gebhart/patrepeval huggingface dataset:
The regulation of carotenoid formation in tomato fruit (2016)

Carotenoid biosynthesis in plants includes a complex series of desaturation/isomerisation reactions, catalyzed by four independent enzymes. In bacteria and fungi one desaturase/isomerase enzyme completes the same series of reactions. In the present study, a bacterial desaturase (crtI) from Pantoea ananatis has been overexpressed in the tangerine mutant of tomato (Solanum lycopersicon) which accumulates cis-carotene isomers in the fruit due to a defective isomerase (CRTISO) and the old gold crimson (og<sup>c</sup> ) tomato mutant, which is defective in the fruit-enhanced lycopene β-cyclase (CYCB). Comprehensive molecular and biochemical characterization of the resulting lines expressing crtI has revealed negative feedback mechanisms, acting predominantly at the level of phytoene synthase-1 (PSY1), and feed-forward mechanisms inducing cyclisation. In both cases, altered transcription appears to be the progenitor, with subsequent post-transcriptional modulation highlighting the complexity of the processes involved in modulating carotenoid homeostasis in plant tissues.
Reversible Enantiofacial Differentiation of a Single Heterocyclic Substrate by Supramolecular Receptors (2003)

Telling top and bottom apart: Supramolecular receptors can discriminate between the “top” and “bottom” sides of a single guest molecule, such as caffeine (see picture). This reversible enantiofacial differentiation results in the preferential formation of the α or β complexes.
Localization of intracellular triacylglycerol and cholesteryl ester transfer activity in rat tissues (1986)

A triacylglycerol and cholesteryl ester transfer activity has been isolated from rat liver. After homogenization, the liver cells were subfractionated into the 10 000 X g pellet, microsomal fraction and postmicrosomal supernatant. Most of the transfer activity appeared to be associated with the microsomal fraction. Rough and smooth microsomes contained nearly equal transfer activities. When isolated microsomes were subject to proteolytic attack, the transfer activity was not inactivated, unless it had been released from the microsomes prior to proteolytic treatment. This indicates that the activity is probably located within the microsomal vesicles. Similar transfer activities were found in the intestinal mucosa of rats, whereas little or no activity was detected in the brain, heart, kidney, or plasma.
Development of a C-band RF Gun with a Coniferous-tree-type Carbon Nanostructure Field Emission Cathode (2015)

A C-band RF gun for compact radiation sources such as a high energy x-ray and a terahertz radiation is developed at AIST, which is designed to work at the frequency of 5.3 GHz*. A coniferous-tree-type carbon nanostructure (CCNS) is used for a field emission cathode in the C-band RF gun. A graphene sheet composed of carbon has a coniferous form, and the tip has a nanometer-size tubular structure that becomes thicker on the substrate side**. Owing to this configuration, the CCNS has a large field enhancement factor, and is considered to be more stable in high electric fields than Carbon nanotubes. We have fabricated the C-band RF gun of the single cell cavity. Emission current depending on the electric field strength on the CCNS cathode surface was measured. When the electric field strength was 30 MV/m, the total charge per a macro pulse was 30 nC. After applying a stronger electric field, a decline of the field enhancement factor was observed. We will present the experimental result of the field emission measurement of the CCNS and the simulation result of a beam trajectory using a C-band RF gun of a multi cell cavity.
Measurement of the cross section fortt¯production inpp¯collisions using the kinematics of lepton+jets events (2005)

We present a measurement of the top pair production cross section in $p\overline{p}$ collisions at $\sqrt{s}=1.96\text{ }\text{ }\mathrm{TeV}$. We collect a data sample with an integrated luminosity of $194\ifmmode\pm\else\textpm\fi{}11\text{ }\text{ }{\mathrm{pb}}^{\ensuremath{-}1}$ with the CDF II detector at the Fermilab Tevatron. We use an artificial neural network technique to discriminate between top pair production and background processes in a sample of 519 lepton+jets events, which have one isolated energetic charged lepton, large missing transverse energy and at least three energetic jets. We measure the top pair production cross section to be ${\ensuremath{\sigma}}_{t\overline{t}}=6.6\ifmmode\pm\else\textpm\fi{}1.1\ifmmode\pm\else\textpm\fi{}1.5\text{ }\text{ }\mathrm{pb}$, where the first uncertainty is statistical and the second is systematic.
Nitazoxanide for the Treatment of Blastocystis hominis in Patients with Irritable Bowel Syndrome (2009)

Purpose: Blastocystis hominis is a protozoan commonly found in the human digestive tract. Surveillance studies from the United States and Europe indicate 11-38% of the population may be infected with this organism. However, the pathogenicity of Blastocystis hominis is controversial despite increasing evidence supporting the role of this protozoan in digestive disorders. While patients with Blastocystis hominis may be asymptomatic, studies indicate a strong association between Blastocystis hominis infection and irritable bowel syndrome (IBS). Nitazoxanide is a thiazolide antibiotic indicated for the treatment of Cryptosporidium parvum and Giardia lamblia in adults and in children. Nitazoxanide also has activity against Blastocystis hominis in both in vivo and in vitro studies. This abstract reports on the use of nitazoxanide for the eradication of Blastocystis hominis in patients with IBS. Methods: Patients with a diagnosis of IBS by ROME II/III criteria had their stool examined via microscopy (Diagnos-Techs, Inc., Kent, WA) for the presence of Blastocystis hominis as part of their serial workup. Those with positive stools were then treated with nitazoxanide 1g twice daily for 14 days. Upon follow-up examination patients had their stools rechecked for the presence of Blastocystis hominis and they were re-evaluated for their IBS symptoms. Microbiologic cure was defined as those with negative stools for Blastocystis hominis after therapy. Clinical response was defined as resolution of IBS related symptoms. Results: Overall 22 patients with IBS were treated for Blastocystis hominis infection, of which there were 10 males and 12 females. The mean age of the population was 53 years. A microbiologic cure was achieved in 82% (18/22) of the patients and a clinical cure in 86% (19/22) of the patients. There was an excellent correlation between the eradication of Blastocystis hominis and the resolution of IBS symptoms, 94% (17/18). Nitazoxanide was well tolerated with most patients reporting yellowing of the urine, and a few complaining of gastrointestinal discomfort during therapy which had resolved at follow-up. Conclusion: In this study, nitazoxanide was effective for the treatment of Blastocystis hominis infection. The pathogenic role of Blastocystis hominis remains unclear, however it should be considered a potential pathogen in symptomatic patients. Furthermore, in patients with IBS, Blastocystis hominis should be considered in the differential diagnosis. Disclosure: Dr Stuppy - Unrestricted educational grant Romark Labs.
Radon alpha-ray detector based on a high-resistivity-silicon BJT and a low-cost readout electronics (2008)

Radon dosimetry yields valuable information about radioactive health risks in closed environments. Indeed, World Health Organization (WHO) and the International Agency for Research on Cancer (IARC) have recently classified radon as a human carcinogen and have demonstrated a correlation between environmental radon concentration and lung cancer risk. Dose measurements are traditionally based on laboratory analysis of alpha-ray traces in ionization chambers exposed to environmental air. In this paper we propose a portable instrument for real-time radon alpha-ray detection based on a previously-developed high-resistivity-silicon BJT sensor and a low-cost, IC-based readout electronics.
Melon Playlist Dataset: A Public Dataset for Audio-Based Playlist Generation and Music Tagging (2021)

One of the main limitations in the field of audio signal processing is the lack of large public datasets with audio representations and high-quality annotations due to restrictions of copyrighted commercial music. We present Melon Playlist Dataset, a public dataset of mel-spectrograms for 649,091 tracks and 148,826 associated playlists annotated by 30,652 different tags. All the data is gathered from Melon, a popular Korean streaming service. The dataset is suitable for music information retrieval tasks, in particular, auto-tagging and automatic playlist continuation. Even though the latter can be addressed by collaborative filtering approaches, audio provides opportunities for research on track suggestions and building systems resistant to the cold-start problem, for which we provide a baseline. Moreover, the playlists and the annotations included in the Melon Playlist Dataset make it suitable for metric learning and representation learning.
Nicotinoyl Azide (NCA)-Mediated Mitsunobu Reaction: An Expedient One-Pot Transformation of Alcohols into Azides (2004)

A practical and simple method that allows preparation of azides from alcohols is described. The process involves oxyphosphonium-type activation and it is based upon the use of nicotinoyl azide (NCA), a cheap and easily accessible azide ion source.
Perlecan Functions in Chondrogenesis: Insights from in vitro and in vivo Models (2004)

Perlecan is a large heparan sulfate proteoglycan that is typically found in basal lamina of adult and embryonic tissues. Recent studies have demonstrated that perlecan accumulates impressively during cartilage development and is maintained as the major heparan sulfate proteoglycan of adult cartilage. In vertebrates, perlecan mutations result in skeletal defects. Moreover, in vitro studies indicate that perlecan can stimulate early stages of cartilage differentiation and cooperate with chondrogenic growth factors to promote this process. This short article will summarize these results and propose a model for perlecan function that incorporates these genetic and cell biological findings.
A Missing PD-L1/PD-1 Coinhibition Regulates Diabetes Induction by Preproinsulin-Specific CD8 T-Cells in an Epitope-Specific Manner (2013)

Coinhibitory PD-1/PD-L1 (B7-H1) interactions provide critical signals for the regulation of autoreactive T-cell responses. We established mouse models, expressing the costimulator molecule B7.1 (CD80) on pancreatic beta cells (RIP-B7.1 tg mice) or are deficient in coinhibitory PD-L1 or PD-1 molecules (PD-L1(-/-) and PD-1(-/-) mice), to study induction of preproinsulin (ppins)-specific CD8 T-cell responses and experimental autoimmune diabetes (EAD) by DNA-based immunization. RIP-B7.1 tg mice allowed us to identify two CD8 T-cell specificities: pCI/ppins DNA exclusively induced K(b)/A(12-21)-specific CD8 T-cells and EAD, whereas pCI/ppinsΔA(12-21) DNA (encoding ppins without the COOH-terminal A(12-21) epitope) elicited K(b)/B(22-29)-specific CD8 T-cells and EAD. Specific expression/processing of mutant ppinsΔA(12-21) (but not ppins) in non-beta cells, targeted by intramuscular DNA-injection, thus facilitated induction of K(b)/B(22-29)-specific CD8 T-cells. The A(12-21) epitope binds K(b) molecules with a very low avidity as compared with B(22-29). Interestingly, immunization of coinhibition-deficient PD-L1(-/-) or PD-1(-/-) mice with pCI/ppins induced K(b)/A(12-21)-monospecific CD8 T-cells and EAD but injections with pCI/ppinsΔA(12-21) did neither recruit K(b)/B(22-29)-specific CD8 T-cells into the pancreatic target tissue nor induce EAD. PpinsΔA(12-21)/(K(b)/B(22-29))-mediated EAD was efficiently restored in RIP-B7.1(+)/PD-L1(-/-) mice, differing from PD-L1(-/-) mice only in the tg B7.1 expression in beta cells. Alternatively, an ongoing beta cell destruction and tissue inflammation, initiated by ppins/(K(b)/A(12-21))-specific CD8 T-cells in pCI/ppins+pCI/ppinsΔA(12-21) co-immunized PD-L1(-/-) mice, facilitated the expansion of ppinsΔA(12-21)/(K(b)/B(22-29))-specific CD8 T-cells. CD8 T-cells specific for the high-affinity K(b)/B(22-29)- (but not the low-affinity K(b)/A(12-21))-epitope thus require stimulatory help from beta cells or inflamed islets to expand in PD-L1-deficient mice. The new PD-1/PD-L1 diabetes models may be valuable tools to study under well controlled experimental conditions distinct hierarchies of autoreactive CD8 T-cell responses, which trigger the initial steps of beta cell destruction or emerge during the pathogenic progression of EAD.
Detection of eye blinks from EEG signals for home lighting system activation (2009)

The improvement in the development of lighting system has not considered eye blinking activity as a parameter to activate the system. In addition, the use of eye blink extracted from EEG signal has not been investigated. This study examines a suitable eye activity for activating home lighting system and then detects the occurrence of this activity from EEG signals. Two types of eye activity were analysed; eye blinks and eye movements. It was found that EEG signal obtained from voluntary eye blink condition produces clearer signals with larger amplitude than that obtained from eye movements. An efficient algorithm for detecting the occurrence of eye blinks was then developed and its performance was investigated. Using this algorithm, the required eye blinks could be detected successfully from 85% of the records. Results from this study show that with proper filtering and accurate detection, the eye blinks could be used for activating home lighting system.
Beta-Cell Function in Obesity (2004)

In nondiabetic subjects, obesity is associated with a modest expansion of beta-cell mass, possibly amounting-according to the best available estimates-to 10-30% for each 10 kg of weight excess. Whether age of onset and duration of obesity, recent changes in body weight, and body fat distribution have any effect on beta-cell mass in humans is unknown. Both fasting insulin secretion and the total insulin response to oral glucose have the following characteristics: 1) they increase with BMI in an approximately linear fashion, 2) both fat-free and fat mass are significant positive correlates, and 3) BMI exerts a positive effect separate from that of insulin resistance (i.e., obesity may be a state of primary insulin hypersecretion). The mechanisms are currently unknown, though chronic small increments in plasma glucose may play a role. In contrast, dynamic properties of beta-cell function, such as glucose sensitivity (i.e., dose-response function), rate sensitivity, and potentiation, do not appear to be substantially altered by the presence of obesity, body fat distribution, or insulin resistance as long as glucose tolerance is maintained. Weight loss, by diet or restrictive bariatric surgery, is associated with consensual decrements in insulin resistance and insulin hypersecretion. The latter, however, seems to be more persistent, suggesting that the postobese state may reproduce the primary insulin hypersecretion of the obese state. Malabsorptive bariatric surgery, in contrast, normalizes insulin sensitivity and abolishes insulin hypersecretion even before achievement of ideal body weight. Lipid-triggered messages from the gastrointestinal tract to the insulin target tissues and endocrine pancreas are the subject of intense investigation.
Improved day ahead heating demand forecasting by online correction methods (2019)

To reduce the heating and cooling energy demand of buildings and districts novel control strategies are constantly being developed that require information on the future demand of the controlled entity. Demand forecasting is commonly done with deterministic white box models or fitted grey-box models, however, recently more and more data and machine learning based approaches are being developed. All approaches have weaknesses: white-box models require major modelling effort, grey-box approaches are limited by their model or parameter complexity and machine learning is dependent on hyperparameters, some of which are randomly chosen, and therefore considered unreliable. Here we develop a forecasting approach based on Artificial Neural Networks (ANN) and introduce error correction methods based on online learning and the learned autocorrelation of the forecasting error. We compare the approach to other regression based and grey-box methods in a real case study of a small-scale district energy system with mixed use and unknown lower-level control. We show that the proposed method outperforms the other forecasting methods in terms of average error and coefficient of determination. We further demonstrate that in our case study the error correction methods significantly reduce variance in ANN performance created by randomly initialized parameters in the networks.
Rational Redesign of Inhibitors of Furin/kexin Processing Proteases. (2001)

Furin/kexin processing proteases catalyze the proteolysis of large protein precursors involved in many biological processes, such as zymogen activation, peptide hormone synthesis, viral protein processing and receptor maturation, making them potential targets for therapeutic agents. Herein, homology modeling and weighted evolutionary tracing were combined to investigate the interactionmechanism of furin/kex2 with eglin C mutants. The model structures showed that there were many acidic residues in the furin (kex2) binding interface, contributing to specificity for multiple basic residues of their corresponding substrates or inhibitors. Besides, some rational explanations were presented for the different inhibitor/substrate specificity of the furin/kexin members by combining the model structures with results of evolutionary tracing. Based on these analyses,an attempt was made to rationally redesign the eglin C by interface engineering with heterogeneous self-consistent ensemble optimization to improve its inhibitory specificity on furin/kex2. With the model complex structures of furin/kex2 and eglin C variants as structural templates, the P(1), P(2) and P(4) of eglin C were redesigned, respectively. The design results show that both furin and kex2 favored basic residues at P(1), P(2) and P(4) in eglin C, in good agreement with the experimental data. The detection of many specific residues in S' part of furin/kexin sequences made possible designing inhibitors with high specific binding to furin and kex2, respectively. As for furin, the best inhibitor designed was eglin C-P(2)'Glu-P(3)'Asp-P(4)'Arg (only these three positions were shown), while the best eglin C variant for kex2 designed was P(2)'Arg-P(3)'Arg-P(4)'Glu. The structures show that furin and kex2 form distinct interactions with these two eglin C variants. Herein, a strategy was proposed that combine homology modeling, evolutionary tracing and rational interface redesign to investigate enzyme-inhibitor interactions and inhibitor engineering. This computational design gives some rational guidance to further experimental inhibitor engineering.
ChemInform Abstract: STRUCTURE AND SYNTHESIS OF A SPIROCYCLIC PHOSPHORANIDE ANION: MODEL OF AN INTERMEDIATE IN A SN2(P) REACTION (1983)

Abstract Das wie bekannt durch Umsetzung von (I) und (II) im Bombenrohr synthetisierte Hydrophosphoran (III) unterwirft sich einer Säure‐Basen‐Reaktion mit Triethylamin unter Bildung des spirocyclischen Phosphoranids (IV).
An Improved Drop-fall Algorithm Based on Background Analysis for Handwritten Digits Segmentation (2009)

Among several contour splitting algorithms, Drop-fall algorithm has shown good performance, but it is defective in locating the start point of the algorithm and the seeping process in vertical direction inside character stroke block. For the purpose of solving the problems produced by the defections, in this paper Drop-fall algorithm is improved by citing water reservoir concept to use the information coming from the background region of touching digits. On the basis of the topological features of background region, the range of searching start point in algorithm is dictated and the optimal position for the seeping process is determined. For connected digits sharing a long stroke segment, instead of the seeping process in vertical direction, centerline is extracted from common touching area to be used as a long tilt path which is cutting across the black block when the drop enters the junction of connected digits. Experimental results show that the improved algorithm obtains more satisfied segmentation and works better than former.
Thrombosis following desmopressin for uremic bleeding (1988)

An elderly patient with evidence of atherosclerosis and uremic bleeding diathesis developed two foci of cerebral thrombosis immediately after an infusion of desmopressin (DDAVP). Because large molecular weight multimers of von Willebrand factor (vWF) have been demonstrated to cause platelet aggregation under conditions of elevated fluid shear stress as occurs in atherosclerotic vessels, we investigated his plasma vWF at the time of the event and compared it to baseline values obtained 2 weeks later. Unusually large vWF multimers induced by the DDAVP infusion were present and likely contributed to the thrombotic process. Consequently, we believe DDAVP should be given with greater caution to patients with atherosclerosis.
Using the local immune response to identify vaccine and diagnostic candidates for Asian schistosomiasis: a novel phage display approach (2017)

Schistosomiasis is one of the most important parasitic diseases in the world, causing high levels of morbidity in the approximately 200 million people that are infected. Chemical therapeutic treatment of infection is currently the only effective mechanism to combat the disease; however this treatment regime has limitations, most significantly that treatment does not prevent re-infection. This thesis developed a new method to identify parasite molecules that could be developed as vaccine and better diagnostic reagents to help combat this insidious disease.
ABCG2/BCRP Expression Modulates d -Luciferin–Based Bioluminescence Imaging (2007)

Bioluminescence imaging (BLI) is becoming indispensable to the study of transgene expression during development and, in many in vivo models of disease such as cancer, for high throughput drug screening in vitro. Because reaction of d-luciferin with firefly luciferase (fLuc) produces photons of sufficiently long wavelength to permit imaging in intact animals, use of this substrate and enzyme pair has become the method of choice for performing BLI in vivo. We now show that expression of the ATP-binding cassette (ABC) family transporter ABCG2/BCRP affects BLI signal output from the substrate d-luciferin. In vitro studies show that d-luciferin is a substrate for ABCG2/BCRP but not for the MDR1 P-glycoprotein (ABCB1/Pgp), multidrug resistance protein 1 (MRP1/ABCC1), or multidrug resistance protein 2 (MRP2/ABCC2). d-Luciferin uptake within cells is shown to be modulated by ABC transporter inhibitors, including the potent and selective ABCG2/BCRP inhibitor fumitremorgin C. Images of xenografts engineered to express transgenic ABCG2/BCRP, as well as xenografts derived from the human prostate cancer cell line 22Rv1 that naturally express ABCG2/BCRP, show that ABCG2/BCRP expression and function within regions of interest substantially influence d-luciferin-dependent bioluminescent output in vivo. These findings highlight the need to consider ABCG2/BCRP effects during d-luciferin-based BLI and suggest novel high throughput methods for identifying new ABCG2/BCRP inhibitors.