bluuebunny/crossref_metadata_2025 huggingface dataset:
Nocturnal Heterothermy and Torpor in the Malachite Sunbird (Nectarinia Famosa)
Authors: Downs Colleen T. , Brown Mark
Published: September 2019

Heterothermy in birds occurs in species that are generally small and whose diet fluctuates. This study of thermoregulation of Malachite Sunbirds (Nectarina famosa) showed that they have circadian fluctuations in Tb and VO2, as in most birds. Of special importance was the high degree of rest-phase hypothermy and exhibition of torpor at ambient temperatures of 10°C and lower. These patterns are significant because they have not been described in detail for a passerine species. Surgically implanted minimitters were used to measure Tb continuously and without disturbing the birds. Minimum VO2 during rest phase was 1.70 (mL O2 g–1 h–1) at 25°C. As ambient temperature decreased, VO2 minimum during the rest phase did not increase to maintain Tb. No birds remained normothermic during scotophase. At 5°C, that resulted in torpor in Malachite Sunbirds with a decrease of 15°C in Tb. Birds increased Tb to active-phase levels with the onset of light. It was difficult to define limits and ranges of physiological parameters associated with observed heterothermy. Individuals showed similar responses; however, those differed with ambient temperature. Malachite Sunbirds conserved energy nocturnally by reducing metabolic rate and, concomitantly, Tb. This plasticity in Tb shows that daily variations in Tb of homeotherms are biologically important. Furthermore, this heterothermy (particularly nocturnal hypothermia and torpor) in a small avian species would be important in an unpredictable environment where food resources fluctuate to prevent an energy deficit.
Rediscovery of a Cryptic Species and Description of a New Subspecies in The Myrmeciza Hemimelaena Complex (Thamnophilidae) of the Neotropics
Authors: Isler Morton L. , Alonso José Alvarez , Isler Phyllis R. , Valqui Thomas , Begazo Alfredo , Whitney Bret M.
Published: September 2019

The recording in 1992 of an unknown antbird loudsong initiated a journey of discovery that led to the resolution of the conflict between John Zimmer (1932) and Melvin Carriker (1934) regarding the taxonomic standing of the population of Myrmeciza hemimelaena, a widespread southern Amazonian antbird, that occurs in lower Andean elevations in San Martín, Peru. Zimmer had described a new subspecies, M. h. castanea, from the Moyobamba Valley, but Carriker, on the basis of specimens he collected at the same elevation in an adjoining valley, could not find morphological differences between his specimens and the widespread nominate form of M. hemimelaena. Both authors were correct. Two cryptic sister taxa coexist in the foothills of San Martín. Diagnostic vocal and morphological characters and syntopy confirm their status as distinct species. Myrmeciza hemimelaena castanea Zimmer is revived and raised to species status. Concurrently, analysis of the vocalizations and morphology of the lowland population north of the Río Marañón in Peru, the loudsong recording of which initiated the project, revealed that this population was closely related to M. castanea of which it is described as a subspecies, M. c. centunculorum, under the biological species concept. The discovery that there are two cryptic species in the Myrmeciza hemimelaena complex exemplifies the continuing need to pursue field knowledge and analysis of avian species limits in the Neotropics required for the development of conservation strategies as well as phylogenetic understanding.
hypeR: an R package for geneset enrichment workflows
Authors: Federico Anthony , Monti Stefano
Published: September 2019

Geneset enrichment is a popular method for annotating high-throughput sequencing data. Existing tools fall short in providing the flexibility to tackle the varied challenges researchers face in such analyses, particularly when analyzing many signatures across multiple experiments. We present a comprehensive R package for geneset enrichment workflows that offers multiple enrichment, visualization, and sharing methods in addition to novel features such as hierarchical geneset analysis and built-in markdown reporting. hypeR is a one-stop solution to performing geneset enrichment for a wide audience and range of use cases.

Availability and implementation

The most recent version of the package is available at https://github.com/montilab/hypeR.
EpiSAFARI: sensitive detection of valleys in epigenetic signals for enhancing annotations of functional elements
Authors: Harmanci Arif , Harmanci Akdes Serin , Swaminathan Jyothishmathi , Gopalakrishnan Vidya
Published: September 2019

Motivation

Functional genomics experiments generate genomewide signal profiles that are dense information sources for annotating the regulatory elements. These profiles measure epigenetic activity at the nucleotide resolution and they exhibit distinctive patterns as they fluctuate along the genome. Most notable of these patterns are the valley patterns that are prevalently observed in assays such as ChIP Sequencing and bisulfite sequencing. The genomic positions of valleys pinpoint locations of cis-regulatory elements such as enhancers and insulators. Systematic identification of the valleys provides novel information for delineating the annotation of regulatory elements. Nevertheless, the valleys are not reported by majority of the analysis pipelines.

Results

We describe EpiSAFARI, a computational method for sensitive detection of valleys from diverse types of epigenetic profiles. EpiSAFARI employs a novel smoothing method for decreasing noise in signal profiles and accounts for technical factors such as sparse signals, mappability and nucleotide content. In performance comparisons, EpiSAFARI performs favorably in terms of accuracy. The histone modification valleys detected by EpiSAFARI exhibit high conservation, transcription factor binding and they are enriched in nascent transcription. In addition, the large clusters of histone valleys are found to be enriched at the promoters of the developmentally associated genes. Differential histone valleys exhibit concordance with differential DNase signal at cell line specific valleys. DNA methylation valleys exhibit elevated conservation and high transcription factor binding. Specifically, we observed enriched binding of transcription factors associated with chromatin structure around methyl-valleys.

Availability and implementation

EpiSAFARI is publicly available at https://github.com/harmancilab/EpiSAFARI.

Supplementary information

Supplementary data are available at Bioinformatics online.
Simple and Rapid Method by Ultra High-Performance Liquid Chromatography (UHPLC) with Ultraviolet Detection for Determination of Efavirenz in Plasma: Application in a Preclinical Pharmacokinetic Study
Authors: dos Santos Martins Evelin , Oliveira Jonata Augusto , Franchin Taísa Busaranho , Silva Bruna Cristina Ulian , Cândido Caroline Damico , Peccinini Rosângela Gonçalves
Published: September 2019

A simple and rapid ultra-high-performance liquid chromatography (UHPLC) method for determination of efavirenz (EFV) in plasma was developed and applied in a preclinical pharmacokinetic study. The method involves only addition of acetonitrile to precipitation of plasma proteins followed by solvent evaporation. The mobile phase consisted of methanol, acetonitrile and 0.1 M formic acid (20:50:30) at a flow rate of 0.3 mL/min with run time of 5 min. A CSH C18 column and a UHPLC-UV system operating at 245 nm were used. There was a linear response in the range of 0.078 to 10 μg/mL, and the equation was obtained by weighting (1/x2) with r2 = 0.9965. The pharmacokinetic disposition of EFV was investigated in rabbits (two groups, n = 7) following a single intravenous administration (IV group) at a dose of 2.7 mg/kg and a single oral administration (oral group) of EFV co-administered with lamivudine (3TC) and tenofovir (TNF) at a dose of 50, 25 and 25 mg, respectively. The study demonstrated the applicability of the method for determination of EFV in plasma without interference from other co-administered drugs, and the pharmacokinetic parameters were calculated. The method showed advantages over other methods in the literature, such as simplicity of sample processing and fast results.
Survival, Emigration, and Winter Population Structure of Harlequin Ducks
Authors: Cooke Fred , Robertson Gregory J. , Smith Cyndi M. , Ian Goudie R. , Sean Boyd W.
Published: September 2019

A population of individually marked Harlequin Ducks (Histrionicus histrionicus) at White Rock, British Columbia, Canada was examined to measure the degree of population differentiation among birds which pair during the winter months. This required an understanding of the patterns of emigration among wintering sites in different segments of the population. Some juveniles arrived at the wintering grounds accompanied by their mothers, thus initially arriving into the same winter population as their parents. Young males were more likely than young females to disperse during the first two years of life. Adult males had higher local survival than adult females during the summer months, probably because of the greater mortality risks to nesting females. During the nonbreeding seasons, local survival was the same in both sexes. Paired males had a local survival of more than 90%, suggesting both high survival and strong philopatry. Unpaired males had a lower local survival rate, suggesting they have higher mortality and/or emigration rates. Young females had the same local survival rate as adult females, suggesting that they did not disperse during the winter. These winter philopatry patterns are similar to the general pattern of breeding philopatry in waterfowl, with females showing stronger philopatry than males, and paired adults stronger philopatry than unpaired and young birds. The dispersal of young males makes local population differentiation unlikely in this species.
Song Post and Foraging Site Characteristics of Breeding Varied Thrushes in Northwestern California
Authors: Beck Maurie J. , George T. Luke
Published: September 2019

We used a hierarchical approach to describe habitat characteristics of song posts and foraging sites used by Varied Thrushes (Ixoreus naevius) in coastal redwood (Sequoia sempervirens) forests of northwestern California. We measured mesohabitat (0.04-ha circular plots) and microhabitat (0.5-m radius) scale attributes centered on occupied and random song posts and foraging locations at four study sites during March–August of 1994 and 1995. Ninety-five percent of song posts were in trees or snags. Male thrushes used song posts with low foliage density near the top of large conifers (microhabitat scale), located on steeper slopes, surrounded by a high density of trees, and centered in drainages closer to water (mesohabitat scale) as compared to random locations. Varied Thrushes foraged predominantly on the ground early in the breeding season, then subsequently included fruit in their diet after the young had fledged. Although many variables were correlated with ground foraging locations, microhabitat foliage density had the greatest explanatory power, indicating thrushes selected foraging locations primarily at the microhabitat scale, and emphasizing the importance of measuring habitat characteristics at the appropriate spatial scale. Abrupt forest edges, such as those produced by clearcuts, may reduce habitat suitability for Varied Thrushes possibly explaining their absence from small forest fragments during the breeding season.
Breeding Bird Communities in Boreal Forest of Western Canada: Consequences of “Unmixing” the Mixedwoods
Authors: Hobson Keith A. , Bayne Erin
Published: September 2019

Silvicultural practices following clearcutting in boreal forest may encourage the creation of monospecific, single-aged stands having less vegetation heterogeneity and diversity than original stands. We conducted point counts in central Saskatchewan, Canada, 1993–1995, in pure and mixedwood stands dominated by black spruce (Picea mariana), jackpine (Pinus banksiana), trembling aspen (Populus tremuloides), or white spruce (Picea glauca). Mixedwood stands supported more individuals and more species than pure stands. Higher abundance in mixedwood stands relative to pure stands was consistent among nesting guilds and migration strategies. Rarefaction revealed similar patterns, although pure trembling aspen stands were predicted to support more species than aspen-dominated mixedwood stands. Increased avian diversity in mixedwood stands was not solely the result of the mixing of bird species associated with coniferous or deciduous forest types. Chipping Sparrow (Spizella passerina), Pine Siskin (Carduelis pinus), White-winged Crossbill (Loxia leucoptera), Red-breasted Nuthatch (Sitta canadensis), Swainson's Thrush (Catharus ustulatus), and Tennessee Warbler (Vermivora peregrina) were more abundant in mixedwood stands than pure stands. Black-throated Green Warbler (Dendroica virens), Magnolia Warbler (D. magnolia), and Blackburnian Warbler (D. fusca) were abundant in stands dominated by white spruce but were absent from jackpine or black spruce. Other species such as American Redstart (Setophaga ruticilla) and Chestnut-sided Warbler (D. pensylvanica) relied exclusively on pure trembling aspen, particularly stands with dense shrub cover. Several bird species in the boreal forest will be adversely affected by forestry practices that target mature to old aspen and white spruce mixedwoods and promote reduction in mixedwood compositions of regenerating stands.
Non-standard Schedules, Work–Family Conflict, and the Moderating Role of National Labour Context: Evidence from 32 European Countries
Authors: Taiji Riley , Mills Melinda C
Published: September 2019

A wide body of research over the past 30 years links non-standard work schedules to increased work–family conflict (WFC), but often only within single country contexts. A relatively under-explored question is the extent to which the effects of non-standard schedules on family life might vary by country or be buffered by institutional context. Building on past research, this study uses multilevel modelling techniques on 2004 and 2010 European Social Survey data to explore whether the effects of non-standard schedules on WFC vary across 32 countries in Europe, and if so, whether this contextual variation can be explained by labour regulations and industrial relations characteristics measured at the country level. Findings show that while non-standard work hours and days are associated with increased WFC across the majority of sampled countries, the strength of this association varies significantly between countries. The strongest factor shaping the social consequences of non-standard schedules is the degree to which workers are covered under collective bargaining agreements in a country, which explains as much as 17% of the observed between-country variation in the effects of non-standard schedules on WFC. These findings highlight collective agreements as one of the central mechanisms through which family-friendly regulations on working times and conditions are generated for non-standard schedule workers across Europe. More broadly, findings suggest that when studying the social consequences of non-standard schedules, these arrangements must be contextualized in the broader institutional frameworks within which they are organized and regulated.
The organizational domain in HTA reports: towards a technology-oriented assessment
Authors: Cacciatore Pasquale , Specchia Maria Lucia , Solinas Maria Giuliana , Ricciardi Walter , Damiani Gianfranco
Published: September 2019

Background

Organizational aspects in Health Technology Assessment (HTA) reports play a significant role in managing policies and strategies to implement new health technologies. The organizational domain, however, is often under-represented in HTA reports. This study explored how organizational assessment is carried out in HTA reports and designed a new perspective through an empirical approach after the comparison with EUnetHTA's Core Model 3.0.

Methods

Full HTA reports were extracted from the websites of members of International Network of Agencies for HTA and the aspects relating to the organizational assessment were analysed. HTA reports were classified into 4 typologies of technologies (device, diagnosis/screening, intervention and organizational procedures) and organizational aspects described were explored through a framework of 5 domains and 15 subdomains from Core Model. Specific Multiple Correspondence Analyses were carried out to identify technology-related domains for organizational assessment in reports.

Results

The analysis showed that domains and subdomains of Core Model were not covered homogeneously by the organizational assessments in the HTA reports. Through Multiple Correspondence Analyses, four new technology-related dimensions were identified and named according to the Core Model’s subdomains in the four new clusters.

Conclusions

This study analyzed the significance of organizational assessments in current literature and the challenges of improving this domain in HTA reports. Through an empirical analysis, we proposed a new methodology to cover the most relevant aspects of organizational appraisal according to new domains to promote support to the assessment of organizational issues in reports and fulfil the needs of future HTA research.
Large-Scale Molecular Evolutionary Analysis Uncovers a Variety of Polynucleotide Kinase Clp1 Family Proteins in the Three Domains of Life
Authors: Saito Motofumi , Sato Asako , Nagata Shohei , Tamaki Satoshi , Tomita Masaru , Suzuki Haruo , Kanai Akio
Published: September 2019

Clp1, a polyribonucleotide 5′-hydroxyl kinase in eukaryotes, is involved in pretRNA splicing and mRNA 3′-end formation. Enzymes similar in amino acid sequence to Clp1, Nol9, and Grc3, are present in some eukaryotes and are involved in prerRNA processing. However, our knowledge of how these Clp1 family proteins evolved and diversified is limited. We conducted a large-scale molecular evolutionary analysis of the Clp1 family proteins in all living organisms for which protein sequences are available in public databases. The phylogenetic distribution and frequencies of the Clp1 family proteins were investigated in complete genomes of Bacteria, Archaea and Eukarya. In total, 3,557 Clp1 family proteins were detected in the three domains of life, Bacteria, Archaea, and Eukarya. Many were from Archaea and Eukarya, but a few were found in restricted, phylogenetically diverse bacterial species. The domain structures of the Clp1 family proteins also differed among the three domains of life. Although the proteins were, on average, 555 amino acids long (range, 196–2,728), 122 large proteins with >1,000 amino acids were detected in eukaryotes. These novel proteins contain the conserved Clp1 polynucleotide kinase domain and various other functional domains. Of these proteins, >80% were from Fungi or Protostomia. The polyribonucleotide kinase activity of Thermus scotoductus Clp1 (Ts-Clp1) was characterized experimentally. Ts-Clp1 preferentially phosphorylates single-stranded RNA oligonucleotides (Km value for ATP, 2.5 µM), or single-stranded DNA at higher enzyme concentrations. We propose a comprehensive assessment of the diversification of the Clp1 family proteins and the molecular evolution of their functional domains.
Health Care Access and Utilization for American Indian Elders: A Concept-Mapping Study
Authors: Sommerfeld David H , Jaramillo Elise Trott , Lujan Erik , Haozous Emily , Willging Cathleen E
Published: September 2019

Objectives

Inequities in access to and utilization of health care greatly influence the health and quality of life of American Indian elders (AIEs). This study explores the importance and perceived prevalence of factors affecting health care use within this population and assesses the changeability of these factors to produce a list of action items that are timely and relevant to improving health care access and utilization.

Method

Concept mapping was conducted with AIEs (n = 65) and professional stakeholders (n = 50), including tribal leaders, administrators of public-sector health systems, outreach workers, and health care providers. Data were analyzed using multidimensional scaling and cluster analyses.

Results

The final concept-map model comprised nine thematic clusters related to factors affecting elder health care: Difficulties Obtaining and Using Insurance; Insecurity from Lack of Knowledge; Limited Availability of Services; Scheduling Challenges; Provider Issues and Relationships; Family and Emotional Challenges; Health-Related Self-Efficacy and Knowledge; Accessibility and Transportation Barriers; and Tribal/National Policy.

Discussion

Findings suggest that improvements in access to and utilization of health care among AIEs will require actions across multiple domains, including health system navigation services, workforce improvements, and tribal, state, and federal policy. A multilevel socioecological approach is necessary to organize and undertake these actions.
The Prospective Association of Social Integration With Life Span and Exceptional Longevity in Women
Authors: Trudel-Fitzgerald Claudia , Zevon Emily S , Kawachi Ichiro , Tucker-Seeley Reginald D , Grodstein Francine , Kubzansky Laura D
Published: September 2019

Objectives

Although stronger social relationships have been associated with reduced mortality risk in prior research, their associations with favorable health outcomes are understudied. We evaluated whether higher social integration levels were associated with longer life span and greater likelihood of achieving exceptional longevity.

Method

Women from the Nurses’ Health Study completed the Berkman–Syme Social Network Index in 1992 (N = 72,322; average age = 58.80 years), and were followed through 2014 with biennial questionnaires. Deaths were ascertained from participants’ families, postal authorities, and death registries. Accelerated failure time models adjusting for relevant covariates estimated percent changes in life span associated with social integration levels; logistic regressions evaluated likelihood of surviving to age 85 years or older among women who could reach that age during follow-up (N = 16,818).

Results

After controlling for baseline demographics and chronic diseases, socially integrated versus isolated women had 10% (95% confidence interval [CI] = 8.80–11.42) longer life span and 41% (95% CI = 1.28–1.54) higher odds of surviving to age 85 years. All findings remained statistically significant after further adjusting for health behaviors and depression.

Discussion

Better social integration is related to longer life span and greater likelihood of achieving exceptional longevity among midlife women. Findings suggest social integration may be an important psychosocial asset to evaluate for promoting longer, healthier lives.
When Frail Older People Relocate in Very Old Age, Who Makes the Decision?
Authors: Scheibl Fiona , Farquhar Morag , Buck Jackie , Barclay Stephen , Brayne Carol , Fleming Jane
Published: September 2019

Background and Objectives

Older people are likely to transition to a new home closer to family who can provide assistance or to long-term residential care as their health declines and their care needs increase. A minority choose to move to “age-friendly” housing before the onset of disability, but the majority prefer to “age in place” and defer moving until health crises compel a transition. Older people living with dementia are likely to move into residential care, but not much is known about the role they play in decision making around these moves. This qualitative study addresses this gap in knowledge by examining how a rare cohort of “older old” people, most with some level of cognitive impairment, were involved in decisions surrounding assistance seeking and moving to a care home.

Research Design and Methods

Thematic analysis of qualitative interview data from Cambridge City over-75s Cohort (CC75C) study participants aged 95 years and older, who had moved in later life, and their proxy informants (n = 26).

Results

Moves at such an old age were made due to a complexity of push and pull factors which had layered dynamics of decision making. In most cases (n = 22), decision making involved other people with varying degrees of decision ownership. Only four older people, who moved voluntarily, had full ownership of the decision to move. Many relatives reported being traumatized by events leading up to the move.

Discussion and Implications

“Older old” people are sometimes unable to make their own decisions about moving due to the urgency of health crisis and cognitive decline. There is a need to support relatives to discuss moving and housing options at timely junctures before health crises intervene in an effort to optimize older people’s participation in decision making.
Advanced glycation end products (AGEs), protein aggregation and their cross talk: new insight in tumorigenesis
Authors: Haque Ejazul , Kamil Mohd , Hasan Adria , Irfan Safia , Sheikh Saba , Khatoon Aisha , Nazir Aamir , Mir Snober S
Published: September 2019

Protein glycation and protein aggregation are two distinct phenomena being observed in cancer cells as factors promoting cancer cell viability. Protein aggregation is an abnormal interaction between proteins caused as a result of structural changes in them after any mutation or environmental assault. Protein aggregation is usually associated with neurodegenerative diseases like Alzheimer’s and Parkinson’s, but of late, research findings have shown its association with the development of different cancers like lung, breast and ovarian cancer. On the contrary, protein glycation is a cascade of irreversible nonenzymatic reaction of reducing sugar with the amino group of the protein resulting in the modification of protein structure and formation of advanced glycation end products (AGEs). These AGEs are reported to obstruct the normal function of proteins. Lately, it has been reported that protein aggregation occurs as a result of AGEs. This aggregation of protein promotes the transformation of healthy cells to neoplasia leading to tumorigenesis. In this review, we underline the current knowledge of protein aggregation and glycation along with the cross talk between the two, which may eventually lead to the development of cancer.
Relationship between shell integrity of pelagic gastropods and carbonate chemistry parameters at a Scottish Coastal Observatory monitoring site
Authors: León Pablo , Bednaršek Nina , Walsham Pam , Cook Kathryn , Hartman Susan E , Wall-Palmer Deborah , Hindson Jennifer , Mackenzie Kevin , Webster Lynda , Bresnan Eileen
Published: September 2019

Ocean acidification (OA), the anthropogenic carbon dioxide-induced changes in seawater carbonate chemistry, is likely to have a significant impact on calcifying plankton. Most planktonic studies on OA are based on “one-off” cruises focused on offshore areas while observations from inshore waters are scarce. This study presents the first analysis on the shell integrity of pelagic gastropods (holoplanktonic pteropods and planktonic larvae of otherwise benthic species) at the Scottish Coastal Observatory monitoring site at Stonehaven on the east coast of Scotland. The shell integrity of archived pelagic gastropods specimens from 2011 to 2013 was examined using Scanning Electron Microscopy and the relationship with OA (pH and aragonite saturation, Ωarg) and other environmental parameters was investigated. Evidence of shell dissolution was detected in all analysed taxa even though the seawater was supersaturated with respect to aragonite. The shell condition matched the temporal pattern observed in Ωarg, with higher proportion of dissolution associated with decreasing Ωarg, suggesting that the seasonality component of carbonate chemistry might affect the shell integrity of pelagic gastropods. The proportion of shell dissolution differed significantly between larvae and adult stages of pteropods, supporting the hypothesis that early-life stages would be more vulnerable to OA-induced changes. Our data also suggest that sensitivity to OA may differ even between closely related taxonomic groups. The strong interannual variability revealed by the year-to-year shell dissolution and Ωarg illustrates the difficulty in assessing the plankton response to OA in the field and the value of time series studies.
Multiplicity One for Pairs of Prasad–Takloo-Bighash Type
Authors: Broussous Paul , Matringe Nadir
Published: September 2019

Let ${\textrm{E}}/{\textrm{F}}$ be a quadratic extension of non-archimedean local fields of characteristic different from $2$. Let ${\textrm{A}}$ be an ${\textrm{F}}$-central simple algebra of even dimension so that it contains ${\textrm{E}}$ as a subfield, set ${\textrm{G}}={\textrm{A}}^\times $ and ${\textrm{H}}$ for the centralizer of ${\textrm{E}}^\times $ in ${\textrm{G}}$. Using a Galois descent argument, we prove that all double cosets ${\textrm{H}} g {\textrm{H}}\subset{\textrm{G}}$ are stable under the anti-involution $g\mapsto g^{-1}$, reducing to Guo’s result for ${\textrm{F}}$-split ${\textrm{G}}$ [ 14], which we extend to fields of positive characteristic different from $2$. We then show, combining global and local results, that ${\textrm{H}}$-distinguished irreducible representations of ${\textrm{G}}$ are self-dual and this implies that $({\textrm{G}},{\textrm{H}})$ is a Gelfand pair $$\begin{equation*}\operatorname{dim}_{\mathbb{C}}(\operatorname{Hom}_{{\textrm{H}}}(\pi,\mathbb{C}))\leq 1\end{equation*}$$for all smooth irreducible representations $\pi $ of ${\textrm{G}}$. Finally we explain how to obtain the multiplicity one statement in the archimedean case using the criteria of Aizenbud and Gourevitch ([ 1]), and we then show self-duality of irreducible distinguished representations in the archimedean case too.
A Combinatorial Formula for the Coefficient of q in Kazhdan–Lusztig Polynomials
Authors: Patimo Leonardo
Published: September 2019

We propose a combinatorial interpretation of the coefficient of $q$ in Kazhdan–Lusztig polynomials and we prove it for finite simply-laced Weyl groups.
Convergence of the Weak Kähler–Ricci Flow on Manifolds of General Type
Authors: Tô Tat Dat
Published: September 2019

We study the Kähler–Ricci flow on compact Kähler manifolds whose canonical bundle is big. We show that the normalized Kähler–Ricci flow has long-time existence in the viscosity sense, is continuous in a Zariski open set, and converges to the unique singular Kähler–Einstein metric in the canonical class. The key ingredient is a viscosity theory for degenerate complex Monge–Ampère flows in big classes that we develop, extending and refining the approach of Eyssidieux–Guedj–Zeriahi.
Dynamical Uniform Bounds for Fibers and a Gap Conjecture
Authors: Bell Jason , Ghioca Dragos , Satriano Matthew
Published: September 2019

We prove a uniform version of the Dynamical Mordell–Lang Conjecture for étale maps; also, we obtain a gap result for the growth rate of heights of points in an orbit along an arbitrary endomorphism of a quasiprojective variety defined over a number field. More precisely, for our 1st result, we assume $X$ is a quasi-projective variety defined over a field $K$ of characteristic $0$, endowed with the action of an étale endomorphism $\Phi $, and $f\colon X\longrightarrow Y$ is a morphism with $Y$ a quasi-projective variety defined over $K$. Then for any $x\in X(K)$, if for each $y\in Y(K)$, the set $S_{x,y}:=\{n\in{\mathbb{N}}\colon f(\Phi ^n(x))=y\}$ is finite, then there exists a positive integer $N_x$ such that $\sharp S_{x,y}\le N_x$ for each $y\in Y(K)$. For our 2nd result, we let $K$ be a number field, $f:X\dashrightarrow{\mathbb{P}}^1$ is a rational map, and $\Phi $ is an arbitrary endomorphism of $X$. If ${\mathcal{O}}_{\Phi }(x)$ denotes the forward orbit of $x$ under the action of $\Phi $, then either $f({\mathcal{O}}_{\Phi }(x))$ is finite, or $\limsup _{n\to \infty } h(f(\Phi ^n(x)))/\log (n)>0$, where $h(\cdot )$ represents the usual logarithmic Weil height for algebraic points.
The frugivorous insectivores? Functional morphological analysis of molar topography for inferring diet in extant treeshrews (Scandentia)
Authors: Selig Keegan R , Sargis Eric J , Silcox Mary T
Published: September 2019

The ecology, and particularly the diet, of treeshrews (order Scandentia) is poorly understood compared to that of their close relatives, the primates. This stems partially from treeshrews having fast food transit times through the gut, meaning fecal and stomach samples only represent a small portion of the foodstuffs consumed in a given day. Moreover, treeshrews are difficult to observe in the wild, leading to a lack of observational data in the literature. Although treeshrews are mixed feeders, consuming both insects and fruit, it is currently unknown how the relative importance of these food types varies across Scandentia. Previous study of functional dental morphology has provided an alternative means for understanding the diet of living euarchontans. We used dental topographic metrics to quantify aspects of functional dental morphology in a large sample of treeshrews (n = 58). We measured relief index, Dirichlet normal energy, and three-dimensional orientation patch count rotated, which quantify crown relief, occlusal curvature, and complexity, respectively. Our results suggest that treeshrews exhibit dental morphology consistent with high levels of insectivory relative to other euarchontans. They also suggest that taxa such as Dendrogale melanura and Tupaia belangeri appear to be best suited to insectivory, whereas taxa such as T. palawanensis and T. gracilis appear to be best adapted to frugivory. Our results suggest that Ptilocercus lowii is characterized by a dentition better adapted to insectivory than the early primate Purgatorius. If P. lowii represents a good modern analogue for primitive euarchontans, this contrast would support models of primate origins that include a shift to greater frugivory.
Inter-fractional variations in the dosimetric parameters of accelerated partial breast irradiation using a strut-adjusted volume implant
Authors: Iijima Kotaro , Okamoto Hiroyuki , Takahashi Kana , Aikawa Ako , Wakita Akihisa , Nakamura Satoshi , Nishioka Shie , Harada Ken , Notake Ryoichi , Sugawara Akimoto , Yoshimura Ryoichi , Kunieda Etsuo , Itami Jun
Published: September 2019

The aim of the study was to evaluate inter-fractional dosimetric variations for high-dose rate breast brachytherapy using a strut-adjusted volume implant (SAVI). For the nine patients included, dosimetric constraints for treatment were as follows: for the planning target volume for evaluation (PTV_Eval), the volume receiving 90, 150 and 200% of the prescribed dose (V90%,150%,200%) should be >90%, ≤50 cm3 and ≤20 cm3, respectively; the dose covering 1 cm3 (D1cc) of the organs at risk should be ≤110% of the prescribed dose; and the air volume should be ≤10% of PTV_Eval. Differences in V90%,150%,200%, D1cc and air volume ($\Delta V$ and $\Delta D$) as inter-fractional dosimetric variations and SAVI displacements were measured with pretreatment and planning computed tomography (CT) images. Inter-fractional dosimetric variations were analyzed for correlations with the SAVI displacements. The patients were divided into two groups based on the distance of the SAVI from the surface skin to assess the relationship between the insertion position of the SAVI and dosimetric parameters. The median ΔV90%,150%,200% for the PTV_Eval in all patients was −0.3%, 0.2 cm3 and 0.2 cm3, respectively. The median (range) ΔD1cc for the chest wall and surface skin was −0.8% (−18.9 to 9.4%) and 0.3% (−7.6 to 5.3%), respectively. SAVI displacement did not correlate with inter-fractional dosimetric variations. In conclusion, the dose constraints were satisfied in most cases. However, there were inter-fractional dosimetric changes due to SAVI displacement.
All roads lead to growth: imaging-based and biochemical methods to measure plant growth
Authors: Olas Justyna Jadwiga , Fichtner Franziska , Apelt Federico
Published: September 2019

We provide a comprehensive description and comparison of the various imaging and non-imaging-based techniques used to measure vegetative plant shoot growth and suggest a terminology for growth rates.
NUSTAR and Swift observations of AMXP Swift J1756.9−2508 during its 2018 outburst
Authors: Rai Binay , Paul Bikash Chandra
Published: September 2019

We present here the timing and spectral analysis of the accreting millisecond pulsar (AMXP) SwiftJ1756.9−2508 during its recent outburst in 2018 using Swift and NUSTAR observations. The simultaneous fitting of the Swift and NUSTAR spectra indicates that the source was in the hard state with a cut-off energy of about 74.58 keV. We also study in detail the pulse profile of the AMXP and its dependence on energy. The colour–colour diagram of the source is different from those previously reported. We performed phase- and time-resolved spectral analysis using NUSTAR data. Pulse phase-resolved spectra were fitted with a power-law model and significant changes in the spectral parameters with pulse phase were observed. The orbital phase and time-resolved spectra were fitted with a cut-off power-law model. The column density and photon index obtained from orbital phase spectral analysis were found to show some anticorrelation with the flux. Through time-resolved spectral analysis, we observed that the spectral parameters show positive correlation with each other and with the flux. We do not observe a softening of the spectrum with time. No emission lines or Compton bump were observed in the spectrum of the AMXP.
Multi-epoch X-ray spectral analysis of the narrow-line Seyfert 1 galaxy Mrk 478
Authors: Waddell S G H , Gallo L C , Gonzalez A G , Tripathi S , Zoghbi A
Published: September 2019

A multi-epoch X-ray spectral and variability analysis is conducted for the narrow-line Seyfert 1 (NLS1) active galactic nucleus (AGN) Mrk 478. All available X-ray data from XMM–Newton and Suzaku satellites, spanning from 2001 to 2017, are modelled with a variety of physical models, including partial covering, soft Comptonization, and blurred reflection, to explain the observed spectral shape and variability over the 16 yr. All models are a similar statistical fit to the data sets, though the analysis of the variability between data sets favours the blurred reflection model. In particular, the variability can be attributed to changes in flux of the primary coronal emission. Different reflection models fit the data equally well, but differ in interpretation. The use of reflionx predicts a low disc ionization and power law dominated spectrum, while relxill predicts a highly ionized and blurred reflection dominated spectrum. A power law dominated spectrum might be more consistent with the normal X-ray-to-UV spectral shape (αox). Both blurred reflection models suggest a rapidly spinning black hole seen at a low inclination angle, and both require a sub-solar (∼0.5) abundance of iron. All physical models require a narrow emission feature at $6.7{\rm \, keV}$ likely attributable to Fe xxv emission, while no evidence for a narrow $6.4{\rm \, keV}$ line from neutral iron is detected.
The CFHT Large Area U-band Deep Survey (CLAUDS)
Authors: Sawicki Marcin , Arnouts Stephane , Huang Jiasheng , Coupon Jean , Golob Anneya , Gwyn Stephen , Foucaud Sebastien , Moutard Thibaud , Iwata Ikuru , Liu Chengze , Chen Lingjian , Desprez Guillaume , Harikane Yuichi , Ono Yoshiaki , Strauss Michael A , Tanaka Masayuki , Thibert Nathalie , Balogh Michael , Bundy Kevin , Chapman Scott , Gunn James E , Hsieh Bau-Ching , Ilbert Olivier , Jing Yipeng , LeFèvre Olivier , Li Cheng , Matsuda Yuichi , Miyazaki Satoshi , Nagao Tohru , Nishizawa Atsushi J , Ouchi Masami , Shimasaku Kazuhiro , Silverman John , de la Torre Sylvain , Tresse Laurence , Wang Wei-Hao , Willott Chris J , Yamada Toru , Yang Xiaohu , Yee Howard K C
Published: September 2019

The Canada-France-Hawaii Telescope (CFHT) Large Area U-band Deep Survey (CLAUDS) uses data taken with the MegaCam mosaic imager on CFHT to produce images of 18.60 deg2 with median seeing of FWHM=0.92″ and to a median depth of U = 27.1 AB (5σ in 2″ apertures), with selected areas that total 1.36 deg2 reaching a median depth of U = 27.7 AB. These are the deepest U-band images assembled to date over this large an area. These data are located in four fields also imaged to comparably faint levels in grizy and several narrowband filters as part of the Hyper Suprime-Cam (HSC) Subaru Strategic Program (HSC-SSP). These CFHT and Subaru datasets will remain unmatched in their combination of area and depth until the advent of the Large Synoptic Survey Telescope (LSST). This paper provides an overview of the scientific motivation for CLAUDS and gives details of the observing strategy, observations, data reduction, and data merging with the HSC-SSP. Three early applications of these deep data are used to illustrate the potential of the dataset: deep U-band galaxy number counts, z∼3 Lyman break galaxy (LBG) selection, and photometric redshifts improved by adding CLAUDS U to the Subaru HSC grizy photometry.
Jean-Philippe Rameau’s Influence on Harmonic Theory in Spain
Authors: Murphy Paul , Gallardo Cristóbal García
Published: September 2019

It is well known that the music-theoretical ideas of Jean-Philippe Rameau (1683–1764) were disseminated throughout much of Europe in large part by the summary editions issued by the mathematician and philosopher Jean Le Rond d’Alembert (1717–83) and certain German, English, and Italian translations that followed. Little is known, however, about how Rameau’s revolutionary and controversial theories appeared in Spain, and even less about how they were received and interpreted. In response, we offer a contextual analysis of the effects that these ideas had on both forward-looking intellectuals as well as on conservative professional musicians grounded in music of the past.
SNP2APA: a database for evaluating effects of genetic variants on alternative polyadenylation in human cancers
Authors: Yang Yanbo , Zhang Qiong , Miao Ya-Ru , Yang Jiajun , Yang Wenqian , Yu Fangda , Wang Dongyang , Guo An-Yuan , Gong Jing
Published: September 2019

Alternative polyadenylation (APA) is an important post-transcriptional regulation that recognizes different polyadenylation signals (PASs), resulting in transcripts with different 3′ untranslated regions, thereby influencing a series of biological processes and functions. Recent studies have revealed that some single nucleotide polymorphisms (SNPs) could contribute to tumorigenesis and development through dysregulating APA. However, the associations between SNPs and APA in human cancers remain largely unknown. Here, using genotype and APA data of 9082 samples from The Cancer Genome Atlas (TCGA) and The Cancer 3′UTR Altas (TC3A), we systematically identified SNPs affecting APA events across 32 cancer types and defined them as APA quantitative trait loci (apaQTLs). As a result, a total of 467 942 cis-apaQTLs and 30 721 trans-apaQTLs were identified. By integrating apaQTLs with survival and genome-wide association studies (GWAS) data, we further identified 2154 apaQTLs associated with patient survival time and 151 342 apaQTLs located in GWAS loci. In addition, we designed an online tool to predict the effects of SNPs on PASs by utilizing PAS motif prediction tool. Finally, we developed SNP2APA, a user-friendly and intuitive database (http://gong_lab.hzau.edu.cn/SNP2APA/) for data browsing, searching, and downloading. SNP2APA will significantly improve our understanding of genetic variants and APA in human cancers.
JS1.2 Increased frequency of paraneoplastic encephalitis with anti-Ma2 antibodies in the cancer immunotherapy era
Authors: Vogrig A , Fouret M , Joubert B , Picard G , Rogemond V , Pinto A , Muñiz Castrillo S , Roger M , Raimbourg J , Dayen C , Grignou L , Pallix-Guyot M , Lannoy J , Ducray F , Desestret V , Psimaras D , Honnorat J
Published: September 2019

BACKGROUND

Given the mechanism of action of immune checkpoint inhibitors (ICIs), a possible association with the development of paraneoplastic neurological syndromes (PNS) has been hypothesized. We sought to determine if ICI treatment might trigger anti-Ma2 antibody-associated paraneoplastic neurological syndromes (Ma2-PNS).

MATERIAL AND METHODS

We performed a retrospective nationwide study of all patients with Ma2-PNS developed during ICI treatment between 2017–2018. The frequency of neuronal-antibody detection before and after ICI implementation was also analyzed.

RESULTS

Our series of patients included 5 men and 1 woman (median age, 63 years). The patients were receiving either nivolumab (n = 3), pembrolizumab (n = 2) or a combination of nivolumab and ipilimumab (n=1), for treatment of neoplasms that included lung (n=4) and kidney (n=1) cancers, and pleural mesothelioma (n=1). Median delay between ICI introduction and onset of the neurological syndrome was 4 months. Clinical syndromes included a combination of limbic encephalitis and diencephalitis (n=3), isolated limbic encephalitis (n=2) and a syndrome characterized by opthalmoplegia and head-drop (n=1). Patients with diencephalitis manifested hyperphagia, weight gain and somnolence. Post-ICI Ma2-PNS accounted for 35% of the total 17 Ma2-PNS diagnosed in our center over the 2017–2018 biennium. Eight cases had been detected in the preceding biennium 2015–2016, corresponding to a 112% increase of Ma2-PNS frequency since the implementation of ICIs in France. No other neuronal-antibody demonstrated a similar increment.

CONCLUSION

We show a clear association between ICI use and increased frequency of Ma2-PNS. Physicians need to be aware that ICIs can trigger Ma2-PNS since clinical presentation can be challenging.
OS1.3 Tumor cell-free DNA detection in CSF for primary CNS lymphoma diagnosis
Authors: Rimelen V , Ahle G , Pencreach E , Zinniger N , Debliquis A , Zalmaï L , Harzallah I , Hurstel R , Alamome I , Lamy F , Brinet A , Voirin J , Drénou B
Published: September 2019

BACKGROUND

Primary CNS lymphoma (PCNSL) is a rare disease accounting for around 3% of the primary brain tumors. In the vast majority of cases, PCNSL are classified as diffuse large B-cell lymphoma according to the WHO classification. The diagnosis is based on cranial MRI, in combination with a brain biopsy. In case of classical MRI findings, the identification of lymphoma cells in the cerebrospinal (CSF) or vitreous fluid by cytology and flow cytometry might obviate brain biopsy. The presence of the somatic mutation p.Leu265Pro (L265P) in MYD88 is detectable in 50 to 80% of PCNSL, and might also be helpful to confirm the diagnosis. The aim of our study was to evaluate the contribution of a highly sensitive digital droplet PCR, targeting the mutation L265P MYD88, for the detection of tumoral circulating DNA from CSF supernatant.

MATERIAL AND METHODS

We identified 9 PCNSL expressing the L265P mutation at diagnosis or relapse. The mutation was found by an allele specific PCR technique either on biopsy or in CSF cells. Circulating DNA was isolated from CSF supernatant with the « QiaAmp® circulating nucleic acid» kit. The quantity of DNA collected was estimated by quantitative PCR for a reference gene (albumine) with 7900HT (Life technologies™) device. Subsequently, the L265P MYD88 mutation was quantified by digital droplet PCR Biorad™: The droplets generated were amplified by PCR, detected with the QX200 Reader, and analyzed with the QuantaSoft™ software.

RESULTS

The circulating DNA concentration was low, varying between 0 and 2.2 ng/mL of CSF. However, the mutation was detected in the circulating DNA from CSF supernatant in 6 out of 9 cases (66%). The fractional abundance varied from 2.6 to 85%. In 3 cases, the mutation was detected even though cytology and flow cytometry did not reveal leptomeningeal disease. For 3 other cases, the mutation was not detected: The genome copy number was below 1 copy/µL, indicating a low analytical sensitivity for theses samples.

CONCLUSION

This study shows that circulating DNA is present in low concentration in CSF and can be amplified by a sensitive digital PCR for the L265P MYD88 mutation. The detection of circulating PCNSL DNA in CSF is possible and might be used to improve the non-invasive diagnosis of PCNSL. It might also help to select patients for targeted therapies.