Miracle-dz/UniFAR-FTUs huggingface dataset:
Genome-wide association studies in asthma; perhaps, the end of the beginning

Purpose of reviewA large number of genetic loci contribute towards an individual's susceptibility to asthma and other complex diseases. Genome-wide association studies (GWASs) have provided us with a wealth of loci associated with asthma susceptibility, asthma endotypes and responsiveness to asthma medications. The reproducibility of these genetic loci across different studies highlights the interplay of general and population-specific risk alleles in asthma. Although GWASs have been successful in identifying disease-associated loci, there is still large potential for such studies to provide further insights into asthma pathogenesis. Recent findingsGWASs over the past year have extended study design well beyond the simple case–control and continuous phenotype association formats, for example, including interactions with environmental factors, integrating GWAS data with epigenetic data and GWASs in animal models, incorporating pathway analyses and utilising emerging sequencing technologies. SummaryMoving beyond traditional GWAS formats is likely to significantly enhance our understanding of the genetic basis for asthma. This review discusses where we are after half a decade of asthma GWASs, and focuses on advances over the past year that show where the GWAS field is headed in the future.
Context models on sequences of covers

We present a class of models that, via a simple construction, enables exact, incremental, non-parametric, polynomial-time, Bayesian inference of conditional measures. The approach relies upon creating a sequence of covers on the conditioning variable and maintaining a different model for each set within a cover. Inference remains tractable by specifying the probabilistic model in terms of a random walk within the sequence of covers. We demonstrate the approach on problems of conditional density estimation, which, to our knowledge is the first closed-form, non-parametric Bayesian approach to this problem
The Subventricular Zone Response to Stroke Is Not a Therapeutic Target of Anti-Nogo-A Immunotherapy

Ischemic stroke is a leading cause of adult disability with no pharmacological treatments to promote the recovery of lost function. Neutralizing antibodies against the neurite outgrowth inhibitor Nogo-A have emerged as a promising treatment for subacute and chronic stroke in animal models; however, whether anti-Nogo-A treatment affects poststroke neurogenesis remains poorly understood. In this study, we confirmed expression of Nogo-A by neuroblasts in the adult rat subventricular zone (SVZ), a major neurogenic niche; however, we found no evidence that Nogo-A was expressed at the surface of these cells. In vitro migration assays demonstrated that Nogo-A signaling induced a modest reduction in neuroblast migration speed, while anti-Nogo-A antibodies had no effect on motility properties. Using a permanent distal middle cerebral artery occlusion model of cortical stroke, we found that the number of proliferating cells in the SVZ was unaffected in response to stroke, while neuroblast mobilization from the SVZ toward the stroke lesion correlated positively with lesion size. However, we found no evidence that proliferation or neuroblast mobilization were affected by anti-Nogo-A antibody treatment. Our results suggest that the SVZ is not a therapeutic target of anti-Nogo-A immunotherapy, and contribute to our understanding of the SVZ response to cortical stroke.
A 105-dB SNDR, 10 kSps multi-level second-order incremental converter with smart-DEM consuming 280 µW and 3.3-V supply

This paper presents a second-order 3-bit incremental converter, which uses a novel Smart-DEM algorithm for mismatch compensation of multi-level DAC unity elements. The circuit, fabricated in a mixed 0.18-0.5-μm CMOS technology, achieves more than 17-bit resolution over a 5-kHz bandwidth using 256 clock periods. A single-step chopping of the input stage leads to a residual offset of 9.7 μV. The measured SFDR and power consumption are -90 dB and 280 μW, respectively. The achieved Figure of Merit is 177.5 dB.
A hybrid neural model for the characterization of a single layer SIW waveguide

In this work, a hybrid neural model (HNM) able to characterize accurately the dispersion behavior of the fundamental TE10 mode of a single layer SIW waveguide, is developed. The HNM combines the analytical expression that models the dispersion characteristics of this guiding structure, with a Multi Layer Perceptron Neural Network (MLPNN) which operates as an estimator of the cutoff angular frequency ωt of the fundamental mode. The comparison among HNM computations, numerical results obtained with methods proposed in literature and full-wave data validate both the accuracy and the effectiveness of the proposed approach.
A Reliable Token-Based MAC Protocol for Delay Sensitive Platooning Applications

Platooning is both a challenging and rewarding application. Challenging since strict timing and reliability requirements are imposed by the distributed control system required to operate the platoon. Rewarding since considerable fuel reductions are possible. As platooning takes place in a vehicular ad hoc network, the use of IEEE 802.11p is close to mandatory. However, the 802.11p medium access method suffers from packet collisions and random delays. Most ongoing research suggests using TDMA on top of 802.11p as a potential remedy. However, TDMA requires synchronization and is not very flexible if the beacon frequency needs to be updated, the number of platoon members changes, or if retransmissions for increased reliability are required. We therefore suggest a token-passing medium access method where the next token holder is selected based on beacon data age. This has the advantage of allowing beacons to be re-broadcasted in each beacon interval whenever time and bandwidth are available. We show that our token-based method is able to reduce the data age and considerably increase reliability compared to pure 802.11p.
Phase modulation for discrete-time wiener phase noise channels with oversampling at high SNR

A discrete-time Wiener phase noise channel model is introduced in which multiple samples are available at the output for every input symbol. A lower bound on the capacity is developed. At high signal-to-noise ratio (SNR), if the number of samples per symbol grows with the square root of the SNR, the capacity pre-log is at least 3/4. This is strictly greater than the capacity pre-log of the Wiener phase noise channel with only one sample per symbol, which is 1/2. It is shown that amplitude modulation achieves a pre-log of 1/2 while phase modulation achieves a pre-log of at least 1/4.
Heritage Tourism in the 21st Century: Valued Traditions and New Perspectives

This article was written as an introduction to the journal by the editors; seeking to examine areas for future research into heritage tourism. The article is one of the most read and most cited of all the articles across the 9 volumes that have been published to date. The paper examined a range of what the authors called 'existing and emerging trends in heritage tourism', including research focused on supply and demand, heritage politics, conservation concerns, heritage economics, authenticity. They also set out more recent and future trends encouraging research in the following: thanatourism, ordinary landscapes, ordinary people, how heritage is linked to other sectors, heritage trails and routes, personal heritage and individual identity, the rise of heritage in the developing world, and religious tourism. The authors (editor and associate editor) set out the case for the need for a journal that focused on heritage tourism research alone and encouraged scholars to develop the field further and publish their findings in the journal.
Book Review: The Context of Youth Violence: Resilience, Risk, and Protection

There is consensus among prevention scholars that to lessen the occurrence of youth violence, interventions must seek to reduce risk influences and also strengthen protection against current and later occurring risks. Risk factors and protective factors have been identified through years of research on the development and behavior of youths in general population and clinical samples. The chapters included in this book detail for the reader much of what currently is known from that research about risk and resilience in children, as well as promising interventions. Contributors to this edited volume are leading scholars who represent several disciplines, including education, psychology, public health, and social work. The editors list as a primary goal the task of integrating theory and research across disciplines so as to establish a risk and protective factor perspective for preventing and reducing youth violence. Although the general perspective the editors espouse is not new to the literature, they succeed here in offering a coherent and rich discussion of the evidence base that informs the perspective. Furthermore, they succeed more so than others in drawing from existing research a range of implications for practice and priorities for the field. To highlight all of what this book has to offer in the way of research overviews and practice recommendations, I briefly describe and comment on each chapter and then elaborate on my overall reactions to the book and its contributions. In Chapter 1, Jack M. Richman and Mark W. Fraser define key terms and then briefly summarize how each chapter that follows contributes to the risk and resilience theme of the book. A particularly useful aspect of this initial chapter is the attention paid to differing conceptualizations of risk, protection, and resilience as the terms are used in the research literature. In Chapter 2, Michael Rutter examines some methodological considerations related to studies on risk and resiliency in children. He also addresses mechanisms that account for ways in which individuals differ in their susceptibility to risks and methods of coping. In this chapter, Rutter clearly communicates to the reader how resilience is defined and reflected in behavior, as well as how individuals come to show resilience after encountering adversity. The chapter concludes with several important implications for prevention that extend from a risk and resilience orientation. Rutter’s expansive knowledge of this topic area and history as a researcher contribute to this being one of the most comprehensive chapters of the book. Chapter 3 by J. Eric Vance focuses on neurobiological mechanisms as they relate to vulnerability and resiliency in children. He notes that although the neurobiolgical underpinnings of resiliency are not well understood, research has expanded knowl-
Inline Measurement of Adhesion Force Using Electrostatic Actuation and Capacitive Readout

A microinstrument with electrostatic actuation and capacitive readout for the measurement of adhesion force is introduced that can be used in packaged systems for the in-line characterization and monitoring of fabricated devices. The test results for different apparent contact areas obtained using these devices are in agreement with previously reported values for adhesion force obtained via optical readout and display a weak correlation between the apparent contact area and the adhesion force.
The last bastion? X chromosome genotyping of Anopheles gambiae species pair males from a hybrid zone reveals complex recombination within the major candidate ‘genomic island of speciation’

Speciation with gene flow may be aided by reduced recombination helping to build linkage between genes involved in the early stages of reproductive isolation. Reduced recombination on chromosome X has been implicated in speciation within the Anopheles gambiae complex, species of which represent the major Afrotropical malaria vectors. The most recently diverged, morphologically indistinguishable, species pair, A. gambiae and Anopheles coluzzii, ubiquitously displays a ‘genomic island of divergence’ spanning over 4 Mb from chromosome X centromere, which represents a particularly promising candidate region for reproductive isolation genes, in addition to containing the diagnostic markers used to distinguish the species. Very low recombination makes the island intractable for experimental recombination studies, but an extreme hybrid zone in Guinea Bissau offers the opportunity for natural investigation of X‐island recombination. SNP analysis of chromosome X hemizygous males revealed: (i) strong divergence in the X‐island despite a lack of autosomal divergence; (ii) individuals with multiple‐recombinant genotypes, including likely double crossovers and localized gene conversion; (iii) recombination‐driven discontinuity both within and between the molecular species markers, suggesting that the utility of the diagnostics is undermined under high hybridization. The largely, but incompletely protected nature of the X centromeric genomic island is consistent with a primary candidate area for accumulation of adaptive variants driving speciation with gene flow, while permitting some selective shuffling and removal of genetic variation.
Ultrastructural and Real-time Microscopic Changes in P. falciparum-infected Red Blood Cells Following Treatment with Antimalarial Drugs

Ultrastructural changes to P. falciparum-infected red blood cells were examined in vitro after treatment with antimalarial drugs. Artesunate had the most rapid parasitocidal effect. All three drugs caused structural changes within the parasite, including dilatation of the parasitophorus vacuole membrane, depletion of ribosomes, mitochondrial swelling, and decreased formation of hemozoin crystals. The structure of surface knobs and Maurer’s clefts were similar to controls but reduced in number. Only depletion of free ribosomes correlated with antimalarial drug exposure. Drug treatment decreased movement of hemozoin granules within parasites on real-time microscopy, before recognizable morphological changes of parasite death.
Modeling Graph Languages with Grammars Extracted via Tree Decompositions

Work on probabilistic models of natural language tends to focus on strings and trees, but there is increasing interest in more general graph-shaped structures since they seem to be better suited for representing natural language semantics, ontologies, or other varieties of knowledge structures. However, while there are relatively simple approaches to defining generative models over strings and trees, it has proven more challenging for more general graphs. This paper describes a natural generalization of the n-gram to graphs, making use of Hyperedge Replacement Grammars to define generative models of graph languages.
Mechanisms and physiological effects of protamine resistance in Salmonella enterica serovar Typhimurium LT2.

OBJECTIVES Protamines are cationic peptides that exert antimicrobial activity. We have examined the evolution of bacterial resistance to protamine sulphate and the resulting effects on fitness and physiology, with the objective of increasing knowledge about mechanisms of bacterial resistance to antimicrobial peptides. METHODS Spontaneous, protamine-resistant Salmonella enterica serovar Typhimurium (i.e. Salmonella Typhimurium) LT2 mutants were isolated on agarose plates containing protamine sulphate. Resistance mutations were identified using transposon insertions and DNA sequencing. Peptide susceptibility was determined by broth dilution tests and antibiotic susceptibility using Etests. Fitness was determined as log-phase growth rates. Growth-compensated strains were isolated by serial passage through population bottlenecks followed by visual screening for large colonies. RESULTS Protamine-resistant mutants appeared at a rate of 2.3 x 10(-7)/cell/generation. These mutants were 2-20 times more resistant to protamine than the parental strain and less susceptible to several other antimicrobials, including colistin, gentamicin, lactoferricin and human defensin HNP-1. The resistance mutations were mapped to genes involved in haem biosynthesis and respiration, and were associated with a reduction in bacterial fitness. Some mutants could, in the absence of protamine, be evolved to higher fitness by acquiring second-site compensatory mutations. CONCLUSIONS Spontaneous mutants resistant to protamine sulphate were readily selected in Salmonella Typhimurium LT2. These mutants were less susceptible to several other peptides and antibiotics, and had the characteristics of small colony variants, a phenotype often associated with persistent and recurrent infections that are difficult to treat and which could be a strategy for bacteria to escape the killing effects of antimicrobial peptides.
Silviculture that sustains : the nexus between silviculture, frequent prescribed fire, and conservation of biodiversity in longleaf pine forests of the southeastern United States

Les ecosystemes forestiers de pin des marais (Pinus palustris Mill.) de la plaine cotiere du sud-est des E. -U. , qui sont parmi les ecosystemes les plus biologiquement diversifies en Amerique du Nord, couvraient a l'origine plus de 24 millions d'hectares mais occupent maintenant moins de 5 % de leur etendue originale. Le facteur cle dans le maintien de leur degre eleve de diversite est l'application frequente du brulage dirige ininterrompu dans le temps et dans l'espace. Les combustibles de pin, essentiels a l'utilisation du feu et regis par la distribution de la canopee, fournissent le lien entre la sylviculture et la gestion du feu dans ce systeme. Les approches sylvicoles typiques pour ce type de foret ont ete en grande partie developpees pour favoriser l'etablissement et la croissance de la regeneration ainsi que la croissance et le rendement en matiere ligneuse sans porter beaucoup d'attention a la facon dont ces pratiques pouvaient influencer la capacite de maintenir un regime de brulage dirige ou la biodiversite qui y est associee. Cependant, plusieurs proprietes dans cette region retiennent maintenant la conservation de la biodiversite comme premier objectif avec le rendement soutenu de matiere ligneuse en tant que but important mais secondaire. Cet article dresse la synthese de la litterature reliee au controle de la biodiversite dans les ecosystemes de pin des marais et compare les approches sylvicoles en fonction de leur capacite a maintenir les perturbations naturelles comme le feu et du degre de fidelite avec lequel elles reproduisent les variations, les comportements et les processus des regimes de perturbation naturelle tout en tenant compte de la regeneration.
Modeling the Optical Afterglow of GRB 030329

The best-sampled afterglow light curves available are for GRB 030329. A distinguishing feature of this event is the obvious rebrightening at around 1.6 days after the burst. Proposed explanations for the rebrightening mainly include the two-component jet model and the refreshed-shock model, although a sudden density jump in the circumburst environment is also a potential choice. Here we reexamine the optical afterglow of GRB 030329 numerically in light of the three models. In the density-jump model, no obvious rebrightening can be produced at the jump moment. In addition, after the density jump, the predicted flux density decreases rapidly to a level that is significantly below observations. A simple density-jump model thus can be excluded. In the two-component jet model, although the observed late afterglow (after 1.6 days) can potentially be explained as emission from the wide component, the emergence of this emission actually is too slow, and it does not manifest as a rebrightening as previously expected. The energy-injection model seems to be the most preferred choice. By engaging a sequence of energy-injection events, it provides an acceptable fit to the rebrightening at ~1.6 days, as well as the whole observed light curve that extends to ~80 days. Further studies on these multiple energy-injection processes may provide a valuable insight into the nature of the central engines of gamma-ray bursts.
Optimal rate allocation for adaptive wireless video streaming in networks with user dynamics

We consider the problem of optimal rate allocation and admission control for adaptive video streaming sessions in wireless networks with user dynamics. The central aim is to achieve an optimal tradeoff between several key objectives: maximizing the average rate utility per user, minimizing the temporal rate variability, and maximizing the number of users supported. We identify the structure of algorithms that achieve asymptotically optimal performance in large-capacity systems, and exploit the insight into this structure to devise parsimonious and robust online algorithms. Extensive simulation experiments demonstrate that the proposed online algorithms perform well, even in systems with relatively small capacity.
Chimeric Yellow Fever Virus 17D-Japanese Encephalitis Virus Vaccine: Dose-Response Effectiveness and Extended Safety Testing in Rhesus Monkeys

ABSTRACT ChimeriVax-JE is a live, attenuated recombinant virus prepared by replacing the genes encoding two structural proteins (prM and E) of yellow fever 17D virus with the corresponding genes of an attenuated strain of Japanese encephalitis virus (JE), SA14-14-2 (T. J. Chambers et al., J. Virol. 73:3095–3101, 1999). Since the prM and E proteins contain antigens conferring protective humoral and cellular immunity, the immune response to vaccination is directed principally at JE. The prM-E genome sequence of the ChimeriVax-JE in diploid fetal rhesus lung cells (FRhL, a substrate acceptable for human vaccines) was identical to that of JE SA14-14-2 vaccine and differed from sequences of virulent wild-type strains (SA14 and Nakayama) at six amino acid residues in the envelope gene (E107, E138, E176, E279, E315, and E439). ChimeriVax-JE was fully attenuated for weaned mice inoculated by the intracerebral (i.c.) route, whereas commercial yellow fever 17D vaccine (YF-Vax) caused lethal encephalitis with a 50% lethal dose of 1.67 log10 PFU. Groups of four rhesus monkeys were inoculated by the subcutaneous route with 2.0, 3.0, 4.0, and 5.0 log10PFU of ChimeriVax-JE. All 16 monkeys developed low viremias (mean peak viremia, 1.7 to 2.1 log10 PFU/ml; mean duration, 1.8 to 2.3 days). Neutralizing antibodies appeared between days 6 and 10; by day 30, neutralizing antibody responses were similar across dose groups. Neutralizing antibody titers to the homologous (vaccine) strain were higher than to the heterologous wild-type JE strains. All immunized monkeys and sham-immunized controls were challenged i.c. on day 54 with 5.2 log10 PFU of wild-type JE. None of the immunized monkeys developed viremia or illness and had mild residual brain lesions, whereas controls developed viremia, clinical encephalitis, and severe histopathologic lesions. Immunized monkeys developed significant (≥4-fold) increases in serum and cerebrospinal fluid neutralizing antibodies after i.c. challenge. In a standardized test for neurovirulence, ChimeriVax-JE and YF-Vax were compared in groups of 10 monkeys inoculated i.c. and analyzed histopathologically on day 30. Lesion scores in brains and spinal cord were significantly higher for monkeys inoculated with YF-Vax. ChimeriVax-JE meets preclinical safety and efficacy requirements for a human vaccine; it appears safer than yellow fever 17D vaccine but has a similar profile of immunogenicity and protective efficacy.