gebhart/patrepeval huggingface dataset:
Multi-modal Imaging: Simultaneous MRI and Ultrasound Imaging for Carotid Arteries Visualization (2007)

The purpose of this study is to examine the feasibility of simultaneous Magnetic Resonance Imaging (MRI) and Ultrasound (US) imaging in visualizing anatomical structures and functions in human carotid arteries. US has high frame rate in visualizing dynamic changes while high resolution MRI is capable of capturing volumetric structures with the best tissue contrast. Concurrent multi-modal image acquisition allows fusion of US Doppler flow measurement with volumetric MRI. We present a method for acquiring MR images in a known orientation with respect to US image by passive fiducial tracking and demonstrate concurrent real-time imaging in the right Common Carotid Artery (CCA) in both modalities. Preliminary results suggest that US and MRI can operate concurrently with proper shielding. Dispensability measurements are feasible on both modalities at the co-incident plane.
Charging insulating barrier by corona in air in large coaxial system (2015)

Results of the experimental study and computer simulations of corona charging of an insulating barrier in a large scale coaxial arrangement are reported. A computational model describing transport of charged species generated by corona and their dynamics on dielectric surfaces is presented. The measured and computed voltage-current characteristics of corona discharge are compared and discussed. It is shown that charges deposited on gas-solid dielectric interfaces reach a steady state after few cycles of the applied triangular ac voltage. The electric field induced by the surface charges modifies the field in the entire system and alter corona characteristics.
Bud8p and Bud9p, Proteins That May Mark the Sites for Bipolar Budding in Yeast (2001)

The bipolar budding pattern of a/alpha Saccharomyces cerevisiae cells appears to depend on persistent spatial markers in the cell cortex at the two poles of the cell. Previous analysis of mutants with specific defects in bipolar budding identified BUD8 and BUD9 as potentially encoding components of the markers at the poles distal and proximal to the birth scar, respectively. Further genetic analysis reported here supports this hypothesis. Mutants deleted for BUD8 or BUD9 grow normally but bud exclusively from the proximal and distal poles, respectively, and the double-mutant phenotype suggests that the bipolar budding pathway has been totally disabled. Moreover, overexpression of these genes can cause either an increased bias for budding at the distal (BUD8) or proximal (BUD9) pole or a randomization of bud position, depending on the level of expression. The structures and localizations of Bud8p and Bud9p are also consistent with their postulated roles as cortical markers. Both proteins appear to be integral membrane proteins of the plasma membrane, and they have very similar overall structures, with long N-terminal domains that are both N- and O-glycosylated followed by a pair of putative transmembrane domains surrounding a short hydrophilic domain that is presumably cytoplasmic. The putative transmembrane and cytoplasmic domains of the two proteins are very similar in sequence. When Bud8p and Bud9p were localized by immunofluorescence and tagging with GFP, each protein was found predominantly in the expected location, with Bud8p at presumptive bud sites, bud tips, and the distal poles of daughter cells and Bud9p at the necks of large-budded cells and the proximal poles of daughter cells. Bud8p localized approximately normally in several mutants in which daughter cells are competent to form their first buds at the distal pole, but it was not detected in a bni1 mutant, in which such distal-pole budding is lost. Surprisingly, Bud8p localization to the presumptive bud site and bud tip also depends on actin but is independent of the septins.
Filament‐based realistic turbulent wake synthesis (2017)

Abstract Turbulent wake is crucial for the visually appealing effects of liquid. Unfortunately, it is challenging to realistically simulate this phenomenon with ring‐shaped vortical structures. To tackle this issue, we propose a filament‐based turbulent wake synthesis method for realistically simulating the turbulent wake with ring‐shaped vortical structures. The filaments are sampled at the separation points on the obstacle surface and emitted into the liquid flow to generate structured turbulent wake. Besides, the surface tension model is incorporated to generate natural turbulent wake diffusion visual effects in liquid by the anticurvature effects. The proposed approach can realistically and effectively synthesize the turbulent wake with ring‐shaped vortical structures and make it diffuse naturally. The experimental results demonstrate that our method outperforms than the vortex particle‐based method in synthesizing appealing turbulent wake.
Uncovering the Conditionally Essential Roles of NAD Kinases in Human Cells (2022)

Forward genetic screens across hundreds of human cancer cell lines have been used to identify genetic dependencies of proliferating human cells and how these vary by genotype and cell lineage. However, while it is appreciated that environmental factors influence cell physiology, there has been little investigation into how nutrient availability impacts gene essentiality. Further, most such screens have been performed in vitro using culture media that poorly reflect the metabolic composition of human blood. Previously, we developed Human Plasma‐Like Medium (HPLM), a physiologic medium designed to more closely reflect the biochemical conditions in human blood. To determine how medium composition affects gene essentiality, we recently performed CRISPR‐based screens of K562 leukemia cells in HPLM versus RPMI, the medium historically used to culture human blood cells. Among the strongest scoring HPLM‐essential genes is Nicotinamide Adenine Dinucleotide Kinase ( NADK ), which encodes one of two human NAD kinases (NADK, cytosolic; NADK2, mitochondrial) that can catalyze the phosphorylation of NAD(H)to NADP(H). While most human cells co‐express both isozymes, only NADK was identified as HPLM‐essential, suggesting that endogenous NADK2 expression is not sufficient to complement NADK knockout in HPLM‐cultured cells. Interestingly, NADK has been annotated as an essential gene in less than 1% of over 1000 genome‐wide CRISPR‐based screens from the Broad Institute Cancer Dependency Map project. To begin to investigate the conditional CRISPR phenotype for NADK , we first engineered NADK ‐knockout cells and then found that they showed a 40% growth defect versus control cells in HPLM relative to RPMI using a short‐term growth assay. Next, to test the hypothesis that cytosolic NAD kinase activity is required for the conditionally essential role of NADK , we performed similar short‐term growth assays with NADK ‐knockout cells expressing cDNAs for wild‐type and cytosol‐restricted NADK2 , as well as kinase‐dead NADK . These experiments revealed that neither kinase‐dead NADK nor NADK2 overexpression could rescue the growth defect of NADK ‐knockout cells, but that cytosol‐restricted NADK2 could. Collectively, these results indicate that the conditionally essential role of NADK is linked to its cytosolic NAD kinase activity. Currently, we are applying systematic approaches in media engineering and metabolomics to identify the medium component(s) that contribute to the NADK gene‐nutrient interaction, and to gain insights into the non‐redundant, context‐dependent role of NADK . Lastly, through further conditional essentiality profiling, we identified NADK2 as DMEM‐essential versus HPLM. Consistent with two recently published studies, we traced this effect to the differential availability of proline between HPLM and DMEM. Collectively, our results demonstrate the human NADKs fulfill distinct cell‐essential roles and form distinct gene‐nutrient interactions that vary with their subcellular localization.
Molecular Cloning and Characterization of Three cDNAs Encoding Putative Mitogen-activated Protein Kinase Kinases (MAPKKs) in Arabidopsis thaliana (1998)

We isolated three Arabidopsis thaliana cDNA clones (ATMKK3, ATMKK4 and ATMKK5) encoding protein kinases with extensive homology to the mitogen-activated protein kinase kinases (MAPKKs) of various organisms in the catalytic domain. ATMKK3 shows high homology (85% identity) to NPK2, a tobacco MAPKK homologue. ATMKK4 and 5 are closely related to each other (84% identity). Phylogenetic analysis showed that the plant MAPKKs constitute at least three subgroups. The recombinant ATMKK3 and ATMKK4 were expressed as a fusion protein with glutathione S-transferase (GST) in Escherichia coli. Affinity purified GST-ATMKK3 and GST-ATMKK4 proteins contained phosphorylation activity, which shows that both the ATMKK3 and ATMKK4 genes encode functional protein kinases. Northern blot analysis revealed that the ATMKK3 gene expressed in all the organs. The levels of ATMKK4 and 5 mRNAs were relatively higher in steins and leaves than in flowers and roots. We determined the map positions of the ATMKK3, 4 and 5 genes on Arabidopsis chromosomes by RFLP mapping using P1 genomic clones.
The model for echolocation of insects by using bat-like sounds (2016)

Bats use frequency-modulated echolocation to identify and capture flying insects in real three dimensional space. Experimental evidence indicates that bats are capable of locating static objects with a range accuracy of less than 1 μs. A previously introduced model could localize objects in two-dimensional space by accurately estimating the object’s range at each timepoint by extracting temporal changes from the time-frequency pattern and interaural range differences while echoes were measured at two receiving points by intermittently emitting LFM sounds. In addition, this model was shown to localize moving objects in two-dimensional space by accurately estimating the object’s range under the influences of the Doppler shift, which was dependent on the movements. However, it was not evaluated whether this model could detect and localize small sized objects, e.g., small moths, whose echoes were weak. In this presentation, the echoes were measured from two kinds of moth, Spodoptera litura and Helicoverpa armigera. The accuracies of estimated range and direction were examined while echoes were measured from flying moths by intermittently emitting bat-like sounds.
Accelerating Correlated Quantum Chemistry Calculations Using Graphical Processing Units (2010)

Graphical processing units are now being used with dramatic effect to accelerate quantum chemistry applications. The authors give a brief introduction to electronic structure methods and describe their efforts to accelerate a correlated quantum chemistry code. They propose and analyze two new tools for accelerating matrix-multiplications where single-precision accuracy is insuffcient.
Using Big Data to Study the Impact of Wellbore Tortuosity on Drilling, Completions, and Production Performance (2019)

Abstract The principal indicators for drilling performance have traditionally been measures of time. For instance, time vs. depth and ROP serve as instant KPIs that are easy to measure and have obvious implications. Other potential performance parameters, such as the quality of the constructed wellbore are not considered in the drilling process. A standardized wellbore quality index has not been established yet. This work aims to narrow the gap between drilling and subsequent completion, production and plug &amp; abandonment operations. The operator gathered large data sets to link wellbore tortuosity with non-productive time (NPT) in drilling and completion and production outcome. A previously published measure of wellbore geometry, tortuosity index developed at the University of Texas (Zhou et al., 2016), was adjusted to better fit the requirements for the tortuosity study presented in this paper. Tortuosity values for horizontal, curve and vertical sections are calculated from about 2400 publicly available directional surveys for a basin in the US. The study uses data from hundreds of these wells to reveal correlations of tortuosity with drilling and completion NPT and correlations with production values in one out of three reservoir layers analyzed in this work.
Discovery and Use of a Natural Mutation that Results in Severe Combined Immuno Deficiency in Pigs (2013)

Piglets from the low residual feed intake (RFI) line at ISU were found to be affected with a lethal autosomal recessive mutation that causes Severe Combined Immunodeficiency (SCID). Bone marrow allotransplantation rescued the immune deficiency in four of nine attempted transfers; the other five exhibited signs of severe graft versus host disease and were euthanized. A genome wide association study identified a 5.6 Mb region that contained the causative mutation. Affected haplotypes were traced back to the founders of the RFI population, who were sourced from the purebred Yorkshire population. The SCID pigs will be useful as a biomedical model, as pigs are anatomically and genetically more similar to humans than SCID mice, which are now widely used. Development of a genetic test for the causative mutation will be valuable to the swine industry, allowing breeders to identify carriers.
Single antenna full duplex communications using a common carrier (2012)

Recently there has been much interest in systems capable of full duplex communications operating with a common RF carrier frequency in both the transmit and receive channels. All the reported systems require transceivers with multiple transmit and receive antennas in order to achieve sufficient isolation between the transmit and receive channels. The technique detailed in this paper is the first reported system to achieve full duplex communication using a common carrier operating with a single antenna resulting in high transmit to receive isolation and low insertion loss. The technique provides over 40 dB isolation between the transmitter and receiver channels and 0.75dB insertion loss for the transmitter-to-antenna and antenna-to-receiver paths.
Influence of Hormones and Hormone Metabolites on the Growth of Schwann Cells Derived From Embryonic Stem Cells and on Tumor Cell Lines Expressing Variable Levels of Neurofibromin (2008)

Abstract A benign human plexiform neurofibroma cell. Note the extensive tubulin networks (red), which become disrupted after addition of 2ME2, an estrogen metabolite implicated in tumor toxicity. The green staining represents S100 staining, indicating the Schwann Cell origin of the tumor cells. Blue is DAPI nuclear staining. See Roth et al., Developmental Dynamics 237:513–524, 2008. © 2008 Wiley‐Liss, Inc.
Improved biological delignification of wood biomass via Ionic liquids pretreatment: A one step process (2013)

The enzymatic pretreatment of wood biomass for degrading lignin, a complex aromatic polymer, has received much attention as an environmentally safe or “green” process. However, this process for lignin degradation has been found to be very slow, even needed several months. To overcome this limitation, this study reports a new approach for enhanced enzymatic delignification of wood biomass using room temperature ionic liquids (RTILs)- a potentially attractive “green” and “designer” solvent- as (co)solvents or/and pretreated agents. The method comprised pretreatment of wood biomass prior to enzymatic delignification in ILs-aqueous systems with the aim of overcoming low delignification efficiency associated with the difficulties in enzyme accessibility to the solid substrate and the poor substrate and products solubility in aqueous system. The results showed that IL [emim] [OAc] (1-ethyl-3-methylimidazolium acetate) was better solvent for wood delignification than IL [bmim][Cl] (1-butyl-3-methylimidazolium chloride). The recovered cellulose rich materials obtained from combination effects of IL and biological pretreatment contained significantly lower amounts of lignin as compared to the amounts found when each method applied alone. The produced cellulose rich materials were characterized by acid hydrolysis, Fourier-transform infrared spectroscopy (FTIR), Scanning electron microscopy (SEM), and X-ray diffractometry (XRD). SEM and XRD revealed considerable microstructural and crystallinity index changes in the pretreated cellulose rich materials.  We believe that this newly developed process will play a great role in converting cellulosic biomass- the most abundant renewable biomaterials in the world- to biomaterials, biopolymers, biofuels, bioplastics and hydrocarbons. Keywords: ionic liquids, wood biomass, cellulose, lignin, laccase, enzymatic delignification.
Digitaltechnik und Entwurfsverfahren, WS 2015/2016, gehalten am 11.01.2016, Vorlesung 16 (2016)

16: Vorlesung | 0:00:00 Starten 0:00:49 Schaltwerke 0:01:55 Einleitung 0:04:37 Formale Grundlagen 0:05:07 Einführung in die Automatentheorie 0:09:18 Arbeitsweise 0:10:03 Mealy- und Moore-Automat 0:10:09 Moore-Automat 0:12:42 Mealy-Automat 0:15:24 Moore-Automat vs. Mealy-Automat 0:17:49 Unterschiede im Verhalten der beiden Automaten 0:22:45 Darstellungsmöglichkeiten 0:22:55 Formalisierte Beschreibung 0:25:18 Zeitdiagramm 0:30:33 Automatentabelle 0:35:17 Automatengraph 0:40:09 Realisierung von Automaten 0:40:41 Beispiel: Rückgekoppeltes NOR-Gatter 0:48:53 Definitionen 0:49:39 Pegelsteuerung 0:52:07 Flankensteuerung 0:54:04 Synchrone Schaltwerke vs. Asynchrone Schaltwerke 0:58:08 Entwurf asynchroner Schaltwerke 1:00:11 Beispiel: Einfacher Speicher 1:01:49 Aufstellung des Automatengraphen 1:01:54 Vorgehensweise 1:03:04 Automatengraph des einfachen Speichers 1:05:46 Funktionsweise 1:06:44 Übertragen des Automatengraphen in die Automatentafel 1:08:56 Stabilitätskriterium 1:11:31 Beispiel: Flussmatrix des einfachen Speichers
Inositol phosphatase activity of theEscherichia coli agp-encoded acid glucose-1-phosphatase (2002)

When screening an Escherichia coli gene library for myo-inositol hexakisphosphate (InsP 6 ) phosphatases (phytases), we discovered that the agp-encoded acid glucose-1-phosphatase also possesses this activity. Purified Agp hydrolyzes glucose-1-phosphate, p-nitrophenyl phosphate, and InsP 6 with pH optima, 6.5, 3.5, and 4.5, respectively, and was stable when incubated at pH values ranging from 3 to 10. Glucose-1-phosphate was hydrolyzed most efficiently at 55°C, while InsP 6 and p-nitrophenyl phosphate were hydrolyzed maximally at 60°C. The Agp exhibited K m values of 0.39 mM, 13 mM, and 0.54 mM for the hydrolysis of glucose-1-phosphate, p-nitrophenyl phosphate, and InsP 6 , respectively. High-pressure liquid chromatography (HPLC) analysis of inositol phosphate hydrolysis products of Agp demonstrated that the enzyme catalyzes the hydrolysis of phosphate from each of InsP 6 , D-Ins(1,2,3,4,5)P 5 , Ins(1,3,4,5,6)P 5 , and Ins(1,2,3,4,6)P 5 , producing D/L-Ins(1,2,4,5,6)P 5 , D-Ins(1,2,4,5)P 4 , D/L-Ins(1,4,5,6)P 4 and D/L-Ins(1,2,4,6)P 4 , respectively. These data support the contention that Agp is a 3-phosphatase. Key words: phosphatase, phytate, bacteria, inositol phosphate, phytase.
Synthesis of a Mg-Cd-Al layered double hydroxide and sorption of selenium (2009)

Abstract Leaching experiments with metallic uranium-aluminum research-reactor fuel elements in repository-relevant MgCl 2 -rich salt brine (brine 2) were performed. A Mg-Al layered double hydroxide (LDH) with chloride as the interlayer anion was identified as a crystalline secondary-phase component. In the present study, the incorporation of Cd into the structure of the Mg-Al-Cl LDH was investigated. Synthesis by a coprecipitation method was performed and the Mg-Cd-Al-Cl LDH obtained was characterized. The sorption behavior of selenium on the LDH was investigated in water, clay pore-water (Mont-Terri-type), and brine 2. Using a LDH concentration of 10 g/L, the sorption kinetics were rapid and equilibrium was reached within 12 h. The sorption of selenium decreased with increasing amount of chloride anions in the solutions. The chloride anions acted as competing anions for the sorption of selenium. The effect of pH on selenium sorption was investigated and a large buffer capacity of the LDH was observed. For the range of selenium concentration used, linear sorption isotherms were obtained which obeyed the Freundlich and Dubinin-Radushkevich models. From these, the energies of selenium sorption were calculated to be in the range of ion-exchange processes.
Preparation of nanostructured porous carbon composite fibers from ferrum alginate fibers (2012)

Abstract Nano‐microstructured porous carbon composite fibers (Fe 2 O 3 @C/FeO@C/Fe@C) were synthesized by the thermal decomposition of ferrum alginate fibers. The ferrum alginate fiber precursors were prepared by wet spinning, and calcined at 300–1000°C in high purity nitrogen. The resulting composite fibers consist of carbon coated Fe 2 O 3 /FeO/Fe nanoparticles and porous carbon fibers. All the prepared nanostructures were investigated using thermal gravimetry, X‐ray diffraction (XRD), Fourier transform infrared spectroscopy, transmission electron microscope (TEM), and nitrogen adsorption–desorption isotherm. The results show that there are five stages in the decomposition process of the ferrum alginate fibers. Transitions between the five stages are affected by the decomposition temperature. XRD results show that maghemite (Fe 2 O 3 ), wüstite (FeO), martensite (Fe) nanoparticles were formed at 300–500°C, 600–700°C, 800–1000°C, respectively. Scanning electron microscopy and TEM results indicate that the composite fibers consist of nanoparticles and porous carbon. The diameter of the nanosized particles increased from 100 to 500 nm with increasing reaction temperature. The nitrogen adsorption–desorption results also show that the composite fibers have a micro‐ and mesoporous structure. © 2012 Wiley Periodicals, Inc. J. Appl. Polym. Sci., 2013
Development and Assessment of Digital Audiovisual Youtube Lectures for an Engineering Course in Numerical Methods (2011)

Cyberlearning is transforming education by offering course content through multiple context and platforms. As part of this transformation, this paper describes the experience of preparing, recording, uploading, organizing, and assessing audiovisual lectures for an engineering course in Numerical Methods. More than 250 short modular videos are currently available that cover the syllabus of a comprehensive undergraduate course in Numerical Methods for Engineers. The motivation for the development of the audiovisual lectures was based on a pilot study that showed that the examination performance and student satisfaction increased with the availability of audiovisual lectures. A final assessment of these resources made via a video analytics tool shows increasing popularity of the videos, gives insight into the audience attention, and presents demographics by gender, age, and geography.addition, a summative rating survey of the courseware shows significant increase in the value of the quality of content and enhancement in student learning.