gebhart/patrepeval huggingface dataset:
Large-Scale Bi-Level Strain Design Approaches and Mixed-Integer Programming Solution Techniques (2011)

The use of computational models in metabolic engineering has been increasing as more genome-scale metabolic models and computational approaches become available. Various computational approaches have been developed to predict how genetic perturbations affect metabolic behavior at a systems level, and have been successfully used to engineer microbial strains with improved primary or secondary metabolite production. However, identification of metabolic engineering strategies involving a large number of perturbations is currently limited by computational resources due to the size of genome-scale models and the combinatorial nature of the problem. In this study, we present (i) two new bi-level strain design approaches using mixed-integer programming (MIP), and (ii) general solution techniques that improve the performance of MIP-based bi-level approaches. The first approach (SimOptStrain) simultaneously considers gene deletion and non-native reaction addition, while the second approach (BiMOMA) uses minimization of metabolic adjustment to predict knockout behavior in a MIP-based bi-level problem for the first time. Our general MIP solution techniques significantly reduced the CPU times needed to find optimal strategies when applied to an existing strain design approach (OptORF) (e.g., from ∼10 days to ∼5 minutes for metabolic engineering strategies with 4 gene deletions), and identified strategies for producing compounds where previous studies could not (e.g., malate and serine). Additionally, we found novel strategies using SimOptStrain with higher predicted production levels (for succinate and glycerol) than could have been found using an existing approach that considers network additions and deletions in sequential steps rather than simultaneously. Finally, using BiMOMA we found novel strategies involving large numbers of modifications (for pyruvate and glutamate), which sequential search and genetic algorithms were unable to find. The approaches and solution techniques developed here will facilitate the strain design process and extend the scope of its application to metabolic engineering.
Building a Robust Implementation of Bearing‐only Inertial SLAM for a UAV (2007)

Abstract This paper presents the on‐going design and implementation of a robust inertial sensor based simultaneous localization and mapping (SLAM) algorithm for an unmanned aerial vehicle (UAV) using bearing‐only observations. A single color vision camera is used to observe the terrain from which image points corresponding to features in the environment are extracted. The SLAM algorithm estimates the complete six degrees‐of‐freedom motion of the UAV along with the three‐dimensional position of the features in the environment. An extended Kalman filter approach is used where a technique of delayed initialization is performed to initialize the three‐dimensional position of features from bearing‐only observations. Data association is achieved using a multihypothesis innovation gate based on the spatial uncertainty of each feature. Results are presented by running the algorithm off‐line using inertial sensor and vision data collected during a flight test of a UAV. © 2007 Wiley Periodicals, Inc.
Using Control Charts to Monitor Process and Product Quality Profiles (2004)

In most statistical process control (SPC) applications, it is assumed that the quality of a process or product can be adequately represented by the distribution of a univariate quality characteristic or by the general multivariate distribution of a vector consisting of several correlated quality characteristics. In many practical situations, however, the quality of a process or product is better characterized and summarized by a relationship between a response variable and one or more explanatory variables. Thus, at each sampling stage, one observes a collection of data points that can be represented by a curve (or profile). In some calibration applications, the profile can be represented adequately by a simple straight-line model, while in other applications, more complicated models are needed. In this expository paper, we discuss some of the general issues involved in using control charts to monitor such process- and product-quality profiles and review the SPC literature on the topic. We relate this application to functional data analysis and review applications involving linear profiles, nonlinear profiles, and the use of splines and wavelets. We strongly encourage research in profile monitoring and provide some research ideas.
Cartilage delivery and open rhinoplasty as two preferred approaches to the nasal tip. (1986)

There seems to be a great difference of opinion among rhinoplastic surgeons concerning incisions to gain access to the nasal tip. Some state that the method of exposure is of secondary importance. This author firmly believes that many unsatisfactory results could be avoided if adequate surgical exposure were used for nasal tip surgery. Alar cartilage delivery and external approach rhinoplasty are recommended as the only methods for all cases. These methods are described in detail, and in accordance with the author's conviction that all pre- and postoperative photographs should be published to allow proper assessment, these are provided in selected cases.
Single-walled carbon nanotubes shell decorating porous silicate materials: A general platform for studying the interaction of carbon nanotubes with photoactive molecules (2011)

Single-walled carbon nanotubes (SWCNTs) have been deposited onto the external surface of porous silicate materials by deposition from a solution of individualized, protonated SWCNTs in chlorosulfonic acid. It is demonstrated that the deposited SWCNTs can be deprotonated on the silicate surface, yielding a microporous or mesoporous material with individual or small bundles of SWCNTs. These carbon nanotubes present all the spectral characteristics of pristine SWCNTs, including van Hove transitions, Raman and NIR photoluminescence. Furthermore, it is shown that these materials can be used as scaffolds to study the interaction of SWCNTs with photoactive molecules loaded in the cavities of the porous silicate materials. As a proof-of-concept, we showed that the photoluminescence of tris(2,2′-bipyridine)ruthenium(II) can be quenched by protonated SWCNTs in the nearby surface decreasing its lifetime by nearly two orders of magnitude. This represents a novel application for these materials, especially considering the large amount of different molecules that can be immobilized in the internal cavities of these porous silicates.
Abrogation of BRAF<sup>V600E</sup>-induced senescence by PI3K pathway activation contributes to melanomagenesis (2012)

Human melanocytic nevi (moles) are benign lesions harboring activated oncogenes, including BRAF. Although this oncogene initially acts mitogenically, eventually, oncogene-induced senescence (OIS) ensues. Nevi can infrequently progress to melanomas, but the mechanistic relationship with OIS is unclear. We show here that PTEN depletion abrogates BRAF(V600E)-induced senescence in human fibroblasts and melanocytes. Correspondingly, in established murine BRAF(V600E)-driven nevi, acute shRNA-mediated depletion of PTEN prompted tumor progression. Furthermore, genetic analysis of laser-guided microdissected human contiguous nevus-melanoma specimens recurrently revealed identical mutations in BRAF or NRAS in adjacent benign and malignant melanocytes. The PI3K pathway was often activated through either decreased PTEN or increased AKT3 expression in melanomas relative to their adjacent nevi. Pharmacologic PI3K inhibition in melanoma cells suppressed proliferation and induced the senescence-associated tumor suppressor p15(INK4B). This treatment also eliminated subpopulations resistant to targeted BRAF(V600E) inhibition. Our findings suggest that a significant proportion of melanomas arise from nevi. Furthermore, these results demonstrate that PI3K pathway activation serves as a rate-limiting event in this setting, acting at least in part by abrogating OIS. The reactivation of senescence features and elimination of cells refractory to BRAF(V600E) inhibition by PI3K inhibition warrants further investigation into the therapeutic potential of simultaneously targeting these pathways in melanoma.
Variabilidade diária da precipitação em regiões de floresta e pastagem na Amazônia (1998)

As estações automáticas do Projeto ABRACOS instaladas na Amazônia Ocidental forneceram os dados horários de precipitação em áreas de pastagem e floresta, durante o trimestre mais chuvoso (j/f/m) no período de 1992 a 1995. A variabilidade diária de precipitação maior que 1 mm h1 mostrou uma frequência relativa de 6,7% dos casos às 14 horas local (hl) na pastagem e 5,7% às 16 hl na floresta. O período da tarde (13-18 hl) registra acima de 30% dos eventos de precipitação em ambos os sítios. Há uma boa regularidade na distribuição horária dos eventos, principalmente na floresta. Para as precipitações maiores que 10 mm h1, existe uma concentração dos casos no final da tarde. Na pastagem 12,3%, e na floresta 11,5% dos eventos ocorrem às 18 hl. O intervalo entre 7-18 hl detém 64,9% dos casos na pastagem, e 57,7% na floresta. Do total de eventos de precipitação, 14% são maiores que 10 mm h1, tanto na floresta como na pastagem. Comparando-se o total de chuva ocorrido nas áreas de floresta e pastagem, o volume precipitado na floresta é cerca de 28% em média superior ao da pastagem.
Structure, Ion Transport, and Rheology of Nanoparticle Salts (2014)

Above a critical surface chemistry-dependent particle loading associated with nanoscale interparticle spacing, ligand–ligand interactions—both electrostatic and steric—come into play and govern the structure and dynamics of charged oligomer-functionalized nanoparticle suspensions. We report in particular on the structure, ion transport, and rheology of suspensions of nanoparticle salts created by cofunctionalization of silica particles with tethered sulfonate salts and oligomers. Dispersion of the hairy ionic particles into medium and high dielectric constant liquids yields electrolytes with unique structure and transport properties. We find that electrostatic repulsion imparted by ion dissociation can be tuned to control the dispersion state and rheology through counterion size (i.e., Li+, Na+, and K+) and dielectric properties of the dispersing medium. Analysis of small-angle X-ray scattering (SAXS) structure factors and the mechanical modulus shows that when the interparticle spacing approaches nanometer dimensions, weakly entangled anchored ligands experience strong and long-lived topological constraints analogous to those normally found in well-entangled polymeric fluids. This finding provides insight into the molecular origins of the surprisingly similar rubbery plateau moduli observed in hairy nanoparticle suspensions and entangled polymers of the same chemistry as the tethered ligands. Additionally, we find that a time–composition superposition (TCS) principle exists for the suspensions, which can be used to substantially extend the observation time over which dynamics are observed in jammed, soft glassy suspensions. Application of TCS reveals dynamical similarities between the suspensions and entangled solutions of linear polymer chains; i.e., a hairy particle trapped in a cage appears to exhibit analogous dynamics to a long polymer chain confined to a tube.
Dip move out processing (DMO) for converted waves in transversely isotropic media (1996)

Converted waves, which are generated with every explosion shot, offer additional information about shearwave velocities. Shearwaves are especially valuable in the presence of anisotropy. However, the processing of converted waves must account for their nonsymmetric raypaths, which become even more complicated when the reflectors are dipping. In the following, the location of the conversion point along a dipping interface and the moveout will be analyzed. The description of reflection moveout enables to map the data to zero offset and image the reflector. A dip-moveout (DMO) operation, here presented for common-offset-gathers, proves to be a useful tool to map reflectors with help of converted waves, even in the presence of anisotropy.
Creating and Using a Computer Networking and Systems Administration Laboratory Built Under Relaxed Financial Constraints (2011)

The Computer Science Department at Slippery Rock University created a laboratory for its Computer Networks and System Administration and Security courses, under relaxed financial constraints. This paper describes the department's experience designing and using this laboratory, including lessons learned and descriptions of some student projects performed in the lab.
Structural analysis to determine the stress induced loading on Wellhead Housing system supported by CAN and sea bed BOP supporter (2012)

The present work investigates the effect of the bending loads on the wellhead systems and predicts\nthe response of the conductor with the introduction of CAN™ (Conductor Anchor Node) and Seabed\nBOP Supporter.\nPerformance of the wellhead and conductor system is dependent on field design parameters. These\nparameters can include local environmental loading, drilling rig motions, marine riser stack-ups and\nBOP (Blow-out Preventer) configuration and soil conditions. These loads may cause severe\ndamage to the wellhead system. In order to reduce the effect of these loads, the possibility of\nincorporating other components such as the CAN™ and Seabed BOP Supporter can be\nconsidered.\nThe present work aims at introducing the mentioned CAN™ and Seabed BOP Supporter in the\nwellhead system and assessing their influence on the bending moment response of the conductor.\nThis has been analyzed considering different load cases outlined below.\nLoad Case 1: The analysis was carried out considering a conventional drilling mode with a 30”\nwellhead system, drilling riser and a BOP system.\nLoad Case 2: The analysis was performed considering Wellhead system with BOP and drilling riser\nsupported in a CAN™ foundation developed by NeoDrill AS.\nLoad Case 3: The analysis also considers Seabed BOP Support in addition to the CAN™. The\nSeabed BOP Supporter is located in between CAN™ and BOP. The purpose of a Sea bed BOP\nsupporter is to transfer pre-set part of BOP weight directly to CAN™ and to counteract riser induced\nBOP moments on Wellhead.\n3-D FE (Finite Element) model based on PIPE element was established for the mentioned three\nload cases. The analyses have been performed by considering various factors that include internal\naxial casing load, external load from BOP, drilling riser tension, foundation soil support stiffness,\nand the cement level within the annulus of the conductor and surface casing. The shear loads that\noccur when the well is configured for drilling operations are applied at the lower flex joint over a\nrange from -490kN to +490kN.\nThe results from the analysis are discussed against the two criteria established to assess the\nstructural integrity of the wellhead conductor. These criteria are: allowable bending capacity of the\nconductor and limiting flex joint rotation angles. The results show that the introduction of CAN™ and Seabed BOP Supporter influences the\nresponse for bending moment of Wellhead conductor considerably. The results further conclude\nthat the reduction in the bending moment of the conductor is in the order of 25% and 80% due to\nintroduction of CAN™ and Seabed BOP Supporter in the wellhead system, respectively.
Synthesis and characterization of a tin(<scp>iv</scp>) antimonophosphate nano-composite membrane incorporating 1-dodecyl-3-methylimidazolium bromide ionic liquid (2017)

Ionic liquid doped PVC based nanocomposite membranes, with varying crystallinity that affects their physicochemical properties, are prepared and characterized.
Preliminary Design and Analysis of a Lidar Based Obstacle Detection System (2006)

This paper outlines the use of a high-resolution laser range scanner to detect terrain features and obstacles and the development of a test bed for the obstacle and terrain feature detection system. Results from tests conducted at Ohio University and simulations from data collected during flight tests in the vicinity of Braxton County Airport (K481), WV are presented.
Over 2000 V FLR termination technologies for SiC high voltage devices (2002)

The Field Limiting Ring (FLR) termination structures are examined in order to confirm the high voltage technology of SiC diodes and FETs. Elemental devices with planar FLR terminations are fabricated and their reverse I-V characteristics are determined using 4H n-type SiC. First demonstrations of breakdown voltages higher than 2000 V are succeeded by using FLR terminations. Optimal FLR spacing of the boron termination is wider than that of the aluminum case. This difference is considered to show that the lateral diffusion is remarkable for the process using boron implantation.
An Infra-Red Sensitive, Low Noise, Single-Photon Avalanche Diode in 90nm CMOS (2024)

A Single-Photon Avalanche Diode (SPAD) is reported in 90nm CMOS imaging technology with a peak photon detection efficiency (PDE) of ≈44% at 690nm and better than ≈20% at 850nm. This represents an eight-fold improvement in near infrared sensitivity over existing SPAD structures. This result has important implications for optical communications, time-of-flight ranging and optical tomography applications. The 6.4µm active diameter SPAD also achieves low dark count rates of typically around 100Hz with ≈51ps FWHM timing resolution; and a low after-pulsing probability of ≈0.375%. The new SPAD structure employs the junction between deep n-well and the p-substrate rather than being fabricated inside its own well, and is in theory compatible with low-resistivity substrate and thin epi-layer CMOS technology and backside illumination.
Peripheral blood and bone marrow abnormalities in patients with HIV related disease (1987)

Between February 1983 and April 1986 we studied peripheral blood and bone marrow samples from 20 patients with human immunodeficiency virus (HIV) related disease. 14 patients had AIDS, three had ARC, two had PGL and one had ITP as a sole manifestation of HIV related disease. Peripheral blood abnormalities included marked anisocytosis and poikilocytosis, rouleaux formation, neutropenia, lymphopenia, monocytopenia, a left shift in the granulocyte series and, in the patients with AIDS, vacuolated monocytes. The most frequent bone marrow abnormalities were reticuloendothelial iron block, dyserythropoiesis, megaloblastic change and erythroid hypoplasia. Excess histiocytes were noted in four marrows, one exhibiting haemophagocytosis. None of the bone marrows showed lymphopenia. Eight of the 20 marrows were difficult or impossible to aspirate. None of the trephine biopsies showed increased reticulin. The causes of these abnormalities are probably multiple and include opportunistic infections, drug therapy, immune mechanisms and possibly direct insult by the HIV virus.
Compaction and Decompaction Algorithms for Sedimentary Carbonates (1997)

The mechanical compaction behavior of shallow marine carbonate sediments has been investigated to develop carbonate compaction algorithms and decompaction curves that can be used in stratigraphic restoration, backstripping analyses, and quantitative models for simulation of carbonate stratigraphy. Deep-water chalks and calcareous oozes are not treated here. Empirical porosity-depth data for carbonate sediments have been compiled and compared with experimentally derived compaction curves to derive appropriate porosity-depth curves for shallow-water carbonate muds and sands. The curves are exponential in form. This review indicates that mud-rich shallow marine carbonates behave differently than sand-rich, grain-supported sediments with regard to reduction in porosity and thickness. Quantitative analysis of compaction behavior in carbonate sediments reveals that, barring early cementation, carbonate muds suffer significant thickness reduction early in their burial history and at shallow depths, e.g., 50% thickness reduction with about 150-200 m overburden. However, primary porosities of carbonate muds, approximately 70-80%, are reduced only to about 42% under that overburden. Thus, the potential exists for significant retention of primary porosity in carbonate muds in the form of microporosity. This indicates that interparticle cementation, with or without chemical compaction, is required to transform muddy carbonate sediments into lithified rock. In the absence of early lithification, carbonate sands compact more slowly than muds. Primary interparticle porosities of about 40-45% can be maintained in the first 200-300 m of burial, with little thickness reduction.
Virus strategies : molecular biology and pathogenesis (1993)

Strategies in Virus Replication DNA Viruses RNA Viruses Viral Membranes and Virus Receptors Regulation of Viral Gene Expression Virus Transformation and Oncogenicity (Cellular Differentiation) DNA Viruses RNA Viruses Viral Latency and Pathogenesis.
Coincidental loss of DOCK8 function in NLRP10-deficient and C3H/HeJ mice results in defective dendritic cell migration (2015)

Dendritic cells (DCs) are the primary leukocytes responsible for priming T cells. To find and activate naïve T cells, DCs must migrate to lymph nodes, yet the cellular programs responsible for this key step remain unclear. DC migration to lymph nodes and the subsequent T-cell response are disrupted in a mouse we recently described lacking the NOD-like receptor NLRP10 (NLR family, pyrin domain containing 10); however, the mechanism by which this pattern recognition receptor governs DC migration remained unknown. Using a proteomic approach, we discovered that DCs from Nlrp10 knockout mice lack the guanine nucleotide exchange factor DOCK8 (dedicator of cytokinesis 8), which regulates cytoskeleton dynamics in multiple leukocyte populations; in humans, loss-of-function mutations in Dock8 result in severe immunodeficiency. Surprisingly, Nlrp10 knockout mice crossed to other backgrounds had normal DOCK8 expression. This suggested that the original Nlrp10 knockout strain harbored an unexpected mutation in Dock8, which was confirmed using whole-exome sequencing. Consistent with our original report, NLRP3 inflammasome activation remained unaltered in NLRP10-deficient DCs even after restoring DOCK8 function; however, these DCs recovered the ability to migrate. Isolated loss of DOCK8 via targeted deletion confirmed its absolute requirement for DC migration. Because mutations in Dock genes have been discovered in other mouse lines, we analyzed the diversity of Dock8 across different murine strains and found that C3H/HeJ mice also harbor a Dock8 mutation that partially impairs DC migration. We conclude that DOCK8 is an important regulator of DC migration during an immune response and is prone to mutations that disrupt its crucial function.