gebhart/patrepeval huggingface dataset:
Quantitative Lateral Flow Assays for Salivary Biomarker Assessment: A Review (2017)

Saliva is an emerging biofluid with a significant number of applications in use across research and clinical settings. The present paper explores the reasons why saliva has grown in popularity in recent years, balancing both the potential strengths and weaknesses of this biofluid. Focusing on reasons why saliva is different from other common biological fluids such as blood, urine, or tears, we review how saliva is easily obtained, with minimal risk to the donor, and reduced costs for collection, transportation, and analysis. We then move on to a brief review of the history and progress in rapid salivary testing, again reviewing the strengths and weaknesses of rapid immunoassays (e.g., lateral flow immunoassay) compared to more traditional immunoassays. We consider the potential for saliva as an alternative biofluid in a setting where rapid results are important. We focus the review on salivary tests for small molecule biomarkers using cortisol as an example. Such salivary tests can be applied readily in a variety of settings and for specific measurement purposes, providing researchers and clinicians with opportunities to assess biomarkers in real time with lower transportation, collection, and analysis costs, faster turnaround time, and minimal training requirements. We conclude with a note of cautious optimism that the field will soon gain the ability to collect and analyze salivary specimens at any location and return viable results within minutes.
Combining Anatomical Constraints and Deep learning for 3-D CBCT Dental Image Multi-label Segmentation (2021)

Machine learning research on medical images is becoming popular as advanced imaging technologies and equipment in medicine become more and more available. Dental Cone-beam Computed Tomography (Dental CBCT), a frequently-used visualization tool for oral diagnosis, provides valuable three-dimensional information, whose development for automation of Dental CBCT analysis, on the other hand, is relatively preliminary. Generally, there are three important characteristics for analyzing Dental CBCT with noisy labels and limited labeled sample size, and availability of oral medicine knowledge. Based on those characteristics, we develop an image segmentation method for Dental CBCT by integrating domain knowledge into deep U-Net for the 3D segmentation. Finally, depending on whether the knowledge can be decomposed into each pixel, the knowledge constraints are classified into two types: separable and non-separable constraints. All knowledge constraints can be represented as a posterior regularization term and solved in different ways in accordance with related types. For separable constraints, the mean-field theory is employed to solve an optimization problem with the independence assumption about the distributions of output variables on each pixel. For non-separable constraints, we propose to combine the importance sampling based approach and the stochastic optimization algorithm. Finally, we propose to formulate the domain knowledge to the learning stage to improve the accuracy and efficiency of automation of Dental CBCT segmentation. Finally, we will apply the proposed methods into the real datasets collected and manually labeled by the doctors at the University of Pennsylvania.
Improved Quantification of Myocardium Scar in Late Gadolinium Enhancement Images: Deep Learning Based Image Fusion Approach (2021)

3 TECHNICAL EFFICACY: 1.
Virtual Screening against Metalloenzymes for Inhibitors and Substrates (2005)

Molecular docking uses the three-dimensional structure of a receptor to screen databases of small molecules for potential ligands, often based on energetic complementarity. For many docking scoring functions, which calculate nonbonded interactions, metalloenzymes are challenging because of the partial covalent nature of metal-ligand interactions. To investigate how well molecular docking can identify potential ligands of metalloenzymes using a "standard" scoring function, we have docked the MDL Drug Data Report (MDDR), a functionally annotated database of 95,000 small molecules, against the X-ray crystal structures of five metalloenzymes. These enzymes included three zinc proteases, the nickel analogue of an iron enzyme, and a molybdenum metalloenzyme. The ability of the docking program to retrospectively enrich the annotated ligands as high-scoring hits for each enzyme and to calculate proper geometries was evaluated. In all five systems, the annotated ligands within the MDDR were enriched at least 20 times over random. To test the approach prospectively, a sixth target, the zinc beta-lactamase from Bacteroides fragilis, was screened against the fragment-like subset of the ZINC database. We purchased and tested 15 compounds from among the top 50 top-ranked ligands from docking, and found 5 inhibitors with apparent K(i) values less than 120 microM, the best of which was 2 microM. A more ambitious test still was predicting actual substrates for a seventh target, a Zn-dependent phosphotriesterase from Pseudomonas diminuta. Screening the Available Chemicals Directory (ACD) identified 25 thiophosphate esters as potential substrates within the top 100 ranked compounds. Eight of these, all previously uncharacterized for this enzyme, were acquired and tested, and all were confirmed experimentally as substrates. These results suggest that a simple, noncovalent scoring function may be used to identify inhibitors of at least some metalloenzymes.
On-Virus Construction of Polyvalent Glycan Ligands for Cell-Surface Receptors (2008)

Glycans arrayed on the exterior of virus particles were used as substrates for glycosyltransferase reactions to build di- and trisaccharides from the virus surface. The resulting particles exhibited tight and specific associations with cognate receptors on beads and cells, in one example defeating in cis cell-surface interactions in a manner characteristic of polyvalent binding. Combined with the ability of viruses to provide structurally well-defined attachment points, the methodology provides a convenient and powerful way to prepare complex carbohydrate ligands for clustered receptors.
Implementing fast cloth simulation with collision response (2002)

The article details and implements efficient techniques for cloth simulation, both in the area of numerical simulation and the area of collision detection and response. Emphasis is put on the efficient implementation of implicit numerical methods with many improvements toward better realism, as well as computation simplicity. A constraint based collision response scheme is adapted to this scheme in order to provide an accurate and stable collision response.
Human high-affinity Fc IgG receptor (Fc gamma RI)-mediated phagocytosis and pinocytosis in COS cells. (1994)

The high-affinity receptor (Fc gamma RI) for the constant (Fc) portion of immunoglobulin G (IgG) is one of three Fc IgG receptor classes (Fc gamma Rs) found on mononuclear phagocytes. The functional specialization of each of the Fc gamma R classes is not well understood. Previous studies utilizing anti-Fc gamma R monoclonal antibodies (mAbs) as opsonins suggest that Fc gamma RI, like the other Fc gamma Rs expressed by macrophages, is able to mediate phagocytosis. The ability of Fc gamma RI to mediate pinocytosis, however, had not been certain, since it binds, but does not mediate, internalization of monomeric IgG in the monocytoid U937 cells. We studied Fc gamma RI-mediated internalization by introducing it into the Fc gamma R-negative fibroblastic COS cells. We found, using electron microscopy and fluorescence microscopy, that COS cells expressing Fc gamma RI are able to phagocytose IgG-coated zymosan particles and sheep red blood cells (SRBC), as well as pinocytose cross-linked IgG. There was no intracellular accumulation of monomeric IgG. Chimeric receptors which retain the extracellular domains of Fc gamma RI but lack the entire wild-type transmembrane and intracellular regions of the receptor mediated both phagocytosis and pinocytosis with equal or increased efficiency when compared to the wild-type receptor. Control COS cells transfected with CD2 rosetted, but did not phagocytose, SRBC. Attachment of phagocytic targets to COS cells is therefore not sufficient for phagocytosis. Taken together, this suggests that the extracellular domain of Fc gamma RI is sufficient for it to mediate phagocytosis and pinocytosis in this system.
Preparation of Porous Carbon by Polymer Blending of Phenolic Resin and Adipic Diacid (2011)

Porous carbons used for electric double layer capacitors(EDLCs) were prepared by chemical blending of phenolic resin(PF) and adipic diacid(DA).Chemical reaction of PF with diacid is manifested by a shift of carbonyl stretching peak of diacid to a higher frequency in FT-IR spectra and a higher decomposition temperature of diacid in TG curves.The influences of the ratio of w(DA) to w(PF) on pore structure,adsorption behavior and capacity per-formance were investigated.The specific surface area and total pore volume increase with the ratio of w(DA) to w(PF) at first and then decrease,reach the maximum at the value of w(PF)/w(DA),which are 550 cm2/g and 0.27 cm3/g,re-spectively.When the porous carbon used for the electrodes of electrochemical double layer capacitor(EDLC),a satis-fied specific capacitances of 145 F/g in 30 wt% KOH aqueous electrolytes is acquired and the capacitance maintenance achieve 70% while the current density enlarged 50 times.
The roles of antibody variable region hypermutation and selection in the development of the memory B‐cell compartment (1998)

Somatic hypermutation and selection of immunoglobulin (Ig) variable (V)-region genes, working in concert, appear to be essential for memory B-cell development in mammals. There has been substantial progress on the nature of the cis-acting DNA elements that regulate hypermutation. The data obtained suggest that the mechanisms of Ig gene hypermutation and transcription are intimately intertwined. While it has long been appreciated that stringent phenotypic selection forces are imposed on the somatically mutated Ig V regions generated during a T-cell dependent B-cell response, the mechanisms involved in this selection have remained enigmatic. Our studies have questioned the role of foreign antigen deposited on follicular dendritic cells in affinity-based positive selection of V regions, and have shown that this selection takes place in a "clone-autonomous" fashion. In addition, our data strongly suggest that affinity for antigen alone is not the driving force for selection of B-cell clones into the memory compartment. In contrast, we suggest that a combination of positive selection for increased foreign antigen binding, and negative selection of antibody V regions that are autoreactive at the onset of the response, or have acquired autoreactivity via hypermutation, results in the "specificity maturation" of the memory B-cell response.
Hyperphagia Alters Expression of Hypothalamic 5-HT2C and 5-HT1B Receptor Genes and Plasma Des-Acyl Ghrelin Levels in A<sup>y</sup>Mice (2006)

The central melanocortin (MC) pathway is suggested to mediate satiety signaling downstream of serotonin (5-HT)2C receptors. 5-HT2C receptor mutant mice consume more food, which leads to late-onset obesity and impaired glucose tolerance. Ay mice with ectopic expression of the agouti peptide, which leads to a perturbation of the central MC pathway, develop obesity and diabetes, associated with low levels of plasma total ghrelin. Here, we report that 5-wk-old Ay mice consumed more food in association with decreases in levels of plasma des-acyl ghrelin, but not active ghrelin, and increases in hypothalamic 5-HT2C and 5-HT1B receptor gene expression compared with wild-type mice matched for age and body weight. These alterations were also observed in 8-wk-old obese Ay mice. Restricted feeding significantly decreased hypothalamic 5-HT2C and 5-HT1B receptor gene expression in association with a reversal of the decreases in plasma des-acyl ghrelin levels in 5-wk-old Ay mice. Moreover, restricted feeding reduced body weight, hyperinsulinemia, and hyperglycemia in association with increases in plasma des-acyl ghrelin levels in 8-wk-old obese Ay mice. Administration of m-chlorophenylpiperazine and fenfluramine, both of which induce anorexic effects via 5-HT2C receptors and/or 5-HT1B receptors, suppressed food intake in 5- and 8-wk-old Ay mice, whereas the anorexic effects were attenuated in food-restricted Ay mice. These findings suggest that the agouti peptide down-regulates hypothalamic 5-HT2C and 5-HT1B receptor gene expression under restricted feeding conditions, whereas chronic hyperphagia increases the expression of these genes and decreases plasma des-acyl ghrelin levels in Ay mice.
The ICSI Meeting Recorder Dialog Act (MRDA) Corpus (2004)

Abstract : We describe a new corpus of over 180,000 hand- annotated dialog act tags and accompanying adjacency pair annotations for roughly 72 hours of speech from 75 naturally-occurring meetings. We provide a brief summary of the annotation system and labeling procedure, inter-annotator reliability statistics, overall distributional statistics, a description of auxiliary files distributed with the corpus, and information on how to obtain the data.
Osmoregulatory changes in <i>Myo</i>‐inositol content and Na<sup>+</sup>/<i>Myo</i>‐inositol contransport in rat cortical astrocytes (1994)

Exposure of cortical astrocytes to 325, 350, or 390 mosM culture media for 48 h caused a 1.4-, 2.1-, and 3.5-fold increase, respectively, in cellular content of the compatible osmolyte myo-inositol. Elevated myo-inositol levels accounted for approximately 56-100% of the solute needed by the cells for complete volume regulation under hypertonic conditions. Myo-inositol accumulation was associated with 4-5-fold (peak rate) and 1.8-2-fold (steady-state rate) increases in the rate of Na(+)-dependent myo-inositol uptake when cells were acclimated to 390 mosM culture medium for 12 h or 24-96 h, respectively. When medium osmolality was elevated by 25 mosM, peak and steady-state increases in myo-inositol uptake of 1.7-fold and 1.3-fold, respectively, were observed. Exposure to 390 mosM medium for 12-48 h induced a 3-8-fold increase in cotransporter mRNA levels suggesting that the increase in myo-inositol uptake is brought about by increased cotransporter gene expression. Abrupt return of hypertonic cells to an isotonic medium induced a rapid increase in myo-inositol efflux and a return of cotransporter mRNA to control values in < 2 h. In contrast, the cotransporter remained fully activated at hypertonic levels for 16 h. Between 16-24 h after the transfer, the rate of myo-inositol uptake returned to control values. The remarkable sensitivity of the cotransporter to hypertonic stress indicates that upregulation of myo-inositol transport in glial cells is likely to occur in a variety of disease states that cause an elevation of plasma osmolality. Slow downregulation of the cotransporter may be responsible in part for the slow loss of myo-inositol and cerebral edema that occurs with too rapid correction of chronic plasma hypertonicity.
Exploring the Mechanisms in STED‐Enhanced Direct Laser Writing (2014)

Stimulated‐emission‐depletion direct laser writing allows for performing 3D optical lithography beyond the Abbe diffraction limit. However, the underlying mechanisms and limitations are poorly understood. In order to clarify for the case of 7‐diethylamino‐3‐thenoylcoumarin (DETC) as photoinitiator in pentaerythritol triacrylate, transient photoluminescence experiments as well as lithography experiments with variable repetition rate are performed. In addition, several coinitiators and DETC derivatives are investigated. While the photoluminescence of the DETC photoresist exhibits a two‐photon excitation behavior and can be largely depleted, lithography under the same conditions surprisingly shows an effective three‐photon excitation behavior at high repetition rates and an effective four‐photon behavior at low repetition rates. From the comprehensive investigation, it is concluded that at high repetition rates, residual absorption of the depletion laser is the limiting mechanism, whereas at low repetition rates an effective four‐photon process leads to direct radical generation that cannot be depleted.
Continuous True-Time Delay Phase Shifter Using Distributed Inductive and Capacitive Miller Effect (2019)

A new true-time delay phase shifter concept is proposed exploiting the distributed Miller effect in coupled transmission lines. Simultaneous change in Miller capacitance and inductance controlled by a single analog voltage changes the propagation delay of a transmission line with constant input impedance and insertion loss. The true-time delay line feature of the proposed architecture accommodates a wide bandwidth signal without group delay distortion. A theoretical framework for understanding Miller inductance from voltage and current duality and the distributed Miller effect using coupled wave equations is presented. As a proof of concept, a four-stage tunable delay line with a high-speed phase modulation capability was fabricated in a 45-nm RF SOI CMOS process and occupies an active area of 0.28 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> . The measured IC demonstrates a broadband tunable true-time delay with a measured group delay tuning range of 18 ± 1 ps from 11 to 24 GHz. The measured phase shift ranges are 173° and 182° with insertion losses of 10.6 ± 0.7 dB and 11.6 ± 1 dB at 28 and 30 GHz, respectively. The measured dc power consumption is 22 mW from a 1.2-V supply.
Novel magnetic techniques for rapidly detecting palaeomagnetically important single-domain iron particles and obtaining directional palaeomagnetic data from “unoriented” lunar rock samples (2011)

Returned lunar samples from the Apollo missions comprise “unoriented” consolidated rock samples (and rock powder samples) containing fine iron particles that hold important information concerning the ancient lunar magnetic fields. Previous magnetic studies have concentrated almost entirely on attempts to obtain palaeointensity data (the strength of the ancient lunar magnetic fields). A major disadvantage of not having any in situ bedrock samples was that no palaeomagnetic directional data could be obtained and thus the emphasis on palaeointensity work. Many samples, however, were not even suitable for palaeointensity studies as they did not contain a high proportion of stable single-domain iron particles (the best recorders of the ancient fields). This study describes a novel magnetic technique for rapidly detecting the most suitable lunar samples for palaeomagnetic purposes (those containing a high proportion of stable single-domain iron particles), with results on some returned Apollo lunar rock samples and laboratory analogue materials. A novel technique, using magnetic anisotropy, for obtaining some directional information from unoriented consolidated rock samples is also presented in this study. In particular, a methodology to potentially obtain the palaeomagnetic inclination angle is presented and applied to the above Apollo samples. This pilot study demonstrates that the novel techniques reported here are feasible even on the small lunar samples made available for scientific study. This paves the way for these techniques to be applied to many more samples. This is potentially important because one could then determine whether or not there were systematic variations of the apparent palaeolatitude (derived from the palaeomagnetic inclination angle data) with the known sample ground locations. Such systematic variations would be strong support for the existence of a global ancient lunar magnetic field of internal origin when the primary component of the natural remanent magnetization of the lunar samples was acquired. Interestingly, the palaeopole for the Apollo samples in this study (derived from the inclination data via the proposed new methodology) is similar to the palaeopoles calculated from magnetic anomalies for Upper Nectarian – Lower Imbrian age (close in age to at least some of the samples studied here). The methodologies described here could also be applied to unoriented consolidated rock samples on other planetary bodies such as Mercury.
A direction-based location update scheme with a line-paging strategy for PCS networks (2000)

On the problem of location update and terminal paging, many schemes using ring-paging strategies have been proposed. However, sequentially paging the rings surrounding the mobile user's last updated location may cause large paging cost. We propose a direction-based location update (DBLU) scheme using a line-paging strategy to reduce the paging cost. A moving direction identification mechanism using only simple computations detects the change of moving direction and updates the mobile's location. The numerical results show that our DBLU scheme achieves good performance when the paging cost is high.
Retrovirus transduction: segregation of the viral transforming function and the herpes simplex virus tk gene in infectious Friend spleen focus-forming virus thymidine kinase vectors. (1983)

A series of deletions and insertions utilizing the herpesvirus thymidine kinase gene (tk) were constructed in the murine retrovirus Friend spleen focus-forming virus (SFFV). In all cases, the coding region for the SFFV-specific glycoprotein (gp55), which is implicated in erythroleukemic transformation, was left intact. These SFFV-TK and SFFV deletion vectors were analyzed for expression of tk and gp55 after DNA-mediated gene transfer. In addition, virus rescued by cotransfection of these vectors with Moloney murine leukemia virus was analyzed for infectious TK-transducing virus, gp55 expression, and erythroleukemia-inducing ability. The experiments demonstrated that deletions or insertions within the intron for the gp55 env gene can interfere with expression of gp55 after both DNA-mediated gene transfer and virus infection. In contrast, the gene transfer efficiency of the tk gene was unaffected in the SFFV-TK vectors, and high-titer infectious TK virus could be recovered. Revertant viruses capable of inducing erythroleukemia and expressing gp55 were generated after cotransfection of the SFFV-TK vectors with murine leukemia virus. The revertant viruses lost both tk sequences and the ability to transduce TK- fibroblasts to a TK+ phenotype. These experiments demonstrate that segregation of the TK and erythroleukemia functions can occur in retrovirus vectors which initially carry both markers.
Recent Developments in Optofluidic Lens Technology (2016)

Optofluidics is a rapidly growing versatile branch of adaptive optics including a wide variety of applications such as tunable beam shaping tools, mirrors, apertures, and lenses. In this review, we focus on recent developments in optofluidic lenses, which arguably forms the most important part of optofluidics devices. We report first on a number of general characteristics and characterization methods for optofluidics lenses and their optical performance, including aberrations and their description in terms of Zernike polynomials. Subsequently, we discuss examples of actuation methods separately for spherical optofluidic lenses and for more recent tunable aspherical lenses. Advantages and disadvantages of various actuation schemes are presented, focusing in particular on electrowetting-driven lenses and pressure-driven liquid lenses that are covered by elastomeric sheets. We discuss in particular the opportunities for detailed aberration control by using either finely controlled electric fields or specifically designed elastomeric lenses.