bluuebunny/crossref_metadata_2025_split huggingface dataset:
HST unveils a compact mildly relativistic broad-line region in the candidate true type 2 NGC 3147
Authors: Bianchi Stefano , Antonucci Robert , Capetti Alessandro , Chiaberge Marco , Laor Ari , Bassani Loredana , Carrera Francisco J , La Franca Fabio , Marinucci Andrea , Matt Giorgio , Middei Riccardo , Panessa Francesca 
Published: May 2019

ABSTRACT
NGC 3147 has been considered the best case of a true type 2 AGN: an unobscured AGN, based on the unabsorbed compact X-ray continuum, which lacks a broad-line region (BLR). However, the very low luminosity of NGC 3147 implies a compact BLR, which produces very broad lines, hard to detect against the dominant background host galaxy. Narrow (0.1 arcsec × 0.1 arcsec) slit HST spectroscopy allowed us to exclude most of the host galaxy light, and revealed an H α line with an extremely broad base (FWZI${\sim }27\, 000$ km s−1). The line profile shows a steep cut-off blue wing and an extended red wing, which match the signature of a mildly relativistic thin accretion disc line profile. It is indeed well fit with a nearly face on thin disc, at i ∼ 23°, with an inner radius at 77 ± 15 rg, which matches the prediction of $62^{+18}_{-14}$rg from the RBLR–L1/2 relation. This result questions the very existence of true type 2 AGN. Moreover, the detection of a thin disc, which extends below 100 rg in an L/LEdd ∼ 10−4 system, contradicts the current view of the accretion flow configuration at extremely low accretion rates.
Modelling and DNA topology of compact 2-start and 1-start chromatin fibres
Authors: Wu Chenyi , Travers Andrew 
Published: May 2019

AbstractWe have investigated the structure of the most compact 30-nm chromatin fibres by modelling those with 2-start or 1-start crossed-linker organisations. Using an iterative procedure we obtained possible structural solutions for fibres of the highest possible compaction permitted by physical constraints, including the helical repeat of linker DNA. We find that this procedure predicts a quantized nucleosome repeat length (NRL) and that only fibres with longer NRLs (≥197 bp) can more likely adopt the 1-start organisation. The transition from 2-start to 1-start fibres is consistent with reported differing binding modes of the linker histone. We also calculate that in 1-start fibres the DNA constrains more torsion (as writhe) than 2-start fibres with the same NRL and that the maximum constraint obtained is in accord with previous experimental results. We posit that the coiling of the fibre is driven by overtwisting of linker DNA which, in the most compact forms - for example, in echinoderm sperm and avian erythrocytes - could adopt a helical repeat of ∼10 bp/turn. We argue that in vivo the total twist of linker DNA could be modulated by interaction with other abundant chromatin-associated proteins and by epigenetic modifications of the C-terminal tail of linker histones.
Review of whole grain and dietary fiber recommendations and intake levels in different countries
Authors: Miller Kevin Burke 
Published: May 2019

Abstract
This review of whole grain and dietary fiber recommendations and intake levels was presented at the symposium on whole grains, dietary fiber, and public health, convened in Beijing, China, on May 11, 2018. The review reflects on inconsistencies among the definitions of whole grains and fiber as well as recommended intake levels in different countries. The lack of consistent dietary recommendations from authoritative sources may delay the regional implementation and consumer adoption of diets that include whole grains and fiber. Currently, few countries include specific intake recommendations for whole grain, and even among those countries with guidance the recommendations can be vague and qualitative. As a result of the well-documented associations between increasing whole grain intake and reduced disease risk, there is compelling evidence to create clear, actionable dietary recommendations for both whole grains and fiber. Furthermore, work is ongoing to develop uniform standards for whole grain and whole-grain food to ensure recommendations are being met. Health and regulatory authorities are encouraged to acknowledge the public health benefits that could be derived from strong, clear whole-grain and dietary fiber recommendations; examine existing definitions (whole grain as an ingredient, whole-grain food, and dietary fiber); and adopt the most appropriate approach to best serve public health needs for their respective populations.
Evolutionary Model of Plastidial RNA Editing in Angiosperms Presumed from Genome-Wide Analysis of Amborella trichopoda
Authors: Ishibashi Kota , Small Ian , Shikanai Toshiharu 
Published: May 2019

Abstract
Amborella trichopoda is placed close to the base of the angiosperm lineage (basal angiosperm). By genome-wide RNA sequencing, we identified 184C-to-U RNA editing sites in the plastid genome of Amborella. This number is much higher than that observed in other angiosperms including maize (44 sites), rice (39 sites) and grape (115 sites). Despite the high frequency of RNA editing, the biased distribution of RNA editing sites in the genome, target codon preference and nucleotide preference adjacent to the edited cytidine are similar to that in other angiosperms, suggesting a common editing machinery. Consistent with this idea, the Amborella nuclear genome encodes 2–3 times more of the E- and DYW-subclass members of pentatricopeptide repeat proteins responsible for RNA editing site recognition in plant organelles. Among 165 editing sites in plastid protein coding sequences in Amborella, 100 sites were conserved at least in one out of 38 species selected to represent key branching points of the angiosperm phylogenetic tree. We assume these 100 sites represent at least a subset of the sites in the plastid editotype of ancestral angiosperms. We then mapped the loss and gain of editing sites on the phylogenetic tree of angiosperms. Our results support the idea that the evolution of angiosperms has led to the loss of RNA editing sites in plastids.
Solidarity and Responsibility in Health Care
Authors: Davies Ben , Savulescu Julian 
Published: May 2019

Abstract
Some healthcare systems are said to be grounded in solidarity because healthcare is funded as a form of mutual support. This article argues that health care systems that are grounded in solidarity have the right to penalise some users who are responsible for their poor health. This derives from the fact that solidary systems involve both rights and obligations and, in some cases, those who avoidably incur health burdens violate obligations of solidarity. Penalties warranted include direct patient contribution to costs, and lower priority treatment, but not typically full exclusion from the healthcare system. We also note two important restrictions on this argument. First, failures of solidary obligations can only be assumed under conditions that are conducive to sufficiently autonomous choice, which occur when patients are given ‘Golden Opportunities’ to improve their health. Second, because poor health does not occur in a social vacuum, an insistence on solidarity as part of healthcare is legitimate only if all members of society are held to similar standards of solidarity. We cannot insist upon, and penalise failures of, solidarity only for those who are unwell, and who cannot afford to evade the terms of public health.
Zoochory of zooplankton: seasonality and bird morphological diversity can influence metacommunity dynamics of temporary ponds
Authors: de Morais-Junior Cláudio Simões , de Melo-Júnior Mauro , Gonçalves-Souza Thiago , de Lyra-Neves Rachel Maria 
Published: May 2019

Abstract
Harsh and unstable aquatic environments present selective forces that influence environmental heterogeneity, dispersal capacity and specific life history strategies that, in turn, affect species distribution and metacommunity dynamics. To date, relatively few studies have examined the potential of bird-mediated dispersal to connect isolated ephemeral habitats. We used zooplankton from temporary ponds to examine the effects of bird morphological diversity and water availability on microcrustacean diversity in temporary ponds. Three bird feet models were constructed based on small, large and webbed anisodactylous forms in order to simulate bird walking on the pond shore. Bird and zooplankton communities were sampled in two temporary ponds and experimentally simulated zooplankton dispersal by bird on dry sediments. We surveyed in two contrasting seasonal periods. Overall, water availability does affect zooplankton composition, and birds with large feet have higher dispersal capacity. In addition, birds with different feet size and shape carry distinct zooplankton species. During the dry season, sediments hold 100% more species than in the wet season, which indicates that birds have higher potential for dispersing zooplankton in drought conditions. Our findings suggest that bird diversity can maintain zooplankton metacommunities by rescuing dormant organisms from dry ponds and connecting to any available aquatic habitats.
The Use of L2 and L3 Lumbar Sympathetic Blockade for Cancer-Related Pain, an Experience and Recommendation in the Oncologic Population
Authors: Spiegel Matthew A , Hingula Lee , Chen Grant H , Legler Aron , Puttanniah Vinay , Gulati Amitabh 
Published: May 2019

Abstract

Objective
The sympathetic nervous system has a recognized role in transmission of pain, and the lumbar sympathetic blockade is intended to provide analgesia. We share our experiences of lumbar sympathetic blockade in the treatment of cancer-related pain.

Methods
We performed a retrospective analysis of patients with cancer-related pain in the back, abdomen, pelvis, or legs treated at Memorial Sloan Kettering Cancer Center between 2000 and 2018 undergoing lumbar sympathetic blockade at L2 or L3. Blocks were accomplished by injection of local anesthetic or local anesthetic with steroid under fluoroscopy. We measured numerical rating scale scores, percent relief, and relief time. The primary end point was defined as “effective” or “ineffective” pain relief. Effective pain relief was defined as ≥30% relief for at least one day.

Results
We identified 124 data points of lumbar sympathetic blockade at L2 or L3, of which 57 were with complete data and used for analysis. Peri-injection, 42 data points had active disease whereas 15 were in remission. Lumbar sympathetic blockade was 67% effective in the back pain cohort, 82% effective in the abdominopelvic pain cohort, and 75% effective in the leg pain cohort. Seventeen data points went on to neurolysis, two to neuromodulation, and eight to intrathecal pump implantation.

Conclusions
Lumbar sympathetic blockade is effective for back, abdominopelvic, and leg pain related to cancer and its treatments. Future research should be aimed at refining its role within multimodal pain management.
Design of catalytic polypeptides and proteins
Authors: Gutte B , Klauser S 
Published: May 2019

AbstractThe first part of this review article lists examples of complete, empirical de novo design that made important contributions to the development of the field and initiated challenging projects. The second part of this article deals with computational design of novel enzymes in native protein scaffolds; active designs were refined through random and site-directed mutagenesis producing artificial enzymes with nearly native enzyme- like activities against a number of non-natural substrates. Combining aspects of de novo design and biological evolution of nature’s enzymes has started and will accelerate the development of novel enzyme activities.
Systematic revision of Mexican threatened tarantulas Brachypelma (Araneae: Theraphosidae: Theraphosinae), with a description of a new genus, and implications on the conservation
Authors: Mendoza Jorge , Francke Oscar 
Published: May 2019

AbstractThe tarantula genus Brachypelma includes colourful species that are highly sought after in the commercial pet trade. They are all included in CITES appendix II. We present phylogenetic analyses using molecular and morphological characters to revise Brachypelma, in which we include all currently known species. Our results agree with a previous study that shows the non-monophyly of Brachypelma. Both phylogenies strongly favour the division of Brachypelma into two smaller genera. The first clade (Brachypelma s.s.) is formed by B.albiceps, B. auratum, B. baumgarteni, B. boehmei, B. emilia, B. hamorii, B. klaasi and B. smithi. The species included in the second clade are transferred to the new genus Tliltocatl and is formed by T. albopilosum comb. nov., T. epicureanum comb. nov., T. kahlenbergi comb. nov., T. sabulosum comb. nov., T. schroederi comb. nov., T. vagans comb. nov. and T. verdezi comb. nov. Both genera can be differentiated by their coloration and the shape of the genitalia. We transfer to Tliltocatl: T. alvarezi, T. andrewi and T. aureoceps, but should be considered as nomina dubia. In addition, we transfer B. fossorium to Stichoplastoris. We discuss the implications of these taxonomical changes for CITES and for the Mexican Laws for wildlife protection.
Estimations of the weather effects on brain functions using functional MRI: a cautionary note
Authors: Di Xin , Wolfer Marie , Kühn Simone , Zhang Zhiguo , Biswal Bharat B. 
Published: May 2019

AbstractThe influences of environmental factors such as weather on the human brain are still largely unknown. A few neuroimaging studies have demonstrated seasonal effects, but were limited by their cross-sectional design or sample sizes. Most importantly, the stability of the MRI scanner hasn’t been taken into account, which may also be affected by environments. In the current study, we analyzed longitudinal resting-state functional MRI (fMRI) data from eight individuals, where the participants were scanned over months to years. We applied machine learning regression to use different resting-state parameters, including the amplitude of low-frequency fluctuations (ALFF), regional homogeneity (ReHo), and functional connectivity matrix, to predict different weather and environmental parameters. For careful control, the raw EPI and the anatomical images were also used for predictions. We first found that daylight length and air temperatures could be reliably predicted with cross-validation using the resting-state parameters. However, similar prediction accuracies could also be achieved by using one frame of EPI image, and even higher accuracies could be achieved by using segmented or raw anatomical images. Finally, the signals outside of the brain in the anatomical images and signals in phantom scans could also achieve higher prediction accuracies, suggesting that the predictability may be due to the baseline signals of the MRI scanner. After all, we did not identify detectable influences of weather on brain functions other than the influences on the baseline signals of MRI scanners. The results highlight the difficulty of studying long-term effects using MRI.
Caenorhabditis elegansmodel for admixed proteinopathy of Huntington’s and Alzheimer-type
Authors: Kapulkin Wadim J. 
Published: May 2019

ABSTRACTFormation of proteinaceous deposits composed of abnormally aggregated proteins characterizes a range of pathological conditions. Proteinaceous inclusions detected in the neurodegenerative conditions such Huntington’s chorea (HD) and Alzheimer’s disease (AD) are often referred as pathognomic and regarded as causally implicated. Despite of differences in aetiology and underlying genetics, rare cases of combined HD and AD were reported and described as admixed proteinopathies. Mixed proteopathies are characterized by the co-occurrence of at least two types of abnormal aggregation-prone variants; pathological deposition of proteinaceous inclusions might however, affect different cell populations. Here, combining plaques derived from human ß-amyloid with mutant HTT-like polyglutamine inclusions in a cell-autonomous manner, we report on theCaenorhabditis elegansmodel for admixed proteinopathy of Alzheimer’s and Huntington’s type. We show both types of intracellular foci are formedin vivo: non-amyloidic extended polyglutamine derived inclusions and distinguish those from the presence of mature ß- amyloid fibers. We found that polyglutamines expanded above pathogenic threshold and ß-amyloid act synergistically to promote the progression of proteotoxicity in a temperature dependent manner. We further, implicate thehsp-1(the predominantC. eleganschaperone interacting with ER-routed Aß42) modulate the proteotoxic insults observed in combined proteopathy model. Our results demonstrate how thein vivomodel of admixed proteopathy could be utilized to probe for human pathogenic variants confined to the same cellular type. In that perspective expanded aggregation-prone polyglutamines appended with fluorescent proteins could be regarded as ‘pathogenic probes’ useful in the proteotoxicity assaysi.e.involving ß-amyloid and possibly other comparable models of disease-associated aggregation prone variants.We anticipate models of combined proteopathies will be informative regarding the underlying pathogenesis and provide the sensitized background for sophisticated screening. For example the combinatorial effects of multiple pathogenic aggregation-prone variants could be tested against mutant backgrounds and pharmacological compounds. Furthermore, we surmise the postulated synergistic actions might explain some of the overlaps in observed progression of clinical symptoms in HD and AD. We also formulate the conjecture regarding the polyQ containing proteins as a contributing factor in degenerative conditions associated with increased ß-amyloid formation and deposition.
Damped oscillations of the probability of random events followed by absolute refractory period: exact analytical results
Authors: Paraskevov A.V. , Minkin A.S. 
Published: May 2019

AbstractThere are numerous examples of natural and artificial processes that represent stochastic sequences of events followed by an absolute refractory period during which the occurrence of a subsequent event is impossible. In the simplest case of a generalized Bernoulli scheme for uniform random events followed by the absolute refractory period, the event probability as a function of time can exhibit damped transient oscillations. Using stochastically-spiking point neuron as a model example, we present an exact and compact analytical description for the oscillations without invoking the standard renewal theory. The resulting formulas stand out for their relative simplicity, allowing one to analytically obtain the amplitude damping of the 2nd and 3rd peaks of the event probability.
Type-3 Secretion System–induced pyroptosis protects Pseudomonas against cell-autonomous immunity
Authors: Eren Elif , Planès Rémi , Buyck Julien , Bordignon Pierre-Jean , Colom André , Cunrath Olivier , Dreier Roland F. , Santos José C. , Duplan-Eche Valérie , Näser Emmanuelle , Peixoto Antonio , Bumann Dirk , Cougoule Céline , Coste Agnès , Neyrolles Olivier , Broz Petr , Meunier Etienne 
Published: May 2019

AbstractInflammasome-induced pyroptosis comprises a key cell-autonomous immune process against intracellular bacteria, namely the generation of dying cell structures. These so-called pore-induced intracellular traps (PITs) entrap and weaken intracellular microbes. However, the immune importance of pyroptosis against extracellular pathogens remains unclear. Here, we report that Type-3 secretion system (T3SS)-expressingPseudomonas aeruginosa(P. aeruginosa) escaped PIT immunity by inducing a NLRC4 inflammasome-dependent macrophage pyroptosis response in the extracellular environment. To the contrary, phagocytosis ofSalmonellaTyphimurium promoted NLRC4-dependent PIT formation and the subsequent bacterial caging. Remarkably, T3SS-deficientPseudomonaswere efficiently sequestered within PIT-dependent caging, which favored exposure to neutrophils. Conversely, both NLRC4 and caspase-11 deficient mice presented increased susceptibility to T3SS-deficientP. aeruginosachallenge, but not to T3SS-expressingP. aeruginosa.Overall, our results uncovered thatP. aeruginosauses its T3SS to overcome inflammasome-triggered pyroptosis, which is primarily effective against intracellular invaders.ImportanceAlthough innate immune components confer host protection against infections, the opportunistic bacterial pathogenPseudomonas aeruginosa(P. aeruginosa) exploits the inflammatory reaction to thrive. Specifically the NLRC4 inflammasome, a crucial immune complex, triggers an Interleukin (IL)-1β and -18 deleterious host response toP. aeruginosa. Here, we provide evidence that, in addition to IL-1 cytokines,P. aeruginosaalso exploits the NLRC4 inflammasome-induced pro-inflammatory cell death, namely pyroptosis, to avoid efficient uptake and killing by macrophages. Therefore, our study reveals that pyroptosis-driven immune effectiveness mainly depends onP. aeruginosalocalization. This paves the way toward our comprehension of the mechanistic requirements for pyroptosis effectiveness upon microbial infections and may initiate targeted approaches in order to ameliorate the innate immune functions to infections.Graphical abstractMacrophages infected with T3SS-expressingP. aeruginosadie in a NLRC4-dependent manner, which allows bacterial escape from PIT-mediated cell-autonomous immunity and neutrophil efferocytosis. However, T3SS-deficientP. aeruginosais detected by both NLRC4 and caspase-11 inflammasomes, which promotes bacterial trapping and subsequent efferocytosis ofP. aeruginosa-containing-PITs by neutrophils.
Low support values and lack of reproducibility of molecular phylogenetic analysis of Copepoda orders
Authors: Mikhailov Kirill V. , Ivanenko Viatcheslav N. 
Published: May 2019

AbstractReanalysis of the dataset used by Khodami et al. (2017) reveals low support values for the key nodes of the copepod (Crustacea) phylogeny and fails to reproduce the results obtained in the study. Maximum likelihood (ML) and Bayesian analyses with the dataset produce phylogenies that are inconsistent with the branching of copepod groups proposed by Khodami et al. (2017). The proposed phylogeny is refuted by the approximately unbiased (AU) statistical test, which undermines several conclusions drawn from the original study.
jackalope: a swift, versatile phylogenomic and high-throughput sequencing simulator
Authors: Nell Lucas A. 
Published: May 2019

AbstractHigh-throughput sequencing (HTS) is central to the study of population genomics and has an increasingly important role in constructing phylogenies. Choices in research design for sequencing projects can include a wide range of factors, such as sequencing platform, depth of coverage, and bioinformatic tools. Simulating HTS data better informs these decisions. However, current standalone HTS simulators cannot generate genomic variants under even somewhat complex evolutionary scenarios, which greatly reduces their usefulness for fields such as population genomics and phylogenomics. Here I present the R package jackalope that simply and efficiently simulates (i) variants from reference genomes and (ii) reads from both Illumina and Pacific Biosciences (PacBio) platforms. Genomic variants can be simulated using phylogenies, gene trees, coalescent-simulation output, population-genomic summary statistics, and Variant Call Format (VCF) files. jackalope can simulate single, paired-end, or mate-pair Illumina reads, as well as reads from Pacific Biosciences. These simulations include sequencing errors, mapping qualities, multiplexing, and optical/PCR duplicates. It can read reference genomes from FASTA files and can simulate new ones, and all outputs can be written to standard file formats. jackalope is available for Mac, Windows, and Linux systems.