gebhart/patrepeval huggingface dataset:
Total Synthesis of (+)‐Dibromophakellin (2009)

Abstract Zwei Mitglieder einer Familie mariner Pyrrol‐Imidazol‐Alkaloide – (+)‐Dibromphakellin und das nichtnatürliche Kongener (+)‐Phakellin – wurden enantioselektiv aus 4‐Hydroxy‐ L ‐prolin synthetisiert. Das chirale Aminal an C10 ließ sich mithilfe einer [3,3]‐sigmatropen Overman‐Umlagerung eines Enamids effizient aufbauen (siehe Schema). magnified image
Kinesin: switch I & II and the motor mechanism (2002)

New crystal structures of the kinesin motors differ from previously described motor-ADP atomic models, showing striking changes both in the switch I region near the nucleotide-binding cleft and in the switch II or 'relay' helix at the filament-binding face of the motor. The switch I region, present as a short helix flanked by two loops in previous motor-ADP structures, rearranges into a pseudo-beta-hairpin or is completely disordered with melted helices to either side of the disordered switch I loop. The relay helix undergoes a rotational movement coupled to a translation that differs from the piston-like movement of the relay helix observed in myosin. The changes observed in the crystal structures are interpreted to represent structural transitions that occur in the kinesin motors during the ATP hydrolysis cycle. The movements of switch I residues disrupt the water-mediated coordination of the bound Mg2+, which could result in loss of Mg2+ and ADP, raising the intriguing possibility that disruption of the switch I region leads to release of nucleotide by the kinesins. None of the new structures is a true motor-ATP state, however, probably because conformational changes at the active site of the kinesins require interactions with microtubules to stabilize the movements.
Neuropeptides accentuate interleukin‐4 induced human immunoglobuline E synthesis in vitro (1996)

Corticotropin releasing factor, adrenocorticotropic hormone (ACTH) and alpha-melanocyte stimulating hormone either inhibit or enhance in a dose-dependent fashion an interleukin-4 (IL-4) driven human IgE synthesis in vitro. Here, we show that culture conditions strongly influence the earlier observed dose- and donor-dependent effects of adrenocorticotropic hormone. The effect of ACTH on IgE synthesis became only apparent late during culture periods, suggesting an indirect effect via the cellular microenvironment rather than by acting directly at the level of B-cell isotype switching. Thus, we studied other proopiomelanocortin (POMC) derived peptides and neuropeptides known to influence the cellular microenvironment. Indeed, similar modulatory effects on IgE synthesis were also observed by the addition of other proopiomelanocortin-derived peptides such as alpha-, beta-, and gamma-endorphins as well as by the opioid binding pentapeptide Leu-enkephalin. Furthermore the neuropeptide substance P accentuated an IL-4 or an IL-4 and anti-CD40 antibody driven class switch to IgE. In contrast to ACTH, substance P interfered not only with IgE synthesis but also with the synthesis of the other immunoglobulin isotypes. Thus, systemically acting neuroendocrine peptides such as ACTH and locally acting neuropeptides such as the enkephalins and substance P can modulate the magnitude of an IL-4 induced IgE response.
Integrating DNA: Transposases and Retroviral Integrases (1999)

Transposable elements appear quite disparate in their organization and in the types of genetic rearrangements they promote. In spite of this diversity, retroviruses and many transposons of both prokaryotes and eukaryotes show clear similarities in the chemical reactions involved in their transposition. This is reflected in the enzymes, integrases and transposases, that catalyze these reactions and that are essential for the mobility of the elements. In this chapter, we examine the structure-function relationships between these enzymes and the different ways in which the individual steps are assembled to produce a complete transposition cycle.
A state-dependent mean-field formalism to model different activity states in conductance based networks of spiking neurons (2019)

Abstract Higher and higher interest has been shown in the recent years to large scale spiking simulations of cerebral neuronal networks, coming both from the presence of high performance computers and increasing details in the experimental observations. In this context it is important to understand how population dynamics are generated by the designed parameters of the networks, that is the question addressed by mean field theories. Despite analytic solutions for the mean field dynamics has already been proposed generally for current based neurons (CUBA), the same for more realistic neural properties, such as conductance based (COBA) network of adaptive exponential neurons (AdEx), a complete analytic model has not been achieved yet. Here, we propose a novel principled approach to map a COBA on a CUBA. Such approach provides a state-dependent approximation capable to reliably predict the firing rate properties of an AdEx neuron with non-instantaneous COBA integration. We also applied our theory to population dynamics, predicting the dynamical properties of the network in very different regimes, such as asynchronous irregular (AI) and synchronous irregular (SI) (slow oscillations, SO). This results show that a state-dependent approximation can be successfully introduced in order to take into account the subtle effects of COBA integration and to deal with a theory capable to correctly predicts the activity in regimes of alternating states like slow oscillations.
Inhibition of CWR22Rν1 tumor growth and PSA secretion in athymic nude mice by green and black teas (2005)

Cancer of the prostate gland (CaP), the most common invasive malignancy and a major cause of cancer related deaths in male population in the USA, is an ideal candidate disease for chemoprevention because it is typically detected in elderly population with a relatively slower rate of growth and progression. Many dietary phytochemicals are showing promising chemopreventive effects, at-least in pre-clinical models of CaP. Our published data in cell culture and animal studies, supported by the work from other laboratories, as well as epidemiological observations and case-control studies, suggest that polyphenols present in green tea possess CaP chemopreventive and possibly therapeutic effects. This present study was designed to compare CaP cancer chemopreventive effects of green tea polyphenols (GTP), water extract of black tea, and their major constituents epigallocatechin-3-gallate and theaflavins, respectively, in athymic nude mice implanted with androgen-sensitive human CaP CWR22Rnu1 cells. Our data demonstrated that the treatment with all the tea ingredients resulted in (i) significant inhibition in growth of implanted prostate tumors, (ii) reduction in the level of serum prostate specific antigen, (iii) induction of apoptosis accompanied with upregulation in Bax and decrease in Bcl-2 proteins, and (iv) decrease in the levels of VEGF protein. Furthermore, we also found that GTP (0.01 or 0.05% w/v; given after establishment of CWR22Rnu1 tumor) causes a significant regression of tumors suggesting therapeutic effects of GTP at human achievable concentrations.
Search for the standard model Higgs boson in the H → ZZ → ℓ+ℓ−τ+τ− decay channel in pp collisions at $ \sqrt {s} = {7}\;{\text{TeV}} $ (2012)

A bstract A search is reported for the standard model Higgs boson in the H → ZZ → ℓ + ℓ − τ + τ − decay mode, where ℓ = μ or e, in proton-proton collisions at $ \sqrt {s} = {7}\;{\text{TeV}} $ , corresponding to an integrated luminosity of 4.7 fb −1 collected with the CMS detector at the LHC. No evidence is found for a significant deviation from the background expectation. An upper limit four to twelve times larger than the predicted value is set at 95% confidence level for the product of the standard model Higgs boson production cross section and decay branching fraction in the mass range 190 &lt; m H &lt; 600 GeV.
Strain Distribution in OSB and GWB in Wood-Frame Shear Walls (2009)

The overall goal of this study is to gain an insight into the load sharing aspect between oriented strand board (OSB) and gypsum wall board (GWB) in shear wall assembly during racking load. Sixteen standard 2,440×2,440mm walls were tested monotonically, in total, out of which 11 (Type A) were sheathed on both sides (OSB on one side and GWB on the other), while five walls were tested without GWB (Type B). Digital image correlation (DIC) was used for data acquisition and analysis which is a full-field, noncontact technique for measurement of displacements and strains. The system returns full-field three-dimensional displacement and strain data measured over the visible specimen surfaces. Overall, these tests suggest that initially during loading of a wall the load is shared between OSB and GWB. However, the proportion of load sharing is not known. As GWB fails first at about 60% of ultimate load capacity of the wall, the load shifts to the OSB panel which resists it until the failure of the wall. The tests also revealed that the load path in wall Types A and B is different and so is the failure pattern. Strains were locally concentrated around the fasteners, while the strains in the field of the panel were below the detection limit of DIC system.
Amino Acids and Peptides. II. A One-Step Synthesis of Atropine and Other Related Alkaloids from dl-Phenylalanine 3α-Tropanyl Ester (1971)

Atropine (VI), littorine (VII), apoatropine (IX), and related compounds have been synthesized by a one-step deamination reaction from dl-phenylalanine 3α-tropanyl ester (V). The amino ester (V) was obtained by coupling tropine with N-phthalyl-dl-phenylalanyl chloride (III) followed by hydrazinolysis with an equimolar amount of hydrazine hydrate.
The use of baculovirus vectors for the production of membrane proteins in insect cells (1999)

Conference Abstract| October 01 1999 The use of baculovirus vectors for the production of membrane proteins in insect cells R.D. Possee; R.D. Possee 1NERC Institute of Virology and Environmental Microbiology, Mansfield Road, Oxford, Oxon OX1 3SR UK Search for other works by this author on: This Site PubMed Google Scholar C.J. Thomas; C.J. Thomas 2School of Biological and Molecular Sciences, Oxford Brookes University, Gipsy Lane Campus, Headington, Oxford OX3 OBP, UK Search for other works by this author on: This Site PubMed Google Scholar L.A. King L.A. King 2School of Biological and Molecular Sciences, Oxford Brookes University, Gipsy Lane Campus, Headington, Oxford OX3 OBP, UK Search for other works by this author on: This Site PubMed Google Scholar Biochem Soc Trans (1999) 27 (5): A142. https://doi.org/10.1042/bst027a142a Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Facebook Twitter LinkedIn MailTo Cite Icon Cite Get Permissions Citation R.D. Possee, C.J. Thomas, L.A. King; The use of baculovirus vectors for the production of membrane proteins in insect cells. Biochem Soc Trans 1 October 1999; 27 (5): A142. doi: https://doi.org/10.1042/bst027a142a Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAll JournalsBiochemical Society Transactions Search Advanced Search This content is only available as a PDF. © 1999 Biochemical Society1999 Article PDF first page preview Close Modal You do not currently have access to this content.
Transcriptomic Profiling Reveals Extraordinary Diversity of Venom Peptides in Unexplored Predatory Gastropods of the Genus Clavus (2020)

Predatory gastropods of the superfamily Conoidea number over 12,000 living species. The evolutionary success of this lineage can be explained by the ability of conoideans to produce complex venoms for hunting, defense, and competitive interactions. Whereas venoms of cone snails (family Conidae) have become increasingly well studied, the venoms of most other conoidean lineages remain largely uncharacterized. In the present study, we present the venom gland transcriptomes of two species of the genus Clavus that belong to the family Drilliidae. Venom gland transcriptomes of two specimens of Clavus canalicularis and two specimens of Clavus davidgilmouri were analyzed, leading to the identification of a total of 1,176 putative venom peptide toxins (drillipeptides). Based on the combined evidence of secretion signal sequence identity, entire precursor similarity search (BLAST), and the orthology inference, putative Clavus toxins were assigned to 158 different gene families. The majority of identified transcripts comprise signal, pro-, mature peptide, and post-regions, with a typically short (<50 amino acids) and cysteine-rich mature peptide region. Thus, drillipeptides are structurally similar to conotoxins. However, convincing homology with known groups of Conus toxins was only detected for very few toxin families. Among these are Clavus counterparts of Conus venom insulins (drillinsulins), porins (drilliporins), and highly diversified lectins (drillilectins). The short size of most drillipeptides and structural similarity to conotoxins were unexpected, given that most related conoidean gastropod families (Terebridae and Turridae) possess longer mature peptide regions. Our findings indicate that, similar to conotoxins, drillipeptides may represent a valuable resource for future pharmacological exploration.
The Influence of Surface Treatment on Photocatalytic Activity of PE CVD TiO2 Thin Films (2009)

Abstract The aim of this paper is investigation of the photocatalytic properties of TiO 2 thin films prepared by PECVD with metal nanoparticles built‐up on the film surface. The deposition of TiO 2 films was carried out in the radio frequency (RF) low‐pressure PECVD reactor. Layers were deposited at two different substrate temperatures (40 and 300 °C). The surface of TiO 2 films was subsequently covered by noble metal nanoparticles—silver, platinum, and gold, deposited by different methods. For determination of the photocatalytic decomposition the Acid orange 7 (AO7) C 16 H 11 N 2 NaO 4 S organic dye was used. Selected samples were used for antibacterial tests (Gram‐negative bacteria Escherichia coli ). The results clearly proved that presence of metal clusters resulted in enhancement of the photocatalytic and antibacterial activity.
Design and Thermal Analysis for Irradiation of Absorber Material Specimens in the High Flux Isotope Reactor (2018)

This report provides a summary of the irradiation vehicle design and thermal analysis of absorber material specimens planned for irradiation in the flux trap of the High Flux Isotope Reactor (HFIR). Four different absorber materials will be inserted in the same capsule: hafnium carbide without additive (HfC), hafnium carbide with molybdenum silicide additive (HfC + MoSi2), samarium hafnate (Sm2HfO5), and europium hafnate (Eu2HfO5). The capsule design,with target temperatures of 300°C,will accommodate twelve specimens. Two capsules are planned to be built and irradiated to two different neutron fluence levels.
Experimental Proof of Microwave Sintering of Nd–Fe–B Powders Toward Fabrication of Permanent Magnets (2014)

The Nd-Fe-B magnets were prepared using conventional and microware sintering processes. A finely tuned microwave cavity operating in the 2.45 GHz, which works in single mode of electric field (e-field), was used to investigate the microwave sintering of Nd-Fe-B powders. The highest sintering temperature used was 1173 K, and the sintering lasted up to 610 s. The density of microwave sintered Nd-Fe-B magnets could reach values as high as 7.43 g/cc. We have managed to sinter Nd-Fe-B powders and produce magnets at a fraction of the time and energy used in conventional resistive/radiant heating, which is in excess of 1273 K for many hours, and in many cases after homogenization at high temperatures.
Comparison of Thermally Optimized SMD Packages for 100 V GaN HEMTs in 300 kHz Buck Converter High Current Applications (2022)

In this work an approach for a direct experimental comparison of the application-oriented performance between two high current GaN DC/DC converters based on 7mΩ, 100V GaN HEMTs in a commercial off-the-shelf top-cooled package and 5mΩ, 100V GaN HEMTs embedded in a thermally-optimized single-chip package is given. The two packaging versions are compared by a maximally identical implementation of the power and gate loops in a 48V, 300kHz buck converter with two parallel GaN HEMTs. In the single-chip package the die is directly mounted on a 12×6mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> copper-heat spreader offering a significantly lower thermal resistance to heatsink (1.69KW <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">−1</sup> ) in comparison to the commercial off-the-shelf version (2.45KW <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">−1</sup> ). For a direct benchmark, the COTS-based converter has an identical power-loop to the SCP-version with a novel gate-drive concept. Both versions have an efficiency of 96.8% at 65A output current (output power: 1.5kW), while the commercial off-the-shelf version has a better efficiency for lower currents, due to its better hard-switching Figure-of-Merits and therefore lower switching losses and reaches an output current of up to 80A (output power: 1.75kW). A detailed analytical loss breakdown for the different transistors in dependence of the temperature and output current is given to proof the measured current point, where the efficiencies of both converters are identical, since the higher switching losses of the SCP version are compensated by lower conduction losses at higher currents and temperatures compared to the smaller COTS transistor. Finally, an outlook on further improvements for reaching higher output currents and potential converters for a more fair comparison of different thermally optimized SMD packages are given.
Co je nového v hodnocení viability myokardu (2000)

Cilem sděleni je předložit souhrn nových poznatků o metodach a významu hodnoceni viability myokardu. Výsledky praci z poslednich 3 let ukazuji důležitost nejen hodnoceni přitomnosti viability myokardu, ale i jeji kvantifikace. Ukazuje se, že pokud je množstvi dysfunkcniho, ale viabilniho myokardu dostatecně velke (alespoň 25-30% masy leve komory), je revaskularizace myokardu spojena s významným zlepsenim globalni funkce leve komory, se zlepsenim funkcniho stavu podle klasifikace NYHA a předevsim s výrazně mensim rizikem srdecnich komplikaci, vcetně umrti. U nemocných s mensi masou hibernovaneho myokardu je funkcni zlepseni po revaskularizaci nevýznamne a přiznivý ucinek na prognozu je nejistý. Nemocným s nevratně poskozeným dysfunkcnim myokardem revaskularizace podle dnesnich znalosti nepřinasi prospěch ve srovnani s medikamentozni lecbou. Revaskularizace hibernovaneho myokardu by měla být provedena co nejdřive, a to vzhledem k progresi strukturalnich změn v hibernovanem myokardu až do nevratneho poskozeni.Zavěrem je vsak třeba řici, že definitivni zhodnoceni významu viability myokardu jestě vyžaduje studie s větsim poctem nemocných a vyřeseni některých dosud sporných otazek.
8-Amino-Adenosine Induces Loss of Phosphorylation of ERK1/2, p38 MAPK, and Akt Kinase: Role in Induction of Apoptosis in Multiple Myeloma. (2004)

Abstract Multiple Myeloma (MM) is a malignancy of monoclonal plasma cell proliferation in the bone marrow, which accounts for 10% of all hematologic cancers. This slow proliferating B-cell malignancy accumulates apoptosis-resistant and replication-quiescent cell populations, posing a challenge for current chemotherapeutics, which target rapidly replicating cells. MM remains an incurable disease in need of new therapeutic approaches. We have previously shown that the nucleoside analog, 8-chloro-adenosine (8-Cl-Ado), has significant activity for MM and that its sister compound, 8-amino-adenosine (8-NH2-Ado), appears to be even more potent, exhibiting greater activity in pre-clinical studies. 8-NH2-Ado is cytotoxic to MM cell lines both sensitive and resistant to conventional chemotherapies. This cytotoxic effect requires phosphorylation of 8-NH2-Ado to its tri-phosphate form, 8-NH2-ATP, and accumulation of 8-NH2-ATP results in a concomitant loss of endogenous ATP levels. 8-NH2-Ado induces apoptosis in MM cells as measured by an increase in Annexin V binding, a decrease in mitochondrial membrane potential, an increase in caspase activity, cleavage of caspase substrates, and an increase in cells with a subG1 DNA content. Here we demonstrate the novel effect of 8-NH2-Ado on the phosphorylation status of key cellular signaling molecules. MM cells treated with 8-NH2-Ado exhibit a dramatic loss of phosphorylation of several important signaling proteins, including ERK1/2, p38 MAPK and Akt kinase, within 30–120 minutes. Cells depleted of ATP by antimycin A or 2-deoxyglucose treatments to mimic 8-NH2-Ado-induced ATP depletion do not exhibit the same decrease in phosphorylation of vital cellular proteins. Therefore, the significant shifts in endogenous ATP pools caused by 8-NH2-Ado treatment cannot account for the changes in phosphorylation levels. Instead, 8-NH2-Ado may be affecting the activity of protein phosphatases involved in the negative regulation of these signaling molecules. Based on studies using the phosphatase inhibitor okadaic acid, it appears that PP2A may play a role in the 8-NH2-Ado-induced decrease in phosphorylation of p38. The distinctive effect of 8-NH2-Ado on the phosphorylation status of cellular proteins is a novel phenomenon for a nucleoside analog drug and appears to be unique to 8-NH2-Ado among this class of drugs. The kinetics of 8-NH2-Ado-mediated changes in phosphorylation levels of critical pro-survival and apoptosis-regulating proteins suggest that the modulation of these proteins by de-phosphorylation at early time-points may be an important mechanistic step in 8-NH2-Ado-induced programmed cell death.
Electromagnetic Fault Injection : How Faults Occur (2019)

Electromagnetic Fault Injection (EMFI) has recently gained popularity as a mean to induce faults because of its inherent advantages. Among them, the most interesting is probably its ability to generate faults in Systems on Chips without removing the package, and this even if only the frontside is exposed to the EM field. Despite this popularity, there is only little information on how EMFI generates faults. Within this context, this paper first aims at filling this lack by proposing a complete modeling of EM induction fault mechanism. In a second step, the introduced model is confronted to experimental data in order to demonstrate its soundness.
Inter- versus Intraannular Ring-Closing Metathesis of Polyallylferrocenes: Five-Fold RCM within a Single Molecule (2013)

Treatment of decaallylferrocene (1) with the Grubbs-II catalyst in refluxing dichloromethane has promoted the 5-fold ring-closing metathesis in 1 to afford single-bridged bis(1,4,5,8-tetrahydrofluorenyl)iron(II) species 3 in excellent yield. The preferential formation of 3 over quintuply bridged “superferrocenophane” 2 was explained as the intraannular RCM process being preferred over the interannular one in the reactions of polyallylferrocenes.
New Labdane-Type Diterpenoids and Anti-Inflammatory Constituents from Hedychium coronarium (2013)

Four new labdane-type diterpenoids: hedychicoronarin (1), peroxycoronarin D (2), 7β-hydroxycalcaratarin A (3), and (E)-7β-hydroxy-6-oxo-labda-8(17),12-diene-15,16-dial (4), have been isolated from the rhizomes of Hedychium coronarium, together with 13 known compounds (5-17). The structures of these new compounds were determined through spectroscopic and MS analyses. Compounds 3, 5, 6, and 10 exhibited inhibition (IC50 values ≤4.52 μg/mL) of superoxide anion generation by human neutrophils in response to formyl-L-methionyl-L-leucyl-L-phenylalanine/cytochalasin B (fMLP/CB). Compounds 3-6, 10, and 11 inhibited fMLP/CB-induced elastase release with IC50 values ≤6.17 μg/mL.