gebhart/patrepeval huggingface dataset:
Expression of cyclooxygenase-2 and inducible nitric oxide synthase in human ovarian tumors and tumor-associated macrophages. (2001)

This study investigates whether and to what extent cyclooxygenase type-2 (COX-2) and inducible nitric oxide-synthase (iNOS), both known to have an immunosuppressive effect, are expressed in human ovarian tumors. Because COX-2 and iNOS can be expressed by activated macrophages, the presence of tumor-associated macrophages and the expression of COX-2 and iNOS by these tumor-associated macrophages were determined. The results obtained may provide insight into the function of COX-2 and iNOS expression by tumors. The expression of COX-2 and iNOS in tumor cells and macrophages was assessed in 18 malignant, 15 borderline, and 14 benign human ovarian tumors by immunohistochemical staining of frozen tissue sections. The intra- and peritumoral macrophages were stained using an anti-CD68 monoclonal antibody. Most of the malignant tumors (15 of 18), 10 of 15 borderline, and 9 of 14 benign tumors showed COX-2 expression in the epithelial cells, a result which indicates that COX-2 expression is not exclusive to malignancy. In addition, COX-2 staining was more intense in the epithelial cells of benign and borderline tumors than in malignant tumors. Weak iNOS staining was observed in 5 of 18 malignant, 4 of 15 borderline, and 5 of 14 benign tumors. The number of tumor-associated macrophages varied widely between the different tumors. The highest number of tumor-associated macrophages (> or =20/0.125 mm(2)) was observed in malignant tumors, whereas low to moderate intra- and peritumoral macrophage infiltration (5-20/0.125 mm(2)) was observed in the borderline and benign tumors. COX-2-positive tumor-associated macrophages were found in 3 of 18 malignant tumors, 7 of 15 borderline tumors, and 1 of 14 benign tumors. The number of COX-2-positive tumor-associated macrophages ranged from 3 to 30% of the total macrophage population. Some malignant (4 of 18), borderline (5 of 15), and benign (2 of 14) tumors contained iNOS-positive macrophages. Notable was that COX-2- and iNOS-positive macrophages were predominantly located in the tumor stroma, the regions between tumor and stroma, and in the lumina of the tumor when located in the tumor tissue. These data indicate that not only malignant but also borderline and benign ovarian tumors can exhibit increased levels of COX-2 and iNOS expression. In addition, a small proportion of the tumor-associated macrophages found in malignant, borderline, and benign tumors seems to be in an activated state, judged by their iNOS and COX-2 expression. This subpopulation of tumor-associated macrophages was invariably located in the tumor stroma or in the lumina of the tumor, specifically suggesting that macrophages outside the tumor can be tumor cytotoxic.
Cannabinoid receptor agonists from Conus venoms alleviate pain-related behavior in rats (2021)

Cannabinoid (CB) receptor agonists show robust antinociceptive effects in various pain models. However, most of the clinically potent CB1 receptor-active drugs derived from cannabis are considered concerning due to psychotomimetic side effects. Selective CB receptor ligands that do not induce CNS side effects are of clinical interest. The venoms of marine snail Conus are a natural source of various potent analgesic peptides, some of which are already FDA approved. In this study we evaluated the ability of several Conus venom extracts to interact with CB1 receptor. HEK293 cells expressing CB1 receptors were treated with venom extracts and CB1 receptor internalization was analyzed by immunofluorescence. Results showed C. textile (C. Tex) and C. miles (C. Mil) samples as the most potent. These were serially subfractionated by HPLC for subsequent analysis by internalization assays and for analgesic potency evaluated in the formalin test and after peripheral nerve injury. Intrathecal injection of C. Tex and C. Mil subfractions reduced flinching/licking behavior during the second phase of formalin test and attenuated thermal and mechanical allodynia in nerve injury model. Treatment with proteolytic enzymes reduced CB1 internalization of subfractions, indicating the peptidergic nature of CB1 active component. Further HPLC purification revealed two potent antinociceptive subfractions within C. Tex with CB1 and possible CB2 activity, with mild to no side effects in the CB tetrad assessment. CB conopeptides can be isolated from these active Conus venom-derived samples and further developed as novel analgesic agents for the treatment of chronic pain using cell based or gene therapy approaches.
High-order Talbot fringes for atomic matter waves (1997)

We observe the interference of de Broglie waves in the diffraction near field of a microfabricated grating. The reduction of the grating period by self-imaging of second to seventh order is spatially resolved. We investigate the dependence of this effect on the de Broglie wavelength by a time-to-flight technique.
An automatic cap arrangement scoring device [abstract] (2010)

Poor color vision can be inherited (an estimated 8% of men and .5% of women have a congenital color vision defect) or acquired as the result of disease, certain medications, trauma, aging, or exposure to particular chemicals and other environmental factors. Cap arrangement tests (e.g. Farnsworth-Munsell 100 Hue, Farnsworth D-15, L'Anthony D-15 Desaturated, etc.) are among the most valid and reliable color vision tests to quantify color deficits currently available. However, these tests, particularly the FM 100, are time consuming to score and are highly susceptible to transcription errors. Researchers at the University of Missouri-St. Louis have developed the Automatic Cap Arrangement Scoring Device (ACASD) to significantly reduce testing time and improve measurement reliability of cap arrangement tests by electronically automating scoring and data entry. Once the patient places the caps in the test tray, the rest will be automatic -- scoring, data entry and printing of results. Upgrading existing cap arrangement devices is easy by transferring existing test papers to the new cap. Potential Areas of Applications: * Standard cap arrangement color vision tests given not only by optometrists and ophthalmologists as part of a visual examination, but employers filling positions with color vision requirements * Other applications where specific sequences of small items are necessary PATENT STATUS: U.S. Patent Application No. 12/522,691 INVENTOR(S): Carl Bassi; Michael Howe; Wayne Garver CONTACT INFO: Tamara Wilgers; wilgerst@umsl.edu; 314-516-6884
Case studies: Public domain, single mining tasks systems: VisDB (2002)

The VisDB system is an interactive data visualization and exploration that uses novel pixel-oriented visualization techniques for effective exploration of large multidimensional data sets. Pixel-oriented techniques use each pixel of the display to visualize one data value and therefore allow the visualization of the largest amount of data possible. Using a slider-based direct-manipulation interface, the user may explore the data interactively and discover interesting patterns in the visualizations generated. The system can be used for the discovery of correlations, functional relationships, and clusters. It has proven to be effective even for data sets with small clusters and a high degree of noise. Application areas include stock market analysis, environmental science, computer-aided design, and molecular biology. The pixel-oriented techniques implemented in the VisDB System may be divided into query-independent techniques, which directly visualize the data (or a certain portion of it) and query-dependent techniques, which visualize the relevance of the data with respect to a specific query. Recently, new pixel-oriented techniques have also been developed for geographically related data, such as telecommunication or census data.
Experimental Investigations of Mode Coupling as Limiting Effect Using Mode Group Diversity Multiplexing on GI-MMF (2006)

We investigate experimentally mode coupling as limiting effect in MMF transmission systems at 21.4 Gb/s. It is shown that this effect has only significant influence for high power levels over 300 m MMF.
Robustness of Coherent 100 Gbps QPSK and 200 Gbps 16QAM-OFDM to Practical Implementation Impairments (2014)

The sensitivity of coherent 100 Gbps QPSK and 200 Gbps 16QAM-OFDM to practical implementation impairments is investigated. In spite of its higher sensitivity when compared to 100 Gbps QPSK-OFDM, we demonstrate that the implementation complexity of 200 Gbps 16QAM-OFDM is manageable experimentally.
Photonic parallel channel estimation of MIMO-OFDM wireless communication systems (2022)

Channel estimation is a key technology in MIMO-OFDM wireless communication systems. Increasingly extensive application scenarios and exponentially growing data volumes of MIMO-OFDM systems have imposed greater challenges on the speed, latency, and parallelism of channel estimation based on electronic processors. Here, we propose a photonic parallel channel estimation (PPCE) architecture which features radio-frequency direct processing. Proof-of-concept experiment is carried out to demonstrate the general feasibility of the proposed architecture at different frequency bands (100 MHz, 4 GHz, and 10 GHz). The mean square errors (MSEs) between the experimental channel estimation results and the theoretically simulated ones lie on the order of 10<sup>-3</sup>. The bit error rates (BERs) are below the pre-forward error correction (pre-FEC) threshold. Besides, we analyze the performance of PPCE under different signal-to-noise ratios (SNRs), baseband symbol forms, and weight tuning precisions. The proposed PPCE architecture has the potential to achieve high-speed, highly parallel channel estimation in large-scale MIMO-OFDM systems after the photonic-electronic chip integration.
Fault-scalable Byzantine fault-tolerant services (2005)

A fault-scalable service can be configured to tolerate increasing numbers of faults without significant decreases in performance. The Query/Update (Q/U) protocol is a new tool that enables construction of fault-scalable Byzantine fault-tolerant services. The optimistic quorum-based nature of the Q/U protocol allows it to provide better throughput and fault-scalability than replicated state machines using agreement-based protocols. A prototype service built using the Q/U protocol outperforms the same service built using a popular replicated state machine implementation at all system sizes in experiments that permit an optimistic execution. Moreover, the performance of the Q/U protocol decreases by only 36% as the number of Byzantine faults tolerated increases from one to five, whereas the performance of the replicated state machine decreases by 83%.
Data compression systems for home-use digital video recording (1992)

The authors focus on image data compression techniques for digital recording. Image coding for storage equipment covers a large variety of systems because the applications differ considerably in nature. Video coding systems suitable for digital TV and HDTV recording and digital electronic still picture storage are considered. In addition, attention is paid to picture coding for interactive systems, such as the compact-disc interactive system. The relation between the recording system boundary conditions and the applied coding techniques is outlined. The main emphasis is on picture coding techniques for digital consumer recording.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Abstract LB-106: A novel TCL1-Tg:p53−/− mouse model of human CLL (2012)

Abstract Chronic lymphocytic leukemia (CLL) is the most common adult leukemia in the United States and Europe. CLL patients with loss of p53 due to chromosome 17p deletion often exhibit more malignant disease phenotype, are refractory to standard treatment, and have poor clinical outcomes. Although there are several mouse models that resemble the chronic disease processes of CLL, no animal model has been reported that mimic the aggressive disease phenotype of CLL with loss of p53. To facilitate the investigation of the biology of aggressive CLL with loss of p53 and the underlying mechanisms, we generated a mouse model with Eu-TCL1-Tg:p53−/− genotype by crossing the Eu-TCL1-Tg mice with p53 knockout mice. The Eu-TCL1-Tg:p53−/- mice developed CLL disease at 3-4 months, significantly earlier than the parental Eu-TCL1-Tg mice that developed CLL disease at 8-12 months. Flow cytometry analysis showed that the IgM+/CD5+ cell population appeared in the peritoneal cavity, bone marrow, and the spleens of Eu-TCL1-Tg:p53−/- mice significantly earlier than that of the parental Eu-TCL1-Tg mice. Massive infiltration and accumulation of leukemia cells were found in the spleen, liver, and peritoneal cavity. In vitro study showed that the leukemia cells isolated from the Eu-TCL1-Tg:p53−/- mice were more resistant to fludarabine treatment than the leukemia cells isolated from spleens of TCL1-Tg mice. Interestingly, TUNEL assay revealed that there was higher apoptotic cell death found in the TCL1-Tg spleen tissue compared to the spleens of the Eu-TCL1-Tg:p53−/- mice, suggesting that the loss of p53 compromises the apoptotic process in vivo, and this might in part explain the drug resistant phenotype of CLL cells with 17p deletion. Further molecular analysis showed that the expression of MCL-1, a key survival molecule for CLL, was significantly increased at the mRNA and protein levels in the leukemia cells isolated from Eu-TCL1-Tg:p53−/- mice, which seemed to be associated with the abnormal expression of certain microRNAs including miR15a and miR-16. Overall, the Eu-TCL1-Tg:p53−/- mice display a disease phenotypes that resemble human CLL with 17p deletion, and represent a useful animal model for mechanistic study as well as evaluation of in vivo therapeutic efficacy of anti-CLL agents. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr LB-106. doi:1538-7445.AM2012-LB-106
Prevention of Dominant IgG Adsorption on Nanocarriers in IgG‐Enriched Blood Plasma by Clusterin Precoating (2019)

Nanocarriers for medical applications must work reliably within organisms, independent of the individual differences in the blood proteome. Variation in the blood proteome, such as immunoglobulin levels, is a result of environmental, nutrition, and constitution conditions. This variation, however, should not influence the behavior of nanocarriers in biological media. The composition of the protein corona is investigated to understand the influence varying immunoglobulin levels in the blood plasma have on the interactions with nanocarriers. Specifically, the composition of the nanocarriers' coronas is analyzed after incubation in plasma with normal or elevated immunoglobulin G (IgG) levels, and cellular uptake is monitored in cell lines containing different immunoglobulin receptors. Here, it is reported that upon doubling the IgG concentration in plasma, the IgG fraction in the protein corona increases by a factor of 40 independent of the nanocarrier material. This results in a significant increase in uptake in cells exhibiting IgG binding receptors. Furthermore, precoating nanocarriers with clusterin successfully prevents dominant IgG-adsorption and additionally reduces cellular internalization, after incubation with IgG-enriched plasma. Therefore, precoating nanocarriers may be utilized as a powerful method to reduce the influence of individual variations in blood composition on the protein corona.
Room temperature continuous wave operation of single-mode, edge-emitting photonic crystal Bragg lasers (2008)

We report the first room temperature CW operation of two dimensional single-mode edge-emitting photonic crystal Bragg lasers. Single-mode lasing with single-lobed, diffraction limited far-fields is obtained for 100μm wide and 550μm long on-chip devices.
Study of High Load Operation Limit Expansion for Gasoline Compression Ignition Engines (2006)

In this research, combustion characteristics of gasoline compression ignition engines have been analyzed numerically and experimentally with the aim of expanding the high load operation limit. The mechanism limiting high load operation under homogeneous charge compression ignition (HCCI) combustion was clarified. It was confirmed that retarding the combustion timing from top dead center (TDC) is an effective way to prevent knocking. However, with retarded combustion, combustion timing is substantially influenced by cycle-to-cycle variation of in-cylinder conditions. Therefore, an ignition timing control method is required to achieve stable retarded combustion. Using numerical analysis, it was found that ignition timing control could be achieved by creating a fuel-rich zone at the center of the cylinder. The fuel-rich zone works as an ignition source to ignite the surrounding fuel-lean zone. In this way, combustion consists of two separate auto-ignitions and is thus called two-step combustion. In the simulation, the high load operation limit was expanded using two-step combustion. An engine system identical to a direct-injection gasoline (DIG) engine was then used to validate two-step combustion experimentally. An air-fuel distribution was created by splitting fuel injection into first and second injections. The spark plug was used to ignite the first combustion. This combustion process might better be called spark-ignited compression ignition combustion (SI-CI combustion). Using the spark plug, stable two-step combustion was achieved, thereby validating a means of expanding the operation limit of gasoline compression ignition engines toward a higher load range.
Meta-uncertainty for particle image velocimetry (2021)

Abstract Uncertainty quantification for particle image velocimetry (PIV) is critical for comparing experimentally measured flow fields with computational fluid dynamics results, and model design and validation. However, PIV features a complex measurement chain with coupled, non-linear error sources, and quantifying the uncertainty is challenging. Multiple assessments show that none of the current methods can reliably measure the actual uncertainty across a wide range of experiments, and estimates can vary. Because the current methods differ in assumptions regarding the measurement process and calculation procedures, it is not clear which method is best to use for an experiment where the error distribution is unknown. To address this issue, we propose a method to estimate an uncertainty method’s sensitivity and reliability, termed the Meta-Uncertainty. The novel approach is automated, local, and instantaneous, and based on perturbation of the recorded particle images. We developed an image perturbation scheme based on adding random unmatched particles to the interrogation window pair considering the signal-to-noise of the correlation plane. Each uncertainty scheme’s response to several trials of random particle addition is used to estimate a reliability metric, defined as the rate of change of the inter-quartile range of the uncertainties with increasing levels of particle addition. We also propose applying the meta-uncertainty as a weighting metric to combine uncertainty estimates from individual schemes, based on ideas from the consensus forecasting literature. We use planar and stereo PIV measurements across a range of canonical flows to assess the performance of the uncertainty schemes. Further, a novel method is introduced to assess an uncertainty scheme’s performance based on a quantile comparison of the error and uncertainty distributions, generalizing the current method of comparing the RMS of the two distributions. The results show that the combined uncertainty method outperforms the individual methods, and this work establishes the meta-uncertainty as a useful reliability assessment tool for PIV uncertainty quantification.
HIV-1 Reverse Transcriptase Variants: Molecular Modeling of Y181C, V106A, L100I, and K103N Mutations with Nonnucleoside Inhibitors Using Monte Carlo Simulations in Combination with a Linear Response Method (2003)

The energies and physical descriptors for the binding of 21 novel 1-(2,6-difluorobenzyl)-2-(2,6-difluorophenyl)-benzimidazole (BPBI) analogs to HIV-1 reverse transcriptase (RT) variants Y181C, L100I, V106A, and K103N have been determined using Monte Carlo (MC) simulations. The crystallographic structure of the lead compound, 4-methyl BPBI, was used as a starting point to model the inhibitors in both the mutant bound and the unbound states. The energy terms and physical descriptors obtained from the calculations were reasonably correlated with the respective experimental EC50 values for the inhibitors against the various mutant RTs. Using the linear response correlations from the calculations, 2 novel BPBI inhibitors have been designed and simulations have been carried out. The results show the computed deltaG(binding) values match the experimental data for the analogs. Given the ongoing problem with drug resistance, the ability to predict the activity of novel analogs against variants prior to synthesis is highly advantageous.
A comparison study of genetic codings for the traveling salesman problem (2002)

In applying the genetic algorithm (GA) to optimization problems, both a genetic coding method and a method of genetic operations are essential for making a search effective. Moreover, freedom in a genetic representation, e.g. redundant coding, is indispensable for achieving a successful self-organization in GA. This paper treats the case of the application of a GA to the traveling salesman problem (TSP), and proposes four ways of redundantly coding a tour plan. Then, based on several computational experiments, the coding methods have been mutually compared from the viewpoints of the search efficiency, i.e. the effects of genetic operators, the quality of the obtained tours, and the number of generations required for finding near-optimal tours. As a result, the search for the optimal tour is found to be most effective in the case of the coding based on the link information, while the simple GA is found not to be sufficient for solving large-scale problems. Then, the GA is modified by supplementing some new mechanisms. The results of the computational experiments suggest the applicability of the modified GA to large-scale problems.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
A generalized HIV vaccine design strategy for priming of broadly neutralizing antibody responses (2019)

Vaccine induction of broadly neutralizing antibodies (bnAbs) to HIV remains a major challenge. Germline-targeting immunogens hold promise for initiating the induction of certain bnAb classes; yet for most bnAbs, a strong dependence on antibody heavy chain complementarity-determining region 3 (HCDR3) is a major barrier. Exploiting ultradeep human antibody sequencing data, we identified a diverse set of potential antibody precursors for a bnAb with dominant HCDR3 contacts. We then developed HIV envelope trimer-based immunogens that primed responses from rare bnAb-precursor B cells in a mouse model and bound a range of potential bnAb-precursor human naïve B cells in ex vivo screens. Our repertoire-guided germline-targeting approach provides a framework for priming the induction of many HIV bnAbs and could be applied to most HCDR3-dominant antibodies from other pathogens.