bluuebunny/crossref_metadata_2025_split huggingface dataset:
Localization of a bacterial group II intron-encoded protein in human cells
Authors: Reinoso-Colacio Mercedes , García-Rodríguez Fernando Manuel , García-Cañadas Marta , Amador-Cubero Suyapa , Pérez José Luis García , Toro Nicolás 
Published: August 2015

AbstractGroup II introns are mobile retroelements that self-splice from precursor RNAs to form ribonucleoparticles (RNP), which can invade new specific genomic DNA sites. This specificity can be reprogrammed, for insertion into any desired DNA site, making these introns useful tools for bacterial genetic engineering. However, previous studies have suggested that these elements may function inefficiently in eukaryotes. We investigated the subcellular distribution, in cultured human cells, of the protein encoded by the group II intron RmInt1 (IEP) and several mutants. We created fusions with yellow fluorescent protein (YFP) and with a FLAG epitope. We found that the IEP was localized in the nucleus and nucleolus of the cells. Remarkably, it also accumulated at the periphery of the nuclear matrix. We were also able to identify spliced lariat intron RNA, which co-immunoprecipitated with the IEP, suggesting that functional RmInt1 RNPs can be assembled in cultured human cells.
Arteriovenous Blood Metabolomics: A Readout of Intra-Tissue Metabostasis
Authors: Ivanisevic Julijana , Elias Darlene , Deguchi Hiroshi , Averell Patricia M. , Kurczy Michael , Johnson Caroline H. , Tautenhahn Ralf , Zhu Zhengjiang , Watrous Jeramie , Jain Mohit , Griffin John , Patti Gary J. , Siuzdak Gary 
Published: August 2015

AbstractThe human circulatory system consists of arterial blood that delivers nutrients to tissues and venous blood that removes the metabolic by-products. Although it is well established that arterial blood generally has higher concentrations of glucose and oxygen relative to venous blood, a comprehensive biochemical characterization of arteriovenous differences has not yet been reported. Here we apply cutting-edge, mass spectrometry-based metabolomic technologies to provide a global characterization of metabolites that vary in concentration between the arterial and venous blood of human patients. Global profiling of paired arterial and venous plasma from 20 healthy individuals, followed up by targeted analysis made it possible to measure subtle (<2 fold), yet highly statistically significant and physiologically important differences in water soluble human plasma metabolome. While we detected changes in lactic acid, alanine, glutamine and glutamate as expected from skeletal muscle activity, a number of unanticipated metabolites were also determined to be significantly altered including Krebs cycle intermediates, amino acids that have not been previously implicated in transport and a few oxidized fatty acids. This study provides the most comprehensive assessment of metabolic changes in the blood during circulation to date and suggests that such profiling approach may offer new insights into organ homeostasis and organ specific pathology.
miRegulome: a knowledge-base of miRNA regulomics and analysis
Authors: Barh Debmalya , Kamapantula Bhanu , Jain Neha , Nalluri Joseph , Bhattacharya Antaripa , Juneja Lucky , Barve Neha , Tiwari Sandeep , Miyoshi Anderson , Azevedo Vasco , Blum Kenneth , Kumar Anil , Silva Artur , Ghosh Preetam 
Published: August 2015

AbstractmiRNAs regulate post transcriptional gene expression by targeting multiple mRNAs and hence can modulate multiple signalling pathways, biological processes and patho-physiologies. Therefore, understanding of miRNA regulatory networks is essential in order to modulate the functions of a miRNA. The focus of several existing databases is to provide information on specific aspects of miRNA regulation. However, an integrated resource on the miRNA regulome is currently not available to facilitate the exploration and understanding of miRNA regulomics. miRegulome attempts to bridge this gap. The current version of miRegulome v1.0 provides details on the entire regulatory modules of miRNAs altered in response to chemical treatments and transcription factors, based on validated data manually curated from published literature. Modules of miRegulome (upstream regulators, downstream targets, miRNA regulated pathways, functions, diseases, etc) are hyperlinked to an appropriate external resource and are displayed visually to provide a comprehensive understanding. Four analysis tools are incorporated to identify relationships among different modules based on user specified datasets. miRegulome and its tools are helpful in understanding the biology of miRNAs and will also facilitate the discovery of biomarkers and therapeutics. With added features in upcoming releases, miRegulome will be an essential resource to the scientific community. Availability: http://bnet.egr.vcu.edu/miRegulome.
Determination of the Cytosolic NADPH/NADP Ratio in Saccharomyces cerevisiae using Shikimate Dehydrogenase as Sensor Reaction
Authors: Zhang Jinrui , Pierick Angela ten , van Rossum Harmen M. , Maleki Seifar Reza , Ras Cor , Daran Jean-Marc , Heijnen Joseph J. , Aljoscha Wahl S. 
Published: August 2015

AbstractEukaryotic metabolism is organised in complex networks of enzyme catalysed reactions which are distributed over different organelles. To quantify the compartmentalised reactions, quantitative measurements of relevant physiological variables in different compartments are needed, especially of cofactors. NADP(H) are critical components in cellular redox metabolism. Currently, available metabolite measurement methods allow whole cell measurements. Here a metabolite sensor based on a fast equilibrium reaction is introduced to monitor the cytosolic NADPH/NADP ratio in Saccharomyces cerevisiae: "Equation missing". The cytosolic NADPH/NADP ratio was determined by measuring the shikimate and dehydroshikimate concentrations (by GC-MS/MS). The cytosolic NADPH/NADP ratio was determined under batch and chemostat (aerobic, glucose-limited, D = 0.1 h−1) conditions, to be 22.0 ± 2.6 and 15.6 ± 0.6, respectively. These ratios were much higher than the whole cell NADPH/NADP ratio (1.05 ± 0.08). In response to a glucose pulse, the cytosolic NADPH/NADP ratio first increased very rapidly and restored the steady state ratio after 3 minutes. In contrast to this dynamic observation, the whole cell NADPH/NADP ratio remained nearly constant. The novel cytosol NADPH/NADP measurements provide new insights into the thermodynamic driving forces for NADP(H)-dependent reactions, like amino acid synthesis, product pathways like fatty acid production or the mevalonate pathway.
Visualizing Non-abrupt Transition of Quantum Well States at Stepped Silver Surfaces
Authors: Kumar Saha Srijan , Manna Sujit , Stepanyuk Valeri S. , Kirschner Jürgen 
Published: August 2015

AbstractWe use scanning tunneling spectroscopy (STS) experiments and first-principles density functional theory (DFT) calculations to address a fundamental question of how quantum well (QW) states for electrons in a metal evolve spatially in the lateral direction when there is a surface step that changes the vertical confinement thickness. This study reveals a clear spatially dependent, nearly continuous trend in the energetic shifts of quantum well (QW) states of thin Ag(111) film grown on Cu(111) substrate, showing the strongest change near the step edge. A large energetic shift equaling up to ~200 meV with a lateral extension of the QW states of the order of ~20 Å is found, even though the step-edge is atomically sharp as evidenced by a line scan. The observed lateral extension and the nearly smooth transition of QW states are understood within the context of step-induced charge oscillation and Smoluchowski-type charge spreading and smoothing.
Molecular mobility on graphene nanoroads
Authors: Jafary-Zadeh Mehdi , Zhang Yong-Wei 
Published: August 2015

AbstractWe study molecular mobility on a graphene nanoroad (GNRD), a pristine graphene strip embedded in between two hydrogenated graphene domains serving as a nanoscale pathway for transporting admolecules. Our molecular dynamics simulations using a prototype physisorbed C60 admolecule demonstrate that the proposed GNRD is able to confine the diffusive motion of the admolecule within the nanoroad up to a certain temperature, depending on its width and edge type. Within the confinement regime, the width and edge-type of the GNRD also play an important role in the molecular motion. Specifically, when the GNRD width is narrower than the admolecule diameter, the admolecule performs one-dimensional hopping motion along the nanoroad. When the GNRD width is larger than the admolecule diameter, the admolecule moves only along one of its edges at low temperatures and shuffle between two edges at high temperatures. We further show the admolecule motion on the zigzag-edged GRND is faster than that on the armchair-edged GRND with the same width and at the same temperature. These results can be well explained by analysing the potential energy surfaces of the systems. Since such hydrogenated graphene nanostructures have been experimentally realized, our results provide a valuable reference for constructing molecular conveyor circuits.
Reduced Expression of Argonaute 1, Argonaute 2 and TRBP Changes Levels and Intracellular Distribution of RNAi Factors
Authors: Matsui Masayuki , Li Liande , Janowski Bethany A. , Corey David R. 
Published: August 2015

AbstractUntil recently, Argonaute 2 (AGO2) and other RNA factors were believed to be restricted to the cytoplasm of mammalian somatic cells. It is now becoming appreciated that RNAi factors can also be found in cell nuclei, but much remains to be learned about their transport, molecular recognition and function. We find that siRNA-mediated reduction of AGO1 or AGO2 increases the proportion of AGO1 or AGO2 in cell nuclei. Inhibition of AGO1 expression led to increased AGO2 levels, while knockdown of AGO2 led to increased levels of AGO1. Blocking AGO1, AGO2, or TRBP expression changed expression levels and nuclear distribution of RNAi factors Dicer, TNRC6A (GW182) and TRBP. These data reveal the expression of RNAi proteins is mutually dependent and that perturbation can affect subcellular distribution of those factors inside cells.
Intrinsic mutagenic properties of 5-chlorocytosine: A mechanistic connection between chronic inflammation and cancer
Authors: Fedeles Bogdan I. , Freudenthal Bret D. , Yau Emily , Singh Vipender , Chang Shiou-chi , Li Deyu , Delaney James C. , Wilson Samuel H. , Essigmann John M. 
Published: August 2015

Significance
Chronic inflammation is a significant risk factor for cancer and other human diseases. During chronic inflammation, cells exposed to neutrophil-derived hypochlorous acid accumulate in their genomes the DNA lesion 5-chlorocytosine (5ClC). Using a battery of chemical, structural, and genetic tools, the present study demonstrates that 5ClC is a mutagenic lesion, suggesting that genomic 5ClC accumulation could have very serious biological consequences. 5ClC induces C→T transitions, a type of mutation commonly observed in tissues under inflammatory stress as well as in the genomes of inflammation-driven cancers. Thus, the mutagenic properties of 5ClC represent an appealing molecular mechanism by which chronic inflammation induces the genetic changes that potentially enable and stimulate carcinogenesis.
Are We Catching What They Eat? Moving Beyond Trends in the Mean Trophic Level of Catch
Authors: Rountos Konstantine J. , Frisk Michael G. , Pikitch Ellen K. 
Published: August 2015

Abstract
The mean trophic level of fisheries catch is commonly used to describe and assess temporal trends in fisheries. Though its value as an indicator to evaluate the relative health of fisheries in marine ecosystems has been hotly debated, the metric calculated is clear. We applied this indicator along with a relatively new indicator, the mean trophic level of predator consumption, to 40 Ecopath models around the world. Together, these measures were used to detect where fisheries and marine predators may be targeting similar trophic levels of prey. Globally, the mean trophic levels caught by all fisheries and finfish fisheries were similar to those consumed by marine mammals but significantly higher than those consumed by seabirds and large predatory fish. We found no significant differences between the median trophic levels targeted by forage fisheries and predators. These indicators can inform ecosystembased management, especially when information on predators and fishery interactions are limited or unavailable.
El nivel trófico promedio de las capturas pesqueras se utiliza comúnmente para describir y evaluar las tendencias de las pesquerías a través del tiempo. Si bien su utilidad como indicador de la salud relativa de las pesquerías en ecosistemas marinos ha sido un tema de intenso debate, el cálculo de esta métrica es claro. En el presente artículo se aplicó este indicador junto con uno nuevo, el nivel trófico promedio del consumo de los depredadores, a 40 modelos Ecopath alrededor del mundo. Juntas, estas dos medidas fueron utilizadas para detectar dónde las pesquerías y los depredadores marinos pueden estar incidiendo en niveles tróficos similares de las presas. De forma global, los niveles tróficos promedio capturados por todas las pesquerías de escama fueron similares a aquellos consumidos por mamíferos marinos, pero sensiblemente más altos que aquellos consumidos por aves marinas y grandes peces depredadores. No se encontraron diferencias significativas entre los niveles tróficos que utilizan las pesquerías de peces forrajeros y los depredadores. Estos indicadores pueden aportar información útil para el manejo de las pesquerías basado en el ecosistema, especialmente cuando la información sobre los depredadores y las interacciones con las pesquerías es limitada o no está disponible.
Characterizing the Human Dimensions of a Hidden Fishery: Riverine Trotline Fishers
Authors: Dickinson Benjamin D. , Orth Donald J. , McMullin Steve L. 
Published: August 2015

Abstract
Hidden fisheries include catfish harvesters who use trotlines and are seldom surveyed. We examined trotline fishers to describe fishing habits and techniques, trotline fishing knowledge, recreational motivations, and opinions of the fishery, regulations, and conflicts with other river users. Trotline fishers on the New River, Virginia, were secretive and solitary, and some were socioeconomically disadvantaged. They placed high importance on catch- and harvest-related factors, in contrast to many other angler groups who use highly specialized methods. They relied on harvesting catfish for varying degrees of sustenance to their diet or income. Trotline fishing appears to be part of a larger “way of life” for some rural individuals, who may also hunt, trap, and garden as part of activities to supplement their diet or income. New River trotline fishers strongly believed that participation in trotline fishing had declined significantly in the New River Valley due to improving socioeconomic status of the region, changing recreational values (such as focus on catch-and-release fishing and paddle sports), increasing recreational boat traffic and law enforcement presence, and decreasing participation in trotline fishing by younger generations.
Las pesquerías escondidas incluyen a los pescadores de bagre quienes usan el palangre artesanal pero que rara vez son contabilizados. En este artículo se examinan a los pescadores de palangre artesanal con el fin de describir sus hábitos y técnicas de pesca, el conocimiento existente sobre pesca con palangre artesanal, motivaciones recreativas, opiniones sobre la pesquería y conflictos con otros usuarios de los ríos. Los pescadores de palangre artesanal en New River, Virginia, mostraron ser reservados, solitarios y algunos estuvieron en condiciones socioeconómicas desventajosas. Ellos consideran muy importante la captura y factores relativos a ésta, en contraste con otros grupos de pescadores que utilizan métodos altamente especializados. Así mismo, dependen de la captura de bagre en grado diverso para el sustento de su dieta o de su ingreso. La pesca artesanal de palangre parece constituir parte de un modo de vida más general para algunos individuos rurales, quienes también pueden cazar, atrapar y hacer jardinería como parte de actividades suplementarias para mantener su dieta e ingreso. Los pescadores de palangre artesanal de New River creen firmemente que la participación en este tipo de pesquería ha declinado significativamente en el Valle de New River debido al incremento del estatus socioeconómico de la región, al cambio en los valores recreativos (tales como la pesca enfocada a captura-recaptura y deportes de remo), el tráfico creciente de botes, presencia del poder judicial y a una reducción en la participación de las generaciones más jóvenes en la pesca artesanal de palangre.
Influence of Ventilation Strategies and Anesthetic Techniques on Regional Cerebral Oximetry in the Beach Chair Position
Authors: Picton Paul , Dering Andrew , Alexander Amir , Neff Mary , Miller Bruce S. , Shanks Amy , Housey Michelle , Mashour George A. 
Published: August 2015

AbstractAbstract
Cerebral oxygenation desaturation in the beach chair position, as estimated by cerebral oximetry, may be attenuated by the combination of normobaric hyperoxia and moderate hypercarbia. This appears independent of anesthetic agent.

Background:
Beach chair positioning during general anesthesia is associated with cerebral oxygen desaturation. Changes in cerebral oxygenation resulting from the interaction of inspired oxygen fraction (Fio
2), end-tidal carbon dioxide (PETco
2), and anesthetic choice have not been fully evaluated in anesthetized patients in the beach chair position.

Methods:
This is a prospective interventional within-group study of patients undergoing shoulder surgery in the beach chair position that incorporated a randomized comparison between two anesthetics. Fifty-six patients were randomized to receive desflurane or total intravenous anesthesia with propofol. Following induction of anesthesia and positioning, Fio
2 and minute ventilation were sequentially adjusted for all patients. Regional cerebral oxygenation (rSo
2) was the primary outcome and was recorded at each of five set points.

Results:
While maintaining Fio
2 at 0.3 and PETco
2 at 30 mmHg, there was a decrease in rSo
2 from 68% (SD, 12) to 61% (SD, 12) (P < 0.001) following beach chair positioning. The combined interventions of increasing Fio
2 to 1.0 and increasing PETco
2 to 45 mmHg resulted in a 14% point improvement in rSo
2 to 75% (SD, 12) (P <0.001) for patients anesthetized in the beach chair position. There was no significant interaction effect of the anesthetic at the study intervention points.

Conclusions:
Increasing Fio
2 and PETco
2 resulted in a significant increase in rSo
2 that overcomes desaturation in patients anesthetized in the beach chair position and that appears independent of anesthetic choice.
The P25 protein ofPotato virus Xsuppresses accumulation of 24nt siRNAs in theN. benthamianatransgenic line 16c
Authors: Garcia Shahinez , Himber Christophe , Voinnet Olivier 
Published: August 2015

AbstractBy transiently expressing viral suppressors of RNA silencing (VSRs) in combination with GFP silencing-inducing constructs in leaves ofNicotiana benthamianaline 16c, Hamilton et al. (2002) could establish a positive correlation between the production of 24nt GFP small interfering (si)RNAs in infiltrated leaves and the systemic onset of GFP silencing in remote tissues. In the context of GFP silencing inducers based on replicatingPotato virus X (PVX), the P25 protein of PVX was found to specifically inhibit the local accumulation of 24nt GFP siRNAs. In the original paper, there were background pixel pattern duplications in the figure reporting the P25 experiments. We have now repeated these experiments with the original clones and the results presented here confirm those reported in the original paper.
Tracking and following pedestrian trajectories, an approach for autonomous surveillance of critical infrastructures
Authors: Garzon Oviedo Mario Andrei , Barrientos Antonio , Del Cerro Jaime , Alacid Andrés , Fotiadis Efstathios , Rodríguez-Canosa Gonzalo R. , Wang Bang-Chen 
Published: August 2015

Purpose
– This paper aims to present a system that is fully capable of addressing the issue of detection, tracking and following pedestrians, which is a very challenging task, especially when it is considered for using in large outdoors infrastructures. Three modules, detection, tracking and following, are integrated and tested over long distances in semi-structured scenarios, where static or dynamic obstacles, including other pedestrians, can be found.

Design/methodology/approach
– The detection is based on the probabilistic fusion of a laser scanner and a camera. The tracking module pairs observations with previously detected targets by using Kalman Filters and a Mahalanobis-distance. The following module allows to safely pursue the target by using a well-defined navigation scheme.

Findings
– The system can track pedestrians from static position to 3.46 m/s (running). It handles occlusions, crossings or miss-detections, keeping track of the position even if the pedestrian is only detected in 55/per cent of the observations. Moreover, it autonomously selects and follows a target at a maximum speed of 1.46 m/s.

Originality/value
– The main novelty of this study is the integration of the three algorithms in a fully operational system, tested in real outdoor scenarios. Furthermore, the addition of labelling to the detection algorithm allows using the full range of a single sensor while preserving the high performance of a combined detection. False-positives’ rate is reduced by handling the uncertainty level when pairing observations. The inclusion of pedestrian speed in the model speeds up and simplifies tracking process. Finally, the most suitable target is automatically selected by a scoring system.
Design and experimental study of a new thrown robot based on flexible structure
Authors: Wang Wei , Wu Shilin , Zhu Peihua , Li Xuepeng 
Published: August 2015

Purpose
– The paper aims to present a new thought for design of a thrown robot based on flexible structures. The aim of the design is to reduce the weight and improve the anti-impact capability for mini thrown robot.

Design/methodology/approach
– A mass-spring wheeled robot model is proposed and an impact analysis is given in this paper. Some principia were derived for configuration design and material choice to get a light and robust thrown reconnaissance robot. Based on the theoretical analysis, flexible elements like flexure hinges or rubber shell were utilized to build two generation of robots that both showed excellent performances of anti-impact ability.

Findings
– A second-generation thrown robot (2,050 g) was developed, which could survive dropping from the height of 6 m more than 10 times without apparent damage.

Originality/value
– The method based on the flexible structure provides the thrown robot with high survivability from impact, as well as light weight. It can be used in the design of the mini thrown reconnaissance robot at low cost.