gebhart/patrepeval huggingface dataset:
Glycoengineered Outer Membrane Vesicles: A Novel Platform for Bacterial Vaccines (2016)

The World Health Organization has indicated that we are entering into a post-antibiotic era in which infections that were routinely and successfully treated with antibiotics can now be lethal due to the global dissemination of multidrug resistant strains. Conjugate vaccines are an effective way to create a long-lasting immune response against bacteria. However, these vaccines present many drawbacks such as slow development, high price, and batch-to-batch inconsistencies. Alternate approaches for vaccine development are urgently needed. Here we present a new vaccine consisting of glycoengineered outer membrane vesicles (geOMVs). This platform exploits the fact that the initial steps in the biosynthesis of most bacterial glycans are similar. Therefore, it is possible to easily engineer non-pathogenic Escherichia coli lab strains to produce geOMVs displaying the glycan of the pathogen of interest. In this work we demonstrate the versatility of this platform by showing the efficacy of geOMVs as vaccines against Streptococcus pneumoniae in mice, and against Campylobacter jejuni in chicken. This cost-effective platform could be employed to generate vaccines to prevent infections caused by a wide variety of microbial agents in human and animals.
Millimeter-wave radar combining Tx beamforming and Rx array processing for precise pedestrians detection (2012)

The advanced radar detection method which combines Tx beamforming and Rx array processing with highresolution direction of arrival (DOA) estimation is proposed. The proposed method associates DOA estimation direction with Tx beamforming direction (TxD-DOA) for a high accuracy detection for multiple targets in millimeter-wave radar system. Computer simulation and experiment evaluation verify the improvement effects of the TxD-DOA method. We have confirmed that the suppression of multiple radar reflection waves by the transmission beam scanning brings the better DOA estimation accuracy and higher angular resolution of the TxD-DOA for multiple human targets.
Shuffling Improves the Acute and Carryover Effect of Subthalamic Coordinated Reset Deep Brain Stimulation (2022)

Coordinated reset deep brain stimulation (CR DBS) in the subthalamic nucleus (STN) has been demonstrated effective for the treatment of the motor signs associated with Parkinson's disease (PD). A critical CR parameter is an order in which stimulation is delivered across contacts. The relative effect of alternating vs. not alternating this order, i.e., shuffling vs. non-shuffling, however, has not been evaluated <i>in vivo</i>. The objective of this study is to compare the effect of shuffled vs. non-shuffled STN CR DBS on Parkinsonian motor signs. Two Parkinsonian non-human primates were implanted with a DBS lead in the STN. The effects of STN CR DBS with and without shuffling were compared with the traditional isochronal DBS (tDBS) using a within-subject design. For each stimulation setting, DBS was delivered for 2 or 4 h/day for 5 consecutive days. The severity of PD was assessed using a modified clinical rating scale immediately before, during, and 1 h after DBS, as well as on days following the discontinuation of the 5 days of daily stimulation, i.e., carryover effect. Shuffled STN CR DBS produced greater acute and carryover improvements on Parkinsonian motor signs compared with non-shuffled CR. Moreover, this difference was more pronounced when more effective stimulation intensity and burst frequency settings were used. tDBS showed limited carryover effects. Given the significant effect of shuffling on the effectiveness of CR DBS, it will be critical for future studies to further define the relative role of different CR parameters for the clinical implementation of this novel stimulation paradigm.
Large-Scale, Nonchromatographic Purification of Plasmid DNA (2006)

A large-scale approach to the purification of plasmid DNA has been developed that overcomes many of the limitations of current chromatography-based processes. The process consists of a scaleable lysis using recombinant lysozyme and a rapid heating and cooling step followed by a selective precipitation with cetyltrimethylammonium bromide (CTAB). Calcium silicate batch adsorption is then utilized to remove residual genomic DNA, linear plasmid, open circular plasmid, endotoxin, detergents, and proteins. Finally, a concentration and diafiltration step utilizing ultrafiltration and a terminal sterile filtration complete the process. The final product exceeds the requirements for clinical-grade plasmid DNA, and the process has been scaled up to yield an average of 18 ± 4 g (over five lots) of pharmaceutically pure plasmid DNA per 140 L of lysate (from approx 1.3 kg Escherichia coli dry cell weight).
Protection against Pneumococcal Colonization and Fatal Pneumonia by a Trivalent Conjugate of a Fusion Protein with the Cell Wall Polysaccharide (2009)

Cell wall polysaccharide (CWPS), pneumolysin, and surface adhesin A (PsaA) are antigens common to virtually all serotypes of Streptococcus pneumoniae (pneumococcus), and all have been studied separately for use in protection. Previously we showed that protection against nasopharyngeal (NP) colonization by intranasal vaccination of mice with killed pneumococci is mediated by T(H)17 cells and correlates with interleukin-17A (IL-17A) expression by T cells in vitro; we have also shown that CWPS and other species-common antigens protect against colonization by a similar mechanism. Here we made a fusion protein of PsaA with the pneumolysin nontoxic derivative PdT and then coupled CWPS to the fusion protein, aiming to enhance immune responses to all three antigens. When given intranasally with cholera toxin adjuvant, the fusion conjugate induced higher serum antibody titers and greater priming for IL-17A responses than an equimolar mixture of the three antigens. The conjugate administered intranasally protected mice against experimental NP colonization by a strain of serotype 6B, while mice immunized with the mixture or with bivalent conjugates were not protected. Subcutaneous immunization with the conjugate and alum adjuvant likewise induced higher antibody titers than the mixture, primed for IL-17A responses, and reduced colonization. The conjugate, but not the antigen mixture, fully protected mice from fatal pneumonia caused by a highly virulent serotype 3 strain. Thus, a covalent construct of three antigens common to all serotypes exhibits protection with both mucosal and systemic administration.
Genome‐scale model for <i>Clostridium acetobutylicum</i>: Part II. Development of specific proton flux states and numerically determined sub‐systems (2008)

A regulated genome-scale model for Clostridium acetobutylicum ATCC 824 was developed based on its metabolic network reconstruction. To aid model convergence and limit the number of flux-vector possible solutions (the size of the phenotypic solution space), modeling strategies were developed to impose a new type of constraint at the endo-exo-metabolome interface. This constraint is termed the specific proton flux state, and its use enabled accurate prediction of the extracellular medium pH during vegetative growth of batch cultures. The specific proton flux refers to the influx or efflux of free protons (per unit biomass) across the cell membrane. A specific proton flux state encompasses a defined range of specific proton fluxes and includes all metabolic flux distributions resulting in a specific proton flux within this range. Effective simulation of time-course batch fermentation required the use of independent flux balance solutions from an optimum set of specific proton flux states. Using a real-coded genetic algorithm to optimize temporal bounds of specific proton flux states, we show that six separate specific proton flux states are required to model vegetative-growth metabolism and accurately predict the extracellular medium pH. Further, we define the apparent proton flux stoichiometry per weak acids efflux and show that this value decreases from approximately 3.5 mol of protons secreted per mole of weak acids at the start of the culture to approximately 0 at the end of vegetative growth. Calculations revealed that when specific weak acids production is maximized in vegetative growth, the net proton exchange between the cell and environment occurs primarily through weak acids efflux (apparent proton flux stoichiometry is 1). However, proton efflux through cation channels during the early stages of acidogenesis was found to be significant. We have also developed the concept of numerically determined sub-systems of genome-scale metabolic networks here as a sub-network with a one-dimensional null space basis set. A numerically determined sub-system was constructed in the genome-scale metabolic network to study the flux magnitudes and directions of acetylornithine transaminase, alanine racemase, and D-alanine transaminase. These results were then used to establish additional constraints for the genome-scale model.
Microscopic tomography by digital interference holography (2004)

We are developing the digital interference holography (DIH) as a novel method of microscopic tomographic imaging by numerical superposition of a number of holographic fields taken with varying wavelengths. The digital interference holography does not involve pixel-by-pixel mechanical scanning of three-dimensional volume and yet achieves high lateral and longitudinal resolutions. The holographic interference pattern of an object is generated optically and recorded digitally using a CCD camera. The hologrpahic image field is numerically calculated using basic diffraction formulas and the process is repeated for a range of varying wavelengths at regular intervals. Numerical superposition, or digital interference, of the holographic image fields yields the desired three-dimensional representation of the object. Experiments have demonstrated a few-micron lateral and axial resolutions. Furthermore, since the DIH is a coherent imaging system, one can form true tomographic images of sub-surface structures, in the presence of diffuse scattering from overlying layers. By being able to generate true tomographic images of subsurface structures, without the need for three-dimensional mechanical scannig, the DIH method can provide a very efficient and versatile imaging modality for a wide range of applications in materials science and biomedical imaging.
Metagenomic evaluation of the dairy farm environment and facilities for evidence of digital dermatitis-associated bacteria (2016)

Bovine digital dermatitis is a common polybacterial disease process and a leading cause of lameness in dairy and beef cattle. Mature lesions are associated with a very high abundance of Treponema spp organisms, while developing lesions have a larger diversity with different populations of organisms. This study was designed to utilize 16S-based phylogenomics to evaluate a variety of environmental samples obtained from various areas of a dairy farm for the presence of bacterial organisms associated with digital dermatitis lesions.
A human cytomegalovirus glycoprotein complex designated gC-II is a major heparin-binding component of the envelope (1992)

The purposes of this study were to determine whether heparin would block human cytomegalovirus (HCMV) infection of skin fibroblast (SF) cells and to identify HCMV envelope glycoproteins which might have affinity for heparin. It was determined that soluble heparin in concentrations of 5 to 20 micrograms/ml was capable of blocking HCMV infection of SF cells. However, after virus had adsorbed to the SF cells, heparin lost its ability to block infection. It was also determined that treatment of SF cells with heparinase to remove cell surface heparinlike moieties prevented HCMV infection of SF cells. These data showed that HCMV, like other herpesviruses, adsorbed to cells by binding cell surface heparin. Heparin affinity chromatography was done to determine which HCMV envelope glycoproteins bound heparin. HCMV envelope glycoproteins were solubilized in a nonionic detergent and applied to a heparin affinity column. An HCMV glycoprotein complex designated gC-II was the major component to bind to immobilized heparin and elute in the presence of soluble heparin.
The Hsp60 protein of <i>Helicobacter pylori</i>: structure and immune response in patients with gastroduodenal diseases (1993)

Helicobacter pylori is a human pathogen that has been associated with gastritis, peptic ulcer and gastric carcinoma. The role of the direct action of H. pylori virulence factors and of the induction of autoreactive immunity in the development of chronic gastritis has not been clarified yet. Here we report the cloning and molecular characterization of a gene of H. pylori coding for a protein of 58 kDa, recognized by sera of patients affected by H. pylori-induced gastroduodenal diseases. This antigen is present in all the H. pylori strains tested and it belongs to the Hsp60 family of heat-shock proteins, with high homology with other bacterial and eukaryotic proteins of the same family. This class of homologous proteins has been implicated in the induction of autoimmune disorders in different systems. The presence in infected patients of anti-H. pylori Hsp60 antibodies, potentially cross-reactivity between human Hsp60 and a rabbit antiserum against H. pylori Hsp60 suggest that a role of this protein in gastroduodenal diseases is possible.
Innate and adaptive immunity to human beta cell lines: implications for beta cell therapy (2015)

We demonstrate that genetically engineered human beta cell lines can be used in vitro to assess diverse immune responses that may be involved in the pathogenesis of type 1 diabetes in humans and beta cell transplantation, enabling preclinical evaluation of novel immune intervention strategies protecting beta cells from immune destruction.
Laboratory tests of a time-domain reflectometry system for frazil ice detection (1999)

A prototype, electromagnetic-based frazil ice detection system (patent pending) has been developed and tested under simulated frazil ice accretion conditions in an environmentally controlled flume. The system employs a time-domain reflectometer (TDR) and specially designed transmission line sensor to monitor the accretion of frazil ice by measuring the propagation time along the sensor when it is submerged. Changes in the round-trip travel time of the TDR pulse result from a decrease in the localized bulk dielectric constant as frazil ice accretes and displaces water around the sensor. Two frazil detection sensor configurations were tested, a parallel transmission line probe and a semicylindrical mesh coaxial probe. During 2 h long experiments, the TDR clearly indicated a decreasing probe propagation time as frazil ice continued to accrete. This is indicative of the decreasing bulk dielectric constant of the frazil ice and water mix. Continuous real-time data from the TDR were recorded. From these data, an estimate of volumetric ice fraction was calculated using a simple linear dielectric mixing equation. Volumetric ice fractions estimates for both probe configurations were calculated to increase from approximately 0.02 to 0.18 during the test. The system shows promise for detection and measurement of frazil ice growth and accretion in freshwater bodies.Key words: frazil ice, trash rack, water intake, icing detection, time-domain reflectometry, TDR.
Transcranial photoacoustic tomography of the monkey brain (2012)

A photoacoustic tomography (PAT) system using a virtual point ultrasonic transducer was developed for transcranial imaging of monkey brains. The virtual point transducer provided a 10 times greater field-of-view (FOV) than finiteaperture unfocused transducers, which enables large primate imaging. The cerebral cortex of a monkey brain was accurately mapped transcranially, through up to two skulls ranging from 4 to 8 mm in thickness. The mass density and speed of sound distributions of the skull were estimated from adjunct X-ray CT image data and utilized with a timereversal algorithm to mitigate artifacts in the reconstructed image due to acoustic aberration. The oxygenation saturation (sO2) in blood phantoms through a monkey skull was also imaged and quantified, with results consistent with measurements by a gas analyzer. The oxygenation saturation (sO2) in blood phantoms through a monkey skull was also imaged and quantified, with results consistent with measurements by a gas analyzer. Our experimental results demonstrate that PAT can overcome the optical and ultrasound attenuation of a relatively thick skull, and the imaging aberration caused by skull can be corrected to a great extent.
Applications of Ultra-Low Field Magnetic Resonance for Imaging and Materials Studies (2009)

Recently it has become both possible and practical to perform MR at magnetic fields from muT to mT, the so-called ultra-low field (ULF) regime. SQUID sensor technology allows for ultra-sensitive detection while pulsed pre-polarizing fields greatly enhance signal. The instrumentation allows for unprecedented flexibility in signal acquisition sequences. Here we present the results from several applications of ULF MR which exploit the unique abilities of the method. These include novel ways to image both brain structure and function either by combination of MRI with magnetoencephalography or direct observation of the interaction of neural currents with the spin population, and ULF relaxometry for detection and characterization of materials relevant to numerous non-invasive inspection applications. We briefly describe the motivation, advantages, and recent results of several new applications of the ULF MR method. Specifically, we present recent data measuring the interaction of weak ( ~ 10 muA) currents with a spin-population in a water phantom, as studied by ULF MRI with implications for neural current imaging. We also present data from a ULF MR relaxometer developed inspecting liquids in a check-point for the presence of hazardous material.
Passive Shroud Cooling Concepts for HP Turbines: Experimental Investigations (2006)

The cooling of rotor shrouds in the first stage of a high-pressure turbine requires special attention as flatter turbine inlet temperature profiles and more highly loaded blades result in increased thermal and mechanical stresses. The use of film cooling and/or internal convective cooling makes the rotor shroud heavier and oversized, restricting the maximum rotational speed. Alternative methods are therefore sought to achieve improved cooling of the shroud. This paper discusses the low speed experimental investigation of two ‘passive’ cooling concepts known as ‘rail cooling’ and ‘platform cooling’. It has been shown experimentally that the modified cooling method, namely the platform cooling, substantially improves the rotor shroud coolant distribution in the critical areas whilst employing significantly lower amounts of coolant.
Scanning tunneling microscope combined with optical microscope for large sample measurement (1990)

A new scanning tunneling microscope (STM) which can easily search the sample area of interest and can observe the whole area of the sample up to 150 mm diameter has been developed. Its key design feature is the built-in piezo driver tube, which scans up to 12 μm and is nearly the same size as the objective lens. This tube is located in the revolver of the optical microscope (OM), which has a rotation position reproducibility of better than 1 μm. Tip position can be easily found for comparing the STM and OM images by scanning the standard patterns before measurement. Tip position accuracy of better than 2 μm has been obtained. The whole system, which has a minimum resonance frequency Rf of around 400 Hz, is built on an air damping table (Rf=1.5 Hz) to isolate it from vibrations. However, care must be taken with larger samples because their low resonant frequencies pick up acoustic vibrations more easily. Thermal drift is another problem, as the lengths of the frame holding the piezo driver and the sample stage are quite long (≂50 cm). Symmetric design is adopted to reduce the surface drift (&lt;2 nm/min) and materials have been chosen to compensate for the vertical drift.
Wireless link signature: measurements, methodologies, and applications (2010)

We study and advance unique representations of physical layer wireless links, and explore opportunities to use them in location distinction, secret key establishment, and perimeter distinction applications.
Location distinction is the ability to determine when a device has changed its position. We compare two existing location distinction methods, and then combine their benefits to develop a new method using a metric that we call complex temporal signature. We use a 2.4 GHz link measurement dataset to evaluate the three methods. We find that the complex temporal signature method performs significantly better than the existing methods. We also perform new measurements to understand and model the temporal behavior of our link signatures. We integrate our model in our location distinction mechanism and significantly reduce false alarms due to temporal variations of link signatures.
We propose an approach where wireless devices, interested in establishing a secret key, sample the link signature space in a physical area to collect and combine uncorrelated measurements to generate the key. We study the impact of mobility patterns in obtaining uncorrelated measurements and find that (i) when movement step size is larger than one foot, the measurements are mostly uncorrelated, and (ii) more diffusion in the mobility results in less correlation in the measurements. We develop efficient mechanisms to encode measurements and reconcile the differences in the bits extracted between the two devices. Our results show that our scheme generates very high entropy secret bits at a high rate. 
Perimeter distinction is the ability to distinguish locations belonging to different perimeters. We examine the use of wireless received signal strength (RSS) and link signature, and propose multiple methods to retain good distinction rates even when the receiver faces power manipulation by malicious transmitters. Using extensive measurements of indoor and outdoor perimeters, we find that link signature outperforms RSS in various fading conditions in terms of accuracy. Even without using signal power, it can achieve accurate perimeter distinction of up to 80%. When we train our perimeter distinction method with multiple measurements within the same perimeter, we can improve the accuracy up to 98%.