gebhart/patrepeval huggingface dataset:
Telomere Restriction Fragment (TRF) Analysis (2015)

While telomerase is expressed in ~90% of primary human tumors, most somatic tissue cells except transiently proliferating stem-like cells do not have detectable telomerase activity (Shay and Wright, 1996; Shay and Wright, 2001). Telomeres progressively shorten with each cell division in normal cells, including proliferating stem-like cells, due to the end replication (lagging strand synthesis) problem and other causes such as oxidative damage, therefore all somatic cells have limited cell proliferation capacity (Hayflick limit) (Hayflick and Moorhead, 1961; Olovnikov, 1973). The progressive telomere shortening eventually leads to growth arrest in normal cells, which is known as replicative senescence (Shay <i>et al.</i>, 1991). Once telomerase is activated in cancer cells, telomere length is stabilized by the addition of TTAGGG repeats to the end of chromosomes, thus enabling the limitless continuation of cell division (Shay and Wright, 1996; Shay and Wright, 2001). Therefore, the link between aging and cancer can be partially explained by telomere biology. There are many rapid and convenient methods to study telomere biology such as Telomere Restriction Fragment (TRF), Telomere Repeat Amplification Protocol (TRAP) (Mender and Shay, 2015b) and Telomere dysfunction Induced Foci (TIF) analysis (Mender and Shay, 2015a). In this protocol paper we describe Telomere Restriction Fragment (TRF) analysis to determine average telomeric length of cells. Telomeric length can be indirectly measured by a technique called Telomere Restriction Fragment analysis (TRF). This technique is a modified Southern blot, which measures the heterogeneous range of telomere lengths in a cell population using the length distribution of the terminal restriction fragments (Harley <i>et al.</i>, 1990; Ouellette <i>et al.</i>, 2000). This method can be used in eukaryotic cells. The description below focuses on the measurement of human cancer cells telomere length. The principle of this method relies on the lack of restriction enzyme recognition sites within TTAGGG tandem telomeric repeats, therefore digestion of genomic DNA, not telomeric DNA, with a combination of 6 base restriction endonucleases reduces genomic DNA size to less than 800 bp.
Direct and Indirect Regulation of Cytokine and Cell Cycle Proteins by EBNA-2 during Epstein-Barr Virus Infection (2001)

We have studied the pathways of regulation of cytokine and cell cycle control proteins during infection of human B lymphocytes by Epstein-Barr virus (EBV). Among 30 cytokine RNAs analyzed by the RNase protection assay, tumor necrosis factor alpha (TNF-alpha), granulocyte colony-stimulating factor, lymphotoxin (LT), and LTbeta were found to be regulated within 20 h of EBV infection of primary B cells. Similar results were obtained using the estrogen-regulated EBNA-2 cell line EREB2.5, in which RNAs for LT and TNF-alpha were induced within 6 h of activation of EBNA-2. Expression of Notch also caused an induction of TNF-alpha RNA. The induction of TNF-alpha RNA by EBNA-2 was indirect, and constitutive expression of either LMP-1 or c-myc proteins did not substitute for EBNA-2 in induction of TNF-alpha RNA. Cyclin D2 is also an indirect target of EBNA-2-mediated transactivation. EBNA-2 was found to activate the cyclin D2 promoter in a transient-transfection assay. A mutant of EBNA-2 that does not bind RBP-Jkappa retained some activity in this assay, and activation did not depend on the presence of B-cell-specific factors. Deletion analysis of the cyclin D2 promoter revealed that removal of sequences containing E-box c-myc consensus DNA binding sequences did not reduce EBNA-2-mediated activation of the cyclin D2 promoter in the transient-transfection assay. The results indicate that cytokines are an early target of EBNA-2 and that EBNA-2 can regulate cyclin D2 transcription in EBV-infected cells by mechanisms additional to the c-myc pathway.
Prevalence of Borrelia Burgdorferi Infection in a Series of 98 Primary Cutaneous Lymphomas (2011)

Borrelia burgdorferi has been variably associated with different forms of primary cutaneous lymphoma. Differences in prevalence rates among reported studies could be a result of geographic variability or heterogeneity in the molecular approaches that have been employed. In the present study, we investigated the prevalence of Borrelia burgdorferi sensu lato DNA in diagnostic tissue samples from fresh cutaneous biopsies of 98 primary cutaneous lymphomas and 19 normal skin controls. Three different polymerase chain reaction (PCR) protocols targeting the hbb, flagellin, and Osp-A genes were used. Direct sequencing of both sense and antisense strands of purified PCR products confirmed the specificity of the amplified fragments. Sequence specificity was assessed using the Basic Local Alignment Search Tool, and MultAlin software was used to investigate the heterogeneity of target gene sequences across the different samples. Borrelia DNA was not detected in 19 controls, 23 cases of follicular lymphoma, 31 cases of extranodal marginal zone lymphoma, or 30 cases of mycosis fungoides. A single case of 14 diffuse large B-cell lymphoma cases was positive for B. burgdorferi. This study does not support a pathogenic role of B. burgdorferi in primary cutaneous B- and T-cell lymphomas from areas nonendemic for this microorganism and the consequent rationale for the adoption of antibiotic therapy in these patients.
Supplemental table 4 from Preclinical Characterization of BET Family Bromodomain Inhibitor ABBV-075 Suggests Combination Therapeutic Strategies (2023)

&lt;p&gt;Apoptosis induction by MS417 across cancer cell lines&lt;/p&gt;
1912: NFKB-Decoy Transfection into the Donor Kidney Using a Novel Approach of "Ultrasound-Optizon Mediated Gene Transfer Technique" Efficiently Prevented Acute Rejection and Prolonged Animal Survival in Rat Renal Allografts (2007)

You have accessJournal of UrologyModerated Poster 60, Wednesday, May 23,2007, 1:00 - 3:00 pm1 Apr 20071912: NFKB-Decoy Transfection into the Donor Kidney Using a Novel Approach of "Ultrasound-Optizon Mediated Gene Transfer Technique" Efficiently Prevented Acute Rejection and Prolonged Animal Survival in Rat Renal Allografts Haruhito Azuma, Kiyoshi Takahara, Hayahito Nomi, Naokazu Ibuki, Naruya Tomita, Ryuichi Morishita, and Yoji Katsuoka Haruhito AzumaHaruhito Azuma More articles by this author , Kiyoshi TakaharaKiyoshi Takahara More articles by this author , Hayahito NomiHayahito Nomi More articles by this author , Naokazu IbukiNaokazu Ibuki More articles by this author , Naruya TomitaNaruya Tomita More articles by this author , Ryuichi MorishitaRyuichi Morishita More articles by this author , and Yoji KatsuokaYoji Katsuoka More articles by this author View All Author Informationhttps://doi.org/10.1016/S0022-5347(18)32085-8AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail "1912: NFKB-Decoy Transfection into the Donor Kidney Using a Novel Approach of "Ultrasound-Optizon Mediated Gene Transfer Technique" Efficiently Prevented Acute Rejection and Prolonged Animal Survival in Rat Renal Allografts." The Journal of Urology, 177(4S), p. 635 © 2016 by American Urological AssociationFiguresReferencesRelatedDetails Volume 177Issue 4SApril 2007Page: 635 Advertisement Copyright & Permissions© 2016 by American Urological AssociationMetricsAuthor Information Haruhito Azuma More articles by this author Kiyoshi Takahara More articles by this author Hayahito Nomi More articles by this author Naokazu Ibuki More articles by this author Naruya Tomita More articles by this author Ryuichi Morishita More articles by this author Yoji Katsuoka More articles by this author Expand All Advertisement PDF downloadLoading ...
Basal plane slip and formation of mixed-tilt boundaries in sublimation-grown hexagonal polytype silicon carbide single crystals (2002)

Optical microscopy, synchrotron white beam x-ray topography (SWBXT), and high resolution x-ray diffraction (HRXRD) were used to study the distribution of basal plane dislocations in bulk 4H silicon carbide crystals grown by the physical vapor transport method. An etch pit array was observed on the silicon face of KOH-etched off-cut wafers. The arrays were aligned parallel to each other and perpendicular to the off-cut direction. The etch pits were oval-shaped, which is characteristic of basal plane dislocations. Corresponding array images have been observed by SWBXT. Based on the characteristic distribution, the etch pit arrays are interpreted as the slip traces of high temperature deformation during the growth process. Thermoelastic stress is proposed as the plausible cause of the deformation. In addition, basal plane dislocation pileups were found in the proximity of polygonized threading edge dislocation arrays. SWBXT and HRXRD were used to study the misorientation related to such dislocation structure. The pileups are interpreted as the origin of the basal-plane-tilt domains in SiC crystals.
Plasma-enhanced chemical vapor deposition of silicon, germanium, and tin nitride thin films from metalorganic precursors (1995)

Nearly stoichiometric silicon, germanium, and tin nitride thin films were deposited from the corresponding homoleptic dimethylamido complexes M (NMe2)4 (M=Si, Ge, Sn; Me=CH3), and an ammonia plasma at low substrate temperatures (&amp;lt;400 °C). Tin nitride films were also deposited from Sn (NMe2)4 and ammonia without plasma activation. The films showed little (&amp;lt;few at. %) or no carbon or oxygen contamination. The barrier properties of the silicon and germanium nitride films were evaluated by using backscattering spectrometry. Homoleptic dimethylamido silicon and germanium compounds are attractive alternatives to silane and germane for use in the plasma-enhanced chemical vapor deposition of nitride thin films.
Polycarbonates (2014)

The article contains sections titled: 1. Introduction 2. Properties 2.1. Bisphenol A Polycarbonate 2.2. Modified Bisphenol A Polycarbonate (Copolymers) 2.3. Bisphenol A Polycarbonate with Additives 2.4 Aliphatic Polycarbonates 3. Blends 4. Production 4.1. Interfacial Polycondensation 4.2. Melt Transesterification 5. Processing 6. Applications 7. Recycling 8. Toxicology and Environmental Aspects
Selbstorganisation zu einer Helix durch Wasserstoffbrückenbindungen (1993)

Das gleiche Strukturmotiv, aber verschiedene räumliche Gestalten kennzeichnen die polymeren 1:1‐Komplexe aus dem Isophthalsäurederivat 1 und den beiden Dicarbonsäuren 2 . Mit der längerkettigen entsteht eine Helixstruktur, mit der kürzerkettigen eine Blattstruktur, obwohl beide Aggregate durch zwei Paare von Wasserstoffbrücken zwischen benachbarten Molekülen stabilisiert werden. magnified image
Optimization of Electron Transfer Dissociation via Informed Selection of Reagents and Operating Parameters (2011)

Electron transfer dissociation (ETD) has improved the mass spectrometric analysis of proteins and peptides with labile post-translational modifications and larger intact masses. Here, the parameters governing the reaction rate of ETD are examined experimentally. Currently, due to reagent injection and isolation events as well as longer reaction times, ETD spectra require significantly more time to acquire than collision-induced dissociation (CID) spectra (>100 ms), resulting in a trade-off in the dynamic range of tandem MS analyses when ETD-based methods are compared to CID-based methods. Through fine adjustment of reaction parameters and the selection of reagents with optimal characteristics, we demonstrate a drastic reduction in the time taken per ETD event. In fact, ETD can be performed with optimal efficiency in nearly the same time as CID at low precursor charge state (z = +3) and becomes faster at higher charge state (z > +3).
Inference of variable-length acoustic units for continuous speech recognition (2002)

In the field of speech recognition, the patterns assumed to structure the speech material (phonemes, triphones, words...) are defined a priori according to a linguistic criterion, whereas the recognition criterion is based on an acoustic similarity measure. From this may result a lack of consistency for the recognition units. We explore the possibility of a more data-driven approach, where recognition units are derived according to an acoustic criterion, and then, mapped to variable length sequences of phonemes in an unsupervised way. Continuous speech recognition experiments are reported to evaluate the consistency of those units as opposed to linguistically defined units.
Heterogeneous Multipath Networks: Flow vs. Packet Based Routing in a Size-Aware Context (2017)

We are facing a steady increase in Internet usages and bandwidth requirements. However, many terrestrial infrastructures remain unchanged due to exorbitant modernization costs, particularly in rural areas. In front of the aging of their infrastructures, concerned users are turning towards satellite internet access. Indeed, these solutions offer a high-throughput internet access at a moderate cost of deployment. Unfortunately, the long delay introduced by GEO satellite degrades significantly the user Quality of Experience (QoE) in many cases. In this paper, we consider a hybrid access, composed of a low data rate terrestrial path and a satellite path, within a Content Delivery Network (CDN) context. Thanks to the CDN, requested content size is known allowing to use this information in routing schemes to maximize the users' QoE. Then, we compare flow and packet based routing in this heterogeneous and size-aware context. We finally conclude on the limited interest in packet-based routing compared to flow-based routing, privileged by its simplicity and good performance from a QoE point of view.
A crucial role for T-bet in selectin ligand expression in T helper 1 (Th1) cells (2005)

Proinflammatory T helper 1 (Th1) cells express high levels of carbohydrate ligands for the endothelial selectins, but the molecular basis for this phenotype is incompletely understood. We document here a significant role in selectin ligand formation for the recently described Th1 transcription factor T-bet. Th1 cells generated from T-bet-/- mice showed significantly lower levels of ligands for both E-selectin and P-selectin, compared with wild-type (WT) Th1 cells. Enforced expression of T-bet in WT Th0 cells only modestly up-regulated P-selectin ligands and had no effect on E-selectin ligands. To define a mechanism for the defects observed in T-bet-/- mice, we examined expression of glycosyltransferases involved in selectin ligand biosynthesis. T-bet-/- Th1 cells expressed significantly lower levels of core 2 beta1,6 N-acetylglucosaminyltransferase I (C2GlcNAcT-I), but no differences in levels of alpha 2,3-sialyltransferase IV (ST3Gal-IV). Further, we show that T-bet is responsible for the signal transducer and activator of transcription 4 (Stat4)-independent increase in Th1 cells of fucosyltransferase VII (FucT-VII). We also identify ST3Gal-VI, which is thought to play an important role in E- and P-selectin ligand formation, as an interleukin 12 (IL-12)-regulated, T-bet-dependent gene. These data show that T-bet controls selectin ligand formation in Th1 cells via control of expression of multiple key enzymes in response to IL-12 signaling and establishes an independent transcriptional pathway for control of Th1 cell traffic.
Self-Assembly of Partially Alkylated Dextran-graft-poly[(2-dimethylamino)ethyl methacrylate] Copolymer Facilitating Hydrophobic/Hydrophilic Drug Delivery and Improving Conetwork Hydrogel Properties (2018)

Key issues of injectable hydrogels are incapability of loading hydrophobic drugs due to insolubility of drugs in aqueous prepolymer solution as well as in hydrogel matrix, and high water swelling, which leads to poor mechanical and bioadhesive properties. Herein, we report that self-assembly of partially long-chain alkylated dextran- graft-poly[(2-dimethylamino)ethyl methacrylate] copolymer in aqueous solution could encapsulate pyrene, a hydrophobic probe, griseofulvin, a hydrophobic antifungal drug, and ornidazole, a hydrophilic antibiotic. Addition of activated chloride terminated poly(ethylene glycol) (PEG) into the guest molecules loaded copolymer solution produced an injectable dextran- graft-poly[(2-dimethylamino)ethyl methacrylate]-linked-PEG conetwork hydrogel. The alkylated hydrogels exhibited zero order release kinetics and were mechanically tough (50-54 kPa storage modulus) and bioadhesive (8-9 kPa). The roles of alkyl chains and dextran on the drug loading-release behavior, degradation behavior, gelation time, and the mechanical property of the hydrogels have been studied in details. Additionally, DNA hybrid composite hydrogel was formed owing to the cationic nature of the prepolymer solution and the hydrogel. Controlled alkylation of a prepolymer thus highlights the potential to induce and enhance the hydrogel property.
Association of Aberrant Posterior Vitreous Detachment and Pathologic Tractional Forces With Myopic Macular Degeneration (2021)

Our study demonstrated an association between tractional (MTM, PS, and persistently incomplete PVD) and degenerative elements of PM independent of age and axial length. These data provide further insights into the pathogenesis of MMD.
Supplemental Figure S5 from Plasma KIM-1 Is Associated with Recurrence Risk after Nephrectomy for Localized Renal Cell Carcinoma: A Trial of the ECOG-ACRIN Research Group (E2805) (2023)

&lt;p&gt;Modelled relationship between KIM-1 and disease free survival&lt;/p&gt;
Generalized modeling and simulation of a modular multilevel converter (2011)

This paper proposes a generalized dynamic model of the modular multilevel converter, which is valid for single-phase or three-phase loads and for DC or single-phase source. The proposed model is simple and easy to simulate, it gives a powerful tool to analyze the entire converter including the circulating currents and simplify the controller design. An analysis of the converter model applied to circulating currents and simulations results are presented.
Floating-island TFT leakage caused by process step reduction (2002)

The leakage mechanism for a top-gate thin-film transistor (TFT) produced using the fewest process steps in the industry is analyzed in order to achieve a high-contrast liquid crystal display (LCD). Using a T-shaped TFT structure, the OFF and ON channel lengths are defined independently, so that the leakage can be reduced with no ON current decrease.
Mathematical Modeling of Oscillometric Blood Pressure Measurement: A Complete, Reduced Oscillogram Model (2022)

The complete, reduced oscillogram model determined herein can potentially improve oscillometric BP measurement accuracy while advancing foundational knowledge.
The rat models of non-insulin dependent diabetes induced by neonatal streptozotocin. (1989)

This review is intended to describe the characteristics of the rat models of non-insulin-dependent diabetes induced by neonatal streptozotocin administration (n-STZ models), to sum-up the information so far collected and to highlight the potential of these models for diabetes research. The n-STZ models can now be recognized as adequate tools for the elucidation of the mechanisms leading to: 1) regeneration of the beta cells, 2) the functional "exhaustion" of the beta cells, 3) the emergence of defects in insulin action. They appear well-suited to study the effects of the modulating factors involved in the appearance and/or deterioration of non-insulin-dependent diabetes (obesity, gestation, content of the diet). They are potentially appropriate for investigations in diabetes pharmacotherapy.
Iron, Copper, and Nickel Behavior in Buffered, Neutral Aluminum Chloride: 1‐Methyl‐3‐ethylimidazolium Chloride Molten Salt (1997)

Iron, copper, and nickel electrodes were examined as possible metal/metal(II) chloride cathodes for the room temperature sodium/metal chloride battery in a molten salt composed of sodium chloride (NaCl), aluminum chloride , and 1‐methyl‐3‐ethylimidazolium chloride (MEIC). The iron electrode was investigated in basic, neutral‐like, and acidic melts. The solubility and the kinetics of the reduction of Fe(II) was a function of acidity. In the basic melt, the was soluble; however, its reduction was not observed due to slow kinetics. In the neutral‐like and acidic melts, the quasi‐reversible reduction of Fe(II) to Fe(0) was observed. The redox potential of copper was approximately 1 V more positive of iron; however, the oxidized copper was soluble in the neutral‐like melt, making it unacceptable without a separator. The oxidized and reduced forms of nickel were insoluble and the redox potential was 2.5 V positive of . The nickel electrode supported a charge density of 3.5 mC/cm2 at room temperature, suggesting that a high‐surface‐area electrode would be needed in a practical device.
INCB050465 (Parsaclisib), a Novel Next-Generation Inhibitor of Phosphoinositide 3-Kinase Delta (PI3Kδ) (2019)

A medicinal chemistry effort focused on identifying a structurally diverse candidate for phosphoinositide 3-kinase delta (PI3Kδ) led to the discovery of clinical candidate INCB050465 (<b>20</b>, parsaclisib). The unique structure of <b>20</b> contains a pyrazolopyrimidine hinge-binder in place of a purine motif that is present in other PI3Kδ inhibitors, such as idelalisib (<b>1</b>), duvelisib (<b>2</b>), and INCB040093 (<b>3</b>, dezapelisib). Parsaclisib (<b>20</b>) is a potent and highly selective inhibitor of PI3Kδ with drug-like ADME properties that exhibited an excellent in vivo profile as demonstrated through pharmacokinetic studies in rats, dogs, and monkeys and through pharmacodynamic and efficacy studies in a mouse Pfeiffer xenograft model.
Randomized self-tuning control of Markov chains (1980)

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<title>Failure mode analysis of high-power laser diodes</title> (2002)

In this paper, we present the results of a preliminary investigation on the reliability of high power optical diodes. Commercially available 970 nm optical diodes were subjected to various levels of stress, including: operating current, optical power and operating temperature. Optical diodes that failed during testing were subsequently analyzed using a variety of techniques, including: optical microscopy, scanning electron microscopy, eletroluminescence, and near-field profiling. It has been observed that the major cause of optical failure can be attributed to damage on the emitting facet of the optical diodes. Preliminary evidence suggests that facet damage is a result of catastrophic optical damage.
ChemInform Abstract: Synthesis of N6‐Substituted 3′‐Ureidoadenosine Derivatives as Highly Potent Agonists at the Mutant A3 Adenosine Receptor (2008)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.