gebhart/patrepeval huggingface dataset:
Estrogen receptor α (ESR1) over-expression mediated apoptosis in Hep3B cells by binding with SP1 proteins (2013)

Previous studies have reported that estrogen receptors (ERs) are expressed in normal human liver, chronic hepatitis, and benign hepatic tumor tissues. However, decreased expression of ERs can be observed in hepatocellular carcinoma (HCC) and the role of ERs in HCC is not fully understood. Thus, the present study aimed to investigate the molecular mechanism induced by the overexpression of ERα (ERα (ESR1)) in Hep3B cells. We first detected the induction of apoptosis in ER-negative Hep3B cells using DNA fragmentation assay and flow cytometry. We found that ERα and ERα plus 17β-estradiol treatment increased apoptosis in Hep3B cells. Additionally, western blotting showed increased expression of active caspase 3 and tumor necrosis factor α (TNFα (TNF)) in ERα-transfected cells. To further understand the importance of SP1-binding sites in the TNFα promoter, ERα-negative Hep3B cells were co-transfected with ERα and a wild-type TNFα plasmid or TNFα with deleted SP1 regions. Deletion of both distant and primal SP1 sites abolished the activity of ERα, and similar results were observed by blocking the expression of SP1 protein using mithramycin (MA). This result indicates that SP1 protein is essential for ERα-activated TNFα promoter activity. Co-immunoprecipitation assay further confirmed the binding interaction between ERα and SP1 in a ligand-dependent manner. In general, we demonstrate that the overexpression of ERα mediates apoptosis in ERα-negative Hep3B cells by the binding of ERα to SP1 protein. Additionally, this ERα-SP1 complex binds to the proximal and distal sites of the TNFα gene promoter and further induces the expression of active caspase 3 in a ligand-dependent manner.
CSR: Speaker Recognition from Compressed VoIP Packet Stream (2005)

VoIP applications require the ability to identify speakers in real time. This paper presents compressed speaker recognition (CSR), an innovative approach to perform speaker recognition directly from the compressed voice packets. CSR performs online speaker recognition from live packet streams of compressed voice packets by performing fast clustering over a defined subset of the features available in each compressed voice packet. Our experimental results show that CSR is highly scalable and accurate across a broad range of speakers
Genome-wide association study identifies 17 new loci influencing concentrations of circulating cytokines and growth factors (2016)

Abstract Circulating cytokines and growth factors are regulators of inflammation and have been implicated in autoimmune and metabolic diseases. In this genome-wide association study (GWAS) up to n=8,293 Finns we identified 27 loci with genome-wide association (P-value&lt;1.2×10 -9 ) for one or more cytokines, including 17 unidentified in previous GWASes. Fifteen of the associated SNPs had expression quantitative trait loci in whole blood. We provide strong genetic instruments to clarify the causal roles of cytokine signaling and upstream inflammation in immune-related and other chronic diseases. We further link known autoimmune disease variants including Crohn's disease, multiple sclerosis and ulcerative colitis with new inflammatory markers, which elucidate the molecular mechanisms underpinning these diseases and suggest potential drug targets.
On Orders of Optimal Normal Basis Generators (1995)

In this paper we give some experimental results on the multiplicative orders of optimal normal basis generators in ${F_{{2^n}}}$ over ${F_2}$ for $n \leq 1200$ whenever the complete factorization of ${2^n} - 1$ is known. Our results show that a subclass of optimal normal basis generators always have high multiplicative orders, at least $O(({2^n} - 1)/n)$, and are very often primitive. For a given optimal normal basis generator $\alpha$ in ${F_{{2^n}}}$ and an arbitrary integer e, we show that ${\alpha ^e}$ can be computed in $O(n \cdot v(e))$ bit operations, where $v(e)$ is the number of 1âs in the binary representation of e.
Development of a novel MALDI-TOF MS-based bile solubility test for rapid discrimination of Streptococcus pneumoniae (2020)

Differentiation of Streptococcus pneumoniae from other Streptococcus mitis group streptococci (SMGS) remains challenging despite the introduction of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). While the bile solubility test (BST) provides most reliable discrimination of pneumococci, its practical implementation is limited by subjective visual interpretation and frequent inconclusive results. We aimed to develop a rapid confirmation BST based on direct-on-target MALDI-TOF MS assay. After establishment of optimal test conditions, test performance was evaluated on 36 consecutive clinical SMGS isolates. Colony material was suspended and pipetted onto a MALDI target. After drying, sodium deoxycholate in different concentrations (2%, 5%, and 10 %) was added. Incubation for 30 min (at room temperature or 35 °C) was followed by liquid removal and spot washing. After adding 70 % formic acid, spots were overlaid with matrix and measured (MALDI Biotyper smart, Bruker). The absence of microbial spectra (Biotyper score <1.7) in samples with sodium deoxycholate indicated efficient removal of bacterial biomass due to bile solubility, thus, identifying pneumococci. In contrast, scores ≥1.7 were interpreted as lack of bile solubility and confirmation as viridans streptococci other than S. pneumoniae. Highest test accuracy was achieved applying 5% sodium deoxycholate at 35 °C and 10 % sodium deoxycholate at room temperature. These test conditions provided 100 % sensitivity and 100 % specificity for discrimination of S. pneumoniae. The developed MALDI-TOF MS-based BST is an easy-to-perform assay with minimum hands-on time and objective readout. The promising results of this proof-of-principle study warrant confirmation with large collections of epidemiologically diverse strains.
Nanocannabinoides como terapia frente a glioma (2019)

Las patologias cerebrales representan un desafio terapeutico por la restriccion al paso de farmacos a traves de la barrera hematoencefalica. Por ello, actualmente se persigue disenar transportadores de farmacos capaces de atravesar de manera eficiente el endotelio cerebral tras su administracion intravenosa. Sin embargo, el impacto traslacional de la nanomedicina es aun discreto. Sin duda, la transicion de un desarrollo empirico hacia un diseno racional adecuado a las necesidades terapeuticas concretas en cada caso aumentara las posibilidades de exito. Bajo esta premisa y aprovechando tanto el tropismo cerebral como la actividad antiproliferativa del cannabidiol, y a fin de contribuir al diseno racional de nanocapsulas dirigidas para el tratamiento de gliomas, hemos evaluado la influencia de distintos parametros en su comportamiento in vitro e in vivo . Efectivamente, hemos demostrado que tanto el paso a traves de barrera hematoencefalica como la captacion por celulas de glioma, asi como la velocidad de liberacion de farmacos pueden modularse variando su tamano de particula. El metodo termico de inversion de fases posibilita la obtencion de nanocapsulas bajo demanda en terminos de tamano gracias al modelo matematico lineal en una variable aqui descrito. Ademas, hemos desarrollado una novedosa estrategia de vectorizacion con cannabidiol (que incluso supera a otras que ya se encuentran en ensayos clinicos). Asimismo, las nanocapsulas sirven como transportadores de liberacion prolongada del cannabidiol, superando asi sus problemas de formulacion que venian limitando su potencial terapeutico. En conjunto, las nanocapsulas lipidicas, cargadas y funcionalizadas con cannabidiol, constituyen prometedores candidatos para el tratamiento de gliomas.
Antigen‐Specific Therapy Promotes Repair of Myelin and Axonal Damage in Established EAE (2006)

Inflammation results in CNS damage in multiple sclerosis (MS) and experimental autoimmune encephalomyelitis (EAE), an animal model of MS. It is uncertain how much repair of injured myelin and axons can occur following highly selective anti-inflammatory therapy in EAE and MS. In this study, SJL/J mice with established EAE were treated successfully with an antigen-specific recombinant T cell receptor ligand (RTL), RTL401, a mouse I-A(s)/PLP-139-151 construct, after the peak of EAE. To define the mechanisms by which late application of RTL401 inhibits EAE, we evaluated mice at different time points to assess the levels of neuroinflammation and myelin and axon damage in their spinal cords. Our results showed that RTL401 administered after the peak of acute EAE induced a marked reduction in inflammation in the CNS, associated with a significant reduction of demyelination, axonal loss and ongoing damage. Electron microscopy showed that RTL-treated mice had reduced pathology compared with mice treated with vehicle and mice at the peak of disease, as demonstrated by a decrease in continued degeneration, increase in remyelinating axons and the presence of an increased number of small, presumably regenerative axonal sprouts. These findings indicate that RTL therapy targeting encephalitogenic T cells may promote CNS neuroregenerative processes.
Online feedback-based estimation of dynamic page service time (2006)

We present a framework for estimating the service time of a dynamic HTTP request by using the service times of past requests to the same URL. Our framework tags incoming requests with a timestamp. As the request is processed, server state relevant to the estimation mechanism, such as the number of threads servicing incoming requests, is stored with each request. When a request is handled, it is timestamped again, allowing us to calculate its service time. This service time is added to the history table and used in the computation of future estimates. The estimators we evaluated do not produce accurate predictions when server resources change, leaving room for further work in estimator design.
New Converter Solution With a Compact Modular Multilevel Structure Suitable for High-Power Medium-Voltage Wind Turbines (2022)

Modern wind turbines with increasing power levels are continuously emerging. These power levels are reaching a point where excessively high currents are obtained if the traditional low-voltage wind-turbine structure is adopted. High currents lead to excessively high losses and the need for bulky and heavy conductors to carry them. A medium-voltage structure should be a more competitive alternative to be adopted in high-power wind turbines. In this article, a new converter solution with a modular multilevel structure suitable for driving modern/future high-power medium-voltage wind turbines is proposed. This converter topology has desirable features common to modular multilevel converters, such as the improved reliability at high voltage levels, and the possibility to synthesize high-power-quality staircase-shape voltages, which leads to low requirements for harmonic and <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex-math notation="LaTeX">${dv}/{dt}$</tex-math></inline-formula> filters. Furthermore, the proposed converter presents reduced capacitance and inductance requirements compared with other well-established modular multilevel converter topologies, which should result in a lighter and more compact solution. The proposed solution could potentially allow for the reduction of the overall costs of the supporting structure required to withstand the weight of the wind turbine. Simulation and experimental results are presented in this article to validate the proposed topology.
Studying the activity of antitubercluosis drugs inside electrospun polyvinyl alcohol, polyethylene oxide, and polycaprolacton nanofibers (2013)

The activity of antituberculosis drugs (streptomycin sulfate, isoniazid, pyrazinamid, and clarithromycin) embedded in biodegradable nanofibers against Mycobacterium avium has been studied by broth dilution assay and by agar plate assay. These drugs have also been embedded in electrospun polyvinyl alcohol (PVA), polyethylene oxide (PEO), and polycaprolacton (PCL) nanofibers to design a new single tablet containing first-line antituberculosis drugs. Our results show that antituberculosis drugs are active at tiny amounts (up to 300 µg mL(-1) of solvent). However, within polymer matrices, high amounts of drugs are required to avoid unwanted weak interactions within PEO and PCL matrices. The successful design of a single tablet containing required amounts of antituberculosis drugs is essential for the full treatment of tuberculosis in patients with HIV.
A Recombinant Influenza A/H1N1 Carrying A Short Immunogenic Peptide of MERS-CoV as Bivalent Vaccine in BALB/c Mice (2019)

Middle East Respiratory Syndrome Coronavirus (MERS-CoV) became a global human health threat since its first documentation in humans in 2012. An efficient vaccine for the prophylaxis of humans in hotspots of the infection (e.g., Saudi Arabia) is necessary but no commercial vaccines are yet approved. In this study, a chimeric DNA construct was designed to encode an influenza A/H1N1 NA protein which is flanking immunogenic amino acids (aa) 736-761 of MERS-CoV spike protein. Using the generated chimeric construct, a novel recombinant vaccine strain against pandemic influenza A virus (H1N1pdm09) and MERS-CoV was generated (chimeric bivalent 5 + 3). The chimeric bivalent 5 + 3 vaccine strain comprises a recombinant PR8-based vaccine, expressing the PB1, HA, and chimeric NA of pandemic 2009 H1N1. Interestingly, an increase in replication efficiency of the generated vaccine strain was observed when compared to the PR8-based 5 + 3 H1N1pdm09 vaccine strain that lacks the MERS-CoV spike peptide insert. In BALB/c mice, the inactivated chimeric bivalent vaccine induced potent and specific neutralizing antibodies against MERS-CoV and H1N1pdm09. This novel approach succeeded in developing a recombinant influenza virus with potential use as a bivalent vaccine against H1N1pdm09 and MERS-CoV. This approach provides a basis for the future development of chimeric influenza-based vaccines against MERS-CoV and other viruses.
Solid Vesicle Membrane Made of meso-Tetrakis[(bixinylamino)-o-phenyl]porphyrins (1997)

Tetrakis(aminophenyl)porphyrin with four bixin side chains in statistical orientation with respect to the porphyrin plane and its zinc(II) complex produced stable colloidal solutions in water at pH 9. Cryoelectron microscopy showed spherical unilamellar vesicles with diameters ranging from 30 to 120 nm and a membrane thickness of 4.7 ± 0.5 nm, corresponding to a monomolecular layer with the bixin side chains tilted by 30°. The stiff vesicle membranes were not sensitive to the addition of sodium chloride and survived adsorption to dry solid surfaces. Furthermore, the vesicles were totally polymerized by visible light. These polymer vesicles remained intact in 95% ethanol, and scanning force microscopy (SFM) images showed perfectly spherical shapes on graphite. A slow collapse is only observed on hydrated mica. The tetrabixinporphyrin also produced stable monolayers on water surface which polymerized upon irradiation. Combination of the polyene vesicle with an electron-accepting porphyrin, namely a synthetic guanidinium porphyrin or 2-anthraquinone sulfonate, led to light-induced long-lived charge separations.
Development of the Caecal Microbiota in Three Broiler Breeds (2019)

The development of the caecal microbiota plays a role in the metabolism and immune competence of chickens. A detailed understanding of normal succession in the caecal microbiota can inform the use of probiotics and other interventions to optimize the caecal microbiota. The development of the microbiota in caecal mucus and lumen samples from three breeds of broiler chicken (Cobb 500, <i>n</i> = 36; Hubbard JA87, <i>n</i> = 38; and Ross 308, <i>n</i> = 36) was observed between 0 and 42 days post hatch. Chicks were housed in the same room of a climate-controlled, biosecure chicken housing unit. Between 0 and 14 days post hatch, chicks were kept in brooder pens ensuring a mixture of breeds in each brooder. From 22 days post hatch, chicks were removed from the brooders and kept in the same room. DNA was extracted from a pooled sample of caecal mucus and luminal contents from five birds of each breed at 0, 3, 7, 14, 21, 28, and 42 days post hatch. High-throughput Illumina sequencing was performed for the V4 hypervariable region of the 16S rRNA gene. The early caecal microbiota was characterized by poor diversity and dominance by one or two bacterial species. Early colonizers of the caecum included <i>Bifidobacteriaceae, Lachnospiraceae, Bacteroidaceae</i> and <i>Burkholderiaceae</i> with some amplicon sequence variants (ASVs) assigned to <i>Ruminococcaceae</i>. Later colonizers of the caecal microbiota were most apparent from 14 d.p.h and included <i>Ruminococcaceae, Clostridiales</i> vadin BB60 group, <i>Christensenellaceae</i> and <i>Bacillaceae</i>. The caecal microbiota continued to change until 42 d.p.h when the microbiota was characterized by a high abundance of <i>Bacteroidaceae, Lachnospiraceae</i> and <i>Ruminococcaceae</i>. The lumen microbiota was significantly different to the mucus with some ASVs assigned to <i>Lachnospiraceae, Ruminococcaceae, Christensenellaceae</i> and <i>Bacillaceae</i> showing increased abundance in the mucus. ASVs assigned to <i>Bacteroidaceae, Lactobacillaceae</i> and <i>Burkholderiaceae</i> showed a preference for the lumen. Analysis of five caecal mucus samples from each breed at 42 days post hatch showed differences in microbiota composition between Ross and Cobb as well as between Ross and Hubbard. Since performance data was not collected no functional inferences as to the significance of this finding can be made.
Biomimetic Engineering of Carbon Nanotubes by Using Cell Surface Mucin Mimics (2004)

Biocompatible nanotubes: Glycosylated polymers designed to mimic natural mucins were assembled on carbon nanotubes (see picture). Carbon nanotubes coated with mucin mimics were soluble in water, resisted nonspecific protein binding, and bound specifically to biomolecules through receptor–ligand interactions. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2002/2004/z460620_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Evaluation of Hydraulic Radial Forces on the Impeller by the Volute in a Centrifugal Rotary Blood Pump (2011)

In many state-of-the-art rotary blood pumps for long-term ventricular assistance, the impeller is suspended within the casing by magnetic or hydrodynamic means. For the design of such suspension systems, profound knowledge of the acting forces on the impeller is crucial. Hydrodynamic bearings running at low clearance gaps can yield increased blood damage and magnetic bearings counteracting high forces consume excessive power. Most current rotary blood pump devices with contactless bearings are centrifugal pumps that incorporate a radial diffuser volute where hydraulic forces on the impeller develop. The yielding radial forces are highly dependent on impeller design, operating point and volute design. There are three basic types of volute design--singular, circular, and double volute. In this study, the hydraulic radial forces on the impeller created by the volute in an investigational centrifugal blood pump are evaluated and discussed with regard to the choice of contactless suspension systems. Each volute type was tested experimentally in a centrifugal pump test setup at various rotational speeds and flow rates. For the pump's design point at 5 L/min and 2500 rpm, the single volute had the lowest radial force (∼0 N), the circular volute yielded the highest force (∼2 N), and the double volute possessed a force of approx. 0.5 N. Results of radial force magnitude and direction were obtained and compared with a previously performed computational fluid dynamics (CFD) study.
Flory Theory of a Polyampholyte Chain (1995)

The behavior of a polyampholyte chain is analyzed in the framework of the two-parameter Flory theory. We consider a N-mer containing N+ positively charged monomers and N- negatively charged ones. There are three different regimes for polyampholytes with charge asymmetry |N+ -N-|>(N+ +N-)1/2 depending on the effective temperature t=N/[u(N++N-)], where u is the ratio of the Bjerrum length lB to the bond size b: (i) Unperturbed regime: at high effective temperatures t>t1 the electrostatic interactions are unimportant and polyampholyte configuration is controlled by the solvent quality for the uncharged backbone, (ii) Polyelectrolyte regime: at intermediate effective temperatures t2 < t < t1 the repulsion between uncompensated charges e(N+-N-) dominates over the charge-fluctuation-induced attraction. The chain is stretched into an array of electrostatic blobs, (iii) Polyampholyte regime (t < t2): when the Debye screening length due to the charges on the chain becomes smaller than the electrostatic blob size, the charge-fluctuation-induced attraction collapses the polyampholyte into an elongated globule with aspect ratio (N+-N-)2/(N+ +N-) independent of the temperature. The nearly symmetric chains with |N+-N-|≤(N+ +N-)1/2 directly cross over from regime (i) to regime (iii), but stay nearly spherical.
P2–157: Effects of APOE‐ε4 on regional cerebral amyloid deposition and gray matter atrophy in mild cognitive impairment with PiB‐PET‐confirmed amyloid pathology: Results from J‐ADNI (2013)

The aim of this study was to reveal the effects of apolipoprotein (APOE) epsilon4 (ε 4) on regional amyloid burden and gray matter atrophy in mild cognitive impairment (MCI) with PiB-PET-confirmed amyloid pathology using PiB-PET and 3D-MRI. Twenty-one MCI subjects with APOE ε 4 and 11 MCI subjects without ApoE ε 4 who underwent both PiB-PET and MRI from the database of Japanese Alzheimer's disease neuroimaging initiative (J-ADNI) were included in this study. Voxel-based morphometry (VBM) with Statistical Parametrical Mapping (SPM) 8 was used to compare the amyloid burden and gray matter volume among MCI subjects with ApoE ε 4, MCI subjects without ApoE ε 4, and with 23 PiB-negative normal controls. Additional ROIs analysis using ANCOVA models for the hippocampus and posterior cingulate was performed for the comparison in the gray matter volume. In MCI with APOE ε 4 group, PiB uptake was greater in the left precuneus and temporal lobe than that in APOE ε 4 noncarriers. MRI demonstrated that the gray matter volume in the hippocampus was more decreased in the MCI with APOE ε 4 group than that in ApoE ε 4 noncarriers (p < 0.03 for ROIs analysis and p<0.05, uncorrected for VBM analysis), whereas the gray matter atrophy in the posterior cingulate in MCI without ApoE ε 4 group was greater than that in APOE ε 4 carriers (p < 0.02 for ROIs analysis and p<0.05, uncorrected for VBM analysis). Possession of APOE ε 4 allele facilitates amyloid accumulation involving the gray matter atrophy especially in the medial temporal lobe, whereas posterior cingulate was affected in the MCI subjects without APOE ε 4. APOE genotype might lead different patterns of gray matter atrophy in the early stage of the disease, suggesting variable mechanisms in the development of AD pathology depending on the APOE genotype.