gebhart/patrepeval huggingface dataset:
Kinesin superfamily protein Kif26b links Wnt5a-Ror signaling to the control of cell and tissue behaviors in vertebrates (2017)

Wnt5a-Ror signaling constitutes a developmental pathway crucial for embryonic tissue morphogenesis, reproduction and adult tissue regeneration, yet the molecular mechanisms by which the Wnt5a-Ror pathway mediates these processes are largely unknown. Using a proteomic screen, we identify the kinesin superfamily protein Kif26b as a downstream target of the Wnt5a-Ror pathway. Wnt5a-Ror, through a process independent of the canonical Wnt/β-catenin-dependent pathway, regulates the cellular stability of Kif26b by inducing its degradation via the ubiquitin-proteasome system. Through this mechanism, Kif26b modulates the migratory behavior of cultured mesenchymal cells in a Wnt5a-dependent manner. Genetic perturbation of Kif26b function in vivo caused embryonic axis malformations and depletion of primordial germ cells in the developing gonad, two phenotypes characteristic of disrupted Wnt5a-Ror signaling. These findings indicate that Kif26b links Wnt5a-Ror signaling to the control of morphogenetic cell and tissue behaviors in vertebrates and reveal a new role for regulated proteolysis in noncanonical Wnt5a-Ror signal transduction.
BELLA: Berkeley Efficient Long-Read to Long-Read Aligner and Overlapper (2018)

Abstract Recent advances in long-read sequencing enable the characterization of genome structure and its intra- and inter-species variation at a resolution that was previously impossible. Detecting overlaps between reads is integral to many long-read genomics pipelines, such as de novo genome assembly. While longer reads simplify genome assembly and improve the contiguity of the reconstruction, current long-read technologies come with high error rates. We present Berkeley Long-Read to Long-Read Aligner and Overlapper (BELLA), a novel algorithm for computing overlaps and alignments via sparse matrix-matrix multiplication that balances the goals of recall and precision, performing well on both. We present a probabilistic model that demonstrates the feasibility of using short k -mers for detecting candidate overlaps. We then introduce a notion of reliable k-mers based on our probabilistic model. Combining reliable k-mers with our binning mechanism eliminates both the k -mer set explosion that would otherwise occur with highly erroneous reads and the spurious overlaps from k -mers originating in repetitive regions. Finally, we present a new method based on Chernoff bounds for separating true overlaps from false positives using a combination of alignment techniques and probabilistic modeling. Our methodologies aim at maximizing the balance between precision and recall. On both real and synthetic data, BELLA performs amongst the best in terms of F1 score, showing performance stability which is often missing for competitor software. BELLA’s F1 score is consistently within 1.7% of the top entry. Notably, we show improved de novo assembly results on synthetic data when coupling BELLA with the Miniasm assembler.
Digital Signal Processor(DSP)-Based Variable Structure Control With Observer For Robot Manipulator (1987)

A variable structure control scheme which consists of continuous adaptive gain feedback and feedforward controls with an equivalent external diturbance observer is developed to achieve accurate (robust) decoupled model following control for a two-degrees-of-freedom manipulator powered by PWM transistor converter-fed dc servomotors. The proposed control scheme is implemented by a fast digital signal processor(DSP). It is confirmed by the experiments that the position trajectories are smooth and track the desired trajectories accurately(robustly).
Cholecystokinin Facilitates Glutamate Release by Increasing the Number of Readily Releasable Vesicles and Releasing Probability (2010)

Cholecystokinin (CCK), a neuropeptide originally discovered in the gastrointestinal tract, is abundantly distributed in the mammalian brains including the hippocampus. Whereas CCK has been shown to increase glutamate concentration in the perfusate of hippocampal slices and in purified rat hippocampal synaptosomes, the cellular and molecular mechanisms whereby CCK modulates glutamatergic function remain unexplored. Here, we examined the effects of CCK on glutamatergic transmission in the hippocampus using whole-cell recordings from hippocampal slices. Application of CCK increased AMPA receptor-mediated EPSCs at perforant path-dentate gyrus granule cell, CA3-CA3 and Schaffer collateral-CA1 synapses without effects at mossy fiber-CA3 synapses. CCK-induced increases in AMPA EPSCs were mediated by CCK-2 receptors and were not modulated developmentally and transcriptionally. CCK reduced the coefficient of variation and paired-pulse ratio of AMPA EPSCs suggesting that CCK facilitates presynaptic glutamate release. CCK increased the release probability and the number of readily releasable vesicles with no effects on the rate of recovery from vesicle depletion. CCK-mediated increases in glutamate release required the functions of phospholipase C, intracellular Ca(2+) release and protein kinase Cgamma. CCK released endogenously from hippocampal interneurons facilitated glutamatergic transmission. Our results provide a cellular and molecular mechanism to explain the roles of CCK in the brain.
Protein-tyrosine phosphorylation regulates apoptosis in human eosinophils and neutrophils. (1994)

Early signaling events that control the process of programmed cell death are largely unknown. Tyrosine phosphorylation plays a major role in transmembrane signal transduction through most cell surface receptors. Granulocyte/macrophage colony-stimulating factor (GM-CSF), a cytokine released by activated T cells, has been shown to increase tyrosine phosphorylation in several cells and to inhibit granulocyte cell death in vitro. In this study, we demonstrate that the effect of GM-CSF on granulocyte cell death can be blocked by the tyrosine kinase inhibitor genistein, suggesting that increases in tyrosine phosphorylation are essential to inhibit cell death. To analyze the role of tyrosine phosphorylation for the regulation of granulocyte cell death more precisely, we increased levels of tyrosine phosphorylation using the protein-tyrosine phosphatase inhibitor phenylarsine oxide (PAO). Similar to GM-CSF, treatment of the cells with PAO was followed by high increases in tyrosine phosphorylation and inhibition of programmed cell death in human eosinophils and neutrophils. Strikingly, at low concentrations of the inhibitor and low induction of tyrosine phosphorylation, acceleration of apoptosis was observed. Genistein and herbimycin A reversed the effects of PAO on tyrosine phosphorylation and granulocyte apoptosis. These results suggest that programmed eosinophil and neutrophil death is regulated by early events of signal transduction pathways such as tyrosine phosphorylation.
The mathematical theory of a countercurrent catalytic reactor (1982)

Abstract The steady-state behaviour of a countercurrent catalytic reactor has been analysed mathematically for a reversible reaction─adsorption system A ⇌ A* ⇌ B* ⇌ B occurring, in the first instance, under the ideal chromatographic conditions in which negligible axial dispersion and instantaneous local adsorption equilibrium are assumed. The system is considered to be one-dimensional and isothermal. The internal discontinuity of the steady-state model was analysed in connection with the transient model, while the boundary behaviour was investigated in relation to the non-equilibrium-adsorption model. Two of the most influential parameters on the system behaviour were found to be the relative adsorptivity of the two chemical species A and B, and the relative carrying capacity of the two moving streams. It has been shown by heuristic examples how the chemical reaction process and the adsorption process interact to break the local thermodynamic equilibrium limitation by the formation of a stationary shock front inside the reactor. The physical meaning of this internal shock appears to be that it is the interface between two different regions; on one side the process is controlled by the reaction rate, and on the other side by the adsorption rate. The effect of non-ideality has also been investigated, and the performance characteristics have been discussed in comparison with those of the conventional fixed-bed reactor.
In Situ Growth of Superconducting Y-Ba-Cu-O Films on Si, SiO<sub>2</sub>, GaAs and Cu/Ag by the High-Pressure DC Sputtering Process (1989)

Superconducting Y-Ba-Cu-O thin films on Si, SiO 2 , GaAs and Cu/Ag substrates have been reproducibly prepared by the high-pressure DC sputtering process without further annealing treatment. The targets were Y-Ba-Cu-O compounds made by the solid-state reaction. The substrate temperature was lower than 450°C. The films (0.6–2 µm) consist of predominantly the superconducting phase of Y 1 Ba 2 Cu 3 O x and impurity phases such as CuO or a mixture of CuO and Y 2 Ba 1 Cu 1 O 5 . The best superconductivity of the films on Si is Tc(onset)=95 K and Tc(zero)=70 K. There are no microcracks on the film surface, and the interdiffusion between film and Si substrate is limited.
Domain instability of a glow discharge (1975)

In an experimental study of the self-excited current oscillations of a glow discharge in an electronegative gas flowing transverse to the discharge axis, bright layers (''domains'') are detected at gas pressures from 10 to 100 torr. These layers are generated periodically near the cathode; they travel to the anode and vanish there. A theoretical model has been worked out. The equations obtained on the basis of this model permit solutions corresponding to a solitary steady-state wave; the velocity of such a wave is evaluated. (AIP)
High Frequency Stimulation of the Basal Ganglia for the Treatment of Movement Disorders: Current Status and Clinical Results (2002)

High frequency stimulation of the basal ganglia has gained much interest during the last years. Based on the reevaluation of the results of functional neurosurgery for movement disorders from Leksell's group, pallidotomy as lesional procedure was the first functional operation that underwent a renaissance for the treatment of movement disorders. The work by Benabid and Siegfried who carried out thalamic high frequency stimulation to suppress tremor, the knowledge about deep brain stimulation (DBS) for the treatment of chronic pain as well as better understanding in basal ganglia physiology and the development of reliable stimulation hardware led to an increasing number of centers worldwide who currently apply high frequency DBS for different movement disorders. In the present review the current status of DBS for movement disorders is presented and the results with high frequency stimulation targeted at different brain areas are summarized.
Partial-ring PET image restoration using a deep learning based method (2019)

PET scanners with partial-ring geometry have been proposed for various imaging purposes. The incomplete projection data obtained from this design cause undesirable artifacts in the reconstructed images. In this study, we investigated the performance of a deep learning (DL) based method for the recovery of partial-ring PET images. Twenty digital brain phantoms were used in the Monte Carlo simulation toolkit, SimSET, to simulate 15 min full-ring PET scans. Partial-ring PET data were generated from full-ring PET data by removing coincidence events that hit these specific detector blocks. A convolutional neural network based on the residual U-Net architecture was trained to predict full-ring data from partial-ring data in either the projection or image domain. The performance of the proposed DL-based method was evaluated by comparing with the PET images reconstructed using the full-ring projection data in terms of the mean squared error (MSE), structural similarity (SSIM) index and recovery coefficient (RC). The MSE results showed the superiority of the image-domain approach in reduction of 91.7% in contrast to 14.3% for the projection-domain approach. Therefore, the image-domain approach was used to study the influence of the number of detector block removal. The SSIM results were 0.998, 0.996 and 0.993 for 3, 5 and 7 detector block removals, respectively. The activity of gray and white matters could be fully recovered even with 7 detector block removal, while the RCs of two artificially inserted small lesions (3 pixels in diameter) in the testing data were 94%, 89% and 79% for 3, 5, and 7 detector block removals, respectively. Our simulation results suggest that DL has the potential to recover partial-ring PET images.
Antioxidative effect of ginseng stem-leaf saponins on oxidative stress induced by cyclophosphamide in chickens (2015)

Previous investigation demonstrated that oral administration of ginseng stem-leaf saponins in chickens could enhance the immune response. The present study was designed to evaluate the effects of ginseng stem-leaf saponins on oxidative stress induced by cyclophosphamide in chickens. One hundred and twenty chickens were randomly divided into 5 groups. Groups 1 to 4 received intramuscular injection of cyclophosphamide to induce oxidative stress while group 5 was injected with saline solution and served as control. Following administration of cyclophosphamide, groups 1 to 3 were orally administered ginseng stem-leaf saponins at 2.5, 5, and 10 mg/kg BW in drinking water for 7 d, respectively. After that, the spleen, thymus, bursa, and serum were collected to measure the indices of the organs and oxidative parameters. The results showed that ginseng stem-leaf saponins significantly inhibited cyclophosphamide-induced oxidative stress by increasing the organ indices, total antioxidant capacity, and the levels of glutathione, ascorbic acid, and α-tocopherol, while elevating the activity of total superoxide dismutase, catalase, and glutathione peroxidase, as well as decreasing the protein carbonyl content and malondialdehyde. Therefore, ginseng stem-leaf saponins could be a promising agent against oxidative stress in the poultry industry.
Rescue of radiation-induced cognitive impairment through cranial transplantation of human embryonic stem cells (2009)

Cranial irradiation remains a frontline treatment for the control of tumor growth, and individuals surviving such treatments often manifest various degrees of cognitive dysfunction. Radiation-induced depletion of stem/precursor cell pools in the brain, particularly those residing in the neurogenic region of the hippocampus, is believed, in part, to be responsible for these often-unavoidable cognitive deficits. To explore the possibility of ameliorating radiation-induced cognitive impairment, athymic nude rats subjected to head only irradiation (10 Gy) were transplanted 2 days afterward with human embryonic stem cells (hESC) into the hippocampal formation and analyzed for stem cell survival, differentiation, and cognitive function. Animals receiving hESC transplantation exhibited superior performance on a hippocampal-dependent cognitive task 4 months postirradiation, compared to their irradiated surgical counterparts that did not receive hESCs. Significant stem cell survival was found at 1 and 4 months postirradiation, and transplanted cells showed robust migration to the subgranular zone throughout the dentate gyrus, exhibiting signs of neuron morphology within this neurogenic niche. These results demonstrate the capability to ameliorate radiation-induced normal tissue injury using hESCs, and suggest that such strategies may provide useful interventions for reducing the adverse effects of irradiation on cognition.
Role of molecular mimicry to HIV-1 peptides in HIV-1–related immunologic thrombocytopenia (2005)

Patients with early HIV-1 infection develop an autoimmune thrombocytopenia in which antibody is directed against an immunodominant epitope of the beta3 (glycoprotein IIIa [GPIIIa]) integrin, GPIIIa49-66. This antibody induces thrombocytopenia by a novel complement-independent mechanism in which platelets are fragmented by antibody-induced generation of H2O2 derived from the interaction of platelet nicotinamide adenine dinucleotide phosphate (NADPH) oxidase and 12-lipoxygenase. To examine whether sharing of epitope between host and parasite may be responsible for this immunodominant epitope, we screened for antibody-reactive peptides capable of inhibiting platelet lysis and oxidation in vitro, using a filamentous phage display 7-mer peptide library. Fourteen of these phage-peptide clones were identified. Five shared close sequence similarity with GPIIIa49-66, as expected. Ten were molecular mimics with close sequence similarity to HIV-1 proteins nef, gag, env, and pol. Seven were synthesized as 10-mers from their known HIV-1 sequence and found to inhibit anti-GPIIIa49-66-induced platelet oxidation/fragmentation in vitro. Three rabbit antibodies raised against these peptides induced platelet oxidation/fragmentation in vitro and thrombocytopenia in vivo when passively transferred into mice. One of the peptides shared a known epitope region with HIV-1 protein nef and was derived from a variant region of the protein. These data provide strong support for molecular mimicry in HIV-1-immunologic thrombocytopenia within polymorphic regions of HIV-1 proteins. A known epitope of nef is particularly incriminated.
A 2.4 kbps variable bit rate ADP-CELP speech coder (2002)

This paper presents a variable bit rate ADP-CELP (adaptive density pulse code excited linear prediction) coder that selects one of four kinds of coding structure in each frame based on short time speech characteristics. To improve speech quality and reduce the average bit rate, we have developed a speech/non-speech classification method using spectrum envelope variation, which is robust for background noise. In addition, we propose an efficient pitch lag coding technique. The technique interpolates consecutive frame pitch lags and quantizes a vector of relative pitch lags consisting of variation between an estimated pitch lag and a target pitch lag in plural subframes. The average bit rate of the proposed coder was approximately 2.4 kbps for speech sources with activity factor of 60%. Our subjective testing indicates the quality of the proposed coder exceeds that of the Japanese digital cellular standard with rate of 3.45 kbps.
Unbinding process of adsorbed proteins under external stress studied by atomic force microscopy spectroscopy (2000)

We report the study of the dynamics of the unbinding process under a force load f of adsorbed proteins (fibrinogen) on a solid surface (hydrophilic silica) by means of atomic force microscopy spectroscopy. By varying the loading rate r(f), defined by f = r(f) t, t being the time, we find that, as for specific interactions, the mean rupture force increases with r(f). This unbinding process is analyzed in the framework of the widely used Bell model. The typical dissociation rate at zero force entering in the model lies between 0. 02 and 0.6 s(-1). Each measured rupture is characterized by a force f(0), which appears to be quantized in integer multiples of 180-200 pN.
Enzymic determination of urea in serum based on pH measurement with the flow injection method (1979)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTEnzymic determination of urea in serum based on pH measurement with the flow injection methodJ. Ruzicka, E. H. Hansen, Animesh K. Ghose, and H. A. MottolaCite this: Anal. Chem. 1979, 51, 2, 199–203Publication Date (Print):February 1, 1979Publication History Published online1 May 2002Published inissue 1 February 1979https://pubs.acs.org/doi/10.1021/ac50038a011https://doi.org/10.1021/ac50038a011research-articleACS PublicationsRequest reuse permissionsArticle Views137Altmetric-Citations61LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Toward Quantitative Prediction of Stereospecificity of Metallocene-Based Catalysts for α-Olefin Polymerization (2000)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTToward Quantitative Prediction of Stereospecificity of Metallocene-Based Catalysts for α-Olefin PolymerizationKlaus Angermund, Gerhard Fink, Vidar R. Jensen, and Ralph KleinschmidtView Author Information Max-Planck Institut für Kohlenforschung, D-45470 Mülheim an der Ruhr, Germany Cite this: Chem. Rev. 2000, 100, 4, 1457–1470Publication Date (Web):March 25, 2000Publication History Received19 October 1999Published online25 March 2000Published inissue 1 April 2000https://pubs.acs.org/doi/10.1021/cr990373mhttps://doi.org/10.1021/cr990373mresearch-articleACS PublicationsCopyright © 2000 American Chemical SocietyRequest reuse permissionsArticle Views1242Altmetric-Citations157LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose SUBJECTS:Alkyls,Catalysts,Energy,Hydrocarbons,Molecular mechanics Get e-Alerts
Molecular Rheology and Statistics of Long Chain Branched Metallocene-Catalyzed Polyolefins (2001)

We derive the rheologically relevant “priority” and “seniority” distributions of entangled segment topology from a kinetic model of long chain branch formation in metallocene-catalyzed polyolefins. For the model considered, the chemistry results in a two-parameter family of molecular distributions; convenient parameters are the typical strand molecular weight between cross-links and a branching probability. Only the branching probability controls the chain topologies. We comment on the different nature of the metallocene ensemble from the usual gelation ensemble that is a candidate model for standard low-density polyethylene. We calculate the extensional rheology of a model system within a decoupling approximation that permits a partial mapping onto the “multimode pompom” constitutive scheme.