Miracle-dz/UniFAR-FTUs huggingface dataset:
Development of simple sequence repeat markers from expressed sequence tags of the black tiger shrimp (Penaeus monodon)

In this study, we describe the development of expressed sequence tag–simple sequence repeat markers from expressed sequence tags of the black tiger shrimp (Penaeus monodon) deposited in public sequence databases. A total of 46 primer pairs were designed and screened on 26 individuals of P. monodon from a natural population. Of these, 16 primer pairs showed polymorphic profiles with between two and five alleles per locus. The average unbiased and direct count heterozygosities were 0.4662 and 0.3516, respectively. Cross‐amplification was tested with five individuals of Penaeus vannamei and polymorphic products were detected at five loci.
SPSD Matrix Approximation vis Column Selection: Theories, Algorithms, and Extensions

Symmetric positive semidefinite (SPSD) matrix approximation is an important problem with applications in kernel methods. However, existing SPSD matrix approximation methods such as the Nystrom method only have weak error bounds. In this paper we conduct in-depth studies of an SPSD matrix approximation model and establish strong relative-error bounds. We call it the prototype model for it has more efficient and effective extensions, and some of its extensions have high scalability. Though the prototype model itself is not suitable for large-scale data, it is still useful to study its properties, on which the analysis of its extensions relies. This paper offers novel theoretical analysis, efficient algorithms, and a highly accurate extension. First, we establish a lower error bound for the prototype model and improve the error bound of an existing column selection algorithm to match the lower bound. In this way, we obtain the first optimal column selection algorithm for the prototype model. We also prove that the prototype model is exact under certain conditions. Second, we develop a simple column selection algorithm with a provable error bound. Third, we propose a so-called spectral shifting model to make the approximation more accurate when the eigenvalues of the matrix decay slowly, and the improvement is theoretically quantified. The spectral shifting method can also be applied to improve other SPSD matrix approximation models.
EZ-Flow: removing turbulence in IEEE 802.11 wireless mesh networks without message passing

Recent analytical and experimental work demonstrate that IEEE 802.11-based wireless mesh networks are prone to turbulence. Manifestations of such turbulence take the form of large buffer build-up at relay nodes, end-to-end delay fluctuations, and traffic congestion. In this paper, we propose and evaluate a novel, distributed flow-control mechanism to address this problem, called EZ-flow. EZ-flow is fully compatible with the IEEE 802.11 standard (i.e., it does not modify headers in packets), can be implemented using off-the-shelf hardware, and does not entail any communication overhead. EZ-flow operates by adapting the minimum congestion window parameter at each relay node, based on an estimation of the buffer occupancy at its successor node in the mesh. We show how such an estimation can be conducted passively by taking advantage of the broadcast nature of the wireless channel. Real experiments, run on a 9-node testbed deployed over 4 different buildings, show that EZ-flow effectively smoothes traffic and improves delay, throughput, and fairness performance. We further corroborate these results with a mathematical stability analysis and extensive ns-2 simulations run for different traffic workloads and network topologies.
A coding system for qualitative studies of the information-seeking process in computer science research

Introduction. In this article we propose a qualitative analysis tool ? a coding system - that can support the formalisation of the information-seeking process in a specific field: research in computer science. Method. In order to elaborate the coding system, we have conducted a set of qualitative studies, more specifically a focus group and some individual interviews, and have analysed their results. Analysis. We provide a detailed description of how the qualitative studies were performed and how the subsequent analysis, refining and validation phases were carried out until we obtained the proposed coding system. Results. The coding system is presented as a list of hierarchically categorised codes that try to cover the full information-seeking process performed by researchers in computer science. In order to facilitate the understanding and later use of the codes, we also include a detailed description of each, together with real examples of use extracted from the qualitative studies. Conclusions. We present a complete list of 169 codes categorised into 13 categories that can help other researchers to analyse further qualitative results related to the information-seeking process, both at the process level and at the user level. In our case, these codes will be in the near future the seed to design a system that can adapt its functionality, visualisation and interaction based on the task at hand, the user and the context of use.
Asymmetric Division and Lineage Commitment at the Level of Hematopoietic Stem Cells

How hematopoietic stem cells (HSCs) commit to a particular lineage is unclear. A high degree of HSC purification enabled us to address this issue at the clonal level. Single-cell transplantation studies revealed that 40% of the CD34−/low, c-Kit+, Sca-1+, and lineage marker− (CD34−KSL) cells in adult mouse bone marrow were able, as individual cells, to reconstitute myeloid and B- and T-lymphoid lineages over the long-term. Single-cell culture showed that >40% of CD34−KSL cells could form neutrophil (n)/macrophage (m)/erythroblast (E)/megakaryocyte (M) (nmEM) colonies. Assuming that a substantial portion of long-term repopulating cells can be detected as nmEM cells within this population, we compared differentiation potentials between individual pairs of daughter and granddaughter cells derived in vitro from single nmEM cells. One of the two daughter or granddaughter cells remained an nmEM cell. The other showed a variety of combinations of differentiation potential. In particular, an nmEM cell directly gave rise, after one cell division, to progenitor cells committed to nm, EM, or M lineages. The probability of asymmetric division of nmEM cells depended on the cytokines used. These data strongly suggest that lineage commitment takes place asymmetrically at the level of HSCs under the influence of external factors.
Model Choice using Reversible Jump Markov Chain

We review the across-model simulation approach to computation for Bayesian model determination, based on the reversible jump Markov chain Monte Carlo method. Advantages, difficulties and variations of the methods are discussed. We also discuss some limitations of the ideal Bayesian view of the model determination problem, for which no computational methods can provide a cure. Some key words: Across-model sampling, Bayes factors, Bayesian model determination, posterior model probabilities, transdimensional inference, variable dimension problems,
Warehousing and inventory management: a simulation tool to determine warehouse efficiencies and storage allocations

Using ProModel simulation language, a universal warehouse storage simulation model has been developed. Applications of the model have been executed with success to analyze the storage capacity and rack efficiency of a medium volume, low stock-keeping unit (SKU) warehouse and a medium volume, large SKU warehouse. The model is scaleable and can be modified to simulate any warehouse configuration, including selective racks, bulk floor storage, push-back, flow-through, drive-in and drive-through racks.
The complete mitochondrial genome of Chrysopa pallens (Insecta, Neuroptera, Chrysopidae)

The complete mitochondrial genome of Chrysopa pallens (Neuroptera, Chrysopidae) was sequenced. It consists of 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA (rRNA) genes, and a control region (AT-rich region). The total length of C. pallens mitogenome is 16,723 bp with 79.5% AT content, and the length of control region is 1905 bp with 89.1% AT content. The non-coding regions of C. pallens include control region between 12S rRNA and trnI genes, and a 75-bp space region between trnI and trnQ genes.
A multi-layered solution for supporting isp traffic demand using genetic algorithm

This paper proposes a unique feedback governed multi layered architectural model to support ISP's traffic demands with multiple quality of service(QoS) constraints. The proposed model consists of different modules each responsible for a particular set of tasks. The most challenging task involved in satisfying the demands is routing the traffic subject to multiple QoS constraints for multiple internet service providers (ISP). Routing the traffic subject to multiple constraints itself is known to be an NP-hard problem. This paper addresses the problem of finding the optimum routes to satisfy the demands of different ISPs, where different ISPs have different demands and their priority of QoS keep changing. A genetic algorithm (GA) which makes use of heuristic technique is proposed in this paper. All the optimum routes are found in one run of the program, therefore the chromosome selected encodes all the demanded routes. This paper also makes use of employing a tournament selection mechanism where the diversity of the population is preserved while the best chromosomes are carried to the next generation. The evolutionary property of GA is utilised in this paper to evolve to suit the changing demands. The performance and the evolutionary property of the proposed solution are shown with the simulation tests.
Novel Regulatory Properties of Human Type 9 Adenylate Cyclase

Nine membrane-bound members of the mammalian adenylate cyclase family have been identified. The least characterized and most divergent in sequence of the nine adenylate cyclase isoforms is AC9. Stimulation by Gαs and inhibition by Ca2+/calcineurin are two modes of regulation that have been reported for AC9. We explored the possibility of additional modes of regulation of human AC9. We now report that quinpirole activation of the inhibitory G protein-coupled D2L dopamine receptor inhibits Gαs stimulation of AC9 by approximately 50%. The effects of quinpirole were reversed by the D2 antagonist spiperone and by pertussis toxin pretreatment. We also report the first evidence for regulation of AC9 by protein kinase C (PKC). Specifically, phorbol ester activation of PKC significantly attenuated (∼50%) Gαs-stimulated AC9 activity. The effect of PKC activation on AC9 was reversed by the PKC inhibitor bisindolylmaleimide. Gαs-stimulated cyclic accumulation was reduced more by simultaneous addition of both quinpirole and phorbol 12-myristate 13-acetate than by either drug alone. Additional studies investigated the role of glycosylation on AC9 activity. The results show that blocking glycosylation of AC9 significantly attenuates Gαs stimulation. In contrast, the ability of PKC and Gαi/o to negatively regulate AC9 did not seem to be affected by the glycosylation state of AC9. These observations demonstrate the diverse regulatory features of AC9 and the ability of AC9 to integrate multiple signals.
STU1, a suppressor of a beta-tubulin mutation, encodes a novel and essential component of the yeast mitotic spindle

We have isolated a cold-sensitive allele of TUB2, the sole gene encoding beta-tubulin in S. cerevisiae, that confers a specific defect in spindle microtubule function. At 14 degrees C, tub2-406 cells lack a normal bipolar spindle but do assemble functional cytoplasmic microtubules. In an attempt to identify proteins that are important for spindle assembly, we screened for suppressors of the cold-sensitivity of tub2-406 and obtained four alleles of a novel gene, STU1. Genetic interactions between stu1 alleles and alleles of TUB1 and TUB2 suggest that Stu1p specifically interacts with microtubules. STU1 is essential for growth and disruption of STU1 causes defects in spindle assembly that are similar to those produced by the tub2-406 mutation. The nucleotide sequence of the STU1 gene predicts a protein product of 174 kD with no significant similarity to known proteins. An epitope-tagged Stulp colocalizes with microtubules in the mitotic spindle of yeast. These results demonstrate that Stulp is an essential component of the yeast mitotic spindle.
A logarithmic poisson execution time model for software reliability measurement

A new software reliability model is developed that predicts expected failures (and hence related reliability quantities) as well or better than existing software reliability models, and is simpler than any of the models that approach it in predictive validity. The model incorporates both execution time and calendar time components, each of which is derived. The model is evaluated, using actual data, and compared with other models.
Literature Review on Digital Image Watermarking

Digital image watermarking is the technology that is used in information security applications like digital image content protection and copyright protection. In this paper, a brief review of literature on digital image watermarking is presented. Watermarking algorithms can be classified based on different criterions. Depending upon the specific application, watermarking algorithm should satisfy certain requirements. Important parameters used to measure the quality of watermarking are Peak Signal to Noise Ratio (PSNR) and Normalized Cross Correlation (NCC). PSNR represents visual quality of the watermarked image. NCC indicates the visual quality of extracted watermark. For comparing the performance of different watermarking algorithms, PSNR and NCC values against various attacks are measured.
TEXTURE CHARACTERIZATION IN REMOTE SENSING IMAGERY USING BINARY CODING TECHNIQUES

In this paper rotation invariant Local Binary Patterns (LBP) texture based descriptors are evaluated experimentally in the context of land-use and land-cover object-based classification. The texture descriptors were employed in the classification of an Ikonos-2 and a Quickbird-2 image. The experiments have shown that texture characterization approaches perform well when combined with the grayscale variance. We further investigate a novel descriptor resulting from the concatenation of the grayscale variance histogram and the histogram of codes generated by LBP. These experiments have demonstrated that the proposed descriptor, though more compact, performs as well as a bidimensional histogram representing the joint distribution of both quantities. Finally, the paper compares the discrimination capacity of the LBP based textural descriptors with that of features derived from the Gray Level Cooccurrence Matrices (GLCM). The related experiments revealed a noteworthy superiority of LBP descriptors over the GLCM features in the context of remote sensing image data classification.
Augmentation of transvascular transport of macromolecules and nanoparticles in tumors using vascular endothelial growth factor.

The goal of this investigation was to measure changes in vascular permeability, pore cutoff size, and number of transvascular transport pathways as a function of time and in response to vascular endothelial growth factor (VEGF), placenta growth factor (PIGF-1 and PIGF-2), or basic fibroblast growth factor (bFGF). Two human and two murine tumors were implanted in the dorsal skin chamber or cranial window. Vascular permeability to BSA (approximately 7 nm in diameter) and extravasation of polyethylene glycol-stabilized long-circulating liposomes (100-400 nm) and latex microspheres (approximately 800 nm) were determined by intravital microscopy. Vascular permeability was found to be temporally heterogeneous. VEGF superfusion (100 ng/ml) significantly increased vascular permeability to albumin in normal s.c. vessels, whereas a 30-fold higher dose of VEGF (3000 ng/ml) was required to increase permeability in pial vessels, suggesting that different tissues exhibit different dose thresholds for VEGF activity. Furthermore, VEGF superfusion (1000 ng/ml) increased vascular permeability to albumin in a hypopermeable human glioma xenograft in cranial window, whereas VEGF superfusion (10-1000 ng/ml) failed to increase permeability in a variety of hyperpermeable tumors grown in dorsal skin chamber. Interestingly, low-dose VEGF treatment (10 ng/ml) doubled the maximum pore size (from 400 to 800 nm) and significantly increased the frequency of large (400 nm) pores in human colon carcinoma xenografts. PIGF-1, PIGF-2, or bFGF did not show any significant effect on permeability or pore size in tumors. These findings suggest that exogenous VEGF may be useful for augmenting the transvascular delivery of larger antineoplastic agents such as gene targeting vectors and encapsulated drug carriers (typical range, 100-300 nm) into tumors.
Identification of urban regions’ functions in Chengdu, China, based on vehicle trajectory data

Data about human trajectories has been widely used to study urban regions that are attractive to researchers and are considered to be hotspots. It is difficult, however, to quantify the function of urban regions based on the varieties of human behavior. In this research, we developed a clustering method to help discover the specific functions that exist within urban regions. This method applies the Gaussian Mixture Model (GMM) to classify regions’ inflow and trip count characteristics. It regroups these urban regions using the Pearson Correlation Coefficient (PCC) clustering method based on those typical characteristics. Using a large amount of vehicle trajectory data (approximately 1,500,000 data points) in the Chinese city of Chengdu, we demonstrate that the method can discriminate between urban functional regions, by comparing the proportion of surface objects within each region. This research shows that vehicle trajectory data in different functional urban regions possesses different time-series curves, while similar types of functional regions can be identified by these curves. Compared with remote sensing images and other statistical methods which can provide only static results, our research can provide a timely and effective approach to determine an urban region’s functions.
Using Ontologies for Semi-automatic Linking VerbaLex with FrameNet

This work presents a method of linking verbs and their valency frames in VerbaLex database developed at the Centre for NLP at the Faculty of Informatics Masaryk University to the frames in Berkeley FrameNet. While completely manual work may take a long time, the proposed semi-automatic approach requires a smaller amount of human effort to reach sufficient results. The method of linking VerbaLex frames to FrameNet frames consists of two phases. The goal of the first one is to find an appropriate FrameNet frame for each frame in VerbaLex. The second phase includes assigning FrameNet frame elements to the deep semantic roles in VerbaLex. In this work main emphasis is put on the exploitation of ontologies behind VerbaLex and FrameNet. Especially, the method of linking FrameNet frame elements with VerbaLex semantic roles is built using the information provided by the ontology of semantic types in FrameNet. Based on the proposed technique, a semi-automatic linking tool has been developed. By linking FrameNet to VerbaLex, we are able to find a non-trivial subset of the interlingual FrameNet frames (including their frame-to-frame relations), which could be used as a core for building FrameNet in Czech.
Screening for Tumour Suppressor p16(CDKN2A) Germline Mutations in Israeli Melanoma Families

Abstract Approximately ten percent of patients with malignant melanoma have family histories of the disease, suggesting a genetic predisposition. Germline mutations in tumour suppressor p16 gene have been implicated as disease causing mutations in some of the melanoma families. The frequency of families with p16 germline mutations among melanoma prone families varies from eight to fifty percent. The range of the variability is influenced apparently by the number of melanoma affected individuals within the family, as well as by other, yet unidentified factors. Ethnic background is known to determine both the frequency and the nature of germline alterations. Recently, specific mutations in tumour suppressor genes involved in breast cancer and in colon cancer were found at elevated frequency among Ashkenazi Jews. This report describes results of a screening for p16 germline alterations in a collection of Israeli melanoma families. We have analyzed genomic DNA from thirty one Ashkenazi and non-Ashkenazi Jewish melanoma families, as well as from thirty melanoma patients without an apparent family history of the disease. The entire coding region of the p16 gene was screened by single strand conformation polymorphism analysis and direct DNA sequencing. We have detected a number of carriers with the Ala148 Thr polymorphism at the end of the second exon and several instances of 500(G⇒C) substitution at the 3′ untranslated portion of the gene.
Tidal Current Turbine Wake and Park Layout in Transient Environments

Due to orbital velocities of the waves, the characteristics of tidal current turbines change over time. Therefore the induction factor and subsequent the wake is time dependent. Within the present research this time dependency is investigated by using Computational Fluid Dynamics (CFD) with Virtual Free Surface (VFS) and Actuator Disc (ACD) models. Based on this setup several different wave and current scenarios are simulated and analyzed with respect to the transient velocities in the turbine wake. Special respect is taken to the velocity undulations radiated by the changing apparent velocities in the rotor plane. These undulations move with the wake of the tidal current turbines and increase wave loads on 2nd row turbines in a park. This paper presents an efficient method for simulation of wave and park interactions and investigates dynamic turbine wakes under a large variety of parameters. Based on these simulations a suggestion for a tidal park design with respect to a balance of fatigue loads and power output is concluded.
Amyloid-like assembly of the low complexity domain of yeast Nab3

ABSTRACT Termination of transcription of short non-coding RNAs is carried out in yeast by the Nab3-Nrd1-Sen1 complex. Nab3 and Nrd1 are hnRNP-like proteins that dimerize and bind RNA with sequence specificity. We show here that an essential region of Nab3 that is predicted to be prion-like based upon its sequence bias, formed amyloid-like filaments. A similar region from Nrd1 also assembled into filaments in vitro. The purified Nab3 domain formed a macroscopic gel whose lattice organization was observed by X-ray fiber diffraction. Filaments were resistant to dissociation in anionic detergent, bound the fluorescent dye thioflavin T, and showed a β-sheet rich structure by circular dichroism spectroscopy, similar to human amyloid β which served as a reference amyloid. A version of the Nab3 domain with a mutation that impairs its termination function, also formed fibers as observed by electron microscopy. Using a protein fragment interaction assay, the purified Nab3 domain was seen to interact with itself in living yeast. A similar observation was made for full length Nab3. These results suggest that the Nab3 and Nrd1 RNA-binding proteins can attain a complex polymeric form and raise the possibility that this property is important for organizing their functional state during termination. These findings are congruent with recent work showing that RNA binding proteins with low complexity domains form a dynamic subcellular matrix in which RNA metabolism takes place but can also aberrantly yield pathological aggregated particles.