gebhart/patrepeval huggingface dataset:
Design of a dynamic biofilm imaging cell for white-light interferometric microscopy (2017)

In microbiology research, there is a strong need for next-generation imaging and sensing instrumentation that will enable minimally invasive and label-free investigation of soft, hydrated structures, such as in bacterial biofilms. White-light interferometry (WLI) can provide high-resolution images of surface topology without the use of fluorescent labels but is not typically used to image biofilms because there is insufficient refractive index contrast to induce reflection from the biofilm’s interface. The soft structure and water-like bulk properties of hydrated biofilms make them difficult to characterize in situ, especially in a nondestructive manner. We build on our prior description of static biofilm imaging and describe the design of a dynamic growth flow cell that enables monitoring of the thickness and topology of live biofilms over time using a WLI microscope. The microfluidic system is designed to grow biofilms in dynamic conditions and to create a reflective interface on the surface while minimizing disruption of fragile structures. The imaging cell was also designed to accommodate limitations imposed by the depth of focus of the microscope’s objective lens. Example images of live biofilm samples are shown to illustrate the ability of the flow cell and WLI instrument to (1) support bacterial growth and biofilm development, (2) image biofilm structure that reflects growth in flow conditions, and (3) monitor biofilm development over time nondestructively. In future work, the apparatus described here will enable surface metrology measurements (roughness, surface area, etc.) of biofilms and may be used to observe changes in biofilm structure in response to changes in environmental conditions (e.g., flow velocity, availability of nutrients, and presence of biocides). This development will open opportunities for the use of WLI in bioimaging.
A new method of characterising gait using a portable, real-time, ultrasound ranging device (2002)

A portable gait analysis system is presented. The device uses direct ultrasound ranging to measure the distance between a base unit and a transponder worn by the subject at the approximate body center of mass. As the subject progresses away from the base unit distance samples are saved and displayed in real time on a computer screen. Immediately following a walking trial these saved distance samples are used to calculate the instantaneous horizontal velocity or the gait velocigram (GVG). The GVG can be considered to be a pictorial representation of that person's gait. Gait parameters such as average walking speed, cadence, stride time, stride length, the step lengths and times for each leg and the peak-to-peak fluctuation of the instantaneous velocity can all be readily calculated from the GVG. The power of this device is that it provides gait data in real-time, enabling a clinician to implement ideas or changes and then to immediately see effect of those ideas or changes on that person's gait. Our direct ultrasound ranging system (DURS) has application in the area of outcome measures for implant or corrective gait surgery as well as in the area of lower limb prosthetic alignment.
Control of Lignin Peroxidase Production by <i>Phanerochaete chrysosporium</i> INA-12 by Temperature Shifting (1988)

There are two temperature optima connected with lignin peroxidase synthesis by Phanerochaete chrysosporium INA-12. One, at 37 degrees C, is for the mycelium-growing phase; the other, at 30 degrees C, is for the lignin peroxidase-producing phase. One of six extracellular proteins with ligninase activity increased when cultures were grown at 30 degrees C for the entire fermentation period or when cultures were grown at 37 degrees C for the first 2 days of incubation and then shifted to 30 degrees C, compared with the activity of control cultures grown at 37 degrees C for the entire fermentation period. The unsaturation of fatty acid (Delta/mole) of P. chrysosporium INA-12 mycelium decreased from 1.25 to 1.03 when the growth temperature was shifted from 20 to 40 degrees C.
Protection of neonatal kittens against feline immunodeficiency virus infection with passive maternal antiviral antibodies (1995)

Maternal antiviral antibodies, including VN antibodies, from either vaccinated or infected queens protected neonatal kittens from FIV inoculation. Thus, maternal antiviral antibodies play a key role in preventing or limiting infection in neonates and such antiviral immunity can be provided by vaccinated queens.
Use of genetic and physical mapping to locate the spinal muscular atrophy locus between two new highly polymorphic DNA markers. (1994)

The gene for autosomal recessive forms of spinal muscular atrophy (SMA) has recently been mapped to chromosome 5q13, within a 4-cM region between the blocks D5S465/D5S125 and MAP-1B/D5S112. We identified two new highly polymorphic microsatellite DNA markers--namely, AFM265wf5 (D5S629) and AFM281yh9 (D5S637)--which are the closest markers to the SMA locus. Multilocus analysis by the location-score method was used to establish the best estimate of the SMA gene location. Our data suggest that the most likely location for SMA is between locus D5S629 and the block D5S637/D5S351/MAP-1B/D5S112/D5S357. Genetic analysis of inbred SMA families, based on homozygosity by descent and physical mapping using mega-YACs, gave additional information for the loci order as follows: cen-D5S6-D5S125/D5S465-D5S435-D5S629-SMA-+ ++D5S637-D5S351-MAP-1B/D5S112-D5S357- D5S39-tel. These data give the direction for bidirectional walking in order to clone this interval and isolate the SMA gene.
Surface Tension Confines Cryogenic Liquid (1989)

New type of Dewar provides passive, constant-temperature cryogenic cooling for scientific instruments under normal-to low-gravity conditions. Known as Surface-Tension-Contained Liquid Cryogen Cooler (STCLCC), keeps liquid cryogen in known location inside the Dewar by trapping liquid inside spongelike material. Unique sponge material fills most of volume of inner tank. Sponge is all-silica, open-cell material similar to that used for Space Shuttle thermal-protection tiles.
Construction of Flocculent<i>Kluyveromyces marxianus</i>Strains Suitable for High-Temperature Ethanol Fermentation (2009)

Flocculating yeasts are highly useful in fermentation processes because these cells can be separated easily from the fermentation mash. However, native yeasts are usually non-flocculating, including Kluyveromyces marxianus, which exhibits a potent high-temperature ethanol fermentation ability. We describe here the construction of flocculent K. marxianus strains via the introduction of the FLO1, FLO5, FLO9, and FLO10 genes from Saccharomyces cerevisiae. The S. cerevisiae FLO genes were overexpressed by upstream insertion of the constitutive TDH3 promoter, resulting in flocculent S. cerevisiae strains. These TDH3p-FLO sequences were then amplified by PCR and introduced directly into a K. marxianus strain. These K. marxianus strains showed a flocculation phenotype, indicating that the introduced S. cerevisiae TDH3 promoter and all FLO genes were functional in this strain. Moreover, a flocculating K. marxianus strain showed the same ethanol production profile as that of its wild-type parent. The K. marxianus flocculating strains we generated should be useful in the future development of cost-effective fed-batch and continuous fermentation systems at high temperatures.
Thymosin α1 (2007)

Thymosin alpha1 (Talpha1), first described and characterized by Allan Goldstein in 1972, is used worldwide for the treatment of some immunodeficiencies, malignancies, and infections. Although Talpha1 has shown a variety of effects on cells and pathways of the immune system, its central role in modulating dendritic cell (DC) function has only recently been appreciated. As DCs have the ability to sense infection and tissue stress and to translate collectively this information into an appropriate immune response, an action on DCs would predict a central role for Talpha1 in inducing different forms of immunity and tolerance. Recent results have shown that Talpha1: (a) primed DCs for antifungal Th1 resistance through Toll-like receptor (TLR)/MyD88-dependent signaling and this translated in vivo in protection against aspergillosis; (b) activated plasmacytoid DCs (pDC) via the TLR9/MyD88-dependent viral recognition, thus leading to the activation of interferon regulatory factor 7 and the promotion of the IFN-alpha/IFN-gamma-dependent effector pathway, which resulted in vivo in protection against primary murine cytomegalovirus infection; (c) induced indoleamine 2,3-dioxygenase activity in DCs, thus affecting tolerization toward self as well as microbial non-self-antigens, and this resulted in vivo in transplantation tolerance and protection from inflammatory allergy. Talpha1 is produced in vivo by cleavage of prothymosin alpha in diverse mammalian tissues. Our data qualify Talpha1 as an endogenous regulator of immune homeostasis and suggest that instructive immunotherapy with Talpha1, via DCs and tryptophan catabolism, could be at work to control inflammation, immunity, and tolerance in a variety of clinical settings.
Flow optimization study of a batch microfluidics PET tracer synthesizing device (2010)

We present numerical modeling and experimental studies of flow optimization inside a batch microfluidic micro-reactor used for synthesis of human-scale doses of Positron Emission Tomography (PET) tracers. Novel techniques are used for mixing within, and eluting liquid out of, the coin-shaped reaction chamber. Numerical solutions of the general incompressible Navier Stokes equations along with time-dependent elution scalar field equation for the three dimensional coin-shaped geometry were obtained and validated using fluorescence imaging analysis techniques. Utilizing the approach presented in this work, we were able to identify optimized geometrical and operational conditions for the micro-reactor in the absence of radioactive material commonly used in PET related tracer production platforms as well as evaluate the designed and fabricated micro-reactor using numerical and experimental validations.
Miniature Laser Doppler Velocimeter for Measuring Wall Shear (2005)

A miniature optoelectronic instrument has been invented as a nonintrusive means of measuring a velocity gradient proportional to a shear stress in a flow near a wall. The instrument, which can be mounted flush with the wall, is a variant of a basic laser Doppler velocimeter. The laser Doppler probe volume can be located close enough to the wall (as little as 100 micron from the surface) to lie within the viscosity-dominated sublayer of a turbulent boundary layer. The instrument includes a diode laser, the output of which is shaped by a diffractive optical element (DOE) into two beams that have elliptical cross sections with very high aspect ratios.
Preferential Growth of Single-Walled Carbon Nanotubes with Metallic Conductivity (2009)

Single-walled carbon nanotubes can be classified as either metallic or semiconducting, depending on their conductivity, which is determined by their chirality. Existing synthesis methods cannot controllably grow nanotubes with a specific type of conductivity. By varying the noble gas ambient during thermal annealing of the catalyst, and in combination with oxidative and reductive species, we altered the fraction of tubes with metallic conductivity from one-third of the population to a maximum of 91%. In situ transmission electron microscopy studies reveal that this variation leads to differences in both morphology and coarsening behavior of the nanoparticles that we used to nucleate nanotubes. These catalyst rearrangements demonstrate that there are correlations between catalyst morphology and resulting nanotube electronic structure and indicate that chiral-selective growth may be possible.
Optical coherence tomography angiography: Technical principles and clinical applications in ophthalmology (2017)

Optical coherence tomography angiography (OCTA) is a functional extension of OCT that provides information on retinal and choroidal circulations without the need for dye injections. With the recent development of high-speed OCT systems and efficient algorithms, OCTA has become clinically feasible. In this review article, we discuss the technical principles of OCTA, including image processing and artifacts, and its clinical applications in ophthalmology. We summarize recent studies which qualitatively or quantitatively assess disease presentation, progression, and/or response to treatment.
Ultrasonic soldering bath having an ultrasonic probe extending into the solder bath (1980)

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ASYMMETRIC DEPTH-FILTRATION – A VERSATILE AND SCALABLE APPROACH FOR ISOLATION AND PURIFICATION OF EXTRACELLULAR VESICLES (2021)

A new method that is based on asymmetric depth-filtration was developed and tested for isolation of extracellular vesicles (EVs) from biological fluids such as human plasma, urine, Wharton's jelly and cell culture. Results showed that such method can be a reliable alternative for EV research and their application in medicine.
A robust internal control for high-precision DNA methylation analyses by droplet digital PCR (2018)

Implementation of a robust internal control, i.e., the 4Plex, and an algorithm for automated threshold determination, PoDCall, in methylation-specific ddPCR increase the precision of DNA methylation analysis.
Broadly Protective Shigella Vaccine Based on Type III Secretion Apparatus Proteins (2011)

Shigella spp. are food- and waterborne pathogens that cause severe diarrheal and dysenteric disease associated with high morbidity and mortality. Individuals most often affected are children under 5 years of age in the developing world. The existence of multiple Shigella serotypes and the heterogenic distribution of pathogenic strains, as well as emerging antibiotic resistance, require the development of a broadly protective vaccine. All Shigella spp. utilize a type III secretion system (TTSS) to initiate infection. The type III secretion apparatus (TTSA) is the molecular needle and syringe that form the energized conduit between the bacterial cytoplasm and the host cell to transport effector proteins that manipulate cellular processes to benefit the pathogen. IpaB and IpaD form a tip complex atop the TTSA needle and are required for pathogenesis. Because they are common to all virulent Shigella spp., they are ideal candidate antigens for a subunit-based, broad-spectrum vaccine. We examined the immunogenicity and protective efficacy of IpaB and IpaD, alone or combined, coadministered with a double mutant heat-labile toxin (dmLT) from Escherichia coli, used as a mucosal adjuvant, in a mouse model of intranasal immunization and pulmonary challenge. Robust systemic and mucosal antibody- and T cell-mediated immunities were induced against both proteins, particularly IpaB. Mice immunized in the presence of dmLT with IpaB alone or IpaB combined with IpaD were fully protected against lethal pulmonary infection with Shigella flexneri and Shigella sonnei. We provide the first demonstration that the Shigella TTSAs IpaB and IpaD are promising antigens for the development of a cross-protective Shigella vaccine.
Crystal growth and characterization of selected high-performance scintillators for national security applications (Conference Presentation) (2018)

Scintillators are important materials for radiation detection applications such as homeland security, geological exploration, and medical imaging. Scintillators for nuclear nonproliferation applications in particular must have excellent energy resolution in order to distinguish the gamma-ray signatures of potentially dangerous radioactive sources, such as highly enriched uranium or plutonium, from non-threat radioactive sources such as radioactive tracers used in medical imaging. There is an established need for scintillators with energy resolution in the 1-2% range at 662 keV. However, there are challenges surrounding the development of this new generation of high light yield/high resolution scintillators; for example, the high cost of production due to low crystal yield and slow growth process, and crystal inhomogeneity. We will discuss efforts focused on developing recently discovered high performance scintillators K(Sr,Ba)2I5:Eu, Cs4(Ca,Sr)I6:Eu and Cs2Hf(Cl,Br)6 that have potential for meeting nuclear security needs. Growth parameters for these materials have been optimized, allowing the growth of excellent quality single crystals measuring up to one-inch in diameter via the vertical Bridgman technique at translation rates between 1 and 5 mm/h. These scintillators materials have excellent properties with light yields between 30,000 and 120,000 ph/MeV, and energy resolutions between 2.3 and 4.6% at 662 keV.
Monoclonal Antibody-Based Antigenic Mapping of Norovirus GII.4-2002 (2011)

Noroviruses are the primary cause of epidemic gastroenteritis in humans, and GII.4 strains cause ∼80% of the overall disease burden. Surrogate neutralization assays using sera and mouse monoclonal antibodies (MAbs) suggest that antigenic variation maintains GII.4 persistence in the face of herd immunity, as the emergence of new pandemic strains is accompanied by newly evolved neutralization epitopes. To potentially identify specific blockade epitopes that are likely neutralizing and evolving between pandemic strains, mice were hyperimmunized with GII.4-2002 virus-like particles (VLPs) and the resulting MAbs were characterized by biochemical and immunologic assays. All of the MAbs but one recognized GII.4 VLPs representing strains circulating from 1987 to 2009. One MAb weakly recognized GII.4-1987 and -1997 while strongly interacting with 2002 VLPs. This antibody was highly selective and effective at blocking only GII.4-2002-ligand binding. Using bioinformatic analyses, we predicted an evolving GII.4 surface epitope composed of amino acids 407, 412, and 413 and subsequently built mutant VLPs to test the impact of the epitope on MAb binding and blockade potential. Replacement of the 2002 epitope with the epitopes found in 1987 or 2006 strains either reduced or ablated enzyme immunoassay recognition by the GII.4-2002-specific blockade MAb. These data identify a novel, evolving blockade epitope that may be associated with protective immunity, providing further support for the hypotheses that GII.4 norovirus evolution results in antigenic variation that allows the virus to escape from protective herd immunity, resulting in new epidemic strains.
Broadband NFC - A system analysis for the uplink (2008)

Near field communication (NFC) is a new, short-range wireless connectivity technology that evolved from a combination of existing contactless identification and interconnection technologies. Products with built-in NFC will have the aim to simplify the way consumer devices interact with one another. Data-intensive applications based on NFC or applications for health care/e-government need an increase from the actual defined and standardised transmission rates of 424 kbit/s to a higher rate. The topic of this paper is to point out physical layer parameters, limitations and concepts, allowing to enhance the transmission rate of the 13.56 MHz NFC-systems. Finally one implementation of a lab scaled prototype with a transmission rate of 6.78 Mbit/s from card to reader is demonstrated and discussed.
Aberration retrieval using the extended Nijboer-Zernike approach (2003)

We give the proof of principle of a new experimental method to determine the aberrations of an optical system in the field. The measurement is based on the observation of the intensity point-spread function of the lens. To analyze and interpret the measurement, use is made of an analytical method, the so-called extended Nijboer-Zernike approach. The new method is applicable to lithographic projection lenses, but also to EUV mirror systems or microscopes such as the objective lens of an optical mask inspection tool. Phase retrieval is demonstrated both analytically and experimentally. The extension of the method to the case of a medium-to-large hole sized test object is presented. Theory and experimental results are given. In addition we present the extension to the case of aberrations comprising both phase and amplitude errors.
Images of a Spin-Torque-Driven Magnetic Nano-Oscillator (2011)

We present the first space- and time-resolved images of the spin-torque-induced steady-state oscillation of a magnetic vortex in a spin-valve nanostructure. We find that the vortex structure in a nanopillar is considerably more complicated than the 2D idealized structure often-assumed, which has important implications for the driving efficiency. The sense of the vortex gyration is uniquely determined by the vortex core polarity, confirming that the spin-torque acts as a source of negative damping even in such a strongly nonuniform magnetic system. The orbit radius is ∼10 nm, in agreement with micromagnetic simulations.
Non-orthogonal screen and its application in moire-free halftoning (2003)

In color reproduction, the most troublesome moire pattern is the second-order moire, or the three-color moire, usually produced by mixing of cyan, magenta and black halftone outputs. A classical 3-color zero-moire solution is using three identical cluster halftone screens with different rotations: 15, 45 and 75°, respectively. However, for most digital printing devices, the size and shape of halftone screens are constrained by the "digital grid", which defines the locations of printed dots; and therefore, an exact 15 or 75° rotation of a cluster screen is impossible. Although there are many alternative approaches for moire-free color halftoning, most of them only provide approximate solutions and/or have a tendency to generate additional artifacts associated with halftone outputs. The difficulty to achieve moire-free color halftoning is greatly relieved by using non-orthogonal halftone screens, i.e., screens in general parallelogram shapes. In this paper, a general condition for 3-color zero-moire solutions is derived. A procedure using integer equations to search moire-free solutions for different applications is also described.
Training-based channel estimation for multiple-antenna broadband transmissions (2003)

This paper addresses the problem of training sequence design for multiple-antenna transmissions over quasi-static frequency-selective channels. To achieve the channel estimation minimum mean square error, the training sequences transmitted from the multiple antennas must have impulse-like auto correlation and zero cross correlation. We reduce the problem of designing multiple training sequences to the much easier and well-understood problem of designing a single training sequence with impulse-like auto correlation. To this end, we propose to encode the training symbols with a space-time code, that may be the same or different from the space-time code that encodes the information symbols. Optimal sequences do not exist for all training sequence lengths and constellation alphabets. We also propose a method to easily identify training sequences that belong to a standard 2/sup m/-PSK constellation for an arbitrary training sequence length and an arbitrary number of unknown channel taps. Performance bounds derived indicate that these sequences achieve near-optimum performance.