Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparison of optimum density of sensor nodes required for desired coverage in a realistic scenario using sensing models

One of the critical quality of service (QoS) parameter that needs consideration in any wireless sensor network (WSN) design is network area coverage which signifies the efficiency with which the network area can be covered by the deployed network. Node sensing models are used to predict the coverage fraction percentage for a given number of sensor nodes in a predetermined network area. Alternatively, a more practical approach is to compute the optimum density of sensor nodes to be deployed such that they can satisfy temporal and spatial requirement within a given economical constraint. In this paper, these node sensing models are revisited to investigate the optimum density of randomly deployed sensor nodes required to attain the desired network area coverage. This investigation can be used to estimate the number of sensor nodes to be deployed in a network area of any given size. The effect of the sensing device characteristics and environmental parameters on the density of sensor nodes is also analyzed to emphasize the fact that these parameters need due consideration in a realistic scenario. This comparative study based on node sensing models can be taken up as a starting point to design and evaluate an effective WSN so as to match the proposed model to a real world scenario.
Effect of Medium-chain Triglyceride (MCT) on Growth Performance, Nutrient Digestibility, Blood Characteristics in Weanling Pigs

One hundred and twenty weanling pigs in experiment 1 (Exp. 1) (6.91±0.99 kg; 21 d of age) and Exp. 2 (10.20±1.09 kg; 28 d of age) were used in two 42-d and 35-d experiments to evaluate the effect of medium-chain-triglyceride (MCT) on growth performance, apparent total tract digestibility (ATTD) of nutrients and blood profile. In both of Exp. 1 and Exp. 2, the same dietary treatments were utilized as follows : i) negative control (NC), ii) positive control (PC), NC+antibiotics (40 mg/kg Tiamulin, 110 mg/kg Tylosin, and 10 mg/kg Enramycin, iii) MCT3, NC+0.32% (phase 1, 2 and 3) MCT, and iv) MCT5, NC+0.55% (phase 1), 0.32% (phase 2 and 3) MCT. In Exp. 1, the pigs fed MCT5 diets had higher (p<0.05) ADG compared to NC treatment during the first 2 wk. From d 15 to 28, the ATTD of energy was improved (p<0.05) by MCT3 compared to the PC treatment. No effect has been observed on the blood profiles [red blood cell (RBC), white blood cell (WBC), immunoglobulin-G (IgG), lymphocyte concentration] measured in this study. In Exp. 2, the ADG were increased (p<0.05) by the MCT5 treatment than the PC treatment from d 0 to 14. Pigs fed PC treatment diet had lower ADFI (p<0.05) and better FCR (p<0.05) than NC treatment, whereas no differences were shown between MCT treatments and NC or PC treatment from d 15 to 35 and overall phase. The ATTD of DM and nitrogen were improved (p<0.05) by the effect of MCT5 related to the NC and PC treatment at the end of 2nd and 5th wk. The pigs fed MCT3 had higher (p<0.05) energy digestibility than PC treatment. No effects were seen in the blood profiles we measured (WBC, RBC, lymphocyte and immunoglobulin-G). In conclusion, the addition of MCT in the weanling pigs diet can improve the ADG and digestibility during the earlier period (first 2 wks), but had little effect on the blood characteristics.
Maraviroc modifies gut microbiota composition in a mouse model of obesity: a plausible therapeutic option to prevent metabolic disorders in HIV-infected patients.

INTRODUCTION The proportion of HIV-infected patients with overweight/obesity has increased in recent years. These patients have an increased metabolic/cardiovascular risk compared with non-obese patients. Modulation of gut microbiota composition arises as a promising tool to prevent the development of obesity and associated disorders. The aim of this study was to investigate the impacts of maraviroc (MVC), a CCR5 antagonist approved for clinical use in HIV-infected patients, on gut microbiota composition in a mouse model of obesity. METHODS Thirty two male C57BL/6 mice were assigned to:a) Control (chow diet), b) MVC (chow diet plus 300 mg/L MVC), c) High-fat diet (HFD) or d) HFD/MVC (HFD plus 300 mg/L MVC) groups. Body weight and food intake was recorded every 2-3 days. Mice were euthanized after 16 weeks of treatment and cecal contents were removed to analyse by real-time PCR four bacterial orders from the most dominant phyla in gut. RESULTS Mice fed with a HFD showed a significant increase in Enterobacteriales (p<0.001 vs. control). MVC treatment induced a significant decrease in control (p<0.05) and HFD fed mice (p<0.001). Interestingly, this order was positively associated with body weight gain, insulin resistance and fatty liver. HFD induced a significant decrease in Bacteroidales and Clostridiales levels (p<0.05 and p<0.01, respectively). MVC decreased the presence of Bacteroidales (p<0.05 vs. control) while an increase was observed in HFD/MVC mice (p=0.01 vs. HFD). No direct effects of MVC were observed on Clostridiales and Lactobacillales. CONCLUSIONS MVC may constitute a new therapeutic option to prevent obesity and related disorders in HIV-infected patients.
Biclustering as a method for RNA local multiple sequence alignment

MOTIVATIONS Biclustering is a clustering method that simultaneously clusters both the domain and range of a relation. A challenge in multiple sequence alignment (MSA) is that the alignment of sequences is often intended to reveal groups of conserved functional subsequences. Simultaneously, the grouping of the sequences can impact the alignment; precisely the kind of dual situation biclustering is intended to address. RESULTS We define a representation of the MSA problem enabling the application of biclustering algorithms. We develop a computer program for local MSA, BlockMSA, that combines biclustering with divide-and-conquer. BlockMSA simultaneously finds groups of similar sequences and locally aligns subsequences within them. Further alignment is accomplished by dividing both the set of sequences and their contents. The net result is both a multiple sequence alignment and a hierarchical clustering of the sequences. BlockMSA was tested on the subsets of the BRAliBase 2.1 benchmark suite that display high variability and on an extension to that suite to larger problem sizes. Also, alignments were evaluated of two large datasets of current biological interest, T box sequences and Group IC1 Introns. The results were compared with alignments computed by ClustalW, MAFFT, MUCLE and PROBCONS alignment programs using Sum of Pairs (SPS) and Consensus Count. Results for the benchmark suite are sensitive to problem size. On problems of 15 or greater sequences, BlockMSA is consistently the best. On none of the problems in the test suite are there appreciable differences in scores among BlockMSA, MAFFT and PROBCONS. On the T box sequences, BlockMSA does the most faithful job of reproducing known annotations. MAFFT and PROBCONS do not. On the Intron sequences, BlockMSA, MAFFT and MUSCLE are comparable at identifying conserved regions. AVAILABILITY BlockMSA is implemented in Java. Source code and supplementary datasets are available at http://aug.csres. utexas.edu/msa/
Experimental Implementation of an All-Optical Interferometric Drop, Add, and Extract Multiplexer for Superchannels

We present the experimental implementation of an all-optical ROADM scheme for routing of an individual subchannel within an all-optical OFDM superchannel. The different functions required of optical node were demonstrated using interferometric technique with the extraction, drop, and addition of individual subchannel in a ten subchannels optically aggregated signal. The scheme we reported enables a fully flexible node compatible with future terabit per second superchannel transmission.
Cytological and Comparative Proteomic Analyses on Male Sterility in Brassica napus L. Induced by the Chemical Hybridization Agent Monosulphuron Ester Sodium

Male sterility induced by a chemical hybridization agent (CHA) is an important tool for utilizing crop heterosis. Monosulphuron ester sodium (MES), a new acetolactate synthase-inhibitor herbicide belonging to the sulphonylurea family, has been developed as an effective CHA to induce male sterility in rapeseed (Brassica napus L.). To understand MES-induced male sterility in rapeseed better, comparative cytological and proteomic analyses were conducted in this study. Cytological analysis indicated that defective tapetal cells and abnormal microspores were gradually generated in the developing anthers of MES-treated plants at various development stages, resulting in unviable microspores and male sterility. A total of 141 differentially expressed proteins between the MES-treated and control plants were revealed, and 131 of them were further identified by MALDI-TOF/TOF MS. Most of these proteins decreased in abundance in tissues of MES-treated rapeseed plants, and only a few increased. Notably, some proteins were absent or induced in developing anthers after MES treatment. These proteins were involved in several processes that may be crucial for tapetum and microspore development. Down-regulation of these proteins may disrupt the coordination of developmental and metabolic processes, resulting in defective tapetum and abnormal microspores that lead to male sterility in MES-treated plants. Accordingly, a simple model of CHA-MES-induced male sterility in rapeseed was established. This study is the first cytological and dynamic proteomic investigation on CHA-MES-induced male sterility in rapeseed, and the results provide new insights into the molecular events of male sterility.
Generalization of the /spl Sigma//sub 0/-rank criteria for space-time codes

Recently, Liu et al., developed the /spl Sigma//sub 0/-rank criteria for space-time codes. It provides a sufficient condition on codeword and generator matrices defined over finite rings /spl Zopf//sub 2k/(j) to ensure full spatial diversity with 2/sup 2k/-QAM modulation. Here, we generalize the /spl Sigma//sub 0/-rank criteria and derive a sufficient condition on the generator matrices defined over finite rings /spl Zopf//sub 2l/(j) to ensure full spatial diversity with 2/sup 2k/-QAM modulation for any positive integer l/spl les/k. We also show that generator matrices defined over GF(2) satisfying the BPSK stacking construction constraint of Mammons and El Gamal achieve full spatial diversity when used with 2/sup 2k/-QAM modulation.
Glutamate Release through Volume-Activated Channels during Spreading Depression

Volume-sensitive organic anion channels (VSOACs) in astrocytes are activated by cell swelling and are permeable to organic anions, such as glutamate and taurine. We have examined the release of glutamate through VSOACs during the propagation of spreading depression (SD). SD was induced by bath application of ouabain in hippocampal brain slices and was monitored by imaging intrinsic optical signals, a technique that provides a measure of cellular swelling. The onset of SD was associated with increased light transmittance, confirming previous studies that cellular swelling occurs during SD. NMDA receptor antagonists, either noncompetitive (MK-801, 10–50 μm) or competitive (CGS-17355, 100 μm), reduced the rate of propagation of SD, indicating that glutamate release contributes to SD onset. SD still occurred in zero Ca2+–EGTA (0-Ca2+–EGTA) solution, a manipulation that depresses synaptic transmission. HPLC measurements indicated that, even in this solution, there was significant glutamate release. Two lines of experiments indicated that glutamate was released through VSOACs during SD. First, 5-nitro-2-(3-phenylpropylamino) benzoic acid (NPPB), a blocker of VSOACs, depressed the rate of propagation of SD in a manner similar to NMDA antagonists. Second, NPPB inhibited the release of glutamate during SD in 0-Ca2+–EGTA external solution. These results indicate that cellular swelling during SD causes the activation of VSOACs and the release of glutamate by permeation through this channel. Cellular swelling is a result of neuronal activity and is observed during excitotoxicity. Therefore, glutamate release from VSOAC activation could occur under conditions of cell swelling and contribute to excitotoxic damage.
Phylogeographic and demographic effects of Pleistocene climatic fluctuations in a montane salamander, Plethodon fourchensis

Climatic changes associated with Pleistocene glacial cycles profoundly affected species distributions, patterns of interpopulation gene flow, and demography. In species restricted to montane habitats, ranges may expand and contract along an elevational gradients in response to environmental fluctuations and create high levels of genetic variation among populations on different mountains. The salamander Plethodon fourchensis is restricted to high‐elevation, mesic forest on five montane isolates in the Ouachita Mountains. We used DNA sequence data along with ecological niche modelling and coalescent simulations to test several hypotheses related to the effects of Pleistocene climatic fluctuations on species in montane habitats. Our results revealed that P. fourchensis is composed of four well‐supported, geographically structured lineages. Geographic breaks between lineages occurred in the vicinity of major valleys and a narrow high‐elevation pass. Ecological niche modelling predicted that environmental conditions in valleys separating most mountains are suitable; however, interglacial periods like the present are predicted to be times of range expansion in P. fourchensis. Divergence dating and coalescent simulations indicated that lineage diversification occurred during the Middle Pleistocene via the fragmentation of a wide‐ranging ancestor. Bayesian skyline plots showed gradual decreases in population size in three of four lineages over the most recent glacial period and a slight to moderate amount of population growth during the Holocene. Our results not only demonstrate that climatic changes during the Pleistocene had profound effects on species restricted to montane habitats, but comparison of our results for P. fourchensis with its parapatric, sister taxon, P. ouachitae, also emphasizes how responses can vary substantially even among closely related, similarly distributed taxa.
Demonstration of a 0.48 THz Amplifier Module Using InP HEMT Transistors

In this letter, we present an amplifier module operating at a frequency of 0.48 THz. This represents almost a 50% increase in solid-state amplifier operating frequency compared to prior state of the art, and is the highest reported amplifier to date. The amplifier demonstrates a peak gain of 11.7 dB measured in a waveguide split-block housing. Sub 50-nm InP HEMT transistors with an estimated f MAX > 1 THz are used to achieve this level of performance. The five stage amplifier is realized in coplanar waveguide, and uses monolithically integrated dipole probes to couple the chip from the WR 2.2 waveguide.
Defending against Sybil Devices in Crowdsourced Mapping Services

Real-time crowdsourced maps such as Waze provide timely updates on traffic, congestion, accidents and points of interest. In this paper, we demonstrate how lack of strong location authentication allows creation of software-based Sybil devices that expose crowdsourced map systems to a variety of security and privacy attacks. Our experiments show that a single Sybil device with limited resources can cause havoc on Waze, reporting false congestion and accidents and automatically rerouting user traffic. More importantly, we describe techniques to generate Sybil devices at scale, creating armies of virtual vehicles capable of remotely tracking precise movements for large user populations while avoiding detection. We propose a new approach to defend against Sybil devices based on co-location edges, authenticated records that attest to the one-time physical co-location of a pair of devices. Over time, co-location edges combine to form large proximity graphs that attest to physical interactions between devices, allowing scalable detection of virtual vehicles. We demonstrate the efficacy of this approach using large-scale simulations, and discuss how they can be used to dramatically reduce the impact of attacks against crowdsourced mapping services.
Receptor-Directed Chimeric Toxins Created by Sortase-Mediated Protein Fusion

Chimeric protein toxins that act selectively on cells expressing a designated receptor may serve as investigational probes and/or antitumor agents. Here, we report use of the enzyme sortase A (SrtA) to create four chimeric toxins designed to selectively kill cells bearing the tumor marker HER2. We first expressed and purified: (i) a receptor recognition-deficient form of diphtheria toxin that lacks its receptor-binding domain and (ii) a mutated, receptor-binding–deficient form of anthrax-protective antigen. Both proteins carried at the C terminus the sortase recognition sequence LPETGG and a H6 affinity tag. Each toxin protein was mixed with SrtA plus either of two HER2-recognition proteins—a single-chain antibody fragment or an Affibody—both carrying an N-terminal G5 tag. With wild-type SrtA, the fusion reaction between the toxin and receptor-recognition proteins approached completion only after several hours, whereas with an evolved form of the enzyme, SrtA*, the reaction was virtually complete within 5 minutes. The four fusion toxins were purified and shown to kill HER2-positive cells in culture with high specificity. Sortase-mediated ligation of binary combinations of diverse natively folded proteins offers a facile way to produce large sets of chimeric proteins for research and medicine. Mol Cancer Ther; 12(10); 2273–81. ©2013 AACR.
Genome-Scale Metabolic Model of Helicobacter pylori 26695

ABSTRACT A genome-scale metabolic model of Helicobacter pylori 26695 was constructed from genome sequence annotation, biochemical, and physiological data. This represents an in silico model largely derived from genomic information for an organism for which there is substantially less biochemical information available relative to previously modeled organisms such as Escherichia coli. The reconstructed metabolic network contains 388 enzymatic and transport reactions and accounts for 291 open reading frames. Within the paradigm of constraint-based modeling, extreme-pathway analysis and flux balance analysis were used to explore the metabolic capabilities of the in silico model. General network properties were analyzed and compared to similar results previously generated for Haemophilus influenzae. A minimal medium required by the model to generate required biomass constituents was calculated, indicating the requirement of eight amino acids, six of which correspond to essential human amino acids. In addition a list of potential substrates capable of fulfilling the bulk carbon requirements of H. pylori were identified. A deletion study was performed wherein reactions and associated genes in central metabolism were deleted and their effects were simulated under a variety of substrate availability conditions, yielding a number of reactions that are deemed essential. Deletion results were compared to recently published in vitro essentiality determinations for 17 genes. The in silico model accurately predicted 10 of 17 deletion cases, with partial support for additional cases. Collectively, the results presented herein suggest an effective strategy of combining in silico modeling with experimental technologies to enhance biological discovery for less characterized organisms and their genomes.
UvA-DARE (Digital Academic Repository) PML-containing nuclear bodies: their spatial distribution in relation to other nuclear components

The PML protein is a human growth suppressor concentrated in 10 to 20 nuclear bodies per nucleus (PML bodies). Disruption of the PML gene has been shown to be related to acute promyelocytic leukaemia (APL). To obtain information about the function of PML bodies we have investigated the 3D-distribution of PML bodies in the nucleus of T24 cells and compared it with the spatial distribution of a variety of other nuclear components, using fluorescence dual-labeling immunocytochemistry and confocal microscopy. Results show that PML bodies are not enriched in nascent RNA, the splicing component U2-snRNP
Implications of Dual Permit Regulation on the Market Values of Limited Entry Permits in the Bristol Bay Salmon Drift Gillnet Fishery

Implications of dual permit regulation on the market values of limited entry permits in the Bristol Bay salmon drift gillnet fishery Lange Taylor Solberg Chair of the Supervisory Committee: Sunny Jardine School of Marine and Environmental Affairs In 2003, a regulation allowing two drift salmon permits to actively fish on one fishing vessel was adopted by the Alaska Board of Fisheries. This thesis aims to determine whether the new dual permit regulation impacted the market values for buyers and sellers of limited entry salmon permits beyond inherent noise in the permit price data by estimating a difference-indifferences (DiD) model. I compare monthly average permit prices between the treatment fishery, Bristol Bay, and two control fisheries, Prince William Sound and Area M. I also account for exogenous drivers of fishermen’s perceptions of discounted future profits by controlling for exvessel prices, sockeye salmon run forecasts, and harvests in the DiD regression. Initial results indicate a 51.3% decrease in Bristol Bay permit prices occurred after the regulation was enacted. This result is statistically significant. The model proved to be extremely sensitive to sockeye salmon run forecasts in particular, however; and running the regression without this variable and others create drastically different outcomes that are not statistically significant. The analysis can be improved by future work refining control variables to more accurately reflect the information fishermen have about future profitability in the fishery.
Evaluating Energy-aware Behavior of Proactive and Reactive Routing Protocols for Mobile Ad Hoc Networks

Ad hoc routing technology has been developed primarily for networks of mobile nodes. In many cases the operational life of a node will be limited by its power source, so power consumption can be a critical issue. All the layers of communication are coupled in power consumption. Ad hoc routing protocols may consume different amounts of power and their routing decisions may be conditioned. Power consumption must be distributed on the nodes of the network and the overall transmission power for each connection must be minimized. We have therefore modelled two contrasting protocols for the MANETs (Mobile Ad Hoc NETworks), namely the reactive protocol DSR (Dynamic Source Routing) and the proactive protocol OLSR (Optimized Link State Routing). DSR and OLSR have been simulated by ns-2 Network Simulator. We will analyze these two protocols with particular attention to their energy performance.