gebhart/patrepeval huggingface dataset:
Analysis of Colubroidea snake venoms by liquid chromatography with mass spectrometry: evolutionary and toxinological implications (2003)

The evolution of the venomous function of snakes and the diversification of the toxins has been of tremendous research interest and considerable debate. It has become recently evident that the evolution of the toxins in the advanced snakes (Colubroidea) predated the evolution of the advanced, front-fanged delivery mechanisms. Historically, the venoms of snakes lacking front-fanged venom-delivery systems (conventionally grouped into the paraphyletic family Colubridae) have been largely neglected. In this study we used liquid chromatography with mass spectrometry (LC/MS) to analyze a large number of venoms from a wide array of species representing the major advanced snake clades Atractaspididae, Colubrinae, Elapidae, Homalopsinae, Natricinae, Psammophiinae, Pseudoxyrhophiinae, Xenodontinae, and Viperidae. We also present the first sequences of toxins from Azemiops feae as well as additional toxin sequences from the Colubrinae. The large body of data on molecular masses and retention times thus assembled demonstrates a hitherto unsuspected diversity of toxins in all lineages, having implications ranging from clinical management of envenomings to venom evolution to the use of isolated toxins as leads for drug design and development. Although definitive assignment of a toxin to a protein family can only be done through demonstrated structural studies such as N-terminal sequencing, the molecular mass data complemented by LC retention information, presented here, do permit formulation of reasonable hypotheses concerning snake venom evolution and potential clinical effects to a degree not possible till now, and some hypotheses of this kind are proposed here. The data will also be useful in biodiscovery.
Co‐transformation of Lec1 CHO cells with N‐acetylgucosaminyltransferase 1 activity and a selectable marker (1990)

In animal cells, the enzyme alpha(1,3)-mannoside-beta(1,2)-N-acetylglucosaminyltransferase I (GlcNAc-TI, EC.2.4.1.101) catalyzes the addition of N-acetylglucosamine to the ASN-linked Man GlcNAc oligosaccharide. The Chinese hamster ovary (CHO) mutant cell line Lec1 is deficient in this enzyme activity and, therefore, accumulates mannose-terminating cell surface ASN-linked oligosaccharides. Consequently, Lec1 cells are sensitive to the cytotoxic effects of the mannose-binding lectin Concanavalin A (Con A). Lec1 cells were co-transformed with human DNA from A431 cells and eukaryotic expression plasmids containing the bacterial neo gene by calcium phosphate/DNA-mediated transformation. Co-transformants were selected for resistance to Con A and G-418. DNA from a primary co-transformant was purified and used to transform Lec1 cells, resulting in secondary co-transformants. Both primary and secondary co-transformants exhibited in vitro GlcNAc-TI-specific enzyme activity. DNA gel blot analysis indicated that secondary co-transformants contained both human and neo sequences.
Functional Diversification of Kaurene Synthase-Like Genes in <i>Isodon rubescens</i> (2017)

<i>Ent</i>-kaurene diterpenoids are the largest group of known <i>Isodon</i> diterpenoids. Among them, oridonin is accumulated in the leaves, and is the most frequently studied compound because of its antitumor and antibacterial activities. We have identified five copalyl diphosphate synthase (CPS) and six kaurene synthase-like (KSL) genes by transcriptome profiling of <i>Isodon rubescens</i> leaves. An in vitro assay assigns ten of them to five different diterpene biosynthesis pathways, except IrCPS3 that has a mutation in the catalytic motif. The Lamiaceae-specific clade genes (IrCPS1 and IrCPS2) synthesize the intermediate copalyl diphosphate (normal-CPP), while IrCPS4 and IrCPS5 synthesize the intermediate <i>ent</i>-copalyl diphosphate (<i>ent</i>-CPP). IrKSL2, IrKSL4, and IrKSL5 react with <i>ent</i>-CPP to produce an <i>ent</i>-isopimaradiene-like compound, <i>ent</i>-atiserene and <i>ent</i>-kaurene, respectively. Correspondingly, the Lamiaceae-specific clade genes IrKSL1 or IrKSL3 combined with normal-CPP led to the formation of miltiradiene. The compound then underwent aromatization and oxidization with a cytochrome P450 forming two related compounds, abietatriene and ferruginol, which were detected in the root bark. IrKSL6 reacts with normal-CPP to produce isopimaradiene. IrKSL3 and IrKSL6 have the γβα tridomain structure, as these proteins tend to possess the bidomain structure of IrKSL1, highlighting the evolutionary history of KSL gene domain loss and further elucidating chemical diversity evolution from a macroevolutionary stance in Lamiaceae.
Femtosecond time-domain measurements of group velocity dispersion in AlGaAs diode lasers (1989)

Femtosecond optical pulses are used to determine the roundtrip propagation delay in AlGaAs diode lasers. By using pulses at different wavelengths, we have determined the dispersion in group index to be dngdλ = − 2.9µm−1 in these devices.
Protein-Protein Interactions at the Adrenergic Receptors (2011)

The adrenergic receptors are among the best characterized G protein-coupled receptors (GPCRs) and knowledge on this receptor family has provided several important paradigms about GPCR function and regulation. One of the most recent paradigms initially supported by studies on adrenergic receptors is that both βarrestins and G proteincoupled receptors themselves can act as scaffolds binding a variety of proteins and this can result in growing complexity of the receptor-mediated cellular effects. In this review we will briefly summarize the main features of βarrestin binding to the adrenergic receptor subtypes and we will review more in detail the main proteins found to selectively interact with distinct AR subtype. At the end, we will review the main findings on oligomerization of the AR subtypes.
Catalyst-TiO(OH)2 could drastically reduce the energy consumption of CO2 capture (2018)

Implementing Paris Climate Accord is inhibited by the high energy consumption of the state-of-the-art CO<sub>2</sub> capture technologies due to the notoriously slow kinetics in CO<sub>2</sub> desorption step of CO<sub>2</sub> capture. To address the challenge, here we report that nanostructured TiO(OH)<sub>2</sub> as a catalyst is capable of drastically increasing the rates of CO<sub>2</sub> desorption from spent monoethanolamine (MEA) by over 4500%. This discovery makes CO<sub>2</sub> capture successful at much lower temperatures, which not only dramatically reduces energy consumption but also amine losses and prevents emission of carcinogenic amine-decomposition byproducts. The catalytic effect of TiO(OH)<sub>2</sub> is observed with Raman characterization. The stabilities of the catalyst and MEA are confirmed with 50 cyclic CO<sub>2</sub> sorption and sorption. A possible mechanism is proposed for the TiO(OH)<sub>2</sub>-catalyzed CO<sub>2</sub> capture. TiO(OH)<sub>2</sub> could be a key to the future success of Paris Climat e Accord.
Identification of the major phosphorylation sites of the Raf-1 kinase (1993)

Treatment of cells with various growth factors and mitogens results in the rapid hyperphosphorylation and activation of the Raf-1 kinase. To determine if phosphorylation events affect Raf-1 activity, we have initiated experiments to identify the phosphorylation sites of Raf-1. In this report, we find that Ser43, Ser259, and Ser621 are the major sites of Raf-1 which are phosphorylated in mammalian cells and in Sf9 insect cells infected with a recombinant baculovirus encoding human Raf-1. Mutant Raf-1 proteins lacking kinase activity are also phosphorylated on these sites in vivo, indicating that these phosphorylation events are not a consequence of autophosphorylation. Furthermore, we find that Thr268 is the predominant Raf-1 residue phosphorylated in in vitro autokinase assays. In addition, we have examined the biochemical activity of baculovirus-expressed Raf-1 proteins containing mutations at these phosphorylation sites. In in vitro protein kinase assays Ser259 mutant proteins were 2-fold more active than wild-type Raf-1 and Ser621 mutant proteins were inactive as kinases. Analysis of the residues surrounding Ser259 and Ser621 indicates that RSXSXP may be a consensus sequence for the kinase responsible for phosphorylation of Raf-1 at these sites. Interestingly, these RSXSXP sequences are completely conserved throughout evolution in all Raf family members.
Synthesis of new 5‐arylazo‐3‐cyano‐4,6‐dimethyl‐2‐acetylchloridethiopyridine reactive disperse dyes and their applications in textile printing (2008)

Purpose The purpose of this paper is to synthesise some disperse dyes containing a reactive group and study their applications on polyamide and wool printing by heat transfer and screen printing. Design/methodology/approach To prepare these dyes, arylhydrazones of acetylacetone were reacted with cyanothioacetamide in boiling ethanolic sodium ethoxide. The resultant salt was collected by filtration and dried, then the salt was dissolved in ethanol and reacted with chloroacetylchloride with stirring for 3 h, where chloroacetylechloride was added dropwise. The final precipitated product was collected by filtration and crystallised with an appropriate solvent. These prepared dyes were used to print polyamide and wool fabrics by using synthetic thickener in the printing paste for all techniques. Findings The structure of the synthesised dyes were established and confirmed for the reaction products on the basis of their elemental analysis and spectral data (MS, IR and 1 H‐NMR). The suitability of the prepared dyestuffs for either heat transfer printing or traditional printing on nylon 6 and wool fabrics was investigated. The prints obtained from dyes possess high‐colour strength as well as excellent overall fastness properties. Research limitations/implications The synthesised heterocyclic reactive disperse azo dyes were prepared from the reaction of arylhydrazones of acetylacetone and thiocyanoacetamide to form the corresponding pyridinethione salts which underwent further reaction with chloroacetylchloride. The obtained dyes were utilised in preparing a paste for polyamide and wool fabric printing. In addition, both of the variation of the substituents on the synthesised dyes and the fastness properties were also studied. Practical implications The synthesis and use of reactive disperse dyes provide practical solution to over come the low fastness on polyamide and wool, when they are printed with disperse dyes only. Originality/value The result of the work aimed to define the scope and limitation of the authors' procedures for the synthesis of novel reactive disperse azo dyes to improve the low‐fastness properties of polyamide and wool, the dyes were synthesised in a simple way.
Influence of perfusion by gaseous oxygen persufflation on rat donor liver. (2006)

Perfusion by gaseous oxygen persufflation in combination with antioxidative agents is promising for resuscitating the ischemically altered livers for successful transplantation.
Effect of Groove Geometry on Viscoseal Performance (1967)

An experimental investigation of the effect of groove geometry on the performance of the grooved-shaft viscoseal is being conducted. Using distilled water as the sealed fluid, the concentric and eccentric performance of ten seals has been determined under laminar and turbulent conditions. An approximate method is devised to predict the empirical factors in the turbulent sealing equation. The findings reveal that the optimum seal geometry for laminar operation is not optimum for turbulent conditions, the seal eccentricity has slight effect on performance, and the phenomenon of air ingestion may present a major problem in the application of the viscoseal.
Infrared Metrics for Fixation-Free Liver Tumor Detection (2013)

Infrared (IR) spectroscopic imaging of human liver tissue slices has been used to identify and characterize liver tumors. Liver tissue, containing a liver metastasis of breast origin (mucinous carcinoma), was surgically removed from a consenting patient and frozen without formalin fixation or dehydration procedures, so that lipids and water remained in the tissues. A set of IR metrics (ratios of various IR peaks) was determined for tumors in fixation-free liver tissues. K-means cluster analysis was used to tell tumor from nontumor. In this case, there was a large reduction in lipid content upon going from nontumor to tumor tissue, and a well-resolved IR spectrum of nontumor liver lipid was obtained and analyzed. These IR metrics may someday guide work on IR spectroscopic diagnostics on patients in the operating room. This work also suggests utility for these methods beyond the identification of liver tumors, perhaps in the study of liver lipids.
Identification of a second transforming region in bovine papillomavirus DNA. (1984)

Bovine papillomavirus type 1 (BPV-1) has been used as a model for studying papillomavirus genetics because BPV-1 virions or BPV-1 genomic viral DNA efficiently induce morphologic transformation of certain cultured cells. Previous studies of BPV-1-induced transformation have found that a cloned 5.4-kilobase (kb) fragment (69T) of the genome is transforming and that a 2.3-kb segment from the 3' end of this fragment is also transforming if activated by a retroviral regulatory element (the long terminal repeat). We now report that 69T contains another transforming segment near its 5' end that can also be activated by a long terminal repeat. Since this second segment does not overlap the 3' transforming segment, we conclude that BPV-1 encodes at least two genes that can independently transform cultured cells. Mutational analysis of the 5' transforming segment suggests that the transforming gene of this segment lies within the E6 open reading frame. The two transforming segments differ in their biological activity in that the E6-containing fragment can transform C127 mouse cells but not NIH3T3 mouse cells, whereas the 3' fragment can transform both cell lines.
RGD-based Therapy: Principles of Selectivity (2016)

Design of selective anticancer drugs that are targeting RGD-binding integrin receptors which are known to be one of the perspective directions in the field of oncology. Significant progress in the development and application of these types compounds is already demonstrated. The accumulating body of basic and clinical evidence demonstrates potential significant effects on both in vitro and in vivo experimental models. However, the specific mechanism of action of these compounds is generally not a fully elucidated or the exact target responsible for the achievement of stated effects hasn't yet been defined sufficiently. To date eight types of integrin receptors, which are capable to recognize RGD-motif in natural ligands, has in fact been identified as (namely αIIbβ3, αvβ1, αvβ3, αvβ5, αvβ6, αvβ8, α5β1, α8β1). Even so, the estimation of the affinity of one particular RGD-bearing anticancer agent is often based on the determination of the binding efficacy to only one or rarely two integrin receptors. Traditionally the range of targets is restricted by the integrins, which are known to be highly expressed in a particular model system. While potential interactions of such an agent with other RGD-recognizing receptors usually remain beyond the research. Nonetheless, such interactions may also affect the viability and behavior of cancer cells. In this review we attempt to critically analyze the principles of selectivity achievement in the case of RGD-bearing natural ligands and the applicability of these principles in the context of the anticancer drug design.
Overlay-Aware Detailed Routing for Self-Aligned Double Patterning Lithography Using the Cut Process (2015)

Self-aligned double patterning (SADP) is one of the most promising techniques for sub-20 nm technology. Spacer-is-dielectric SADP using a cut process is getting popular because of its higher design flexibility; for example, it can decompose odd cycles without the need of inserting any stitch. This paper presents the first work that applies the cut process for decomposing odd cycles during routing. For SADP, further, overlay control is a critical issue for yield improvement; while published routers can handle only partial overlay scenarios, this paper identifies all the scenarios that induce overlays and proposes a novel constraint graph to model all overlays. With the developed techniques, our router can achieve high-quality routing results with significantly fewer overlays (and thus better yields). Compared with three state-of-the-art studies, our algorithm can achieve the best quality and efficiency, with zero cut conflicts, smallest overlay length, highest routability, and fastest running time.
Regulation of the Pax6 : Pax6(5a) mRNA ratio in the developing mammalian brain (2005)

These changes in vivo are similar in magnitude to those shown previously to alter target gene activity in vitro and might, therefore, allow the single mammalian Pax6 gene to carry out different functions at different times in mammalian brain development.
Whiteboard documentation through foreground object detection and stroke classification (2008)

Digitization of classroom content has been receiving widespread attention in recent days. The whiteboard/blackboard contents are valuable components of classroom contents. Capturing these contents in the presence of foreground objects has been a challenging task. In this paper we propose a model for whiteboard content documentation through foreground object detection. These detected object regions are inpainted with the recent whiteboard content. This virtually provides an experience of viewing the whiteboard content without any occlusion. The resulting frames are either sent to storage as a movie file or can be streamed online to remote locations.
An Algorithm for the nt Pairing Calculation in Characteristic Three and its Hardware Implementation (2007)

In this paper, we propose a modified eta <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">T</sub> pairing algorithm in characteristic three which does not need any cube root extraction. We also discuss its implementation on a low cost platform which hosts an Altera Cyclone II FPGA device. Our pairing accelerator is ten times faster than previous known FPGA implementations in characteristic three.
Multiple In Vivo Roles for the −12-Region Elements of Sigma 54 Promoters (1998)

Alignment of sigma 54-dependent promoters indicates conservation of two sequence elements. Six nucleotides in the downstream -12 element were mutated individually to each nonconsensus nucleotide. mRNA levels were measured in vivo for each promoter under strongly activating conditions. The results showed that the consensus sequence was not the strongest promoter. Instead, the -12 consensus element consists of two subregions that behave differently when mutated. Single changes in the upstream TTT consensus subregion can lead to increases in transcription, whereas single changes in the downstream GC(A/T) can lead to decreases in transcription. Selected double mutations with changes in both subregions were constructed and studied in vivo. No double mutation increased promoter strength, and some decreased it. Mutant promoters were also assayed under nonactivating conditions in vivo. No mRNA was detected in 23 of the 24 promoters tested. However, one double mutant showed substantial levels of transcript, indicating that the -12 sequence was capable of specifying basal transcription under nonactivating conditions. Overall, the results show that the -12 region has multiple roles in transcription in vivo, including modulating both basal and induced RNA levels.
Transient getter scheme for the Tokamak Fusion Test Reactor (1980)

The ability of the Tokamak Fusion Test Reactor (TFTR) to attain the largest fusion power gain depends critically on minimizing plasma contamination and controlling the densities of the reacting deuterium and tritium. Experiments on a number of tokamaks have demonstrated that gettering over an appreciable surface area (? 10%) of the vacuum vessel greatly facilitates both of these objectives. One particular problem in implementing a surface pumping system in TFTR, however, is a restriction on the maximum allowable tritium content of the getter. This restriction could require regeneration of the absorbed tritium after as few as 50 machine pulses. We have developed a scheme utilizing SAES Zr/Al getter modules which obviates the need for such frequent interruptions of machine operation by taking advantage of the pulsed operation of TFTR. With the Zr/Al getter at temperatures between 500°–600°C it is possible to achieve a quasisteady state in the tritium loading where the quantity of tritium desorbed between pulses is equal to the quantity which is absorbed during a pulse. Since frequent thermal cycling is not required, this scheme also reduces the possibility of Zr/Al getter material fatigue.
Simulation of networks of spiking neurons: A review of tools and strategies (2006)

We review different aspects of the simulation of spiking neural networks. We start by reviewing the different types of simulation strategies and algorithms that are currently implemented. We next review the precision of those simulation strategies, in particular in cases where plasticity depends on the exact timing of the spikes. We overview different simulators and simulation environments presently available (restricted to those freely available, open source and documented). For each simulation tool, its advantages and pitfalls are reviewed, with an aim to allow the reader to identify which simulator is appropriate for a given task. Finally, we provide a series of benchmark simulations of different types of networks of spiking neurons, including Hodgkin-Huxley type, integrate-and-fire models, interacting with current-based or conductance-based synapses, using clock-driven or event-driven integration strategies. The same set of models are implemented on the different simulators, and the codes are made available. The ultimate goal of this review is to provide a resource to facilitate identifying the appropriate integration strategy and simulation tool to use for a given modeling problem related to spiking neural networks.
Secured Handover Key Management among LTE Entities Using Device Certification (2014)

Cellular wireless network technology has been progressing in last 3 decades through different generations. Each generation adds new features to make the network attractive to the users. The long term evolution (LTE) is newly adopted technology to offer enhanced capacity, coverage and speed for current mobility networks. However the new distinctive features bring some new challenges in the design of the security mechanisms. Hence in this paper, we propose an improved approach such as device certification based key agreement among all the entities in the LTE. The purpose is increasing the security levels between eNB and MME and the same status should be followed for MME and EPC, whenever UE moves from one eNB to another. And the Proposed algorithm for fast and secure access by key management is implemented using MATLAB GUI.