gebhart/patrepeval huggingface dataset:
Development of a potent and protective germline-like antibody lineage against Zika virus in a convalescent human (2019)

Abstract Zika virus (ZIKV) specific neutralizing antibodies hold a great promise for antibody-based interventions and vaccine design against ZIKV infection. However, their development in infected patients remain unknown. Here, we report on the dynamic development of a potent and protective ZIKV-specific human antibody ZK2B10 initially isolated from a ZIKV convalescent individual using next-generation sequencing (NGS). The unbiased repertoire analysis showed dramatic changes in many families of heavy and light chain variable regions. However, lineage tracing of ZK2B10 revealed limited somatic hypermutation throughout the 12 months since the onset of symptom. In particular, NGS-derived germline-like somatic variants neutralized and protected mice from lethal challenge of ZIKV without detectable cross-reactivity with Dengue virus (DENV). Site-directed mutagenesis identified two residues within λ chain, N31 and S91 that are essential to the functional maturation. The dynamic features unveiled here will assist us to better understand the pathogenesis of ZIKV infection and inform rational design of vaccines. Author summary Recently emerged ZIKV is associated with severe neurological complications such as Guillain–Barré syndrome in adults and congenital microcephaly in newborns. No ZIKV-specific therapeutics or vaccines are currently available. We and others have identified a number of neutralizing antibodies capable of protecting experimental animals from ZIKV infection. However, the development of these potent antibodies during ZIKV natural infection remains unknown. Here, we report on the longitudinal analysis of one such antibody ZK2B10 using next-generation sequencing (NGS), bioinformatics and functional analysis. We found that the ZK2B10 germline-like antibodies possess strong neutralizing activity in vitro and impressive protectivity against lethal ZIKV infection in vivo . These findings suggest that the potent and protective antibody response against ZIKV can be generated within relative short term with high germline identity which provide great hope and promise for successful vaccine development against ZIKV.
Multiple Domain and Multiple Kernel Outcome-Weighted Learning for Estimating Individualized Treatment Regimes (2022)

Individualized treatment rules (ITRs) recommend treatments that are tailored specifically according to each patient's own characteristics. It can be challenging to estimate optimal ITRs when there are many features, especially when these features have arisen from multiple <i>data domains</i> (e.g., demographics, clinical measurements, neuroimaging modalities). Considering data from complementary domains and using multiple similarity measures to capture the potential complex relationship between features and treatment can potentially improve the accuracy of assigning treatments. Outcome weighted learning (OWL) methods that are based on support vector machines using a predetermined single kernel function have previously been developed to estimate optimal ITRs. In this paper, we propose an approach to estimate optimal ITRs by exploiting multiple kernel functions to describe the similarity of features between subjects both within and across data domains within the OWL framework, as opposed to preselecting a single kernel function to be used for all features for all domains. Our method takes into account the heterogeneity of each data domain and combines multiple data domains optimally. Our learning process estimates optimal ITRs and also identifies the data domains that are most important for determining ITRs. This approach can thus be used to prioritize the collection of data from multiple domains, potentially reducing cost without sacrificing accuracy. The comparative advantage of our method is demonstrated by simulation studies and by an application to a randomized clinical trial for major depressive disorder that collected features from multiple data domains. Supplemental materials for this article are available online.
Acoustic temperature measurement in a rocket noise field (2010)

A 1 μm diameter platinum wire resistance thermometer has been used to measure temperature fluctuations generated during a static GEM-60 rocket motor test. Exact and small-signal relationships between acoustic pressure and acoustic temperature are derived in order to compare the temperature probe output with that of a 3.18 mm diameter condenser microphone. After preliminary plane wave tests yielded good agreement between the transducers within the temperature probe's ∼2 kHz bandwidth, comparison between the temperature probe and microphone data during the motor firing show that the ±∼3 K acoustic temperature fluctuations are a significant contributor to the total temperature variations.
Optically pumped cesium plasma neutralization of space charge in photon-enhanced thermionic energy converters (2012)

Photon-enhanced thermionic emission from semiconducting cathodes is a promising means of increasing cathode current density in low temperature vacuum thermionic energy devices [J. W. Schwede et al., Nature Mater. 9, 762 (2010)]. However, the space charge resulting from high emission current densities prevents emitted electrons from reaching the collector, even with gaps as small as 100 μm and at voltages as high as 1 V. We demonstrate by particle-in-cell simulations that one possible solution to overcoming the space charge is to add cesium filling and generation of a space charge-neutralizing plasma by continuous laser excitation of the cesium resonance level.
Use of a fluorescent probe to assess the activities of candidate agents against intracellular forms of Encephalitozoon microsporidia (1997)

Microsporidia are obligate intracellular protozoan parasites. Three species of the genus Encephalitozoon are among the microsporidia that infect immunodeficient humans. These species, Encephalitozoon cuniculi, Encephalitozoon hellem, and Encephalitozoon intestinalis, all develop in a parasitophorous vacuole within a host cell. The present study describes a method that uses the fluorescent probe calcein and confocal microscopy to detect drug-induced effects in Encephalitozoon-infected green monkey kidney cells. The effects were as follows: (i) changes in parasite organization within the parasitophorous vacuole; (ii) swelling and gross morphological changes of parasite developing stages in situ; (iii) killing of developing parasite stages in situ, detected by their uptake of the fluorescent probe; and (iv) reduction in the viability of the host cell population, assessed by the loss of the probe. Verapamil and itraconazole were used to increase the vital dye loading by both uninfected and infected cells. Agents with known antimicrosporidial activity, albendazole and fumagillin, caused all three types of parasite changes at concentrations that had no detectable effect on host cell viability. The effective doses of albendazole and fumagillin that caused swelling and disorganization of parasite developing stages were 5 x 10(-7) and 10(-6) M respectively. Killing of developing stages was detected at 10-fold-higher concentrations for these agents and at 10(-5) M for metronidazole. This method can be used to screen candidate antimicrosporidial agents in infected cultured cells.
A crosssectional analysis of Facebook comments to study public perception of a new diagnostic test called the Cytosponge (2018)

Social media provides a useful platform for informal discussions about healthcare. Acceptability is key to the uptake of diagnostic devices and this can be difficult to gauge from questionnaires and qualitative studies. The aim of this study is to investigate whether Facebook could be used to gauge public perception toward uptake of a new diagnostic test for Barrett's esophagus called the Cytosponge. We retrospectively reviewed Facebook comments relating to a video on the Cytosponge. We categorized comments into: (1) Positive, (2) Negative, (3) Unknown and (4) Questions. Recurring themes that arose were compared to a qualitative study on the Cytosponge. The video received 22.5 million views and 2837 comments within four months. Of these, 525 comments were positive, 215 were unknown, 179 were negative, 71 were questions, and 1847 were 'Tagged' comments. Among positive comments, recurrent themes were that it was innovative, could lead to early cancer-detection, and more favorable than endoscopy. Among negative comments, a recurring theme was concern about the risk of gagging and vomiting. Among 'questions', a recurring theme was related to the risk of Cytosponge detachment. We compared our analysis to a published qualitative study and found similar themes arose across both studies. Facebook provides a rich source of qualitative data, which could be used to augment studies to gauge public perception toward a new diagnostic test.
Novel strategies for the biocontrol of noctuid pests (Lepidoptera) based on improving ascovirus infectivity using Bacillus thuringiensis (2020)

Identifying novel biocontrol agents and developing new strategies are urgent goals in insect pest biocontrol. Ascoviruses are potential competent insect viruses that may be developed into bioinsecticides, but this aim is impeded by their poor oral infectivity. To improve the per os infectivity of ascovirus, Bacillus thuringiensis kurstaki (Btk) was employed as a helper to damage the midgut of lepidopteran larvae (Helicoverpa armigera, Mythimna separata, Spodoptera frugiperda, and S. litura) in formulations with Heliothis virescens ascovirus isolates (HvAV-3h and HvAV-3j). Btk and ascovirus mixtures (Btk/HvAV-3h and Btk/HvAV-3j) were fed to insect larvae (3rd instar). With the exception of S. frugiperda larvae, which exhibited low mortality after ingesting Btk, the larvae of the other tested species showed three types of response to feeding on the formulas: type I, the tested larvae (H. armigera) were killed by Btk infection so quickly that insufficient time and resources remained for ascoviral invasion; type II, both Btk and the ascovirus were depleted by their competition, such that neither was successfully released or colonized the tissue; type III, Btk was eliminated by the ascovirus, and the ascovirus achieved systemic infection in the tested larvae. The feeding of Btk/ascovirus formulas led to a great reduction in larval diet consumption and resulted in a significant decrease in the emergence rate of H. armigera, M. separata, and S. litura larvae, which suggested that the formulas exerted marked oral control effects on both the contemporary individuals and the next generation of these tested pest species.
A new 3-D attributed data model for archiving and interchanging of coronary vessel systems (2002)

Morphology analysis on coronary vessel systems and the quantification of vessel parameters are important aids in clinical diagnosis. Biplane angiographic images are the common source for coronary disease assessment. 3-D reconstruction methods were established to extract the morphologic data. A quantitative coronary analysis system was used to determine important stenosis parameters. Further results, e.g. from other imaging modalities like intra-vasal ultrasound, deliver additional parameters. Usually these methods co-exist without any interconnection. A new 3-D data model for the coronary tree is presented here, which is capable of integrating the results of different applications. It contains the topology of the vessel tree as well as quantitative data in a hierarchic order.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Processing and design techniques for InGaAs/InAlAs/InP photoFETs and MSMs (2002)

Despite the theoretical advantages of InGaAs/InAlAs/InP photoFETs for electro-optical system applications, fully optimized device structures and processing protocols have yet to be developed. We report here results from several device variations directed toward such optimization. This includes variation of HEMT channel thickness and current density, grading of the hole-blocking InGaAs/InAlAs heterojunction. A novel substrate removal process with backside illumination, and frontside and backside passivation is explored for optimized discrete components as well as integrated devices. Many of these advances are applicable to both MSM photodetectors and photoFETs; results from each are presented.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Surface Modifications of Superparamagnetic Iron Oxide Nanoparticles with Polylactic Acid-Polyethylene Glycol Diblock Copolymer and Graphene Oxide for a Protein Delivery Vehicle (2019)

As a protein delivery vehicle, superparamagnetic iron oxide nanoparticles (SPION) with an average size of 19.6 4.8 nm were coated with polylactic acid (PLA) (5000)-polyethylene glycol (PEG) (10000) diblock copolymer and single layer graphene oxide (GO). Bovine serum -1 albumin was selected as the model protein, and the drug loading capacity of the designed vehicle is 2013 79 mg g . The drug release result shows that the average percentage of cumulative drug release after 47 days in vitro is 37.7% 1.4%.
Proflavin and microwave radiation: Absence of a mutagenic interaction (1990)

The potential ability of radiofrequency electromagnetic radiation (RFR) in the microwave range to induce mutagenesis, chromosomal aberrations, and sister chromatid exchanges in mammalian cells is being explored in our laboratories. In addition, we have also been examining the ability of simultaneous exposure to RFR and chemical mutagens to alter the genotoxic damage induced by chemical mutagens acting alone. We have performed experiments to determine whether there is an interaction between 2.45-GHz, pulsed-wave, RFR and proflavin, a DNA-intercalating drug. The endpoint studied was forward mutation at the thymidine kinase locus in L5178Y mouse leukemic cells. Any effect on the size distribution of the resulting colonies of mutated cells was also examined. The exposures were performed at net forward powers of 500 or 600 W, resulting in a specific absorption rate (SAR) of approximately 40 W/kg. The culture-medium temperature reached a 3 degrees C maximal increase during the 4-h exposure; appropriate 37 degrees C and convection-heating temperature controls (TC) were performed. In no case was there any indication of a statistically significant increase in the induced mutant frequency due to the simultaneous exposure to RFR and proflavin, as compared with the proflavin exposures alone. There was also no indication of any change in the colony-size distribution of the resulting mutant colonies, neither, and there was no evidence in these experiments of any mutagenic action by the RFR exposure alone.
The Design and Measurement of Pulsed Magnetic Field (2011)

To investigate the solidification behavior of metallic melt under the pulsed magnetic field (PMF), a method of capacitors discharging to a pair of solenoid was utilized to produce the desired PMF. Based on the principle of R-L-C circuit and the calculation of magnetic intensity, the appropriate coil parameters of excitation solenoid, such as winding turns, layers and size, were determined. The electromagnetic induction method was chosen to measure the magnetic intensity of PMF effect zone, and the magnetic distribution curves of peak value intensity along horizontal central axes of magnetic field were obtained. The multipoint measuring results indicates that the experimental results are in close agreement with the results of calculation of electromagnetic theory and finite element analysis, which demonstrates that the design of magnetic settings is reasonable.
A practical guide and software for analysing pairwise comparison\n experiments (2017)

Most popular strategies to capture subjective judgments from humans involve\nthe construction of a unidimensional relative measurement scale, representing\norder preferences or judgments about a set of objects or conditions. This\ninformation is generally captured by means of direct scoring, either in the\nform of a Likert or cardinal scale, or by comparative judgments in pairs or\nsets. In this sense, the use of pairwise comparisons is becoming increasingly\npopular because of the simplicity of this experimental procedure. However, this\nstrategy requires non-trivial data analysis to aggregate the comparison ranks\ninto a quality scale and analyse the results, in order to take full advantage\nof the collected data. This paper explains the process of translating pairwise\ncomparison data into a measurement scale, discusses the benefits and\nlimitations of such scaling methods and introduces a publicly available\nsoftware in Matlab. We improve on existing scaling methods by introducing\noutlier analysis, providing methods for computing confidence intervals and\nstatistical testing and introducing a prior, which reduces estimation error\nwhen the number of observers is low. Most of our examples focus on image\nquality assessment.\n
Modeling Brain Dynamics in Brain Tumor Patients Using the Virtual Brain (2018)

Presurgical planning for brain tumor resection aims at delineating eloquent tissue in the vicinity of the lesion to spare during surgery. To this end, noninvasive neuroimaging techniques such as functional MRI and diffusion-weighted imaging fiber tracking are currently employed. However, taking into account this information is often still insufficient, as the complex nonlinear dynamics of the brain impede straightforward prediction of functional outcome after surgical intervention. Large-scale brain network modeling carries the potential to bridge this gap by integrating neuroimaging data with biophysically based models to predict collective brain dynamics. As a first step in this direction, an appropriate computational model has to be selected, after which suitable model parameter values have to be determined. To this end, we simulated large-scale brain dynamics in 25 human brain tumor patients and 11 human control participants using The Virtual Brain, an open-source neuroinformatics platform. Local and global model parameters of the Reduced Wong-Wang model were individually optimized and compared between brain tumor patients and control subjects. In addition, the relationship between model parameters and structural network topology and cognitive performance was assessed. Results showed (1) significantly improved prediction accuracy of individual functional connectivity when using individually optimized model parameters; (2) local model parameters that can differentiate between regions directly affected by a tumor, regions distant from a tumor, and regions in a healthy brain; and (3) interesting associations between individually optimized model parameters and structural network topology and cognitive performance.
A practical method to measure the MTF of CT scanners (1982)

A method has been devised which enables the modulation transfer function (MTF) of computerized tomographic (CT) scanners to be simply and rapidly determined. The method relies upon the measurement of the standard deviation of the pixel values within the image of cyclic bar patterns. The method is shown to produce results which are indistinguishable from those derived by less practical conventional methods.
Phonemic awareness and early spelling skills in urban Australian Aboriginal and non-Aboriginal children (2010)

This study investigated the phonological awareness and early spelling skills of 10 Australian Aboriginal and 10 non-Aboriginal children in their first year of schooling at urban schools. Phonological awareness was assessed using a standardized test (the Queensland University Inventory of Literacy), and children completed a standard spelling task that required them to generate spelling attempts in response to 12 line drawings of familiar animals. Spelling was analysed using the Spelling Scoring Sensitivity procedure. All children performed within the normal range for scores on the QUIL. However, as a group, Aboriginal children performed more poorly than their non-Aboriginal peers. Statistically significant differences were found on the subtests non-word spelling, non-word reading, and phoneme segmentation. Both formal scoring and informal observations were used to examine the spelling skills of participants. Possible explanations of the differences between groups are discussed in terms of health and cultural factors, and implications for the education of Aboriginal children are suggested.
The future is now for rare genetic diseases (2012)

We agree with the cautionary note sounded by Roger Collier with respect to the hype surrounding genomic medicine.[1][1] In most cases a careful medical and family history combined with a thorough physical examination has as much, and very likely more, clinical prognostic power than does a complete
Ultra‐High Capacity Lithium‐Ion Batteries with Hierarchical CoO Nanowire Clusters as Binder Free Electrodes (2015)

Although transition metal oxide electrodes have large lithium storage capacity, they often suffer from low rate capability, poor cycling stability, and unclear additional capacity. In this paper, CoO nanowire clusters (NWCs) composed of ultra‐small nanoparticles (≈10 nm) directly grown on copper current collector are fabricated and evaluated as an anode of binder‐free lithium‐ion batteries, which exhibits an ultra‐high capacity and good rate capability. At a rate of 1 C (716 mA g −1 ), a reversible capacity as high as 1516.2 mA h g −1 is obtained, and even when the current density is increased to 5 C, a capacity of 1330.5 mA h g −1 could still be maintained. Importantly, the origins of the additional capacity are investigated in detail, with the results suggesting that pseudocapacitive charge and the higher‐oxidation‐state products are jointly responsible for the large additional capacity. In addition, nanoreactors for the CoO nanowires are fabricated by coating the CoO nanowires with amorphous silica shells. This hierarchical core–shell CoO@SiO 2 NWC electrode achieves an improved cycling stability without degrading the high capacity and good rate capability compared to the uncoated CoO NWCs electrode.
Drop-Based Modeling of Extraction Equipment (2019)

The design of equipment for solvent extraction is a challenging task. Two major types of equipment shall be regarded, namely extraction columns and mixer-settlers. The challenge in designing a mixer-settler with respect to its major dimensions lies in the difficulty of predicting coalescence and thus settling behavior, which strongly depends on the material system due to the significant influence of trace impurities like salts and surfactants on the drop coalescence. Since the models for the drop-based simulation of extraction-column behavior also need to take the interaction between the drop swarms and the column internals properly into account, the lab-scale measuring cells for drop behavior have been augmented correspondingly. In the extraction column, coalescence and breakage of the drops determine the drop-size distribution and, therefore, the volume-specific interfacial area for mass transfer. The results of the drop-based simulations show that they allow the prediction of the behavior of extraction equipment on a pilot-plant and technical scale with good accuracy.