gebhart/patrepeval huggingface dataset:
Cationic phosphorus-containing dendrimers reduce prion replication both in cell culture and in mice infected with scrapie (2004)

Over the last 30 years, many drugs have been tested both in cell culture and in vivo for their ability to prevent the generation of prions and the development of transmissible spongiform encephalopathies. Among the compounds tested, dendrimers are defined by their branched and repeating molecular structure. The anti-prion activity of new cationic phosphorus-containing dendrimers (P-dendrimers) with tertiary amine end-groups was tested. These molecules had a strong anti-prion activity, decreasing both PrP(Sc) and infectivity in scrapie-infected cells at non-cytotoxic doses. They can bind PrP and decrease the amount of pre-existing PrP(Sc) from several prion strains, including the BSE strain. More importantly, when tested in a murine scrapie model, the dendrimers were able to decrease PrP(Sc) accumulation in the spleen by more than 80 %. These molecules have a high bio-availability and therefore exhibit relevant potential for prion therapeutics for at least post-exposure prophylaxis.
Properties of two isoforms of human blood platelet α‐actinin (1985)

The structural and functional properties of the aa (2 X 97 kDa) and cc (2 X 94 kDa) isoforms of platelet alpha-actinin have been compared. Structural differences between aa and cc are revealed by their peptide maps, obtained from limited proteolysis, and by their immunological cross-reactivity. Both isoforms stimulate the Mg ATPase activity of actomyosin, bind to F-actin (high-speed sedimentation) and cross-link or gel actin filaments (low-speed sedimentation and viscometry), in a calcium-dependent manner. The study of the interaction with F-actin indicates that the binding of 1 molecule of aa or cc alpha-actinin/9-11 actin monomers is sufficient to produce maximal gelation in the presence of EGTA. CaCl2 at 0.1 mM strongly inhibits the binding of aa to F-actin and weakly that of cc, while it inhibits similarly the cross-linking of either aa or cc. The cross-linking efficiency of cc is 9, 7, 1.7 and 1.3 times higher than that of aa at 4, 20, 30 and 37 degrees C, respectively. The bb form (2 X 96 kDa), which is a proteolytic product of aa [Y. Gache et al. (1984) Biochem. Biophys. Res. Commun. 124, 877-881], behaves roughly as aa, but the calcium sensitivity of its binding to F-actin is intermediate between that of aa and cc. These results suggest that the effect of Ca2+ concentration on the binding of platelet alpha-actinin to F-actin may be partly dissociated from the effect on the cross-linking.
Epigenetic Control of Centromere Behavior (2007)

The centromere is the DNA region that ensures genetic stability and is therefore of vital importance. Paradoxically, centromere proteins and centromeric structural domains are conserved despite that fact that centromere DNA sequences are highly variable and are not conserved. Remarkably, heritable states at the centromere can be propagated independent of the underlying centromeric DNA sequences. This review describes the epigenetic mechanisms governing centromere behavior, i.e., the mechanisms that control centromere assembly and propagation. A centromeric histone variant, CenH3, and histone modifications play key roles at centromeric chromatin. Histone modifications and RNA interference are important in assembly of pericentric heterochromatin structures. The molecular machinery that is directly involved in epigenetic control of centromeres is shared with regulation of gene expression. Nucleosome remodeling factors, histone chaperones, histone-modifying enzymes, transcription factors, and even RNA polymerase II itself control epigenetic states at centromeres.
Capillary electrophoresis of carbohydrates (1994)

Capillary electrophoresis has emerged as a highly promising technique for the analysis of mono- and oligosaccharides. The approaches developed for overcoming the lack of chromophoric and fluorophoric functions in most carbohydrates involve the use of indirect photometric detection, amperometry, mass spectrometry, and precolumn derivatization with various tags. The merits and drawbacks of the derivatizing agents, including 2-aminopyridine, 4-amino-benzoic acid and its analogues, which for the first time permitted the reproducible determination of aldoses, uronic acids and even ketoses in the low femtomole range by means of readily available UV detection, and other agents such as 8-aminonaphthalene-1,3,6-trisulphonic acid, 1-phenyl-3-methyl-5-pyrazolone and 3-(4-carboxybenzoyl)-2-quinoline-carboxaldehyde, are discussed in detail. Means to secure electromigration of the usually neutral carbohydrates are: (i) ionization of hydroxyl groups at high pH; (ii) complexation of vicinal or alternate hydroxyl groups with borate or other charged compounds such as alkaline earth metal ions; (iii) derivatization with a reagent possessing ionizable functions; and (iv) partitioning into a pseudostationary phase such as sodium dodecyl sulphate micelles. Each alternative has its own analytical rewards, and combinations of the above mechanisms allow the two-dimensional and perhaps even three-dimensional mapping of oligosaccharides. Pyridylaminated oligosaccharides, for instance, have been separated both according to size by exploiting differences in the charge-to-mass ratio, with the charge being identical for each oligomer under acidic conditions due to protonation of the imino group incorporated by precolumn derivatization, as well as on the basis of structural differences, as a consequence of differences in the ease of borate complexation of the peripheral monosaccharide residues. It is also shown that the 4-aminobenzonitrile derivatives of mono- and disaccharides can be separated by micellar electrokinetic chromatography with a resolving power superior to that achieved by capillary zone electrophoresis of sugar-borate complexes. Based on the progress made, it can be concluded that capillary electrophoresis represents a powerful alternative and complement to existing methodology in the area of carbohydrate analysis.
Triggering Fbw7-Mediated Proteasomal Degradation of c-Myc by Oridonin Induces Cell Growth Inhibition and Apoptosis (2012)

The transcription factor c-Myc is important in cell fate decisions and is frequently overexpressed in cancer cells, making it an attractive therapeutic target. Natural compounds are among the current strategies aimed at targeting c-Myc, but their modes of action still need to be characterized. To explore the mechanisms underlying the anticancer activity of a natural diterpenoid, oridonin, we conducted miRNA expression profiling and statistical analyses that strongly suggested that c-Myc was a potential molecular target of oridonin. Furthermore, experimental data showed that oridonin significantly reduced c-Myc protein levels in vitro and in vivo and that this reduction was mediated by the ubiquitin-proteasome system. Fbw7, a component of the ubiquitin-proteasome system and an E3 ubiquitin ligase of c-Myc, was upregulated rapidly in K562 cells and other leukemia and lymphoma cells, resulting in the rapid turnover of c-Myc. In cell lines harboring mutations in the WD domain of Fbw7, the degradation of c-Myc induced by oridonin was attenuated during short-term treatment. GSK-3, an Fbw7 priming kinase, was also activated by oridonin, along with an increase in T58-phosphorylated c-Myc. Furthermore, the knockdown of Fbw7 or the forced expression of stable c-Myc resulted in reduced sensitization to oridonin-induced apoptosis. Our observations help to clarify the anticancer mechanisms of oridonin and shed light on the application of this natural compound as an Fbw7-c-Myc pathway targeting agent in cancer treatment.
Human complement in thrombin-mediated platelet function: uptake of the C5b-9 complex. (1979)

Thrombin-mediated platelet aggregation and release is enhanced by the presence of C3, C5, C6, C7, C8, and C9 of human complement. The interaction of thrombin with its receptor on the platelet membrane initiates activation of complement on the platelet surface. Trypsin-mediated platelet function is not enhanced by the addition of complement, probably because trypsin has no receptor on the platelet surface so activation of complement is triggered in the fluid phase and not on the platelet surface. Activation of complement by thrombin led to production of dimers of the C5b-9 complex on the platelet surface. These complexes were eluted from the platelet membrane and were identified physicochemically and morphologically. The mechanism of complement-induced enhancement of platelet function is not clear, however, it probably is mediated via the arachidonic acid transormation pathway because this activity was blocked by known inhibitors of cyclo-oxygenase, namely, aspirin and indomethacin.
A General Introduction To Graph Visualization Techniques.. (2011)

Generally, a graph is an abstract data type used to represent relations among a given set of data entities. Graphs are used in numerous applications within the field of information visualization, such as VLSI (circuit schematics), state-transition diagrams, and social networks. The size and complexity of graphs easily reach dimensions at which the task of exploring and navigating gets crucial. Moreover, additional requirements have to be met in order to provide proper visualizations. In this context, many techniques already have been introduced. This survey aims to provide an introduction on graph visualization techniques helping the reader to gain a first insight into the most fundamental techniques. Furthermore, a brief introduction about navigation and interaction tools is provided.
Randomized Study of the Crush Technique Versus Provisional Side-Branch Stenting in True Coronary Bifurcations (2008)

In most bifurcations with a significant stenosis in both branches, a provisional strategy of stenting the main branch only is effective, with the need to implant a second stent on the side branch occurring in approximately one third of cases. The implantation of 2 stents does not appear to be associated with a higher incidence of adverse events at 6 months.
Harmonic radar tag measurement and characterization (2004)

Conventional radar systems transmit and receive at a single, fundamental frequency. It is sometimes challenging to identify a small object against a large background with these radars due to the relatively large return from the background. In effect, the background represents a clutter environment. Harmonic radar tags can be attached to an item, such as insects, and then used to track that item against the background. To do so, the radar must transmit a signal at the fundamental frequency but receive at twice that frequency. Since the clutter return is at the fundamental frequency, the radar is able to discriminate the return from the tag. This paper describes equipment constructed at Michigan State University to conduct research on harmonic tags.
Periodic and aperiodic neural activity displays age-dependent changes across early-to-middle childhood (2022)

The neurodevelopmental period spanning early-to-middle childhood represents a time of significant growth and reorganisation throughout the cortex. Such changes are critical for the emergence and maturation of a range of social and cognitive processes. Here, we utilised both eyes open and eyes closed resting-state electroencephalography (EEG) to examine maturational changes in both oscillatory (i.e., periodic) and non-oscillatory (aperiodic, '1/f-like') activity in a large cohort of participants ranging from 4-to-12 years of age (N = 139, average age=9.41 years, SD=1.95). The EEG signal was parameterised into aperiodic and periodic components, and linear regression models were used to evaluate if chronological age could predict aperiodic exponent and offset, as well as well as peak frequency and power within the alpha and beta ranges. Exponent and offset were found to both decrease with age, while aperiodic-adjusted alpha peak frequency increased with age; however, there was no association between age and peak frequency for the beta band. Age was also unrelated to aperiodic-adjusted spectral power within either the alpha or beta bands, despite both frequency ranges being correlated with the aperiodic signal. Overall, these results highlight the capacity for both periodic and aperiodic features of the EEG to elucidate age-related functional changes within the developing brain.
Study on n-gram language models for topic and out-of-vocabulary words (2011)

Language models (LMs) are an important field of study in automatic speech recognition (ASR) systems. LM helps acoustic models find the corresponding word sequence of a given speech signal. Without it, ASR systems would not understand the language and it would be hard to find the correct word sequence. A data sparseness problem for modeling a language often occurs in LMs. The problem is caused by the insufficiency of training data, which in turn, makes the infrequent words have unreliable probability. In this research, we investigated a class LM based on a latent semantic analysis (LSA). A word-document matrix is commonly used to represent a collection of text (corpus) in LSA framework. This matrix tells how many times a word occurs in a certain document. In other words, this matrix ignores the word order in the sentence. We propose several word co-occurrence matrices that keep the word order. By applying LSA to these matrices, words in the vocabulary are projected to a continues vector space according to their position in the sentences. To support these matrices, we define a context dependent class (CDC) based ngram. Unlike traditional class-based n-gram LM, CDC LM distinguishes classes according to their context in the sentences. Experiments on Wall Street Journal (WSJ) corpus show that the word co-occurrence matrix works 3.62%-12.72% better in terms of perplexity than word-document matrix. Furthermore, the CDC improves the performance and achieves better perplexity than the traditional class-based n-gram LM based on LSA. When the model is linearly interpolated with the word-based 3-gram, it gives improvements about 2.01% for 3-gram model and 9.47% for 4-gram model on relative perplexity against a standard word-based 3-gram LM. During the past few years, researchers have tried to incorporate long-range dependencies into statistical word-based n-gram LMs. One of these long-range dependencies is topic. Unlike words, topic is unobservable. Thus, it is required to find the meanings behind the words to get into the topic. As the second part of this research, we proposed a new approach for a topic-dependent LM called topic dependent class (TDC) based n-gram, where the topic is decided in
Biochemical Changes in Testicular Varicocele (1989)

The precise mechanism of the hypospermatogenesis associated with varicocele has remained uncertain, although there have been a number of speculations on the etiology of the associated infertility. The altered spermatogenesis has been attributed to the reflux of toxic metabolites from either adrenal or renal origin, disturbed hormone status, spermatic venous hypertension, testicular hypoxia secondary to stasis, and abnormal temperature regulation. However, the biochemical changes of the testicular tissue with varicocele have been only partially explored. This overview includes the available information on the biochemical change in the testes associated with varicocele as well as the introduction of basic biochemical aspects on the testes, which may give new insights into the possible pathophysiological mechanism of male infertility.
Resonant Hydrophones Based on Coated Fiber Bragg Gratings (2012)

In this paper, we report on recent experimental results obtained with fiber-Bragg-grating (FBG) hydrophones for underwater acoustic detection. The optical hydrophones under investigation consist of FBGs coated with ring-shaped polymers of different size and mechanical properties. The coating materials were selected and designed in order to provide mechanical amplification, via judicious choice of their acousto-mechanical properties and by exploiting selected resonances occurring in different frequency ranges. Our underwater acoustic measurements, carried out within the range 4–35 kHz, reveal the resonant behavior of these optical hydrophones, as well as its dependence on the coating size and type of material. These experimental data are also in good agreement with our previously published numerical results. By comparison with bare (i.e., uncoated) FBGs, responsivity enhancements of up to three orders of magnitude were found, demonstrating the effectiveness of polymeric coatings in tailoring the acoustic response of FBG-based hydrophones.
A multi-modeling electro-optical transfer function for display and transmission of high dynamic range content (2017)

This paper proposes a multi-modeling Electro-Optical Transfer Function (EOTF) enabling efficient use of the code word to preserve the contrast details in the quantized High Dynamic Range (HDR) content. Different from the classic EOTF that employs one single model, the proposed EOTF considers four models to adjust the reproducible contrast according to the luminance level of the HDR content. Furthermore, the proposed EOTF and its inverse process functions can be integrated on HDR cameras and displays with a low computational cost. In order to evaluate the performance of the proposed EOTF, it has been applied into a HDR video transmission chain based on the High Efficiency Video Coding (HEVC) codec. The standardized Perceptual Quantizer (PQ) EOTF and Hybrid Log-Gamma (HLG) Opto-Electronic Transfer Function (OETF) are also introduced and compared with the proposed EOTF in terms of the reproducible contrast. The objective evaluation results show that the proposed EOTF brings a better quality of the decoded HDR video than that generated by the standard function. A subjective test was also conducted in a commercial HDR television and the results show that the proposed EOTF can present more visible details than PQ, particularly for the HDR content with dark scenes. Therefore, the proposed multi-modeling EOTF is useful for the transmission and display of the HDR content in the consumer electronics.
E1A 13S and 12S mRNA Products Made in <i>Escherichia coli</i> Both Function as Nucleus-Localized Transcription Activators but Do Not Directly Bind DNA (1985)

We previously purified and characterized functionally the Escherichia coli-expressed product of the human subgroup C adenovirus E1A 13S mRNA (B. Ferguson, N. Jones, J. Richter, and M. Rosenberg, Science 224:1343-1346, 1984; B. Krippl, B. Ferguson, M. Rosenberg, and H. Westphal, Proc. Natl. Acad. Sci. USA 81:6988-6992, 1984). We have now expressed in E. coli and purified the protein product encoded by the human subgroup C adenovirus E1A 12S mRNA and have compared the functional properties of this protein with those of the E1A 13S mRNA product. Using microinjection techniques to introduce these proteins into mammalian cells, we found that the E1A 12S mRNA product, like the 13S mRNA product, localized rapidly to the cell nucleus and induced adenovirus gene expression. Although both E1A gene products localized to the nucleus and stimulated adenovirus gene transcription, these proteins did not directly bind to DNA under conditions in which a known DNA-binding protein, the human c-myc gene product, bound DNA efficiently. Thus, the E1A and myc gene products, which have been related both structurally and functionally, exhibit distinctly different biochemical properties.
Cytotoxicity and potency of mesocellular foam-26 in comparison to layered clays used as hemostatic agents (2012)

Uncontrolled hemorrhage is a leading cause of potentially preventable death. The most effective commercial hemostatic products employ layered clays. Due to safety concerns only a product containing kaolin is currently recommended by the U. S. Department of Defense. A problem related to layered clays, including kaolin, is their cytotoxicity. Also, material left in the wound can lead to thrombosis and other adverse effects. Recently, it has been shown that pure silica mesocellular foams (MCF) with cell window sizes >20 nm are effective in promoting blood clotting. Here, we tested the potency and cytotoxicity of layered clays in comparison to MCF with a cell window size of 26 nm (MCF-26) in vitro. The results showed that the potencies of MCF-26 and layered clays in promoting clotting were comparable. Effects on cell viability were assessed with relevant primary human cell types. The cytotoxic effects of all compounds were cell type-specific and most sensitive were endothelial cells. The IC50 values of MCF-26 were in the mg ml−1 range and its cytotoxicity was ∼1–2 orders of magnitude lower than the cytotoxicity of layered clays. Further, MCF-26 did not adhere strongly to cell surfaces and was not taken up by cells as observed for the layered clays. This suggests that it would be easier to remove MCF-26 from wounds. Altogether, the results suggest that MCF-26 would be effective and safer than currently used hemostatic agents.
SH2 and PTB Domains in Tyrosine Kinase Signaling (2003)

Intracellular signaling pathways that involve protein tyrosine kinases (PTKs) are critical for the control of most cellular processes. Dysfunctions in PTKs, or in the signaling pathways that they regulate, result in a variety of diseases such as cancer, diabetes, immune deficiency, and many others. SH2 (Src homology region 2) and PTB (phosphotyrosine-binding) domains are small protein modules that mediate protein-protein interactions involved in many signal transduction pathways. Both domains were initially identified as modules that recognize phosphorylated tyrosines in receptor tyrosine kinases and other signaling proteins. Subsequent studies have shown that, while binding of SH2 domains to their target proteins is strictly regulated by tyrosine phosphorylation, most PTB domains actually bind to their (nonphosphorylated) targets constitutively. The functions of SH2 and PTB domains include targeting of their host proteins to different cellular compartments, assembly of key components of signaling pathways in response to extracellular signals, and the control of autoinhibition, activation and dimerization of their host proteins. The information flow from the cell surface to different cellular compartments to regulate the cell cycle, cell shape and movement, cell proliferation, differentiation and cell survival are all controlled in part by SH2 and PTB domains that can recognize phosphotyrosine or particular amino acid sequence motifs in a wide variety of target molecules.
A Self-controlled Incremental Method for Vector Quantization (2004)

A new vector quantization method is proposed which generates codebooks incrementally. New vectors are inserted in areas of the input vector space where the quantization error is highest until the desired error threshold is reached. After the desired error threshold is reached, a remove-insert phase fine tunes the codebook. The proposed method can (1) solve the main shortcoming of traditional vector quantization LBG algorithm: the dependence on initial conditions; (2) work better than some recently published efficient algorithm such as Enhanced LBG (Patane 2001) for the traditional task: with fixed number of codewords, to find a suitable codebook to minimize distortion error. (3) work for new task that is not solved with traditional methods: with fixed distortion error, to minimize the number of codewords and find a suitable codebook. By solving some image compression problems, a comparison with ELBG was performed. The results indicate that the new method is significantly better than ELBG.