gebhart/patrepeval huggingface dataset:
Virtual angiography using CFD simulations based on patient-specific parameter optimization (2012)

Computational fluid dynamics (CFD) simulations of blood flow within intracranial aneurysms may provide important hemodynamic information for treatment planning. However, reliable validation is required prior to applications in clinical environments. For that purpose, we introduce a workflow for generating virtual digital subtraction angiographies (DSA) based on CFD results and real patient-individual contrast injection protocols. This allows for comparing virtual and acquired DSA and thus drawing first conclusions about the reliability of the CFD simulation. Due to the possibility of simulating arbitrary x-ray system angulations, both mechanically impossible angulations as well as multiple projection views are representable using the proposed virtual DSA workflow.
Relaxin family peptides: structure–activity relationship studies (2016)

This article is part of a themed section on Recent Progress in the Understanding of Relaxin Family Peptides and their Receptors. To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v174.10/issuetoc.
Model Based Diagnostics for Vehicle Systems (2000)

Abstract In recent years, increasing interest and requirement for improved vehicle performance, reliability and safety has focused attention on the use of Fault Detection & Isolation when designing vehicle control systems. In order to achieve this FDI schemes, particular vehicle subsystems integrated with a controller have been proposed. This paper introduces a new Model-Based Fault Detection and Fault Diagnosis method for monitoring the overall vehicle system performance.
Applications of Air Plasma for Wound Bleeding Control and Healing (2012)

The design and the electric and emission characteristics of a handheld air plasma spray are presented. The plasma is generated by 60-Hz periodic discharges between two concentrically cylindrical electrodes. A ring magnet is used to rotate arc discharges, which sprays outward by an airflow. The rotation of arc discharges keeps the generated plasma in nonequilibrium state and at relatively low temperature . The plasma effluent still contains high-energy electrons which dissociate molecular oxygen into atomic oxygen. The emission spectroscopy of the plasma plume reveals that the plasma effluent, which carries abundant atomic oxygen, extends from the cap of the plasma spray about 25 mm. Using pigs as the animal model, in vivo tests of stopping wound bleeding and postoperative observation of wound healing by this air plasma spray were performed. The results show that the bleeding from a cut to an ear artery is stopped swiftly; this air plasma spray also shortens wound healing time to about half (from 14 days to 8 days) after stopping the bleeding of a cross-cut wound in the ham area.
Availability aware cost modeling of mesh architectures for long-haul networks (2004)

Carriers determined to stay competitive in the market have learned that simply going for the cheapest networking solution in terms of CAPEX is not enough, as the total cost includes OPEX as well. Availability of the network, which is too important to ignore in terms of providing meaningful service to customers, also relates to OPEX cost through maintenance and repair efforts. This study introduces a modeling methodology that incorporates availability awareness in to the cost modeling in order to propose a mesh architecture for a given core network with an acceptable trade-off between cost-efficiency and availability.
Endotoxin of <i>Neisseria meningitidis</i> Composed Only of Intact Lipid A: Inactivation of the Meningococcal 3-Deoxy- <scp>d</scp> -Manno-Octulosonic Acid Transferase (2002)

Lipopolysaccharide, lipooligosaccharide (LOS), or endotoxin is important in bacterial survival and the pathogenesis of gram-negative bacteria. A necessary step in endotoxin biosynthesis is 3-deoxy-D-manno-octulosonic acid (Kdo) glycosylation of lipid A, catalyzed by the Kdo transferase KdtA (WaaA). In enteric gram-negative bacteria, this step is essential for survival. A nonpolar kdtA::aphA-3 mutation was created in Neisseria meningitidis via allelic exchange, and the mutant was viable. Detailed structural analysis demonstrated that the endotoxin of the kdtA::aphA-3 mutant was composed of fully acylated lipid A with variable phosphorylation but without Kdo glycosylation. In contrast to what happens in other gram-negative bacteria, tetra-acylated lipid IV(A) did not accumulate. The LOS structure of the kdtA::aphA-3 mutant was restored to the wild-type structure by complementation with kdtA from N. meningitidis or Escherichia coli. The expression of a fully acylated, unglycosylated lipid A indicates that lipid A biosynthesis in N. meningitidis can proceed without the addition of Kdo and that KdtA is not essential for survival of the meningococcus.
Coherent-array imaging using phased subarrays. Part I: basic principles (2005)

The front-end hardware complexity of a coherent array imaging system scales with the number of active array elements that are simultaneously used for transmission or reception of signals. Different imaging methods use different numbers of active channels and data collection strategies. Conventional full phased array (FPA) imaging produces the best image quality using all elements for both transmission and reception, and it has high front-end hardware complexity. In contrast, classical synthetic aperture (CSA) imaging only transmits on and receives from a single element at a time, minimizing the hardware complexity but achieving poor image quality. We propose a new coherent array imaging method--phased subarray (PSA) imaging--that performs partial transmit and receive beam-forming using a subset of adjacent elements at each firing step. This method reduces the number of active channels to the number of subarray elements; these channels are multiplexed across the full array and a reduced number of beams are acquired from each subarray. The low-resolution subarray images are laterally upsampled, interpolated, weighted, and coherently summed to form the final high-resolution PSA image. The PSA imaging reduces the complexity of the front-end hardware while achieving image quality approaching that of FPA imaging.
Genes encoding high-molecular-weight adhesion proteins of nontypeable Haemophilus influenzae are part of gene clusters (1994)

We previously reported the cloning and sequencing of genes designated hmw1 and hmw2 from a prototype nontypeable Haemophilus influenzae strain. The genes encode proteins which are related to filamentous hemagglutinin of Bordetella pertussis and promote attachment of the nontypeable H. influenzae strain to human epithelial cells (J. W. St. Geme III, S. Falkow, and S. J. Barenkamp, Proc. Natl. Acad. Sci. USA 90:2875-2879, 1993). Subcloning studies suggested that correct processing of these high-molecular-weight proteins required the products of additional downstream genes. In the present study we analyzed the 3'-flanking regions of the hmw1A and hmw2A structural genes and found that both genes are flanked by two additional downstream open reading frames (ORFs), designated B and C, respectively. The B ORFs are 1,635 bp long. Their derived amino acid sequences are 99% identical and demonstrate similarity to the derived amino acid sequences of two genes that encode proteins required for secretion and activation of hemolysins of Proteus mirabilis and Serratia marcescens. The C ORFs are 1,950 bp long, and their derived amino acid sequences are 96% identical. In Escherichia coli transformants, interruption of the hmw1C or both the hmw1B and hmw1C genes resulted in defective processing of the hmw1A structural gene product and loss of the ability of the transformants to adhere to human epithelial cells. The precise interactions of the proteins encoded by these gene clusters are yet to be defined, but their elucidation may further our understanding of the biology of nontypeable H. influenzae bacteria and the interaction of these organisms with the human host.
Contrast-Use Metrics for Tone Mapping Images (2015)

Existing tone mapping operators (TMOs) provide good results in well-lit scenes, but often perform poorly on im-ages in low light conditions. In these scenes, noise is prevalent and gets amplified by TMOs, as they confuse contrast created by noise with contrast created by the scene. This paper presents a principled approach to produce tone mapped images with less visible noise. For this purpose, we leverage established models of camera noise and human contrast perception to design two new quality scores: contrast waste and contrast loss, which measure image quality as a function of contrast allocation. To produce tone mappings with less visible noise, we apply these scores in two ways: first, to automatically tune the parameters of existing TMOs to reduce the amount of noise they produce; and second, to propose a new noise-aware tone curve
Valine requirement of the high-producing lactating sow. (1996)

Two hundred three (40 or 41/treatment, average parity 4.3) Large White x Landrace or Large White x Chester White x Landrace sows were used to determine the valine requirement of sows with a genetic capacity for high milk production. All diets were formulated to contain .90% total lysine, with all amino acids other than valine formulated to be at least 110% of their suggested estimates relative to lysine based on ratios derived from the National and Agricultural Research Councils. The control diet was formulated to .75% total valine, and crystalline valine replaced cornstarch to provide additional treatments containing .85, .95, 1.05, and 1.15% total dietary valine. Corresponding valine:lysine ratios were 83, 94, 106, 117, and 128%. Mean litter size after adjustment was 10.3 pigs across treatments, and average lactation length was 26 d. Number of pigs weaned was not affected by dietary valine (mean = 10.2 pigs), nor was daily sow feed (mean = 6.24 kg) or lysine (mean = 56 g) intake. Valine intake increased (linear, P < .001) as dietary valine increased. Litter weight at d 21 and at weaning (d 26) increased (linear, P < .02) with increasing dietary valine (62.4 to 65.5 kg and 76.1 to 79.9 kg, respectively). Litter weight gain increased from d 0 to 7 (linear, P < .06) and from d 0 to 21 and d 0 to weaning (linear, P < .02) as dietary valine increased. Dietary valine had no effect (P > .10) on sow weight change, 10th rib, or last lumbar backfat change from d 0 to 21 or d 0 to weaning or on days from weaning to estrus. These results demonstrate that increasing dietary valine for high-producing sows (21-d litter weights > 60 kg) results in improved litter weight gain. Based on the linear responses observed, the requirement is at least 1.15% of the diet (72 g/d of valine intake) to maximize litter weaning weight and litter weight gain, much greater than recommended currently by the National Research Council (100% of lysine, 36.5 g/d) or the Agricultural Research Council (70% of lysine, 25.5 g/d).
A DIVA vaccine for cross-protection against Salmonella (2016)

Swine are often asymptomatic carriers of Salmonella spp., a leading cause of human bacterial foodborne disease. Vaccination against Salmonella is effective for protecting animal health and enhancing food safety. However, with >2500 Salmonella serovars, current vaccines for swine offer limited cross-protection against heterologous serovars. Also, existing vaccines can interfere with surveillance programs that monitor the Salmonella status of swine herds. To overcome Salmonella vaccine limitations, we rationally designed and constructed an attenuated Salmonella enterica serovar Typhimurium vaccine (BBS 866) by deleting multiple small regulatory RNA (sRNA) genes (omrA, omrB, rybB, micA, and invR) in combination with an rfaH mutation. We vaccinated swine intranasally at 3-weeks of age with PBS (mock-vaccinated), BBS 866 or BBS 202 (S. Typhimurium rfaH, Bearson et al., Front Vet Sci 2014;1:9.) and challenged at 7-weeks of age with virulent S. Choleraesuis, a swine pathogen. Vaccination with BBS 866 enhanced protection against S. Choleraesuis by significantly limiting the duration of fever, weight loss, the levels of circulating INFγ, and the total number of swine with S. Choleraesuis septicemia. Vaccination with either BBS 866 or BBS 202 significantly reduced S. Choleraesuis colonization of both systemic (spleen and liver) and gastrointestinal (Peyer's Patch, Ileocecal lymph nodes, and cecum) tissues. Similar to our earlier report for BBS 202, the BBS 866 vaccine strain can be used in swine without compromising the differentiation of infected from vaccinated animals (DIVA). Therefore, the attenuated S. Typhimurium BBS 866 strain, containing mutations in rfaH and multiple sRNAs, addresses the limitations of current Salmonella vaccines by providing cross-protection against Salmonella serovars in swine without interfering with established monitoring programs for Salmonella surveillance.
Mock-object generation with behavior (2006)

Unit testing is a popular way to guide software development and testing. Each unit test should target a single feature, but in practice it is difficult to test features in isolation. Mock objects are a well-known technique to substitute parts of a program which are irrelevant for a particular unit test. Today mock objects are usually written manually supported by tools that generate method stubs or distill behavior from existing programs. We have developed a prototype tool based on symbolic execution of .NET code that generates mock objects including their behavior by analyzing all uses of the mock object in a given unit test. It is not required that an actual implementation of the mocked behavior exists. We are working towards an integration of our tool into Visual Studio Team System
C-axis-Oriented (Sr,Ca)<sub>2</sub>NaNb<sub>5</sub>O<sub>15</sub> Multilayer Piezoelectric Ceramics Fabricated Using High-Magnetic-Field Method (2008)

We formed a c-axis-oriented (Sr,Ca)2NaNb5O15 (SCNN) sheets using a rotation magnetic field, and succeeded in realizing a c-axis-oriented SCNN multilayer piezoelectric ceramic (O-MLPC). The Lotgering factor of both the c-axis-oriented SCNN sheet and inner piezoelectric ceramic of the O-MLPC were approximately 0.80 after sintering. The applied voltage dependences of displacement for both the O-MLPC and a conventional multilayer piezoelectric ceramic (MLPC) with randomly oriented ceramics were examined. As a result, we confirmed that the displacement characteristic of the O-MLPC increased up to a value 2.5 times larger than that of the MLPC.
Constructing Virtual Architectures on a Tiled Processor (2006)

As the amount of available silicon resources on one chip increases, we have seen the advent of ever increasing parallel resources integrated on-chip. Many architectures use these resources as individually controllable, parallel processing elements. While such architectures excel at parallel applications, they seldom support legacy single-threaded applications. In this work, we propose using parallel resources to facilitate execution of legacy codes with acceptable performance on parallel architectures containing a drastically different instruction set through the use of an all software parallel dynamic binary translation engine. This engine spatially implements different portions of a superscalar processor across distinct parallel elements thus exploiting the pipeline parallelism inherent in a superscalar. This virtual micro architecture facilitates changing the allocation of silicon resources between different superscalar units in software which is not possible when special purpose physical resources are built. We propose building dynamically reconfigurable architectures that inspect the current virtual machine configuration along with the dynamic instruction stream and change the configuration to best suit the program's needs at runtime. An x86 to Raw parallel translation engine was built in which tiles dedicated to translation can be traded for tiles dedicated to the memory system as an example of dynamic reconfiguration.
Template-Synthesized Protein Nanotubes (2005)

A layer-by-layer deposition strategy for preparing protein nanotubes within the pores of a nanopore alumina template membrane is described. This method entails alternately exposing the template membrane to a solution of the desired protein and then to a solution of glutaraldehyde, which acts as cross-linking agent to hold the protein layers together. The number of layers of protein that make up the nanotube walls can be controlled at will by varying the number of alternate protein/glutaraldehyde cycles. After the desired number of layers have been deposited on the pore walls, the alumina template can be dissolved to liberate the protein nanotubes. We show here that glucose oxidase nanotubes prepared in this way catalyze glucose oxidation and that hemoglobin nanotubes retain their heme electroactivity. Furthermore, for the glucose oxidase nanotubes, the enzymatic activity increases with the nanotube wall thickness.
Buried heterostructure quantum cascade lasers (1998)

We report on the fabrication and characterization of buried heterostructure quantum cascade (BH-QC) lasers. The buried heterostructure is formed by regrowth of InP lateral on the side walls and on top of the InAlAs/InGaAs laser structure by molecular beam epitaxy (MBE) after in situ surface cleaning. Thermal Cl<SUB>2</SUB> etching is applied to the etched laser structure to remove the native oxides of the ternaries prior to regrowth of InP. Buried heterostructure QC lasers demonstrated excellent performances with lower threshold current densities (as low as 4.5kA/cm<SUP>2</SUP> at T equals 300K) and higher slope efficiencies that we attribute to lower waveguide losses and a better heat dissipation.
Non-Tumorigenic Pluripotent Reparative Muse Cells Provide a New Therapeutic Approach for Neurologic Diseases (2021)

Muse cells are non-tumorigenic endogenous reparative pluripotent cells with high therapeutic potential. They are identified as cells positive for the pluripotent surface marker SSEA-3 in the bone marrow, peripheral blood, and connective tissue. Muse cells also express other pluripotent stem cell markers, are able to differentiate into cells representative of all three germ layers, self-renew from a single cell, and are stress tolerant. They express receptors for sphingosine-1-phosphate (S1P), which is actively produced by damaged cells, allowing circulating cells to selectively home to damaged tissue. Muse cells spontaneously differentiate on-site into multiple tissue-constituent cells with few errors and replace damaged/apoptotic cells with functional cells, thereby contributing to tissue repair. Intravenous injection of exogenous Muse cells to increase the number of circulating Muse cells enhances their reparative activity. Muse cells also have a specific immunomodulatory system, represented by HLA-G expression, allowing them to be directly administered without HLA-matching or immunosuppressant treatment. Owing to these unique characteristics, clinical trials using intravenously administered donor-Muse cells have been conducted for myocardial infarction, stroke, epidermolysis bullosa, spinal cord injury, perinatal hypoxic ischemic encephalopathy, and amyotrophic lateral sclerosis. Muse cells have the potential to break through the limitations of current cell therapies for neurologic diseases, including amyotrophic lateral sclerosis. Muse cells provide a new therapeutic strategy that requires no HLA-matching or immunosuppressant treatment for administering donor-derived cells, no gene introduction or differentiation induction for cell preparation, and no surgery for delivering the cells to patients.
Wide-field Fourier ptychographic microscopy using laser illumination source (2016)

Fourier ptychographic (FP) microscopy is a coherent imaging method that can synthesize an image with a higher bandwidth using multiple low-bandwidth images captured at different spatial frequency regions. The method's demand for multiple images drives the need for a brighter illumination scheme and a high-frame-rate camera for a faster acquisition. We report the use of a guided laser beam as an illumination source for an FP microscope. It uses a mirror array and a 2-dimensional scanning Galvo mirror system to provide a sample with plane-wave illuminations at diverse incidence angles. The use of a laser presents speckles in the image capturing process due to reflections between glass surfaces in the system. They appear as slowly varying background fluctuations in the final reconstructed image. We are able to mitigate these artifacts by including a phase image obtained by differential phase contrast (DPC) deconvolution in the FP algorithm. We use a 1-Watt laser configured to provide a collimated beam with 150 mW of power and beam diameter of 1 cm to allow for the total capturing time of 0.96 seconds for 96 raw FPM input images in our system, with the camera sensor's frame rate being the bottleneck for speed. We demonstrate a factor of 4 resolution improvement using a 0.1 NA objective lens over the full camera field-of-view of 2.7 mm by 1.5 mm.
Features of Modularly Assembled Compounds That Impart Bioactivity Against an RNA Target (2013)

Transcriptomes provide a myriad of potential RNAs that could be the targets of therapeutics or chemical genetic probes of function. Cell-permeable small molecules, however, generally do not exploit these targets, owing to the difficulty in the design of high affinity, specific small molecules targeting RNA. As part of a general program to study RNA function using small molecules, we designed bioactive, modularly assembled small molecules that target the noncoding expanded RNA repeat that causes myotonic dystrophy type 1 (DM1), r(CUG)(exp). Herein, we present a rigorous study to elucidate features in modularly assembled compounds that afford bioactivity. Different modular assembly scaffolds were investigated, including polyamines, α-peptides, β-peptides, and peptide tertiary amides (PTAs). On the basis of activity as assessed by improvement of DM1-associated defects, stability against proteases, cellular permeability, and toxicity, we discovered that constrained backbones, namely, PTAs, are optimal. Notably, we determined that r(CUG)(exp) is the target of the optimal PTA in cellular models and that the optimal PTA improves DM1-associated defects in a mouse model. Biophysical analyses were employed to investigate potential sources of bioactivity. These investigations show that modularly assembled compounds have increased residence times on their targets and faster on rates than the RNA-binding modules from which they were derived. Moreover, they have faster on rates than the protein that binds r(CUG)(exp), the inactivation of which gives rise to DM1-associated defects. These studies provide information about features of small molecules that are programmable for targeting RNA, allowing for the facile optimization of therapeutics or chemical probes against other cellular RNA targets.