gebhart/patrepeval huggingface dataset:
A new method for measuring small local vibrations in the heart using ultrasound (1993)

In order to diagnose ventricular dysfunction based on the acoustic characteristics of the heart muscle of the ventricle, it is necessary to detect vibration signals from various parts of the ventricular wall. This is, however, difficult using previously proposed ultrasonic diagnostic methods or systems. The reason is that the amplitude of the cardiac motion is large during one beat period which produces large fluctuations in the transit time required for ultrasonic waves to travel from the transducer to the heart and back. This paper proposes a new method for overcoming this problem and accurately measuring small vibrations of the ventricle wall using ultrasound. In this method, the demodulated ultrasound signal reflected at the heart wall is converted from analogue to digital (A/D) signal at a high sampling frequency; from the resultant digital signal, the velocity of the wall is accurately obtained over a wide dynamic range based on the Doppler effect. The proposed method is preliminarily applied to the detection of small vibrations on the aortic wall and the interventricular septum. The new method offers potential for research in acoustical diagnosis of heart and artery dysfunction.
Effects of primer-template mismatches on the polymerase chain reaction: Human immunodeficiency virus type 1 model studies (1990)

We investigated the effects of various primer-template mismatches on DNA amplification of an HIV-1 gag region by the polymerase chain reaction (PCR). Single internal mismatches had no significant effect on PCR product yield while those at the 3'-terminal base had varied effects. A:G, G:A, and C:C mismatches reduced overall PCR product yield about 100-fold, A:A mismatches about 20-fold. All other 3'-terminal mismatches were efficiently amplified, although the G:G mismatches appeared to be more sensitive to sequence context and dNTP concentrations than other mismatches. It should be noted that mismatches of T with either G, C, or T had a minimal effect on PCR product yield. Double mismatches within the last four bases of a primer-template duplex where one of the mismatches is at the 3' terminal nucleotide, in general, reduced PCR product yield dramatically. The presence of a mismatched T at the 3'-terminus, however, allowed significant amplification even when coupled with an adjacent mismatch. Furthermore, even two mismatched Ts at the 3'-terminus allowed efficient amplification.
NARRATIVE SPECIFICITY OF THE SHORT STORY "HEY YOU, LITTLE BARRELL..." BY V. VYNNYCHENKO (2021)

The paper discusses the methodological potential of narratology that extends beyond the boundaries of traditional poetics taking the text of Volodymyr Vynnychenko’s short story "Hey you, little barrell..." as a case study. G. Genette’s definitions of the basic categories of narratology, such as story, discourse, anachronies, narrator’s types and functions, narrative distance and focalization are discussed. First and foremost, categories and paradigms introduced by G. Genette increase the possibilities of literary analysis. For example, there is no concept of a subject of vision (a focalizer) in traditional poetics. The paradigm of narrative perspective (focalization) developed by G. Genette is very important for studies of the narratives, besides, the narrative technique of modernism without this category is incomprehensible at all. Traditional poetics does not pay enough attention to anachrony, considering it together with other "off-plot elements", although analepsis and prolepsis are neither discursive nor descriptive. G. Genette presents detailed classification of analepsises and prolepsises, that determines the functionality of the analysis in context. Secondly, the paper clarifies, that the method of G. Genette’s narratology is not limited to tracing narrative categories as elements – it is also about their constant interrelation, i.e. the narrative model of the stories.&#x0D; Vynnychenko’s short story is analyzed in terms of correlations between telling, showing and talking, as well as displays of character’s discourse and attributive discourse. The artistic viability of anachronies (analepses and prolepses) is examined in the compositional and semantic aspects. The paper focuses on some specific features of Vynnychenko’s narrative style, such as dominance of mimesis over diegesis, as well as narrative distance and the author’s self-elimination by means of focalization (both the internal and external one) that are typical for modernist writing.
Deep Voice 2: Multi-Speaker Neural Text-to-Speech (2017)

We introduce a technique for augmenting neural text-to-speech (TTS) with lowdimensional trainable speaker embeddings to generate different voices from a single model. As a starting point, we show improvements over the two state-ofthe-art approaches for single-speaker neural TTS: Deep Voice 1 and Tacotron. We introduce Deep Voice 2, which is based on a similar pipeline with Deep Voice 1, but constructed with higher performance building blocks and demonstrates a significant audio quality improvement over Deep Voice 1. We improve Tacotron by introducing a post-processing neural vocoder, and demonstrate a significant audio quality improvement. We then demonstrate our technique for multi-speaker speech synthesis for both Deep Voice 2 and Tacotron on two multi-speaker TTS datasets. We show that a single neural TTS system can learn hundreds of unique voices from less than half an hour of data per speaker, while achieving high audio quality synthesis and preserving the speaker identities almost perfectly.
Transcriptome analysis and molecular signature of human retinal pigment epithelium (2010)

Retinal pigment epithelium (RPE) is a polarized cell layer critical for photoreceptor function and survival. The unique physiology and relationship to the photoreceptors make the RPE a critical determinant of human vision. Therefore, we performed a global expression profiling of native and cultured human fetal and adult RPE and determined a set of highly expressed 'signature' genes by comparing the observed RPE gene profiles to the Novartis expression database (SymAtlas: http://wombat.gnf.org/index.html) of 78 tissues. Using stringent selection criteria of at least 10-fold higher expression in three distinct preparations, we identified 154 RPE signature genes, which were validated by qRT-PCR analysis in RPE and in an independent set of 11 tissues. Several of the highly expressed signature genes encode proteins involved in visual cycle, melanogenesis and cell adhesion and Gene ontology analysis enabled the assignment of RPE signature genes to epithelial channels and transporters (ClCN4, BEST1, SLCA20) or matrix remodeling (TIMP3, COL8A2). Fifteen RPE signature genes were associated with known ophthalmic diseases, and 25 others were mapped to regions of disease loci. An evaluation of the RPE signature genes in a recently completed AMD genomewide association (GWA) data set revealed that TIMP3, GRAMD3, PITPNA and CHRNA3 signature genes may have potential roles in AMD pathogenesis and deserve further examination. We propose that RPE signature genes are excellent candidates for retinal diseases and for physiological investigations (e.g. dopachrome tautomerase in melanogenesis). The RPE signature gene set should allow the validation of RPE-like cells derived from human embryonic or induced pluripotent stem cells for cell-based therapies of degenerative retinal diseases.
T Cell Receptor Signaling Precedes Immunological Synapse Formation (2002)

The area of contact between a T cell and an antigen-presenting cell (APC) is known as the immunological synapse. Although its exact function is unknown, one model suggests that it allows for T cell receptor (TCR) clustering and for sustained signaling in T cells for many hours. Here we demonstrate that TCR-mediated tyrosine kinase signaling in naïve T cells occurred primarily at the periphery of the synapse and was largely abated before mature immunological synapses had formed. These data suggest that many hours of TCR signaling are not required for T cell activation. These observations challenge current ideas about the role of immunological synapses in T cell activation.
A Blocking Antibody to Nerve Growth Factor Attenuates Skeletal Pain Induced by Prostate Tumor Cells Growing in Bone (2005)

Abstract Prostate cancer is unique in that bone is often the only clinically detectable site of metastasis. Prostate tumors that have metastasized to bone frequently induce bone pain which can be difficult to fully control as it seems to be driven simultaneously by inflammatory, neuropathic, and tumorigenic mechanisms. As nerve growth factor (NGF) has been shown to modulate inflammatory and some neuropathic pain states in animal models, an NGF-sequestering antibody was administered in a prostate model of bone cancer where significant bone formation and bone destruction occur simultaneously in the mouse femur. Administration of a blocking antibody to NGF produced a significant reduction in both early and late stage bone cancer pain–related behaviors that was greater than or equivalent to that achieved with acute administration of 10 or 30 mg/kg of morphine sulfate. In contrast, this therapy did not influence tumor-induced bone remodeling, osteoblast proliferation, osteoclastogenesis, tumor growth, or markers of sensory or sympathetic innervation in the skin or bone. One rather unique aspect of the sensory innervation of bone, that may partially explain the analgesic efficacy of anti-NGF therapy in relieving prostate cancer–induced bone pain, is that nearly all nerve fibers that innervate the bone express trkA and p75, and these are the receptors through which NGF sensitizes and/or activates nociceptors. The present results suggest that anti-NGF therapy may be effective in reducing pain and enhancing the quality of life in patients with prostate tumor–induced bone cancer pain.
Effect of pH and temperature on peroxidase and polyphenoloxidase activities of litchi pericarp (2010)

After harvesting litchi, the red color of the fruit pericarp is rapidly lost resulting in discoloration and browning during storage and marketing. The loss of the red color is caused by the degradation or loss of stability of anthocyanins. The action of peroxidase and polyphenoloxidase is usually related to the browning and discoloration of fruits of various species. This study aimed to evaluate the influence of pH and temperature on peroxidase and polyphenoloxidase activities, in a partially purified preparation of pericarp of the litchi cultivar Bengal. Fruits were harvested at the ripe stage and polyphenoloxidase was partially purified by sequential saturation in 80% ammonium sulfate. At concentrations of 40-50% and 60-70% ammonium sulfate the activities of polyphenoloxidase and peroxidase were, respectively, 124 times and 158 times higher than in the crude extract. The activity of peroxidase and polyphenoloxidase was maximum at pH 6.5 and 7.0, respectively, and no activity was detected at pH 2.5 and 9.5. Pre-incubation of the enzyme extract for 45 min at pH 2.5 or 9.5 completely inactivated the enzymes, with the highest degree of efficiency at pH 2.5. Peroxidase activity was highest at 70ºC and remained active for a period of 120 min at 70 and 80ºC. Peroxidase became completely inactive when maintained at 90ºC for 10 min or 1 min at 100ºC. Polyphenoloxidase activity was highest at 20ºC and remained active for a period of 120 min at 40 and 50ºC and was inactivated after 10 min at 60ºC. Due to the high temperature of inactivation of the peroxidase and polyphenoloxidase activities, the enzymes can be inactivated more easily in fruits using acid or alkaline solutions.
A novel star PEG–derived surface coating for specific cell adhesion (2005)

In this study a novel approach for the coating and functionalization of substrates for cell culture and tissue engineering is presented. Glass, silicon, and titanium panes were coated with an ultrathin film (30 +/- 5 nm) of reactive star-shaped poly(ethylene glycol) prepolymers (Star PEG). Homogeneity of the films was checked by optical microscopy and scanning force microscopy. These coatings prevent unspecific protein adsorption as monitored by fluorescence microscopy and ellipsometry. In order to allow specific cell adhesion the films were modified with linear RGD peptides (gRGDsc) in different concentrations. After sterilization, fibroblast, SaOS, and human mesenchymal stem cells (hMSC) were seeded on these substrates. Cell adhesion, spreading, and survival was observed for up to 30 days on linear RGD peptide (gRGDsc)-modified coatings, whereas no cell adhesion could be detected on unmodified Star PEG layers. By variation of the RGD concentration within the film the amount of cells that became adhesive could be controlled. When differentiation conditions are used for cultivation of hMSCs the cells show the expression of osteogenic marker genes after 14 days which is comparable to cultivation on cell culture plastic. Thus, the Star PEG/RGD film did not negatively influence the differentiation process. The high flexibility of the system considering the incorporation of biologically active compounds opens a broad field of future experiments.
Overexpression of a BAHD Acyltransferase, OsAt10, Alters Rice Cell Wall Hydroxycinnamic Acid Content and Saccharification (2013)

Grass cell wall properties influence food, feed, and biofuel feedstock usage efficiency. The glucuronoarabinoxylan of grass cell walls is esterified with the phenylpropanoid-derived hydroxycinnamic acids ferulic acid (FA) and para-coumaric acid (p-CA). Feruloyl esters undergo oxidative coupling with neighboring phenylpropanoids on glucuronoarabinoxylan and lignin. Examination of rice (Oryza sativa) mutants in a grass-expanded and -diverged clade of BAHD acyl-coenzyme A-utilizing transferases identified four mutants with altered cell wall FA or p-CA contents. Here, we report on the effects of overexpressing one of these genes, OsAt10 (LOC_Os06g39390), in rice. An activation-tagged line, OsAT10-D1, shows a 60% reduction in matrix polysaccharide-bound FA and an approximately 300% increase in p-CA in young leaf tissue but no discernible phenotypic alterations in vegetative development, lignin content, or lignin composition. Two additional independent OsAt10 overexpression lines show similar changes in FA and p-CA content. Cell wall fractionation and liquid chromatography-mass spectrometry experiments isolate the cell wall alterations in the mutant to ester conjugates of a five-carbon sugar with p-CA and FA. These results suggest that OsAT10 is a p-coumaroyl coenzyme A transferase involved in glucuronoarabinoxylan modification. Biomass from OsAT10-D1 exhibits a 20% to 40% increase in saccharification yield depending on the assay. Thus, OsAt10 is an attractive target for improving grass cell wall quality for fuel and animal feed.
Direct-ambient decomposition and upmix of surround signals (2011)

Various direct-ambient signal decompositions, applicable to two-channel stereophonic signals, have been proposed previously. Strategies to enhance these decompositions for multi-channel surround audio signals are not obvious. A method is proposed, which estimates direct and ambient signal components in a downmix of a given surround signal. Those estimates are then used to compute filters to obtain direct and ambient surround signals. Approaches on how to use the decomposed signals for upmixing of surround audio signals in two and three dimensions are also discussed.
High-resolution Z-contrast Imaging by the HAADF-STEM Method (2005)

Characteristic features of the high-angle annular dark-field scanning transmission electron microscope method are described from an experimental viewpoint. Examples of experimental HAADF-STEM images are shown.
Recombinant tumor necrosis factor induces procoagulant activity in cultured human vascular endothelium: characterization and comparison with the actions of interleukin 1. (1986)

Human recombinant tumor necrosis factor (rTNF) was found to act directly on cultured human vascular endothelium to induce a tissue factor-like procoagulant activity (PCA). After a 4-hr incubation in rTNF (100 units/ml), serially passaged endothelial cells isolated from umbilical veins, saphenous veins, iliac arteries, and thoracic aortae demonstrated a dramatic increase (4- to 15-fold, 21 experiments) in total cellular PCA as measured with a one-stage clotting assay. rTNF-induced PCA was also expressed at the surface of intact viable endothelial monolayers. Induction of PCA by rTNF was concentration dependent (maximum, 500 units/ml), time dependent, reversible, and blocked by cycloheximide and actinomycin D, and it occurred without detectable endothelial cell damage. Actions of rTNF were compared with those of natural human interleukin 1 (IL-1) derived from stimulated monocytes and two distinct species of recombinant IL-1, each of which also induced endothelial PCA. The use of recombinant polypeptides and specific neutralizing antisera established the distinct natures of the mediators. The kinetics of the endothelial PCA responses to TNF and IL-1 were similar, demonstrating a rapid rise to peak activity at approximately equal to 4 hr, and a decline toward basal levels by 24 hr. This characteristic decline in PCA after prolonged incubation with TNF or IL-1 was accompanied by selective endothelial hyporesponsiveness to the initially stimulating monokine. Interestingly, the effects of TNF and IL-1 were found to be additive even at apparent maximal doses of the individual monokines. Endothelial-directed actions of TNF, alone or in combination with other monokines, may be important in the initiation of coagulation and inflammatory responses in vivo.
Evolving artificial neural network ensembles (2008)

Using a coordinated group of simple solvers to tackle a complex problem is not an entirely new idea. Its root could be traced back hundreds of years ago when ancient Chinese suggested a team approach to problem solving. For a long time, engineers have used the divide-and-conquer strategy to decompose a complex problem into simpler sub-problems and then solve them by a group of solvers. However, knowing the best way to divide a complex problem into simpler ones relies heavily on the available domain knowledge. It is often a manual process by an experienced engineer. There have been few automatic divide-and-conquer methods reported in the literature. Fortunately, evolutionary computation provides some of the interesting avenues to automatic divide-and-conquer methods. An in-depth study of such methods reveals that there is a deep underlying connection between evolutionary computation and ANN ensembles. Ideas in one area can be usefully transferred into another in producing effective algorithms. For example, using speciation to create and maintain diversity had inspired the development of negative correlation learning for ANN ensembles, and an in-depth study of diversity in ensembles. This paper will review some of the recent work in evolutionary approaches to designing ANN ensembles.
Caveolae require intact VAMP for targeted transport in vascular endothelium (1999)

Caveolae appear to function in vesicular trafficking of specific molecular cargo into and across vascular endothelial and other cells. They contain the molecular machinery for docking and fusion, similar to other vesicular trafficking systems, yet the mechanisms mediating ligand internalization and targeted intracellular transport by caveolae remain unclear. Using immunoelectron microscopy, we show that caveolae in the microvascular endothelium of rat lung express vesicle-associated membrane protein (VAMP)-2 (also called synaptobrevin) on their cytoplasmic surface. Immunofluorescence studies of cholera toxin B (CTB)-FITC internalization in toxin-treated cells demonstrate that intact VAMP-2 is necessary for the efficient trafficking of caveolar ligands. The CTB subunit binds preferentially to GM1 in caveolae, and N-ethylmaleimide treatment drastically inhibits the intracellular accumulation of CTB. The cleavage of caveolar VAMP-2 with VAMP-specific neurotoxins (botulinum D and F but not A) significantly inhibits CTB endocytosis and targeted intracellular accumulation in cultured endothelial cells. This impairment of caveolae-mediated trafficking provides evidence that caveolae require intact VAMP-2 for efficient targeted delivery via vesicle docking with target organelles.
Transitive functional annotation by shortest-path analysis of gene expression data (2002)

Current methods for the functional analysis of microarray gene expression data make the implicit assumption that genes with similar expression profiles have similar functions in cells. However, among genes involved in the same biological pathway, not all gene pairs show high expression similarity. Here, we propose that transitive expression similarity among genes can be used as an important attribute to link genes of the same biological pathway. Based on large-scale yeast microarray expression data, we use the shortest-path analysis to identify transitive genes between two given genes from the same biological process. We find that not only functionally related genes with correlated expression profiles are identified but also those without. In the latter case, we compare our method to hierarchical clustering, and show that our method can reveal functional relationships among genes in a more precise manner. Finally, we show that our method can be used to reliably predict the function of unknown genes from known genes lying on the same shortest path. We assigned functions for 146 yeast genes that are considered as unknown by the Saccharomyces Genome Database and by the Yeast Proteome Database. These genes constitute around 5% of the unknown yeast ORFome.
Fast B1 mapping based on interleaved‐three‐flip‐angle (ITFA) excitation (2013)

ITFA excitations made it possible to reduce the T1-effects on B1 mapping of the human-brain-mimicking phantom and the human brain at 3T. The authors expect the ITFA method can be used for B1 shimming once the optimal flip angles have been predetermined for the target imaging region and for the preferred TR.
Flow-controlled therapeutic embolization: a physiologic and safe technique (1980)

A feared complication of therapeutic embolization is loss of control of one or more particles with resultant ischemic infarction of normal tissues. To avoid passage of emboli into normal arteries, the delivery catheter may be wedged tightly into the artery or the artery completely occluded with a balloon catheter during embolus injection. These techniques, termed occlusion control, were a valuable forward step and significantly enhanced patient safety. However, occluding the vessel completely may cause spasm, and allows the operator to introduce fluid and emboli under higher than normal perfusion pressures which can open extra- to intracranial shunts and cause disastrous intracranial embolization. A further refinement is suggested. First, the emboli are suspended in contrast agent; then the particles are introduced while arterial runoff of the contrast agent is watched so the acceptance rate of the artery is not exceeded. Normal perfusion pressures and flow then carry the embolus distally into the abnormality being treated. This technique is safe, easily learned, and gives the radiologist direct vision control over the embolization process. It has been used in39 patients with only one serious complication.