bluuebunny/crossref_metadata_2025 huggingface dataset:
The effects of initial void and dislocation on the onset of plasticity in copper single crystals
Authors: Hu Jianqiao , Ye Xuan , Liu Xiaoming , Chen Zhen
Published: October 2019

Based on molecular dynamics, the effects of void and initial dislocation structure on incipient plasticity are investigated with single crystal copper samples. By introducing a void of different sizes and shapes and dislocations of different initial structures around the void in copper single crystals, we explore their effects on yielding as well as the dominated deformation mechanism. The main findings from this study are as follows: (1) for the samples with a void of the same size, the yield stress approaches to a specific value as the initial dislocation density increases; (2) for samples with a void of varying size, the yield stress becomes independent of the void size as it reaches a certain level, due to the saturation of preexisting dislocations around the void; and (3) as the strain rate increases, the effects of voids and preexisting dislocations on the yield stress become limited due to the response inertia, for which the phase transition from face-centered cubic to an amorphous phase occurs at an extremely high strain rate.
Mitigation of self-focusing in Thomson scattering experiments
Authors: Hansen A. M. , Turnbull D. , Katz J. , Froula D. H.
Published: October 2019

A fundamental challenge associated with measuring Thomson scattering comes from the small scattering cross section associated with the interaction. To improve photon statistics, a powerful Thomson-scattering probe laser is required. Ponderomotive self-focusing limits the maximum power in the Thomson-scattering probe and was shown to limit the maximum achievable Thomson-scattering signal-to-noise ratio. Operating the laser at powers above the self-focusing critical power was shown to cause beam degradation, which reduced the amount of collected Thomson-scattered light. Using a phase plate was shown to improve laser beam propagation and consequently improve the signal-to-noise ratio in the measured spectrum.
The effect of TiCl4 treatment on the performance of dye-sensitized solar cells
Authors: Adhikari Sunita G. , Shamsaldeen Altaf , Andersson Gunther G.
Published: October 2019

Titanium dioxide (TiO2) is used to form the anode in dye sensitized solar cells (DSSCs) and is thus one of the crucial components of this type of solar cell. A large range of treatments of the titania anode before deposition of the dye have been applied to improve the performance of DSSCs among which the TiCl4 treatment is the most frequently used treatment. The present study investigates how the TiCl4 treatment of the TiO2 changes the anode. For this purpose, different sample sets, nontreated, post-treated, and pre-post treated cells, were fabricated and analyzed with electron and ion scattering spectroscopy to investigate how they change the titania surface and consequently influence the cell performance. After the TiCl4 treatment, the short circuit current density (Jsc), open-circuit voltage (Voc), and efficiency significantly improved. An upward shift in the conduction band of the semiconductor as an effect of TiCl4 treatment was measured using inverse photoemission spectroscopy and UV-photoelectron spectroscopy. An increase in dye adsorption due to the treatment was found through neutral impact collision ion scattering spectroscopy measurement. The change in the energy level alignment of the titania and the adsorbed dye and the increase in dye loading explain the threefold increase of power conversion of the cells.
Assessment of fish vulnerability to climate change in the Yellow Sea and Bohai Sea
Authors: Chen Yunlong , Shan Xiujuan , Wang Ning , Jin Xianshi , Guan Lisha , Gorfine Harry , Yang Tao , Dai Fangqun
Published: October 2019

Vulnerability assessments provide a feasible yet infrequently used approach to expanding our understanding and evaluating the effects of climate change on fish assemblages. Here, we first used a fuzzy-logic expert system to quantitatively estimate the vulnerability and potential impact risks of climate change for fish species in the Bohai Sea and Yellow Sea (BSYS). The mean (±s.d.) vulnerability and the impact-risk indices for 25 dominant fish species were 51±22 and 62±12 respectively (with the highest possible value being 100 under the Representative Concentration Pathway 8.5 scenario). Miiuy croaker (Miichthys miiuy) was found to have the highest impact risk, whereas the glowbelly (Acropoma japonicum) had the lowest. Demersal fishes tended to be more vulnerable than pelagic fishes, whereas the opposite was found for impact risks. No significant correlation was found between species biomass and vulnerability (P>0.05). The assessment provided a comprehensive framework for evaluating climate effects in the BSYS and suggested that interspecific and habitat group differences should be considered when developing future climate-adaptive fishery policies and management measures in this region, as well as similar systems elsewhere in the world.
Impoundment led to spatial trophic segregation of three closely related catfish species in the Three Gorges Reservoir, China
Authors: Liao Chuansong , Chen Sibao , Correa Sandra Bibiana , Li Wei , Zhang Tanglin , Liu Jiashou
Published: October 2019

The construction of the Three Gorges Reservoir (TGR), the largest dam in the world, created novel spatial and seasonal fluctuations in food availability along the Yangtze River. We studied changes in diet and niche overlap of three co-occurring catfish species between the upper and lower sections of the TGR and across four hydrological seasons to investigate whether the diets of native catfish species reflect the fluctuations in food availability. Zoobenthos dominated the diets of the three species in the upper section, but shrimp made the bulk of the diet in the lower section. This was the case in every season except during the rising-water season when all three species increased the consumption of allochthonous foods. Diet breadth was significantly broader in the upper section relative to the lower section, and expanded during the rising-water season in the lower section. Niche overlap was significantly lower in the upper section than in the lower section. A non-significant trend of reduced niche overlap during the rising-water season was observed in both sections. Our results suggest that, in less than a decade, dietary plasticity facilitated the adaptation of these species to novel habitats and a shifted food-resource base formed by the impoundment.
Core 1–derived mucin-type O-glycosylation protects against spontaneous gastritis and gastric cancer
Authors: Liu Fei , Fu Jianxin , Bergstrom Kirk , Shan Xindi , McDaniel J. Michael , McGee Samuel , Bai Xia , Chen Weichang , Xia Lijun
Published: October 2019

Core 1–derived mucin-type O-glycans (O-glycans) are a major component of gastric mucus with an unclear role. To address this, we generated mice lacking gastric epithelial O-glycans (GEC C1galt1−/−). GEC C1galt1−/− mice exhibited spontaneous gastritis that progressed to adenocarcinoma with ∼80% penetrance by 1 yr. GEC C1galt1−/− gastric epithelium exhibited defective expression of a major mucus forming O-glycoprotein Muc5AC relative to WT controls, which was associated with impaired gastric acid homeostasis. Inflammation and tumorigenesis in GEC C1galt1−/− stomach were concurrent with activation of caspases 1 and 11 (Casp1/11)–dependent inflammasome. GEC C1galt1−/− mice genetically lacking Casp1/11 had reduced gastritis and gastric cancer progression. Notably, expression of Tn antigen, a truncated form of O-glycan, and CASP1 activation was associated with tumor progression in gastric cancer patients. These results reveal a critical role of O-glycosylation in gastric homeostasis and the protection of the gastric mucosa from Casp1-mediated gastric inflammation and cancer.
Death by microglia
Authors: Kemal Shahrnaz , Vassar Robert
Published: October 2019

The roles of microglia and ApoE in tauopathies, such as Alzheimer’s disease, remain elusive. In this issue, Shi et al. (https://doi.org/10.1084/jem.20190980) demonstrate that microglia-mediated innate immunity collaborates with ApoE to drive neurodegeneration and disease progression in a mouse model of tauopathy.
Synthetic aperture source localization
Authors: Waddington Chad , Cheney Margaret , Given James A
Published: October 2019

Many state-of-the-art methods in source localization require large numbers of sensors and perform poorly or require additional sensors when emitters of interest transmit highly correlated waveforms. We present a new source localization technique which employs a cross correlation measure of the time difference of arrival (TDOA) for signals recorded at two separate platforms, at least one of which is in motion. This data is backprojected through a process of synthetic aperture source localization (SASL) to form an image of the locations of the emitters in a region of interest (ROI) This method has the advantage of not requiring any a priori knowledge of the number of emitters in the scene. Nor does it rest on an ability to identify regions of the data which come from individual emitters, though if this capability is present it may improve image quality. We demonstrate that this method is capable of localizing emitters which transmit highly correlated waveforms, though complications arise when several such emitters are present in the scene. We discuss these complications and strategies to mitigate them.
Contrasting changes of urban heat island intensity during hot weather episodes
Authors: Fenner Daniel , Holtmann Achim , Meier Fred , Langer Ines , Scherer Dieter
Published: October 2019

Cities typically exhibit higher air temperatures than their rural surroundings, a phenomenon known as the urban heat island (UHI) effect. Contrasting results are reported as to whether UHI intensity (UHII) is exacerbated or reduced during hot weather episodes (HWEs). This contrast is investigated for a four-year period from 2015 to 2018, utilising a set of observational data from high-quality meteorological stations, as well as from hundreds of crowdsourced citizen weather stations, located in the urban region of Berlin, Germany. It can be shown that if HWEs, defined here as the ten percent hottest days or nights during May–September, are identified via daytime conditions, or by night-time conditions at inner-city sites, then night-time UHII is exacerbated. However, if HWEs are identified via night-time conditions at rural sites, then night-time UHII is reduced. These differences in UHII change can be linked with prevalent weather conditions, namely radiation, cloud cover, wind speed, precipitation, and humidity. This highlights that, beside land cover changes, future changes in weather conditions due to climate change will control UHIIs, and thus heat-stress hazards in cities.
Stranded asset implications of the Paris Agreement in Latin America and the Caribbean
Authors: Binsted Matthew , Iyer Gokul , Edmonds James , Vogt-Schilb Adrien , Arguello Ricardo , Cadena Angela , Delgado Ricardo , Feijoo Felipe , Lucena André F P , McJeon Haewon , Miralles-Wilhelm Fernando , Sharma Anjali
Published: October 2019

Achieving the Paris Agreement’s near-term goals (nationally determined contributions, or NDCs) and long-term temperature targets could result in pre-mature retirement, or stranding, of carbon-intensive assets before the end of their useful lifetime. We use an integrated assessment model to quantify the implications of the Paris Agreement for stranded assets in Latin America and the Caribbean (LAC), a developing region with the least carbon-intensive power sector in the world. We find that meeting the Paris goals results in stranding of $37–90 billion and investment of $1.9–2.6 trillion worth of power sector capital (2021–2050) across a range of future scenarios. Strengthening the NDCs could reduce stranding costs by 27%–40%. Additionally, while politically shielding power plants from pre-mature retirement or increasing the role of other sectors (e.g. land-use) could also reduce power sector stranding, such actions could make mitigation more expensive and negatively impact society. For example, we find that avoiding stranded assets in the power sector increases food prices 13%, suggesting implications for food security in LAC. Our analysis demonstrates that climate goals are relevant for investment decisions even in developing countries with low emissions.
A pan-South-America assessment of avoided exposure to dangerous extreme precipitation by limiting to 1.5 °C warming
Authors: Li Sihan , Otto Friederike E L , Harrington Luke J , Sparrow Sarah N , Wallom David C H
Published: October 2019

This study investigates the future changes in dangerous extreme precipitation event in South America, using the multi-model ensemble simulations from the HAPPI experiments. The risks of dangerous extreme precipitation events occurrence, and changes in area and population exposure are quantified. Our results show that the likelihood of dangerous extreme precipitation increases in large parts of South America under future warming; changes in extreme precipitation are nonlinear with increasing global mean temperatures; and exposure plays a minor role compared to hazard. In all the models, limiting warming to 1.5 °C as opposed to 2 °C shows a general reduction in both area and population exposure to dangerous extreme precipitation throughout South America. The southeast region of South America exhibited the highest multi-model median percentage of avoided area exposure at 13.3%, while the southwest region shows the lowest percentage at 3.1%. Under all shared socioeconomic pathways, South America Monsoon region and southern South America region yielded the highest multi-model median percentage of avoided population exposure (>10%). The strong spatial heterogeneity in projected changes in all the models highlights the importance of considering location-specific information when designing adaptation measures and investing in disaster preparedness.
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
<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" alttext="normal upper Phi Subscript u Baseline element-of upper I d plus script upper B Superscript n comma alpha comma p Baseline left-parenthesis double-struck upper R Superscript d Baseline comma double-struck upper R Superscript d Baseline right-parenthesis">

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
<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" alttext="upper L Superscript 1 Baseline left-parenthesis upper I comma script upper B Superscript n comma alpha comma p Baseline left-parenthesis double-struck upper R Superscript d Baseline comma double-struck upper R Superscript d Baseline right-parenthesis right-parenthesis">

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
<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" alttext="upper L Superscript 1 Baseline left-parenthesis upper I comma script upper B Superscript n comma beta comma p Baseline left-parenthesis double-struck upper R Superscript d Baseline comma double-struck upper R Superscript d Baseline right-parenthesis right-parenthesis right-arrow upper C left-parenthesis upper I comma script upper B Superscript n comma alpha comma p Baseline left-parenthesis double-struck upper R Superscript d Baseline comma double-struck upper R Superscript d Baseline right-parenthesis right-parenthesis comma u right-arrow normal upper Phi Subscript u Baseline minus upper I d">

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

.
Universal bounds and monotonicity properties of ratios of Hermite and parabolic cylinder functions
Authors: Koch Torben
Published: October 2019

We obtain so far unproved properties of a ratio involving a class of Hermite and parabolic cylinder functions. Those ratios are shown to be strictly decreasing and bounded by universal constants. Differently from the usual analytic approaches, we employ simple purely probabilistic arguments to derive our results. In particular, we exploit the relation between Hermite and parabolic cylinder functions and the eigenfunctions of the infinitesimal generator of the Ornstein-Uhlenbeck process. As a byproduct, we obtain Turán-type inequalities.
Global surfaces of section for dynamically convex Reeb flows on lens spaces
Authors: Schneider A.
Published: October 2019

We show that a dynamically convex Reeb flow on the standard tight lens space

(
L
(
p
,
1
)
,

ξ

s
t
d

)

(L(p, 1),\xi _\mathrm {std})

,

p
>
1
,

p>1,

admits a

p
p

-unknotted closed Reeb orbit

P
P

which is the binding of a rational open book decomposition with disk-like pages. Each page is a rational global surface of section for the Reeb flow and the Conley-Zehnder index of the

p
p

th iterate of

P
P

is

3
3

. We also check dynamical convexity in the Hénon-Heiles system for low positive energies. In this case the rational open book decomposition follows from the fact that the sphere-like component of the energy surface admits a

Z

3

\mathbb {Z}_3

-symmetric periodic orbit and the flow descends to a Reeb flow on the standard tight

(
L
(
3
,
2
)
,

ξ

s
t
d

)

(L(3,2),\xi _\mathrm {std})

.
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

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

Background and Aims

The 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].

Methods

Resident 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.

Results

Systemically, 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.

Conclusions

A 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

Ornamental 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

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

A 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

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

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

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

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

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

The 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

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

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.
80. Opioid Analgesics Are Associated with Increased Clostridioides difficile Infection Risk in a National Cohort of Veterans
Authors: Young Eric H , Lalani Falak S , Reveles Kelly R
Published: October 2019

Background

Clostridioides difficile infection (CDI) is the leading cause of healthcare-associated diarrhea. Several drugs are known to increase CDI risk, although the association between opioids and CDI risk has not been clearly established. Opioid analgesics have gastrointestinal antimotility and immunomodulatory effects, which may predispose patients to infection. The purpose of this study was to determine the association between opioid use and CDI risk.

Methods

This was a retrospective case–control study that utilized inpatient and outpatient data from the national United States Veterans Health Administration (VHA). CDI patients included those age 18 to 89 years with an ICD-9-CM code for CDI (008.45), a positive stool test, and active CDI therapy between October 1, 2002 and September 30, 2014. A control cohort of VHA patients was created by randomly sampling patients without a CDI ICD-9-CM code during the study period and matched to CDI patients by visit setting and fiscal year. Opioid use was defined as at least one prescription for morphine, hydromorphone, hydrocodone, and/or codeine in the 90 days prior to study inclusion. The χ 2 test was used to compare the proportion of patients who received an opioid in the CDI and control groups. Opioid risk factors for CDI were analyzed using a multivariable logistic regression model that included 33 covariates.

Results

A total of 85,451 patients were included in this study (26,149 CDI patients and 59,302 controls). Overall, 50.1% and 30.1% of patients were prescribed an opioid in the CDI and cohort group, respectively. Overall, opioids were associated with significantly increased CDI risk (OR 1.92, 95% CI 1.86–2.00) and was even greater for >1 opioid (OR 2.40; 95% CI 2.25–2.55). Opioids with the strongest association with CDI risk include morphine (OR 2.04, 95% CI 1.95–2.13), followed by hydromorphone (OR 1.74, 95% CI 1.63–1.87), codeine (OR 1.56, 95% CI 1.44–1.70), and hydrocodone (OR 1.14; 95% CI 1.09–1.19).

Conclusion

In a national cohort of veterans, patients with recent opioid analgesic use had an increased risk of developing CDI compared with a control group. Opioid analgesics with greater immunomodulatory and constipating effects were associated with increased risk compared with other opioids.

Disclosures

All Authors: No reported Disclosures.
85. Use of Dual Statistical Process Control Charts for Early Detection of Surgical Site Infection Outbreaks at a Community Hospital Network
Authors: Baker Arthur W , Nehls Nicole , Ilieş Iulian , Benneyan James C , Anderson Deverick J
Published: October 2019

Background

We recently showed that the empirical use of a combination of 2 moving average (MA) statistical process control (SPC) charts was highly sensitive and specific for detecting potentially important increases in surgical site infection (SSI) rates. We performed this follow-up study to examine the performance of these same SPC charts when applied to known SSI outbreaks.

Methods

We retrospectively applied 2 MA SPC charts to all 30 SSI outbreaks investigated from 2007 to 2015 in a network of over 50 community hospitals. These outbreaks were detected via routine SSI surveillance activities that occurred in the network. We reviewed prior outbreak investigation documentation to determine the estimated time of outbreak onset and time of traditional surveillance outbreak detection. The first SPC chart utilized procedure-specific, composite SSI data from the hospital network for its baseline; the baseline for the second chart was calculated from SSI data from the outbreak hospital undergoing analysis. Both charts used rolling baseline windows but varied in baseline window size, rolling baseline lag, and MA window size. SPC chart outbreak detection occurred when either chart had a data point above the upper control limit of 1 standard deviation. Time of SPC detection was compared with both time of outbreak onset and time of traditional surveillance detection.

Results

With the dual chart approach, SPC detected all 30 outbreaks, including detection of 25 outbreaks (83%) prior to their estimated onset (Figure 1). SPC detection occurred a median of 16 months (interquartile range, 12–21 months) prior to the date of traditional outbreak detection, which never occurred prior to outbreak onset. Both individual SPC charts exhibited at least 90% sensitivity in outbreak detection, but the dual chart approach showed superior sensitivity and speed of detection (Figure 2).

Conclusion

A strategy that employed optimized, dual MA SPC charts retrospectively detected all SSI outbreaks that occurred over 9 years in a network of community hospitals. SPC outbreak detection occurred earlier than traditional surveillance detection. These optimized SPC charts merit prospective study to evaluate their ability to promote early detection of SSI clusters in real-world scenarios.

Disclosures

All Authors: No reported Disclosures.
86. Ventilator-Associated Pneumonia in Trauma Intensive Care Unit, a Dilemma in Quality Metrics
Authors: Karnatak Rajendra , Schlitzkus Lisa , Hinkle Lauren , Lyden Elizabeth , Cawcutt Kelly , Cawcutt Kelly
Published: October 2019

Background

Ventilator-associated pneumonia (VAP) definition remains controversial. Ventilator-associated event (VAE) and probable/possible VAPs are reported to the National Healthcare Network (NHSN). In trauma patients, VAPs are also reported to the Trauma Quality Improvement Project (TQIP) utilizing the National Trauma Data Bank (NTDB)’s definition.

Methods

We reviewed all VAPs reported to NHSN and TQIP in trauma patients at the University of Nebraska Medical Center between January 1, 2015 and June 30, 2018. The primary objective was to determine the discordance rates between NHSN and NTDB definitions. VAPs identified by both NHSN+NTDB considered concordant; if identified by only one definition, considered discordant. Secondary objectives were mortality, intensive care unit (ICU) length of stay (LOS), and ventilator (vent) days. Fisher’s exact test and the Kruskal–Wallis test were used where appropriate; P < 0.05 = statistical significance.

Results

In total, 998 patients had 5,624 days of vent support during the study period. One hundred and one patients were diagnosed with VAP. The median age was 43 years (range 2–92), median vent days were 14 days (range 3–128), and median ICU LOS was 16 days (range 6–47). Of the 101 patients, 28 (27%) met VAP definition by NHSN and 88 (87%) by NTDB. Of the 101 patients, 15 (15%) were concordant and 85 (85%) were discordant. Cumulative all-cause mortality was 23/101 (23%). Composite analysis showed mortality 5/15 (33%) in concordant group, 3/13 (23%) in NHSN group, and 15/73 (20%) in NTDB group (P = 0.52). Median vent days between concordant, NHSN, and NTDB groups were 14 days, 16 days, and 14 days, respectively (P = 0.71). Median ICU LOS was 17 days in concordant, 21 days in NHSN, and 14 days in NTDB group (P = 0.094). Similarly, comparison of NHSN VAE with NTDB VAP definition showed 67/101 (66%) were discordant. There was no statistically significant difference in mortality between concordant (NHSN VAE+NDTB VAP) 9/34 (26%), NHSN VAE 3/13 (23%), and NTDB VAP 11/54 (20%) (P = 0.84).

Conclusion

Our study showed very high discordant (85%) reporting of VAP to different agencies. No difference in mortality, ICU LOS, and vent days was noted. The high discordance of reported VAPs results in inconsistency in quality metrics and hinders initiatives to decrease VAPs depending on which definition is followed. Improved standardization is needed.

Disclosures

All Authors: No reported Disclosures.