Miracle-dz/UniFAR-FTUs huggingface dataset:
Sequence Diversity of Pseudomonas aeruginosa: Impact on Population Structure and Genome Evolution

ABSTRACT Comparative sequencing of Pseudomonas aeruginosa genesoriC, citS, ampC, oprI,fliC, and pilA in 19 environmental and clinical isolates revealed the sequence diversity to be about 1 order of magnitude lower than in comparable housekeeping genes ofSalmonella. In contrast to the low nucleotide substitution rate, the frequency of recombination among different P. aeruginosa genotypes was high, leading to the random association of alleles. The P. aeruginosa population consists of equivalent genotypes that form a net-like population structure. However, each genotype represents a cluster of closely related strains which retain their sequence signature in the conserved gene pool and carry a set of genotype-specific DNA blocks. The codon adaptation index, a quantitative measure of synonymous codon bias of genes, was found to be consistently high in the P. aeruginosa genome irrespective of the metabolic category and the abundance of the encoded gene product. Such uniformly high codon adaptation indices of 0.55 to 0.85 fit the ubiquitous lifestyle ofP. aeruginosa.
Medium access control in vehicular ad hoc networks

The distinguishing properties of Vehicular Ad hoc wireless Networks (VANETs) strongly challenge the design of Medium Access Control (MAC) protocols, which are responsible for the medium access coordination among active vehicles, as well as the accommodation of both driving safety applications and non-safety applications. In this paper, we focus on a comprehensive survey of VANET MAC schemes by integrating various related issues and challenges. Our analysis not only deepens the understanding of MAC techniques in VANETs but also presents the key ideas and potential directions for future research in this area. In order to significantly improve the communication performance of VANETs, more research efforts on MAC techniques must be made for optimizing multichannel coordination and allocation approaches, enhancing the Quality of Service (QoS) capability, and combating the hidden terminal problem, broadcast storm problem and even ACK (acknowledgment) explosion problem. Copyright © 2009 John Wiley & Sons, Ltd.
Fish Farms and Sea Lice Infestations of Wild Juvenile Salmon in the Broughton Archipelago—A Rebuttal to Brooks (2005)

Contrary to several recent studies, a review (Brooks, 2005) of sea lice (Lepeophtheirus salmonis) interactions between wild and farm salmon in the Broughton Archipelago, British Columbia, Canada, concluded that there is little potential for sea lice transmission from farm to wild salmon. In this rebuttal, we show that this conclusion was based on a flawed interpretation of how salinity affects louse development, a misunderstanding of how the timing of salinity changes corresponds to the timing of the juvenile salmon migration, models of larval dispersion that overestimate the transport of louse larvae, and a selective and misleading assessment of the literature. We analyze and extend the current models of larval dispersion and demonstrate the (perhaps counter-intuitive) result that sustained high abundances of infectious larvae should be expected near lice-infested salmon farms. We also highlight important studies overlooked in Brooks (2005) and clarify some misinterpretations. Counter to the conclusions in Brooks (2005), the modeling and empirical work to date on sea lice interactions between wild and farm salmon are consistent and point to a strong association between salmon farming and recurrent infestations of wild juvenile salmon in the Broughton Archipelago.
The need for measured data in computer system performance analysis or garbage in, garbage out

There are three general techniques for studying the design, operation and optimization of any type of system: implementation, modeling, and simulation. Implementation can be used when the time is available and the effort is justified. Mathematical modeling can be used if the system is simple enough or if gross approximations are acceptable. Simulation is needed for the remaining cases. In all three cases, a crucial element is the need for accurate estimates of the "workload. " For example, for a computer main or cache memory system, the workload may at one level of detail be the timing and sequence of memory addresses referenced; at another level of detail, it could be just the ratio of loads to stores. No matter how accurate the model of a system may be, any results from it are useless if the workload is not accurately represented. We discuss various types of models and when and what type of accurate workload data is needed. We pay particular attention to performance analysis of memory hierarchies and the use of trace driven simulation. <<ETX>>
Machine Learning Fairness in Justice Systems: Base Rates, False Positives, and False Negatives

Machine learning best practice statements have proliferated, but there is a lack of consensus on what the standards should be. For fairness standards in particular, there is little guidance on how fairness might be achieved in practice. Specifically, fairness in errors (both false negatives and false positives) can pose a problem of how to set weights, how to make unavoidable tradeoffs, and how to judge models that present different kinds of errors across racial groups. This paper considers the consequences of having higher rates of false positives for one racial group and higher rates of false negatives for another racial group. The paper examines how different errors in justice settings can present problems for machine learning applications, the limits of computation for resolving tradeoffs, and how solutions might have to be crafted through courageous conversations with leadership, line workers, stakeholders, and impacted communities.
MODIS and VIIRS geometric performance comparison

The VIIRS instrument was launched on the NASA/NOAA Suomi NPP satellite in October 2011. This instrument is the first of a series of VIIRS instruments meant to continue the operational and long-term measurements of NASA, NOAA and DOD heritage instruments such as the MODIS instruments on the NASA EOS Terra and Aqua satellites and other. The VIIRS Sensor Data Record product recently achieved Beta Maturity in geometric and radiometric performance after the initial on-orbit instrument characterization and calibration. In this paper, we compare MODIS and VIIRS instrument's geometric characteristics and geolocation accuracy. This VIIRS geometric characterization is on-going and the product to be much more mature by the end of the year. At this time, the MODIS and VIIRS instruments have different but comparable geometric performance and that the VIIRS geometric characteristics will enable it to fulfill the mission objectives.
Fair energy-efficient virtual machine scheduling for Internet of Things applications in cloud environment

With the rapid resource requirements of Internet of Things applications, cloud computing technology is regarded as a promising paradigm for resource provision. To improve the efficiency and effectiveness of cloud services, it is essential to improve the resource fairness and achieve energy savings. However, it is still a challenge to schedule the virtual machines in an energy-efficient manner while taking into consideration the resource fairness. In view of this challenge, a fair energy-efficient virtual machine scheduling method for Internet of Things applications is designed in this article. Specifically, energy and fairness are analyzed in a formal way. Then, a virtual machine scheduling method is proposed to achieve the energy efficiency and further improve the resource fairness during the executions of Internet of Things applications. Finally, experimental evaluation demonstrates the validity of our proposed method.
High-Efficiency Transformerless Single-phase Photovoltaic Inverter

Grid-connected photovoltaic (PV) systems usually include a line transformer in their power conversion stage. This transformer guarantees galvanic isolation between the grid and the PV system, thus providing personal protection and avoiding leakage currents between the PV system and the ground. Furthermore, it also ensures that no continuous current is injected into the grid. However, because of its low frequency (50 Hz), the transformer is big, heavy and expensive. As an alternative to the grid-connected PV systems with line transformer, new transformerless inverter topologies are being studied. If no transformer is used, a galvanic connection between the grid and the PV array exists. In these conditions, leakage currents due to the capacitance between the photovoltaic array and earth could occur and increase the electromagnetic emissions. To avoid these leakage currents, it is necessary to use inverter topologies that avoid commonmode voltages. In this paper, a new transformerless singlephase PV inverter with six IGBTs and one diode is proposed. This topology generates no common-mode voltage and has a higher efficiency than the existing topologies. The topology has been validated by simulation.
Cell aggregation in thawed haematopoietic stem cell products visualised using micro‐flow imaging

Dear Sir, Cell aggregation is often observed after thawing peripheral blood progenitor cell products used in haematopoietic stem cell transplantation, and some groups have described methods to reduce cell clumping (Querol et al., 2000; Allan et al., 2002). Transplant centres typically follow standard procedures that guide the thawing conditions and rates of stem cell product infusion to limit cellular injury and prevent cell clumping. The impact on cells reinfused into recipients, however, is unknown and precise quantification of cell clumping has been difficult. Micro-flow imaging (MFI) is a novel method of imaging biologic fluids (Sharma et al., 2007; Huang et al., 2009) and provides a means for investigating cell aggregation following cryopreservation. MFI systems are specialised flow microscopes designed to measure the size distribution, concentration and morphological properties of multi-component populations of sub-visible particles in solution with high sensitivity and statistical accuracy. MFI is broadly used for evaluating populations of micro-particles encountered during bio-formulation development (Sharma et al., 2007; Huang et al., 2009). In this study, we used MFI as a new approach to analyse cell clumping in thawed haematopoietic progenitor cell products. Aliquots (1 mL) of autologous haematopoietic progenitor cells (HPC-A) products were utilised for our study in accordance with the protocol approved by our Research Ethics Board (REB). HPC-A products were volume reduced and cryopreserved in 5% dimethylsulfoxide (DMSO), 12% plasma-Lyte A (Baxter, Deerfield, IL, USA) and 2·2% (w/v) pentastarch by transferring directly to the vapour phase of liquid nitrogen in cryogenic vials. Haematopoietic progenitor products derived from umbilical cord blood (HPC-C) were collected using standard collection kits following informed consent and in accordance with the protocol approved by our institutional ethics review board. Mononuclear cells from HPC-C units were isolated by Ficoll gradient centrifugation and cryopreserved at a concentration of 1·5–2·5 × 107 cells mL−1 in cryogenic 2-mL vials in RPMI-1640 media (1 mL) with a final concentration of 5% DMSO, 12% Plasma-Lyte A and 2·2% (w/v) pentastarch by rate controlled freezing to −80◦C and then transferring the cryovials to the
Some EPPS Differences between Smokers and Non-Smokers

30 smokers and 30 non-smokers were found to differ significantly on the EPPS in Change (Chg), Nurturance (Nur), Exhibition (Exh), and Deference (Def). Smokers scored higher in Change and Exhibition while non-smokers were higher in Nurturance and Deference. The differences supported previous findings regarding less social responsibility among smokers.
Planar Inverted-F Antennas for Small Multi-Standard Handsets

Three small multi-band planar inverted-F antennas (PIFAs) are presented. They have been developed to be used in future small multi-standard handsets. Mobile communication (GSM1800, UMTS), wireless local area network (WLAN) (IEEE 802.11b, HiperLAN2) and wireless personal area network (WPAN) (Bluetooth) standards have been envisaged. Prototypes have been designed, fabricated and tested. Good agreement has been obtained between numerical simulations and experimental results
Modelling of defect formation and evolution in metals and silicon

Defects always exists in a crystal lattice at temperatures above absolute zero. Our knowledge of defect concentration and mobility is crucial, due to their profound influence on the material properties. By the means of thermodynamics it is possible to estimate defect concentrations at the equilibrium conditions. Near the melting point of pure metals the vacancy fraction is typically about 10−4. However, it has been shown that the presence of light impurities may enhance vacancy formation in many metals and metal alloys. The main reason for this phenomenon, often referred to as the superabundant vacancy formation, is the lowering of the vacancy formation energy due to the impurity trapping. In this thesis a theoretical thermodynamics model has been developed to study the equilibrium vacancy concentrations as a function of impurity concentration and temperature. Our model takes into account monovacancy and divacancy thermodynamics as well as the binding energy of each trapped impurity and the vibrational entropy of defects. The diffusion of monovacancies and hydrogen in tungsten is studied due to its relevance to fusion research. Extraordinary thermal and mechanical properties, like high melting temperature, high heat conductivity, low sputtering yield and low hydrogen retention makes tungsten a prime candidate for a divertor plate material in the next step fusion device ITER. At this region of the fusion reactor, the material is exposed to the highest heat and particle fluxes producing damage in the plasma facing components. Open volume defects are known to trap hydrogen and, thus, are the main reasons for hydrogen retention in tungsten. The radioactive hydrogen isotope tritium retention in the fusion reactor is especially undesirable due to efficiency and safety reasons. The molecular dynamics method has been used to simulate the diffusion of hydrogen in tungsten. The commonly accepted and so far used H diffusion migration barrier is revised and a new analysis method to determine diffusion coefficients that accounts for the random oscillation of atoms around the equilibrium position is presented. At high hydrogen concentrations, a dramatic reduction in the diffusion coefficient is observed, due to the neighbouring interstitial
Angiotensin II inhibits interleukin-1 beta-induced nitric oxide production in cultured rat mesangial cells.

BACKGROUND Macrophage-type nitric oxide synthase (NOS-II) is expressed in glomerular mesangial cells in response to inflammatory cytokines. Nitric oxide (NO) has antithrombotic and cytostatic activities in glomerular diseases. Recent studies have suggested that several vasoactive substances and growth factors modulate NO production in a tissue-specific manner. The aim of this study was to examine whether angiotensin II and transforming growth factor-beta (TGF-beta) modulate cytokine-stimulated NO production and NOS-II gene expression in rat glomerular mesangial cells. METHODS Cultured rat mesangial cells were incubated with interleukin-1 beta (IL-1 beta) for 24 hours. The effects of angiotensin II and TGF-beta on stimulated nitrite accumulation and NOS-II mRNA levels were determined. RESULTS Angiotensin II and TGF-beta significantly decreased IL-1 beta-stimulated nitrite accumulation. The angiotensin type 1 receptor antagonist CV11974 prevented angiotensin II-mediated inhibition of NO production. TGF-beta-neutralizing antibody reversed the effect of TGF-beta without affecting angiotensin II-mediated inhibition of NO production. TGF-beta markedly decreased steady-state levels of NOS-II mRNA and the half-life of the message, whereas angiotensin II did not alter these parameters. CONCLUSIONS These results suggest that in mesangial cells, angiotensin II and TGF-beta participate in the inhibitory regulation of cytokine-induced NO production. TGF-beta inhibits NO production by decreasing NOS-II mRNA levels, whereas angiotensin II may regulate NO production at the levels after NOS-II gene expression. An autocrine action of TGF-beta induced by angiotensin II is unlikely to contribute to angiotensin II-mediated inhibition of NO production.
Time Delay Compensation For A DSP-Based Current-Source Converter Using Observer-Predictor Controller

The inevitable time delay of the digital controller can degrade the performance of a converter system. Further, this time delay may depend on both sampling and switching cycles of the converter. Therefore, with applications where the converter operates at low or medium switching frequency, the time delay can severely affect the system dynamics. Further, in controlling a current-source converter, this time delay can cause oscillation in the system. The paper proposes the use of an observer-predictor state feedback algorithm to compensate the time delay in a DSP based controller. Experimental result shows that the time delay in a DSP-based controller can have significant effect on the CSC performance. Simulation and experimental results also shows the proposed control approach can successfully compensate the time delay and provides fast dynamics to the CSC.
Elevated KIAA0101 expression is a marker of recurrence in human gastric cancer

Gastric cancer (GC) is one of the most common malignant tumors with a high rate of recurrence, which results in surgery being unsuccessful. Therefore, it is important to find the reason for the surgery failing. The purpose of the present study was to investigate a factor related to recurrence. Expression of KIAA0101 was assessed in 61 paired human primary GC and non‐cancerous gastric tissue using immunohistochemistry. After surgery, all 61 patients were followed regularly for more than 24 months or until death to analyze the 2‐year survival rate and recurrence. After suppressing KIAA0101 by RNA interference in human GC cell lines, the cell viability was detected using MTT. We are first to find that KIAA0101 was elevated in GC tissues compared with paired non‐cancerous gastric tissues. Immunohistochemical staining also revealed the predominant nuclear localization of KIAA0101 protein. Despite these findings, GC patients with elevated KIAA0101 expression levels exhibited a high recurrence and subsequently poor prognosis in the survival study. Also, cell viability was significantly inhibited after suppressing KIAA0101 in GC cells, suggesting that KIAA0101 might promote cancer cell proliferation. KIAA0101 is increased in human GC and is a marker of recurrence.
Usage of Classification based Association for Removal of Noisy Attributes

mining is a process of extracting knowledge from underlying huge multidimensional data. Data mining techniques discovers hidden patterns from a given data. Classification is one of the techniques of data mining. Data Classification consists of categorization of data under the known class labels for its most effective and efficient utilization. There are different algorithms available for classification. Association rule mining is used to generate the rules for strongly associated attributes. It helps to uncover the association between seemingly unrelated attributes. Association rules are identified by analyzing patterns which satisfies the confidence and support criteria. This paper explains pre-processing for a given bank data set along with classification and association rule mining. Association followed by classification method helps in finding the noisy data attributes. Experimental setup uses WEKA tool for data mining. WEKA is a collection of machine learning algorithms for data mining tasks. Experiment has shown that classification with guidance of strongly supported rules from association rule mining helps in removal of noise and has increased the accuracy of classifier for a given data set.
Determination of the mRNA Sequence of Cathepsin Y, a Cysteine Endopeptidase from Rat Spleen, and Confirmation of Its Ubiquitous

Abstract A cysteine endopeptidase from rat spleen was purified, characterized and its gene cloned. This enzyme was originally recognized by its action of producing kininpotentiating peptide from a plasma protein. We named it cathepsin Y due to its localization, acidic pH optimum and the presence of the same set of active site amino acids as in other thiol cathepsins. Here we show the total sequence of the mRNA obtained by means of TaKaRa 5 Full RACE Core Set and complete the previously reported sequence. This completion of the mRNA sequence resulted in the omission of the strangely attached Cterminal peptide from cathepsin Y.
Multipath Routing with Reliable Nodes in Large-Scale Mobile Ad-Hoc Networks

We propose a Multiple Zones-based (M-Zone) routing protocol to discover node-disjoint multiplath routing efficiently and effectively in large-scale MANETs. Compared with single path routing, multipath routing can improve robustness, load balancing and throughput of a network. However, it is very difficult to achieve node-disjoint multipath routing in large-scale MANETs. To ensure finding node-disjoint multiple paths, the M-Zone protocol divides the region between a source and a destination into multiple zones based on geographical location and each path is mapped to a distinct zone. Performance analysis shows that M-Zone has good stability, and the control complexity and storage complexity of M-Zone are lower than those of the well-known AODVM protocol. Simulation studies show that the average end-to-end delay of M-Zone is lower than that of AODVM and the routing overhead of M-Zone is less than that of AODVM.
Solution structure of the C1‐subdomain of Bacillus stearothermophilus translation initiation factor IF2

IF2 is one of three bacterial translation initiation factors that are conserved through all kingdoms of life. It binds the 30S and 50S ribosomal subunits, as well as fMet‐tRNAfMet. After these interactions, fMet‐tRNAfMet is oriented to the ribosomal P‐site where the first amino acid of the nascent polypeptide, formylmethionine, is presented. The C‐terminal domain of Bacillus stearothermophilus IF2, which is responsible for recognition and binding of fMet‐tRNAfMet, contains two structured modules. Previously, the solution structure of the most C‐terminal module, IF2‐C2, has been elucidated by NMR spectroscopy and direct interactions between this subdomain and fMet‐tRNAfMet were reported. In the present NMR study we have obtained the spectral assignment of the other module of the C‐terminal domain (IF2‐C1) and determined its solution structure and backbone dynamics. The IF2‐C1 core forms a flattened fold consisting of a central four‐stranded parallel β‐sheet flanked by three α‐helices. Although its overall organization resembles that of subdomain III of the archaeal IF2‐homolog eIF5B whose crystal structure had previously been reported, some differences of potential functional significance are evident.