gebhart/patrepeval huggingface dataset:
Coenzyme Q Biosynthesis: Evidence for a Substrate Access Channel in the FAD-Dependent Monooxygenase Coq6 (2016)

Coq6 is an enzyme involved in the biosynthesis of coenzyme Q, a polyisoprenylated benzoquinone lipid essential to the function of the mitochondrial respiratory chain. In the yeast Saccharomyces cerevisiae, this putative flavin-dependent monooxygenase is proposed to hydroxylate the benzene ring of coenzyme Q (ubiquinone) precursor at position C5. We show here through biochemical studies that Coq6 is a flavoprotein using FAD as a cofactor. Homology models of the Coq6-FAD complex are constructed and studied through molecular dynamics and substrate docking calculations of 3-hexaprenyl-4-hydroxyphenol (4-HP6), a bulky hydrophobic model substrate. We identify a putative access channel for Coq6 in a wild type model and propose in silico mutations positioned at its entrance capable of partially (G248R and L382E single mutations) or completely (a G248R-L382E double-mutation) blocking access to the channel for the substrate. Further in vivo assays support the computational predictions, thus explaining the decreased activities or inactivation of the mutated enzymes. This work provides the first detailed structural information of an important and highly conserved enzyme of ubiquinone biosynthesis.
A new monocomponent xylanase improves performance, ileal digestibility of energy and nutrients, intestinal morphology, and intestinal microbiota in young broilers (2022)

Supplementation of feed enzymes such as xylanases has been shown to lower intestinal digesta viscosity and improve nutrient digestion thereby resulting in better gut health due to the reduced availability of undigested nutrients for the growth of harmful bacteria. Oligosaccharides produced by xylanase in situ from dietary non-starch polysaccharides with potential prebiotic effects could modulate the gut microbiome. This paper reports the positive effects of a new monocomponent xylanase in improving performance and nutrient digestion and modulating the intestinal microbiota of broilers. A corn-wheat-soybean meal-based diet was formulated and used to develop 3 dietary treatments using different doses (0, 45,000 U/kg and 90,000 U/kg) of the xylanase. A total of 288, one-day-old male broiler (Ross 308) chicks were allocated to 36 cages (12 replicates per treatment and 8 chicks per cage) and offered the experimental diets from d 0 to 21 post-hatch. The data were subjected to ANOVA using the General Linear Models procedure of SAS. The results confirm that supplemental xylanase at both dose levels improved (P < 0.05) broiler performance and nutrient digestibility. Xylanase supplementation had significant (P < 0.05) effects in modulating the intestinal microbiota with a higher relative abundance of commensal bacteria such as Lactobacillus and a lower abundance of potentially non-beneficial bacteria such as E. shigella indicating a prebiotic mode of action.
Engineering for Patient Safety: Issues in Minimally Invasive Procedures (2009)

Contents: Series Foreword. Preface. H.G. Stassen, C.A. Grimbergen, J. Dankelman, Introduction to Minimally Invasive Surgery. K.T. den Boer, D.J. Gouma, C.A. Grimbergen, J. DankelmanEvaluation of the Surgical Process. P. Breedveld, D.W. Meijer, J.J. Jakimowicz, T. van Lunteren, Observation and Manipulation in Laparoscopic Surgery. P. Breedveld, M. Wentink, L.P.S. Stassen, P.A. Wieringa, Eye-Hand Coordination in Laparoscopy. W. Sjoerdsma, K.T. den Boer, T. Jansen, J.L. Herder, C.A. Grimbergen, Force Transmission of Laparoscopic Graspers. E.A.M. Heijnsdijk, H. de Visser, D.J. Gouma, P.V. Pistecky, J. Dankelman, Safe Manipulation of Bowel Tissue. J.E.N. Jaspers, K.T. den Boer, B.A.J.M. de Mol, C.A. Grimbergen, Design and Evaluation of Endoscope Positioners. G.J.M. Tuijthof, C.N. van Dijk, P.V. Pistecky, Design of Arthroscopic Instruments. F.M. Vos, R.E. van Gelder, I.W.O. Serlie, J. Florie, C.Y. Nio, F.H. Post, R. Truyen, A.M. Vossepoel, J. Stoker, Virtual Colonoscopy. N.H. Bakker, D. Tanase, J.A. Reekers, P.J. French, C.A. Grimbergen, Steering of Catheters. J.F.L. Goosen, J.J. Piek, P.J. French, Sensors for Catheters and Guidewires. H.G. Stassen, H.J. Bonjer, C.A. Grimbergen, J. Dankelman, The Future of Minimally Invasive Surgery and Training.
Reasoning about the Value of Decision-Model Refinement: Methods and\n Application (2013)

We investigate the value of extending the completeness of a decision model\nalong different dimensions of refinement. Specifically, we analyze the expected\nvalue of quantitative, conceptual, and structural refinement of decision\nmodels. We illustrate the key dimensions of refinement with examples. The\nanalyses of value of model refinement can be used to focus the attention of an\nanalyst or an automated reasoning system on extensions of a decision model\nassociated with the greatest expected value.\n
Reversal of Metabolic Deficits by Lipoic Acid in a Triple Transgenic Mouse Model of Alzheimer's Disease: A 13C NMR Study (2013)

Alzheimer's disease is an age-related neurodegenerative disease characterized by deterioration of cognition and loss of memory. Several clinical studies have shown Alzheimer's disease to be associated with disturbances in glucose metabolism and the subsequent tricarboxylic acid (TCA) cycle-related metabolites like glutamate (Glu), glutamine (Gln), and N-acetylaspartate (NAA). These metabolites have been viewed as biomarkers by (a) assisting early diagnosis of Alzheimer's disease and (b) evaluating the efficacy of a treatment regimen. In this study, 13-month-old triple transgenic mice (a mouse model of Alzheimer's disease (3xTg-AD)) were given intravenous infusion of [1- 13 C]glucose followed by an ex vivo 13 C NMR to determine the concentrations of 13 C-labeled isotopomers of Glu, Gln, aspartate (Asp), GABA, myo-inositol, and NAA. Total ( 12 C+ 13 C) Glu, Gln, and Asp were quantified by high-performance liquid chromatography to calculate enrichment. Furthermore, we examined the effects of lipoic acid in modulating these metabolites, based on its previously established insulin mimetic effects. Total 13 C labeling and percent enrichment decreased by ∼50% in the 3xTg-AD mice. This hypometabolism was partially or completely restored by lipoic acid feeding. The ability of lipoic acid to restore glucose metabolism and subsequent TCA cycle-related metabolites further substantiates its role in overcoming the hypometabolic state inherent in early stages of Alzheimer's disease.
ChemInform Abstract: Studies on the Electrochemical Behavior of the FeS2 Electrode in Molten AlCl3‐NaCl by the ac Impedance Method (1988)

Abstract show that the faradaic impedance values in the basic melt (50 mol% AlCl 3 ‐50 mol% NaCl) are much smaller than those in the acidic melt (52:48 mol%).
<title>Holoplanar optical interconnects</title> (1990)

A novel optical interconnect technology is presented. It combines single mode waveguides with multiplexed volume waveguide holograms to provide a highly parallel, very wide bandwidth system for VLSI, computer board or backplane computer interconects. Interconnect density and system performance are analyzed. Experimental results of a 1-to-20 waveguide interconnection are presented.
Lapatax: a phase I study of neoadjuvant lapatinib combined with docetaxel in Her2/neu overexpressing breast cancer (BC). EORTC protocol 10054. (2009)

Abstract Abstract #5112 Background: Lapatinib (L) has been shown to be an effective anti-HER2 therapy in advanced breast cancer, and is under study as an adjuvant therapy in the ALTTO and TEACH studies. Whilst there are ongoing neoadjuvant studies with the combination of Lapatinib and paclitaxel, there are none with docetaxel (D), considered by many to be the most active taxane in breast cancer, mainly due to the limited data available on the safety and efficacy of this combination. Hence there is a need for this dose-finding study which is being conducted as a prelude to a randomized phase II trial.&amp;#x2028; Objective: The objectives are to establish the maximum tolerated dose (MTD), to characterize Dose limiting toxicity (DLT) and to define the recommended dose for phase II.&amp;#x2028; Patients and Methods: Female patients (pts) with locally advanced, inflammatory or large operable BC are treated with escalating doses of L from 1000 to 1250 mg/d, administered orally once daily continuously in combination with D given every 21 days at dose ranges of 75 to 100 mg/m² for 4 cycles. At least three pts are treated at each dose level (DL). DLT is defined during cycle 1: any grade 3-4 non hematological toxicity, ANC&amp;lt;0.5 G/L lasting for 7days or more, Febrile neutopenia or thrombocytopenia &amp;lt;25 G/L. Growth factors are given only in case of clinical symptoms. Core biopsies are mandatory at baseline and after cycle 4. Pharmacokinetic samples are collected on day 1 of cycles 1 and 2.&amp;#x2028; Results: As of June 10, 10 pts with a median age of 56 years (range 17-64) were enrolled and 3 DLs (DL 3: L 1000 mg/day, D: 85 mg/m²) have been fully investigated. No pt had a DLT during cycle 1. The toxicity profile for 30 documented cycles is summarized in this table.&amp;#x2028; &amp;#x2028; The 4th cycles LVEF has been documented in 4 patients, one of whom had a drop by 16% to a value of 55%.&amp;#x2028; Conclusions: The toxicity of docetaxel-lapatinib during the first 3 dose levels is excellent. Final toxicity data and PK results of this phase 1 will be presented at the meeting. Citation Information: Cancer Res 2009;69(2 Suppl):Abstract nr 5112.
Synchronization of Elliptic Bursters (2001)

Periodic bursting behavior in neurons is a recurrent transition between a quiescent state and repetitive spiking. When the transition to repetitive spiking occurs via a subcritical Andronov--Hopf bifurcation and the transition to the quiescent state occurs via fold limit cycle bifurcation, the burster is said to be of elliptic type (also known as a "subHopf/fold cycle" burster). Here we study the synchronization dynamics of weakly connected networks of such bursters. We find that the behavior of such networks is quite different from the behavior of weakly connected phase oscillators and resembles that of strongly connected relaxation oscillators. As a result, such weakly connected bursters need few (usually one) bursts to synchronize, and synchronization is possible for bursters having quite different quantitative features. We also find that interactions between bursters depend crucially on the spiking frequencies. Namely, the interactions are most effective when the presynaptic interspike frequency matches the frequency of postsynaptic oscillations. Finally, we use the FitzHugh--Rinzel, Morris--Lecar, and Hodgkin--Huxley models to illustrate our major results.
Interaction of platelet-derived autotaxin with tumor integrin αVβ3 controls metastasis of breast cancer cells to bone (2014)

Autotaxin (ATX), through its lysophospholipase D activity controls physiological levels of lysophosphatidic acid (LPA) in blood. ATX is overexpressed in multiple types of cancers, and together with LPA generated during platelet activation promotes skeletal metastasis of breast cancer. However, the pathophysiological sequelae of regulated interactions between circulating LPA, ATX, and platelets remain undefined in cancer. In this study, we show that ATX is stored in α-granules of resting human platelets and released upon tumor cell-induced platelet aggregation, leading to the production of LPA. Our in vitro and in vivo experiments using human breast cancer cells that do not express ATX (MDA-MB-231 and MDA-B02) demonstrate that nontumoral ATX controls the early stage of bone colonization by tumor cells. Moreover, expression of a dominant negative integrin αvβ3-Δ744 or treatment with the anti-human αvβ3 monoclonal antibody LM609, completely abolished binding of ATX to tumor cells, demonstrating the requirement of a fully active integrin αvβ3 in this process. The present results establish a new mechanism for platelet contribution to LPA-dependent metastasis of breast cancer cells, and demonstrate the therapeutic potential of disrupting the binding of nontumor-derived ATX with the tumor cells for the prevention of metastasis.
Developing Ionic Liquid Know-How for the Design of Modular Functionality, Versatile Platforms, and New Synthetic Methodologies for Energetic Materials (2013)

Abstract : To address Objective 1 of the proposed work, the dual-functional nature of ILs has been exploited towards selective formation of new salts, where cation/anions are varied by structural modification and or ion exchange techniques. New classes of azolium azolate salts featuring nitro functional groups, nitrate anions, and dicyanamide anions have been synthesized and their energetic properties have been determined. As electron-withdrawing groups (e.g., nitro, nitrile) directly appended to the azole core tends to deactivate the nucleophilicity of the ring for further substitution (e.g., N-alkylation to form quaternized azolium cation), the synthesis of ILs with either stable azolate anions or cations with energetic group appended to N-alkyl chains both represented strategies for EIL synthesis to circumvent synthetic obstacles. Special attention has also been placed in developing new crystallographic methods for obtaining solid state structures of low melting EILs. Full details on the crystallographic results have been included in Appendix D. These solid state structures have served as models for the development of new synthetic pathways, achieving target properties, and understanding the interactions in the liquid state.
Arabinogalactan‐like Glycoproteins from Ulva lactuca (Chlorophyta) Show Unique Features Compared to Land Plants AGPs (2020)

Arabinogalactan proteins (AGPs) encompass a diverse group of plant cell wall proteoglycans, which play an essential role in plant development, signaling, plant-microbe interactions, and many others. Although they are widely distributed throughout the plant kingdom and extensively studied, they remain largely unexplored in the lower plants, especially in seaweeds. Ulva species have high economic potential since various applications were previously described including bioremediation, biofuel production, and as a source of bioactive compounds. This article presents the first experimental confirmation of AGP-like glycoproteins in Ulva species and provides a simple extraction protocol of Ulva lactuca AGP-like glycoproteins, their partial characterization and unique comparison to scarcely described Solanum lycopersicum AGPs. The reactivity with primary anti-AGP antibodies as well as Yariv reagent showed a great variety between Ulva lactuca and Solanum lycopersicum AGP-like glycoproteins. While the amino acid analysis of the AGP-like glycoproteins purified by the β-d-glucosyl Yariv reagent showed a similarity between algal and land plant AGP-like glycoproteins, neutral saccharide analysis revealed unique glycosylation of the Ulva lactuca AGP-like glycoproteins. Surprisingly, arabinose and galactose were not the most prevalent monosaccharides and the most outstanding was the presence of 3-O-methyl-hexose, which has never been described in the AGPs. The exceptional structure of the Ulva lactuca AGP-like glycoproteins implies a specialized adaptation to the marine environment and might bring new insight into the evolution of the plant cell wall.
Intraoperative assessment (2020)

Thorough intraoperative margin assessment is valuable when partial breast reconstruction is undertaken as an immediate procedure. The pathologist cannot assess the entire surface of a wide local excision specimen with frozen section examination; correlation with intraoperative radiological examination allows targeting of the area(s) of greatest concern in order to provide a sufficiently rapid result which is of value to the surgeon. The former incorporates selection of areas of concern and a process of “pressing” these onto glass microscope slides, immediately fixing the sample and staining with subsequent light microscopic assessment of the cytological preparations produced. Diathermy is damaging to epithelial cells and may cause potential problems especially with assessment of intraductal epithelial proliferations. Narrow margins between the breast tumor and edges of the surgical specimen are increasingly being accepted by multidisciplinary teams as sufficiently adequate for margin clearance.
Transparent Interconnection of Lots of Links (TRILL) Transparent Transport over MPLS (2018)

This document specifies methods to interconnect multiple Transparent
Interconnection of Lots of links (TRILL) sites with an intervening
MPLS network using existing TRILL and VPLS standards. This draft
addresses two problems as follows: 1) Providing connection between
more than two TRILL sites that are separated by an MPLS provider
network. 2) Providing a single logical virtualized TRILL network for
different tenants that are separated by an MPLS provider network.
5-Hydroxymethylcytosine signatures in cell-free DNA provide information about tumor types and stages (2017)

5-Hydroxymethylcytosine (5hmC) is an important mammalian DNA epigenetic modification that has been linked to gene regulation and cancer pathogenesis. Here we explored the diagnostic potential of 5hmC in circulating cell-free DNA (cfDNA) using a sensitive chemical labeling-based low-input shotgun sequencing approach. We sequenced cell-free 5hmC from 49 patients of seven different cancer types and found distinct features that could be used to predict cancer types and stages with high accuracy. Specifically, we discovered that lung cancer leads to a progressive global loss of 5hmC in cfDNA, whereas hepatocellular carcinoma and pancreatic cancer lead to disease-specific changes in the cell-free hydroxymethylome. Our proof-of-principle results suggest that cell-free 5hmC signatures may potentially be used not only to identify cancer types but also to track tumor stage in some cancers.
Supplementary Figure 3 from Transient Antiangiogenic Treatment Improves Delivery of Cytotoxic Compounds and Therapeutic Outcome in Lung Cancer (2023)

&lt;p&gt;PDF file - 665KB, Imaging of tumor cell proliferation using 18FFLT PET in H1975 tumors.&lt;/p&gt;
Heliquinomycin, a New Inhibitor of DNA Helicase, Produced by Streptomyces sp. MJ929-SF2. III. Biosynthesis. (1997)

In the course of our screening program for a novel DNAhelicase inhibitor, we have isolated heliquinomycin, which is produced by Streptomyces sp. M.J929-SF2X). The absolute structure of heliquinomycin (Fig.
<title>Application of ion imaging to the study of unimolecular and bimolecular reactions</title> (1993)

We use the photofragment ion imaging technique to investigate the 266 nm photodissociation dynamics of hydrogen iodide. We show the quantitative features of ion imaging by comparing determinations of photofragment recoil velocity distributions, product branching ratios and the HI bond dissociation energy with previously published results. Excellent agreement with previous experimental and theoretical results is obtained. The H atoms produced from this process are then used as reactants in the reaction of H + HI and H + D<SUB>2</SUB>. Imaging techniques are used to measure the velocity distributions of the products of these reactions.
Real-life experiments of Multi-Radio Multi-Channel wireless mesh networks: 802.11n is not any better than 802.11a! (2011)

Wireless Mesh Network (WMN) has become a popular access network architecture in the community due to its low cost and readily deployable nature. However, it is well known that multi-hop transmission in WMN is vulnerable to bandwidth degradation, primarily due to contention and radio interference. A straightforward solution to this problem is to use mesh nodes with multiple radios and channels. In this paper, we demonstrate through real-world experiments that the use of multiple radios and channels solely cannot solve the multi-hop TCP throughput degradation problem in IEEE 802.11n mesh networks. We verify that it is because the round trip time (RTT) for wireless communication path increases significantly with the number of hops, and the TCP throughput is limited inversely by the RTT. Due to this TCP throughput limitation, we also found interestingly that the multi-hop TCP throughput (up to five hops) of 802.11a is comparable to that of 802.11n. Our results give a key message that a new generation of TCP needs to be proposed and adopted so as to support the ever advancing wireless technologies and growing demand of multi-hop communications in wireless mesh networks.
Relationships between Structure and Rheology in Model Nanocomposites of Ethylene−Vinyl-Based Copolymers and Organoclays (2005)

A series of nanocomposites prepared by melt-blending of Cloisite organoclays with ethylene-co-vinyl acetate (EVA) and ethylene-co-methyl acrylate (EMA) copolymers were investigated by using small-angle X-ray scattering (SAXS), wide-angle X-ray diffraction (WAXD), transmission electron microscopy (TEM), thermogravimetric analysis (TGA), and rheological techniques. SAXS and TEM results confirmed mixed clay intercalation and exfoliation in all tested nanocomposites. The melting temperature, Tm, and crystalline structure (orthorhombic) in EMA and EVA were not significantly affected by the presence of organoclays, indicating that the clay particles were predominantly confined to the amorphous phase. Rheological properties above Tm were very similar in EVA and EMA nanocomposites. Both systems exhibited pseudo-solid rheological behavior in small-strain oscillatory shear experiments, yet they could yield and flow under a steady shear, which is characteristic of physical gelation. The pseudo-solid rheological behavior in EVA and EMA nanocomposites becomes more pronounced at higher contents of organoclay and at higher temperatures. SAXS results indicated that the silicate gallery spacings (d), intercalated by EVA and EMA chains, decreased with increasing temperature. This can be attributed to the reduced compatibility between organoclay and polymer (i.e., a LCST-type phase behavior). The unusual rheological properties of the nanocomposites at high temperatures were probably due to the formation of a 3D network of clay tactoids. Novel analytic models were proposed to describe rheological data from meltlike to gellike behaviors in EVA− and EMA−organoclay nanocomposites.
Virtual Power Management simulation framework for computer systems (2013)

We developed a Virtual Power Management (VPM) simulation methodology for pre-silicon design and validation of power management hardware and firmware. VPM integrates a realistic hardware interface with high-level workload and power models to achieve fast and effective system-wide simulation. VPM models are used independently for algorithmic and architectural exploration, and in conjunction with the Simics simulation environment to execute real firmware for verification. In this paper, we present an overview of the VPM architecture and results from two studies using the simulation framework.
Modeling of Alternative High-k Dielectrics for Memory Based Applications (2009)

Significant research efforts are devoted to the development of alternative high dielectric constant oxides (high-k) to sustain the requirements of the next generations of DRAM and FLASH memories. For the metal-insulator-metal applications, the identification of an oxide with a dielectric constant higher than 50 and a crystallization temperature lower than 650 C is a corner stone in the selection of the materials; while for non volatile memory (NVM) applications, an oxide with a dielectric constant ranging between 9 and 30, a large band gap (&gt; 6 eV) are targeted. While significant efforts have been dedicated to the integration of possible material candidates, little is known on their intrinsic properties. Through this paper, we provide an overview of the parameters that determine the electronic and the polarizability response of tantalates, niobiates and rare-earth based scandates oxides eligible for the development of the next generation of memory based applications.