gebhart/patrepeval huggingface dataset:
Site-directed Mutagenesis of Heparin-binding EGF-like Growth Factor (HB-EGF): Analysis of <i>O</i> -glycosylation Sites and Properties (2001)

Heparin-binding epidermal growth factor-like growth factor (HB-EGF) is a 22 kDa, O-glycosylated protein. HeLa cells infected with a recombinant vaccinia virus expressing human HB-EGF produced a secreted, bioactive protein, with Mr 22,000 that was decreased to 14,000 by treatment with O-glycanase. Site-directed mutagenesis of HB-EGF cDNA using oligonucleotide- and PCR-directed techniques was performed to change the potential glycosylation sites, Thr75 and Thr85, to alanine residues to prevent O-glycosylation. Purification and characterization of the mutant proteins demonstrated that: (i) both O-glycosylation sites of HB-EGF are utilized, (ii) HB-EGF secretion does not require O-glycosylation, (iii) removal of O-glycans does not affect proteolytic cleavage of the HB-EGF precursor, nor does it influence HB-EGF intracellular trafficking or subcellular localization, and (iv) HB-EGF produced by HeLa cells is heavily sialylated. Comparisons between glycosylation mutants and wild-type HB-EGF revealed no significant apparent differences in receptor binding activity.
PCR-Based Tandem Epitope Tagging System for <i>Escherichia Coli</i> Genome Engineering (2006)

Biological discovery in the postgenomic era requires a systematic and high-throughput experimental approach. To this end, a versatile PCR-based tandem epitope tagging system is described, which inserts a tandem epitope coding sequence into any desired position of the Escherichia coli chromosome. Template plasmids were constructed that carry tandem copies of the epitope encoding sequence, Flp recombinase target (FRT) sites, and antibiotic resistance genes. The linear DNA fragment, amplified from the template plasmid with extensions homologous to the end of the target gene and part of its downstream region, was transformed into E. coli K-12 MG1655 harboring the bacteriophage gamma Red recombination system. The antibiotic resistance gene was then removed from the inserted heterologous PCR fragment using Flp recombinase. This epitope tagging system was applied to global transcription factors of E. coli to obtain proteins fused with tandem c-myc epitope tags. The tandem myc epitope-fused transcription factors were successfully detected by Western blot analysis and chromatin immunoprecipitation with increased detection sensitivity and higher yield. Higher copy numbers of the epitope molecule allowed the use of more stringent experimental conditions to increase the signal-to-noise ratio in subsequent experimental applications. Furthermore, judging from the measurement of gene expression using reverse transcription PCR (RT-PCR), the epitope-fused transcription factors retained their normal function for gene regulation in vivo.
Recessive truncating titin gene, <i>TTN</i> , mutations presenting as centronuclear myopathy (2013)

Our study identifies truncating TTN mutations as a cause of congenital myopathy that is reported as CNM. Unlike the classic CNM genes that are all involved in excitation-contraction coupling at the triad, TTN encodes the giant sarcomeric protein titin, which forms a myofibrillar backbone for the components of the contractile machinery. This study expands the phenotypic spectrum associated with TTN mutations and indicates that TTN mutation analysis should be considered in cases of possible CNM without mutations in the classic CNM genes.
Recreating life-like motion in robotic limbs (2002)

A study in which the motion of living limbs was characterized and formulated for the control of mechanical limbs is discussed. Trajectories of human elbow joints performing a blind reaching motion were digitized and smoothed using an A/D converter on a personal computer. Waveforms for position over time were recorded and velocity and acceleration waveforms derived from them. Trajectories were normalized with respect to time and amplitude and a polynomial curve and its first two derivatives fitted to them. Finally, the human trajectories were compared to that of a robotic arm controlled by a biologically based algorithm using artificial nerve cells.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Development of radioimmunoassay for eel growth hormone. (1988)

A highly specific and homologous radioimmunoassay (RIA) for the measurement of growth hormone (GH) in the plasma and the pituitary of the eel was developed using a rabbit antiserum to eel GH. Two forms of eel GH: eGHI and II, were purified from the media from organ-cultures of pituitaries of the Japanese eel Anguilla japonica. An antiserum against eGH I, which does not distinguish between the two forms, was used to measure total GH levels. Pituitary extracts from the Japanese eel and the European eel A. anguilla exhibited displacement curves parallel to the eGHI standard, whereas extracts from chum salmon, rainbow trout, Japanese charr, carp, goldfish and tilapia pituitaries showed no cross-reactivity. GH or prolactin preparations from sheep, whale, chum salmon and tilapia also did not cross-react with the antibody. RIA sensitivity was 0.2ng/ml of plasma when 50μl of plasma were employed. Most of the plasma GH levels were low or undetectable in starved eels either in fresh water or in seawater, or in fed eels in fresh water. On the other hand, plasma samples from seawater-adapted male eels receiving injections of human chorionic gonadotropin showed high GH levels. Apparent plasma half-life of eGH I injected intravascularly through a cannula into the pneumogastric artery was about 15 min.
Gefitinib reverses breast cancer resistance protein–mediated drug resistance (2004)

Breast cancer resistance protein (BCRP) is an ATP binding cassette transporter that confers resistance to a series of anticancer agents such as 7-ethyl-10-hydroxycamptothecin (SN-38), topotecan, and mitoxantrone. In this study, we evaluated the possible interaction of gefitinib, a selective epidermal growth factor receptor tyrosine kinase inhibitor, with BCRP. BCRP-transduced human epidermoid carcinoma A431 (A431/BCRP) cells acquired cellular resistance to gefitinib, suggesting that BCRP could be one of the determinants of gefitinib sensitivity in a certain sort of cells. Next, the effect of gefitinib on BCRP-mediated drug resistance was examined. Gefitinib reversed SN-38 resistance in BCRP-transduced human myelogenous leukemia K562 (K562/BCRP) or BCRP-transduced murine lymphocytic leukemia P388 (P388/BCRP) cells but not in these parental cells. In addition, gefitinib sensitized human colon cancer HT-29 cells, which endogenously express BCRP, to SN-38. Gefitinib increased intracellular accumulation of topotecan in K562/BCRP cells and suppressed ATP-dependent transport of estrone 3-sulfate, a substrate of BCRP, in membrane vesicles from K562/BCRP cells. These results suggest that gefitinib may overcome BCRP-mediated drug resistance by inhibiting the pump function of BCRP. Furthermore, P388/BCRP-transplanted mice treated with combination of irinotecan and gefitinib survived significantly longer than those treated with irinotecan alone or gefitinib alone. In conclusion, gefitinib is shown to interact with BCRP. BCRP expression in a certain sort of cells is supposed to be one of the determinants of gefitinib sensitivity. Gefitinib inhibits the transporter function of BCRP and reverses BCRP-mediated drug resistance both in vitro and in vivo.
MOEA/D: A Multiobjective Evolutionary Algorithm Based on Decomposition (2007)

Decomposition is a basic strategy in traditional multiobjective optimization. However, it has not yet been widely used in multiobjective evolutionary optimization. This paper proposes a multiobjective evolutionary algorithm based on decomposition (MOEA/D). It decomposes a multiobjective optimization problem into a number of scalar optimization subproblems and optimizes them simultaneously. Each subproblem is optimized by only using information from its several neighboring subproblems, which makes MOEA/D have lower computational complexity at each generation than MOGLS and nondominated sorting genetic algorithm II (NSGA-II). Experimental results have demonstrated that MOEA/D with simple decomposition methods outperforms or performs similarly to MOGLS and NSGA-II on multiobjective 0-1 knapsack problems and continuous multiobjective optimization problems. It has been shown that MOEA/D using objective normalization can deal with disparately-scaled objectives, and MOEA/D with an advanced decomposition method can generate a set of very evenly distributed solutions for 3-objective test instances. The ability of MOEA/D with small population, the scalability and sensitivity of MOEA/D have also been experimentally investigated in this paper.
The Experimental Paradigm in Reverse Engineering: Role, Challenges, and Limitations (2006)

In many areas of software engineering, empirical studies are playing an increasingly important role. This stems from the fact that software technologies are often based on heuristics and are moreover expected to be used in processes where human intervention is paramount. As a result, not only it is important to assess their cost-effectiveness under conditions that are as realistic and representative as possible, but we must also understand the conditions under which they are more suitable and applicable. There exists a wealth of empirical methods aimed at maximizing the validity of results obtained through empirical studies. However, in the case of reverse engineering, as for other domains of investigation, researchers and practitioners are faced with specific constraints and challenges. This is the focus of this keynote address and what the current paper attempts to clarify
Oleoyl‐CoA is not an immediate substrate for fatty acid elongation in developing seeds of <i>Brassica napus</i> (1995)

Summary The substrate specificity of fatty acid elongase was studied using an oil body fraction from developing seeds of Brassica napus . ATP was essential for high rates of elongase activity, but there was no apparent requirement for oleoyl‐CoA, oleic acid (18:1) or CoA. Furthermore, 14 C from 18:1‐CoA was incorporated into eicosenoic (20:1) and erucic (22:1) acids at a much slower rate than 14 C from malonyl‐CoA. Incubation of [ 14 C]18:1‐CoA with the oil body fraction resulted in a rapid loss of [ 14 C]18:1‐CoA into several lipid fractions whether in the absence or presence of ATP, but the loss of 18:1‐CoA had a comparatively small effect on the overall rate of elongation. Acyl‐CoAs were derivatized to their respective acylbutylamide and analyzed by gas chromatography‐mass spectrometry. This analysis of acyl‐CoAs demonstrated that there was no detectable 20:1‐CoA or 22:1‐CoA at 0 min incubation, while newly synthesized 20:1‐CoA and 22:1‐CoA were present at 10 min. Analysis of the % 14 C of the substrates and products of the elongation reaction revealed that the endogenous pool of 18:1‐CoA is quite small in elongase preparations. In addition, [ 14 C]18:1‐CoA added to the incubation, although incorporated into lipids, was not significantly diluted by turnover or new synthesis. In contrast, the % 14 C of the 20:1‐CoA was two‐ to threefold less than that of the 18:1‐CoA. Taken together, these results indicate that the [ 14 C]18:1 from the [ 14 C]18:1‐CoA was diluted in an intermediate 18:1 pool and that the 18:1‐CoA was not the major donor of the acyl group to the elongase reaction.
Efficacy of non‐surgical treatments for androgenetic alopecia: a systematic review and network meta‐analysis (2018)

Androgenetic alopecia, or male/female pattern baldness, is the most common type of progressive hair loss disorder. The aim of this study was to review recent advances in non-surgical treatments for androgenetic alopecia and identify the most effective treatments. A network meta-analysis (NMA) was conducted of the available literature of the six most common non-surgical treatment options for treating androgenetic alopecia in both men and women; dutasteride 0.5 mg, finasteride 1 mg, low-level laser therapy (LLLT), minoxidil 2%, minoxidil 5% and platelet-rich plasma (PRP). Seventy-eight studies met the inclusion criteria, and 22 studies had the data necessary for a network meta-analysis. Relative effects show LLLT as the superior treatment. Relative effects show PRP, finasteride 1 mg (male), finasteride 1 mg (female), minoxidil 5%, minoxidil 2% and dutasteride (male) are approximately equivalent in mean change hair count following treatment. Minoxidil 5% and minoxidil 2% reported the most drug-related adverse events (n = 45 and n = 23, respectively). The quality of evidence of minoxidil 2% vs. minoxidil 5% was high; minoxidil 5% vs. placebo was moderate; dutasteride (male) vs. placebo, finasteride (female) vs. placebo, minoxidil 2% vs. placebo and minoxidil 5% vs. LLLT was low; and finasteride (male) vs. placebo, LLLT vs. sham, PRP vs. placebo and finasteride vs. minoxidil 2% was very low. Results of this NMA indicate the emergence of novel, non-hormonal therapies as effective treatments for hair loss; however, the quality of evidence is generally low. High-quality randomized controlled trials and head-to-head trials are required to support these findings and aid in the development of more standardized protocols, particularly for PRP. Regardless, this analysis may aid physicians in clinical decision-making and highlight the variety of non-surgical hair restoration options for patients.
A toolbox for simulation-based optimization of supply chains (2007)

In this paper we present a general framework for simulating and optimizing the operational decisions in a supply chain network. We developed a supply chain network library for the simulation software AnyLogic (copyXJ Technologies) and a linearized version as an optimization model implemented using XpressMP (copy Dash Optimization). Aggregated results for the simulation experiments are fed into the optimization model. The solution of the optimization model is used to improve operational decision in the supply chain. In order to gain good results this process is repeated until a stable solution is reached. This approach enriches the simulation framework by a powerful tool to improve the supply chain by simultaneously optimizing a large number of possible decisions.
Hole Mobility Behavior in Strained SiGe-on-SOI p-MOSFETs (2008)

A compressive strained SiGe channel grown-on-SOI structure which can be applicable to next generation high performance C-MOSFETs was applied to p-MOSFETs. The mobility behavior depending on effective fields, Eeff, was investigated by varying Ge concentrations in the SiGe layer. We confirmed that the mobility enhancement factor increases with both Ge concentration and Eeff, and quite depends on Eeff. In particular, we demonstrated that hole mobility enhancement factor at the effective fields of 0.13 MV/cm amounted to 1.51 for 34 at% Ge. In addition, we observed that the strain of 0.23 induced by 56.5-at% Ge concentration in SiGe grown-on-SOI structure could not increase hole mobility at the effective fields range from 0.05 to 0.13 MV/cm because of high density of dislocations.
A syntax-directed translation for the synthesis of delay-insensitive circuits (1994)

A syntax-directed translation procedure for the synthesis of delay-insensitive circuits from graph-theoretic specifications is presented. No isochronic fork assumption is required for the correct operation of the synthesized circuits. The synthesized circuits are different from those obtained from Ebergen's synthesis method. In Ebergen's circuits, the voltage levels of a set of wires are used to encode which input events are most recently received. Special circuit elements (the N-element or the RCEL element) and two-phase to four-phase converters are needed to change the voltage levels of the encoding wires when input events are received. In the circuits obtained from the method in this paper, the wires encoding which input events are most recently received are the outputs of the toggles. When input events are received, they are sent directly or via demultiplexers to the toggles to change the voltage levels at their outputs. Two-phase to four-phase converters are not needed. The synthesis method is compared with Ebergen's synthesis method.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Gating of IsK expressed in Xenopus oocytes depends on the amount of mRNA injected. (1994)

IsK is a K+ channel of the delayed rectifier type widely distributed throughout both excitable and nonexcitable cells. Its structure is different from other cloned K+ channels and molecular details of its gating remain obscure. Here we show that the activation kinetics of IsK expressed in Xenopus oocytes depend upon the amount of its mRNA injected, with larger amounts resulting in slower activation kinetics with a longer initial delay during activation. Similar changes in activation kinetics occur with time after a single injection of IsK mRNA. We present two kinetic schemes which illustrate how our experimental results could arise. Both imply an interaction among individual channel proteins during IsK activation. The dependence of channel gating on mRNA concentration provides a novel mechanism for long term regulation of ion current kinetics.
A locally encodable and decodable compressed data structure (2009)

In a variety of applications, ranging from highspeed networks to massive databases, there is a need to maintain histograms and other statistics in a streaming manner. Motivated by such applications, we establish the existence of efficient source codes that are both locally encodable and locally decodable. Our solution is an explicit construction in the form of a (randomized) data structure for storing N integers. The construction uses multi-layered sparse graph codes based on Ramanujan graphs, and has the following properties: (a) the structure utilizes minimal possible space, and (b) the value of any of the integers can be read or updated in near constant time (on average and with high probability). By contrast, data structures proposed in the context of streaming algorithms and compressed sensing in recent years (e.g., various sketches) support local encodability, but not local decodability; and those known as succinct data structures are locally decodable, but not locally encodable.
The common stress responsive transcription factor ATF3 binds genomic sites enriched with p300 and H3K27ac for transcriptional regulation (2016)

These results suggest that ATF3 likely bookmarks genomic sites and interacts with other transcription regulators to control gene expression.
NITSOL: A Newton Iterative Solver for Nonlinear Systems (1998)

We introduce a well-developed Newton iterative (truncated Newton) algorithm for solving large-scale nonlinear systems. The framework is an inexact Newton method globalized by backtracking. Trial steps are obtained using one of several Krylov subspace methods. The algorithm is implemented in a Fortran solver called NITSOL that is robust yet easy to use and provides a number of useful options and features. The structure offers the user great flexibility in addressing problem specificity through preconditioning and other means and allows easy adaptation to parallel environments. Features and capabilities are illustrated in numerical experiments.
Pharmacokinetics and effect on caffeine metabolism of the proton pump inhibitors, omeprazole, lansoprazole, and pantoprazole (1998)

The approximately 5 fold difference in AUC between EMs and PMs indicates that approximately 80% of the dose for all three proton pump inhibitors is metabolized by the polymorphically expressed CYP2C19. None of the three proton pump inhibitors, administered in therapeutically recommended doses, is an inducer of CYP1A2--neither in PMs nor in EMs.
Characterization of Landraces of rice following DUS guidelines (2012)

For the establishment of the distinctness among fifty one landraces of rice, fortysix characters were used. Characterization of fifty one landraces of rice was done using 46agro-morphological traits following Distinctiveness, Uniformity and Stability test (DUS)during kharif season of 2008 2009 and 2010 at the Zonal Adaptive Research Station,Krishnagar, Nadia, West Bengal. Out of fifty one varieties studied, twenty seven werefound to be distinctive on the basis of twenty two essential and twenty four additionalcharacters. This study will be useful for breeders, researchers and farmers to identify andchoose the restoration and conservation of beneficial genes for crop improvement andalso to seek protection under Protection of Plant Varieties and Farmerâ€™s Rights Act.
Fluorescence background suppression in Raman spectroscopy (2010)

Raman spectroscopy provides a non-invasive method to study biological samples. We demonstrate the powerful capabilities of our novel Raman modulation technique to detect weak Raman signals hidden by a strong fluorescent background.
A high performance current mirror for low voltage designs (2002)

A novel current mirror having high input and output voltage swing capability and which can operate at /spl plusmn/1.0 V supply, is proposed. PSPICE simulations confirm the input current range of 1 /spl mu/A to 500 /spl mu/A with 2 GHz bandwidth. Resistive and capacitive compensation are introduced to increase the bandwidth.
Evaluating the impact of automated intrusion response mechanisms (2003)

Intrusion detection systems (IDSs) have reached a high level of sophistication and are able to detect intrusions with a variety of methods. Unfortunately, system administrators neither can keep up with the pace that an IDS is delivering alerts, nor can they react upon these within adequate time limits. Automatic response systems have to take over that task. In case of an identified intrusion, these components have to initiate appropriate actions to counter emerging threats. Most current intrusion response systems (IRSs) utilize static mappings to determine adequate response actions in reaction to detected intrusions. The problem with this approach is its inherent inflexibility. Countermeasures (such as changes of firewall rules) often do not only defend against the detected attack but may also have negative effects on legitimate users of the network and its services. To prevent a situation where a response action causes more damage that the actual attack, a mechanism is needed that compares the severity of an attack to the effects of a possible response mechanism. In this paper, we present a network model and an algorithm to evaluate the impact of response actions on the entities of a network. This allows the IRS to select the response among several alternatives which fulfills the security requirements and has a minimal negative effect on legitimate users.