gebhart/patrepeval huggingface dataset:
Generation of collimated beams of relativistic ions in laser-plasma interactions (2000)

A method is proposed for generating collimated beams of fast ions in laser-plasma interactions. Two-dimensional and three-dimensional particle-in-cell simulations show that the ponderomotive force expels electrons from the plasma region irradiated by a laser pulse. The ions with unneutralized electric charge that remain in this region are accelerated by Coulomb repulsive forces. The ions are focused by tailoring the target and also as a result of pinching in the magnetic field produced by the electric current of fast ions.
Novel therapeutic approaches for pulmonary fibrosis (2011)

Pulmonary fibrosis represents the end stage of a number of heterogeneous conditions and is, to a greater or lesser degree, the hallmark of the interstitial lung diseases. It is characterized by the excessive deposition of extracellular matrix proteins within the pulmonary interstitium leading to the obliteration of functional alveolar units and in many cases, respiratory failure. While a small number of interstitial lung diseases have known aetiologies, most are idiopathic in nature, and of these, idiopathic pulmonary fibrosis is the most common and carries with it an appalling prognosis - median survival from the time of diagnosis is less than 3 years. This reflects the lack of any effective therapy to modify the course of the disease, which in turn is indicative of our incomplete understanding of the pathogenesis of this condition. Current prevailing hypotheses focus on dysregulated epithelial-mesenchymal interactions promoting a cycle of continued epithelial cell injury and fibroblast activation leading to progressive fibrosis. However, it is likely that multiple abnormalities in a myriad of biological pathways affecting inflammation and wound repair - including matrix regulation, epithelial reconstitution, the coagulation cascade, neovascularization and antioxidant pathways - modulate this defective crosstalk and promote fibrogenesis. This review aims to offer a pathogenetic rationale behind current therapies, briefly outlining previous and ongoing clinical trials, but will focus on recent and exciting advancements in our understanding of the pathogenesis of idiopathic pulmonary fibrosis, which may ultimately lead to the development of novel and effective therapeutic interventions for this devastating condition.
Notch 1–Deficient Common Lymphoid Precursors Adopt a B Cell Fate in the Thymus (2001)

We have recently reported that Notch 1, a member of the Notch multigene family, is essential for the development of murine T cells. Using a mouse model in which Notch 1 is inactivated in bone marrow (BM) precursors we have shown that B cells instead of T cells are found in the thymus of BM chimeras. However, it is not clear whether these B cells develop by default from a common lymphoid precursor due to the absence of Notch 1 signaling, or whether they arise as a result of perturbed migration of BM-derived B cells and/or altered homeostasis of normal resident thymic B cells. In this report we show that Notch 1-deficient thymic B cells resemble BM B cells in phenotype and turnover kinetics and are located predominantly in the medulla and corticomedullary junction. Peripheral blood lymphocyte analysis shows no evidence of recirculating Notch1(-/)- BM B cells. Furthermore, lack of T cell development is not due to a failure of Notch1(-/)- precursors to home to the thymus, as even after intrathymic reconstitution with BM cells, B cells instead of T cells develop from Notch 1-deficient precursors. Taken together, these results provide evidence for de novo ectopic B cell development in the thymus, and support the hypothesis that in the absence of Notch 1 common lymphoid precursors adopt the default cell fate and develop into B cells instead.
Using robotic exploratory procedures to learn the meaning of haptic adjectives (2013)

Delivering on the promise of real-world robotics will require robots that can communicate with humans through natural language by learning new words and concepts through their daily experiences. Our research strives to create a robot that can learn the meaning of haptic adjectives by directly touching objects. By equipping the PR2 humanoid robot with state-of-the-art biomimetic tactile sensors that measure temperature, pressure, and fingertip deformations, we created a platform uniquely capable of feeling the physical properties of everyday objects. The robot used five exploratory procedures to touch 51 objects that were annotated by human participants with 34 binary adjective labels. We present both static and dynamic learning methods to discover the meaning of these adjectives from the labeled objects, achieving average F1 scores of 0.57 and 0.79 on a set of eight previously unfelt items.
Peroxisome Proliferator-activated Receptor α Inhibits Hepatic S14 Gene Transcription (1996)

The peroxisome proliferator-activated receptor (PPARalpha) has been implicated in fatty acid regulation of gene transcription. Lipogenic gene transcription is inhibited by polyunsaturated fatty acids (PUFA). We have used the PUFA-sensitive rat liver S14 gene as a model to examine the role PPARalpha plays in fatty acid regulation of hepatic lipogenic gene transcription. Both PPARalpha and the potent peroxisome proliferator, WY14643, inhibit S14CAT activity in transfected primary hepatocytes. WY14643 and PPARalpha target the S14 T3 regulatory region (TRR, -2.8 to -2.5 kilobases), a region containing 3 T3 response elements (TRE). Transfer of the TRR to the thymidine kinase (TK) promoter conferred negative control to the TKCAT gene following WY14643 and PPARalpha treatment. Gel shift analysis showed that PPARalpha, either alone or with RXRalpha, did not bind the S14TRR. However, PPARalpha interfered with TRbeta/RXRalpha binding to a TRE (DR+4). Functional studies showed that co-transfected RXRalpha, but not T3 receptor beta1 (TRbeta1), abrogated the inhibitory effect of PPARalpha on S14 gene transcription. These results suggest that WY14643 and PPARalpha functionally interfere with T3 regulation of S14 gene transcription by inhibiting TRbeta1/RXR binding to S14 TREs. Previous studies had established that the cis-regulatory targets of PUFA control were located within the proximal promoter region of the S14 gene, i.e. between -220 and -80 bp. Finding that the cis-regulatory elements for WY14643/PPARalpha and PUFA are functionally and spatially distinct argues against PPARalpha as the mediator of PUFA suppression of S14 gene transcription.
RIBOSOMAL RNA AND TRANSLATION (1991)

The Hippo pathway was initially discovered in Drosophila melanogaster as a key regulator of tissue growth. It is an evolutionarily conserved signaling cascade regulating numerous biological processes, including cell growth and fate decision, organ size ...Read More
An Agent-Based Model for the Socio-Economic Monitoring of Vis-itor Streams A Study Using the Example of the Harz National Park, Germany (2018)

The Harz National Park (NP) offers a well-developed path network with a total length of 813 km, as well as a high number of starting and destination points for hikes. It was visited by about 1.7 million visitors in 2014. Due to its large extent, an accurate measurement of visitor numbers and their spatio-temporal distribution is not feasible. This paper demonstrates the possibility of simulating visitor streams around Mt. Brocken buy using the agent-based model (ABM) methodology. The GAMA v1.7 RC2 modelling environment was chosen, be-cause it has very extensive spatial operators and simulation tasks, combined with an easy-to-understand modelling language. To reduce the simulation effort, a model reduction factor MRF = 10 was tested successfully: no significant change to the model was required. After an initial parameterization, a sensitivity analysis was conducted, with the results in-cluded in the final calibration. The observed error value was significantly reduced, from RMSEparam=0,3817 to RMSEcalib=0,1069, and therefore the model was applied to the study area. For the final validation, visitor numbers from other, independent investigations were used. In addition to the 12 main routes and 7 hotspots identified, basic socio-economic indicators emerged. Hikersâ changes in behaviour according to framework conditions were analysed, demonstrating the impact of current measures on the reduction of path use. The final result is a flexible and expandable baseline model, which provides a realistic picture of the spatial distribution of hikers in the study area and additional key so-cio-economic figures.
Laser Biostimulation of Healing Wounds: Specific Effects and Mechanisms of Action (1988)

The purpose of this article was to synthesize the scientific knowledge relevant to laser biostimulation of healing wounds. The literature reviewed suggests that biostimulation with lasers: 1) accelerates the inflammatory phase of wound healing by altering the levels of various prostaglandins, 2) increases ATP synthesis by enhancing electron transfer in the inner membrane of mitochondria, 3) quickens protein (collagen) synthesis by quickening DNA and RNA synthesis, 4) augments fibroplasia by a mechanism that is still being explored, and 5) enhances the ability of immune cells to combat invading pathogens. Although these findings were made in vitro and in vivo in various animal models, their clinical implications are quite clear. Laser biostimulation is potentially a useful tool in the treatment of wounds, particularly those cutaneous and subcutaneous wounds that are either complicated by infection or inherently require a prolonged period of time to heal. The precise dosage and frequency of treatment required to promote healing even in animal models remain elusive, as is experimental determination of the depth of penetration of lasers.J Ortho Sports Phys Ther 1988;9(10):333-338.
Super-SILAC Allows Classification of Diffuse Large B-cell Lymphoma Subtypes by Their Protein Expression Profiles (2012)

Correct classification of cancer patients into subtypes is a prerequisite for acute diagnosis and effective treatment. Currently this classification relies mainly on histological assessment, but gene expression analysis by microarrays has shown great promise. Here we show that high accuracy, quantitative proteomics can robustly segregate cancer subtypes directly at the level of expressed proteins. We investigated two histologically indistinguishable subtypes of diffuse large B-cell lymphoma (DLBCL): activated B-cell-like (ABC) and germinal-center B-cell-like (GCB) subtypes, by first developing a general lymphoma stable isotope labeling with amino acids in cell culture (SILAC) mix from heavy stable isotope-labeled cell lines. This super-SILAC mix was combined with cell lysates from five ABC-DLBCL and five GCB-DLBCL cell lines. Shotgun proteomic analysis on a linear ion trap Orbitrap mass spectrometer with high mass accuracy at the MS and MS/MS levels yielded a proteome of more than 7,500 identified proteins. High accuracy of quantification allowed robust separation of subtypes by principal component analysis. The main contributors to the classification included proteins known to be differentially expressed between the subtypes such as the transcription factors IRF4 and SPI1/PU.1, cell surface markers CD44 and CD27, as well as novel candidates. We extracted a signature of 55 proteins that segregated subtypes and contained proteins connected to functional differences between the ABC and GCB-DLBCL subtypes, including many NF-κB-regulated genes. Shortening the analysis time to single-shot analysis combined with use of the new linear quadrupole Orbitrap analyzer (Q Exactive) also clearly differentiated between the subtypes. These results show that high resolution shotgun proteomics combined with super-SILAC-based quantification is a promising new technology for tumor characterization and classification.
An Organometallic B12-Rotaxane and a B12-Dimer, Relaxed and Loaded Forms of a Molecular Spring (1997)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTAn Organometallic B12-Rotaxane and a B12-Dimer, Relaxed and Loaded Forms of a Molecular SpringRenate B. Hannak, Gerald Färber, Robert Konrat, and Bernhard KräutlerView Author Information Institute of Organic Chemistry, University of Innsbruck A-6020 Innsbruck, Austria Cite this: J. Am. Chem. Soc. 1997, 119, 9, 2313–2314Publication Date (Web):March 5, 1997Publication History Received11 July 1996Published online5 March 1997Published inissue 1 March 1997https://pubs.acs.org/doi/10.1021/ja962376bhttps://doi.org/10.1021/ja962376brapid-communicationACS PublicationsCopyright © 1997 American Chemical SocietyRequest reuse permissionsArticle Views386Altmetric-Citations67LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information SUBJECTS:Alkyls,Hydrophobicity,Oligomers,Rotaxanes,Solution chemistry Get e-Alerts
Purification and Properties of l-erythro-3,5-Diaminohexanoate Dehydrogenase from a Lysine-fermenting Clostridium (1972)

Abstract A DPN-dependent dehydrogenase catalyzing the oxidative deamination of l-erythro-3,5-diaminohexanoate to 3-keto-5-aminohexanoate was purified about 30-fold from extracts of the lysine-fermenting Clostridium SB4. The best preparations have a specific activity of 34 units per mg and are relatively homogeneous. In the presence of sodium dodecyl sulfate the enzyme has a subunit molecular weight of about 37,000. The most active form of the enzyme is a tetramer of molecular weight about 140,000; at high pH or in solutions of low ionic strength it dissociates readily to a dimer of molecular weight about 68,000 which appears to be about one-third as active. The enzyme is highly specific with respect to substrate utilization and consequently is useful for the identification and quantitative estimation of l-erythro-3,5-diaminohexanoate and 3-keto-5-amino-hexanoate. The equilibrium of the dehydrogenase reaction is more favorable for amino acid oxidation than are the equilibria of other similar reactions.
Impaired Proteasome Function in Alzheimer's Disease (2000)

Inhibition of proteasome activity is sufficient to induce neuron degeneration and death; however, altered proteasome activity in a neurodegenerative disorder has not been demonstrated. In the present study, we analyzed proteasome activity in short-postmortem-interval autopsied brains from 16 Alzheimer's disease (AD) and nine age- and sex-matched controls. A significant decrease in proteasome activity was observed in the hippocampus and parahippocampal gyrus (48%), superior and middle temporal gyri (38%), and inferior parietal lobule (28%) of AD patients compared with controls. In contrast, no significant decrease in proteasome activity was observed in either the occipital lobe or the cerebellum. The loss of proteasome activity was not associated with a decrease in proteasome expression, suggesting that the proteasome may become inhibited in AD by a posttranslational modification. Together, these data indicate a possible role for proteasome inhibition in the neurodegeneration associated with AD.
Graphoepitaxy of cylinder-forming block copolymers for use as templates to pattern magnetic metal dot arrays (2005)

We report a method to fabricate high-quality patterned magnetic dot arrays using block copolymer lithography, metal deposition, and a dry lift-off technique. Long-range order of cylindrical domains oriented perpendicular to the substrate and in hexagonal arrays was induced in the block copolymer films by prepatterning the substrate with topographic features and chemically modifying the surface to exhibit neutral wetting behaviour towards the blocks of the copolymer. The uniformity of the domain size and row spacing of block copolymer templates created in this way was improved compared to those reported in previous studies that used graphoepitaxy of sphere-forming block copolymers. The pattern of block copolymer domains was transferred to a pattern of magnetic metal dots, demonstrating the potential of this technology for the fabrication of patterned magnetic recording media.
[An experimental study on high intensity focused ultrasound combined with mitomycin treatment of bladder tumor]. (2003)

HIFU group, HIFU combined chemotherapy group can distinctively inhibit tumor growth; HIFU combined with mitomycin has notable synergistic inhibitory effect. HIFU may induce the apoptosis of tumor cell.
The Plk1 inhibitor BI 2536 in patients with refractory or relapsed non-Hodgkin lymphoma: a phase I, open-label, single dose-escalation study (2012)

Polo-like kinase 1 (Plk1) is expressed during mitosis and overexpressed in multiple cancers, including non-Hodgkin lymphoma (NHL). This phase I study determined the maximum tolerated dose (MTD) of BI 2536, a Plk1 inhibitor, as a 1 h infusion once every 3 weeks in post-transplant relapsed (n = 17) and transplant-naive (n = 24) patients with relapsed/refractory NHL. Median treatment cycles were 2 and 1.5, respectively. MTD was 175 mg for both populations; dose-limiting toxicities were grade 4 thrombocytopenia and neutropenia. Most treatment-related adverse events were grade 1/2; drug-related grade 3/4 events included thrombocytopenia and neutropenia. Four patients achieved responses (three complete and one partial at doses ≥ 150 mg, all post-transplant relapsed patients) for an overall response rate of 9.8%. BI 2536 exhibited multi-compartmental pharmacokinetics with a high volume of distribution. The activity and safety of BI 2536 in this pretreated patient population support Plk inhibitors as a therapeutic strategy in oncology.
From a Helix to a Small Cycle: Metadynamics‐Inspired αvβ6 Integrin Selective Ligands (2018)

The RGD-recognizing αvβ6 integrin has only recently emerged as a major target for cancer diagnosis and therapy. Thus, the development of selective, low-molecular-weight ligands of this receptor is still in great demand. Here, a metadynamics-driven design strategy allowed us to successfully convert a helical nonapeptide into a cyclic pentapeptide (6) showing remarkable potency and αvβ6 specificity. NMR and docking studies elucidated the reasons for the high affinity and selectivity of this compound, setting the ground for the rational design of new αvβ6-specific small peptides or even peptidomimetics. In vivo PET imaging studies demonstrated the potential use of 6 for medical applications.
Voltage gating of conductance in lipid bilayers induced by porin from outer membrane of Neisseria gonorrhoeae. (1988)

Porins, polypeptides of approximately 35 kDa, are present as integral membrane proteins in the outer membranes of a variety of Gram-negative bacteria. As reported previously for a purified porin from Escherichia coli, voltage gating of conductance was found to be induced in a lipid bilayer by the solubilized purified porin, protein I, from Neisseria gonorrhoeae. The unitary response to an applied potential showed a cascade of current from an initial level through at least three levels, more or less equal, to a persisting lower level. The initial level of current corresponded to 1.0-1.3 nS for 0.2 M NaCl on either side of the bilayer. Briefly reducing the potential to zero restored the current to its initial level. Interpretation of the unitary response is suggested by electron microscopic data obtained on negatively stained outer membranes of E. coli indicating the presence of "pores" appearing in triplets. Moreover, low-resolution x-ray and neutron diffraction studies on crystals obtained with an E. coli porin show that three polypeptides associate to form a unit. Combining such structural data with the present electrical data lends support for the hypothesis that the unitary response results from three pores acting as a unit in response to an applied potential. Evidence obtained with the patch-clamp technique is mounting for a similar mechanism of many channels operating as a unit in a variety of cell membranes. The porin channel holds promise as a concrete model for the analysis of voltage gating of ionic conductance.
Zur Kenntnis der komplexen Wolframcyanide K4[W(CN)8], 2H2O und K3[W(CN)8], H2O (1955)

Abstract 1. Es wurden K 4 [W(CN) 8 ], 2H 2 O und K 3 [W(CN) 8 ], H 2 O rein dargestellt und deren magnetische Suszeptibilitäten gemessen. Dabei wurden die folgenden Werte gefunden: . Wie erwartet für die d 4 sp 3 ‐Bindung der 8 CN − Liganden, erwies sich K 4 [W(CN) 8 ], 2H 2 O als diamagnetisch und K 3 [W(CN) 8 ], H 2 O als paramagnetisch mit einer Suszeptibilität entsprechend einem unpaaren Elektron.
Antioxidant, Antimalarial and Antimicrobial Activities of Tannin-Rich Fractions, Ellagitannins and Phenolic Acids from Punica granatum L. (2007)

The Punica granatum L. (pomegranate) by-product POMx was partitioned between water, EtOAc and n-BuOH, and the EtOAc and n-BuOH extracts were purified by XAD-16 and Sephadex LH-20 column chromatography to afford ellagic acid (1), gallagic acid (2), punicalins (3), and punicalagins (4). Compounds 1 - 4 and the mixture of tannin fractions (XAD-16 eluates) were evaluated for antioxidant, antiplasmodial, and antimicrobial activities in cell-based assays. The mixture of tannins (TPT), XAD-EtOAc, XAD-H2O, XAD-PJ and XAD-BuOH, exhibited IC50 values against reactive oxygen species (ROS) generation at 0.8 - 19 microg/mL. Compounds 1 - 4 showed IC50 values of 1.1, 3.2, 2.3 and 1.4 microM, respectively, against ROS generation and no toxicity up to 31.25 microg/mL against HL-60 cells. Gallagic acid (2) and punicalagins (4) exhibited antiplasmodial activity against Plasmodium falciparum D6 and W2 clones with IC50 values of 10.9, 10.6, 7.5 and 8.8 microM, respectively. Fractions XAD-EtOAc, XAD-BuOH, XAD-H2O and XAD-PJ compounds 1 - 4 revealed antimicrobial activity when assayed against Escherichia coli, Pseudomonas aeruginosa, Candida albicans, Cryptococcus neoformans, methicillin-resistant Staphylococcus aureus (MRSA), Aspergillus fumigatus and Mycobacterium intracellulare. Compounds 2 and 4 showed activity against P. aeruginosa, C. neoformans, and MRSA. This is the first report on the antioxidant, antiplasmodial and antimicrobial activities of POMx isolates, including structure-activity relationships (SAR) of the free radical inhibition activity of compounds 1 - 4. Our results suggest a beneficial effect from the daily intake of POMx and pomegranate juice (PJ) as dietary supplements to augment the human immune system's antioxidant, antimalarial and antimicrobial capacities.
Quantitative Data Cleaning for Large Databases (2008)

Data collection has become a ubiquitous function of large organizations – not only for record keeping, but to support a variety of data analysis tasks that are critical to the organizational mission. Data analysis typically drives decision-making processes and efficiency optimizations, and in an increasing number of settings is the raison d’etre of entire agencies or firms.
Early Treatment of NOD Mice With B7-H4 Reduces the Incidence of Autoimmune Diabetes (2011)

Our data demonstrate the protective role of B7-H4 in the development of autoimmune diabetes, suggesting a potential means of preventing type 1 diabetes by targeting the B7-H4 pathway.