bluuebunny/crossref_metadata_2025_split huggingface dataset:
On time-dependent Besov vector fields and the regularity of their flows
Authors: Nenning David 
Published: October 2019

We show ODE-closedness for a large class of Besov spaces

B

n
,
α
,
p

(

R

d

,

R

d

)

\mathcal {B}^{n,\alpha ,p}(\mathbb {R}^d,\mathbb {R}^d)

, where

n
≥
1
,

α
∈
(
0
,
1
]
,

p
∈
[
1
,
∞
]

n \ge 1,~\alpha \in (0,1],~p \in [1,\infty ]

. ODE-closedness means that pointwise time-dependent

B

n
,
α
,
p

\mathcal {B}^{n,\alpha ,p}

-vector fields

u
u

have unique flows

Φ
u

∈
Id
+

B

n
,
α
,
p

(

R

d

,

R

d

)

\Phi _u \in \operatorname {Id}+\mathcal {B}^{n,\alpha ,p}(\mathbb {R}^d,\mathbb {R}^d)

. The class of vector fields under consideration contains as a special case the class of Bochner integrable vector fields

L
1

(
I
,

B

n
,
α
,
p

(

R

d

,

R

d

)
)

L^1(I, \mathcal {B}^{n,\alpha ,p}(\mathbb {R}^d,\mathbb {R}^d))

. In addition, for

n
≥
2

n \ge 2

and

α
>
β

\alpha > \beta

, we show continuity of the flow mapping

L
1

(
I
,

B

n
,
β
,
p

(

R

d

,

R

d

)
)
→
C
(
I
,

B

n
,
α
,
p

(

R

d

,

R

d

)
)
,

u
→

Φ
u

−
Id

L^1(I,\mathcal {B}^{n,\beta ,p}(\mathbb {R}^d,\mathbb {R}^d)) \rightarrow C(I,\mathcal {B}^{n,\alpha ,p}(\mathbb {R}^d,\mathbb {R}^d)), ~ u \to \Phi _u-\operatorname {Id}

. We even get

γ
\gamma

-Hölder continuity for any

γ
>
β
−
α

\gamma > \beta - \alpha

.
PlanExp: intuitive integration of complex RNA-seq datasets with planarian omics resources
Authors: Castillo-Lara S , Pascual-Carreras E , Abril J F 
Published: October 2019

Abstract

Motivation
There is an increasing amount of transcriptomic and genomic data available for planarians with the advent of both traditional and single-cell RNA sequencing technologies. Therefore, exploring, visualizing and making sense of all these data in order to understand planarian regeneration and development can be challenging.

Results
In this work, we present PlanExp, a web-application to explore and visualize gene expression data from different RNA-seq experiments (both traditional and single-cell RNA-seq) for the planaria Schmidtea mediterranea. PlanExp provides tools for creating different interactive plots, such as heatmaps, scatterplots, etc. and links them with the current sequence annotations both at the genome and the transcript level thanks to its integration with the PlanNET web application. PlanExp also provides a full gene/protein network editor, a prediction of genetic interactions from single-cell RNA-seq data, and a network expression mapper that will help researchers to close the gap between systems biology and planarian regeneration.

Availability and implementation
PlanExp is freely available at https://compgen.bio.ub.edu/PlanNET/planexp. The source code is available at https://compgen.bio.ub.edu/PlanNET/downloads.

Supplementary information
Supplementary data are available at Bioinformatics online.
Deficient Resident Memory T Cell and CD8 T Cell Response to Commensals in Inflammatory Bowel Disease
Authors: Noble Alistair , Durant Lydia , Hoyles Lesley , Mccartney Anne L , Man Ripple , Segal Jonathan , Costello Samuel P , Hendy Philip , Reddi Durga , Bouri Sonia , Lim Dennis N F , Pring Toby , O’Connor Matthew J , Datt Pooja , Wilson Ana , Arebi Naila , Akbar Ayesha , Hart Ailsa L , Carding Simon R , Knight Stella C 
Published: October 2019

AbstractBackground and AimsThe intestinal microbiota is closely associated with resident memory lymphocytes in mucosal tissue. We sought to understand how acquired cellular and humoral immunity to the microbiota differ in health versus inflammatory bowel disease [IBD].MethodsResident memory T cells [Trm] in colonic biopsies and local antibody responses to intraepithelial microbes were analysed. Systemic antigen-specific immune T and B cell memory to a panel of commensal microbes was assessed.ResultsSystemically, healthy blood showed CD4 and occasional CD8 memory T cell responses to selected intestinal bacteria, but few memory B cell responses. In IBD, CD8 memory T cell responses decreased although B cell responses and circulating plasmablasts increased. Possibly secondary to loss of systemic CD8 T cell responses in IBD, dramatically reduced numbers of mucosal CD8+ Trm and γδ T cells were observed. IgA responses to intraepithelial bacteria were increased. Colonic Trm expressed CD39 and CD73 ectonucleotidases, characteristic of regulatory T cells. Cytokines/factors required for Trm differentiation were identified, and in vitro-generated Trm expressed regulatory T cell function via CD39. Cognate interaction between T cells and dendritic cells induced T-bet expression in dendritic cells, a key mechanism in regulating cell-mediated mucosal responses.ConclusionsA previously unrecognised imbalance exists between cellular and humoral immunity to the microbiota in IBD, with loss of mucosal T cell-mediated barrier immunity and uncontrolled antibody responses. Regulatory function of Trm may explain their association with intestinal health. Promoting Trm and their interaction with dendritic cells, rather than immunosuppression, may reinforce tissue immunity, improve barrier function, and prevent B cell dysfunction in microbiota-associated disease and IBD aetiology.
More Than Meets the Eye? The Role of Annual Ornamental Flowers in Supporting Pollinators
Authors: Erickson E , Adam S , Russo L , Wojcik V , Patch H M , Grozinger C M 
Published: October 2019

AbstractOrnamental flowers are commonly planted in urban and suburban areas to provide foraging resources for pollinator populations. However, their role in supporting broad pollinator biodiversity is not well established as previous studies have been conducted in urban landscapes with pollinator communities that are distinct from those in natural systems. We observed pollinator visitation patterns to five ornamental annual plant genera and their cultivars over multiple years at two semi-natural sites in Pennsylvania to understand their potential for supporting diverse pollinator communities. There was significant variation in visitor abundance and diversity by season and year for many annual ornamental cultivars. Within some genera, cultivars had similar visitor abundance, diversity, and main visitor taxa, while cultivars in other genera varied greatly in these measures. We observed only polylectic (pollen generalist) bee species visiting annual ornamentals, despite the presence of oligolectic (pollen specialist) bee species in the background population. We conclude that the attractiveness of annual ornamental plants likely depends on both cultivar characteristics and environmental context. While their role in supporting complex pollinator populations is limited both based on the number of and dietary breadth of the species they support, ornamental plants may nonetheless provide long-lasting supplemental foraging resources for the generalist pollinator communities characteristic of urban and suburban environments.
Atrial fibrillation and cardiac fibrosis
Authors: Sohns Christian , Marrouche Nassir F 
Published: October 2019

Abstract
The understanding of atrial fibrillation (AF) evolved from a sole rhythm disturbance towards the complex concept of a cardiomyopathy based on arrhythmia substrates. There is evidence that atrial fibrosis can be visualized using late gadolinium enhancement cardiac magnetic resonance imaging and that it is a powerful predictor for the outcome of AF interventions. However, a strategy of an individual and fibrosis guided management of AF looks promising but results from prospective multicentre trials are pending. This review gives an overview about the relationship between cardiac fibrosis and AF focusing on translational aspects, clinical observations, and fibrosis imaging to emphasize the concept of personalized paths in AF management taking into account the individual amount and distribution of fibrosis.
Histone demethylase KDM5C is a SAHA-sensitive central hub at the crossroads of transcriptional axes involved in multiple neurodevelopmental disorders
Authors: Poeta Loredana , Padula Agnese , Attianese Benedetta , Valentino Mariaelena , Verrillo Lucia , Filosa Stefania , Shoubridge Cheryl , Barra Adriano , Schwartz Charles E , Christensen Jesper , van Bokhoven Hans , Helin Kristian , Lioi Maria Brigida , Collombat Patrick , Gecz Jozef , Altucci Lucia , Di Schiavi Elia , Miano Maria Giuseppina 
Published: October 2019

AbstractA disproportional large number of neurodevelopmental disorders (NDDs) is caused by variants in genes encoding transcription factors and chromatin modifiers. However, the functional interactions between the corresponding proteins are only partly known. Here, we show that KDM5C, encoding a H3K4 demethylase, is at the intersection of transcriptional axes under the control of three regulatory proteins ARX, ZNF711 and PHF8. Interestingly, mutations in all four genes (KDM5C, ARX, ZNF711 and PHF8) are associated with X-linked NDDs comprising intellectual disability as a core feature. in vitro analysis of the KDM5C promoter revealed that ARX and ZNF711 function as antagonist transcription factors that activate KDM5C expression and compete for the recruitment of PHF8. Functional analysis of mutations in these genes showed a correlation between phenotype severity and the reduction in KDM5C transcriptional activity. The KDM5C decrease was associated with a lack of repression of downstream target genes Scn2a, Syn1 and Bdnf in the embryonic brain of Arx-null mice. Aiming to correct the faulty expression of KDM5C, we studied the effect of the FDA-approved histone deacetylase inhibitor suberanilohydroxamic acid (SAHA). In Arx-KO murine ES-derived neurons, SAHA was able to rescue KDM5C depletion, recover H3K4me3 signalling and improve neuronal differentiation. Indeed, in ARX/alr-1-deficient Caenorhabditis elegans animals, SAHA was shown to counteract the defective KDM5C/rbr-2-H3K4me3 signalling, recover abnormal behavioural phenotype and ameliorate neuronal maturation. Overall, our studies indicate that KDM5C is a conserved and druggable effector molecule across a number of NDDs for whom the use of SAHA may be considered a potential therapeutic strategy.
Simulating the galactic system in interaction AM 2229-735 and the formation of its polar structure
Authors: Quiroga Luis F , Muñoz-Cuartas J C , Rodrigues I , Libeskind Noam I 
Published: October 2019

Abstract
We study the formation of polar ring galaxies via minor mergers. We used N-body+hydrodynamics simulations to reproduce the dynamics of the observed system AM 2229-735 that is a minor merger whose interaction signals are those of a progenitor for a polar ring galaxy. We used the observational information of the system to get initial conditions for the orbit and numerical realisations of the galaxies to run the simulations. Our simulations reproduce the global characteristics of interaction observed in the system such as arms and a material bridge connecting the galaxies. As a merger remnant, we found a quasi-stable and self gravitating planar tidal stream with dark matter, stars and gas orbiting in a plane approximately perpendicular to the main galaxy disk leading in the future to a polar ring galaxy. We studied the dynamical conditions of the polar structure and found evidence suggesting that this kind of merger remnant can settle down in a disk-like structure with isothermal support, providing inspiring evidence about the process of formation of galactic disks and providing a potentially independent scenario to study the presence of dark matter in this kind of galaxies.
Small-scale clustering of nano-dust grains in supersonic turbulence
Authors: Mattsson L , Fynbo J P U , Villarroel B 
Published: October 2019

ABSTRACT
We investigate the clustering and dynamics of nano-sized particles (nano dust) in high-resolution (10243) simulations of compressible isothermal hydrodynamic turbulence. It is well established that large grains will decouple from a turbulent gas flow, while small grains will tend to trace the motion of the gas. We demonstrate that nano-sized grains may cluster in a turbulent flow (fractal small-scale clustering), which increases the local grain density by at least a factor of a few. In combination with the fact that nano-dust grains may be abundant in general, and the increased interaction rate due to turbulent motions, aggregation involving nano dust may have a rather high probability. Small-scale clustering will also affect extinction properties. As an example we present an extinction model based on silicates, graphite, and metallic iron, assuming strong clustering of grain sizes in the nanometre range, could explain the extreme and rapidly varying ultraviolet extinction in the host of GRB 140506A.
Pulsar candidate classification using generative adversary networks
Authors: Guo Ping , Duan Fuqing , Wang Pei , Yao Yao , Yin Qian , Xin Xin , Li Di , Qian Lei , Wang Shen , Pan Zhichen , Zhang Lei 
Published: October 2019

ABSTRACT
Discovering pulsars is a significant and meaningful research topic in the field of radio astronomy. With the advent of astronomical instruments, the volume and rate of data acquisition have grown exponentially. This development necessitates a focus on artificial intelligence (AI) technologies that can mine large astronomical data sets. Automatic pulsar candidate identification (APCI) can be considered as a task determining potential candidates for further investigation and eliminating the noise of radio-frequency interference and other non-pulsar signals. As reported in the existing literature, AI techniques, especially convolutional neural network (CNN)-based techniques, have been adopted for APCI. However, it is challenging to enhance the performance of CNN-based pulsar identification because only an extremely limited number of real pulsar samples exist, which results in a crucial class imbalance problem. To address these problems, we propose a framework that combines a deep convolution generative adversarial network (DCGAN) with a support vector machine (SVM). The DCGAN is used as a sample generation and feature learning model, and the SVM is adopted as the classifier for predicting the label of a candidate at the inference stage. The proposed framework is a novel technique, which not only can solve the class imbalance problem but also can learn the discriminative feature representations of pulsar candidates instead of computing hand-crafted features in the pre-processing steps. The proposed method can enhance the accuracy of the APCI, and the computer experiments performed on two pulsar data sets verified the effectiveness and efficiency of the proposed method.
On the black hole content and initial mass function of 47 Tuc
Authors: Hénault-Brunet V , Gieles M , Strader J , Peuten M , Balbinot E , Douglas K E K 
Published: October 2019

ABSTRACT
The globular cluster (GC) 47 Tuc has recently been proposed to host an intermediate-mass black hole (IMBH) or a population of stellar mass black holes (BHs). To shed light on its dark content, we present an application of self-consistent multimass models with a varying mass function and content of stellar remnants, which we fit to various observational constraints. Our best-fitting model successfully matches the observables and correctly predicts the radial distribution of millisecond pulsars and their gravitational accelerations inferred from long-term timing observations. The data favours a population of BHs with a total mass of $430^{+386}_{-301}$ M⊙, but the most likely model has very few BHs. Since our models do not include a central IMBH and accurately reproduce the observations, we conclude that there is currently no need to invoke the presence of an IMBH in 47 Tuc. The global present-day mass function inferred is significantly depleted in low-mass stars (power-law slope $\alpha =-0.52^{+0.17}_{-0.16}$). Given the orbit and predicted mass-loss history of this massive GC, the dearth of low-mass stars is difficult to explain with a standard initial mass function (IMF) followed by long-term preferential escape of low-mass stars driven by two-body relaxation, and instead suggests that 47 Tuc may have formed with a bottom-light IMF. We discuss alternative evolutionary origins for the flat mass function and ways to reconcile this with the low BH retention fraction. Finally, by capturing the effect of dark remnants, our method offers a new way to probe the IMF in a GC above the current main-sequence turn-off mass, for which we find a slope of −2.49 ± 0.08.
x-cigale: fitting AGN/galaxy SEDs from X-ray to infrared
Authors: Yang(杨光) G , Boquien M , Buat V , Burgarella D , Ciesla L , Duras F , Stalevski M , Brandt W N , Papovich C 
Published: October 2019

ABSTRACT
Code Investigating GALaxy Emission (cigale) is a powerful multiwavelength spectral energy distribution (SED) fitting code for extragalactic studies. However, the current version of cigale is not able to fit X-ray data, which often provide unique insights into active galactic nucleus (AGN) intrinsic power. We develop a new X-ray module for cigale, allowing it to fit SEDs from the X-ray to infrared (IR). We also improve the AGN fitting of cigale from UV-to-IR wavelengths. We implement a modern clumpy two-phase torus model, skirtor. To account for moderately extincted type 1 AGNs, we implement polar-dust extinction. We publicly release the source code (named ‘x-cigale’). We test x-cigale with X-ray detected AGNs in SDSS, COSMOS, and AKARI-NEP. The fitting quality (as indicated by reduced χ2) is good in general, indicating that x-cigale is capable of modelling the observed SED from X-ray to IR. We discuss constrainability and degeneracy of model parameters in the fitting of AKARI-NEP, for which excellent mid-IR photometric coverage is available. We also test fitting a sample of AKARI-NEP galaxies for which only X-ray upper limits are available from Chandra observations, and find that the upper limit can effectively constrain the AGN SED contribution for some systems. Finally, using x-cigale, we assess the ability of Athena to constrain the AGN activity in future extragalactic studies.
ELM—the eukaryotic linear motif resource in 2020
Authors: Kumar Manjeet , Gouw Marc , Michael Sushama , Sámano-Sánchez Hugo , Pancsa Rita , Glavina Juliana , Diakogianni Athina , Valverde Jesús Alvarado , Bukirova Dayana , Čalyševa Jelena , Palopoli Nicolas , Davey Norman E , Chemes Lucía B , Gibson Toby J 
Published: October 2019

AbstractThe eukaryotic linear motif (ELM) resource is a repository of manually curated experimentally validated short linear motifs (SLiMs). Since the initial release almost 20 years ago, ELM has become an indispensable resource for the molecular biology community for investigating functional regions in many proteins. In this update, we have added 21 novel motif classes, made major revisions to 12 motif classes and added >400 new instances mostly focused on DNA damage, the cytoskeleton, SH2-binding phosphotyrosine motifs and motif mimicry by pathogenic bacterial effector proteins. The current release of the ELM database contains 289 motif classes and 3523 individual protein motif instances manually curated from 3467 scientific publications. ELM is available at: http://elm.eu.org.
MGnify: the microbiome analysis resource in 2020
Authors: Mitchell Alex L , Almeida Alexandre , Beracochea Martin , Boland Miguel , Burgin Josephine , Cochrane Guy , Crusoe Michael R , Kale Varsha , Potter Simon C , Richardson Lorna J , Sakharova Ekaterina , Scheremetjew Maxim , Korobeynikov Anton , Shlemov Alex , Kunyavskaya Olga , Lapidus Alla , Finn Robert D 
Published: October 2019

Abstract
MGnify (http://www.ebi.ac.uk/metagenomics) provides a free to use platform for the assembly, analysis and archiving of microbiome data derived from sequencing microbial populations that are present in particular environments. Over the past 2 years, MGnify (formerly EBI Metagenomics) has more than doubled the number of publicly available analysed datasets held within the resource. Recently, an updated approach to data analysis has been unveiled (version 5.0), replacing the previous single pipeline with multiple analysis pipelines that are tailored according to the input data, and that are formally described using the Common Workflow Language, enabling greater provenance, reusability, and reproducibility. MGnify's new analysis pipelines offer additional approaches for taxonomic assertions based on ribosomal internal transcribed spacer regions (ITS1/2) and expanded protein functional annotations. Biochemical pathways and systems predictions have also been added for assembled contigs. MGnify's growing focus on the assembly of metagenomic data has also seen the number of datasets it has assembled and analysed increase six-fold. The non-redundant protein database constructed from the proteins encoded by these assemblies now exceeds 1 billion sequences. Meanwhile, a newly developed contig viewer provides fine-grained visualisation of the assembled contigs and their enriched annotations.
79. Mucosal Interferon (IFN) Responses in Infants with Respiratory Syncytial Virus (RSV) Infection to Inform Live Attenuated Vaccine (LAV) Development
Authors: Taveras Jeanette , Garcia-Maurino Cristina , Mertz Sara , Peeples Mark E , Ramilo Octavio , Ramilo Octavio , Mejias Asuncion 
Published: October 2019

Abstract

Background
Respiratory syncytial virus (RSV) is a leading cause of hospitalization for infants. Several vaccine strategies for RSV are being developed. Among those, live attenuated vaccine (LAV) represent an attractive alternative for young children as they mimic natural infection and induce protective immunity without causing enhanced disease. However, markers of reactogenicity and/or innate immune protection in the respiratory mucosa are not well defined. The objective of this study was to assess mucosal markers, including innate immune cytokine profiles and RSV loads (VL), and their potential association with protection from severe disease in infants with natural RSV infection.

Methods
Single-center, prospective study in previously healthy infants with mild (outpatients; OP) and severe (inpatients; IP) RSV infection, and aged-matched healthy controls (HC). Nasopharyngeal (NP) swabs were obtained at enrollment in all subjects to measure VL by PCR, and cytokine concentrations (conc.) using a 13-plex panel that included: Type-I, type-II, and type-III IFN, and inflammatory cytokines. Cytokine conc. and VL were compared according to hospitalization status (OP vs. IP).

Results
From 2014 to 2017 we enrolled 105 infants: 48 with severe RSV infection (IP; median IQR age: 2.3 [1.1–5.5] months), 36 with mild disease (OP; 6.4 [3.8–9.3] months), and 20 HC (4.9 [2.8–7.2] months). The median duration of symptoms at enrollment was 4 days for both IP and OP. IL-1β, TNF-α, and IL-10 were detected more frequently in RSV infants than in HC (39% vs. 5%, respectively), but median conc. in IP and OP were not different (P > 0.05). Detection and/or conc. of IFN-β, IP-10, IFN-γ and type III IFN (IFN-λ1, IFN-λ2/3) were significantly greater in OP vs. IP, who also had higher VL (Table 1). In addition, IP-10 (r = 0.6; P < 0.001) and IFN-λ conc. (r = 0.55, P < 0.0001) significantly correlated with RSV VL.

Conclusion
Infants with mild RSV infection had higher VL and a more robust type-I, -II, and -III IFN responses than those hospitalized with severe disease. These findings suggest that increase conc. of mucosal IFNs are associated with protection against severe RSV infection, and could potentially be used as surrogate markers to help the development of LAV for RSV infection in young children.

Disclosures
Octavio Ramilo, MD, Bill & Melinda Gates Foundation: Research Grant; Janssen: Research Grant; Merck: Advisory Board; NIH: Research Grant; Ohio Children’s Hospital Association (OCHA): Research Grant; Pfizer: Advisory Board, Consultant, Lectures; Sanofi/Medimmune: Advisory Board.