gebhart/patrepeval huggingface dataset:
Intermedilysin Is Essential for the Invasion of Hepatoma HepG2 Cells by Streptococcus intermedius (2005)

Streptococcus intermedius causes endogenous infections leading to abscesses. This species produces intermedilysin (ILY), a human-specific cytolysin. Because of the significant correlation between higher ILY production levels by S. intermedius and deep-seated abscesses, we constructed ily knockout mutant UNS38 B3 and complementation strain UNS38 B3R1 in order to investigate the role of ILY in deep-seated infections. Strain UNS38 reduced the viability of human liver cell line HepG2 at infection but not of rat liver cell line BRL3A. Isogenic mutant strain UNS38 B3 was not cytotoxic in either cell line. Quantification of S. intermedius revealed that in infected HepG2 cells UNS38 but not UNS38 B3 increased intracellularly concomitantly with increasing cell damage. This difference between UNS38 and UNS38 B3 was not observed with UNS38 B3R1. Invasion and proliferation in BRL3A cells was not observed. Masking UNS38 or UNS38 B3R1 with ILY antibody drastically decreased adherence and invasion of HepG2. Moreover, coating strain UNS38 B3 with ILY partially restored adherence to HepG2 but without subsequent bacterial growth. At 1 day post-infection, many intact UNS38 were detected in the damaged phagosomes of HepG2 with bacterial proliferation observed in the cytoplasm of dead HepG2 after an additional 2 day incubation. These results indicate that surface-bound ILY on S. intermedius is an important factor for invasion of human cells by this bacterium and that secretion of ILY within host cells is essential for subsequent host cell death. These data strongly implicate ILY as an important factor in the pathogenesis of abscesses in vivo by this streptococcus.
Planarization of Patterned Recording Media (2010)

The planarization of patterned recording media is essential to overcome the ¿flying height reduction¿ and ¿flying instability¿ of the head-slider. This paper reports two planarization techniques; one by compressing a morphological smooth surface onto a low glass transition temperature T <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">g</sub> /UV curable polymer/material coated patterned sample, while the other employs spin coating to coat patterned disks. A roughness of 0.3 nm was achieved by planarization using compression of smooth Si onto 35 K PMMA (heated above T <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">g</sub> to decrease its viscosity). It was also found that decreasing the spin speed from 5000 rpm to 1000 rpm improves the filling of grooves using spin coating of hydrogen silsesquioxane (HSQ) decreasing the height difference between the filled groove region and the land region from about 6 nm to 4 nm. Initial investigation using compression of smooth Si onto diluted HSQ also shows a decrease of roughness as dilution increases from 50.0% to 66.6%. Both techniques were applied in the planarization of a UV curable resist. The results show that about 1 nm is observed between the patterned and unpatterned regions using only spin coating. However, with compression using a flat mold, no height difference on average is observed.
Bonding Wood Veneer with Biobased Poly(Lactic Acid) Thermoplastic Polyesters: Potential Applications for Consolidated Wood Veneer and Overlay Products (2020)

This study reports on the use of poly(lactic acid) (PLA) as a renewable thermoplastic adhesive for laminated panels using birch, spruce, and pine veneers. Consolidated panels were prepared from veneer and PLA foils by hot-pressing from 140 to 180 °C to achieve minimum bondline temperatures. Evaluation of panel properties revealed that the PLA-bonded panels met minimum tensile strength and internal bond strength performance criteria. However, the adhesion interface which developed within individual bondlines varied with distinctions between hardwood and softwood species and PLA grades. Birch samples developed greater bondline strength with a higher pressing temperature using semi-crystalline PLA, whereas higher temperatures produced a poorer performance with the use of amorphous PLA. Panels formed with spruce or pine veneers had lower bondline performance and were also similarly distinguished by their pressing temperature and PLA grade. Furthermore, the potential for PLA-bonded laminated panels was demonstrated by cold water soak testing. Samples exhibiting relatively greater bondline adhesion had wet tensile strength values comparable to those tested in dry state. Our study outcomes suggest the potential for PLA bonding of veneers and panel overlays with the added benefits of being renewable and a no added formaldehyde system.
Nucleic Acid Hybridization Enhanced Luminescence for Rapid and Sensitive RNA and DNA Based Diagnostics (2022)

Long-lived emissive nucleic acid probes are widely used in biochemical analysis due to their programmable structures, high signal-to-background ratio, and high sensitivity. Homogeneous detection based on long-lived emissive nucleic acid probes is often achieved through Förster resonance energy transfer (FRET), which suffers from the limitation of a narrow effective distance range. Herein, a new strategy of accessing nucleic acid hybridization-responsive luminescent probes is presented. The photoluminescence (PL) of a Lumi4-Tb complex internally modified with DNA is switched on by nucleic acid hybridization, after which the PL is increased up to 20 times. PL lifetime analysis revealed a possible mechanism of luminescence enhancement. Due to the flexibility of single-stranded nucleic acid chains, the bases and phosphate groups can coordinate with the Tb(III), which reduces the stability of the Tb complex and results in weak PL. After hybridization, the rigid double helix structure suppresses the coordination between Tb(III) and the bases or phosphate groups, causing luminescence enhancement. As the DNA sequence can be freely designed, an array of probes for different DNA or RNA targets can be created with the same Tb complex. Moreover, the novel probe design can afford pM detection limits of DNA or RNA without any nucleic acid amplification and exhibits great potential for nucleic acid detection in clinical diagnosis.
SMTP Service Extension for Delivery Status Notifications (1996)

This memo defines an extension to the SMTP service, which allows an SMTP client to specify (a) that delivery status notifications (DSNs) should be generated under certain conditions, (b) whether such notifications should return the contents of the message, and (c) additional information, to be returned with a DSN, that allows the sender to identify both the recipient(s) for which the DSN was issued, and the transaction in which the original message was sent.
Cervical Cancer Screening: From the Papanicolaou Smear to the Vaccine Era (2003)

In the next 20 years, cervical cancer screening will have evolved through four phases. The first was traditional screening, which has been associated with a two-thirds reduction in cancer incidence and death rates in the last 50 years and currently is ending. We are entering a second phase, human papillomavirus (HPV) testing, for managing cytologic abnormalities and possibly for primary screening. A third phase, new in development, proposes the use of host biomarkers (or combinations thereof) as either surrogates of HPV infection or, potentially, indicators to assess cancer risk and concentrate available resources on a subset of women. The fourth and, likely, final phase will be screening in an era of vaccines. If HPV vaccines are successful, the pool of at-risk individuals and the prevalence of papillomaviruses that place them at risk will gradually shrink. In this climate, screening strategies that target HPVs alone (as opposed to cytologic testing) may become more economical. If so, previous strategies may become obsolete as the balance of cervical cancer prevention shifts from traditional screening to primary prevention coupled with HPV testing.
Bivalent Aptasensor Based on Silver-Enhanced Fluorescence Polarization for Rapid Detection of Lactoferrin in Milk (2017)

Here we report a novel type of bivalent aptasensor based on silver-enhanced fluorescence polarization (FP) for detection of lactoferrin (Lac) in milk powder with high sensitivity and specificity. The novel two split aptamers were obtained from the aptamer reported in our previous SELEX (systematic evolution of ligands by exponential enrichment) selection, and their minimal structural units were optimized on the basis of their affinity and specificity. Also, dual binding sites of split aptamers were verified. The bivalent aptamers were modified to be linked with signal-molecule fluorescein isothiocyanate (FITC) and enhancer silver decahedral nanoparticles (Ag<sub>10</sub>NPs). The split aptamers could bind to different sites of Lac and assemble into a split-aptamers-target complex, narrowing the distance between Ag<sub>10</sub>NPs and FITC dye. As a result, Ag<sub>10</sub>NPs could produce a mass-augmented and metal-enhanced fluorescence (MEF) effect. In general, ternary amplification based on Ag<sub>10</sub>NPs, split aptamers, and the MEF effect all contributed to the significant increase of FP values. It was proved that the sensitivity of this assay was about 3 orders of magnitude over traditional aptamer-based homogeneous assays with a detection limit of 1.25 pM. Furthermore, this design was examined by actual milk powder with rapid and high-throughout detection.
Integrated optimum design of structure and H-infinity control system (1996)

An approach for an integrated optimum design of a structure and an H∞ control system is presented. The complex method and the genetic algorithm are adopted in the optimization process in the integrated design. The structural shape and the control system, including the locations of both sensors and actuators, are optimized simultaneously by the proposed approach. The improvement of frequency response shaping under the constraint of the structural mass can be realized by the integrated optimum design presented in this paper. The desired properties with respect to the control performance and the robustness are realized by the frequency shaping ability of H∞ control. Effectiveness of the presented approach is verified by both simulation and experiment by the integrated design of a panel structure and H∞ control system.
Transcriptomic analysis of CFTR-impaired endothelial cells reveals a pro-inflammatory phenotype (2020)

Cystic fibrosis (CF) is a life-threatening disorder characterised by decreased pulmonary mucociliary and pathogen clearance, and an exaggerated inflammatory response leading to progressive lung damage. CF is caused by bi-allelic pathogenic variants of the cystic fibrosis transmembrane conductance regulator (CFTR) gene, which encodes a chloride channel. CFTR is expressed in endothelial cells (ECs) and EC dysfunction has been reported in CF patients, but a role for this ion channel in ECs regarding CF disease progression is poorly described.We used an unbiased RNA sequencing approach in complementary models of CFTR silencing and blockade (by the CFTR inhibitor CFTRinh-172) in human ECs to characterise the changes upon CFTR impairment. Key findings were further validated <i>in vitro</i> and <i>in vivo</i> in CFTR-knockout mice and <i>ex vivo</i> in CF patient-derived ECs.Both models of CFTR impairment revealed that EC proliferation, migration and autophagy were downregulated. Remarkably though, defective CFTR function led to EC activation and a persisting pro-inflammatory state of the endothelium with increased leukocyte adhesion. Further validation in CFTR-knockout mice revealed enhanced leukocyte extravasation in lung and liver parenchyma associated with increased levels of EC activation markers. In addition, CF patient-derived ECs displayed increased EC activation markers and leukocyte adhesion, which was partially rescued by the CFTR modulators VX-770 and VX-809.Our integrated analysis thus suggests that ECs are no innocent bystanders in CF pathology, but rather may contribute to the exaggerated inflammatory phenotype, raising the question of whether normalisation of vascular inflammation might be a novel therapeutic strategy to ameliorate the disease severity of CF.
Supplementary Figure Legends from Cyclophosphamide Induces Differentiation of Th17 Cells in Cancer Patients (2023)

Supplementary Figure Legends from Cyclophosphamide Induces Differentiation of Th17 Cells in Cancer Patients
Challenges of Implementing Cyber-Physical Security Solutions in Body Area Networks (2009)

Cyber-physical approach to securing Body Area Networks (BANs) provides solutions that are plug-n-play and trans- parent to its users. These Cyber-Physical Security Solutions (CPSS) actively involve characteristics from the physical en- vironment. As a result they require a combination of signal proc
Organochlorines and risk of non‐Hodgkin lymphoma (2007)

Organochlorine chemicals and polychlorinated biphenyls (PCBs) have been suspected as possible risk factors for non-Hodgkin lymphoma (NHL). We investigated PCBs and organochlorine pesticides and risk of NHL in a population-based case-control study in British Columbia, Canada. Congeners of PCBs (including dioxinlike congeners) and pesticides or pesticide metabolites were measured in plasma of 422 pretreatment cases and 460 control subjects. This is so far the largest study to examine organochlorines in plasma to date. Several dioxin-like PCB congeners were associated with increased risk of NHL, including dioxin-like PCB nos. 118 and 156 with odds ratios (OR) for the highest versus lowest quartile between 1.6 and 1.8. Several non-dioxin-like congeners also showed significant associations. The PCB congener with the strongest association was no. 180 with an OR for the highest versus the lowest quartile of 1.83 (95% confidence interval = 1.18-2.84). Six pesticide analytes also showed a significant association with NHL; beta-hexachlorocyclohexane, p,p'-DDE, hexachlorobenzene, mirex, oxychlordane and trans-nonachlor. The strongest association was found for oxychlordane, a metabolite of the pesticide chlordane (highest vs. lowest quartile OR = 2.68, 95% confidence interval = 1.69-4.24). Our results provide further evidence that organochlorines contribute to NHL risk.
Load balancing in overlapping wireless LAN cells (2004)

We propose a load-balancing scheme for overlapping wireless LAN cells. Agents running in each access point broadcast periodically the local load level via the Ethernet backbone and determines whether the access point is overloaded, balanced or under-loaded by comparing it with the received reports. The load metric is the access point throughput. Overloaded access points force the handoff of some stations to balance the load. Only the under-loaded access points accept the roaming stations in minimizing the number of handoffs. We show via experimental evaluation that our balancing scheme increases the total wireless network throughput and decreases the cell delay.
Damage Evolution in Complex-Phase and Dual-Phase Steels during Edge Stretching (2017)

The role of microstructural damage in controlling the edge stretchability of Complex-Phase (CP) and Dual-Phase (DP) steels was evaluated using hole tension experiments. The experiments considered a tensile specimen with a hole at the center of specimen that is either sheared (sheared edge condition) or drilled and then reamed (reamed edge condition). The damage mechanism and accumulation in the CP and DP steels were systematically characterized by interrupting the hole tension tests at different strain levels using scanning electron microscope (SEM) analysis and optical microscopy. Martensite cracking and decohesion of ferrite-martensite interfaces are the dominant nucleation mechanisms in the DP780. The primary source of void nucleation in the CP800 is nucleation at TiN particles, with secondary void formation at martensite/bainite interfaces near the failure strain. The rate of damage evolution is considerably higher for the sheared edge in contrast with the reamed edge since the shearing process alters the microstructure in the shear affected zone (SAZ) by introducing work-hardening and initial damage behind the sheared edge. The CP microstructures were shown to be less prone to shear-induced damage than the DP materials resulting in much higher sheared edge formability. Microstructural damage in the CP and DP steels was characterized to understand the interaction between microstructure, damage evolution and edge formability during edge stretching. An analytical model for void evolution and coalescence was developed and applied to predict the damage rate in these rather diverse microstructures.
Myocardial fibrosis and calcification are attenuated by microRNA–129-5p targeting Asporin and Sox9 in cardiac fibroblasts (2023)

Myocardial fibrosis and calcification associate with adverse outcomes in nonischemic heart failure. Cardiac fibroblasts (CF) transition into myofibroblasts (MF) and osteogenic fibroblasts (OF) to promote myocardial fibrosis and calcification. However, common upstream mechanisms regulating both CF-to-MF transition and CF-to-OF transition remain unknown. microRNAs are promising targets to modulate CF plasticity. Our bioinformatics revealed downregulation of miR-129-5p and upregulation of its targets small leucine-rich proteoglycan Asporin (ASPN) and transcription factor SOX9 as common in mouse and human heart failure (HF). We experimentally confirmed decreased miR-129-5p and enhanced SOX9 and ASPN expression in CF in human hearts with myocardial fibrosis and calcification. miR-129-5p repressed both CF-to-MF and CF-to-OF transition in primary CF, as did knockdown of SOX9 and ASPN. Sox9 and Aspn are direct targets of miR-129-5p that inhibit downstream β-catenin expression. Chronic Angiotensin II infusion downregulated miR-129-5p in CF in WT and TCF21-lineage CF reporter mice, and it was restored by miR-129-5p mimic. Importantly, miR-129-5p mimic not only attenuated progression of myocardial fibrosis, calcification marker expression, and SOX9 and ASPN expression in CF but also restored diastolic and systolic function. Together, we demonstrate miR-129-5p/ASPN and miR-129-5p/SOX9 as potentially novel dysregulated axes in CF-to-MF and CF-to-OF transition in myocardial fibrosis and calcification and the therapeutic relevance of miR-129-5p.
Restoring oral health (1996)

During the last decade, a continuous decrease in dental caries has been observed among schoolchildren in Iceland. In this paper, various epidemiological studies have been reviewed and summarized to illustrate caries prevalence, and how it has changed during the last decades. Furthermore, an attempt has been made to describe some of the factors involved and their possible effects on caries disease. During this period, sugar consumption increased, especially in the form of sweets and soft drinks. At the same time, the import of toothpaste increased, and preventive measures such as fissure sealants and fluoride rinsing programs were intensified. Other factors likely to have had an impact were changes in treatment philosophy and increased personnel resources. There does not seem to be any single factor responsible for the onset of the caries decline. It rather looks as if this was a multifactorial effect due to a number of different preventive measures. During recent years, a change in treatment philosophy, the evident increase in fluoride toothpaste consumption, and possible changes in the oral microbial flora, together with the use of fluoride varnishes, sealants, and increased manpower, may explain the decline.
Is Quantum Mechanics Falsifiable? A computational perspective on the foundations of Quantum Mechanics (2012)

Quantum computation teaches us that quantum mechanics exhibits exponential complexity. We argue that the standard scientific paradigm of "predict and verify" cannot be applied to testing quantum mechanics in this limit of high complexity. We describe how QM can be tested in this regime by extending the usual scientific paradigm to include {\it interactive experiments}.
Physical Properties of Candidate X-ray Detector Material Rb4Ag2BiBr9 (2021)

Recently, metal halide perovskites have emerged as promising semiconductor candidates for sensitive X-ray photon detection due to their suitable bandgap energies, excellent charge transport properties, and low material cost afforded by their low-temperature solution-processing preparation. Here, we report an improved methodology for single crystal (SC) growth, thermal and electrical properties of a two-dimensional (2D) layered halide material Rb<sub>4</sub>Ag<sub>2</sub>BiBr<sub>9</sub>, which has been identified as a potential candidate for X-ray radiation detection applications. The measured heat capacity for Rb<sub>4</sub>Ag<sub>2</sub>BiBr<sub>9</sub> implies that there are no structural phase transitions upon cooling. Temperature dependence of thermal transport measurements further suggest remarkably low thermal conductivities of Rb<sub>4</sub>Ag<sub>2</sub>BiBr<sub>9</sub> that are comparable to the lowest reported in literature. The bulk crystal resistivity is determined to be 2.59×10<sup>9</sup> Ω·cm from the current-voltage (I-V) curve. Density of trap states are estimated to be ~10<sup>10</sup> cm<sup>-3</sup> using the space-charge-limited-current (SCLC) measurements. The fabricated Rb<sub>4</sub>Ag<sub>2</sub>BiBr<sub>9</sub>-based X-ray detector shows good operational stability with no apparent current drift, which may be ascribed to the 2D crystal structure of Rb<sub>4</sub>Ag<sub>2</sub>BiBr<sub>9</sub>. Finally, by varying the X-ray tube current to change the corresponding dose rate, the Rb<sub>4</sub>Ag<sub>2</sub>BiBr<sub>9</sub> X-ray detector sensitivity is determined to be 222.03 uCGy<sup>-1</sup>cm<sup>-2</sup> (at an electric field of E = 24 V/mm).
Explicit 3-D migration using equiripple polynomial expansion and Laplacian synthesis (1996)

Abstract In f-x explicit finite-difference depth migration schemes, wavefield downward extrapolation is carried out through spatial convolution using finite-length filters. Existing methods for computing these filters are based on nonlinear least-squares, with a high computational cost, or on Taylor series expansion, which is suboptimal. In the 3-D case, the physics of wavefield extrapolation requires 2-D extrapolation filters with circular symmetry. Recently, McClellan transformation has been used to design circularly symmetric extrapolation operators. But this approach exhibits artifacts when the data are not spatially oversampled. We describe an alternative method to take advantage of the circular symmetry: the radial response of the filter is expanded as a polynomial in the Laplacian, which is synthesized as the sum of two 1-D second-derivative filters. Using the Laplacian rather than the McClellan transform yields an artifact-free impulse response for wavenumbers much closer to the Nyquist wavenumber at the same computational cost. Other advantages of the proposed method are the easy extension to a rectangular grid and the possibility of time-migration implementation. The coefficients of the polynomials are optimized in the L∞ norm, because the stability condition is expressed more easily with this norm. The Remez exchange algorithm, which is a fast L∞ norm spectral synthesis algorithm, is adapted to obtain these L∞-optimized coefficients of the polynomials, as well as the coefficients of the second derivative filters.