gebhart/patrepeval huggingface dataset:
Structural Basis for the Feedback Regulation of Escherichia coli Pantothenate Kinase by Coenzyme A (2000)

Pantothenate kinase (PanK) is a key regulatory enzyme in the coenzyme A (CoA) biosynthetic pathway and catalyzes the phosphorylation of pantothenic acid to form phosphopantothenate. CoA is a feedback inhibitor of PanK activity by competitive binding to the ATP site. The structures of the Escherichia coli enzyme, in complex with a nonhydrolyzable analogue of ATP, 5'-adenylimido-diphosphate (AMPPNP), or with CoA, were determined at 2.6 and 2.5 A, respectively. Both structures show that two dimers occupy an asymmetric unit; each subunit has a alpha/beta mononucleotide-binding fold with an extensive antiparallel coiled coil formed by two long helices along the dimerization interface. The two ligands, AMPPNP and CoA, associate with PanK in very different ways, but their phosphate binding sites overlap, explaining the kinetic competition between CoA and ATP. Residues Asp(127), His(177), and Arg(243) are proposed to be involved in catalysis, based on modeling of the pentacoordinate transition state. The more potent inhibition by CoA, compared with the CoA thioesters, is explained by a tight interaction of the CoA thiol group with the side chains of aromatic residues, which is predicted to discriminate against the CoA thioesters. The PanK structure provides the framework for a more detailed understanding of the mechanism of catalysis and feedback regulation of PanK.
Rabconnectin-3, a Novel Protein That Binds Both GDP/GTP Exchange Protein and GTPase-activating Protein for Rab3 Small G Protein Family (2002)

Rab3A, a member of the Rab3 small G protein family, regulates Ca(2+)-dependent exocytosis of neurotransmitter. The cyclical activation and inactivation of Rab3A are essential for the Rab3A action in exocytosis. GDP-Rab3A is activated to GTP-Rab3A by Rab3 GDP/GTP exchange protein (Rab3 GEP), and GTP-Rab3A is inactivated to GDP-Rab3A by Rab3 GTPase-activating protein (Rab3 GAP). It remains unknown how or in which step of the multiple exocytosis steps these regulators are activated and inactivated. We isolated here a novel protein that was co-immunoprecipitated with Rab3 GEP and GAP by their respective antibodies from the crude synaptic vesicle fraction of rat brain. The protein, named rabconnectin-3, bound both Rab3 GEP and GAP. The cDNA of rabconnectin-3 was cloned from a human cDNA library and its primary structure was determined. Human rabconnectin-3 consisted of 3,036 amino acids and showed a calculated M(r) of 339,753. It had 12 WD domains. Tissue and subcellular distribution analyses in rat indicated that rabconnectin-3 was abundantly expressed in the brain where it was enriched in the synaptic vesicle fraction. Immunofluorescence and immunoelectron microscopy revealed that rabconnectin-3 was concentrated on synaptic vesicles at synapses. These results indicate that rabconnectin-3 serves as a scaffold molecule for both Rab3 GEP and GAP on synaptic vesicles.
Doxorubicin downregulates cell surface B7-H1 expression and upregulates its nuclear expression in breast cancer cells: role of B7-H1 as an anti-apoptotic molecule (2010)

Our findings explain the previously reported immunomodulatory effect of anthracyclines on cancer cells, and provide a link between immunoresistance and chemoresistance. Finally these results suggest the use of dual combinatorial agents to inhibit B7-H1 beside chemotherapy, in breast cancer patients.
Fragment-Based Discovery of Low-Micromolar ATAD2 Bromodomain Inhibitors (2015)

Overexpression of ATAD2 (ATPase family, AAA domain containing 2) has been linked to disease severity and progression in a wide range of cancers, and is implicated in the regulation of several drivers of cancer growth. Little is known of the dependence of these effects upon the ATAD2 bromodomain, which has been categorized as among the least tractable of its class. The absence of any potent, selective inhibitors limits clear understanding of the therapeutic potential of the bromodomain. Here, we describe the discovery of a hit from a fragment-based targeted array. Optimization of this produced the first known micromolar inhibitors of the ATAD2 bromodomain.
Identification of the full-length KIAA0591 gene encoding a novel kinesin-related protein which is mapped to the neuroblastoma suppressor gene locus at 1p36.2. (2000)

The distal region of a short arm of chromosome 1p is frequently deleted in many human cancers including neuroblastoma (NBL), in which it has been narrowed down to the smallest region of overlap between D1S244 and D1S214 (approximately 7 cM). During the search for the candidate tumor suppressor genes mapped within the region, we found the KIAA0591 gene which encoded a new human kinesin-related protein with a homology to human axonal transporter of synaptic vesicles (ATSV). The kinesin is an intracellular motor protein and often associated with neuronal differentiation and survival. Here we identified a complete open reading frame of the KIAA0591 gene by screening a cDNA library derived from human substantia nigra. The KIAA0591 protein contains a possible pleckstrin homology (PH) domain at its carboxy-terminus. However, it did not possess a force-generating motor domain which is well conserved among kinesin superfamily members (KIFs). Northern blot analysis demonstrated that KIAA0591 mRNA was preferentially expressed in both adult and fetal brains, kidney, skeletal muscle and pancreas. KIAA0591 was expressed in favorable NBLs at higher levels than in unfavorable NBLs, although RT-PCR SSCP analysis showed no mutation within the coding region of the KIAA0591 gene, when 8 neuroblastoma tissues and 15 neuroblastoma-derived cell lines were examined. Thus, the full-length KIAA0591 gene may be a novel member of human KIF superfamily which lacks motor domain and might function as a tumor suppressor in an epigenetic but not a classic Knudson's manner.
Randomized Evaluation of efficacy and safety of ferric carboxymaltose in Patients with iron deficiency Anaemia and Impaired Renal function (REPAIR-IDA): rationale and study design (2010)

REPAIR-IDA will assess the efficacy and safety of two 750-mg infusions of FCM compared to an FDA-approved IV iron regimen in patients with NDD-CKD at increased risk for cardiovascular disease.
Selective high metabolic lability of uridine, guanosine and cytosine triphosphates in response to glucose deprivation and refeeding of untransformed and polyoma virus‐transformed hamster fibroblasts (1979)

Abstract Sugar deprivation of hamster fibroblasts (NIL Abbreviations: ATP, ADP and AMP, adenosine 5′‐tri‐, di‐ and monophosphate respectively; CTP, CDP and CMP, cytosine 5′‐tri‐, di and monophosphate respectively; GTP, GDP and GMP, guanosine 5′‐tri‐, di‐ and monophosphate respectively; IMP, inosine 5′‐monophosphate; Gal‐1‐P, α‐D‐galactose‐1‐phosphate; UDP‐Gal, uridine 5′‐diphosphogalactose; D‐MEM, Dulbecco's modified Eagle's minimal essential medium; D‐PBS, Dulbecco's phosphate‐buffered saline (pH 7.2); NIL, a line of Syrian hamster fibroblasts; PyNIL, a polyoma virus‐transformed line of NIL cells. ) affected the steady state levels (pool sizes) of cellular acid soluble nucleotides in the following fashion; the pools of UTP, GTP and CTP decreased to a much greater extent than the cellular ATP pools, with the UTP pools undergoing the most dramatic reduction. Sugar deprivation of polyoma‐transformed NIL cells (PyNIL) yielded even sharper decreases in the nucleoside triphosphate pools with relative changes similar to those of the untransformed cells. Inhibition of protein synthesis by cycloheximide, initiated at the onset of (and continued during) sugar deprivation, prevented the reduction in pool sizes and yielded values slightly higher than those observed for pool sizes in cells cultured in sugar‐supplemented medium. Refeeding glucose to sugar‐depleted hamster fibroblasts led to rapid increases (within 1 hour) in the UTP and CTP pools to levels well above the pool sizes observed in cells which were continuously cultured (16 hours) in sugar supplemented medium. Feeding NIL or PyNIL cells with fructose instead of glucose as the only hexose source did not appreciably affect any of the ribonucleoside triphosphate pool sizes. Measurements of hexose uptake by NIL and PyNIL cells under a variety of conditions suggest that hexose transport is not regulated by the total cellular pools of ATP or any of the other ribonucleoside triphosphates.
Reconfigurable processing with field programmable gate arrays (2002)

In-system-programmable, SRAM-based Field Programmable Gate Arrays (FPGAs) can be used to create processors and coprocessors whose internal architecture as well as interconnections can be reconfigured to match the needs of a given application. Exploiting the inherent speed and parallelism of a hardware solution, FPGA-based coprocessors can execute computationally-intensive tasks while maintaining the flexibility of a programmable solution. The successes of this approach have led to the introduction of the first FPGA devices designed for coprocessing applications; the XC6200 FPGA architecture features an SRAM control store, abundant registers, on-chip memory capability, support for high-speed full or partial reconfiguration, and a flexible, hierarchical routing scheme.
High-Density Renewable Fuels Based on the Selective Dimerization of Pinenes (2009)

High-density fuel candidates have been synthesized in up to 90% yield from β-pinene, a renewable strained bicyclic compound derived from wood and plant sources. The process is based on the heterogeneous acidic catalysts Montmorillonite-K10 and Nafion, which promote selective isomerization and dimerization of pinenes under moderate conditions (100 °C and atmospheric pressure). Montmorillonite-K10 was shown to be a highly active catalyst for dimerization but was also active in the ring opening of β-pinene followed by dehydrogenation to produce p-cymene, which limited the yield of the dimer to ca. 75%. Nafion was capable of producing dimers in up to 90% yield primarily through isomerization followed by dimerization. Amberlyst-15, a common industrial catalyst had very poor activity and conversion even at 150 °C. The dimer mixtures were upgraded through hydrogenation over PtO2 and fractional distillation. The synthesized fuels have a density of 0.94 g/cm3 and a net volumetric heating value of 39.5 MJ/L (141 745 BTU/gallon). These values are nearly identical to those for the widely used tactical fuel JP-10 (primarily composed of exotetrahydrodicyclopentadiene), suggesting that these renewable fuels may have applications for rocket propulsion.
A Discourse-Based Approach for Arabic Question Answering (2016)

The treatment of complex questions with explanatory answers involves searching for arguments in texts. Because of the prominent role that discourse relations play in reflecting text producers’ intentions, capturing the underlying structure of text constitutes a good instructor in this issue. From our extensive review, a system for automatic discourse analysis that creates full rhetorical structures in large-scale Arabic texts is currently unavailable. This is due to the high computational complexity involved in processing a large number of hypothesized relations associated with large texts. Therefore, more practical approaches should be investigated. This article presents a new Arabic Text Parser oriented for question-answering systems dealing with لماذا “why” and كيف “how to” questions. The Text Parser presented here considers the sentence as the basic unit of text and incorporates a set of heuristics to avoid computational explosion. With this approach, the developed question-answering system reached a significant improvement over the baseline with a Recall of 68% and MRR of 0.62.
Prevalence and Treatment Outcome in Anxious Versus Nonanxious Depression (2010)

http://www.germanctr.de/ Identifier: DRKS00000161.
N-terminal domains of putative helicases of flavi- and pestiviruses may be serine proteases (1989)

Recently we tentatively identified, by sequence comparison, central domains of the NS3 proteins of flaviviruses and the respective portion of the pestivirus polyprotein as RNA helicases (A.E.G. et al., submitted). Alignment of the N-proximal domains of the same proteins revealed conservation of short sequence stretches resembling those around the catalytic Ser, His and Asp residues of chymotrypsin-like proteases. A statistically significant similarity has been detected between the sequences of these domains and those of the C-terminal serine protease domains of alphavirus capsid proteins. It is suggested that flavivirus NS3 and the respective pestivirus protein contain at least two functional domains, the N-proximal protease and the C-proximal helicase one. The protease domain is probably involved in the processing of viral non-structural proteins.
Acute hydrocephalus in nonketotic hyperglycinemia (2000)

We present four patients with typical neonatal onset non-ketotic hyperglycinemia (NKH) who developed hydrocephalus requiring shunting in early infancy. Brain imaging revealed acute hydrocephalus, a megacisterna magna or posterior fossa cyst, pronounced atrophy of the white matter, and an extremely thin corpus callosum in all. The three older patients had profound developmental disabilities. This suggests that the development of hydrocephalus in NKH is an additional poor prognostic sign.
Monolithic PDM-DQPSK receiver in silicon (2010)

We present a monolithic silicon polarization-division multiplexed (PDM) differential quadrature phase-shift keying (DQPSK) receiver front-end. It contains an endless polarization controller, two Mach-Zehnder delay interferometers, two hybrids, and eight photodetectors. We demonstrate 43-Gb/s PDM-DQPSK reception and automatic endless polarization tracking.
One-Pot Synthesis of Highly Luminescent CdSe/CdS Core−Shell Nanocrystals via Organometallic and “Greener” Chemical Approaches (2003)

We report different approaches to the synthesis of size series of highly luminescent CdSe/CdS core−shell nanocrystals. The mixture of hexadecylamine (HDA)−trioctylphosphine oxide (TOPO)−trioctylphosphine (TOP) as stabilizing solvent was found to be very suitable for one-pot synthesis of nearly monodisperse CdSe nanocrystals followed by growing the CdS shell of a desired thickness. The obtained CdSe/CdS nanocrystals exhibited a narrow PL band (fwhm ∼27−35 nm) with reproducible room-temperature quantum yields as high as 50−85%. The emission color is tunable from green to red with increasing diameter of CdSe cores and/or thickness of the CdS shell. The possibility of preparing high-quality CdSe/CdS core−shell nanocrystals from the precursors cadmium acetate and H2S, which are more environmentally benign than conventional ones (e.g., dimethylcadmium) used in the organometallic synthesis of nanocrystals, was demonstrated. General aspects of the nanocrystal nucleation and growth as well as applicability of “greener” synthetic schemes for synthesis of core−shell nanocrystals are discussed.
A hierarchical Bayesian network approach for linkage disequilibrium modeling and data-dimensionality reduction prior to genome-wide association studies (2011)

The forest of hierarchical latent class models offers several advantages for genome-wide association studies: accurate modeling of linkage disequilibrium, flexible data dimensionality reduction and biological meaning borne by latent variables.
Stochastic Detection of Monovalent and Bivalent Protein–Ligand Interactions (2004)

Single-molecule study on multivalency: The binding kinetics of a tetravalent lectin can be examined at the single-molecule level by using an engineered protein pore carrying up to seven carbohydrate ligands. The binding of the lectin to the pore (see molecular model) produces short and long reversible blockades in single-channel current recordings, which are interpreted as monovalent and bivalent binding events, respectively. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2002/2004/z52614_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Pyridopyrimidines. 7. Ribonucleosides structurally related to the antitumor antibiotic sangivamycin (1977)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPyridopyrimidines. 7. Ribonucleosides structurally related to the antitumor antibiotic sangivamycinGary L. Anderson and Arthur D. BroomCite this: J. Org. Chem. 1977, 42, 6, 997–1000Publication Date (Print):March 1, 1977Publication History Published online1 May 2002Published inissue 1 March 1977https://pubs.acs.org/doi/10.1021/jo00426a014https://doi.org/10.1021/jo00426a014research-articleACS PublicationsRequest reuse permissionsArticle Views115Altmetric-Citations25LEARN 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
A comparison of wireless geolocation algorithms in the indoor environment (2004)

This paper presents a quantitative comparison of various geolocation algorithms for the indoor wireless environment. Using models recently developed for time-of-arrival (TOA) distance measurement errors in the indoor environment, we characterize the performance of standard least-square (LS), closest-neighbor (CN), and the residual weighting (RWGH) algorithms in line-of-sight (LOS), obstructed LOS (OLOS), and mixed LOS/OLOS channel conditions. We also evaluate the performance of these algorithms in relation to the size of the indoor area over which a user is to be located.
Flow Trees: A Lower Bound Computation Tool with Applications to Rearrangeable Multihop Lightwave Network Optimization (1995)

This paper presents a new method for computing the lower bounds for multihop network design problems which is particularly well suited to optical networks. More specifically, given N stations each with d transceivers and pairwise average traffic values of the stations, the method provides a lower bound for the combined problem of finding optimum (i) allocation of wavelengths to the stations to determine a configuration, and (ii) routing of the traffic on this configuration while minimizing congestion – defined as the maximum flow assigned on any link. The lower bounds can be computed in time polynomial in the network size. Consequently, the results in this work yield a tool which can be used in (i) evaluating the quality of heuristic design algorithms, and (ii) determining a termination criteria during minimization. The lower bound computation is based on first building flow trees to find a lower bound on the total flow, and then distributing the total flow over the links to minimize the congestion.
Continuous wave terahertz generation up to 2THz by photomixing on ion-irradiated In0.53Ga0.47As at 1.55μm wavelengths (2007)

We report the generation of continuous terahertz waves from microwave frequencies of up to 2THz obtained by photomixing two optical waves at 1.55μm wavelengths in ion-irradiated In0.53Ga0.47As interdigitated photomixers. A 200nm thick silicon nitride coating is used for antireflection and passivation layer, improving the reliability and the heat tolerance of the photomixer. In such devices, output powers greater than 40nW at 0.5THz and 10nW at 1THz have been achieved. Considering the observed saturation of the output power with the increase of bias voltage, the optimum excitation conditions regarding optical power and bias voltage are discussed.
The Design of the UNIX Operating System (1986)

1. General Review of the System. 2. Introduction to the Kernel. 3. The Buffer Cache. 4. Internal Representation of Files. 5. System Calls for the File System. 6. The System Representation of Processes. 7. Process Control. 8. Process Scheduling and Time. 9. Memory Management Policies. 10. Interprocess Communication. 11. Multiprocessor Systems. 12. Distributed UNIX System.
Asymmetric β-Boration of α,β-Unsaturated Esters with Chiral (NHC)Cu Catalysts (2008)

Copper complexes containing chiral N-heterocyclic carbene ligands catalyze the regioselective nucleophilic boryl attack at the β-carbon of α,β-unsaturated esters with enantioselectivities up to 74% ee, depending on the nature of the ester group.
Efficient epoxidation of unsaturated fatty acids by a hydroperoxide-dependent oxygenase. (1990)

Detergent-solubilized and partially purified soybean peroxygenase was shown to actively catalyze, in the presence of alkylhydroperoxides as co-substrates, the epoxidation of mono- and polyunsaturated fatty acids such as oleic and linoleic acids. Octadecenoic acids were found to be better substrates than shorter mono-unsaturated fatty acids (C16:1 or C14:1), but the position of their double bond (at positions 6, 9, or 11) had little effect on the rates of epoxidation. The peroxygenase exhibits a strong stereospecificity since octadecenoic acids with double bonds in trans-configuration were not epoxidized at detectable rates. Oxidation of linoleic acid yielded the two positional monoepoxide isomers and, as the minor product, the diepoxide. An important regioselectivity was, however, observed in this case; i.e. the unsaturation at position 9,10 was epoxidized preferentially to that at 12, 13. Oxidation of oleic acid in the presence of 18O-labeled hydroperoxy-linoleic acid revealed an incorporation of about 80% of the label into the epoxide ring. Products similar to those formed by the peroxygenase by epoxidation of unsaturated free fatty acids such as linoleic acid have been described as important metabolites (leukotoxins) in the defense of plants, e.g. in fungal agressions. This aspect underlines the physiological relevance of this new and potent catalytic activity of the peroxygenase.