gebhart/patrepeval huggingface dataset:
Transcript Profiling of T Lymphocytes and Dendritic Cells in a Co–culture System Using Anti‐CD3 and Allergen Activation (2004)

The interaction of antigen‐specific T lymphocytes with hapten‐bearing dendritic cells (DC) and the subsequent activation and clonal expansion of specific T lymphocyte populations are critical steps in the induction of skin sensitization. Therefore, we have sought to characterize changes in gene expression in T lymphocytes stimulated by incubation with allergen‐treated DC compared with anti‐CD3‐treated T cell‐DC cocultures as a method to identify potential markers of skin sensitization. Human T cells and autologous, mature peripheral blood‐derived DC were co–cultured in the presence or absence of anti‐CD3 monoclonal antibody (mAb) for 6 hours at a 10:1 responder:stimulator ratio. In a separate experiment, autologous DC and T cells from a donor sensitized to the potent contact allergen dinitrochlorobenzene (DNCB) were isolated. T cells were cultured for 6 hours at a responder to stimulator ratio of 20:1 with mature DC that had been treated with either 1 mM 2,4‐dinitrobenzenesulfonic acid (DNBS; the water soluble analog of DNCB), or media alone for 15 minutes. Total RNA was prepared and changes in gene expression were analyzed using Affymetrix U95Av2 GeneChips®. Comparative analysis of Affymetrix mean signal values from triplicate control cultures with those from anti‐CD3‐treated samples revealed highly significant (p ≤ 0.001) changes in the expression of 344 transcripts of the total of approximately 12,000 represented on the chip. However, mean signal values for T cells cocultured with allergen‐treated DC compared to vehicle‐treated DC‐T cell co–cultures identified only 17 significant gene changes (p ≤ 0.001), 11 of which were also identified as having changed significantly in response to stimulation with anti‐CD3. In parallel assays, antigen‐specific T cell proliferative responses were assessed as a function of tritiated thymidine incorporation. Increased T cell proliferative responses were observed in the cultures that contained both DNBS‐treated DC and T cells as well as the anti‐CD3 treated cultures compared with their respective controls. These data suggest that this approach can be used to identify genes that might serve as indicators of contact allergy and may be used in an in vitro predictive assay for skin sensitization.
Pretargeted Molecular Imaging and Radioimmunotherapy (2012)

Pretargeting is a multi-step process that first has an unlabeled bispecific antibody (bsMAb) localize within a tumor by virtue of its anti-tumor binding site(s) before administering a small, fast-clearing radiolabeled compound that then attaches to the other portion of the bsMAb. The compound's rapid clearance significantly reduces radiation exposure outside of the tumor and its small size permits speedy delivery to the tumor, creating excellent tumor/nontumor ratios in less than 1 hour. Haptens that bind to an anti-hapten antibody, biotin that binds to streptavidin, or an oligonucleotide binding to a complementary oligonucleotide sequence have all been radiolabeled for use by pretargeting. This review will focus on a highly flexible anti-hapten bsMAb platform that has been used to target a variety of radionuclides to image (SPECT and PET) as well as treat tumors.
Fast parallel recursive aggregation methods for simulation of dynamical systems (1994)

A novel recursive aggregation algorithm for numerical simulations of dynamic systems is proposed and analyzed. The algorithm exploits a special structure of the linear equation problem resulting from the discretization of the dynamic system and an aggregation/disaggregation procedure. The algorithm has a time complexity of (I(q)+2M(q)+3)logN for solving linear systems with q states for N discrete time instants, using O(q/sup 3/N) processors, where I(q) is the parallel time complexity for inverting a q/spl times/q matrix, M(q) is the parallel time complexity for matrix multiplication of two q/spl times/q matrices. The competing parallel cyclic reduction method for the same problem has a time complexity of (I(q)+3M(q)+4)logN. Thus, the proposed algorithm has a definite speed advantage over the cyclic reduction method. An approximation technique for the unknown boundary conditions in boundary value problems is also proposed. The algorithm was implemented to simulate some dynamical (stable and unstable) systems, and the numerical results show that the accumulation of roundoff errors is insignificant as compared to the discretization errors.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Inactivation of Flavoenzyme-Encoding Gene flsO1 in Fluostatin Biosynthesis Leads to Diversified Angucyclinone Derivatives (2021)

Inactivation of the flavoenzyme-encoding gene <i>flsO1</i> in fluostatin biosynthesis led to the isolation of four new angucyclinone derivatives (<b>11</b>, <b>12</b>, <b>14</b>, and <b>15</b>), among which fluostarenes A (<b>14</b>) and B (<b>15</b>) featured the unprecedented 6/6/5/6/6 pentacyclic skeleton with fusion of a benzo[<i>b</i>]fluorene and a six-membered lactone ring. Both <b>14</b> and <b>15</b> were putatively generated via quinone methide-mediated nonenzymatic reactions. Fluostarene B (<b>15</b>) exhibited cytotoxicity against several cancer cell lines with IC<sub>50</sub> values ranging from 7 to 10 μM. Fluostarenes A (<b>14</b>), B (<b>15</b>), and PK1 (<b>16</b>) showed α-glucosidase inhibition activity with IC<sub>50</sub> of 0.89, 1.58, and 0.13 μM, respectively. Successful complementation of the Δ<i>flsO1</i> mutant with <i>alpK</i> from kinamycin biosynthesis suggests that FlsO1 should function equivalently to AlpK as a putative C-5 hydroxylase.
Architectural Approaches For Gallium Arsenide Exploitation In High-Speed Computer Design (1985)

Continued advances in the capability of Gallium Arsenide (GaAs)technology have finally drawn serious interest from computer system designers. The recent demonstration of very large scale integration (VLSI) laboratory designs incorporating very fast GaAs logic gates herald a significant role for GaAs technology in high-speed computer design:1 In this thesis we investigate design approaches to best exploit this promising technology in high-performance computer systems. We find significant differences between GaAs and Silicon technologies which are of relevance for computer design. The advantage that GaAs enjoys over Silicon in faster transistor switching speed is countered by a lower transistor count capability for GaAs integrated circuits. In addition, inter-chip signal propagation speeds in GaAs systems do not experience the same speedup exhibited by GaAs transistors; thus, GaAs designs are penalized more severely by inter-chip communication. The relatively low density of GaAs chips and the high cost of communication between them are significant obstacles to the full exploitation of the fast transistors of GaAs technology. A fast GaAs processor may be excessively underutilized unless special consideration is given to its information (instructions and data) requirements. Desirable GaAs system design approaches encourage low hardware resource requirements, and either minimize the processor’s need for off-chip information, maximize the rate of off-chip information transfer, or overlap off-chip information transfer with useful computation. We show the impact that these considerations have on the design of the instruction format, arithmetic unit, memory system, and compiler for a GaAs computer system. Through a simulation study utilizing a set of widely-used benchmark programs, we investigate several candidate instruction pipelines and candidate instruction formats in a GaAs environment. We demonstrate the clear performance advantage of an instruction pipeline based upon a pipelined memory system over a typical Silicon-like pipeline. We also show the performance advantage of packed instruction formats over typical Silicon instruction formats, and present a packed format which performs better than the experimental packed Stanford MIPS format.
Fate and Dissemination of Bacillus subtilis Spores in a Murine Model (2001)

Bacterial spores are being consumed as probiotics, although little is known about their efficacy or mode of action. As a first step in characterizing spore probiotics, we have studied the persistence and dissemination of Bacillus subtilis spores given orally to mice. Our results have shown that spores do not appear to disseminate across the mucosal surfaces. However, we found that the number of spores excreted in the feces of mice was, in some experiments, larger than the original inoculum. This was an intriguing result and might be explained by germination of a proportion of the spore inoculum in the intestinal tract, followed by limited rounds of cell growth and then sporulation again. This result raises the interesting question of whether it is the spore or the germinated spore that contributes to the probiotic effect of bacterial spores.
Applying Kernel Logistic Regression in data mining to classify credit risk (2008)

Credit risk evaluation is an interesting and important data mining problem in financial analysis domain. This problem domain, do require estimable class probabilities as well as accurate classification method. One of classification methods in the kernel-machine techniques and data mining communities that allows non linear probabilistic classification, transparent reasoning, and competitive discriminative ability is Kernel Logistic Regression. Kernel Logistic Regression model is a kernelized version of Logistic Regression, which well known classification method in the field of statistical learning. The parameters of kernel model are given by the solution of a convex optimization problem, that can be found using the efficient Iteratively Re-weighted Least Squares (IRLS) algorithm. In this paper, we investigated the classification performance of applying Kernel Logistic Regression to classify risk credit problem. The result demonstrated that Kernel Logistic Regression has good accuracy to evaluate credit risk, comparable with another well known kernel machine, Support Vector Machine.
Identification and sequence analysis of a methylase gene inPorphyromonas gingivalis (1991)

A gene from the periodontal organism Porphyromonas gingivalis has been identified as encoding a DNA methylase. The gene, referred to as pgiIM, has been sequenced and found to contain a reading frame of 864 basepairs. The putative amino acid sequence of the encoded methylase was 288 amino acids, and shared 47% and 31% homology with the Streptococcus pneumoniae DpnII and E. coli Dam methylases, respectively. The activity and specificity of the pgi methylase (M.PgiI) was confirmed by cloning the gene into a dam- strain of E. coli (JM110) and performing a restriction analysis on the isolated DNA with enzymes whose activities depended upon the methylation state of the DNA. The data indicated that M.PgiI, like DpnII and Dam, methylated the adenine residue within the sequence 5'-GATC-3'.
Differential growth rates and in vitro drug susceptibility to currently used drugs for multiple isolates of Naegleria fowleri (2021)

Abstract The free-living amoeba, Naegleria fowleri , which typically dwells within warm, freshwater environments, can opportunistically cause Primary Amoebic Meningoencephalitis (PAM), a disease with a mortality rate of &gt;98%, even with the administration of the best available drug regimens. The lack of positive outcomes for PAM has prompted a push for the discovery and development of more effective therapeutics, but most studies only utilize one or two clinical isolates in their drug discovery assays. The inability to assess possible heterogenic responses to drugs among isolates from varying geographical regions hinders progress in the field due to a lack of proven universal efficacy for novel therapeutics. Herein we conducted drug efficacy and growth rate determinations for 11 different clinical isolates, including one obtained from a successful treatment outcome, by applying a previously developed CellTiter-Glo 2.0 screening technique and flow cytometry. We found some significant differences in the susceptibility of these isolates to 7 of 8 different drugs tested, all of which comprise the cocktail that is recommended to physicians by the Centers for Disease Control. We also discovered significant variances in growth rates among isolates which draws attention to the dissidence among the amoebae populations collected from different patients. The findings of this study reiterate the need for inclusion of additional clinical isolates of varying genotypes in drug assays and highlight the necessity for more targeted therapeutics with universal efficacy across N. fowleri isolates. Our data establishes a needed baseline for drug susceptibility among clinical isolates and provides a segue for future combination therapy studies as well as research related to phenotypic or genetic differences that could shed light on mechanisms of action or predispositions to specific drugs.
Optimal water supply reservoir operation by leveraging the meta-heuristic Harris Hawks algorithms and opposite based learning technique (2023)

To ease water scarcity, dynamic programming, stochastic dynamic programming, and heuristic algorithms have been applied to solve problem matters related to water resources. Development, operation, and management are vital in a reservoir operating policy, especially when the reservoir serves a complex objective. In this study, an attempt via metaheuristic algorithms, namely the Harris Hawks Optimisation (HHO) Algorithm and the Opposite Based Learning of HHO (OBL-HHO) are made to minimise the water deficit as well as mitigate floods at downstream of the Klang Gate Dam (KGD). Due to trade-offs between water supply and flood management, the HHO and OBL-HHO models have configurable thresholds to optimise the KGD reservoir operation. To determine the efficacy of the HHO and OBL-HHO in reservoir optimisation, reliability, vulnerability, and resilience are risk measures evaluated. If inflow categories are omitted, the OBL-HHO meets 71.49% of demand compared to 54.83% for the standalone HHO. The HHO proved superior to OBL-HHO in satisfying demand during medium inflows, achieving 38.60% compared to 20.61%, even though the HHO may have experienced water loss at the end of the storage level. The HHO is still a promising method, as proven by its reliability and resilience indices compared to other published heuristic algorithms: at 62.50% and 1.56, respectively. The Artificial Bee Colony (ABC) outcomes satisfied demand at 61.36%, 59.47% with the Particle Swarm Optimisation (PSO), 55.68% with the real-coded Genetic Algorithm (GA), and 23.5 percent with the binary GA. For resilience, the ABC scored 0.16, PSO scored 0.15, and real coded GA scored 0.14 whilst the binary-GA has the worst failure recovery algorithm with 0.09.
Bio-inspired framework for automatic image quality enhancement (2011)

We propose a bio-inspired framework for automatic image quality enhancement. Restoration algorithms usually have fixed parameters whose values are not easily settable and depend on image content. In this study, we show that it is possible to correlate no-reference visual quality values to specific parameter settings such that the quality of an image could be effectively enhanced through the restoration algorithm. In this paper, we chose JPEG blockiness distortion as a case study. As for the restoration algorithm, we used either a bilateral filter, or a total variation denoising detexturer. The experimental results on the LIVE database will be reported. These results will demonstrate that a better visual quality is achieved through the optimized parameters over the entire range of compression, with respect to the algorithm default parameters.
Cryptanalysis of a Homomorphic Encryption Scheme (2016)

Homomorphic encryption allows to make specific operations on private data which stays encrypted. While applications such as cloud computing require to have a practical solution, the encryption scheme must be secure. In this article, we detail and analyze in-depth the homomorphic encryption scheme proposed by Zhou and Wornell in~\\cite{zhou}. From the analysis of the encryption scheme, we are able to mount three attacks. The first attack enables to recover a secret plaintext message broadcasted to multiple users. The second attack performs a chosen ciphertext key recovery attack and it was implemented and verified. The last attack is a related chosen plaintext decryption attack.
Supplementary Figure 4 from Contextual Synthetic Lethality of Cancer Cell Kill Based on the Tumor Microenvironment (2023)

Supplementary Figure 4 from Contextual Synthetic Lethality of Cancer Cell Kill Based on the Tumor Microenvironment
Stereochemistry of formation of the hydroxymethyl group of hydroxymethylbilane, the precursor of uro'gen-III (1987)

A new synthetic route to (11S)- and (11R)-[11-3H1]porphobilinogen (PBG) is described and the configurations of the products are assigned by degradation to (2S)- and (2R)-[2-3H1]glycollic acids; these PBG samples are used to establish that hydroxymethylbilane synthase converts PBG into the hydroxymethylbilane with overall retention of configuration at the HOCH2– group.
Inconsistent screening for lead endangers vulnerable children: policy lessons from South Bend and Saint Joseph County, Indiana, USA (2018)

Lead exposure is a major health hazard affecting children and their growth and is a concern in many urban areas around the world. One such city in the United States (US), South Bend Indiana, gained attention for its high levels of lead in blood and relatively low testing rates for children. We assessed current lead screening practices in South Bend and the surrounding St. Joseph County (SJC). The 2005-2015 lead screening data included 18,526 unique children. Lead screening rates ranged from 4.7 to 16.7%. More than 75% of children had 'elevated blood lead levels' (EBLL) ≥ 1 micrograms per deciliter (µg/Dl) and 9.7% had an EBLL ≥ 5 μg/dL. Over 65% of the census tracts in SJC had mean EBLL ≥ 5 μg/dL, suggesting widespread risk. Inconsistent lead screening rates, coupled with environmental and societal risk factors, put children in SJC at greater risk for harmful lead exposure than children living in states with provisions for universal screening. Indiana and other states should adhere to the US Centers for Disease Control's guideline and use universal lead testing to protect vulnerable populations.
Plasmonic resonances in optomagnetic metamaterials based on double dot arrays (2010)

We study optical properties of optomagnetic metamaterials produced by regular arrays of double gold dots (nanopillars). Using combined data of spectroscopic ellipsometry, transmission and reflection measurements, we identify localized plasmon resonances of a nanopillar pair and measure their dependences on dot sizes. We formulate the necessary condition at which an effective field theory can be applied to describe optical properties of a composite medium and employ interferometry to measure phase shifts for our samples. A negative phase shift for transmitted green light coupled to an antisymmetric magnetic mode of a double-dot array is observed.
Reconfigurable computing for space-time adaptive processing (2002)

Space-time adaptive processing (STAP) refers to a class of signal processing techniques used to process returns of an antenna array radar system. STAP algorithms are designed to extract desired target signals from returns comprised of Doppler shifts, ground clutter, and jamming interference. STAP simultaneously and adaptively combines the signals received on multiple elements of an antenna array-the spatial domain-and from multiple pulse repetition periods-the temporal domain. The output of STAP is a weighted sum of multiple returns, where the weights for each return in the sum are calculated adaptively and in real-time. The most computationally intensive portion of most STAP approaches is the calculation of the adaptive weight values. Calculation of the weights involves solving a set of linear equations based on an estimate of the covariance matrix associated with the radar return data. Existing approaches for STAP typically rely on the use of multiple digital signal processors (DSPs) or general-purpose processors (GPPs) to calculate the adaptive weights. These approaches are often based on solving multiple sets of linear equations and require the calculation of numerous vector inner products. This paper proposes the use of FPGAs as vector coprocessors capable of performing inner product calculation. Two different "inner-product co-processor" designs are introduced for use with the host DSP or GPP. The first has a multiply-and-accumulate structure, and the second uses reduction-style tree structure having two multipliers and an adder.
Feeding by the small calanoid copepod Paracalanus sp. on heterotrophic dinoflagellates and ciliates (1999)

Feeding of the calanoid copepod Paracalanus sp. past 15 yr. They indicated that copepods including -on natural populations of heterotrophic (h-) dinoflagellates 'herbivorous1 species ingest ciliates actively and have a and ciliates was examined during the summer in the Seto significant impact on ciliate populations Stoecker Inland Sea, Japan. Paracalanus sp. ingested h-&noflagellates with clearance rates of 35 to 146 m1 ind.-' d-l, comparable to & Capuzzo l g g o l 1991~ Sanders & Wickham those for autotrophic (a-) dinoflagellates. Feeding rates of the 1993, Fessendenn & Cowells 1994, Froneman et al. copepod on h-dinoflagellates (0.35 to 0.93 pg C incl.-' d-'1 1996, Merrell & Stoecker 1998). On the other hand, were close to, or in some cases exceeded, the basic metabolic studies on the interactions between h-dinoflagellates demands (0.5 pg C ind.-' d-l) of the copepod. Ciliates were also ingested by Paracalanus sp., but the corresponding clear-and copepods are rather restricted (Jeong 1994, Froneance rates (23 to 60 m1 ind.-' d-l) \yere lower than those for man et al. 1996, Verity & Paffenhofer 1996, ~a k a m u r a h-dinoflagellates. These results, together with data on the & Turner 1997) abundance/biomass of Paracalanus sp, and h-dinoflagellates A calanoid copepod, Paracalanus sp., which has in the study area, indicate that the population of Paracalanus been identified as P, parvus (Hirota 1979), but is sp. can have a significant feeding impact on h-dinoflagellates.
The use of Histochoice™® for histological examination of articular and growth plate cartilages, intervertebral disc and meniscus (2008)

Histochoice is a proprietary nontoxic, non-cross-linking fixative designed by the manufacturer to replace formaldehyde based fixation protocols. We compared Histochoice and formalin fixation for several cartilaginous tissues including, articular and growth plate cartilage, meniscus and intervertebral disc. The tissues were stained with general histology stains including toluidine blue for tissue proteoglycans, picrosirius red to evaluate collagenous organization, and hematoxylin and eosin to assess cell morphology. The chondroitin sulfate and heparin sulfate substituted proteoglycans aggrecan and perlecan were also immunolocalized in some of the tissues to provide a comparison. Histochoice did not fix deep into the tissue blocks resulting in focal loss of aggrecan and other matrix components from the more central regions of the blocks. This was evident in toluidine blue stained sections of immature tibial articular cartilage where loss of glycosaminoglycan was significant in Histochoice fixed tissues. Histochoice fixation worked well, however, in the aggrecan and perlecan immunohistology applications where its non-cross-linking traits were conducive to epitope retrieval and identification by primary antibodies to extracellular matrix components.