gebhart/patrepeval huggingface dataset:
MicroRNA therapy of heart failure (2014)

MicroRNAs (miRNAs) are short, noncoding RNAs that have revolutionized the way we interpret genetic regulation. A component of what was once considered junk DNA, miRNAs regulate virtually every protein-coding gene in a highly dynamic fashion. Growing evidence has indicated that miRNAs are cen- trally involved in the pathogenesis of heart failure and strategies to modulate their activity therapeutically are under intense investigation. miRNA expression can be modified using several different approaches by either upregulating or blocking function. This article will describe these promising strategies and the challenges that must be overcome to develop meaningful therapies for heart failure. L Heart Metab. 2014;65:31-33
BioFET Technology: Aggressively Scaled pMOS FinFET as Biosensor (2019)

We report for the first time on a BioFET sensor using FinFETs with 10nm wide fins built in a 300 mm pilot line. Our minimally modified finfet process uses a `Replacement Gate' strategy whereby the Si gate is pulled at the end of the process to form the cavity that holds the electrolyte. We used a pMOS FinFET as our electrolytic gate typically has a high work function of 5.0 eV. Changing the pH or binding biomolecules to the gate dielectric surface changes the threshold voltage (VT). Measuring the VT shift provides high sensitivity due to our high-quality gate dielectric. The median voltage referred 1/f noise of only ~500 μV <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> μm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> /Hz (at 1Hz, at threshold), is significantly lower than other reported bioFETs. We obtain a pH sensitivity near the Nernstian limit of 57 mV/pH for HfO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> . Drift of the sensor has been found to be adequate at -1 mV/hour. Finally, we have verified our device to act as a biomolecular transducer. We find the VT shift due to surface bound biomolecules for DNA grafting and PNA-DNA hybridization to be as expected from simulation. Based on our quantification of transduction and simulations we project which single molecule signal-to-noise ratios could ultimately be obtained in the future.
Human papillomavirus detection by non isotopic in situ hybridization, in situ hybridization with signal amplification and in situ polymerase chain reaction. (1999)

Classical in situ hybridization (ISH) with biotinylated probes makes it possible to detect and localize human papillomavirus (HPV) nucleic acid sequences in cytological and histological materials. This method is however of limited value in the detection of a few copies of the virus. Moreover the specificity of such a technique is not always convincing when ISH signals are small and/or of low intensity. Recently, much attention has been focused on the utility of the in vitro polymerase chain reaction (PCR) and especially on PCR-single strand conformation polymorphism (SSCP) to amplify small amounts of viral DNA with accurate hybrid specificity. But the latter method requires nucleic acid extraction and tissue destruction. Thus, correlation between the PCR results and histological findings is not possible. Hence, the aim of our current study was to apply to HeLa cells and cervical formalin-fixed and paraffin-embedded biopsies, a novel procedure of ISH signal amplification, the catalyzed signal amplification (CSA). Such a procedure is based on the deposition of streptavidin-horseradish peroxidase catalyzing the deposition of biotinylated tyramide molecules on the location of the probed target. The biotin accumulation is then detected with streptavidin peroxidase and diaminobenzidine. The results were compared with those obtained by direct and indirect in situ PCR. The catalysed signal amplification successfully increased the sensitivity and efficiency of ISH for the detection of rare sequences in HPV infected cells and histological materials. Such a method was found simpler and faster than in situ PCR and tissue morphology was better preserved.
Online Training from Streaming Data with Concept Drift on FPGAs (2023)

In dynamic environments, the inputs to machine learning models may exhibit statistical changes over time, through what is called concept drift. Incremental training can allow machine learning models to adapt to changing conditions and maintain high accuracy by continuously updating network parameters. In the context of FPGA-based accelerators however, online incremental learning is challenging due to resource and communication constraints, as well as the absence of labelled training data. These challenges have not been fully evaluated or addressed in existing research. In this paper, we present and evaluate strategies for performing incremental training on streaming data with concept drift on FPGA-based platforms. We first present FPGA-based implementations of existing training algorithms to demonstrate the viability of online training with concept shift and to evaluate design tradeoffs. We then propose a technique for online training without labelled data and demonstrate its potential in the context of FPGA-based hardware acceleration.
Technetium-99m-labeled monoclonal antibodies: influence of technetium-99m binding sites. (1994)

In these 99mTc labeling procedures, the amino group-mediated nonspecific binding of 99mTc to Mabs can be as high as 16% and contributes to increased liver uptake and decreased tumor uptake of radioactivity.
Thrombin Regulates Insulin-Like Growth Factor-1 Receptor Transcription in Vascular Smooth Muscle (2001)

We have previously demonstrated that thrombin upregulation of insulin-like growth factor-1 receptor (IGF-1R) is essential for thrombin-induced mitogenic signaling. To characterize the mechanisms involved, we studied transcription of the IGF-1R gene in rat aortic smooth muscle cells. Thrombin markedly increased IGF-1R mRNA levels, peaking at 3 hours (112+/-7% above control). This effect was mimicked by the hexapeptide SFFLRN (that functions as a tethered ligand) and was blocked by the thrombin inhibitor hirudin. Nuclear run-on assays indicated that thrombin stimulated IGF-1R gene transcription by 2.1-fold, and this was confirmed with the use of actinomycin D. Thrombin-mediated upregulation of IGF-1R mRNA and protein levels was protein kinase C independent but was completely inhibited by the protein tyrosine kinase inhibitor genistein and by the antioxidants N-acetyl-L-cysteine and pyrrolidinedithiocarbamate, suggesting the involvement of reactive oxygen species. The thrombin-induced increase in IGF-1R mRNA was inhibitable by diphenyleneiodonium chloride but not by other inhibitors of cellular oxidase systems, suggesting that NAD(P)H oxidase was necessary for the increase. Furthermore, inhibitors of the epidermal growth factor receptor kinase, Janus kinase-2 kinase, and Src kinase did not block the effect. Thus, thrombin transcriptionally regulates the IGF-1R gene via a redox-sensitive protein tyrosine kinase-dependent pathway that does not require protein kinase C activation. In view of our prior data indicating that IGF-1R density is a critical determinant of vascular smooth muscle cell growth, our findings have particular relevance to understanding mechanisms whereby growth factors such as thrombin regulate vascular proliferation in vivo.
Key paradigms of emerging imaging sensor technologies (1998)

In this paper, key paradigms of emerging imaging technologies from different technological areas, are presented. Examples of transfer, utilization, and exchange of the imaging technology are offered and discussed. These phenomena, will create advanced solutions for potential development in different areas of science and technology. Overall, new imaging technologies will merge and are expected to play an ever-expanding role in the civilian and military applications of the next century.
Expression of the Stress-Related Genes for Glutathione S-Transferase and Ascorbate Peroxidase in the Most-Glycinin-Deficient Soybean Cultivar Tousan205 during Seed Maturation (2010)

Global analysis of gene expression profiles in most-glycinin-deficient cultivar Tousan205, was performed by DNA microarray analysis. It was confirmed that Tousan205 lacks mRNA expression of three glycinin subunit precursor genes, G1 (A1aB1x), G2 (A2B1a), and G5 (A3B4), and lacks G4 (A5A4B3) protein. Most glycinin subunits were deficient in mature seeds of Tousan205. We compared the gene expression of Tousan205 with those of parent cultivar, Tamahomare, which was used for crossbreeding of Tousan205. As a result, Tousan205 exhibited higher expression of some seed maturation proteins, and stress-related genes such as glutathione S-transferase and ascorbate peroxidase. This result indicates the possibility that the decrease of main storage protein, glycinin causes stress in soybean.
How bacteria move without flagella (2020)

生命にとって動きは本質的である。多くのバクテリアは、べん毛という繊維構造を使って水中を自由自在に泳ぐことができる。一方、このような優雅な運動様式を持たずに動き回るものもたくさん存在する。この不思議な生体運動は、多種多様なバクテリアにおいて観察されており、多くの研究者を魅了してきた。しかし、べん毛を使わずに、一体どのようにバクテリアが動くのか、そして推進力を発生する装置は何なのか、こういった点について不明のままであった。ところが、この 10-20 年の間に顕微鏡の可視化技術が発達することで、バクテリア個体やそこに含まれる運動装置の動きや構造を詳細に観察できるようになり、これらの運動メカニズムの理解は飛躍的に進展した。本総説では、「スパイダーマン」のように「糸」の伸縮による動きまわる仕組み、「キャタピラ」のように膜表面の流れを使って這う仕組み、「ドリル戦車」のように高粘性環境を潜りながら動く仕組みなど、バクテリアという小さな生命体が独自に発達させた生体運動様式について解説し、我々が得た最新の知見について紹介する。
ChemInform Abstract: Rearrangement Mechanisms of Some Cyclic Sulfoxides. (1991)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 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.
Optimal linearized Poisson–Boltzmann theory applied to the simulation of flexible polyelectrolytes in solution (2004)

Optimal linearized Poisson-Boltzmann (OLPB) theory is applied to the simulation of flexible polyelectrolytes in solution. As previously demonstrated in the contexts of the cell model [H. H. von Grunberg, R. van Roij, and G. Klein, Europhys. Lett. 55, 580 (2001)] and a particle-based model [B. Beresfordsmith, D. Y. C. Chan, and D. J. Mitchell, J. Colloid Interface Sci. 105, 216 (1985)] of charged colloids, OLPB theory is applicable to thermodynamic states at which conventional, Debye-Huckel (DH) linearization of the Poisson-Boltzmann equation is rendered invalid by violation of the condition that the electrostatic coupling energy of a mobile ion be much smaller than its thermal energy throughout space, |nu(alpha)e psi(r)|<<k(B)T. As a demonstration of its applicability to flexible polyelectrolytes, OLPB theory is applied to a concentrated solution of freely jointed chains. The osmotic pressure is computed at various reservoir ionic strengths and compared with results from the conventional DH model for polyelectrolytes. Through comparison with the cylindrical cell model for polyelectrolytes, it is demonstrated that the OLPB model yields the correct osmotic pressure behavior with respect to nonlinear theory where conventional DH theory fails, namely at large ratios of mean counterion density to reservoir salt density, when the Donnan potential is large.
Local Conformation and Cocrystallization Phenomena in Renewable Diaminoisoidide-Based Polyamides Studied by FT-IR, Solid State NMR, and WAXD (2012)

Biobased polyamides synthesized from diaminoisoidide (DAII), 1,4-diaminobutane, and sebacic acid are investigated by FT-IR, 13C{1H} magic-angle spinning/cross-polarization (CP/MAS) NMR spectroscopy, and WAXD. Their molecular conformation and mobility undergo distinct changes as a function of temperature and diaminoisoidide content in the compositions. The presence of randomly distributed diaminoisoidide (DAII) in the polyamides reduces their hydrogen bond density and affects the trans/gauche conformer population. FT-IR and 13C{1H} CP/MAS NMR were successfully employed to prove the incorporation of DAII both in the crystalline and amorphous phase of these materials. Changes in the position and intensities of the diaminoisoidide-assigned FT-IR and NMR signals prove that the DAII monomer causes a conformational disorder of the polyamides and thus influences the crystal structure of these materials, as also shown by WAXD experiments. Extensive ab initio calculations using a combination of DFT and MP2 methods reveal a number of stable conformers of DAII and thus an unexpectedly high flexibility of the isohexide unit.
Immunological Cross-Reactivity of the Major Allergen from Perennial Ryegrass <i>(Lolium perenne</i><i>)</i>, <i>Lol</i> <i>p</i> I, and the Cysteine Proteinase, Bromelain (1997)

Antibodies prepared in rabbits against the major allergen from ryegrass ( Lolium perenne), Lol p I, cross-reacted with the cysteine proteinase bromelain from pineapple and vice versa. Deglycosylation of the proteins showed that the cross-reaction was based on recognition of the carbohydrate moiety of the allergen, but for bromelain the cross-reaction was most likely due to a combination of factors. The results indicate that the carbohydrate residues from these allergens play an important role in cross-reactions found between them and possibly those from other species.
Oligo(ethylene glycol) Containing Polymer Brushes as Bioselective Surfaces (2005)

The nitroxide-mediated polymerization of styrenic monomers containing oligo(ethylene glycol) (OEGn) moieties was chosen for the preparation of biocompatible polymer brushes tethered to silicon oxide surfaces due to the broad range of monomer structures available and the use of a nonmetallic initiator. These surfaces were characterized by near-edge X-ray absorption fine structure and water contact angle measurements. The biocompatibility of these grown polymer brushes was studied and compared with deposited assemblies of surface-bound OEGn-terminated silanes with selected chain lengths. Grown polymer brushes with short OEGn side chains suppressed protein adsorption significantly more than the deposited assemblies of short OEGn chains, and this was attributed to higher surface coverage by the brushes. Cell adhesion studies confirmed that OEGn-containing polymer brushes are particularly effective in preventing nonspecific adhesion. Studies of protein adsorption and cell localization carried out with specific ligands on surfaces patterned demonstrated the potential of these surface-tethered polymer brushes for the formation of micro- and nanoscale devices.
Characterization of thegltFgene product ofEscherichia coli (1999)

The glt operon of Escherichia coli comprises the structural genes for the glutamate synthase subunits (gltB and gltD) and gltF, whose product was previously suggested to have regulatory functions. The A/T-rich region between gltD and gltF contains a weak promoter and a translation initiation site for gltF. The GltF protein is preceded by a signal peptide, which is cleaved off during export into the periplasmic space. A gltF::Km(R) insertion mutant was constructed and shown here to have no detectable phenotype with respect to amino acid utilization or ammonium transport. Thus, GltF is apparently not involved in regulation of nitrogen catabolism.
Influence of V/III growth flux ratio on trap states in m-plane GaN grown by ammonia-based molecular beam epitaxy (2012)

Deep level transient spectroscopy (DLTS) and deep level optical spectroscopy (DLOS) were utilized to investigate the behavior of deep states in m-plane, n-type GaN grown by ammonia-based molecular beam epitaxy (NH3-MBE) as a function of systematically varied V/III growth flux ratios. Levels were detected at EC − 0.14 eV, EC − 0.21 eV, EC − 0.26 eV, EC − 0.62 eV, EC − 0.67 eV, EC − 2.65 eV, and EC − 3.31 eV, with the concentrations of several traps exhibiting systematic dependencies on V/III ratio. The DLTS spectra are dominated by traps at EC − 0.14 eV and EC − 0.67 eV, whose concentrations decreased monotonically with increasing V/III ratio and decreasing oxygen impurity concentration, and by a trap at EC − 0.21 eV that revealed no dependence of its concentration on growth conditions, suggestive of different physical origins. Higher concentrations of deeper trap states detected by DLOS with activation energies of EC − 2.65 eV and EC − 3.31 eV in each sample did not display measureable sensitivity to the intentionally varied V/III ratio, necessitating further study on reducing these deep traps through growth optimization for maximizing material quality of NH3-MBE grown m-plane GaN.
Automatic Identification For Singing Style Based On Sung Melodic Contour Characterized In Phase Plane. (2009)

[TODO] Add abstract here.
Tunable slow-wave optical delay lines (2006)

Tunable delay lines exploiting slow-light in directly-coupled ring-resonators are presented. Time delay can be tuned from zero to maximum. Experimental results showing delays of 300ps and slowing factor of 7.5 over 3GHz bandwidth are reported.
The Heat Shock Protein 32 (Hsp32)/HO-1-Targeting Drug SMA-ZnPP and the Triterpenoid CDDO-Me Exert Synergistic Growth-Inhibitory Effects on TKI-Resistant Leukemic Cells in Ph+ CML (2011)

Abstract Abstract 4414 Resistance against one or more tyrosine kinase inhibitors (TKI) prevents eradication of Ph+ chronic myeloid leukemia (CML). In many patients BCR/ABL1 mutations are detectable. We have recently identified two targeted drugs that exert major growth-inhibitory effects on drug-resistant CML cells, the triterpenoid CDDO-Me (Bardoxolone-methyl, REATA Pharma) that blocks several signalling molecules including mTOR, Akt, and STAT3, and upregulates expression of heat shock protein 32 (Hsp32 = heme oxygenase 1, HO-1), and styrene-maleic acid-copolymer micelle-encapsulated ZnPP (SMA-ZnPP), a water-soluble inhibitor of Hsp32/HO-1. In the current project, we asked whether CDDO-Me exerts inhibitory effects on growth of TKI-resistant CML cells and whether the combination of CDDO-Me and SMA-ZnPP would produce synergistic effects in drug-resistant CML cells. As determined by 3H-thymidine incorporation, CDDO-Me was found to inhibit the proliferation of imatinib-responsive and imatinib-resistant K562, imatinib-resistant KCL-22, KU812, and Ba/F3 cells transfected with various TKI-resistant mutants of BCR/ABL1 (T315I, E255K, Y253F, H396P). In each case, IC50 values &lt;1 μM were obtained without major differences between imatinib-responsive and imatinib-resistant cells. Growth-inhibition was accompanied by apoptosis as assessed by combined AnnexinV/PI staining as well as by an increase in expression of HO-1 in KU812 and KCL-22 cells. CDDO-Me was also found to inhibit proliferation of leukemic cells in all patients with TKI-resistant CML (n=4), with IC50 values ranging between &lt;0.1 and 0.5 μM. No differences in IC50 values were observed between treatment-naïve and TKI-resistant cells. Next, we applied the combination CDDO-Me+SMA-ZnPP and found that this combination acts highly synergistically on imatinib-responsive and imatinib-resistant K562 cells as well as primary CML cells isolated from imatinib-naïve CML patients (n=2) or from patients with imatinib-resistant CML (n=2), including one patient in whom BCR/ABL1 T315I was detected. We also examined whether CDDO-Me would exert synergistic effects on CML cells when combined with BCR/ABL1 TKI. In these experiments, we applied the combinations CDDO-Me+dasatinib and CDDO-Me+nilotinib on K562 cells. Both combinations were found to synergistically induce growth inhibition. In conclusion, CDDO-Me inhibits the proliferation of imatinib-resistant BCR/ABL1+ cells, including primary CML cells isolated from untreated patients and cells derived from patients with TKI-resistant CML carrying the BCR/ABL1 mutant T315I. Our data also show that CDDO-Me + SMA-ZnPP and CDDO-Me + BCR/ABL1 TKI synergize in producing growth inhibition in CML cells. Whether these drug combinations also produce synergistic effects in vivo in patients with TKI-resistant CML remains to be evaluated. Disclosures: Valent: Novartis: Consultancy, Honoraria, Research Funding.
Plasma DNA End-Motif Profiling as a Fragmentomic Marker in Cancer, Pregnancy, and Transplantation (2020)

Plasma DNA fragmentomics is an emerging area of research covering plasma DNA sizes, end points, and nucleosome footprints. In the present study, we found a significant increase in the diversity of plasma DNA end motifs in patients with hepatocellular carcinoma (HCC). Compared with patients without HCC, patients with HCC showed a preferential pattern of 4-mer end motifs. In particular, the abundance of plasma DNA motif CCCA was much lower in patients with HCC than in subjects without HCC. The aberrant end motifs were also observed in patients with other cancer types, including colorectal cancer, lung cancer, nasopharyngeal carcinoma, and head and neck squamous cell carcinoma. We further observed that the profile of plasma DNA end motifs originating from the same organ, such as the liver, placenta, and hematopoietic cells, generally clustered together. The profile of end motifs may therefore serve as a class of biomarkers for liquid biopsy in oncology, noninvasive prenatal testing, and transplantation monitoring. SIGNIFICANCE: Plasma DNA molecules originating from the liver, HCC and other cancers, placenta, and hematopoietic cells each harbor a set of characteristic plasma DNA end motifs. Such markers carry tissue-of-origin information and represent a new class of biomarkers in the nascent field of fragmentomics.<i>This article is highlighted in the In This Issue feature, p. 627</i>.
Music structure analysis by finding repeated parts (2006)

The structure of a musical piece can be described with segments having a certain time range and a label. Segments having the same label are considered as occurrences of a certain structural part. Here, a system for finding structural descriptions is presented. Theproblemisformulated in terms of a cost function for structural descriptions. A method for creating multiple candidate descriptions from acoustic input signal is presented, and an efficient algorithm is presented to find the optimal description with regard to the cost function from the candidate set. The analysis system is evaluated with simulations on a database of 50 popular music pieces.
Congestion-free Multiflow Quantum Tree Network with Logarithmic Overhead (2022)

We propose quantum tree network (QTN) designs that are 1) free from congestion in multiflow communications, 2) optimal routing with only local information (self-information) and 3) completely covers 2D surface, 4) with only logarithmic overhead. If the channel is dominated by the insertion loss and the communication is limited by the local gates, as in current state-of-the-art technologies, the overhead is log(N), while this is relaxed to the general cases with poly-log overhead by engaging repeater chains in the long range communication.