gebhart/patrepeval huggingface dataset:
Effects of Allicin on the Formation of Pseudomonas aeruginosa Biofilm and the Production of Quorum-Sensing Controlled Virulence Factors (2013)

The Gram-negative Pseudomonas aeruginosa bacterial pathogen is reputed for its resistance to multiple antibiotics, and this property is strongly associated with the development of biofilms. Bacterial biofilms form by aggregation of microorganisms on a solid surface and secretion of an extracellular polysaccharide substances that acts as a physical protection barrier for the encased bacteria. In addition, the P aeruginosa quorum-sensing system contributes to antibiotic resistance by regulating the expression of several virulence factors, including exotoxin A, elastase, pyoverdin and rhamnolipid. The organosulfur compound allicin, derived from garlic, has been shown to inhibit both surface-adherence of bacteria and production of virulence factors. In this study, the effects of allicin on P aeruginosa biofilm formation and the production of quorum-sensing controlled virulence factors were investigated. The results demonstrated that allicin could inhibit early bacterial adhesion, reduce EPS secretion, and down-regulate virulence factors' production. Collectively, these findings suggest the potential of allicin as a therapeutic agent for controlling P aeruginosa biofilm.
Paramagnetic NMR Analysis of the Seven‐Iron Ferredoxin from the Hyperthermoacidophilic Archaeon Desulfurolobus ambivalens Reveals Structural Similarity to other Dicluster Ferredoxins (1996)

The seven-iron ferredoxin from the hyperthermophilic archaeon Desulfurolobus ambivalens has been investigated by one-dimensional and two-dimensional 1H-NMR in its oxidized and dithionite-reduced states. All iron atoms of both the three-iron and the four-iron cluster are bound to cysteine residues whose hyperfine-shifted resonances were characterized. The pattern of these resonances is similar to those from three-iron, four-iron and eight-iron ferredoxins previously described in the literature, but the four-iron cluster has a shift pattern different from that in other seven-iron proteins. A second set of hyperfine-shifted resonances clearly indicates sample heterogeneity, which possibly involves the four-iron cluster. The observation of interresidue NOEs between two different cysteine residues proves the existence of close spatial proximity of the two clusters in D. ambivalens ferredoxin and therefore indicates structural homology to other dicluster ferredoxins. Moreover, this feature is crucial for the sequence-specific assignment of the hyperfine-shifted resonances. The C alpha-C beta-S-Fe dihedral angles of the cysteine residues coordinating the four-iron cluster could be estimated, and the electronic structure of the three-iron cluster is discussed.
Thermal effects on the dielectric and electrical properties of relaxor ferroelectric ceramic-based MLCs (2002)

The effects of different thermal shock treatments on dielectric and electrical properties of relaxor based and BaTiO/sub 3/ based "0805" Y5V multilayer ceramic chip capacitors (MLCs) were investigated. It was found that thermal shock generally resulted in larger leakage currents and lower breakdown voltages. It is also confirmed that the thermal shock resistance of relaxer MLCs is in disadvantage to that of the barium titanate MLCs. Nevertheless, no obvious failure was found when the relaxor-based MLCs were subjected to the thermal effects in the normal infrared solder reflow process. Besides the relatively lower mechanical strength, low insulation resistivity and breakdown strength were also proposed to be important contributors to the undesirable reliability of relaxor MLCs.
Upper bounds for convergence rates of vector extrapolation methods on linear systems with initial iterations. Ph.D. Thesis (1992)

The application of the minimal polynomial extrapolation (MPE) and the reduced rank extrapolation (RRE) to a vector sequence obtained by the linear iterative technique x(sub j) + 1 = Ax(sub j) = b,j = 1,2,..., is considered. Both methods produce a two dimensional array of approximations s(sub n,k) to the solution of the system (I - A)x = b. Here, s(sub n,k) is obtained from the vectors x(sub j), n is less than or equal to j is less than or equal to n + k + 1. It was observed in an earlier publication by the first author that the sequence s(sub n,k), k = 1,2,..., for n greater than 0, but fixed, possesses better convergence properties than the sequence s(sub 0,k), k = 1,2,.... A detailed theoretical explanation for this phenomenon is provided in the present work. This explanation is heavily based on approximations by incomplete polynomials. It is demonstrated by numerical examples when the matrix A is sparse that cycling with s(sub n,k) for n greater than 0, but fixed, produces better convergence rates and costs less computationally than cycling with s(sub 0,k). It is also illustrated numerically with a convection-diffusion problem that the former may produce excellent results where the latter may fail completely. As has been shown in an earlier publication, the results produced by s(sub 0,k) are identical to the corresponding results obtained by applying the Arnoldi method or generalized minimal residual scheme (GMRES) to the system (I - A)x = b.
Testing Virtual Network Functions Auto-Scaling using Open-Source Management and Orchestration (2021)

Recently, the open-source management and orchestration (OSM) platform has attracted significant interest from academia and industry, potentially providing network function virtualization (NFV) management and orchestration solutions for European Telecommunications Standards Institute (ETSI) compliant NFV implementations. OSM has a built-in monitoring module (MON), a policy-management module (POL), and a Prometheus time-series database for metrics collection, which are the main components of ensuring service assurance in OSM. In this work, auto-scaling testing is performed with OSM after instantiating network service using the OSM community-developed virtual network functions (VNFs) and the Grafana tool for data visualization. The Prometheus database collects the metrics from the MON exporter, and scaling actions are defined in POL. Finally, we performed auto-scaling testing and demonstrated the results using the Grafana dashboard. The results showed that the auto-scaling policy was automated successfully after the virtual infrastructure manager (VIM) and VNF metrics triggered threshold violation alarms (already defined) and scaling actions were performed successfully as defined in POL.
The Role of Posteriorly Directed Shear Loads Acting on a Pre-rotated Growing Spine: a Hypothesis on the Pathogenesis of Idiopathic Scoliosis (2010)

Despite years of extensive research, the etiology of idiopathic scoliosis still has not been resolved. A hypothesis on the role of posteriorly directed shear loads was studied in several biomechanical and imaging studies. So far, it has been shown that: on the human erect spine these posteriorly directed shear loads act; these loads decrease the rotational stability of the spine vitro and in vivo; once rotation occurs, it logically follows an already built-in vertebral rotational pattern, that is pre-existent in the human spine; this pre-existent rotational pattern is related to organ anatomy, and not to handedness; certain areas in the female spine are more subject to posteriorly directed shear loads as certain areas in the female spine are more backwardly inclined. Although it is appreciated that the cause of idiopathic scoliosis is multi-factorial, we believe that the delicate upright spinal sagittal balance and the unique posteriorly directed shear loads acting on the erect human spine play a crucial role in the rotational stability of the human spine, and thus in the pathogenesis of idiopathic scoliosis.
Global Histone Modifications in Breast Cancer Correlate with Tumor Phenotypes, Prognostic Factors, and Patient Outcome (2009)

Post-translational histone modifications are known to be altered in cancer cells, and loss of selected histone acetylation and methylation marks has recently been shown to predict patient outcome in human carcinoma. Immunohistochemistry was used to detect a series of histone lysine acetylation (H3K9ac, H3K18ac, H4K12ac, and H4K16ac), lysine methylation (H3K4me2 and H4K20me3), and arginine methylation (H4R3me2) marks in a well-characterized series of human breast carcinomas (n = 880). Tissue staining intensities were assessed using blinded semiquantitative scoring. Validation studies were done using immunofluorescence staining and Western blotting. Our analyses revealed low or absent H4K16ac in the majority of breast cancer cases (78.9%), suggesting that this alteration may represent an early sign of breast cancer. There was a highly significant correlation between histone modifications status, tumor biomarker phenotype, and clinical outcome, where high relative levels of global histone acetylation and methylation were associated with a favorable prognosis and detected almost exclusively in luminal-like breast tumors (93%). Moderate to low levels of lysine acetylation (H3K9ac, H3K18ac, and H4K12ac), lysine (H3K4me2 and H4K20me3), and arginine methylation (H4R3me2) were observed in carcinomas of poorer prognostic subtypes, including basal carcinomas and HER-2-positive tumors. Clustering analysis identified three groups of histone displaying distinct pattern in breast cancer, which have distinct relationships to known prognostic factors and clinical outcome. This study identifies the presence of variations in global levels of histone marks in different grades, morphologic types, and phenotype classes of invasive breast cancer and shows that these differences have clinical significance.
Configuration Database for BaBar On-line (2003)

The configuration database is one of the vital systems in the BaBar on-line system. It provides services for the different parts of the data acquisition system and control system, which require run-time parameters. The original design and implementation of the configuration database played a significant role in the successful BaBar operations since the beginning of experiment. Recent additions to the design of the configuration database provide better means for the management of data and add new tools to simplify main configuration tasks. We describe the design of the configuration database, its implementation with the Objectivity/DB object-oriented database, and our experience collected during the years of operation.
A Robust Computational Technique for Model Order Reduction of Two-Time-Scale Discrete Systems via Genetic Algorithms (2015)

A robust computational technique for model order reduction (MOR) of multi-time-scale discrete systems (single input single output (SISO) and multi-input multioutput (MIMO)) is presented in this paper. This work is motivated by the singular perturbation of multi-time-scale systems where some specific dynamics may not have significant influence on the overall system behavior. The new approach is proposed using genetic algorithms (GA) with the advantage of obtaining a reduced order model, maintaining the exact dominant dynamics in the reduced order, and minimizing the steady state error. The reduction process is performed by obtaining an upper triangular transformed matrix of the system state matrix defined in state space representation along with the elements of B, C, and D matrices. The GA computational procedure is based on maximizing the fitness function corresponding to the response deviation between the full and reduced order models. The proposed computational intelligence MOR method is compared to recently published work on MOR techniques where simulation results show the potential and advantages of the new approach.
Severe neonatal alloimmune thrombocytopenia caused by antibodies to human platelet antigen 3a (Baka) detectable only in whole platelet assays (2003)

The two antibodies appear to recognize an epitope on the HPA-3a+ form of glycoprotein IIb that is lost when PLTs are solubilized in detergent, as required for solid-phase assays. The diagnosis was made in these cases because no HLA antibodies were present, allowing an HPA-3a-specific reaction to be identified with intact PLTs as targets. Such antibodies are likely to be overlooked when HLA antibodies are also present.
Supplementary Figure 10 from Olaparib, Monotherapy or with Ionizing Radiation, Exacerbates DNA Damage in Normal Tissues: Insights from a New p21 Reporter Mouse (2023)

&lt;p&gt;Figure S10: Beta-gal staining of various organs from control and etoposide-treated p21 reporter mice.&lt;/p&gt;
Bottom-reflectance discrimination using water-leaving radiance from coastal zone color scanner (1990)

A method of discriminating radiance due to bright bottom reflectance from water volume reflectance has been developed for evaluating Coastal Zone Color Scanner products of chlorophyll concentrations and diffuse attenuation coefficients. A simple three-band thresholding algorithm is applied to CZCS water leaving radiance at 443, 520 and 550 nanometers. Thirty CZCS images were processed to characterize normalized water leaving radiances in three-channels. Statistics were obtained from reflectance signatures in areas of known bottom reflectance and areas of high volume scattering (significant sediment concentrations and low chlorophyll concentrations). High bottom reflectance areas located in clear shallow waters (optically shallow) of Bahamian and Florida Keys were found to have higher water leaving radiance in all three channels than areas of exclusively high volume scattering (optically deep), e.g. Mississippi Delta, Chesapeake Bay, and Sargasso Sea. Radiances exceeding thresholds in any of the three spectral channels are assumed to be corrupted by bottom reflectance and derived bio-optical products assumed invalid. Comparisons of bottom corrupted pixels are in close agreement with charted bathymetry and in-situ ship radiance data.
Cytokine profile and cytotoxicity in response to acute intratracheal dose ofMetarhizium anisopliaein BALB/c mice (2010)

Metarhizium anisopliae has been considered neither pathogenic nor toxic to mammals. However, some recent reports demonstrate that it is capable of causing infections in mammals including humans. Therefore, there is an urgent need to investigate the nature of infections this fungus induces in these animals. We therefore investigated the immunological and cytotoxic responses to acute intratracheal dose (108 conidia/50 μl) of crude conidial suspension (CCS) of M. anisopliae (ARSEF 7487) in BALB/c mice. The secretion of proinflammatory cytokine IL-6 significantly increased at all the evaluated time points post infection. The titers of IFN-γ, TNF-α, IL-12/IL-23-total p40 and IL-12-p70 showed continuous increasing trends from 6 h post infection (h PI) onwards and increased significantly at 24 h PI. While IL-10 activity was almost constant throughout the observation period, the IL-4 activity first increased at 6 h PI, beyond which it continuously decreased at the evaluated periods of time. The lactate dehydrogenase (LDH) and total protein levels increased significantly at the evaluated h PI. Collectively, the cytokine data suggested that the activation of IL-23/Th17 pathways leading to uncontrolled Th1 type response (elevated production of TNF-α, IFN-γ and IL-6) in the early hours of infection contributed to neutrophilia and tissue damage. On the other hand significantly elevated levels of total protein, LDH and albumin indicated cytotoxicity.
Improving the throughput of synchronization by insertion of delays (2002)

Efficiency of synchronization mechanisms can limit the parallel performance of many shared-memory applications. In addition, the ever increasing performance gap between processor and interprocessor communication may further compromise the scalability of these primitives. Ideally, synchronization primitives should provide high performance under both high and low contention without requiring substantial programmer effort and software support. QOLR has been shown to offer substantial speedups and to outperform other synchronization primitives consistently, but at the cost of software support and protocol complexity. This paper proposes the use of speculation and delays to implement a purely hardware-based queueing mechanism called Implicit QOLB. Making use of the pervasiveness of the Load-Linked/Store-Conditional primitives, we present a series of hardware mechanisms to optimize performance for sharing patterns exhibited by locks and associated data. The mechanisms do not require any change to existing software or instruction sets. IQOLB sits alongside the cache-coherence protocol and guides the decisions the protocol makes with respect to lock (and associated data) transfers. Preliminary evaluations indicate that IQOLB may perform as well as, if not better than, QOLB without the additional software and protocol complexity.
Polyhydroxyalkanoates: Properties and chemical modification approaches for their functionalization (2017)

Polyhydroxyalkanoates (PHAs) have become an attractive biomaterial in research in the past few years due to their extensive potential industrial applications. Being long chain hydroxyl fatty acid molecules, the PHAs are hydrophobic in nature, and have less functional groups. These features limit their applications in various areas. To enhance their usage, these polymers may need to be modified including surface and chemical modifications. Such modifications may alter their mechanical properties, surface structure, amphiphilic character and rate of degradation to fulfil the requirements for their future applications. Chemical modifications allow incorporation of functional groups to PHAs that could not be introduced through biotechnological methods. These chemically reformed PHAs, with enhanced properties, could be used for broad range of applications. This review aims to introduce different chemical modification approaches including some recent methods that had not been explored or discussed so far for PHAs as possible technologies for widening the range of product and application potentials. © 2017 American Institute of Chemical Engineers Biotechnol. Prog., 34:29-41, 2018.
Natural Products–Market Development and Potentials (2011)

This chapter contains sections titled: Introduction Natural Product Market Overview Natural Products in Food and Functional Food Natural Products for Pharmaceutical Applications Summary References
Effects of a fragment of human growth hormone-releasing factor in normal and 'Little' mice (1985)

The 'Little' mouse is characterized by a body growth rate 60% of normal due to a defect in the synthesis and storage of GH in the anterior pituitary gland. We have now investigated the effects of GH releasing factor (GRF) in these mice and in normal animals. The pituitary GH content in Little mice was only 4% of that in normal C57: +/+ mice, and was not affected by twice daily i.p. injections of human (h) GRF1-29NH2 (0.2-2 micrograms) for 14 days. This treatment also had no effect on body growth. In anaesthetized normal mice, single i.v. injections of 0.1 or 2 micrograms hGRF1-29NH2 released large amounts of GH into the plasma, whereas this peptide was ineffective in Little mice, whether or not they had been pretreated with GRF. Therefore, although pituitaries of Little mice contain significant amounts of GH, this pool is not releasable by GRF. This suggests that the dwarfism in Little mice may be partly due to a pituitary defect in GRF receptors or their stimulus-secretion coupling, rather than a deficiency in hypothalamic GRF.
Coordinate changes in the expression of troponin subunit and myosin heavy‐chain isoforms during fast‐to‐slow transition of low‐frequency‐stimulated rabbit muscle (1993)

The purpose of this study was to follow the time course of changes in the expression of myosin heavy chain (HC) and troponin (Tn) subunit isoforms during fast-to-slow transition as induced in rabbit fast-twitch muscle by low-frequency stimulation. The evaluation of changes in the relative concentrations of myosin and troponin subunit isoforms were supplemented by measurements of relative protein synthesis rates using an in situ labeling technique. Changes in the amounts of mRNA encoding fast troponin C (TnC) were followed by Northern blot analysis, those for fast and slow troponin I (TnI) by in vitro translation of total RNA. The various fast myosin heavy chain (HC) and fast troponin T (TnT) isoforms were exchanged sequentially. Myosin HCIId which is the predominant fast isoform in rabbit tibialis anterior, was exchanged with HCIIa and, finally, the latter was replaced by the slow myosin HCI. The replacement of HCIId by HCIIa was accompanied by an exchange of TnT1f and TnT2f with TnT3f. The expression of HCI was accompanied by an exchange of TnT3f with the slow TnT isoforms, TnT1s and TnT2s. The changes in the relative concentrations of the TnT isoforms were preceded by similar changes of their relative synthesis rates. Pronounced decreases in the fast TnI and TnC isoforms occurred only with prolonged stimulation and were preceded by changes of the specific mRNAs and decreases in relative synthesis rates. The parallel time courses of the sequential transitions in both the myosin heavy chain and troponin T isoforms suggest the existence of coordinate programs of expression serving specific functional requirements.
Image Synthesis From Reconfigurable Layout and Style (2019)

Despite remarkable recent progress on both unconditional and conditional image synthesis, it remains a long-standing problem to learn generative models that are capable of synthesizing realistic and sharp images from reconfigurable spatial layout (i.e., bounding boxes + class labels in an image lattice) and style (i.e., structural and appearance variations encoded by latent vectors), especially at high resolution. By reconfigurable, it means that a model can preserve the intrinsic one-to-many mapping from a given layout to multiple plausible images with different styles, and is adaptive with respect to perturbations of a layout and style latent code. In this paper, we present a layout- and style-based architecture for generative adversarial networks (termed LostGANs) that can be trained end-to-end to generate images from reconfigurable layout and style. Inspired by the vanilla StyleGAN, the proposed LostGAN consists of two new components: (i) learning fine-grained mask maps in a weakly-supervised manner to bridge the gap between layouts and images, and (ii) learning object instance-specific layout-aware feature normalization (ISLA-Norm) in the generator to realize multi-object style generation. In experiments, the proposed method is tested on the COCO-Stuff dataset and the Visual Genome dataset with state-of-the-art performance obtained. The code and pretrained models are available at \url{https://github.com/iVMCL/LostGANs}.
In vitrovascularization of a combined system based on a 3D printing technique (2014)

A vital challenge in complex organ manufacturing is to vascularize large combined tissues. The aim of this study is to vascularize in vitro an adipose-derived stem cell (ADSC)/fibrin/collagen incorporated three-dimensional (3D) poly(d,l-lactic-co-glycolic acid) (PLGA) scaffold (10 × 10 × 10 mm<sup>3</sup> ) with interconnected channels. A low-temperature 3D printing technique was employed to build the PLGA scaffold. A step-by-step cocktail procedure was designed to engage or steer the ADSCs in the PLGA channels towards both endothelial and smooth muscle cell lineages. The combined system had sufficient mechanical properties to support the cell/fibrin/collagen hydrogel inside the predefined PLGA channels. The ADSCs encapsulated in the fibrin/collagen hydrogel differentiated to endothelial and smooth muscle cell lineage, respectively, corresponding to their respective locations in the construct and formed vascular-like structures. This technique allows in vitro vascularization of the predefined PLGA channels and provides a choice for complex organ manufacture. Copyright © 2014 John Wiley & Sons, Ltd.