Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparative Genomics Integrated with Association Analysis Identifies Candidate Effector Genes Corresponding to Lr20 in Phenotype-Paired Puccinia triticina Isolates from Australia

Leaf rust is one of the most common and damaging diseases of wheat, and is caused by an obligate biotrophic basidiomycete, Puccinia triticina (Pt). In the present study, 20 Pt isolates from Australia, comprising 10 phenotype-matched pairs with contrasting pathogenicity for Lr20, were analyzed using whole genome sequencing. Compared to the reference genome of the American Pt isolate 1-1 BBBD Race 1, an average of 404,690 single nucleotide polymorphisms (SNPs) per isolate was found and the proportion of heterozygous SNPs was above 87% in the majority of the isolates, demonstrating a high level of polymorphism and a high rate of heterozygosity. From the genome-wide SNPs, a phylogenetic tree was inferred, which consisted of a large clade of 15 isolates representing diverse presumed clonal lineages including 14 closely related isolates and the more diverged isolate 670028, and a small clade of five isolates characterized by lower heterozygosity level. Principle component analysis detected three distinct clusters, corresponding exactly to the two major subsets of the small clade and the large clade comprising all 15 isolates without further separation of isolate 670028. While genome-wide association analysis identified 302 genes harboring at least one SNP associated with Lr20 virulence (p < 0.05), a Wilcoxon rank sum test revealed that 36 and 68 genes had significant (p < 0.05) and marginally significant (p < 0.1) differences in the counts of non-synonymous mutations between Lr20 avirulent and virulent groups, respectively. Twenty of these genes were predicted to have a signal peptide without a transmembrane segment, and hence identified as candidate effector genes corresponding to Lr20. SNP analysis also implicated the potential involvement of epigenetics and small RNA in Pt pathogenicity. Future studies are thus warranted to investigate the biological functions of the candidate effectors as well as the gene regulation mechanisms at epigenetic and post-transcription levels. Our study is the first to integrate phenotype-genotype association with effector prediction in Pt genomes, an approach that may circumvent some of the technical difficulties in working with obligate rust fungi and accelerate avirulence gene identification.
Scale-freeness for networks as a degenerate ground state: A Hamiltonian formulation

The origin of scale-free degree distributions in the context of networks is addressed through an analogous non-network model in which the node degree corresponds to the number of balls in a box and the rewiring of links to balls moving between the boxes. A statistical mechanical formulation is presented and the corresponding Hamiltonian is derived. The energy, the entropy, as well as the degree distribution and its fluctuations are investigated at various temperatures. The scale-free distribution is shown to correspond to the degenerate ground state, which has small fluctuations in the degree distribution and yet a large entropy. We suggest an implication of our results from the viewpoint of the stability in evolution of networks.
Face-name association learning and brain structural substrates in alcoholism.

BACKGROUND Associative learning is required for face-name association and is impaired in alcoholism, but the cognitive processes and brain structural components underlying this deficit remain unclear. It is also unknown whether prompting alcoholics to implement a deep level of processing during face-name encoding would enhance performance. METHODS Abstinent alcoholics and controls performed a levels-of-processing face-name learning task. Participants indicated whether the face was that of an honest person (deep encoding) or that of a man (shallow encoding). Retrieval was examined using an associative (face-name) recognition task and a single-item (face or name only) recognition task. Participants also underwent 3T structural MRI. RESULTS Compared with controls, alcoholics had poorer associative and single-item learning and performed at similar levels. Level of processing at encoding had little effect on recognition performance but affected reaction time (RT). Correlations with brain volumes were generally modest and based primarily on RT in alcoholics, where the deeper the processing at encoding, the more restricted the correlations with brain volumes. In alcoholics, longer control task RTs correlated modestly with smaller tissue volumes across several anterior to posterior brain regions; shallow encoding correlated with calcarine and striatal volumes; deep encoding correlated with precuneus and parietal volumes; and associative recognition RT correlated with cerebellar volumes. In controls, poorer associative recognition with deep encoding correlated significantly with smaller volumes of frontal and striatal structures. CONCLUSIONS Despite prompting, alcoholics did not take advantage of encoding memoranda at a deep level to enhance face-name recognition accuracy. Nonetheless, conditions of deeper encoding resulted in faster RTs and more specific relations with regional brain volumes than did shallow encoding. The normal relation between associative recognition and corticostriatal volumes was not present in alcoholics. Rather, their speeded RTs occurred at the expense of accuracy and were related most robustly to cerebellar volumes.
Inversion Formulas for the Dunkl Intertwining Operator and Its Dual on Spaces of Functions and Distributions

In this paper we prove inversion formulas for the Dunkl intertwining operator $V_k$ and for its dual ${}^tV_k$ and we deduce the expression of the representing distributions of the inverse operators $V_k^{-1}$ and ${}^tV_k^{-1}$, and we give some applications.
FRAMES: Software tools for modeling, rendering and animation of 3D scenes

FRAMES is a set of flexible software tools, developed for the UNIX programming environment, that can be used to generate images and animation of 3D scenes. In FRAMES, each stage of the image-rendering pipeline is assigned to a UNIX System filter. The following is a typical FRAMES pipe sequence where each filter performs a task implied by its name:cat scene.frm|euclid|mover|shade|camera|abufFRAMES was designed to be easy to use, to permit flexible experimentation with new ideas in image rendering and geometric modeling, to allow distribution of different parts of the rendering pipeline to different processors, and to specify images in a common format for display on a variety of devices.The user communicates with FRAMES via a command language. This language is extended whenever a software developer needs to incorporate a new idea into the system by adding new commands. Data flowing through the pipeline is modified by a collection of filter programs and passed through the pipe in text or binary format.The modular and pipe-based nature of FRAMES allows for multi/parallel processor implementations and device independence. FRAMES has generated images on a local-area network of minicomputers (each filter runs on a different processor) and on a 64-processor hypercube machine (one filter runs on 64 processors). Applications of FRAMES have ranged from reconstruction of neurons from serial sections to rendering of antialiased octree objects with subpixel detail.
Modeling macroeconomic time series via heavy tailed distributions

It has been shown that some macroeconomic time series, especially those where outliers could be present, can be well modelled using heavy tailed distributions for the noise components. Methods for deciding when and where heavy-tailed models should be preferred are investigated. These investigations primarily focus on automatic methods for model identification and selection. Current methods are extended to incorporate a non-Gaussian selection element, and various different criteria for deciding on which overall model should be used are examined.
Joint kinetics of the ankle and knee when running over obstacles.

AIM When running over obstacles of increasing height, heelstrike (HS) runners switch to a forefoot (FF) landing pattern once a critical obstacle height is reached. The primary purpose of this study was to determine whether ankle or knee joint kinetic variables trigger the gait change from a HS to a FF striking pattern as obstacle height increases. METHODS Ten subjects were filmed from the sagittal plane as they ran at their preferred running speed over a force platform during 6 obstacle height conditions ranging from 10% to 22.5% of standing height, as well as an additional baseline condition with no obstacle (0%). An inverse dynamics approach was utilized to calculate ankle and knee joint kinetics at each condition. RESULTS Differences in joint kinetics did not occur until a height was reached at which the landing strategy changed from a HS to a FF landing pattern. Most differences occurred at the ankle joint, at which there was a greater maximum plantar flexor moment and a greater amount of energy absorbed when obstacles of sufficient height to require a FF landing pattern were negotiated. CONCLUSIONS Although no variables were found which met all of the criteria necessary to be considered a determinant of the gait transition, there were variables which distinguished between a HS and FF strike landing pattern as obstacle height increased.
Caveolae control the anti-inflammatory phenotype of senescent endothelial cells

Senescent endothelial cells (EC) have been identified in cardiovascular disease, in angiogenic tumour associated vessels and in aged individuals. We have previously identified a novel anti‐inflammatory senescent phenotype of EC. We show here that caveolae are critical in the induction of this anti‐inflammatory senescent state. Senescent EC induced by either the overexpression of ARHGAP18/SENEX or by H2O2 showed significantly increased numbers of caveolae and associated proteins Caveolin‐1, cavin‐1 and cavin‐2. Depletion of these proteins by RNA interference decreased senescence induced by ARHGAP18 and by H2O2. ARHGAP18 overexpression induced a predominantly anti‐inflammatory senescent population and depletion of the caveolae‐associated proteins resulted in the preferential reduction in this senescent population as measured by neutrophil adhesion and adhesion protein expression after TNFα treatment. In confirmation, EC isolated from the aortas of CAV‐1−/− mice failed to induce this anti‐inflammatory senescent cell population upon expression of ARHGAP18, whereas EC from wild‐type mice showed a significant increase. NF‐κB is one of the major transcription factors mediating the induction of E‐selectin and VCAM‐1 expression, adhesion molecules responsible for leucocyte attachment to EC. TNFα‐induced activation of NF‐κB was suppressed in ARHGAP18‐induced senescent EC, and this inhibition was reversed by Caveolin‐1 knock‐down. Thus, out results demonstrate that an increase in caveolae and its component proteins in senescent ECs is associated with inhibition of the NF‐kB signalling pathway and promotion of the anti‐inflammatory senescent pathway.
Non-Critical Open Strings Beyond the Semiclassical Approximation

We studied the lowest order quantum corrections to the macroscopic wave functions Γ(A,l) of non-critical string theory using the semiclassical expansion of Liouville theory. By carefully taking the perimeter constraint into account we obtained a new type of boundary condition for the Liouville field which is compatible with the reparametrization invariance of the boundary and which is not only a mixture of Dirichlet and Neumann types but also involves an integral of an exponential of the Liouville field along the boundary. This condition contains an unknown function of A/l2. We determined this function by computing part of the one-loop corrections to Γ(A,l).
Assessment of high-heat-flux thermal management schemes

This paper explores the recent research developments in high-heat-flux thermal management. Cooling schemes such as pool boiling, detachable heat sinks, channel flow boiling, micro-channel and mini-channel heat sinks, jet-impingement, and sprays, are discussed and compared relative to heat dissipation potential, reliability, and packaging concerns. It is demonstrated that, while different cooling options can be tailored to the specific needs of individual applications, system considerations always play a paramount role in determining the most suitable cooling scheme. It is also shown that extensive fundamental electronic cooling knowledge has been amassed over the past two decades. Yet there is now a growing need for hardware innovations rather than perturbations to those fundamental studies. An example of these innovations is the cooling of military avionics, where research findings from the electronic cooling literature have made possible the development of a new generation of cooling hardware which promise order of magnitude increases in heat dissipation compared to today's cutting edge avionics cooling schemes.
Analysis of Mismatched Transcriptions Generated by Humans and Machines for Under-Resourced Languages

When speech data with native transcriptions are scarce in an under-resourced language, automatic speech recognition (ASR) must be trained using other methods. Semi-supervised learning first labels the speech using ASR from other languages, then re-trains the ASR using the generated labels. Mismatched crowdsourcing asks crowd-workers unfamiliar with the language to transcribe it. In this paper, self-training and mismatched crowdsourcing are compared under exactly matched conditions. Specifically, speech data of the target language are decoded by the source language ASR systems into source language phone/word sequences. We find that (1) human mismatched crowdsourcing and cross-lingual ASR have similar error patterns, but different specific errors. (2) These two sources of information can be usefully combined in order to train a better target-language ASR. (3) The differences between the error patterns of non-native human listeners and non-native ASR are small, but when differences are observed, they provide information about the relationship between the phoneme systems of the annotator/source language (Mandarin) and the target language (Vietnamese).
Gating of myotonic Na channel mutants defines the response to mexiletine and a potent derivative

Background: Myotonia and periodic paralysis caused by sodium channel mutations show variable responses to the anti-myotonic drug mexiletine. Objective: To investigate whether variability among sodium channel mutants results from differences in drug binding affinity or in channel gating. Methods: Whole-cell sodium currents (INa) were recorded in tsA201 cells expressing human wild-type (WT) and mutant skeletal muscle sodium channels (A1156T, hyperkalemic periodic paralysis; R1448C, paramyotonia congenita; G1306E, potassium-aggravated myotonia). Results: At a holding potential (hp) of −120 mV, mexiletine produced a tonic (TB, 0.33 Hz) and a use-dependent (UDB, 10 Hz) block of peak INa with a potency following the order rank R1448C > WT ≈ A1156T > G1306E. Yet, when assayed from an hp of −180 mV, TB and UDB by mexiletine were similar for the four channels. The different midpoints of channel availability curves found for the four channels track the half-maximum inhibitory value (IC50) measured at −120 mV. Thus differences in the partitioning of channels between the closed and fast-inactivated states underlie the different IC50 measured at a given potential. The mexiletine-derivative, Me7 (α-[(2-methylphenoxy)methyl]-benzenemethanamine), behaved similarly but was ∼5 times more potent than mexiletine. Interestingly, the higher drug concentrations ameliorated the abnormally slower decay rate of myotonic INa. Conclusions: These results explain the basis of the apparent difference in block of mutant sodium channels by mexiletine and Me7, opening the way to a more rationale drug use and to design more potent drugs able to correct specifically the biophysical defect of the mutation in individual myotonic patients.
MIMO: State of the Art and the Future in Focus

Antennas of transmitters and receivers have been manipulated to increase the capacity of transmission and reception of signals. Using many elements in antennas to shape beams and direct nulls in a particular point for optimum signal transmission and reception has over decades, had tremendous positive influence in received power and signal to noise ratio (SNR). However, since the antenna elements manipulation can be done both at base station and device terminal, it gives rise to an important method of using several antennas to put and obtain signals to and from space with increased capacity. This principle is termed Multiple-input and Multiple-output (MIMO). This paper discusses application of MIMO in the state of the art and next generation of wireless systems (5G). It also discusses four models of MIMO; SISO, SIMO, MISO and MIMO, considering three method of combing the signals from multipath propagations; Selection combining (SC), Equal gain combing (EGC) and maximum ratio combining (MRC). Spatial diversity and spatial multiplexing are also discussed as form of MIMO. Finally, Massive or Hyper MIMO which is a new method of increasing transmission capacity by very large scale for fifth generation of wireless system is discussed with its challenges and opportunities. Key terms-Diversity combining techniques, spatial multiplexing, channel state information (CSI). Massive MIMO
An sEMG-driven musculoskeletal model of shoulder and elbow based on neural networks

In this paper, an sEMG-driven musculoskeletal model of human shoulder and elbow joints is built based on time delay neural network (TDNN). Six principal muscles of the upper arm and forearm are included, and the experiment was conducted under isometric contractions with the aid of a planar haptic interface. Both force amplitude and direction were regulated continuously, and the experiment results proved the effectiveness and performance of this modeling method. The model was proved to have less overfitting risk than the most-used basic multilayer forward networks, and the isometric model was proved to be still effective in estimation of slow movement cases.
Challenges to Evaluating Respiratory Syncytial Virus Mortality in Bangladesh, 2004–2008

Background Acute lower respiratory illness is the most common cause of death among children, globally. Data are not available to make accurate estimates on the global mortality from respiratory syncytial virus (RSV), specifically. Methods Respiratory samples collected from children under 5 years of age during 2004 to 2008 as part of population-based respiratory disease surveillance in an urban community in Dhaka, Bangladesh were tested for RSV, human metapneumovirus (HMPV), human parainfluenza virus (PIV) types 1, 2, and 3, influenza and adenovirus by RT-PCR. Verbal autopsy data were used to identify children who died from respiratory illness in a nearby rural community. Significance of the correlation between detections and community respiratory deaths was determined using Spearman's coefficient. Results RSV activity occurred during defined periods lasting approximately three months but with no clear seasonal pattern. There was no significant correlation between respiratory deaths and detection of any of the respiratory viruses studied. Conclusion Outbreaks of respiratory viruses may not be associated with deaths in children in the study site; however, the few respiratory deaths observed and community-to-community variation in the timing of outbreaks may have obscured an association. An accurate assessment of respiratory virus-associated deaths will require detections and death data to come from the same location and a larger study population.
Transient expression of NADPH‐diaphorase in the lateral geniculate nucleus of the ferret during early postnatal development

Retinogeniculate projections in the ferret are refined during postnatal development so that inputs from the two eyes become segregated into eye‐specific laminae, and each eye‐specific lamina is further divided into sublaminae containing inputs from on‐center or off‐center afferents. Segregation into eye‐specific laminae and on/off sublaminae is dependent on neuronal activity; sublamination depends on activation of N‐methyl‐d‐aspartate (NMDA) receptors. By analogy with the suggested role of nitric oxide in NMDA‐mediated long‐term potentiation in the hippocampus, we investigated a possible role for nitric oxide in ferret retinogeniculate development. The expression of NADPH‐diaphorase, a nitric oxide synthase, was examined histologically in the lateral geniculate nucleus of ferrets at several postnatal ages. At birth, neuropil is labeled in the nucleus, although no cell bodies are visible. After the first postnatal week, some labeled cells appear, predominantly in the C laminae. By three postnatal weeks, cell bodies are clearly labeled in all geniculate laminae. Staining reaches a peak in density at about four postnatal weeks, then declines such that by six postnatal weeks labeled cells are no longer visible. This transient expression of NADPH‐diaphorase activity is consistent with a role for nitric oxide in the development of mature connections within the ferret lateral geniculate nucleus. © 1995 Wiley‐Liss, Inc.
The Evolution of SDN and OpenFlow: A Standards Perspective

 The Evolution of SDN and OpenFlow: A Standards Perspective Jean Tourrilhes; Puneet Sharma; Sujata Banerjee; Justin Pettit HP Laboratories HPL-2014-41 SDN; OpenFlow; Networking SDN is designed to address networking needs that are poorly addressed by existing networks, and therefore the OpenFlow protocol and its specification process are significantly different from most traditional network protocols. The evolution of the OpenFlow API is guided by a large number of unrelated use cases, the main elements of SDN and classical guidelines of API development. However the goal of addressing a wide range of network devices, hardware and software, and the volunteer process in the Extensibility WG make the specification process quite complex. To address these challenges, the specification process for OpenFlow was made very dynamic and quite similar to the process of open source projects, and the deliverables include both a stable long term support branch and a more experimental main branch. External Posting Date: December 6, 2014 [Fulltext] Approved for External Publication Internal Posting Date: December 6, 2014 [Fulltext] Copyright 2014 Hewlett-Packard Development Company, L.P. 1 The Evolution of SDN and OpenFlow: A Standards Perspective Jean Tourrilhes, Puneet Sharma, Sujata Banerjee – HP-Labs {FirstName.LastName}@hp.com Justin Pettit – VMware – jpettit@vmware.com
European Culture and the Media

We are witnessing a dynamic reshaping of the European 'mediascape'. This has been underway for more than a decade since the fall of the Berlin wall in 1989, the growing impact of globalisation, and the birth of new technologies and new media, or the convergence between old and new media. A new and more intense 'mediatisation' of society and everyday life is emerging. This is happening alongside the rapid reconstruction of the cultural and economic landscape of Europe itself. In this transformation the communicative and ideological dimensions, the digitalisation of technology, and changes in culture - 'the imaginary', the discursive universe of politics and communication, are all crucial areas for research. The cultural industries, (film, television, books, magazines, entertainment and music), but also the world of news, actuality, 'infotainment' and the internet, are key areas for the study of what we may begin to understand as a changing European culture in all its complexity and with all its differences and conflicts. The media and the cultural industries are among the fastest growing sectors in the global economy. This book presents new research and thinking, with particular foc