gebhart/patrepeval huggingface dataset:
Defining the adult hippocampal neural stem cell secretome: In vivo versus in vitro transcriptomic differences and their correlation to secreted protein levels (2020)

Adult hippocampal neural stem and progenitor cells (NSPCs) secrete a variety of proteins that affect tissue function. Though several individual NSPC-derived proteins have been shown to impact key cellular processes, a broad characterization is lacking. Secretome profiling of low abundance stem cell populations is typically achieved via proteomic characterization of in vitro, isolated cells. Here, we identified hundreds of secreted proteins in conditioned media from in vitro adult mouse hippocampal NSPCs using an antibody array and mass spectrometry. Comparison of protein abundance between antibody array and mass spectrometry plus quantification of several key secreted proteins by ELISA revealed notable disconnect between methods in what proteins were identified as being high versus low abundance, suggesting that data from antibody arrays in particular should be approached with caution. We next assessed the NSPC secretome on a transcriptional level with single cell and bulk RNA sequencing (RNAseq) of cultured NSPCs. Comparison of RNAseq transcript levels of highly secreted proteins revealed that quantification of gene expression did not necessarily predict relative protein abundance. Interestingly, comparing our in vitro NSPC gene expression data with similar data from freshly isolated, in vivo hippocampal NSPCs revealed strong correlations in global gene expression between in vitro and in vivo NSPCs. Understanding the components and functions of the NSPC secretome is essential to understanding how these cells may modulate the hippocampal neurogenic niche. Cumulatively, our data emphasize the importance of using proteomics in conjunction with transcriptomics and highlights the need for better methods of unbiased secretome profiling.
Pushing the limits of HiFi assemblies reveals centromere diversity between two Arabidopsis thaliana genomes (2022)

ABSTRACT Although long-read sequencing can often enable chromosome-level reconstruction of genomes, it is still unclear how one can routinely obtain gapless assemblies. In the model plant Arabidopsis thaliana , other than the reference accession Col-0, all other accessions de novo assembled with long-reads until now have used PacBio continuous long reads (CLR). Although these assemblies sometimes achieved chromosome-arm level contigs, they inevitably broke near the centromeres, excluding megabases of DNA from analysis in pan-genome projects. Since PacBio high-fidelity (HiFi) reads circumvent the high error rate of CLR technologies, albeit at the expense of read length, we compared a CLR assembly of accession Ey15-2 to HiFi assemblies of the same sample performed by five different assemblers starting from subsampled data sets, allowing us to evaluate the impact of coverage and read length. We found that centromeres and rDNA clusters are responsible for 71% of contig breaks in the CLR scaffolds, while relatively short stretches of GA/TC repeats are at the core of &gt;85% of the unfilled gaps in our best HiFi assemblies. Since the HiFi technology consistently enabled us to reconstruct gapless centromeres and 5S rDNA clusters, we demonstrate the value of the approach by comparing these previously inaccessible regions of the genome between two A. thaliana accessions.
GaInN light-emitting diodes with RuO2/SiO2/Ag omni-directional reflector (2004)

A GaInN light-emitting diode (LED) employing an omni-directional reflector (ODR) is presented. The ODR consists of a RuO2 ohmic contact to p-type GaN, a quarter-wave thick SiO2 low-index layer perforated by an array of micro-contacts, and an Ag layer. Calculations predict a 98% angle-averaged reflectivity at λ=450 nm for an GaN/SiO2/Ag ODR, much higher than that for a 20 period Al0.25Ga0.75N/GaN distributed Bragg reflector (49%) and an Ag reflector (94%). It is shown that the RuO2/SiO2/Ag ODR has higher reflectivity than Ni/Au and even Ag reflectors, leading to a higher light extraction efficiency of GaInN LEDs with ODR. The electrical properties of the ODR-LED are comparable to those LEDs with a conventional Ni/Au contact.
ALPURT Motorway - Sector A: Pavements Design and Consideration (1998)

This paper summaries the pavement design procedures, pavement alternatives, and considerations of the pavement for the 15km ALPURT extension to the Auckland Northern Motorway. Two contracts were let in late 1997, Sector A1 the southern 7 km, and Sector A2 the northern 7km. At this time the motorway is under construction but the pavement construction has not commenced and the details of the methodology are still under review. ALPURT is the first major highway to be designed under the AUSTROADS Pavement Design introduced by TNZ in 1996 to replace the 1988 NRB State Highway Design and Rehabilitation Manual. The design brief called for a conventional flexible unbound aggregate pavement on a stabilised subgrade with a chip/friction mix seal. With a design traffic design of 1.7 x 107 ESA's the pavement designed under AUSTROADS is significantly thinner than would be the case under the NRB design. This emphasises the risk of using low grade materials and poor construction techniques. All previous experience on the current Auckland motorways has been with the thicker NRB pavements and while pavement performance has been adequate, it has not been shown to be conservative. The pavement construction for the motorway and ramps totals some 320,000m2 and the cost is a significant proportion of the total construction cost of the project. The quantity of aggregate required (100,000m3) is unprecedented for Auckland roading projects to date. The minimise the aggregate requirement, and to qualify the costs of more robust materials, alternative pavement systems were investigated. Alternative options reviewed include structural Asphalitic Concrete, unbound over Lean-Mix concrete (upside down Pavement), and a Portland Cement rigid concrete pavement. The paper will outlise the traffic design procedures, the choice of design parameters for mechanistic design, and compare the Present Day Worth Costs of the pavement options. The results of repetitive load triaxial tests on representative high grade and marginal aggregates will be shown. The results will indicate that the use of a stabilised local marginal aggregate for subbase in place of a higher grade aggregate is promising. Throughout the paper AUSTROADS limitations will be reviewed relative to practical considerations and design philosophy.
Study on the transmission line vulnerability index and its application based on the transient power angle stability mechanism (2018)

In some cases, the weak transmission line is the key to limiting the transmission capacity of a power transmission section. The transmission capability of a weak-connected power system is usually limited by its transient stability limit. Therefore, the weak line identification of the transmission section needs to consider the transient stability impact. Based on the equal area criterion, this paper proposes the identification index of weak transmission lines in two-area power grids. This index can identify weak lines in two-area grids connected by multiple lines in series or in parallel, and it can sort the severity of the faults affecting the weak lines. This indicator takes into account the impact of power flow transferring after a fault and it can directly judge the weak lines of the system and the faults that have serious impact on it under certain conditions without time domain simulation which can save a lot of simulation time. It can be used to calculate the system's transmission capacity and monitor the system's operating status which is of great significance to the system's safety and stability analysis and the transmission capacity calculation.
Evaluation of a selective medium for Brucella isolation using natamycin (2002)

Cycloheximide has become unavailable worldwide and is currently an anti-fungal constituent of the medium often used for isolation of Brucella organisms. The use of natamycin as a replacement in the formulation did not inhibit growth of Brucella and was effective at eliminating most contaminants.
The effect of supplemental zinc on the height and weight percentiles of children. (2006)

It was concluded that supplemental zinc increases height and weight percentiles.
ChemInform Abstract: Diastereocontrolled Synthesis of an Enantiopure 4,4‐Disubstituted Cyclohex‐2‐en‐ol: A New Route to (+)‐Quebrachamine. (2002)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
ChemInform Abstract: SELENIUM DIOXIDE OXIDATIONS IN THE β‐CARBOLINE AREA (1980)

Abstract Die Selendioxid‐Oxidation des Tetrahydro‐β‐carbolins (I) führt zu einem Gemisch der vier Verbindungen (II) bis (V), während aus dem N‐Benzoylderivat (VI) nur das Ketoamid (VII) gebildet wird.
Flat Surface Damage Detection System (FSDDS) (2013)

The Flat Surface Damage Detection system (FSDDS} is a sensory system that is capable of detecting impact damages to surfaces utilizing a novel sensor system. This system will provide the ability to monitor the integrity of an inflatable habitat during in situ system health monitoring. The system consists of three main custom designed subsystems: the multi-layer sensing panel, the embedded monitoring system, and the graphical user interface (GUI). The GUI LABVIEW software uses a custom developed damage detection algorithm to determine the damage location based on the sequence of broken sensing lines. It estimates the damage size, the maximum depth, and plots the damage location on a graph. Successfully demonstrated as a stand alone technology during 2011 D-RATS. Software modification also allowed for communication with HDU avionics crew display which was demonstrated remotely (KSC to JSC} during 2012 integration testing. Integrated FSDDS system and stand alone multi-panel systems were demonstrated remotely and at JSC, Mission Operations Test using Space Network Research Federation (SNRF} network in 2012. FY13, FSDDS multi-panel integration with JSC and SNRF network Technology can allow for integration with other complementary damage detection systems.
Binding of an arm repeat protein to the kinase domain of the S -locus receptor kinase (1998)

Screening of a yeast two-hybrid library for proteins that interact with the kinase domain of an S-locus receptor kinase (SRK) resulted in the isolation of a plant protein called ARC1 (Arm Repeat Containing). This interaction was mediated by the C-terminal region of ARC1 in which five arm repeat units were identified. Using the yeast two-hybrid system and in vitro binding assays, ARC1 was found to interact specifically with the kinase domains from SRK-910 and SRK-A14 but failed to interact with kinase domains from two different Arabidopsis receptor-like kinases. In addition, treatment with a protein phosphatase or the use of a kinase-inactive mutant reduced or abolished the binding of ARC1 to the SRK-910 kinase domain, indicating that the interaction was phosphorylation dependent. Lastly, RNA blot analysis revealed that the expression of ARC1 is restricted to the stigma, the site of the self-incompatibility response.
Assessment of biodiversity in Chilean cattle using the distribution of major histocompatibility complex class IIBoLA‐DRB3 allele (2014)

Bovine leukocyte antigens (BoLAs) are used extensively as markers for bovine disease and immunological traits. In this study, we estimated BoLA-DRB3 allele frequencies using 888 cattle from 10 groups, including seven cattle breeds and three crossbreeds: 99 Red Angus, 100 Black Angus, 81 Chilean Wagyu, 49 Hereford, 95 Hereford × Angus, 71 Hereford × Jersey, 20 Hereford × Overo Colorado, 113 Holstein, 136 Overo Colorado, and 124 Overo Negro cattle. Forty-six BoLA-DRB3 alleles were identified, and each group had between 12 and 29 different BoLA-DRB3 alleles. Overo Negro had the highest number of alleles (29); this breed is considered in Chile to be an 'Old type' European Holstein Friesian descendant. By contrast, we detected 21 alleles in Holstein cattle, which are considered to be a 'Present type' Holstein Friesian cattle. Chilean cattle groups and four Japanese breeds were compared by neighbor-joining trees and a principal component analysis (PCA). The phylogenetic tree showed that Red Angus and Black Angus cattle were in the same clade, crossbreeds were closely related to their parent breeds, and Holstein cattle from Chile were closely related to Holstein cattle in Japan. Overall, the tree provided a thorough description of breed history. It also showed that the Overo Negro breed was closely related to the Holstein breed, consistent with historical data indicating that Overo Negro is an 'Old type' Holstein Friesian cattle. This allelic information will be important for investigating the relationship between major histocompatibility complex (MHC) and disease.
TepiTool: A Pipeline for Computational Prediction of T Cell Epitope Candidates (2016)

Abstract Computational prediction of T cell epitope candidates is currently being used in several applications including vaccine discovery studies, development of diagnostics, and removal of unwanted immune responses against protein therapeutics. There have been continuous improvements in the performance of MHC binding prediction tools, but their general adoption by immunologists has been slow due to the lack of user‐friendly interfaces and guidelines. Current tools only provide minimal advice on what alleles to include, what lengths to consider, how to deal with homologous peptides, and what cutoffs should be considered relevant. This protocol provides step‐by‐step instructions with necessary recommendations for prediction of the best T cell epitope candidates with the newly developed online tool called TepiTool. TepiTool, which is part of the Immune Epitope Database (IEDB), provides some of the top MHC binding prediction algorithms for number of species including humans, chimpanzees, bovines, gorillas, macaques, mice, and pigs. The TepiTool is freely accessible at http://tools.iedb.org/tepitool/ . © 2016 by John Wiley &amp; Sons, Inc.
Effects of IgY against Candida albicans and Candida spp. Adherence and Biofilm Formation. (2009)

The fungal pathogen Candida albicans is an opportunistic fungal pathogen that causes oral and vaginal mucosal infections as well as systemic disease. The ability of C. albicans to adhere to host surfaces is positively correlated with its pathogenicity. We prepared a polyclonal anti-Candida albicans antibody in chicken egg yolk (anti-C. albicans IgY) and investigated its in vitro effectiveness in preventing C. albicans adherence and biofilm formation. Anti-C. albicans IgY significantly reduced the adherence of C. albicans SC5314 to human oral epithelial cells in a dose-dependent manner. The same effect was also observed in other Candida spp. including C. albicans serotype A and B. Further, the IgY inhibited biofilm formation of C. albicans in medium without serum, but the inhibition was slightly restored in medium conditioned with 10% serum. The data indicate that anti-C. albicans IgY cross-reacted with various Candida spp. and may have a protective effect against oral candidiasis and reduce the dissemination of Candida spp. This effect may be due to the blocking of the binding of Candida spp. to the host cells. However, the blocking did not play a role when Candida formed a germ tube in the presence of serum. Therefore, anti-C. albicans IgY may be considered as a prophylactic immunotherapy or possibly an adjunctive antifungal therapy under limited conditions.
Improving the Rate Capability of LiFePO4 Electrode by Controlling Particle Size Distribution (2019)

&lt;p&gt;In this study, the rate performance of a LiFePO&lt;sub&gt;4&lt;/sub&gt; (LFP) electrode has been enhanced by optimization of the particle size distribution of the LFP particles. Two LFP samples with different particle sizes (∼50 and ∼350 nm) are mixed with various ratios and the electrochemical performance has been evaluated. Reduction of the contact resistance and increase of the Li diffusion coefficient have been achieved. The electrode with a mixing ratio of 50:50 shows an improved initial capacity at C/10 and superior rate capability compared with the two pristine materials.&lt;/p&gt;
Practical Issues with Unloaded Resonant Inductive WPT Link Operating in Load-Independent Regime (2019)

The paper reveals practical issues present in series-series compensated unloaded inductive wireless power transfer system operating in load-independent regime. It was recently shown, that due to existence of parasitic resistances, corresponding output voltage is not completely load-independent. Based on time-domain analysis, DC voltage gain of an unloaded system was predicted for a wide range of operation frequencies. However, parasitic lumped capacitance of the receiving coil was not taken into account. It is therefore shown that parasitic oscillations appearing in an unloaded secondary impose significant overvoltage at DC output, which may cause safety issues. Two possible solutions are discussed, allowing damping the oscillations thus making the unloaded operation feasible. The presented analysis is well-verified by simulation results and experiments of a 400V, 1kW inductive wireless power transfer link.
Neuer langwelliger Fluoreszenzfarbstoff zur biomolekularen Erkennung von Protein-Protein-Wechselwirkungen über den Förster Energie-Transfer (2001)

Poster ____________________________________________________________ Fluoreszenz-Bioassays dienen dem sensitiven Nachweis biomolekularer Wechselwirkungen zwischen Rezeptor und Ligand, Antikorper und Antigen oder DNA und DNA. Fur den Nachweis der spezifischen Bindung von einem Protein an ein anderes eignet sich der Fluoreszenz Resonante Energie Transfer (FRET). Der Energietransfer erfolgt zwischen zwei fluoroforen Gruppen, die an das jeweilige Protein gekoppelt sind, wenn eine biomolekulare Erkennung erfolgt. Der FRET ist stark abstandsabhangig (110 nm) und hangt nicht wie andere homogene Nachweisverfahren (die Fluoreszenz Korrelationsspektroskopie oder die Fluoreszenz Anisotropie) vom Unterschied des Molekulargewichts ab.
A paper-based electrostatic zipper actuator for printable robots (2014)

A paper-based electrostatic zipper actuator for printable robotics has been designed, fabricated and characterized. A simple fabrication process that utilizes paper with a carbon nanotube ink is used to create electrodes separated by either a mylar or parylene dielectric layer. A 5 cm × 1 cm actuator demonstrated a maximum static deflection of 1.8 cm and a bandwidth of approximately 12 Hz. Static power dissipation was under 1 μW. Two of these actuators are combined to demonstrate simple motion in a 6 cm × 1 cm × 1 cm robot using assymetric friction with the ground, achieving speeds up to 33 mm/min.
Water soluble cucurbit[6]uril derivative as a potential Xe carrier for 129Xe NMR-based biosensors (2008)

The water soluble cucurbit[6]uril derivative CB*[6] forms a thermodynamically and kinetically stable host-guest complex with xenon in water, the binding affinity of which is about 3 x 10(3) M(-1), comparable to those of cryptophanes, suggesting that it may serve as an effective molecular "carrier" for 129Xe NMR-based biosensors.
Sociolect-Based Community Detection (2013)

'Sociolects' are specialized vocabularies used by social subgroups defined by common interests or origins. We applied methods to retrieve large quantities of Twitter data based on expert-identified sociolects and then applied and developed network-analysis methods to relate sociolect use to network (sub-) structure. We show that novel methods including consideration of node populations, as well as edge counts, provide substantially enhanced performance compared to standard assortativity. We explain these methods, show their utility in analyzing large corpora of social media data, and d iscuss their further extensions and potential applications. © 2013 IEEE.
INTERSTATE SHIPMENT AND STORAGE OF FRESH MUSCADINE GRAPES (1999)

ABSTRACT Muscadine grapes (Vitis rotundifolia michx.) are highly perishable, with a short harvest season. The objective of this study was to enhance the commercial viability of muscadine grapes by developing harvesting and handling systems through interstate shipment studies, using sulfur dioxide and/or polyethylene overwrap treatments. Cultivars Fry, Summit and Granny Val from Florida, Arkansas and Mississippi, respectively, were shipped from each region to the other in refrigerated trucks for subsequent storage at OC and evaluation at 0, 2, 4 and 6 weeks. Biochemical properties: pH, titratable acidity and degrees Brix, remained fairly constant with time for all cultivars, under all treatments. The cultivar, Granny Val, which was shipped, wrinkled after 2 weeks' storage, but maintained 6 weeks' shelf‐life in the in‐house study. ‘Summit’ shelf‐life was increased to 4 weeks with SO 2 treatment at all test sites while ‘Fry’ became bleached by SO 2 . The shelf‐life of ‘Fry’ was 6 weeks in the in‐house study using
Profile of David J. Thouless, J. Michael Kosterlitz, and F. Duncan M. Haldane, 2016 Nobel Laureates in Physics (2017)

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans the biological, physical, and social sciences.
Mucus and Surfactant Synthesis and Secretion by Cultured Hamster Respiratory Cells (1980)

Procedures for the selective isolation and cultivation in monolayer of respiratory cells have been developed. This technique requires repeated protease treatment and gradient centrifugation of hamster tracheal or lung tissues and permits the establishment of proliferating cultures of epithelial cells with biologic specialization. Mucus synthesis was monitored in cultured tracheal cells by incorporation of 3H-labeled N-acetyl-D-galactosamine and 14C-serine into glycoprotein as determined by trichloroacetic acid precipitation of growth medium followed by acrylamide gel electrophoresis. For comparative purposes tracheal explants and several established cell lines were also examined. Synthesis and secretion of the glycoprotein macromolecule by tracheal cell monolayers appeared to be regulated by vitamin A since its addition to the culture medium significantly increased both the number of cell-associated granules and glycoprotein secretion. Lung-originated cell cultures were grown to confluence and radio-labeled with 3H-choline in serum-free medium for 24 hr to examine surfactant synthesis. Cell monolayers and growth medium were then extracted by the Folch method, and total radioactive phosphatidylcholine as well as disaturated phosphatidylcholine were determined by thin-layer chromatography and alumina gel fractionation of osmium tetroxide-reactive phospholipid, respectively. Data indicate that these cultures have a marked ability to synthesize and secrete surfactant when compared to other established cell lines. In addition, naturally transformed cells that arose during passage and senescence of the primary cultures were analyzed for their biosynthetic capabilities.