gebhart/patrepeval huggingface dataset:
Deciphering the Chitin Code in Plant Symbiosis, Defense, and Microbial Networks (2021)

Chitin is a structural polymer in many eukaryotes. Many organisms can degrade chitin to defend against chitinous pathogens or use chitin oligomers as food. Beneficial microorganisms like nitrogen-fixing symbiotic rhizobia and mycorrhizal fungi produce chitin-based signal molecules called lipo-chitooligosaccharides (LCOs) and short chitin oligomers to initiate a symbiotic relationship with their compatible hosts and exchange nutrients. A recent study revealed that a broad range of fungi produce LCOs and chitooligosaccharides (COs), suggesting that these signaling molecules are not limited to beneficial microbes. The fungal LCOs also affect fungal growth and development, indicating that the roles of LCOs beyond symbiosis and LCO production may predate mycorrhizal symbiosis. This review describes the diverse structures of chitin; their perception by eukaryotes and prokaryotes; and their roles in symbiotic interactions, defense, and microbe-microbe interactions. We also discuss potential strategies of fungi to synthesize LCOs and their roles in fungi with different lifestyles.
J044033 Frictional analysis of hydrophilic PVA brush for cleaning (2013)

In order to gain insights into the mechanism of PVA brush cleaning in semiconductor device fabrication, we measure the coefficient of friction (COF) between PVA brush and substrates. To obtain the coefficient of friction, the share and normal forces caused by horizontal brush movements are independently measured using load cell and brush traverse apparatus. As a result, the COF values decrease with increasing the brush traverse speed and increase with the brush compression. This result implies that the brush and surface are directly contacted condition and the real contact area of the brush increases over the contact time.
Pandemic H1N1 Influenza Isolated from Free-Ranging Northern Elephant Seals in 2010 off the Central California Coast (2013)

Interspecies transmission of influenza A is an important factor in the evolution and ecology of influenza viruses. Marine mammals are in contact with a number of influenza reservoirs, including aquatic birds and humans, and this may facilitate transmission among avian and mammalian hosts. Virus isolation, whole genome sequencing, and hemagluttination inhibition assay confirmed that exposure to pandemic H1N1 influenza virus occurred among free-ranging Northern Elephant Seals (Mirounga angustirostris) in 2010. Nasal swabs were collected from 42 adult female seals in April 2010, just after the animals had returned to the central California coast from their short post-breeding migration in the northeast Pacific. Swabs from two seals tested positive by RT-PCR for the matrix gene, and virus was isolated from each by inoculation into embryonic chicken eggs. Whole genome sequencing revealed greater than 99% homology with A/California/04/2009 (H1N1) that emerged in humans from swine in 2009. Analysis of more than 300 serum samples showed that samples collected early in 2010 (n = 100) were negative and by April animals began to test positive for antibodies against the pH1N1 virus (HI titer of ≥1∶40), supporting the molecular findings. In vitro characterizations studies revealed that viral replication was indistinguishable from that of reference strains of pH1N1 in canine kidney cells, but replication was inefficient in human epithelial respiratory cells, indicating these isolates may be elephant seal adapted viruses. Thus findings confirmed that exposure to pandemic H1N1 that was circulating in people in 2009 occurred among free-ranging Northern Elephant Seals in 2010 off the central California coast. This is the first report of pH1N1 (A/Elephant seal/California/1/2010) in any marine mammal and provides evidence for cross species transmission of influenza viruses in free-ranging wildlife and movement of influenza viruses between humans and wildlife.
Alternative Forms of the BCR-ABL Oncogene Have Quantitatively Different Potencies for Stimulation of Immature Lymphoid Cells (1989)

The Philadelphia chromosome (t9:22;q34:q11) is found in more than 90% of patients with chronic myelogenous leukemia, in 10 to 20% of patients with acute lymphocytic leukemia, and in 1 to 2% of patients with acute myelogenous leukemia. Alternative chimeric oncogenes are formed by splicing different sets of BCR gene exons on chromosome 22 across the translocation breakpoint to a common set of ABL oncogene sequences on chromosome 9. This results in an 8.7-kilobase mRNA that encodes the P210 BCR-ABL gene product commonly found in patients with chronic myelogenous leukemia or a 7.0-kilobase mRNA that produces the P185 BCR-ABL gene product found in most Philadelphia chromosome-positive patients with acute lymphocytic leukemia. To compare the efficiency of growth stimulation by these two proteins, we derived cDNA clones for each with identical 5' and 3' untranslated regions and expressed them from retrovirus vectors. Matched stocks were compared for potency to transform immature B-lymphoid lineage precursors. The growth-stimulating effects of P185 for this cell type were found to be significantly greater than those of P210. Structural changes in BCR may regulate the effectiveness of the ABL tyrosine kinase function, as monitored by lymphocyte growth response. Changes in mitogenic potency may help to explain the more acute leukemic presentation usually associated with expression of the P185 BCR-ABL oncogene.
Potential antitumor agents. 30. Mutagenic activity of some 9-anilinoacridines: relationships between structure, mutagenic potential, and antileukemic activity (1979)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPotential antitumor agents. 30. Mutagenic activity of some 9-anilinoacridines: relationships between structure, mutagenic potential, and antileukemic activityLynnette R. Ferguson and William A. DennyCite this: J. Med. Chem. 1979, 22, 3, 251–255Publication Date (Print):March 1, 1979Publication History Published online1 May 2002Published inissue 1 March 1979https://doi.org/10.1021/jm00189a006RIGHTS & PERMISSIONSArticle Views77Altmetric-Citations37LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (712 KB) Get e-Alerts Get e-Alerts
Potency assays and biomarkers for cell-based advanced therapy medicinal products (2023)

Advanced Therapy Medicinal Products (ATMPs) based on somatic cells expanded <i>in vitro</i>, with or without genetic modification, is a rapidly growing area of drug development, even more so following the marketing approval of several such products. ATMPs are produced according to Good Manufacturing Practice (GMP) in authorized laboratories. Potency assays are a fundamental aspect of the quality control of the end cell products and ideally could become useful biomarkers of efficacy <i>in vivo</i>. Here we summarize the state of the art with regard to potency assays used for the assessment of the quality of the major ATMPs used clinic settings. We also review the data available on biomarkers that may substitute more complex functional potency tests and predict the efficacy <i>in vivo</i> of these cell-based drugs.
The Effect of Fiber Type and Yarn Diameter on Superhydrophobicity, Self-Cleaning Property, and Water Spray Resistance (2021)

In this study, we proved that micro/micro hierarchical structures are enough to achieve a superhydrophobic surface using polydimethylsiloxane (PDMS) dip-coating. Furthermore, the effect of fiber type and yarn diameter on superhydrophobicity and water spray resistance was investigated. Polyester fabrics with two types of fibers (staple fabric and filament) and three types of yarn diameters (177D, 314D, and 475D) were used. The changes in the surface properties and chemical composition were investigated. Static contact angles and shedding angles were measured for superhydrophobicity, and the self-cleaning test was conducted. Water spray repellency was also tested, as well as the water vapor transmission rate and air permeability. The PDMS-coated staple fabric showed better superhydrophobicity and oleophobicity than the PDMS-coated filament fabric, while the filament fabric showed good self-cleaning property and higher water spray repellency level. When the yarn diameter increased, the fabrics needed higher PDMS concentrations and longer coating durations for uniform coating. The water vapor transmission rate and air permeability did not change significantly after coating. Therefore, the superhydrophobic micro/micro hierarchical fabrics produced using the simple method of this study are more practical and have great potential for mass production than other superhydrophobic textiles prepared using the chemical methods.
MMP-1 is a Prognostic Marker for Hematogenous Metastasis of Colorectal Cancer (2000)

MMP-1 expression may be a novel marker for hematogenous metastasis of colorectal cancer, and its inhibition may be a strategy for prevention of metastasis.
Proceedings of the Ninth International Workshop on Dynamic Analysis (2012)

Proceedings of the International Workshop on Dynamic Analysis: held in conjunction with the ACM SIGSOFT International Symposium on Software Testing and Analysis (ISSTA 2012), WODA 2012, Minneapolis, MN, USA, Sunday, July 15, 2012
A preliminary study of sperm identification in microdissection testicular sperm extraction samples with deep convolutional neural networks (2020)

Sperm identification and selection is an essential task when processing human testicular samples for in vitro fertilization. Locating and identifying sperm cell(s) in human testicular biopsy samples is labor intensive and time consuming. We developed a new computer-aided sperm analysis (CASA) system, which utilizes deep learning for near human-level performance on testicular sperm extraction (TESE), trained on a custom dataset. The system automates the identification of sperm in testicular biopsy samples. A dataset of 702 de-identified images from testicular biopsy samples of 30 patients was collected. Each image was normalized and passed through glare filters and diffraction correction. The data were split 80%, 10%, and 10% into training, validation, and test sets, respectively. Then, a deep object detection network, composed of a feature extraction network and object detection network, was trained on this dataset. The model was benchmarked against embryologists' performance on the detection task. Our deep learning CASA system achieved a mean average precision (mAP) of 0.741, with an average recall (AR) of 0.376 on our dataset. Our proposed method can work in real time; its speed is effectively limited only by the imaging speed of the microscope. Our results indicate that deep learning-based technologies can improve the efficiency of finding sperm in testicular biopsy samples.
On historical diagnosis of sensor streams (2015)

In this paper, we will examine the problem of historical storage and diagnosis of massive numbers of simultaneous streams. Such streams are common in very large sensor systems which collect many data streams simultaneously. For example, in a typical monitoring application, we may desire to determine specific abnormalities at sensor nodes or diagnose local regions of abnormal behavior. In other applications, a user may wish to query the streams for specific behavior of the data over arbitrary time horizons. This can be a very difficult task if it is not possible to store the voluminous sensor information at different nodes. In many cases, it is only possible to store aggregated data over different nodes. In this paper, we discuss the problem of storage-efficient monitoring and diagnosis of sensor networks with the use of summary representations. The goal of the summary representation is to providing worst-case guarantees on query functions computed over the sensor stream, while storing the streams compactly. We present experimental results on a number of real data sets showing the effectiveness of the approach.
Ocean Renewable Energy Storage (ORES) System: Analysis of an Undersea Energy Storage Concept (2013)

Due to its higher capacity factor and proximity to densely populated areas, offshore wind power with integrated energy storage could satisfy > 20% of U.S. electricity demand. Similar results could also be obtained in many parts of the world. The offshore environment can be used for unobtrusive, safe, and economical utility-scale energy storage by taking advantage of the hydrostatic pressure at ocean depths to store energy by pumping water out of concrete spheres and later allowing it to flow back in through a turbine to generate electricity. The storage spheres are an ideal complement to energy harvesting machines, such as floating wind turbines (FWTs). The system could provide near-base-load-quality utility-scale renewable energy and do double duty as the anchoring point for the generation platforms. Analysis indicates that storage can be economically feasible at depths as shallow as 200 m, with cost per megawatt hour of storage dropping until 1500 m before beginning to trend upward. The sweet spot occurs when the concrete wall thickness to withstand the hydrostatic pressure provides enough ballast mass, and this will depend on the strength of used concrete and reinforcement. In addition, the required concrete would use significant amounts of fly ash from coal-fired power plants, and the spheres can serve as artificial reefs.
Intratympanic Gentamicin Therapy for Ménière’s Disease: A Meta-analysis (2004)

The titration method of gentamicin delivery demonstrated significantly better complete (81.7%, p = 0.001) and effective (96.3%, p < 0.05) vertigo control compared with other methods. The low-dose method of delivery demonstrated significantly worse complete vertigo control (66.7%, p < 0.001) and trends toward worse effective vertigo control (86.8%, p = 0.05) compared with other methods. The weekly method of delivery trends toward less overall hearing loss (13.1%, p = 0.08), and the multiple daily method demonstrated significantly more overall hearing loss (34.7%, p < 0.01) compared with other groups. No significant difference in profound hearing loss was found between groups. Degree of vestibular ablation after gentamicin therapy is not significantly correlated with the resulting vertigo control or hearing loss status.
Overlapping Shockley/Frank Faults in 4H-SiC PiN Diodes (2006)

This DOI is not currently attached to any metadata records. DOIs can’t actually ever be deleted (they’re persistent), but sometimes our members create DOIs in error. We do have a process to approximate deletion which we follow only in rare cases where the DOI has been genuinely created in error, and most crucially, if the DOI has never been published anywhere online or in print and never otherwise distributed to or communicated with anyone (authors, readers, reviewers, etc.
Identification of age‐related changes in gene expression in adult versus geriatric dogs (2008)

Thirty adult (&lt;10 years of age) and thirty geriatric (&gt;10 years of age) neutered/spayed beagles were identified for this study. Animals were fed a control food for 30 days and then a blood sample was drawn into a PAXgene Blood RNA tube. RNA was extracted according to the procedures provided in the PAXgene Blood RNA Kit Handbook (Qiagen, Valencia, CA). RNA was hybridized to an Affymetrix GeneChip Canine‐2 Genome Arrays and normalized using Robust Multi‐Array Average. Transcripts having a P &lt; 0.01 (following a false discovery rate adjustment value of 0.1) and a fold change range of at least 1.5 were considered different among the two groups. Analysis of the RNA found differences in 580 genes between the geriatric and adult groups. Of the genes identified, 310 were up‐regulated and 270 down‐regulated in geriatric dogs when compared to adult dogs. Genes associated with immune system activation, cancer formation, B and T‐cell receptor signaling, protein ubiquitination, and branched chain amino acid degradation were increased, while cell‐cell signaling, cell cycle regulation, and blood coagulation were decreased in geriatric compared to adult dogs.
In Search of a Universal Rough Wall Model (2023)

Abstract This work compares various existing rough-wall models on a large collection of rough surfaces with different characteristics and studies the potential of these models in accommodating new datasets. We consider three empirical roughness correlations, two physics-based models, and one data-driven machine-learning model on 68 rough surfaces inside and outside the Roughness Database1. Results show that correlation-type models and machine-learning models do not extrapolate outside the dataset against which they are calibrated or trained. In contrast, the physics-based sheltering model performs well in extrapolation. Recalibrating a roughness correlation against a large dataset proves unfruitful. However, retraining a machine learning model yields good results. We do not pursue further retraining and recalibrating of a physics-based model, as it requires new physical insights. Overall, our findings suggest that a universal rough-wall model is yet to be found. The capability of extrapolation will likely come from incorporating physics. Data, on the other hand, benefits machine learning models.
Tiny Videos: A Large Dataset for Image and Video Frame Categorization (2009)

This paper presents a new method for video and image categorization based on a database of over 50,000 videos collected from YouTube and down-sampled to tiny size. The categorization results achieved by tiny videos are compared with the tiny images framework for a variety of recognition tasks. The tiny images dataset consists of 80 million images collected from the Internet. These are the largest labeled research datasets of videos and images available to date. We show that tiny videos are better suited for classifying sports activities and scenery, while tiny images perform better at recognizing objects. Furthermore, we demonstrate that combining the tiny images and tiny videos datasets improves categorization precision in a wider range of categories.
Integration of cell line and process development to overcome the challenge of a difficult to express protein (2015)

This case study addresses the difficulty in achieving high level expression and production of a small, very positively charged recombinant protein. The novel challenges with this protein include the protein's adherence to the cell surface and its inhibitory effects on Chinese hamster ovary (CHO) cell growth. To overcome these challenges, we utilized a multi-prong approach. We identified dextran sulfate as a way to simultaneously extract the protein from the cell surface and boost cellular productivity. In addition, host cells were adapted to grow in the presence of this protein to improve growth and production characteristics. To achieve an increase in productivity, new cell lines from three different CHO host lines were created and evaluated in parallel with new process development workflows. Instead of a traditional screen of only four to six cell lines in bioreactors, over 130 cell lines were screened by utilization of 15 mL automated bioreactors (AMBR) in an optimal production process specifically developed for this protein. Using the automation, far less manual intervention is required than in traditional bench-top bioreactors, and much more control is achieved than typical plate or shake flask based screens. By utilizing an integrated cell line and process development incorporating medium optimized for this protein, we were able to increase titer more than 10-fold while obtaining desirable product quality. Finally, Monte Carlo simulations were performed to predict the optimal number of cell lines to screen in future cell line development work with the goal of systematically increasing titer through enhanced cell line screening.
Revision der Struktur von Tolyporphin A (1999)

Aus vier monocyclischen Vorstufen gelang die Totalsynthese der für (+)-Tolyporphin-A-O,O-diacetat vorgeschlagenen Struktur 1-A (X = Ac). Ein Vergleich der spektroskopischen Daten ergab, daß das synthetische Tolyporphin-O,O-diacetat nicht mit dem aus natürlichem (+)-Tolyporphin A (X = H) hergestellten O,O-Diacetat übereinstimmte – eine Korrektur der Struktur dieser Naturstoffklasse war gefordert. Aus einer Reihe von NMR-Experimenten, unter anderem an synthetischen Zwischenprodukten, ließ sich als wahrscheinliche Struktur für den Naturstoff die Struktur 1-B folgern, in der die Konfigurationen der quartären Kohlenstoffzentren C7 und C17 umgekehrt wie ursprünglich angenommen sind.
Quantitating intracellular transport of polyplexes by spatio-temporal image correlation spectroscopy (2005)

Quantitatively understanding how nonviral gene delivery vectors (polyplexes) are transported inside cells is essential before they can be optimized for gene therapy and medical applications. In this study, we used spatio-temporal image correlation spectroscopy (ICS) to follow polymer-nucleic acid particles (polyplexes) of various sizes and analyze their diffusive-like and flow behaviors intracellularly to elucidate the mechanisms responsible for their transport. ICS is a quantitative imaging technique that allows the assessment of particle motion in complex systems, although it has not been widely used to date. We find that the internalized polyplexes are able to use microtubule motors for intracellular trafficking and exhibit different transport behaviors for short (<10 s) versus long (approximately 60 s) correlation times. This motion can be explained by a memory effect of the microtubule motors. These results reveal that, although microtubule motor biases may be present for short periods of time, resulting in a net directional velocity, the overall long-term motion of the polyplexes is best described as a random walk-like process. These studies suggest that spatio-temporal ICS is a powerful technique for assessing the nature of intracellular motion and provides a quantitative tool to compare the transport of different objects within a living cell.
Local Relaxation Behavior and Dynamic Fragility in Hydrogen Bonded Polymer Blends (2010)

The dynamics of intermolecularly hydrogen-bonded polymer blends of poly(p-(hexafluoro-2-hydroxyl-2-propyl)styrene) with poly(vinyl acetate), poly(ethylene[30]-co-vinyl acetate[70]) and poly(ethylene[55]-co-vinyl acetate[45]) are investigated by broadband dielectric relaxation spectroscopy and Fourier transform infrared spectroscopy. Each blend component exhibits a glassy state (β) relaxation, and these relaxations are affected by the formation of intermolecular associations. The glassy state behavior of the blends can be modeled using the Painter−Coleman association model. All blends exhibit a single Tg and a single dielectric segmental (α) relaxation, indicative of strong segmental-level coupling. The fragility of the glass-formers depends on the volume fraction of intermolecularly associated segments, and the association model predicts which compositions have the highest fragilities. A relaxation related to the breaking and reforming of hydrogen bonds is observed at temperatures above the α process, and its temperature dependence varies systematically with ethylene content.