Selective Sorting Research Articles

Exploring mechanisms and origins of reduced dispersal in island Komodo dragons.

Loss of dispersal typifies island biotas, but the selective processes driving this phenomenon remain contentious. This is because selection via, both indirect (e.g. relaxed selection or island syndromes) and direct (e.g. natural selection or spatial sorting) processes may be involved, and no study has yet convincingly distinguished between these alternatives. Here, we combined observational and experimental analyses of an island lizard, the Komodo dragon (Varanus komodoensis, the world's largest lizard), to provide evidence for the actions of multiple processes that could contribute to island dispersal loss. In the Komodo dragon, concordant results from telemetry, simulations, experimental translocations, mark-recapture, and gene flow studies indicated that despite impressive physical and sensory capabilities for long-distance movement, Komodo dragons exhibited near complete dispersal restriction: individuals rarely moved beyond the valleys they were born/captured in. Importantly, lizard site-fidelity was insensitive to common agents of dispersal evolution (i.e. indices of risk for inbreeding, kin and intraspecific competition, and low habitat quality) that consequently reduced survival of resident individuals. We suggest that direct selection restricts movement capacity (e.g. via benefits of spatial philopatry and increased costs of dispersal) alongside use of dispersal-compensating traits (e.g. intraspecific niche partitioning) to constrain dispersal in island species.

Comparison Study of Sorting Techniques in Static Data Structure

To manage and organize large data is imperative in order to formulate the data analysis and data processing efficiency. Therefore, this paper investigates the set of sorting techniques to observe which technique to provide better efficiency. Five types of sorting techniques of static data structure, Bubble, Insertion, Selection with O(n2) complexity and Merge, Quick with O(n log n) complexity have been used and tested on four groups between (100–30000) of dataset. To validate the performance of sorting techniques, three performance metrics which are time complexity, execution time and size of dataset were used. All experimental setups were accomplished using simple linear regression. The experimental results illustrate that Quick sort is more efficiency than other sorting and Selection sort is more efficient than Bubble and Insertion in large data size using array. In addition, Bubble, Insertion and Selection have good performance for small data size using array thus, sorting technique with behaviour O(n log n) is more efficient than sorting technique with behaviour O(n2) using array.

Secure architecture to circumvent collision using RSSI measurement in WSN: a cross layer design approach

‘Wireless sensor networks’ (WSNs) follow layered architecture for the fruitful and reliable working of distributed WSNs. The region of WSN is attaining importance in the research field on account of its wide-ranging scope of applications in different domains. The CLD (cross-layer design) is a rising trend in the network layer architectures. And it normally involves significant connections between disparate layers. This paper manages CLD instead of single layer in order to attain good performance. Collision amid packet transmission is the chief issues that directly influence the performance and lifetime of distributed WSNs. This present model specifically provided a secure solution to avoid collision utilizing cross-layer in WSNs. For the foremost time, the transport layer was chosen as a primary platform for the calculation of RSSI (‘received signal strength indicator’) values to enrich cross-layer interaction. Effectively, this sort of selection in the order of nodes bypasses the collision in packet transmission and hence extends the network lifetime by avoiding transmission failure.

Local microtubule organization promotes cargo transport in C. elegans dendrites.

The specific organization of the neuronal microtubule cytoskeleton in axons and dendrites is an evolutionarily conserved determinant of neuronal polarity that allows for selective cargo sorting. However, how dendritic microtubules are organized and whether local differences influence cargo transport remains largely unknown. Here, we use live-cell imaging to systematically probe the microtubule organization in Caenorhabditiselegans neurons, and demonstrate the contribution of distinct mechanisms in the organization of dendritic microtubules. We found that most non-ciliated neurons depend on unc-116 (kinesin-1), unc-33 (CRMP) and unc-44 (ankyrin) for correct microtubule organization and polarized cargo transport, as previously reported. Ciliated neurons and the URX neuron, however, use an additional pathway to nucleate microtubules at the tip of the dendrite, from the base of the cilium in ciliated neurons. Since inhibition of distal microtubule nucleation affects distal dendritic transport, we propose a model in which the presence of a microtubule-organizing center at the dendrite tip ensures correct dendritic cargo transport.

Analysis of ukrainian and foreign wheat samples for the presence of stem rust resistance genes using molecular markers

Aim. The aim of the study was a search of Sr2 and Sr33 gene resistance alleles in foreign and domestic wheat samples using molecular genetic markers. Methods. The PCR with provided molecular genetic markers and with specific primers of own design was used; CTAB method was used for DNA extraction; electrophoresis in agarose gel was used. Results. The analysis of 16 wheat samples using molecular genetic markers for stem rust resistance genes Sr2 and Sr33 was performed. In general, among 16 analyzed samples only two have Sr2 gene resistance allele, and another two – Sr33 gene resistance allele. There were no alleles of resistance of Sr-genes among the sorts of Ukrainian selection (Kharkivska 6 and Kharkivska 12), which were used in this study. Conclusions. There were four samples among the wheat lines/sorts with valuable traits of domestic and foreign selection that have Sr2 and Sr33 gene resistance alleles.
 Keywords: wheat, molecular and genetic markers, resistance genes, stem rust.

Selective sorting of polymers with different terminal groups using metal-organic frameworks

Separation of high-molecular-weight polymers differing just by one monomeric unit remains a challenging task. Here, we describe a protocol using metal-organic frameworks (MOFs) for the efficient separation and purification of mixtures of polymers that differ only by their terminal groups. In this process, polymer chains are inserted by threading one of their extremities through a series of MOF nanowindows. Selected termini can be adjusted by tuning the MOF structure, and the insertion methodology. Accordingly, MOFs with permanently opened pores allow for the complete separation of poly(ethylene glycol) (PEG) based on steric hindrance of the terminal groups. Excellent separation is achieved, even for high molecular weights (20 kDa). Furthermore, the dynamic character of a flexible MOF is used to separate PEG mixtures with very similar terminal moieties, such as OH, OMe, and OEt, as the slight difference of polarity in these groups significantly changes the pore opening kinetics.

Costorage of High Molecular Weight Neurotransmitters in Large Dense Core Vesicles of Mammalian Neurons.

It is today widely accepted that several types of high molecular weight (MW) neurotransmitters produced by neurons are synthesized at the cell body, selectively stored within large dense core vesicles (LDCVs) and anterogradely transported to terminals where they elicit their biological role(s). Among these molecules there are neuropeptides and neurotrophic factors, the main focus of this perspective article. I here first provide a brief resume of the state of art on neuronal secretion, with primary emphasis on the molecular composition and mechanism(s) of filling and release of LDCVs. Then, I discuss the perspectives and future directions of research in the field as regarding the synthesis and storage of multiple high MW transmitters in LDCVs and the possibility that a selective sorting of LDCVs occurs along different neuronal processes and/or their branches. I also consider the ongoing discussion that diverse types of neurons may contain LDCVs with different sets of integral proteins or dial in a different fashion with LDCVs containing the same cargo. In addition, I provide original data on the size of LDCVs in rat dorsal root ganglion neurons and their central terminals in the spinal cord after immunogold labeling for calcitonin gene-related peptide (CGRP), neuropeptide K, substance P, neurokinin A or somatostatin. These data corroborate the idea that, similarly to endocrine cells, LDCVs undergo a process of maturation which involves a homotypic fusion followed by a reduction in size and condensation of cargo. They also give support to the conjecture that release at terminals occurs by cavicapture, a process of partial fusion of the vesicle with the axolemma, accompanied by depletion of cargo and diminution of size.

Engineering Riboswitches in Vivo Using Dual Genetic Selection and Fluorescence-Activated Cell Sorting.

Riboswitches, noncoding RNAs that bind a small molecule effector to control gene expression at the level of transcription or translation, are uniquely suited to meet challenges in synthetic biology. To expand the limited set of existing riboswitches, we developed a riboswitch discovery platform that couples dual genetic selection and fluorescence-activated cell sorting to identify novel riboswitches from a 108 random-sequence library in which the aptamer domain of the ThiM#2 riboswitch was replaced with an N40 sequence. In a proof-of-principle validation, we identified novel riboswitches for the small molecule theophylline. Our best riboswitch (Hit 3-5) displays 2.3-fold activation of downstream gene expression in the presence of theophylline. Random mutagenesis of Hit 3-5, coupled with selections and screens, afforded improved riboswitches displaying nearly 3-fold activation. To the best of our knowledge, this is the first report of in vivo directed evolution of an aptamer domain to generate a functional riboswitch.

GRAIN SIZE AND MORPHOMETRICAL CHARACTERISTICS OF BOEOTIAN KIFISOS STREAM GRAVEL-BED AND THEIR GEOLOGICAL IMPORTANCE

This work studies the lithology, mean size, roundness, sphericity and form of gravels of Boeotian Kifisos river bed, in eleven stations of sampling in middlestream area. The lithology of gravels are limestone, sandstone, chert and igneous. Limestone percentage averages 78.89%, sandstone 11.40%, chert 6.48% and igneous 7.23%. The changes in litho logy with distance of transport is due mostly to influx of new material and partly to abration and breakage of less resistant lithologies (limestone, igneous, sandstone). The mean size of the gravels of all lithologies decreases with the distance of transport. This is due to mainly in the selective sorting because of the reduction of the river slope. The roundness according to Powers (1982) for limestone, sandstone, chert and igneous gravels is 3,81, 4,65, 2,13 and 3,01 respectively. The sphericity of the limestone, sandstone, chert and igneous gravels is 0,70, 0,66, 0,72 and 0,70 respectively. The arithmetic mean of sphericity of total of gravels is 0,69. The roundness is not related with the distance of transport. This suggests that this parameter has acquired the biggest values of degree of roundness before the first station of sampling. Also, the sphericity of the non-resistance lithologies (limestone, sandstone, igneous) does not show any relationship with distance. This suggests a breakage along the bedding in combination with anisotropic wear. On the contrary the sphericity of chert decreases with distance because it were chipped during transport. Boeotian Kifisos river has the tendency to produce more spherical and discoidal gravels than blade and prolate. Moreover the two first forms tend to decrease with the distance of transport while this does not happen with the remainder two forms.

Gate-enhanced photocurrent of (6,5) single-walled carbon nanotube based field effect transistor

A visible sensing field effect transistor (FET) with a channel length of 100 nm for individual (6,5) single-walled carbon nanotubes (SWCNTs) is fabricated via a selective sorting method using 9,9-dioctyfluorenyl-2,7-diyl–bipyridine (PFO–BPy) polymer. The FET of the (6,5) SWCNTs shows p-type behavior with hundreds of on-off ratios and on-state conductivity of 50 ± 4.0 (Ω m)−1. In addition, the photocurrent of the FET of the (6,5) SWCNTs in the visible range increases (maximum 200 times at 620 nm) with higher gate voltage. E22 transition and PFO-BPy transition are observed in the FET of the (6,5) SWCNTs without application of a gate voltage. Interestingly, exciton-phonon coupled E22 transition due to gate-doping (p-type), which has been reported in photoluminescence and absorption studies, is expected to occur in the photocurrent of the FET at negatively higher gate voltage (≤−4 V). In addition, the exciton-phonon coupled E22 transition is prominently observable when carrier concentration by gate doping becomes approximately two-hundred sixty times (260 ± 43) larger than carrier concentration without application of a gate voltage. This demonstration would be useful for the development of SWCNT-based visible sensors with gate control in the SWCNT devices.

Bacteriophage-Assisted Magnetic Separation and Electrochemical Detection of Pathogenic Bacteria from Food Matrix

This work describes a microfluidic cell sorting device that uses magnetophoresis to detect, separate, and concentrate tagged Listeria monocytogenes from food samples. Bacteriophage-functionalized magnetic particles were used to tag the bacteria in a food sample for pre-enrichment, which allowed for more rapid and selective cell sorting. We report on the effect of flow rate on the sorting efficiency, as well as the effect of two different channel designs on the sorting efficiency and purity of tagged bacteria within the food matrices of milk and ground beef. These enriched bacterial samples will be used in various biosensor applications for detection and identification of pathogenic bacteria in food samples.

Bacteriophage-Assisted Magnetic Separation and Electrochemical Detection of Pathogenic Bacteria from Food Matrix

Foodborne illnesses caused by pathogenic microorganisms are a major threat to worldwide public health. Listeria monocytogenes is among the most common pathogens contributing to domestically acquired foodborne illnesses (1). Most foodborne cases of listeriosis present as life-threatening illnesses in the forms of neonatal listeriosis, blood stream infection, and meningoencephalitis. There is a high priority amongst public health officials to identify Listeria outbreak sources and reduce mortality rates of this disease (2). Since the current methods for bacteria enrichment are time consuming and require sophisticated instruments, they are impossible to reproduce in a non-laboratory setting. There is a growing need to develop field-deployable technologies that are able to rapidly and accurately detect harmful pathogens in complex food matrices such as milk, juice, vegetables, meat, and poultry (3, 4). This work describes a microfluidic cell sorting device that uses magnetophoresis to detect, separate, and concentrate tagged Listeria monocytogenes from food samples. Bacteriophage-functionalized magnetic particles will be used to isolate the bacteria in a food sample for pre-enrichment, which will allow for more rapid and selective cell sorting followed by impedimetric detection of Listeria in an electrochemical cell. We will report on the effects of flow rate and viscosity of the sample feed on the separation efficiency, as well as the throughput of enriched target bacteria from different food matrices. These enriched samples will be used in various biosensor applications for detection and identification of pathogenic bacteria in food samples. References E. Scallan, R. M. Hoekstra, F. J. Angulo, R. V. Tauxe, M. A. Widdowson, S. L. Roy, J. L. Jones and P. M. Griffin, Emerg Infect Dis, 17, 7 (2011).B. Swaminathan and P. Gerner-Smidt, Microbes Infect, 9, 1236 (2007).X. Weng and S. Neethirajan, Trends in Food Science & Technology, 65, 10 (2017).Y. Jiang, S. Zou and X. Cao, Anal. Methods, 8, 6668 (2016).

New Methods Towards Designer DNA Sequences for Enantiomeric-Chiral Selective Sorting of Single-Wall Carbon Nanotubes

To date methods in producing structurally defined single-wall carbon nanotubes are inadequate leaving purification or sorting a viable option for obtaining nanotubes of a certain chirality. While several procedures have been developed for structure specific isolation of nanotubes, there are differences in purity, scalability, and economic feasibility. The use of single-stranded DNA sequences has evolved and been refined to select for both nanotube helicity and handedness. These developments through brute force screening of hundreds of sequences show the unique recognition of DNA for nanotube structure. Going a step further DNA recognition combined with a second technique, aqueous two-phase separation, allows for high purity sorting of multiple chiralities. We introduce a few new experimental and computational methods as the next step in discovering new DNA sequences for sorting single-wall carbon nanotubes. Utilizing these new methods followed by experimental verification, novel DNA sequences are discovered for dispersing and sorting single-wall carbon nanotubes.

On the effectiveness of virtual reality in the education of software engineering

AbstractThe popularity of virtual reality headsets have been rapidly increasing. With this technology, students can efficiently interact with the course content and learn the material faster than the traditional methodologies. In addition to this benefit, virtual reality devices also draw the attention of young generation and this helps to the widespread use of this technology among students. In this study, we investigate the use of virtual reality on the performance of computer engineering bachelor science (BS) students within the scope of Data Structures course and develop a software‐intensive system called “Virtual Reality Enhanced Interactive Teaching Environment” (VR‐ENITE). Specifically, we focus on the sorting algorithms such as selection sort, bubble sort, insertions sort, and merge sort which are relatively hard to be understood by the BS students at first glance. For the evaluation of VR‐ENITE, students were divided into two groups: a group which uses VR‐ENITE in addition to the traditional teaching material and the control group which utilizes from only the traditional material. In order to evaluate the performance of these two groups having 36 students in total, a multiple choice exam was delivered to all of them. According to the test results, students who used the VR‐ENITE system got 12% more successful results in average than the students who are in the control group. This study experimentally shows that VR‐ENITE which is based on virtual reality technology is effective for teaching software engineering courses and it has assistive capabilities for traditional teaching approaches.

Novel L-type lectin from fresh water prawn, Macrobrachium rosenbergii participates in antibacterial and antiviral immune responses

L-type lectins (LTLs) play important roles in the secretory pathway of animals, including selective protein trafficking, sorting, and targeting. They have a leguminous lectin domain and can bind to high-mannose-type oligosaccharides. In this study, a novel LTL, designated as MrVIP36, was identified from Macrobrachium rosenbergii. The full-length cDNA of MrVIP36 was 1687 bp with a 972 bp open reading frame encoding a putative protein of 323 deduced amino acids. The deduced MrVIP36 protein contained an LTL-like domain (LTLD) and a transmembrane domain. Phylogenetic tree analysis indicated that MrVIP36 was a member of invertebrate LTLs. It has a closer evolutionary distance with invertebrate LTLs than vertebrate LTLs. Quantitative real time polymerase chain reaction showed that MrVIP36 is expressed widely in all tested tissues, especially in the hepatopancreas and intestine. MrVIP36 was significantly up-regulated in hemocytes of prawns at different time points after Staphylococcus aureus, Vibrio parahaemolyticus, and White spot syndrome virus (WSSV) infections. The recombinant protein MrLTLD (rMrLTLD) could bind and agglutinate all tested bacteria. Sugar binding assay revealed that rMrLTLD could also bind to the glycoconjugates of the bacterial surface, such as lipopolysaccharide and peptidoglycan. Moreover, rMrLTLD could inhibit the growth activities of microorganisms in vitro and accelerate the bacterial clearance in vivo. rMrLTLD could also inhibit WSSV replication in vivo. Survival rate analysis showed that rMrLTLD could protect prawns against WSSV infection. Taken together, our results suggested that MrVIP36 functioned as a pattern recognition receptor involved in the antibacterial and antiviral immune responses of M. rosenbergii.

Cdc48 and ubiquilins confer selective anterograde protein sorting and entry into the multivesicular body in yeast.

Cdc48/p97 and the ubiquilin family of UBA-UBL proteins are known for their role in the retrotranslocation of damaged proteins from the endoplasmic reticulum. We demonstrate that Cdc48 and the ubiquilin-like proteins in yeast also play a role in the anterograde trafficking of proteins, in this case the vacuolar protease, Cps1.

Continuous Change in Membrane and Membrane-Skeleton Organization During Development From Proerythroblast to Senescent Red Blood Cell.

Within the context of erythropoiesis and the possibility of producing artificial red blood cells (RBCs) in vitro, a most critical step is the final differentiation of enucleated erythroblasts, or reticulocytes, to a fully mature biconcave discocyte, the RBC. Reviewed here is the current knowledge about this fundamental maturational process. By combining literature data with our own experimental evidence we propose that the early phase in the maturation of reticulocytes to RBCs is driven by a membrane raft-based mechanism for the sorting of disposable membrane proteins, mostly the no longer needed transferrin receptor (TfR), to the multivesicular endosome (MVE) as cargo of intraluminal vesicles that are subsequently exocytosed as exosomes, consistently with the seminal and original observation of Johnstone and collaborators of more than 30 years ago (Pan BT, Johnstone RM. Cell. 1983;33:967-978). According to a strikingly selective sorting process, the TfR becomes cargo destined to exocytosis while other molecules, including the most abundant RBC transmembrane protein, band 3, are completely retained in the cell membrane. It is also proposed that while this process could be operating in the early maturational steps in the bone marrow, additional mechanism(s) must be at play for the final removal of the excess reticulocyte membrane that is observed to occur in the circulation. This processing will most likely require the intervention of the spleen, whose function is also necessary for the continuous remodeling of the RBC membrane all along this cell's circulatory life.

Silt content approximation of Neogene Surma group mudrocks, Sitakund anticline, Bengal basin

Petrography of the Neogene mudrocks in this study incorporates laser particle size analysis, thin sections and scanning electron microscopy (SEM). Ten representative mudrock samples were collected from outcrops of the Sitakund structure. From the studies, it is evident that mudrocks of Sitakund structure are characteristically silty. The silt content, as estimated by laser grain size analysis, of the mudrocks ranges from 39 to 77% with average of 58%. Significant amount of granular silt with the platy clay minerals is also evident from the SEM micrographs. The silts are mainly quartz, feldspar and micas. The high silt content in the Neogene mudrocks implies an enormous flux of silty sediments with a very high rate of sedimentation allowing little time for a more selective sorting. This supports the geologic history that the uplifting and erosion of Himalaya was at the peak during Miocene and the Ganges mega delta received highest rate of sedimentation and growth rendering shale consistently silty.Bangladesh J. Sci. Res. 30(1&2): 35-43, December-2017

Determination of lateral and vertical dielectrophoresis forces using tapered microelectrode array

The authors have introduced a method to generate and determine lateral and vertical dielectrophoresis forces simultaneously through a new configuration of microelectrodes arrays with tapered side wall profile. Two directions of motion are established based on obtaining a new crossover frequency, which they called as adjustment frequency (f adj) with the value between the crossover frequency of targeted and untargeted cells. The target particles could be particular biological cell in a mixture of cell and other particles or a mixture of cells with various physical and biological properties. The special design of microelectrodes arrays enables dielectrophoresis forces to manipulate and separate target species at two different locations via contactless technique by electrical driven but soft selective capture and sorting for higher efficiency and accuracy.

Analysis of Energy Consumption of Sorting Algorithms on Smartphones

Despite the improvement in hardware and technology, Limited Battery power in Smartphone is still challenging task. Battery lifetime of mobile phones is needed to be improved. As compare to CPU power, HDD capacity, RAM and other hardware components the improvement in battery power consumption and lifetime in the past years is very low. The battery power of a Smartphone may be prolonged by optimizing hardware or software. This paper presents an approach for saving energy through software by choosing the appropriate sorting algorithm. Energy consumption of sorting algorithms like Bubble sort, Insertion sort, Quick sort, Selection sort and Merge sort were measured. The results show that Quick sort is the most energy efficient sorting method on average cases. Bubble sort is the most energy consuming algorithm. Insertion sort is also energy efficient but as the number of input data items increase after a certain value Merge sort outperforms the Insertion sort. This work provides the general guideline to select appropriate sorting algorithm in development of energy efficient Smartphone application. A new term Energy Complexity is also introduced in this paper.