIDES. XVIII. D‐ARABINOFURANOSYL S‐TRIAZOLOPYRIDINES AND D PYRAZINES (1980)

Abstract Kondensation des D‐Arabinofuranosylthioimidates (I) mit den Hydrazinopyridinen (II) und (IV) bzw. dem Hydrazinopyrazin (VI) gibt die C‐a‐Arabinofuranosylnucleoside (IIIa), (Va), (Vb) bzw. (VIIa), die durch Folgereaktionen in die Derivate (IIIb),(Vc)‐(Vg) bzw. (VIIb)‐(VIIe) übergeführt werden (Strukturuntersuchungen).
Supplementary material from "Latch-based control of energy output in spring actuated systems" (2020)

The inherent force-velocity trade-off of muscles and motors can be overcome by instead loading and releasing energy in springs to power extreme movements. A key component of this paradigm is the latch that mediates the release of spring energy to power the motion. Latches have traditionally been considered as switches; they maintain spring compression in one state and allow the spring to release energy without constraint in the other. Using a mathematical model of a simplified contact latch, we reproduce this instantaneous release behaviour and also demonstrate that changing latch parameters (latch release velocity and radius) can reduce and delay the energy released by the spring. We identify a critical threshold between instantaneous and delayed release that depends on the latch, spring, and mass of the system. Systems with stiff springs and small mass can attain a wide range of output performance, including instantaneous behaviour, by changing latch release velocity. We validate this model in both a physical experiment as well as with data from the Dracula ant, <i>Mystrium camillae</i>, and propose that latch release velocity can be used in both engineering and biological systems to control energy output.
Targeting of Primary Breast Cancers and Metastases in a Transgenic Mouse Model Using Rationally Designed Multifunctional SPIONs (2012)

Breast cancer remains one of the most prevalent and lethal malignancies in women. The inability to diagnose small volume metastases early has limited effective treatment of stage 4 breast cancer. Here we report the rational development and use of a multifunctional superparamagnetic iron oxide nanoparticle (SPION) for targeting metastatic breast cancer in a transgenic mouse model and imaging with magnetic resonance (MR). SPIONs coated with a copolymer of chitosan and polyethylene glycol (PEG) were labeled with a fluorescent dye for optical detection and conjugated with a monoclonal antibody against the neu receptor (NP-neu). SPIONs labeled with mouse IgG were used as a nontargeting control (NP-IgG). These SPIONs had desirable physiochemical properties for in vivo applications such as near neutral zeta potential and hydrodynamic size around 40 nm and were highly stable in serum containing medium. Only NP-neu showed high uptake in neu expressing mouse mammary carcinoma (MMC) cells which was reversed by competing free neu antibody, indicating their specificity to the neu antigen. In vivo, NP-neu was able to tag primary breast tumors and significantly, only NP-neu bound to spontaneous liver, lung, and bone marrow metastases in a transgenic mouse model of metastatic breast cancer, highlighting the necessity of targeting for delivery to metastatic disease. The SPIONs provided significant contrast enhancement in MR images of primary breast tumors; thus, they have the potential for MRI detection of micrometastases and provide an excellent platform for further development of an efficient metastatic breast cancer therapy.
Construction of a Transplantable Tissue-Engineered Artificial Peritoneum (2004)

Our artificial peritoneum may be a useful transplantable bioengineered material for repair of surgical peritoneal defects.
Distributed Solution of Large-Scale Linear Systems Via Accelerated Projection-Based Consensus (2018)

Solving a large-scale system of linear equations is a key step at the heart of many algorithms in scientific computing, machine learning, and beyond. When the problem dimension is large, computational and/or memory constraints make it desirable, or even necessary, to perform the task in a distributed fashion. In this paper, we consider a common scenario in which a taskmaster intends to solve a large-scale system of linear equations by distributing subsets of the equations among a number of computing machines/cores. We propose a new algorithm called Accelerated Projection-based Consensus, in which at each iteration every machine updates its solution by adding a scaled version of the projection of an error signal onto the nullspace of its system of equations, and the taskmaster conducts an averaging over the solutions with momentum. The convergence behavior of the proposed algorithm is analyzed in detail and analytically shown to compare favorably with the convergence rate of alternative distributed methods, namely distributed gradient descent, distributed versions of Nesterov's accelerated gradient descent and heavy-ball method, the block Cimmino method, and Alternating Direction Method of Multipliers. On randomly chosen linear systems, as well as on real-world data sets, the proposed method offers significant speed-up relative to all the aforementioned methods. Finally, our analysis suggests a novel variation of the distributed heavy-ball method, which employs a particular distributed preconditioning and achieves the same theoretical convergence rate as that in the proposed consensus-based method.
A Thermal Skin Model for Comparing Contact Skin Temperature Sensors and Assessing Measurement Errors (2021)

To improve the measurement and subsequent use of human skin temperature (<i>T</i><sub>sk</sub>) data, there is a need for practical methods to compare <i>T</i><sub>sk</sub> sensors and to quantify and better understand measurement error. We sought to develop, evaluate, and utilize a skin model with skin-like thermal properties as a tool for benchtop <i>T</i><sub>sk</sub> sensor comparisons and assessments of local temperature disturbance and sensor bias over a range of surface temperatures. Inter-sensor comparisons performed on the model were compared to measurements performed in vivo, where 14 adult males completed an experimental session involving rest and cycling exercise. Three types of <i>T</i><sub>sk</sub> sensors (two of them commercially available and one custom made) were investigated. Skin-model-derived inter-sensor differences were similar (within ±0.4 °C) to the human trial when comparing the two commercial <i>T</i><sub>sk</sub> sensors, but not for the custom <i>T</i><sub>sk</sub> sensor. Using the skin model, all surface <i>T</i><sub>sk</sub> sensors caused a local temperature disturbance with the magnitude and direction dependent upon the sensor and attachment and linearly related to the surface-to-environment temperature gradient. Likewise, surface <i>T</i><sub>sk</sub> sensors also showed bias from both the underlying disturbed surface temperature and that same surface in its otherwise undisturbed state. This work supports the development and use of increasingly realistic benchtop skin models for practical <i>T</i><sub>sk</sub> sensor comparisons and for identifying potential measurement errors, both of which are important for future <i>T</i><sub>sk</sub> sensor design, characterization, correction, and end use.
Rapid and accurate structure‐based therapeutic peptide design using GPU accelerated thermodynamic integration (2018)

Peptide-based therapeutics are an alternative to small molecule drugs as they offer superior specificity, lower toxicity, and easy synthesis. Here we present an approach that leverages the dramatic performance increase afforded by the recent arrival of GPU accelerated thermodynamic integration (TI). GPU TI facilitates very fast, highly accurate binding affinity optimization of peptides against therapeutic targets. We benchmarked TI predictions using published peptide binding optimization studies. Prediction of mutations involving charged side-chains was found to be less accurate than for non-charged, and use of a more complex 3-step TI protocol was found to boost accuracy in these cases. Using the 3-step protocol for non-charged side-chains either had no effect or was detrimental. We use the benchmarked pipeline to optimize a peptide binding to our recently discovered cancer target: EME1. TI calculations predict beneficial mutations using both canonical and non-canonical amino acids. We validate these predictions using fluorescence polarization and confirm that binding affinity is increased. We further demonstrate that this increase translates to a significant reduction in pancreatic cancer cell viability.
Rheological fingerprinting of gastropod pedal mucus and synthetic complex fluids for biomimicking adhesive locomotion (2007)

Nonlinear rheological properties are often relevant in understanding the response of a material to its intended environment. For example, many gastropods crawl on a thin layer of pedal mucus using a technique called adhesive locomotion, in which the gel structure is periodically ruptured and reformed. We present a mechanical model that captures the key features of this process and suggests that the most important properties for optimal inclined locomotion are a large, reversible yield stress, followed by a small shear viscosity and a short thixotropic restructuring time. We present detailed rheological measurements of native pedal mucus in both the linear and nonlinear viscoelastic regimes and compare this "rheological fingerprint" with corresponding observations of two bioinspired slime simulants, a polymer gel and a clay-based colloidal gel, that are selected on the basis of their macroscopic rheological similarities to gastropod mucin gels. Adhesive locomotion (of snails or mechanical crawlers) imposes a large-amplitude pulsatile simple shear flow onto the supporting complex fluid, motivating the characterization of nonlinear rheological properties with large amplitude oscillatory shear (LAOS). We represent our results in the form of Lissajous curves of oscillatory stress against time-varying strain. The native pedal mucus gel is found to exhibit a pronounced strain-stiffening response, which is not imitated by either simulant.
Near field wavefront measurements of semiconductor laser arrays by shearing interferometry (1990)

A reliable technique for measuring near field phase fronts of phased-array semiconductor lasers is proposed and demonstrated. Laterally sheared interferograms are generated in a ring-type interferometer with zero optical path difference between two beams, eliminating problems due to equal optical path requirements in other systems. Fourier transform methods are used to extract phase difference information from the nonuniformly illuminated interferograms, and phase discontinuities between adjacent stripes of carrierguided laser arrays are observed. Test data agree with theoretical predictions and far field interpretations.