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Tagging and capture

Dieter Galea, Ivan Laponogov, Kirill Veselkov
Motivation: Recognition of biomedical entities from scientific text is a critical component of natural language processing and automated information extraction platforms. Modern named entity recognition approaches rely heavily on supervised machine learning techniques, which are critically dependent on annotated training corpora. These approaches have been shown to perform well when trained and tested on the same source. However, in such scenario, the performance and evaluation of these models may be optimistic, as such models may not necessarily generalize to independent corpora, resulting in potential non-optimal entity recognition for large-scale tagging of widely diverse articles in databases such as PubMed...
March 10, 2018: Bioinformatics
J D Armstrong, S McKelvey, G W Smith, P Rycroft, R J Fryer
Groups of wild-reared Atlantic salmon Salmo salar smolts were captured during their seaward migration on a tributary of the River Conon, Scotland, U.K., from 1999 to 2014 and tagged with passive integrated transponders (PIT). Fish that subsequently returned to the river after growing at sea were recorded automatically by a PIT-detector in a fish pass. Return rate was related directly to length and condition and inversely to day of the year that the smolt was tagged. Over years, as the study progressed, there was a significant increase in the proportion of smolts returning after two or more years at sea and no trend in returns of salmon having spent one winter at sea...
March 2018: Journal of Fish Biology
Masanori Nomoto, Kaoru Inokuchi
Behavioral tagging is the transformation of a short-term memory induced by a weak experience into a long-term memory through temporal association with a novel experience. This phenomenon was discovered to recapitulate synaptic tagging and capture at the behavioral level. Significant progress has been made in determining the molecular machinery associated with synaptic tagging and capture and behavioral tagging theories. However, the tag setting and recruitment of plasticity-related proteins that occur within the spatiotemporally constrained cell ensemble at the network level (cellular tagging) in the brain where multimodal sensory information is input are just beginning to be understood...
March 10, 2018: Neurobiology of Learning and Memory
Sajal Shrivastava, Won-Il Lee, Nae-Eung Lee
A critical unmet need in the diagnosis of bacterial infections, which remain a major cause of human morbidity and mortality, is the detection of scarce bacterial pathogens in a variety of samples in a rapid and quantitative manner. Herein, we demonstrate smartphone-based detection of Staphylococcus aureus in a culture-free, rapid, quantitative manner from minimally processed liquid samples using aptamer-functionalized fluorescent magnetic nanoparticles. The tagged S. aureus cells were magnetically captured in a detection cassette, and then fluorescence was imaged using a smartphone camera with a light-emitting diode as the excitation source...
March 6, 2018: Biosensors & Bioelectronics
A Monadjem, A Kane, A Botha, C Kelly, C Murn
Obligate scavengers such as vultures provide critical ecosystem services and their populations have undergone severe declines in Asia and Africa. Intentional poisoning is a major threat to vultures in Africa, yet the impact on vulture populations of where poisoned carcasses are positioned is not known. We used re-sightings of 183 African white-backed vultures captured and tagged in two regions of South Africa, some 200 km apart, to estimate spatial differences in relative survival rates across life stages...
March 12, 2018: Scientific Reports
Muhammed Veli, Aydogan Ozcan
We present a cost-effective and portable platform based on contact lenses for non-invasively detecting Staphylococcus aureus, which is part of the human ocular microbiome and resides on the cornea and conjunctiva. Using Staphylococcus aureus-specific antibodies and a surface chemistry protocol that is compatible with human tear, contact lenses are designed to specifically capture Staphylococcus aureus. After the bacteria capture on the lens, and right before its imaging, the captured bacteria are tagged with surface-functionalized polystyrene microparticles...
March 9, 2018: ACS Nano
Xiao Rui
The detection of hepatocellular carcinoma (HCC) circulating tumor cells (CTCs) from a blood sample can be a very powerful noninvasive approach for the early detection and therapy of liver cancer. However, the extremely rare cells in blood containing billions of other cells make the capture and identification of CTCs with sufficient sensitivity and specificity a real challenge. Here, a magnetically assisted surface-enhanced Raman scattering (SERS) biosensor for HCC CTCs detection is reported for the first time...
March 9, 2018: Chemistry: a European Journal
Merideth A Cooper, Joseph E Taris, Changhua Shi, David W Wood
In this work, we describe a novel self-cleaving tag technology based on a highly modified split-intein cleaving element. In this system, the N-terminal segment of an engineered split intein is expressed in E. coli and covalently immobilized onto a capture resin, while the smaller C-terminal intein segment is fused to the N-terminus of the desired target protein. The tagged target can then be expressed in an appropriate expression system, without concern for premature intein cleaving. During the purification, strong association between the intein segments effectively captures the tagged target onto the capture resin while simultaneously generating a cleaving-competent intein complex...
February 21, 2018: Current Protocols in Protein Science
Honghai Wang, Yan Sun, Weiwei Yue, Qi Kang, Huijuan Li, Dazhong Shen
Sensitive detection of cancer biomarkers is valuable for clinical diagnosis and treatment assessment of cancers. Herein, we report a simple smartphone-based double-channel fluorescence setup for immunoassay. Not including the smartphone, the total cost of the detection device itself is about 80 $, including a laser pointer, a twinning measurement cell, a collective lens, and an outside box. The fluorescence images of the sample and reference areas were captured by the camera in the smartphone and the brightness ratio was calculated using a user-edited smartphone app...
March 7, 2018: Analyst
Patricia Arranz, Kelly J Benoit-Bird, Brandon L Southall, John Calambokidis, Ari S Friedlaender, Peter L Tyack
Humans remember the past and use that information to plan future actions. Lab experiments that test memory for the location of food show that animals have a similar capability to act in anticipation of future needs, but less work has been done on animals foraging in the wild. We hypothesized that planning abilities are critical and common in breath-hold divers who adjust each dive to forage on prey varying in quality, location and predictability within constraints of limited oxygen availability. We equipped Risso's dolphins with sound-and-motion recording tags to reveal where they focus their attention through their externally observable echolocation and how they fine tune search strategies in response to expected and observed prey distribution...
February 28, 2018: Journal of Experimental Biology
Michael F Cameron, Kathryn J Frost, Jay M Ver Hoef, Greg A Breed, Alex V Whiting, John Goodwin, Peter L Boveng
The first year of life is typically the most critical to a pinniped's survival, especially for Arctic phocids which are weaned at only a few weeks of age and left to locate and capture prey on their own. Their seasonal movements and habitat selection are therefore important factors in their survival. During a cooperative effort between scientists and subsistence hunters in October 2004, 2005, and 2006, 13 female and 13 male young (i.e., age <2) bearded seals (Erignathus barbatus) were tagged with satellite-linked dive recorders (SDRs) in Kotzebue Sound, Alaska...
2018: PloS One
Marta Robledo, Ana M Matia-González, Natalia I García-Tomsig, José I Jiménez-Zurdo
The identification of the protein partners of bacterial small noncoding RNAs (sRNAs) is essential to understand the mechanistic principles and functions of riboregulation in prokaryotic cells. Here, we describe an optimized affinity chromatography protocol that enables purification of in vivo formed sRNA-protein complexes in Sinorhizobium meliloti, a genetically tractable nitrogen-fixing plant symbiotic bacterium. The procedure requires the tagging of the desired sRNA with the MS2 aptamer, which is affinity-captured by the MS2-MBP protein conjugated to an amylose resin...
2018: Methods in Molecular Biology
Masaharu Iwasaki, Petra Minder, Yíngyún Caì, Jens H Kuhn, John R Yates, Bruce E Torbett, Juan C de la Torre
Several mammalian arenaviruses (mammarenaviruses) cause hemorrhagic fevers in humans and pose serious public health concerns in their endemic regions. Additionally, mounting evidence indicates that the worldwide-distributed, prototypic mammarenavirus, lymphocytic choriomeningitis virus (LCMV), is a neglected human pathogen of clinical significance. Concerns about human-pathogenic mammarenaviruses are exacerbated by of the lack of licensed vaccines, and current anti-mammarenavirus therapy is limited to off-label use of ribavirin that is only partially effective...
February 20, 2018: PLoS Pathogens
Danuta Maria Wisniewska, Mark Johnson, Jonas Teilmann, Ursula Siebert, Anders Galatius, Rune Dietz, Peter Teglberg Madsen
Shipping is the dominant marine anthropogenic noise source in the world's oceans, yet we know little about vessel encounter rates, exposure levels and behavioural reactions for cetaceans in the wild, many of which rely on sound for foraging, communication and social interactions. Here, we used animal-borne acoustic tags to measure vessel noise exposure and foraging efforts in seven harbour porpoises in highly trafficked coastal waters. Tagged porpoises encountered vessel noise 17-89% of the time and occasional high-noise levels coincided with vigorous fluking, bottom diving, interrupted foraging and even cessation of echolocation, leading to significantly fewer prey capture attempts at received levels greater than 96 dB re 1 µPa (16 kHz third-octave)...
February 14, 2018: Proceedings. Biological Sciences
Xue-Jian Zhang, Xiao-Wei Wang, Xiao-Di Da, Yanlin Shi, Chunli Liu, Fei Sun, Shuguang Yang, Wen-Bin Zhang
Protein-based materials call for innovative processing techniques to integrate their unique biologically enabled functions with other materials of complementary features. Herein, we report the covalent protein layer-by-layer assembly via orthogonal "Tag-Catcher" reactions as a facile and robust approach to make entirely protein-based multilayers on a variety of substrates. Programmed assembly of native telechelic proteins not only endows the materials valuable stimuli-sensitive behaviors, but also unique properties unparalleled by any synthetic counterparts...
February 14, 2018: Biomacromolecules
Xiaofei Wang, Hongfang Gao, Honglan Qi, Qiang Gao, Chengxiao Zhang
A simple electrochemiluminescence (ECL) immunoassay based on proximity hybridization-regulated strategy was developed for highly sensitive and specific detection of cell surface protein and protein-overexpressing cancer cells. A biosensor was fabricated by self-assembling a thiolated capture ss-DNA3 (partially hybridize with ss-DNA1 and ss-DNA2) and blocking with 6-mercapto-1-hexanol on gold electrode surface. Target protein was simultaneously bound by two ss-DNA-tagged antibody probes (DNA1-Ab1 and DNA2-Ab2), while DNA1 and DNA2 were brought in sufficient proximity and hybridized with capture DNA3 on the surface of the biosensor...
February 13, 2018: Analytical Chemistry
Renato Assis Machado, Hercílio Martelli-Júnior, Silvia Regina de Almeida Reis, Darlene Camati Persuhn, Ricardo D Coletta
Nonsyndromic oral clefts are common congenital birth defects that exhibit variable prevalence around the world, often influenced by population-dependent genetic predisposition. Few studies have been performed with nonsyndromic cleft palate only (NSCPO), limiting the knowledge of the genetic risk factors related to this type of oral cleft. Genetic variants in golgin subfamily B member 1 (GOLGB1), a gene that is essential for normal murine palatogenesis, were analyzed in this study to establish its potential association with NSCPO risk in the Brazilian population...
February 12, 2018: Annals of Human Genetics
Hui Ouyang, Xinman Tu, Zhifeng Fu, Wenwen Wang, Shaofang Fu, Chengzhou Zhu, Dan Du, Yuehe Lin
Graphitic carbon nitride/bismuth ferrite nanocomposites (g-C3N4/BiFeO3 NCs) were synthesized by a facile one step sol-gel combustion method and employed as a peroxidase-like catalyst. Based on the catalytical activity on the luminol-H2O2 reaction, the nanocomposites were utilized as a colorimetric/chemiluminescent dual-readout immunochromatographic assay (ICA) for the multiplexed detection of pesticide residues by utilizing chlorpyrifos and carbaryl as the model analytes. In the proposed protocol, chlorpyrifos antibody and carbaryl antibody were tagged to g-C3N4/BiFeO3 NCs for developing the spatially-resolved multianalyte ICA...
January 31, 2018: Biosensors & Bioelectronics
Floris M van Beest, Jonas Teilmann, Line Hermannsen, Anders Galatius, Lonnie Mikkelsen, Signe Sveegaard, Jeppe Dalgaard Balle, Rune Dietz, Jacob Nabe-Nielsen
Knowledge about the impact of anthropogenic disturbances on the behavioural responses of cetaceans is constrained by lack of data on fine-scale movements of individuals. We equipped five free-ranging harbour porpoises (Phocoena phocoena) with high-resolution location and dive loggers and exposed them to a single 10 inch3 underwater airgun producing high-intensity noise pulses (2-3 s intervals) for 1 min. All five porpoises responded to capture and tagging with longer, faster and more directed movements as well as with shorter, shallower, less wiggly dives immediately after release, with natural behaviour resumed in less than or equal to 24 h...
January 2018: Royal Society Open Science
Di Yun, Yinghan Zhuang, Michael R Kreutz, Thomas Behnisch
Posttranslational modification and degradation of proteins by the ubiquitin-proteasome system (UPS) is crucial to synaptic transmission. It is well established that 19S proteasome associated deubiquitinases (DUBs) reverse the process of ubiquitination by removing ubiquitin from their substrates. However, their potential contribution to hippocampal synaptic plasticity has not been addressed in detail. Here, we report that inhibition of the 19S proteasome associated DUBs, ubiquitin C-terminal hydrolase 5 (UCHL5) and ubiquitin-specific peptidase 14 (USP14) by b-AP15 results in an accumulation of polyubiquitinated proteins and a reduction of monomeric ubiquitin without overt effects on 26S proteasome activity...
January 30, 2018: Neuropharmacology
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