bluuebunny/crossref_metadata_2025_split huggingface dataset:
A reverse-transcription/RNase H based protocol for depletion of mosquito ribosomal RNA facilitates viral intrahost evolution analysis, transcriptomics and pathogen discovery
Authors: Fauver Joseph R. , Akter Shamima , Morales Aldo Ivan Ortega , Black William C. , Rodriguez Americo D. , Stenglein Mark D. , Ebel Gregory D. , Weger-Lucarelli James 
Published: October 2018

AbstractStudies aimed at identifying novel viral sequences or assessing intrahost viral variation require sufficient sequencing coverage to assemble contigs and make accurate variant calling at low frequencies. Many samples come from host tissues where ribosomal RNA represents more than 90% of total RNA preparations, making unbiased sequencing of viral samples inefficient and highly expensive, as many reads will be wasted on cellular RNAs. In the presence of this amount of ribosomal RNA, it is difficult to achieve sufficient sequencing depth to perform analyses such as variant calling, haplotype prediction, virus population analyses, virus discovery or transcriptomic profiling. Many methods for depleting unwanted RNA or enriching RNA of interest have been devised, including poly-A selection, RNase H based specific depletion, duplex-specific nuclease treatment and hybrid capture selection, among others. Although these methods can be efficient, they either cannot be used for some viruses (i.e. non-polyadenylated viruses), have been optimized for use in a single species, or have the potential to introduce bias. In this study, we describe a novel approach that uses an RNaseH possessing reverse transcriptase coupled with selective probes for ribosomal RNA designed to work broadly for three medically relevant mosquito genera;Aedes,Anopheles,andCulex.We demonstrate significant depletion of rRNA using multiple assessment techniques from a variety of sample types, including whole mosquitoes and mosquito midgut contents from FTA cards. To demonstrate the utility of our approach, we describe novel insect-specific virus genomes from numerous species of field collected mosquitoes that underwent rRNA depletion, thereby facilitating their detection. The protocol is straightforward, relatively low-cost and requires only common laboratory reagents and the design of several small oligonucleotides specific to the species of interest. This approach can be adapted for use with other organisms with relative ease, thus potentially aiding virus population genetics analyses, virus discovery and transcriptomic profiling in both laboratory and field samples.
HypermorphicSERK1mutations function via aSOBIR1pathway to activate floral abscission signaling
Authors: Taylor Isaiah , Baer John , Calcutt Ryan , Walker John C. 
Published: October 2018

AbstractIn Arabidopsis, the abscission of floral organs is regulated by two related receptor-like protein kinases (RLKs), HAESA and HAESA-like 2 (HAE/HSL2). HAE/HSL2, in complex with members of the SERK family of coreceptor protein kinases, are activated by the binding of the proteolytically processed peptide ligand IDA. This leads to expression of genes encoding secreted cell wall remodeling and hydrolase enzymes.hae hsl2mutants fail to induce expression of these genes and retain floral organs indefinitely. In this paper we report identification of an allelic series ofhae hsl2suppressor mutations in theSERK1coreceptor protein kinase gene. Genetic and transcriptomic evidence indicates these alleles represent a novel class of gain of function mutations that activate signaling independent of HAE/HSL2. We show that the suppression effect surprisingly does not rely on protein kinase activity of SERK1, and that activation of signaling relies on the RLK geneSOBIR1. The effect of these mutations can be mimicked by loss of function ofBIR1,a known negative regulator ofSERK-SOBIR1signaling. These results suggestBIR1functions to negatively regulateSERK-SOBIR1signaling during abscission, and that the identifiedSERK1mutations likely interfere with this negative regulation.
Red squirrels mitigate costs of territory defence through social plasticity
Authors: Siracusa Erin R. , Wilson David R. , Studd Emily K. , Boutin Stan , Humphries Murray M. , Dantzer Ben , Lane Jeffrey E. , McAdam Andrew G. 
Published: October 2018

AbstractFor territorial species, the ability to be behaviourally plastic in response to changes in their social environment may be beneficial by allowing individuals to mitigate conflict with conspecifics and reduce the costs of territoriality. Here we investigated whether North American red squirrels (Tamiasciurus hudsonicus) were able to minimize costs of territory defence by adjusting behaviour in response to the familiarity of neighbouring conspecifics. Since red squirrels living in familiar neighbourhoods face reduced intrusion risk, we predicted that increasing familiarity among territorial neighbours would allow squirrels to spend less time on territorial defence and more time in the nest. Long-term behavioural data (1995-2004) collected from the same squirrels across several different social environments indicated that red squirrels reduced rates of territorial vocalizations and increased nest use in response to increasing familiarity with neighbours. In contrast, cross-sectional data (2015-2016), which provided observations from each individual in a single social environment, did not provide evidence of this plasticity. Post-hoc analyses revealed that evidence of social plasticity in this system was primarily due to within-individual changes in behaviour, which we were unable to estimate in the cross-sectional data. Our results demonstrate that red squirrels can reduce the costs of territoriality by appropriately adjusting behaviour in response to changes in their social environment. However, our results also suggest that estimating plasticity by comparing behaviour among individuals (i.e. cross-sectional analyses) may not always be reliable. Our ability to detect these effects may therefore depend on having data with multiple observations from the same individuals across different social environments.
Bright split red fluorescent proteins with enhanced complementation efficiency for the tagging of endogenous proteins and visualization of synapses
Authors: Feng Siyu , Varshney Aruna , Villa Doris Coto , Modavi Cyrus , Kohler John , Farah Fatima , Ali Nebat , Mueller Joachim Dieter , VanHoven Miri , Huang Bo 
Published: October 2018

AbstractSelf-associating split fluorescent proteins (FPs) have been widely used for labeling proteins, scaffolding protein assembly and detecting cell-cell contacts. Newly developed self-associating split FPs, however, have suffered from suboptimal fluorescence signal. Here, by investigating the complementation process, we have demonstrated two approaches to improve split FPs: assistance through SpyTag/SpyCatcher interaction and directed evolution. The latter has yielded two split sfCherry3 variants with substantially enhanced overall brightness, facilitating the tagging of endogenous proteins by gene editing. Based on sfCherry3, we have further developed a new red-colored trans-synaptic marker called Neuroligin-1 sfCherry3 Linker Across Synaptic Partners (NLG-1 CLASP) for multiplexed visualization of neuronal synapses in living animals, demonstrating its broad applications.
Probability cueing of singleton-distractor locations in visual search: priority-map‐ or dimension-based inhibition?
Authors: Zhang Bei , Allenmark Fredrik , Liesefeld Heinrich R. , Shi Zhuanghua , Müller Hermann J. 
Published: October 2018

ABSTRACTObservers can learn the likely locations of salient distractors in visual search, reducing their potential to capture attention (Ferrante et al., 2018; Sauter et al., 2018a; Wang & Theeuwes, 2018a). While there is agreement that this involves positional suppression of the likely distractor location(s), it is contentious at which stage of search guidance the suppression operates: the supra-dimensional priority map or feature-contrast signals within the distractor dimension. On the latter account, advocated by Sauter et al., target processing should be unaffected by distractor suppression when the target is defined in a different (non-suppressed) dimension to the target. At odds with this, Wang and Theeuwes found strong suppression not only of the (color) distractor, but also of the (shape) target when it appeared at the likely distractor location. Adopting their paradigm, the present study ruled out that increased cross-trial inhibition of the single frequent (frequently inhibited) as compared to any of the rare (rarely inhibited) distractor locations is responsible for this target-location effect. However, a reduced likelihood of the target appearing at the frequent vs. a rare distractor location contributes to this effect: removing this negative bias abolished the cost to target processing with increasing practice, indicative of a transition from priority-map‐ to dimension-based – and thus a flexible locus of – distractor suppression.Public Significance StatementDistraction by a salient visual stimulus outside the ‘focus’ of the task at hand occurs frequently. The present study examined whether and how ‘knowledge’ of the likely location(s) where the distractors occur helps the observer to mitigate distraction. The results confirmed that observers can learn to suppress distracting stimuli at likely locations. Further, they showed that, the suppression may occur at different levels in the hierarchically organized visual system where the priorities of which objects to be attended in the environment are determined.
A Whole-Genome Association Approach for Large-scaled Inter-species Trait
Authors: Wu Qi , Fan Huizhong , Chen Lei , Hu Yibo , Wei Fuwen 
Published: October 2018

AbstractGenome wide association studies (GWAS) have provided an avenue for the association between common genetic variants and complex traits. However, using SNP as a genetic marker, GWAS has been confined to detect genetic basis traits only for within species but not for the large-scale inter-species traits. Here, we propose a practical statistical approach that is using kmer frequencies as the genetic markers to associate genetic variants with large scale inter-species traits. We applied this new approach to the trait of chromosome number in 96 mammalian proteomes, and we prioritized 130 genes including TP53 and BAD, of which 6 were candidate genes. These genes were proved to be associated with cellular reaction of DNA double-strand breaks caused by chromosome fission/fusion. Our study provides a new effective genomic strategy to perform association studies for large-scaled inter-species traits, using the chromosome number as a case. We hope this approach could provide exploration for broadly widely traits.
In vitro model of inflammatory, hypoxia, and cancer stem cell signaling in pancreatic cancer using heterocellular 3-dimensional spheroids
Authors: Suresh Megha , Mattheolabakis George , Singh Amit , Amiji Mansoor 
Published: October 2018

AbstractIntroductionAs one of the most aggressive cancers worldwide, pancreatic cancer is associated with an extremely poor prognosis. The pancreatic tumor microenvironment consists of cancer cells and other tumor associated cells. Cross-talk between these different cell types through various signaling molecules results in the development of a more aggressive and malignant phenotype. Additionally, due to the highly dysregulated vasculature of tumors, the inner tumor core becomes hypoxic and eventually necrotic. Therefore, there is a need for the development of a physiologically relevant in vitro model that recapitulates these dynamic cell-cell interactions and the 3-dimensional (3D) structure of pancreatic tumors.MethodsFour different 3D co-culture spheroid models using different combinations of Panc-1 tumor cells, J774.A1 macrophages, and NIH-3T3 fibroblast cell lines were reproducibly developed using the hanging drop technique in order to mimic the tumor microenvironment and to evaluate the differences in expression of various inflammatory, hypoxia, and cancer stem cell markers, including IL-8, TNF-α, TGF-β, HIF-1α HIF-2α, SCF, and LDH-A. Additionally, immunofluorescence studies were employed to investigate whether these spheroids tested positive for a cancer stem cell population.ResultsPronounced differences in morphology as well as expression of signalling markers were observed using qPCR, indicative of strong influences of co-culturing different cell lines. These models also tested positive for cancer stem cell (CSCs) markers based on immunofluorescence and qPCR analysis.ConclusionOur results demonstrate the potential of 3D co-culture spheroid models to capture the inflammatory and hypoxic markers of pancreatic tumor microenvironment. We further demonstrate the presence of cancer cells with stem cell markers, similar to actual pancreatic cancer tumor. These spheroids present excellent in vitro system to study tumor-immune-stromal cell interactions as well as test deliverability of potential therapeutics in the tumor microenvironment with accurate physical and physiological barriers.
Effects of the Salinity under Soilless Culture Systems on Gamma Linolenic Acid Levels in Borage Seed Oil
Authors: Urrestarazu Miguel , Manuel Gallegos-Cedillo Victor , Ferrón-Carrillo Francisca , Luis Guil-Guerrero José , Lao Teresa , Eugenio Álvaro Juan 
Published: October 2018

AbstractBorage is a well-known plant of great importance in human nutrition and health. Expanding knowledge of particular plants that have anti-cancer products is a global concern. There is substantial information regarding the benefits, presence and extraction of gamma linolenic acid (GLA) in different plants around the world, especially in borage seeds. However, there is little information concerning the effects of the salinity of the nutrient solution on the growth and presence of GLA in borage seeds. The objective of this work was to determine the optimal salinity of the nutrient solution for obtaining GLA in soilless cultivation systems. Borage plants were grown in coconut fibre and provided three treatments of nutrient solution of 2.20, 3.35 and 4.50 dS m−1, increasing solution salinity with the standard nutrient solution of concentrated macronutrients as a reference. Vegetative growth, seed production and GLA ratio were measured. The results of vegetative development and GLA production doubled and tripled with the increase in salinity of the nutrient solution, respectively.
Enumeration, Antagonism and Enzymatic Activities of Microorganisms Isolated from Railway Station Soil
Authors: Sharma Megha , Kaushik Prashant , Chaturvedi Pawan 
Published: October 2018

AbstractSoil is the well-known hotspot for microbial diversity. Therefore, for our investigation, we isolated, characterized, and identified microorganisms from railway station soil. Sampling was done subsequently after every 15 days interval, and from two different soil depths i.e. 0-15 cm and below during March to May of 2013. Further, soil isolates were examined for their antagonistic activity, against four soil born plant pathogens namely,Rhizoctonia solani, Aspergillus niger, Fusarium f sp pisi, andSclerotinia sclerotiorum. Subsequently, isolates were screened for the presence of amylases, proteases, lipases and cellulases. For each interval of soil sampling, a gradual reduction in the microbial count was noticed from month March to May. Mucor species was observed only in the rainy days. The most promising enzymes producers wereBacillus sp., Aspergillus and Penicillium sp. Overall, the fungal isolates were better producers of enzymes as compared to bacterial isolates.
Positioning variation analysis and control for automated drilling in aircraft manufacturing
Authors: Mei Biao , Zhu Weidong , Ke Yinglin 
Published: October 2018

Purpose
Aircraft assembly demands high position accuracy of drilled fastener holes. Automated drilling is a key technology to fulfill the requirement. The purpose of the paper is to conduct positioning variation analysis and control for an automated drilling to achieve a high positioning accuracy.

Design/methodology/approach
The nominal and varied connective models of automated drilling are constructed for positioning variation analysis regarding automated drilling. The principle of a strategy for reducing positioning variation in drilling, which shortens the positioning variation chain with the aid of an industrial camera-based vision system, is explored. Moreover, other strategies for positioning variation control are developed based on mathematical analysis to further reduce the position errors of the drilled fastener holes.

Findings
The propagation and accumulation of an automated drilling system’s positioning variation are explored. The principle of reducing positioning variation in an automated drilling using a monocular vision system is discussed from the view of variation chain.

Practical implications
The strategies for reducing positioning variation, rooted in the constructed positioning variation models, have been applied to a machine-tool based automated drilling system. The system is developed for a wing assembly of an aircraft in the Aviation Industry Corporation of China.

Originality/value
Propagation, accumulation and control of positioning variation in an automated drilling are comprehensively explored. Based on this, the positioning accuracy in an automated drilling is controlled below 0.13 mm, which can meet the requirement for the assembly of the aircraft.
Aircraft positioning using SPP method in GPS system
Authors: Krasuski Kamil 
Published: October 2018

PurposeThe purpose of this paper is based on implementation of Global Navigation Satellite System (GNSS) technique in civil aviation for recovery of aircraft position using Single Point Positioning (SPP) method in kinematic mode.Design/methodology/approachThe aircraft coordinates in ellipsoidal frame were obtained based on Global Positioning System (GPS) code observations for SPP method. The numerical computations were executed in post-processing mode in the Aircraft Positioning Software (APS) package. The mathematical scheme of equation observation of SPP method was solved using least square estimation in stochastic processing. In the experiment, airborne test using Cessna 172 aircraft on September 07, 2011 in the civil aerodrome in Mielec was realized. The aircraft position was recovery using observations data from Topcon HiperPro dual-frequency receiver with interval of 1 second.FindingsIn this paper, the average value of standard deviation of aircraft position is about 0.8 m for Latitude, 0.7 m for Longitude and 1.5 m for ellipsoidal height, respectively. In case of the Mean Radial Spherical Error (MRSE) parameter, the average value equals to 1.8 m. The standard deviation of receiver clock bias was presented in this paper and the average value amounts to 34.4 ns. In this paper, the safety protection levels of Horizontal Protection Level (HPL) and Vertical Protection Level (VPL) were also showed and described.Research limitations/implicationsIn this paper, the analysis of aircraft positioning is focused on application the least square estimation in SPP method. The Kalman filtering operation can be also applied in SPP method for designation the position of the aircraft.Practical implicationsThe SPP method can be applied in civil aviation for designation the position of the aircraft in Non-Precision Approach (NPA) GNSS procedure at the landing phase. The typical accuracy of aircraft position is better than 220 m for lateral navigation in NPA GNSS procedure. The limit of accuracy of aircraft position in vertical plane in NPA GNSS procedure is not available.Social implicationsThis paper is destined for people who works in the area of aviation and air transport.Originality/valueThe work presents that SPP method as a universal technique for recovery of aircraft position in civil aviation, and this method can be also used in positioning of aircraft based on Global Navigation Satellite System (GLONASS) code observations.
Constant-gain EKF algorithm for satellite attitude determination systems
Authors: Hua Song , Huang Huiyin , Yin Fangfang , Wei Chunling 
Published: October 2018

Purpose
This paper aims to propose a constant-gain Kalman Filter algorithm based on the projection method and constant dimension projection, which ensures that the dimension of the observation matrix obtained is maintained when there is a satellite with multiple sensors.

Design/methodology/approach
First, a time-invariant observation matrix is determined with the projection method, which does not require the Jacobi matrix to be calculated. Second, the constant-gain matrix replaces the EKF (extended Kalman filter) gain matrix, which requires online computation, considerably improving the stability and real-time properties of the algorithm.

Findings
The simulation results indicate that compared to the EKF algorithm, the constant-gain Kalman filter algorithm has a considerably lower computational burden and improved real-time properties and stability without a significant loss of accuracy. The algorithm based on the constant dimension projection has better real-time properties, simpler computations and greater fault tolerance than the conventional EKF algorithm when handling an attitude determination system with three or more star trackers.

Originality/value
In satellite attitude determination systems, the constant-gain Kalman Filter algorithm based on the projection method reduces the large computational burden and improve the real-time properties of the EKF algorithm.
Control of pendular motion on tethered satellites systems
Authors: Tirop Paul Kimutai , Jingrui Zhang 
Published: October 2018

Purpose
This paper aims to present the control laws to be used in the control of pendular motion on tethered satellite systems in space during orbiting by using a nonlinear design technique.

Design/methodology/approach
This work presents both physical and mathematical models represented in a circular orbit. Euler equation of the rigid body is applied under reasonable assumption so as to form the equations of pendular motion. These equations are then used to develop the control laws using a nonlinear design technique. The control laws are required to drive the in-plane angles and out-of-plane angles of the pendular motion to the required trajectories. Simulations are then conducted to study the control results.

Findings
Simulation results show that the control laws in both plane angles of motions considered are able to move the pendular motion to the required trajectory. It was also eminent that a lot of effort is required in the case of the reference trajectory that corresponds to the constant inside-plane. To control the pendular motion of the plane, one requires an extended period of time and it should be controlled within a reasonable range. In the outside-of-plane pendular motion, minimal or no effort is required for the control. The reason is that the trajectory is natural planar.

Practical implications
This research is expected to provide a dynamic control strategy for all tethered satellite space systems.

Originality/value
The research proposes a combined dynamic method for the purpose of improving the control of all types of tether satellites.