gebhart/patrepeval huggingface dataset:
Characterization of the Colchicine Binding Site on Avian Tubulin Isotype βVI (2010)

Tubulin, the basic component of microtubules, is present in most eukaryotic cells as multiple gene products, called isotypes. The major tubulin isotypes are highly conserved in terms of structure and drug binding capabilities. Tubulin isotype betaVI, however, is significantly divergent from the other isotypes in sequence, assembly properties, and function. It is the major beta-tubulin isotype of hematopoietic tissue and forms the microtubules of platelet marginal bands. The interaction of the major tubulin isotypes betaI, betaII, betaIII, and betaIotaV with antimicrotubule drugs has been widely studied, but little is known about the drug binding properties of tubulin isotype betaVI. In this investigation, we characterize the activity of various colchicine site ligands with tubulin isolated from Gallus gallus erythrocytes (CeTb), which is approximately 95% betaVI. Colchicine binding is thought to be a universal property of higher eukaryotic tubulin; however, we were unable to detect colchicine binding to CeTb under any experimental conditions. Podophyllotoxin and nocodazole, other colchicine site ligands with divergent structures, were able to inhibit paclitaxel-induced CeTb assembly. Surprisingly, the colchicine isomer allocolchicine also inhibited CeTb assembly and displayed measurable, moderate affinity for CeTb (K(a) = 0.18 x 10(5) M(-1) vs 5.0 x 10(5) M(-1) for bovine brain tubulin). Since allocolchicine and colchicine differ in their C ring structures, the two C ring colchicine analogues were also tested for CeTb binding. Kinetic experiments indicate that thiocolchicine and chlorocolchicine bind to CeTb, but very slowly and with low affinity. Molecular modeling of CeTb identified five divergent amino acid residues within 6 A of the colchicine binding site compared to betaI, betaII, and betaIV; three of these amino acids are also altered in betaIII-tubulin. Interestingly, the altered amino acids are in the vicinity of the A ring region of the colchicine binding site rather than the C ring region. We propose that the amino acid differences in the binding site constrict the A ring binding domain in CeTb, which interferes with the positioning of the trimethoxyphenyl A ring and prevents C ring binding site interactions from efficiently occurring. Allocolchicine is able to accommodate the altered binding mode because of its smaller ring size and more flexible C ring substituents. The sequence of the colchicine binding domain of CeTb isotype betaVI is almost identical to that of its human hematopoietic counterpart. Thus, through analysis of the interactions of ligands with CeTb, it may be possible to discover colchicine site ligands that specifically target tubulin in human hematopoietic cells.
Sphingolipids and Glycerolipids. IV. Syntheses and Ionophoretic Activities of Several Analogues of Soya-cerebroside II, a Calcium Ionophoretic Sphingoglycolipid Isolated from Soybean. (1993)

For examination of the structure-activity relationship five analogues [(2'R)-2'-hydroxypalmitoyl (3), palmitoyl (4), (2'S)-2'-hydroxypalmitoyl (5), β-D-galactosyl (6), and 8, 9-dihydro (7) relevancies] of soya-cerebroside II (2), which is a calcium ionophoretic sphingoglycolipid isolated from soybean, have been synthesized by using our previously reported synthetic method for sphingoglycolipids. Examinations by using a W-08 (liquid-membrane type) apparatus and by means of the human erythrocyte membrane method, have shown that the (2'R)-2'-hydroxypalmitoyl analogue (3) exhibits higher ion-binding and ion-permeation activities for calcium ion than soya-cerebroside II (2), which contains 3 as the major component. It has also been found that the other analogues(5, 6, 7, 8) do not show those ionophoretic activities.An enantiomer (8) of the (2'R)-2'-hydroxypalmitoyl analogue (3) has been synthesized and its calcium ionophoretic activity examined. Compound 8 exhibits calcium ion-binding activity equal to that of 3, but 8 lacks the ability to support calcium ion-permeation through human erythrocyte membrane. Thus, human erythrocyte membrane precisely distinguishes the absolute configurations of 3 and 8 as regards calcium ionophoretic activity.
Environmental Impact Study and Experience Sharing of Produced Water Reinjection from Unconventional Gas Development (2019)

Abstract The world has seen a peak in unconventional gas development in recent years. Based on the practice of unconventional gas field development domestic in China and abroad, it is risky that the reinjection water may contaminate groundwater in local or adjacent areas during reinjected fluid migration. Ensuring environmental safety of the reinjection is a multi-disciplinary system project. This paper carries out the analysis and shares the experience of China's practice based on the actual cases from the following aspects. 1) The screening of the well location and the formation of the reinjection. 2) The drilling and cementing construction of the reinjection well, which considers the factors such as cementing quality and cement height and casing material. 3) The estimation of the total reinjection capacity, and the factors such as porosity and permeability of the geologic trap and reservoir fracture pressure is considered. 4) The monitoring of well and migration of reinjection fluids. Further environmental risk study of produced water reinjection is presented in this paper, on both sandstone formation of tight sand gas field and carbonate karst formation of shale gas field in China's typical unconventional gas development areas, using laboratory geochemistry experiments and large area geophysical test to obtain seismic data.
Mechanical harvest and in-field handling of tree fruit crops. (2017)

This chapter provides a general overview and description of various components of mechanized and automated fruit harvesting and handling systems. The chapter also introduces two case studies: one in shake-and-catch cherry harvesting; and another in robotic apple harvesting. As the design of crop canopies is a critical consideration for the successful development and implementation of harvesting solutions, the chapter begins with a description of several relevant crop architectures and the suitability of each for mechanized or automated harvesting. The chapter ends with a brief discussion on the current challenges and limitations and potential directions for future research and development in tree fruit harvesting.
Supramolecular Host‐Guest Systems in Zeolites Prepared by Ship‐in‐a‐Bottle Synthesis (2004)

Abstract Zeolites have a microporous system defining large cavities interconnected by smaller windows. These cages can accommodate large molecules whose size, however, can be too big to cross the windows. The most important examples of these tridirectional zeolites are faujasites X and Y, but examples of other suitable zeolites are Beta, EMT and MCM‐22. The inclusion of large guests inside the cavities starts from smaller precursors that can diffuse through the zeolite pores and then react inside the cavities to form the target guest. This microreview discusses the special characterisation techniques necessary to study these systems, differentiating those that serve to assess the identity and purity of the guests from those that address the internal vs. external location of the guests with respect to the zeolite host. It is organized by grouping the examples of ship‐in‐a‐bottle synthesis according to the potential application of the system as catalysts, photocatalysts, sensors, in molecular machines, etc. Although proper credit is given to the pioneering reports on ship‐in‐a‐bottle synthesis, the emphasis is placed on the most recent examples of the literature covering up to mid 2003. (© Wiley‐VCH Verlag GmbH &amp; Co. KGaA, 69451 Weinheim, Germany, 2004)
Extensibility safety and performance in the SPIN operating system (1995)

This paper describes the motivation, architecture and performance of SPIN, an extensible operating system. SPIN provides an extension infrastructure, together with a core set of extensible services, that allow applications to safely change the operating system's interface and implementation. Extensions allow an application to specialize the underlying operating system in order to achieve a particular level of performance and functionality. SPIN uses language and link-time mechanisms to inexpensively export fine-grained interfaces to operating system services. Extensions are written in a type safe language, and are dynamically linked into the operating system kernel. This approach offers extensions rapid access to system services, while protecting the operating system code executing within the kernel address space. SPIN and its extensions are written in Modula-3 and run on DEC Alpha workstations.
Thermally stable amorphous (AlMoNbSiTaTiVZr)50N50 nitride film as diffusion barrier in copper metallization (2008)

Results on copper metallization diffusion barriers using high-entropy alloy (HEA) nitride are reported. The HEA nitride (AlMoNbSiTaTiVZr)50N50 is amorphous in the as-deposited state and remains its noncrystallinity up to a high temperature of 850°C. To evaluate its diffusion barrier characteristics, Cu∕(AlMoNbSiTaTiVZr)50N50∕Si test structures were prepared and annealed under 750–900°C for 30min. The results show that the current nitride prevents the reaction between Cu and Si before its failure at 900°C. The outstanding barrier performance and high thermal stability of amorphous structure are suggested to originate from multiprincipal-element effects.
Advances on separation diastereomers of acyclic isoprenoid alkanes by gas chromatography and its geochemical significance (2018)

The abundant acyclic isoprene alkanes, including norpristane (2, 6, 10-tetramethyltetradecane), pristane (2, 6, 10, 14-tetramethylpentadecane), phytane (2, 6, 10, 14-tetramethylhexadecane) and their diastereomers, were detected and separated by GC-MS/MS in the coal sample of the Junggar Basin. Furthermore, the optimized condition of separation were discussed in terms of column type, length, and column temperature program. The results showed that the separation degree (R) of their diastereomers (i.e., 6(R)10(S)), 6(S)10(S) + 6(R)10(R)) of norpristane, pristane and phytane reached 0.6, 0.8 and 0.9, respectively. It indicated that the method was versatile, simple, rapid and efficient to separate the diastereomers of acyclic isoprene alkanes.
Supercritical CO2 Extraction of Volatile Oil from Rose Concrete (1997)

Rose concrete obtained from Rosa damascena Mill. was fractionated by supercritical CO2 extraction at 80 bar pressure and 40°C temperature by using a two-stage separation procedure. Two products, containing mainly paraffins and volatile oil, were recovered in the first and in the second separator, respectively. The volatile oil was analysed by GC–MS and compared with the products obtained from rose concrete by steam distillation and ethyl alcohol solubilization. The supercritical rose oil and the steam distilled product had very different compositions. The major difference was in the 2-phenylethanol content which was 50.0% in the SFE product and 10.4% in the steam-distilled rose oil. The liquid product obtained by ethyl alcohol solubilization contained 28.3% of 2-phenylethanol but more than 46% of paraffins, whereas the supercritical volatile oil contained only 15.1% of these compounds. © 1997 by John Wiley & Sons, Ltd.
[Preparation and release characterization in vitro of pulsed-release tablets of compound Danshen]. (2009)

Successfully obtained the PTS of a certain lag-time behind the rapid release which indicate that after bed time administration of such device, the drug plasma concentration-time curve CAN meet the requirements of chronotherapy of cardiovascular disease.
Data from Telatinib Is an Effective Targeted Therapy for Pseudomyogenic Hemangioendothelioma (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; Pseudomyogenic hemangioendothelioma (PHE) is an extremely rare locally aggressive neoplasm with endothelial differentiation, which often presents with multiple lesions. These tumors have characteristic SERPINE1–FOSB fusions. We report a 17 years old patient with advanced unresectable PHE with a durable complete remission to the multi-tyrosine kinase inhibitor telatinib. The aim of this study was to generate an &lt;i&gt;in vitro&lt;/i&gt; model for PHE, to study the functional consequences of SERPINE1–FOSB in endothelial cells, and its interaction with telatinib, to biologically substantiate the complete response to telatinib.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental Design:&lt;/b&gt; As the fusion results in overexpression of a truncated form of FOSB, we overexpressed truncated FOSB in normal endothelial cells.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; Truncated FOSB significantly affected tumor growth in three-dimensional (3D) on matrigel with increased and sustained sprouting. Moreover, truncated FOSB acted as an active transcription factor capable to regulate its own transcription, as well as to upregulate &lt;i&gt;PDGFRA&lt;/i&gt; and &lt;i&gt;FLT1&lt;/i&gt; expression (four-fold). Telatinib decreased proliferation and tumor growth in 3D and induced apoptosis. As expected, telatinib blocked VEGF signaling as phosphorylation of ERK was abolished. Interestingly, in FOSB overexpressing cells, telatinib specifically affected PDGFRA, FLT1, and FLT4 signaling and downregulated SERPINE1, thereby affecting the self-regulation of the fusion gene.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusions:&lt;/b&gt; We provide a biological substantiation of a complete clinical remission that was seen in a patient with PHE, showing that telatinib indirectly interferes with the self-regulated expression of the fusion product. Thus, telatinib or any other currently available VEGFR1-4/PDGFRA inhibitor could be a highly specific treatment option for patients with multifocal unresectable PHE. &lt;i&gt;Clin Cancer Res; 24(11); 2678–87. ©2018 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
IL-18 Attenuates Experimental Choroidal Neovascularization as a Potential Therapy for Wet Age-Related Macular Degeneration (2014)

Age-related macular degeneration (AMD) is the most common form of central retinal blindness globally. Distinct processes of the innate immune system, specifically activation of the NLRP3 inflammasome, have been shown to play a central role in the development of both "dry" and neovascular ("wet") forms of the disease. We show that the inflammatory cytokine interleukin-18 (IL-18) can regulate choroidal neovascularization formation in mice. We observed that exogenous administration of mature recombinant IL-18 has no effect on retinal pigment epithelial (RPE) cell viability, but that overexpression of pro-IL-18 or pro-IL-1β alone can cause RPE cell swelling and subsequent atrophy, a process that can be inhibited by the promotion of autophagy. A direct comparison of local and systemic administration of mature recombinant IL-18 with current anti-VEGF (vascular endothelial growth factor)-based therapeutic strategies shows that IL-18 treatment works effectively alone and more effectively in combination with anti-VEGF therapy and represents a novel therapeutic strategy for the treatment of wet AMD.
High-Q microsphere biosensor - analysis for adsorption of rodlike bacteria (2007)

Theory is developed for frequency shift and linewidth-broadening induced by rodlike bacteria bound to micro-optical resonators. Optical shift of whispering gallery modes (WGMs) is modeled by introducing a form factor that accounts for random horizontal orientation of cylindrical bacteria bound by their high refractive index cell walls. Linewidth-broadening is estimated from scattering losses. Analytic results are confirmed by measurement using E.Coli as model system (~10(2) bacteria/mm(2) sensitivity), establishing the WGM biosensor as sensitive technique for detection and analysis of micro-organisms.
Progesterone and 6α-Methyl-17α-hydroxyprogesterone Acetate as Inhibitors of Spermatogenesis and Accessory Gland Function in the Ram (1965)

Journal Article Progesterone and 6α-Methyl-17α-hydroxyprogesterone Acetate as Inhibitors of Spermatogenesis and Accessory Gland Function in the Ram Get access R. J. ERICSSON, R. J. ERICSSON 1Department of Animal Science, University of Kentucky Lexington, Kentucky Search for other works by this author on: Oxford Academic Google Scholar R. H. DUTT R. H. DUTT 1Department of Animal Science, University of Kentucky Lexington, Kentucky Search for other works by this author on: Oxford Academic Google Scholar Endocrinology, Volume 77, Issue 1, 1 July 1965, Pages 203–208, https://doi.org/10.1210/endo-77-1-203 Published: 01 July 1965 Article history Received: 10 September 1964 Published: 01 July 1965
Influence of Indenter Tip Geometry on Elastic Deformation during Nanoindentation (2005)

Nanoindentation with a Berkovich indenter is commonly used to investigate the mechanical behavior of small volumes of materials. To date, most investigators have made the simplifying assumption that the tip is spherical. In reality, indenter tips are much more complex. Here, we develop a new method to describe the tip shape using the experimentally determined area function of the indenter at small depths (0-100 nm). Our analysis accurately predicts the elastic load-displacement curve and allows the theoretical strength of a material to be determined from pop-in data. Application of our new method to single crystal Cr3Si shows that the predicted theoretical strengths are within 12% of the ideal strength G/2pi, where G is the shear modulus.
Effect of Schottky barrier alteration on the low-frequency noise of InP-based HEMTs (1998)

For the first time the effect of increasing the Schottky barrier's Al content of InP-based InAlAs-InGaAs HEMTs from 48 to 60% on the low-frequency (LF) drain and gate current noise is investigated. It is shown that the LF gate current noise S/sub IG/(f) for the 60% case decreases by almost three decades, while the LF drain current noise S/sub IDS/(f) stays at the same level. From small coherence values, it can be concluded that drain and gate noise sources can be treated separately which facilitates the LF noise modeling of these HEMTs.
A key role of nuclear factor Y in the refeeding response of fatty acid synthase in adipocytes (2017)

Fatty acid synthase (Fasn) is a key component of energy metabolism that is dynamically induced by food intake. Although extensive studies have revealed a number of transcription factors involved in the fasting/refeeding transition of Fasn expression in hepatocytes, much less evidence is available for adipocytes. Using the in vivo Ad-luc analytical system, we identified the inverted CCAAT element (ICE) around -100 nucleotides in the Fasn promoter as a critical cis-element for the refeeding response in adipocytes. Electrophoretic mobility shift assays and chromatin immunoprecipitation show that nuclear factor Y (NF-Y) binds to ICE specifically in refeeding states. Notably, the NF-Y binding to ICE is differently regulated between adipocytes and hepatocytes. These findings provide insights into the specific mechanisms controlling energy metabolism in adipocytes.
Military anti-shock garment: Historical relic or a device with unrealized potential? (2008)

Military anti-shock trousers represents a medical device which has engendered very divergent views, even up to today. From the time the concept was formulated in 1903 by surgeon George W Crile, there have been significant swings in opinion and evidence. The guidelines, where available, are often kept relatively general and cautious. As a spin-off to the mechanism and technology, several alternative devices have been proposed or developed over the years. This include the auto-transfusion torniquet, the non pneumatic anti-shock garment (Life Wrap) and the non inflatable antishock garment, which are discussed in this paper.
Copper(II)-Catalyzed Silylation of Activated Alkynes (2014)

Key words diastereodivergent silylation - α,β-unsaturated alkynes - Z-β-silyl-α,β-unsaturated carbonyls - E-β-silyl-α,β-unsaturated carboxylates - copper
ChemInform Abstract: UNTERSUCHUNGEN ZUR SYNTH. HETEROCYCLISCHER VERBINDUNGEN 483. MITT. SYNTH. VON HOMOAPORPHIN UND VERSUCHE ZUR DARST. VON C‐NORAPORPHIN DURCH PSCHORR‐RK. (1972)

Abstract Die Behandlung der substituierten Phenyl‐propionsäure (I) mit Salpetersäure in Essigsäure ergibt das 2‐Nitrophenyl‐Derivat (II), das mit 4‐Benzyloxy‐3‐methoxy‐phenäthylamin zum Carbonsäureamid (III) kondensiert wird.
Multi-objective design of antenna structures using variable-fidelity EM simulations and co-kriging (2014)

A methodology for low-cost multi-objective design of antenna structures is proposed. To reduce the computational effort of the design process the initial Pareto front is obtained by optimizing the response surface approximation (RSA) model obtained from low-fidelity EM simulations of the antenna structure of interest. The front is further refined by iterative incorporation of a limited number of high-fidelity training points into the RSA surrogate using co-kriging. Our considerations are illustrated using two examples of antenna structure.
2q31.1 microdeletion syndrome: redefining the associated clinical phenotype (2010)

These results reinforce the hypothesis that the variable skeletal phenotype in 2q31 deletion patients is a result of hemizygosity for the HOXD genes and that the 2q31.1 microdeletion syndrome is a well defined and clinically recognisable phenotype.
On the specification and synthesis of hazard-free asynchronous control circuits (2002)

Two related approaches to the specification and synthesis of hazard-free asynchronous control circuits are described. The first approach is based on signal transition graphs (STGs), a type of interpreted Petri nets. The second is based on a subclass of state machines called asynchronous finite state machines (AFSMs).< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Analyses of thrombocytopenia in idiopathic thrombocytopenic purpura- prone mice by platelet transfer experiments between (NZW x BXSB)F1 and normal mice (1990)

Male (NZW x BXSB) F1 (W/B F1) mice, which develop lupus nephritis, myocardial infarction, and thrombocytopenia, showed reduced platelet lifespan (PLS) and increased platelet-associated antibody (PAA) values. There were statistically significant correlations between the increase in PAA values and either the reduction in PLS or the decrease in platelet counts. This and the results of platelet transfer experiments between old male W/B F1 mice and either female W/B F1 or normal BALB/c mice indicate that PAAs on the platelet surface play a crucial role in the destruction of platelets in W/B F1 mice. The mechanism of thrombocytopenia observed here appears similar to that of human idiopathic thrombocytopenic purpura (ITP). Therefore, we think that W/B F1 mice are a potentially useful animal model for investigating the effectiveness and mode of action of therapeutic agents in human ITP, and that they may provide additional information on the basic mechanisms of this autoimmune phenomenon.