gebhart/patrepeval huggingface dataset:
Early transcriptional alteration of histone deacetylases in a murine model of doxorubicin-induced cardiomyopathy (2017)

Doxorubicin is a potent chemotherapeutic agent that is widely-used to treat a variety of cancers but causes acute and chronic cardiac injury, severely limiting its use. Clinically, the acute side effects of doxorubicin are mostly manageable, whereas the delayed consequences can lead to life-threatening heart failure, even decades after cancer treatment. The cardiotoxicity of doxorubicin is subject to a critical cumulative dose and so dosage limitation is considered to be the best way to reduce these effects. Hence, a number of studies have defined a "safe dose" of the drug, both in animal models and clinical settings, with the aim of avoiding long-term cardiac effects. Here we show that a dose generally considered as safe in a mouse model can induce harmful changes in the myocardium, as early as 2 weeks after infusion. The adverse changes include the development of fibrotic lesions, disarray of cardiomyocytes and a major transcription dysregulation. Importantly, low-dose doxorubicin caused specific changes in the transcriptional profile of several histone deacetylases (HDACs) which are epigenetic regulators of cardiac remodelling. This suggests that cardioprotective therapies, aimed at modulating HDACs during doxorubicin treatment, deserve further exploration.
Self-expanding metal stents in malignant esophageal obstruction: a comparison between two stent types. (1997)

In malignant esophageal obstruction, both stents markedly improved dysphagia. Uncovered Wallstents seem to cause more early severe complications than knitted nitinol stents. In contrast, stent dysfunction, reintervention rate, and costs appear to be higher in the nitinol stent group.
REMOVAL OF CADMIUM FROM AQUEOUS ENVIRONMENTS BY ELECTROCOAGULATION PROCESS USING ALUMINUM ELECTRODES (2007)

: Background: The purpose of this study was the evaluation of cadmium removal from industrial
wastewater by electro coagulation process using aluminum electrodes.
Methods and Materials: For this study a glass tank with 1.87 liter volume containing four plate
aluminum electrodes was used to do experiments. The electrodes were connected to the positive and
negative poles of DC power supply (bipolar mode). The tank was filled with synthetic wastewater
containing cadmium ion in concentration of 5, 50 and 500 mg/l and then it was started up. The
amount of cadmium ion removal was measured at pH 3, 7 and 10 and in electric potential range of
20, 30 and 40 volts.
Results: The results obtained at different electrical potentials showed that initial concentration
of cadmium can affect on efficiency removal; moreover, for higher concentration of cadmium,
higher electrical potential or more reaction time is needed. On the other hand, if the initial
concentration increased, the time required of process had to increase too. The final pH was always
higher than initial pH. As expected, the results showed that in a given time, the removal efficiency
increased significantly with the increase for the current density. The highest electrical potential (40
v) produced the quickest treatment with >99% cadmium reduction occurring after only 20 min.
Conclusions: The results showed that, in this process, the use of different electrical potentials
can provide a wide range of pH for doing this process. The method was found to be highly efficient
and relatively fast compared to conventional existing techniques and, it can also be concluded that
the EC process has the potential to be utilized for the cost-effective removal of heavy metals from
water and wastewater.
Intracellular Disposition and Cytotoxicity of Transferrin-Mitomycin C Conjugate in HL60 Cells as a Receptor-Mediated Drug Targeting System. (1998)

A macromolecular conjugate of mitomycin C (MMC) with transferrin (TF) which possessed binding ability for TF receptor was synthesized. The conjugate (TF-MMC) was internalized into the human leukemia cell line HL60 cells and distributed into intracellular fractions, then exocytosed into an incubation medium. Although these phenomena were similar to those of TF, part of the internalized TF-MMC was degraded to a trichloroacetic acid (TCA)-soluble fraction. Therefore, the intracellular disposition of the conjugate was analyzed kinetically. The mean time of internalization of TF-MMC (7.14 min) was longer than that of TF (5.46 min). The mean exocytosis time of TF-MMC (22.1 min) was also longer than that of TF (13.0 min). Although elongation of both the internalization and exocytosis steps was responsible for the increase in recycling time of the conjugate, the binding process to the TF receptor in the internalization stage was found to be markedly retarded. The recycling times of TF-MMC and TF were 29.2 and 18.5 min, respectively. The mean decomposition time of TF-MMC was 76.3 min. Proliferation of HL60 cells was inhibited by TF-MMC in vitro. These results indicate that the TF-MMC was internalized via a TF receptor and a part of the internalized TF-MMC was degraded, so the released MMC might represent antitumor activity. TF-MMC was demonstrated to be a useful hybrid as a receptor-mediated targeting system.
Presence versus absence of end-to-end nonlocal conductance correlations in Majorana nanowires: Majorana bound states versus Andreev bound states (2019)

By calculating the differential tunneling conductance spectra from the two ends of a Majorana nanowire with a quantum dot embedded at one end, we establish that a careful examination of the nonlocal correlations of the zero-bias conductance peaks, as measured separately from the two ends of the wire, can distinguish between topological Majorana bound states and trivial Andreev bound states. In particular, there will be identical correlated zero-bias peaks from both ends for Majorana bound states, and thus the presence of correlated zero-bias conductance from the two wire ends could imply the presence of topological Majorana zero modes in the system. On the contrary, there will not be identical correlated zero-bias peaks from both ends for Andreev bound states, so the absence of correlated zero-bias conductance from the two wire ends implies the absence of topological Majorana zero modes in the system. We present detailed results for the calculated conductance, energy spectra, and wave functions for different chemical potentials at the same magnetic field values to motivate end-to-end conductance correlation measurements in Majorana nanowires.
Structure of the Complex between the Antibiotic Cerulenin and Its Target, β-Ketoacyl-Acyl Carrier Protein Synthase (1999)

In the biosynthesis of fatty acids, the beta-ketoacyl-acyl carrier protein (ACP) synthases catalyze chain elongation by the addition of two-carbon units derived from malonyl-ACP to an acyl group bound to either ACP or CoA. The enzyme is a possible drug target for treatment of certain cancers and for tuberculosis. The crystal structure of the complex of the enzyme from Escherichia coli, and the fungal mycotoxin cerulenin reveals that the inhibitor is bound in a hydrophobic pocket formed at the dimer interface. Cerulenin is covalently attached to the active site cysteine through its C2 carbon atom. The fit of the inhibitor to the active site is not optimal, and there is thus room for improvement through structure based design.
Multi-class blue noise sampling (2010)

Sampling is a core process for a variety of graphics applications. Among existing sampling methods, blue noise sampling remains popular thanks to its spatial uniformity and absence of aliasing artifacts. However, research so far has been mainly focused on blue noise sampling with a single class of samples. This could be insufficient for common natural as well as man-made phenomena requiring multiple classes of samples, such as object placement, imaging sensors, and stippling patterns.
Pervanadate inhibits mitogen‐activated protein kinase kinase‐1 in a p38<sup>MAPK</sup>‐dependent manner (1998)

In baboon smooth muscle cells (SMCs), pervanadate has a biphasic dose-dependent effect on MEK-1 activity. After a 30 min incubation period, low concentrations (1-10 microM) activate, while higher doses (30-100 microM) fail to stimulate MEK-1. One possibility is that higher doses of pervanadate induce an additional signaling pathway that inhibits MEK-1. Three lines of investigations provide support for the conclusion that this inhibitory effect is mediated by p38MAPK. First, pervanadate induces p38MAPK activity at concentrations that fail to activate MEK-1. Second, pervanadate-stimulated p38MAPK activity is maximal after a 10 min incubation, at a time, when MEK-1 activity disappears. Third, addition of the specific p38MAPK inhibitor SB203580 preserves MEK-1 activation by 100 microM pervanadate. The inhibitory effect of p38MAPK is probably not due to a phosphorylation of MEK-1 although we can not rule out that other p38MAPK isoforms such as SAPK3 and SAPK4 may be involved, and may directly phosphorylate and inhibit MEK-1.
A total synthesis of dl-cerulenin (1979)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTA total synthesis of dl-ceruleninRobert K. Boeckman Jr. and Edward W. ThomasCite this: J. Am. Chem. Soc. 1979, 101, 4, 987–994Publication Date (Print):February 1, 1979Publication History Published online1 May 2002Published inissue 1 February 1979https://pubs.acs.org/doi/10.1021/ja00498a032https://doi.org/10.1021/ja00498a032research-articleACS PublicationsRequest reuse permissionsArticle Views507Altmetric-Citations27LEARN 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
Randomized recovery for boolean compressed sensing (2013)

We consider the problem of boolean compressed sensing, which is also known as group testing. The goal is to recover a small number of defective items in a large set from a few collective binary tests. This problem can be formulated as a binary linear program, which is NP hard in general. To overcome the computational burden, it was recently proposed to relax the binary constraint on the variables, and apply a rounding to the solution of the relaxed linear program. In this paper, we introduce a randomized algorithm to replace the rounding procedure. We show that the proposed algorithm considerably improves the success rate with only a slight increase in computational cost.
Targeted Oncolytic Herpes Simplex Virus Type 1 Eradicates Experimental Pancreatic Tumors (2014)

As many other cancers, pancreatic ductal adenocarcinoma (PDAC) progression is associated with a series of hallmark changes for cancer cells to secure their own growth success. Yet, these very changes render cancer cells highly sensitive to viral infection. A promising strategy may rely on and exploit viral replication for tumor destruction, whereby infection of tumor cells by a replication-conditional virus may lead to cell destruction and simultaneous release of progeny particles that can spread and infect adjacent tumor cells, while sparing healthy tissues. In the present study, we used Myb34.5, a second-generation replication-conditional herpes simplex virus type 1 (HSV-1) mutant in which ICP6 gene expression is defective and expression of the HSV-1 γ134.5 gene is regulated by the cellular B-myb promoter. We found that B-myb is present in experimental PDAC and tumors, and is overexpressed in patients' tumors, as compared with normal adjacent pancreas. Myb34.5 replicates to high level in human PDAC cell lines and is associated with cell death by apoptosis. In experimental models of PDAC, mice receiving intratumoral Myb34.5 injections appeared healthy and tumor progression was inhibited, with evidence of tumor necrosis, hemorrhage, viral replication, and cancer cell death by apoptosis. Combining standard-of-care chemotherapy with Myb34.5 successfully led to a very impressive antitumoral effect that is rarely achieved in this experimental model, and resulted in a greater reduction in tumor growth than chemotherapy alone. These promising results warrant further evaluation in early phase clinical trial for patients diagnosed with PDAC for whom no effective treatment is available.
Facts and artifacts in near-field optical microscopy (1997)

Near-field optical (NFO) microscopes with an auxiliary gap width regulation (shear force, tunneling) may produce images that represent the path of the probe rather than optical properties of the sample. Experimental and theoretical evidence leads us to the conclusion that many NFO results reported in the past might have been affected or even dominated by the resulting artifact. The specifications derived from such results for the different types of NFO microscopes used therefore warrant reexamination. We show that the resolving power of aperture NFO microscopes, 30–50 nm, is of genuine NFO origin but can be heavily obscured by the artifact.
Chromosome Classification with Convolutional Neural Network Based Deep Learning (2018)

Karyotyping plays a crucial role in genetic disorder diagnosis. Currently Karyotyping requires considerable manual efforts, domain expertise and experience, and is very time consuming. Automating the karyotyping process has been an important and popular task. This study focuses on classification of chromosomes into 23 types, a step towards fully automatic karyotyping. This study proposes a convolutional neural network (CNN) based deep learning network to automatically classify chromosomes. The proposed method was trained and tested on a dataset containing 10304 chromosome images, and was further tested on a dataset containing 4830 chromosomes. The proposed method achieved an accuracy of 92.5%, outperforming three other methods appeared in the literature. To investigate how applicable the proposed method is to the doctors, a metric named proportion of well classified karyotype was also designed. An result of 91.3% was achieved on this metric, indicating that the proposed classification method could be used to aid doctors in genetic disorder diagnosis.
The ECVAM International Validation Study on <i>In Vitro</i> Embryotoxicity Tests: Results of the Definitive Phase and Evaluation of Prediction Models (2002)

From 1996 to 2000, ZEBET (Centre for Documentation and Evaluation of Alternative Methods to Animal Experiments at the BgVV, Berlin, Germany) coordinated the European Centre for the Validation of Alternative Methods (ECVAM) prevalidation and validation study on three embryotoxicity tests: a) a test employing embryonic stem cell lines (EST); b) the micromass (MM) test; and c) the postimplantation rat whole-embryo culture assay (WEC test). The main objectives of the study were to assess the performance of these three in vitro tests in discriminating between non- embryotoxic, weakly embryotoxic and strongly embryotoxic compounds. Phase I of the study (1997) was designed as a prevalidation phase, for test protocol optimisation, and for the establishment of a comprehensive database of in vivo and in vitro data on embryotoxic compounds. Phase II (1998-2000) involved a formal validation trial, conducted under blind conditions on 20 test compounds selected from the database, which were coded and distributed to the participating laboratories. In the preliminary phase of the validation study, six chemicals out of the 20, which showed embryotoxic potential, were tested. These results were used to define new biostatistically based prediction models (PMs) for the MM and WEC tests, and to evaluate those developed previously for the EST. As a next step, the PMs were evaluated by using the results for the remaining 14 chemicals of the definitive phase of the validation study. The three in vitro embryotoxicity tests proved to be applicable to testing a diverse group of chemicals with different embryotoxic potentials (non-embryotoxic, weakly embryotoxic, and strongly embryotoxic). The reproducibility of the three in vitro embryotoxicity tests were acceptable according to the acceptance criteria defined by the Management Team. The concordances between the embryotoxic potentials derived from the in vitro data and from the in vivo data were good for the EST and the WEC (PM2) test, and sufficient for the MM test and the WEC (PM1) tests according to the performance criteria defined by the Management Team before the formal validation study. When applying the PM of the EST to the in vitro data obtained in the definitive phase of the formal validation study, chemicals were classified correctly in 78% of the experiments. For the MM and the WEC tests, the PMs provided 70% and 80% (PM2) correct classifications, respectively. And, very importantly, an excellent predictivity (100%, except for PM1 of the WEC test, with 79%, considered as good) was obtained with strong embryotoxic chemicals in each of the three in vitro tests.
Stroke Transiently Increases Subventricular Zone Cell Division from Asymmetric to Symmetric and Increases Neuronal Differentiation in the Adult Rat (2004)

The orientation of mitotic cleavage regulates neurogenesis during neural development. We examined the orientation of mitotic cleavage of dividing progenitor cells in the subventricular zone (SVZ) of adult rats subjected to stroke. In nonstroke rats, 55% of dividing cells were oriented horizontally, whereas 40% were oriented vertically. Horizontal and vertical cleavage orientations produce asymmetric and symmetric divisions, respectively. Four days after stroke, the number of dividing cells increased twofold, whereas the proportion of symmetric dividing cells significantly (p < 0.01) increased from 40% before stroke to 60%. Fourteen days after stroke, the percentage of symmetric dividing cells was 47%. Stroke-increased numbers of dividing cells in M-phase were confirmed by immuostaining. In nonstroke rats, 37 and 33% of symmetric and asymmetric dividing cells, respectively, exhibited a neuronal marker (TuJ1). Four days after stroke, rats exhibited a significant (p < 0.05) augmentation of the frequency (47%) of neuronal distribution showing TuJ1 immunoreactivity in cells with symmetric division but not cells with asymmetric division (33%). Numb immunoreactivity was detected in SVZ cells of nonstroke rats. Stroke did not change Numb distribution. Our data suggest that neurons are produced by both asymmetric and symmetric cell divisions in the adult SVZ, and the transient increases in symmetric division and neuronal differentiation may result in stroke-induced neurogenesis.
Trying to Understand the Cerebellum Well Enough to Build One (2002)

The development of an increasingly detailed computer simulation of the cerebellum is briefly described. Specific and relatively direct evaluation of the performance of this simulation is made possible by the straightforward way in which pavlovian eyelid conditioning engages the cerebellum. Inputs to the simulation are based on recordings of mossy fiber and climbing fiber responses to the stimuli used in eyelid conditioning, and the output of the simulation can be evaluated with respect to the extensively characterized behavioral properties of eyelid conditioning. Because construction of the simulation has been guided by a strong aversion to errors of commission, both failures and successes of the simulation have proven informative. The behavior of the simulation related to the inhibitory nucleo-olivary feedback connection and spontaneous activity of climbing fibers is described. A prediction of the simulation concerning extinction is confirmed by experiment.
Overexpression, purification, crystallization and preliminary X-ray crystal analysis of<i>Bacillus pallidus</i><scp>D</scp>-arabinose isomerase (2008)

D-Arabinose isomerase catalyzes the isomerization of D-arabinose to D-ribulose. Bacillus pallidus D-arabinose isomerase has broad substrate specificity and can catalyze the isomerization of D-arabinose, L-fucose, L-xylose, L-galactose and D-altrose. Recombinant B. pallidus D-arabinose isomerase was overexpressed, purified and crystallized. A crystal of the enzyme was obtained by the sitting-drop method at room temperature and belonged to the orthorhombic space group P2(1)2(1)2, with unit-cell parameters a = 144.9, b = 127.9, c = 109.5 A. Diffraction data were collected to 2.3 A resolution.
Extracellular Glutathione Decreases the Ability of Burkholderia cenocepacia to Penetrate into Epithelial Cells and to Induce an Inflammatory Response (2012)

Extracellular GSH modulates the interaction between B. cenocepacia and epithelial respiratory cells and inhibits the bacterial invasion into these cells. This suggests that therapies aimed at restoring normal levels of GSH in the ASL might be beneficial to control CF lung infections.
Magnitude detection and phase synchronization of unbalanced and distorted grid voltage with novel extended PLL loop filter (2015)

In gird-connected power electronic systems, a fast and accurate tracking method of fundamental grid voltage is required to synchronize the converters with the mains. The Synchronous Reference Frame (SRF) based voltage magnitude and phase detection method is able to track three phase balanced grid voltage. But its performance is very poor when the gird-voltage is unbalanced and/or distorted. Improved SRF based detection methods can partially achieve either fast postfault resynchronization or steady-state unbalanced and distorted voltage rejection. However, its overall performance is not satisfying. This paper proposes a novel detection method based on SRF Phase-Locked Loop (PLL), in which a Low Pass Filter (LPF) and a Phase Sequence Separator (PSS) are combined to reach a tradeoff between fast detection speed and steady-state detection accuracy. Simulation including comparison of traditional methods and the proposed one under different grid fault conditions has been performed. The results validate the correctness and effectiveness of the proposed strategy.
Structure of the active 27‐residue fragment of human calpastatin (1991)

A synthetic 27-residue peptide corresponding to exon 1B of the endogenous inhibitor calpastatin contains a well-conserved region and has an ability to inhibit the cysteine endopeptidase calpain specifically. We examined the solution structure of this peptide in DMSO-d6 by two-dimensional 1H NMR spectroscopy. Although regular secondary structures such as alpha-helix and beta-sheet were not found, the region from Ile18 to Arg23 formed a well-defined structure with a type I beta-turn. This region coincided well with the highly conserved region of calpastatin. The result strongly suggests that this turn structure is essential for the inhibitory activity of calpastatin.