gebhart/patrepeval huggingface dataset:
RNA-Seq Analysis and De Novo Transcriptome Assembly of Jerusalem Artichoke (Helianthus tuberosus Linne) (2014)

Jerusalem artichoke (Helianthus tuberosus L.) has long been cultivated as a vegetable and as a source of fructans (inulin) for pharmaceutical applications in diabetes and obesity prevention. However, transcriptomic and genomic data for Jerusalem artichoke remain scarce. In this study, Illumina RNA sequencing (RNA-Seq) was performed on samples from Jerusalem artichoke leaves, roots, stems and two different tuber tissues (early and late tuber development). Data were used for de novo assembly and characterization of the transcriptome. In total 206,215,632 paired-end reads were generated. These were assembled into 66,322 loci with 272,548 transcripts. Loci were annotated by querying against the NCBI non-redundant, Phytozome and UniProt databases, and 40,215 loci were homologous to existing database sequences. Gene Ontology terms were assigned to 19,848 loci, 15,434 loci were matched to 25 Clusters of Eukaryotic Orthologous Groups classifications, and 11,844 loci were classified into 142 Kyoto Encyclopedia of Genes and Genomes pathways. The assembled loci also contained 10,778 potential simple sequence repeats. The newly assembled transcriptome was used to identify loci with tissue-specific differential expression patterns. In total, 670 loci exhibited tissue-specific expression, and a subset of these were confirmed using RT-PCR and qRT-PCR. Gene expression related to inulin biosynthesis in tuber tissue was also investigated. Exsiting genetic and genomic data for H. tuberosus are scarce. The sequence resources developed in this study will enable the analysis of thousands of transcripts and will thus accelerate marker-assisted breeding studies and studies of inulin biosynthesis in Jerusalem artichoke.
Human cerebral organoids capture the spatiotemporal complexity and disease dynamics of UBE3A (2019)

SUMMARY Human neurodevelopment and its associated diseases are complex and challenging to study. This has driven recent excitement for human cerebral organoids (hCOs) as research and screening tools. These models are steadily proving their utility; however, it remains unclear what limits they will face in recapitulating the complexities of neurodevelopment and disease. Here we show that their utility extends to key (epi)genetic and disease processes that are complex in space and time. Specifically, hCOs capture UBE3A’s dynamically imprinted expression and subcellular localization patterns. Furthermore, given UBE3A’s direct links to Angelman Syndrome and Autism Spectrum Disorder, we show that hCOs respond to candidate small molecule therapeutics. This work demonstrates that hCOs can provide important insights to focus the scope of mechanistic and therapeutic strategies including revealing difficult to access prenatal developmental time windows and cell types key to disease etiology.
Emissive color preferences of Colorado potato beetle larvae (2011)

The Colorado potato beetle, Leptinotarsa decemlineata (Say), is an important pest of potato, as well as other solanaceous crops. While orientation of adult beetles to visual stimuli has been reported, nothing, up until now, has been known about whether the larvae also display positive phototactic behavior. In this study, we investigated the orientation behavior of Colorado potato beetle larvae in response to emissive colors produced by light emitting diodes of narrow band widths in a dual-choice arena adapted to a servosphere. Our results show that the larvae preferred to orient toward blue (472 nm), orange (590 nm), red (660 nm), green (570 nm), white (420–775 nm), and yellow (585 nm) over darkness when both alternatives were offered. No orientation preferences were elicited by infrared (940 nm) or ultraviolet (351 nm) light. When paired light choices were offered, the larvae showed a strong preference to some wavelengths more than others. This research characterizes visual preferences for Colorado potato beetle larvae and suggests that visual cues may be important in host plant orientation for these larvae, and perhaps, other immature insects. Our results suggest the potential for using photic stimuli for manipulation of larvae for control strategies. This research was carried out during the sabbatical leave of V.D.C.S. at the USDA, Beltsville, MD
Across kingdom biased CYP-mediated metabolism via small-molecule ligands docking on P450 oxidoreductase (2020)

Abstract Metabolic control is mediated by the dynamic assemblies and function of multiple redox enzymes. A key element in these assemblies, the P450 oxidoreductase (POR), donates electrons and selectively activates numerous (&gt;50 in humans and &gt;300 in plants) cytochromes P450 (CYPs) controlling metabolism of drugs, steroids and xenobiotics in humans and natural product biosynthesis in plants. The mechanisms underlying POR-mediated CYP metabolism remain poorly understood and to date no ligand binding has been described to regulate the specificity of POR. Here, using a combination of computational modeling and functional assays, we identified ligands that dock on POR and bias its specificity towards CYP redox partners. Single molecule FRET studies revealed ligand docking to alter POR conformational sampling, which resulted in biased activation of metabolic cascades in whole cell assays. We propose the model of biased metabolism , a mechanism akin to biased signaling of GPCRs, where ligand docking on POR stabilizes different conformational states that are linked to distinct metabolic outcomes. Biased metabolism may allow designing pathway-specific therapeutics or personalized food suppressing undesired, disease related, metabolic pathways.
Effect of Granulocyte-Macrophage Colony-Stimulating Factor With or Without Supervised Exercise on Walking Performance in Patients With Peripheral Artery Disease (2017)

clinicaltrials.gov Identifier: NCT01408901.
Vitamin K and hepatocellular carcinoma: The basic and clinic (2015)

Vitamin K (VK), which was originally identified as a cofactor involved in the production of functional coagulation factors in the liver, has been shown to be involved in various aspects of physiological and pathological events, including bone metabolism, cardiovascular diseases and tumor biology. The mechanisms and roles of VK are gradually becoming clear. Several novel enzymes involved in the VK cycle were identified and have been shown to be linked to tumorigenesis. The VKs have been shown to suppress liver cancer cell growth through multiple signaling pathways via the transcription factors and protein kinases. A VK2 analog was applied to the chemoprevention of hepatocellular carcinoma (HCC) recurrence after curative therapy and was shown to have beneficial effects, both in the suppression of HCC recurrence and in patient survival. Although a large scale randomized control study failed to demonstrate the suppression of HCC recurrence, a meta-analysis suggested a beneficial effect on the long-term survival of HCC patients. However, the beneficial effects of VK administration alone were not sufficient to prevent or treat HCC in clinical settings. Thus its combination with other anti-cancer reagents and the development of more potent novel VK derivatives are the focus of ongoing research which seeks to achieve satisfactory therapeutic effects against HCC.
Linking postglacial landscapes to glacier dynamics using swath radar at Thwaites Glacier, Antarctica - Supporting Data (2019)

This archive contains profile and gridded radar data referenced in the paper "Linking postglacial landscapes to glacier dynamics using swath radar at Thwaites Glacier, Antarctica", published in the journal Geology in 2019.
Colonic motor response to eating: a manometric investigation in proximal and distal portions of the viscus in man. (1989)

The motor response of the human colon to a meal is still poorly characterized. Such data as are available were obtained chiefly for the distal colonic portions with myoelectrical techniques. For these reasons, we investigated proximal and distal colonic motor responses to food ingestion in a rather large group of healthy subjects. Twenty-nine healthy volunteers were studied with a colonoscopically positioned multilumen manometric probe and low-compliance infusion system. Recordings were obtained for 2 h during fasting and for 3 h after the subjects had eaten a 1000-kcal standard mixed meal. During fasting, motility was quite low, and no significant differences between proximal and distal portions were seen. After eating, each portion significantly increased its motor activity throughout the subsequent recording period, but there were differences in the time course in the response to eating for different colonic segments. Proximal portions (especially the transverse colon) had first a sudden maximal increase and then a decrease, whereas the distal ones had a slower and more sustained increase in activity. These findings are of interest, especially for comparison with those of patients with suspected motor dysfunction of the large bowel.
Characterization of the Electron Beam Curing of Cationic Polymerization of Diglycidylether of Bisphenol A Epoxy Resin (2005)

The characterization of electron beam (E-beam) curing of diglycidyl-ether of bisphenol A-diaryliodonium hexafluoroantimonate epoxy resin-initiator system is reported as a function of (i) diaryliodonium hexafluoroantimonate catalyst (initiator) concentrations of 0.1-10 parts per hundred (phr) and (ii) total electron beam doses of 5-150 kilogray (kGy). The in situ E-beam temperature of the resin is monitored as a function of dose-time characteristics. The degree of cure is monitored after radiation exposure by Fourier transform infrared spectrometry (FTIR) and the glass transition temperatures (T g ) by differential scanning calorimetry (DSC). The degree of cure and cure rate increased with total dose exposure and initiator concentration. The maximum cure rate occurred at 5 kGy exposure and, thereafter, decreased as reactive species concentration decreased. The maximum in situ E-beam temperature of 76°C was recorded for the resin containing 10 phr of initiator, with a maximum degree of cure of 94% and a glass transition temperature of 86 C, indicating that the cure reactions under E-beam are glassy state diffusion controlled. The resin glass transition temperatures are considerably lower than the thermally cured glass transition temperatures of 170 C because of H 2 O termination reactions at the lower E-beam cure temperatures that result in a poor cross-linked network. In addition, the diaryliodonium hexafluoroantimonate catalytic activity for epoxide cationic polymerization is retarded by H 2 O. E-beam exposure causes the diaryliodonium hexafluoroantimonate to dissociate into active catalytic species, such as HSbF 6 , well below 100°C compared to catalytic thermal induced dissociation near 200°C. The E-beam cure reaction rate is modeled as a function of degree of cure and dose exposure by a standard autocatalytic kinetic model.
Synthesis of [<sup>13</sup>C<sub>6</sub>]primaquine (2013)

In support of a program to identify toxic metabolites of the antimalarial, primaquine, its [(13)C6] analog was prepared from [(13)C6] anisole in seven steps.
Enhancement of device performance of organic solar cells by an interfacial perylene derivative layer (2010)

We report that device performance of organic solar cells consisting of zinc phthalocyanine and fullerene (C(60)) can be enhanced by insertion of a perylene derivative interfacial layer between fullerene and bathocuproine (BCP) exciton blocking layer (EBL). The morphology of the BCP is influenced by the underlying N,N'-dihexyl-perylene-3,4,9,10-bis(dicarboximide) (PTCDI-C6), which promotes migration of the cathode metal into the BCP layer. Insertion of a PTCDI-C6 layer between fullerene and BCP layers enhances the power conversion efficiency to 2.5%, an improvement of 32% over devices without PTCDI-C6 layer. The enhancement in device performance by insertion of PTCDI-C6 is attributed to a reduction in series resistance due to promoted metal migration into BCP and optimized optical interference effects in multilayered devices.
Polyethylene Glycol in the Treatment of Experimental Diffuse Brain Injury (2009)

McCanna, Shannon P. M.D.; Bradbury, Jamie L. M.D.; Smucker, Philip Yoder M.D.; Koob, Andrew Ph.D.; Shapiro, Scott A. M.D.; Borgens, Richard B. Ph.D.
Elevated Serum Angiopoietin-like Protein 2 Correlates with the Metastatic Properties of Colorectal Cancer: A Serum Biomarker for Early Diagnosis and Recurrence (2014)

Serum ANGPTL2 is a novel diagnostic and recurrence-predictive biomarker in patients with colorectal cancer.
Designing a Green Replacement for the Lindlar Catalyst for Alkyne Semi-hydrogenation Using Silica-Supported Nickel Nanoparticles Modified by N-Doped Carbon (2022)

A lead- and palladium-free alternative to the Lindlar catalyst has been developed for industrially relevant alkyne semi-hydrogenation using silica-supported nickel nanoparticles modified by nitrogen-doped carbon. The optimal nickel catalyst acts under mild conditions (5 bar H2, 100 °C, and 4 h) for the selective semi-hydrogenation of a range of alkynes, including vitamin precursors that are important food supplements. Notably, this novel catalyst is selective for alkynes in the presence of easily reducible groups such as carbonyl and nitrile, which also makes it attractive for other synthetic applications.
A Quantitative Determination of 4-Methylthio-3-Butenyl Glucosinolate in Daikon (Raphanus sativus L.) Roots by Gas Liquid Chromatography (1989)

A method was developed for the quantitative determination of 4-methylthio-3-butenyl glucosinolate, which is predominantly contained in daikon root, using gas chromatography (GC) after enzymatic conversion to its isothiocyanate. This method is based on the extraction of glucosinolate with ethanol, purification with anion exchange resin, and hydrolysis with crude myrosinase which was prepared from daikon root. The formed 4-methylthio-3-butenyl isothiocyanate was dissolved into methylene chloride, and measured by GC. The coefficient of variance of 5 samples from one daikon root was about 4% through all procedures in this method.
Diverse Heterocycles from a Naphthofuran Hydroxypropenone Sodium Salt Synthon (2012)

Key words pyrazolo[5,1-c]triazines - pyrazolo[1,5-a]pyrimidines - naphthofurans - Japp–Klingemann reaction - Michael addition
A Protein Microsensor by Detection of Leakage Current from Interaction between an Electrolyte-Entrapping Liposome and Protein (2009)

Abstract We have newly made a specific biomolecule microsensor measuring leakage current and impedance with minute liposome solution that interacts with biomolecules such as protein. The microsensor was fabricated with a Si surface-bulk-micromachining process. K 4 [Fe(CN) 6 ] solution was entrapped inside of liposome of 1,2-dipalmitoyl- sn -glycero-3-phosphocholline (DPPC) and Carbonic Anhydrase from Bovine (CAB) was used as added protein for the interaction. A clear leakage in nA order was observed for the CAB, indicating the microsensor detects the CAB through the liposome-protein interaction. The detectivity increased by about 7 times and the volume of solution was decreased by about 10,000 from the previous result.
Low-loss and low-dispersion-slope highly nonlinear fibers (2005)

In recent technologies, various optical signal processing systems have been reported. In many of these applications, highly nonlinear fibers (HNLFs) are used as key parts. Especially, low loss and low dispersion slope are critical features of the HNLFs. In this paper, their design and characteristics, packaging technology, and applications are introduced.
Hybrid multichannel signal separation using supervised nonnegative matrix factorization with spectrogram restoration (2014)

In this paper, we propose a new hybrid method that concatenates directional clustering and advanced nonnegative matrix factorization (NMF) for the purpose of the specific sound extraction from the multichannel music signal. Multichannel music signal separation technology is aimed to extract a specific target signal from observed multichannel signals that contain multiple instrumental sounds. In the previous studies, various methods using NMF have been proposed, but they remain many problems, e.g., poor convergence in update rules in NMF and lack of robustness. To solve these problems, we propose a new supervised NMF (SNMF) with spectrogram restoration and its hybrid method that concatenates the proposed SNMF after directional clustering. Via extrapolation of supervised spectral bases, the proposed SNMF attempts both target signal separation and reconstruction of the lost target components, which are generated by preceding directional clustering. In addition, we theoretically reveal the trade-off between separation and extrapolation abilities and propose a new scheme for multi-divergence, where optimal divergence can be automatically changed in each time frame according to the local spatial conditions. The results of an evaluation experiment show that our proposed hybrid method outperforms the conventional music signal separation methods.
Data from Noninvasive Measurement of mTORC1 Signaling with &lt;sup&gt;89&lt;/sup&gt;Zr-Transferrin (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; mTOR regulates many normal physiological processes and when hyperactive can drive numerous cancers and human diseases. However, it is very challenging to detect and quantify mTOR signaling noninvasively in clinically relevant animal models of disease or man. We hypothesized that a nuclear imaging tool measuring intracellular mTOR activity could address this unmet need.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental Design:&lt;/b&gt; Although the biochemical activity of mTOR is not directly amenable to nuclear imaging probe development, we show that the transferrin receptor can be used to indirectly measure intracellular changes in mTOR activity.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; After verifying that the uptake of radiolabeled transferrin (the soluble ligand of the transferrin receptor) is stimulated by active mTORC1 &lt;i&gt;in vitro&lt;/i&gt;, we showed that &lt;sup&gt;89&lt;/sup&gt;Zr-labeled transferrin (Tf) can measure mTORC1 signaling dynamics in normal and cancerous mouse tissues with PET. Finally, we show that &lt;sup&gt;89&lt;/sup&gt;Zr-Tf can detect the upregulation of mTORC1 by tumor cells to escape the antitumor effects of a standard-of-care antiandrogen, which is to our knowledge the first example of applying PET to interrogate the biology of treatment resistant cancer.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusions:&lt;/b&gt; In summary, we have developed the first quantitative assay to provide a comprehensive measurement of mTOR signaling dynamics &lt;i&gt;in vivo&lt;/i&gt;, in specific normal tissues, and during tumor development in genetically engineered animal models using a nuclear imaging tool that is readily translatable to man. &lt;i&gt;Clin Cancer Res; 23(12); 3045–52. ©2016 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
Capture of Magnetic Microspheres in Electrokinetic Flow for Application in Lab-on-Chip Devices (2012)

Isolation of bio-molecules, cells and pathogens for immunoassays is a critical component in micro total analysis systems (μTAS). Magnetophoretic technique is often used for separation of such target species, where magnetic beads tagged with specific antibodies against cell surface epitopes, are captured in the microfluidic device. In this study, a numerical model is developed for capture of beads under an external magnetic field in electrokinetically driven flow. The results indicate an increase in the number of beads captured when the magnetic field is higher and the flow is driven by lower electric fields.
ON THE SCANNING PROPERTIES OF IMAGING ANTENNAS BASED ON DUAL CONFOCAL PARABOLOIDAL REFLECTORS (2014)

In this paper the scanning properties of dual reflector antenna systems constituted by two confocal paraboloidal reflectors fed by a planar array are investigated. This antenna architecture combines the interesting features of reflectors and array antennas. Because of the offset configuration the radiation pattern exhibits an anomalous deviation in the beam pointing when the beam is scanned out of the boresight direction. Heuristic equations, representing an extension of the linear equations available in the literature, are derived, which permit predicting the pointing direction of the overall system as a function of the pointing direction of the feeding array in a significant field of view.
Identification of a Novel Calotropis procera Protein That Can Suppress Tumor Growth in Breast Cancer through the Suppression of NF-κB Pathway (2012)

Breast cancer is the most common cancer among women. To date, improvements in hormonal and cytotoxic therapies have not yet led to a sustained remission or cure. In the present study, we investigated the in vitro and in vivo antitumor activities of a novel Calotropis procera protein (CP-P) isolated from root bark. CP-P protein inhibited the proliferation and induced apoptosis of breast cancer cells through the suppression of nuclear factor kappaB (NF-kB) activation. CP-P, when administered individually or in combination with cyclophosphamide (CYC, 0.2 mg/kg) to rats with 7, 12-dimethyl benz(a)anthracene (DMBA)-induced breast cancer decreased tumor volume significantly without affecting the body weight. To elucidate the anticancer mechanism of CP-P, antioxidant activities such as superoxide dismutase (SOD), catalase (CAT), glutathione-s-transferase (GST) and non-enzymatic antioxidant - reduced glutathione (GSH), vitamin E and C generation in the breast were analyzed by various assays. SOD, CAT, GST, GSH, vitamin E and C levels were high in combination-treated groups (CP-P+CYC) versus the CYC alone-treated groups. Also, the combination was more effective in down-regulating the expression of NF-kB-regulated gene products (cyclin D1 and Bcl-2) in breast tumor tissues. Our findings indicate that CP-P possesses significant antitumor activity comparable to a commonly used anticancer drug, cyclophosphamide, and may form the basis of a novel therapy for breast cancer.
Supplementary Figure Legends 1-5 from NPM-ALK Oncogenic Tyrosine Kinase Controls T-Cell Identity by Transcriptional Regulation and Epigenetic Silencing in Lymphoma Cells (2023)

Supplementary Figure Legends 1-5 from NPM-ALK Oncogenic Tyrosine Kinase Controls T-Cell Identity by Transcriptional Regulation and Epigenetic Silencing in Lymphoma Cells
Utiliy of armonic scalpel for laparoscopic partial nephrectomy: correlation with the extent of resection (1997)

Utiliy of armonic scalpel for laparoscopic partial nephrectomy: correlation with the extent of resection
SYNTHESIS OF AMPHIPHILIC COIL-ROD-COIL BLOCK COPOLYMERS USING ATOM TRANSFER RADICAL POLYMERIZATION (2002)

ABSTRACT Coil-rod-coil block copolymers composed from luminescent rigid units and acrylate flexible blocks have been synthesized using atom transfer radical polymerization. α,ω-Difunctionalized oligophenylenes properly modified to act as ATRP initiators have been used for the polymerization of the various acrylates. Copolymers with controlled shape and in some cases, relatively low polydispersities have been obtained as proved by size exclusion chromatography and NMR. In cases, where t-butyl acrylate blocks have been used as the flexible part, selective hydrolysis resulted in coil-rod-coil copolymers containing poly(acrylic acid) blocks. The solution behavior of the synthesized copolymers was explored in various solvents. The poly(acrylic acid) copolymers in aqueous solutions form large aggregates, while in organic selective solvents for the flexible block, monomolecular micelles seem to be formed. Keywords: Polymer synthesesRod-coil copolymersAtom Transfer RadicalPolymerizationLuminescence ACKNOWLEDGMENT This work was supported by the Operational Program for Education and Initial Vocational Training on “Polymer Science and Technology” –3.2a, 33H6, administered through the Ministry of Education and Religious Affairs in Greece.