bluuebunny/crossref_metadata_2025 huggingface dataset:
Modeling of aluminum erosion by neutral particles in dedicated EAST experiments using the 3D-GAPS code
Authors: Shi X.Z. , Ding R. , Matveev D. , Mu L. , Liu N.X. , Xie H. , Xu G.L. , Chen J.L.
Published: March 2023

To evaluate the erosion effects of charge exchange (CX) neutrals on first wall materials, aluminum (Al) coated samples installed in a cylindrical sleeve were exposed to EAST plasmas with the Material and Plasma Evaluation System (MAPES). The 3D-GAPS code was firstly used to simulate the dedicated experiments with the neutral energy spectrums measured by the Low Energy Neutral Particle Analyzer located at the MAPES. The modeled Al erosion rates with isotropic angular distributions for incident D neutrals are consistent with the measured erosion thicknesses of Al layer by Rutherford backscattering spectrometry before and after the plasma exposure. The effects of neutral reflection coefficients and the heights of cylindrical sleeve on material erosion are also studied. The measured material erosion rate by CX neutrals in EAST verified by the modeling can help to us understand the effects of neutrals on first wall erosion, which is an important erosion process in future fusion reactors.
Specifications and pre-production of n+-in-p large-format strip sensors fabricated in 6-inch silicon wafers, ATLAS18, for the Inner Tracker of the ATLAS Detector for High-Luminosity Large Hadron Collider
Authors: Unno Y. , Abidi H. , Affolder A. , Affolder K. , Allport P.P. , Beaupre S. , Beck G.A. , Bernabeu J. , Bevan A.J. , Chisholm A. , Ciungu B. , Dawson I. , Dowling A. , Fadeyev V. , Federicova P. , Fernandez-Tejero J. , Fleta C. , Fournier A. , George W. , Gignac M. , Gonella L. , Greig G. , Gunnell J. , Hara K. , Hirose S. , Hommels B. , Ishii T. , Jessiman C. , Johnson J. , Jones D. , Kachiguin S. , Kang N. , Keller J. , Klein C. , Koffas T. , Kopsalis I. , Kroll J. , Kvasnicka J. , Lacasta C. , Latonova V. , Lomas J. , Martinez-Mckinney F. , Mikestikova M. , Miyagawa P.S. , Orr R.S. , Poley L. , Rousso D. , Shah A. , Solaz C. , Soldevila U. , Staats E. , Stack T.L. , Stelzer B. , Ullan M. , Yarwick J. , Zenz S.C.
Published: March 2023

The ATLAS experiment is constructing new all-silicon inner
tracking system for HL-LHC. The strip detectors cover the radial
extent of 40 to 100 cm. A new approach is adopted to use p-type
silicon material, making the readout in n+-strips, so-called
n+-in-p sensors. This allows for enhanced radiation tolerance
against an order of magnitude higher particle fluence compared to
the LHC. To cope with varying hit rates and occupancies as a
function of radial distance, there are two barrel sensor types, the
short strips (SS) for the inner 2 and the long strips (LS) for the
outer 2 barrel cylinders, respectively. The barrel sensors exhibit a
square, 9.8 × 9.8 cm2, geometry, the largest possible
sensor area from a 6-inch wafer. The strips are laid out in
parallel with a strip pitch of 75.5 μm and 4 or 2 rows of
strip segments. The strips are AC-coupled and biased via
polysilicon resistors. The endcap sensors employ a
“stereo-annulus” geometry exhibiting a skewed-trapezoid shapes
with circular edges. They are designed in 6 unique shapes, R0 to R5,
corresponding to progressively increasing radial extents and which
allows them to fit within the petal geometry and the 6-inch wafer
maximally. The strips are in fan-out geometry with an in-built
rotation angle, with a mean pitch of approximately 75 μm and
4 or 2 rows of strip segments. The eight sensor types are labeled
as ATLAS18xx where xx stands for SS, LS, and R0 to R5. According to
the mechanical and electrical specifications, CAD files for wafer
processing were laid out, following the successful designs of
prototype barrel and endcap sensors, together with a number of
optimizations. A pre-production was carried out prior to the full
production of the wafers. The quality of the sensors is reviewed
and judged excellent through the test results carried out by vendor.
These sensors are used for establishing acceptance procedures and to
evaluate their performance in the ATLAS collaboration, and
subsequently for pre-production of strip modules and stave and petal
structures.
Can future cities grow a carbon storage equal to forests?
Authors: Talvitie Ilmari , Kinnunen Antti , Amiri Ali , Junnila Seppo
Published: March 2023

Urban areas have experienced exponential growth since the industrial revolution and by virtue, the urban population has followed. Current projections suggest that this growth has yet to reach its peak implying that urban developments will continue to sprawl into untouched territories. This growth and subsequent sprawl will undoubtedly come at the expense of forested areas. This study presents a carbon storage factor indicator for new urban developments. It is a novel concept which integrates urban planning, land use changes and wooden construction. The factor sets a carbon storage requirement for new urban areas that are developed at the expense of forested areas. The study is conducted in four parts. First, we estimate the carbon storage potential of forest areas via existing literature and databases. Then we collect all new development and construction estimates up to the year 2050 for the whole metropolitan region in Finland. Next, we conduct scenario analyzes for different demand levels of wood in projected residential developments. Finally, we compare the carbon storage potential of the future building stock to the forest areas planned for development. The data used is provided by the regional authority. The results detail that the future residential building stock can store between 128–733 kt of carbon. The lower level implies that current construction methods can only partially preserve the carbon storage of an area in buildings. However, the higher level suggests future buildings to be able to exceed the carbon storage potential of forest areas by nearly 47 tC ha−1. The study reminds that an increased use of wood is dependent on sustainable forest management practices. Furthermore, it is not our purpose to promote urban development into entirely new areas but rather encourage urban planners to consider the carbon balance when it is the only viable option.
Coupling to multi-mode waveguides with space-time shaped free-space pulses
Authors: Jolly Spencer W , Kockaert Pascal
Published: March 2023

Guided wave optics, including most prominently fiber optics and integrated photonics, very often considers only one or very few spatial modes of the waveguides. Despite being known and utilized for decades, multi-mode guided wave optics is currently rapidly increasing in sophistication in parallel with technological improvements and advancing simulation tools. The physics of multi-mode interactions are usually driven by some initial energy distribution in a number of spatial modes. In this work we introduce how, with free-space input beams having space-time couplings, the different modes can be excited with different complex frequency or time profiles. We cover fundamentals, the coupling with a few simple space-time aberrations, different waveguides, and a number of technical nuances. This concept of space-time initial conditions in multi-mode waveguides will provide yet another tool to study the rich nonlinear interactions in such systems.
Atomic-scale engineering of advanced catalytic and energy materials via atomic layer deposition for eco-friendly vehicles
Authors: Liu Xiao , Su Yu , Chen Rong
Published: March 2023

Highlights

Recent process of atomic layer deposition on catalytic and energy materials is summarized.

The enhanced catalytic and electrochemical performances are presented.

Atomic layer deposition reactors for mass production are highlighted.

The challenges on future applications of atomic layer deposition are discussed.
From neuromorphic to neurohybrid: transition from the emulation to the integration of neuronal networks
Authors: Bruno Ugo , Mariano Anna , Rana Daniela , Gemmeke Tobias , Musall Simon , Santoro Francesca
Published: March 2023

The computation of the brain relies on the highly efficient communication among billions of neurons. Such efficiency derives from the brain’s plastic and reconfigurable nature, enabling complex computations and maintenance of vital functions with a remarkably low power consumption of only ∼20 W. First efforts to leverage brain-inspired computational principles have led to the introduction of artificial neural networks that revolutionized information processing and daily life. The relentless pursuit of the definitive computing platform is now pushing researchers towards investigation of novel solutions to emulate specific brain features (such as synaptic plasticity) to allow local and energy efficient computations. The development of such devices may also be pivotal in addressing major challenges of a continuously aging world, including the treatment of neurodegenerative diseases. To date, the neuroelectronics field has been instrumental in deepening the understanding of how neurons communicate, owing to the rapid development of silicon-based platforms for neural recordings and stimulation. However, this approach still does not allow for in loco processing of biological signals. In fact, despite the success of silicon-based devices in electronic applications, they are ill-suited for directly interfacing with biological tissue. A cornucopia of solutions has therefore been proposed in the last years to obtain neuromorphic materials to create effective biointerfaces and enable reliable bidirectional communication with neurons. Organic conductive materials in particular are not only highly biocompatible and able to electrochemically transduce biological signals, but also promise to include neuromorphic features, such as neuro-transmitter mediated plasticity and learning capabilities. Furthermore, organic electronics, relying on mixed electronic/ionic conduction mechanism, can be efficiently coupled with biological neural networks, while still successfully communicating with silicon-based electronics. Here, we envision neurohybrid systems that integrate silicon-based and organic electronics-based neuromorphic technologies to create active artificial interfaces with biological tissues. We believe that this approach may pave the way towards the development of a functional bidirectional communication between biological and artificial ‘brains’, offering new potential therapeutic applications and allowing for novel approaches in prosthetics.
Thermal acclimation of plant photosynthesis and autotrophic respiration in a northern peatland
Authors: Ma Shuang , Jiang Lifen , Wilson Rachel M , Chanton Jeff , Niu Shuli , Iversen Colleen M , Malhotra Avni , Jiang Jiang , Huang Yuanyuan , Lu Xingjie , Shi Zheng , Tao Feng , Liang Junyi , Ricciuto Daniel , Hanson Paul J , Luo Yiqi
Published: March 2023

Peatlands contain one-third of global soil carbon (C), but the responses of peatland ecosystems to long-term warming are not well understood. Here, we pursue an emergent understanding of warming effects on ecosystem C fluxes at peatlands by constraining a process-oriented model, the terrestrial ECOsystem model, with observational data from a long-term warming experiment at the Spruce and Peatland Responses Under Changing Environments site. Model-based assessments show that ecosystem-level photosynthesis and autotrophic respiration exhibited significant thermal acclimation, with temperature sensitivities being linearly decreased with warming. Using the thermal-acclimated parameter values, simulated gross primary production, net primary production, and plant autotrophic respiration (R
a), were all lower than those simulated with non-thermal acclimated parameter values. In contrast, ecosystem respiration simulated with thermal acclimated parameter values was higher than that simulated with non-thermal acclimated parameter values. Net ecosystem CO2 exchange was much higher after constraining model parameters with observational data from the warming treatments, releasing C at a rate of 28.3 g C m−2 yr−1 °C−1. Our data-model integration study suggests that peatlands are likely to release more C than previously estimated. Earth system models may overestimate C uptake by peatlands under warming if physiological thermal acclimation of plants is not incorporated. Thus, it is critical to consider the long-term physiological thermal acclimation of plants in the models to better predict global C dynamics under future climate and their feedback to climate change.
Wildfires and the COVID-19 pandemic: a systematized literature review of converging health crises
Authors: Clark Kathleen A , Sheehan Mary
Published: March 2023

The emergence and global spread of the COVID-19 pandemic in 2020 converged with wildfire seasons of unprecedented extent. These co-occurring crises brought the potential for amplified health impacts. A systematized literature review was conducted to identify the health impacts from co-exposure to wildfires and the COVID-19 pandemic. A search of PubMed and Scopus identified 373 distinct references which were screened according to predetermined criteria. A total of 22 peer-reviewed publications were included in the final analysis. Studies were located in Australia and the western United States, with a single study in the Amazonian region of Brazil. The studies identified focused primarily on the impact of wildfire smoke exposure on COVID-19 infection and mortality, and the impact of exposure to both crises on mental health. The collective evidence shows that wildfire exposure within the context of the pandemic exacerbated COVID-19 infection and mortality as well as various adverse mental health effects. Additional research is needed in more diverse contexts and with individual-level data. Findings highlight the need for public health preparedness to anticipate overlapping, related crises and to advance climate change mitigation to protect public health.
Remarks on the anisotropic Calderón problem
Authors: Cârstea Cătălin , Feizmohammadi Ali , Oksanen Lauri
Published: March 2023

We show uniqueness results for the anisotropic Calderón problem stated on transversally anisotropic manifolds. Moreover, we give a convexity result for the range of Dirichlet-to-Neumann maps on Riemannian manifolds near the zero potential. Finally, we present results for Calderón type inverse problems associated to semilinear elliptic equations on Riemannian manifolds.
A smooth variational principle on Wasserstein space
Authors: Bayraktar Erhan , Ekren Ibrahim , Zhang Xin
Published: March 2023

In this note, we provide a smooth variational principle on Wasserstein space by constructing a smooth gauge-type function using the sliced Wasserstein distance. This function is a crucial tool for optimization problems and in viscosity theory of PDEs on Wasserstein space.
Three dimensions of metric-measure spaces, Sobolev embeddings and optimal sign transport
Authors: Nikolski N.
Published: March 2023

A sign interlacing phenomenon for Bessel sequences, frames, and Riesz bases(uk)(u_{k})inL2L^2spaces over the spaces of homogeneous typeΩ=(Ω,ρ,μ)\Omega =(\Omega ,\rho ,\mu )satisfying the doubling/halving conditions is studied. Under some relations among three basic metric-measure parameters ofΩ\Omega, asymptotics is obtained for the mass moving norms‖uk‖KR\|u_k\|_{KR}in the sense of Kantorovich–Rubinstein, as well as for the singular numbers of the Lipschitz and Hajlasz–Sobolev embeddings. The main observation shows that, quantitatively, the rate of convergence‖uk‖KR→0\|u_k\|_{KR}\to 0mostly depends on the Bernstein–Kolmogorovnn-widths of a certain compact set of Lipschitz functions, and the widths themselves mostly depend on the interplay between geometric doubling and measure doubling/halving numerical parameters. The “more homogeneous” is the space, the sharper are the results.
Gromov-Witten invariants of 𝑆𝑦𝑚^{𝑑}ℙ^{𝕣}
Authors: Silversmith Rob
Published: March 2023

We give a graph-sum algorithm that expresses any genus-

g
g

Gromov-Witten invariant of the symmetric product orbifold

Sym
d

⁡

P

r

≔

\operatorname {Sym}^d\mathbb {P}^r≔

[
(

P

r

)
d

/

S
d

]

[(\mathbb {P}^r)^d/S_d]

in terms of “Hurwitz-Hodge integrals” – integrals over (compactified) Hurwitz spaces. We apply the algorithm to prove a mirror-type theorem for

Sym
d

⁡

P

r

\operatorname {Sym}^d\mathbb {P}^r

in genus zero. The theorem states that a generating function of Gromov-Witten invariants of

Sym
d

⁡

P

r

\operatorname {Sym}^d\mathbb {P}^r

is equal to an explicit power series

I

Sym
d

⁡

P

r

I_{\operatorname {Sym}^d\mathbb {P}^r}

, conditional upon a conjectural combinatorial identity. This is a first step in the direction of proving Ruan’s Crepant Resolution Conjecture for the resolution

H
i
l

b

(
d
)

(

P

2

)

Hilb^{(d)}(\mathbb {P}^2)

of the coarse moduli space of

Sym
d

⁡

P

2

.

\operatorname {Sym}^d\mathbb {P}^2.
Simple closed curves in stable covers of surfaces
Authors: Salter Nick
Published: March 2023

Let

f
:
X
→
Y

f: X \to Y

be a regular covering of a surface

Y
Y

of finite type with nonempty boundary, with finitely-generated (possibly infinite) deck group

G
G

. We give necessary and sufficient conditions for an integral homology class on

X
X

to admit a representative as a connected component of the preimage of a nonseparating simple closed curve on

Y
Y

, possibly after passing to a “stabilization”, i.e. a

G
G

-equivariant embedding of covering spaces

X
↪

X
+

X \hookrightarrow X^+

.
AGPs as molecular determinants of reproductive development
Authors: Lopes Ana Lúcia , Moreira Diana , Pereira Ana Marta , Ferraz Ricardo , Mendes Sara , Pereira Luís Gustavo , Colombo Lucia , Coimbra Sílvia
Published: March 2023

Background and Aims

Morphogenesis occurs through accurate interaction between essential players to generate highly specialized plant organs. Fruit structure and function are triggered by a neat transcriptional control involving distinct regulator genes encoding transcription factors (TFs) or signalling proteins, such as the C2H2/C2HC zinc-finger NO TRANSMITTING TRACT (NTT) or the MADS-box protein SEEDSTICK (STK), which are important in setting plant reproductive competence, feasibly by affecting cell wall polysaccharide and lipid distribution. Arabinogalactan proteins (AGPs) are major components of the cell wall and are thought to be involved in the reproductive process as important players in specific stages of development. The detection of AGPs epitopes in reproductive tissues of NTT and other fruit development-related TFs, such as MADS-box proteins including SHATTERPROOF1 (SHP1), SHP2 and STK, was the focus of this study.

Methods

We used fluorescence microscopy to perform immunolocalization analyses on stk and ntt single mutants, on the ntt stk double mutant and on the stk shp1 shp2 triple mutant using specific anti-AGP monoclonal antibodies. In these mutants, the expression levels of selected AGP genes were also measured by quantitative real-time PCR and compared with the respective expression in wild-type (WT) plants.

Key Results

The present immunolocalization study collects information on the distribution patterns of specific AGPs in Arabidopsis female reproductive tissues, complemented by the quantification of AGP expression levels, comparing WT, stk and ntt single mutants, the ntt stk double mutant and the stk shp1 shp2 triple mutant.

Conclusions

These findings reveal distinct AGP distribution patterns in different developmental mutants related to the female reproductive unit in Arabidopsis. The value of the immunofluorescence labelling technique is highlighted in this study as an invaluable tool to dissect the remodelling nature of the cell wall in developmental processes.
Breast Augmentation in the Digital Era: The Power of Social Media in a Surgeon's New Practice
Authors: Montemurro Paolo , Savani Luca , Toninello Paolo
Published: March 2023

Background

Opening a new practice is always challenging, and one of the main problems is how to engage patients. Most of them use social media to gather information about surgery and surgeons.

Objectives

The aim was to evaluate social media's impact on a new practice, compared with a long-standing practice run by the same surgeon. Furthermore, changes in patients’ and surgeons’ perspectives regarding social media in recent years were studied.

Methods

In the 2 aforementioned practices, a questionnaire was administered to patients seen in consultation for primary breast augmentation regarding their interaction with social media before booking the visit. Another questionnaire was administered to 152 surgeons to assess their perceptions of social media.

Results

Two hundred forty-seven patients in Italy and 129 in Sweden answered the questionnaire. In the first year of the Italian practice, 97.2% of patients booked a consultation with the surgeon thanks to social media; after 3 years, the percentage dropped to 68.02%. Comparing Italian and Swedish patients, 68.02% vs 28.68%, respectively, booked a consultation with the surgeon specifically thanks to social media, 91.09% vs 79.84% did research about the surgeon before booking a consultation, and 36.03% vs 10.08% contacted the surgeon before booking an appointment. One hundred fifty-two surgeons from 24 different countries answered the questionnaire, and 77.9% opined that social media positively affected their practice.

Conclusions

Social media is fundamental in patient-surgeon interaction and can strongly influence patient inflow, especially at the beginning of a new practice. Surgeons should be capable of using these tools to engage patients, bearing in mind the important role of these media in patients’ education.
easyPheno: An easy-to-use and easy-to-extendPythonframework for phenotype prediction using Bayesian optimization
Authors: Haselbeck Florian , John Maura , Grimm Dominik G
Published: March 2023

Predicting complex traits from genotypic information is a major challenge in various biological domains. With easyPheno, we present a comprehensive Python framework enabling the rigorous training, comparison and analysis of phenotype predictions for a variety of different models, ranging from common genomic selection approaches over classical machine learning and modern deep learning-based techniques. Our framework is easy-to-use, also for non-programming-experts, and includes an automatic hyperparameter search using state-of-the-art Bayesian optimization. Moreover, easyPheno provides various benefits for bioinformaticians developing new prediction models. easyPheno enables to quickly integrate novel models and functionalities in a reliable framework and to benchmark against various integrated prediction models in a comparable setup. In addition, the framework allows the assessment of newly developed prediction models under pre-defined settings using simulated data. We provide a detailed documentation with various hands-on tutorials and videos explaining the usage of easyPheno to novice users.

Availability and implementation

easyPheno is publicly available at https://github.com/grimmlab/easyPheno and can be easily installed as Python package via https://pypi.org/project/easypheno/ or using Docker. A comprehensive documentation including various tutorials complemented with videos can be found at https://easypheno.readthedocs.io/.

Supplementary information

Supplementary data are available at Bioinformatics Advances online.
Identification of a gene expression signature associated with breast cancer survival and risk that improves clinical genomic platforms
Authors: Bueno-Fortes Santiago , Berral-Gonzalez Alberto , Sánchez-Santos José Manuel , Martin-Merino Manuel , De Las Rivas Javier
Published: March 2023

Motivation

Modern genomic technologies allow us to perform genome-wide analysis to find gene markers associated with the risk and survival in cancer patients. Accurate risk prediction and patient stratification based on robust gene signatures is a key path forward in personalized treatment and precision medicine. Several authors have proposed the identification of gene signatures to assign risk in patients with breast cancer (BRCA), and some of these signatures have been implemented within commercial platforms in the clinic, such as Oncotype and Prosigna. However, these platforms are black boxes in which the influence of selected genes as survival markers is unclear and where the risk scores provided cannot be clearly related to the standard clinicopathological tumor markers obtained by immunohistochemistry (IHC), which guide clinical and therapeutic decisions in breast cancer.

Results

Here, we present a framework to discover a robust list of gene expression markers associated with survival that can be biologically interpreted in terms of the three main biomolecular factors (IHC clinical markers: ER, PR and HER2) that define clinical outcome in BRCA. To test and ensure the reproducibility of the results, we compiled and analyzed two independent datasets with a large number of tumor samples (1024 and 879) that include full genome-wide expression profiles and survival data. Using these two cohorts, we obtained a robust subset of gene survival markers that correlate well with the major IHC clinical markers used in breast cancer. The geneset of survival markers that we identify (which includes 34 genes) significantly improves the risk prediction provided by the genesets included in the commercial platforms: Oncotype (16 genes) and Prosigna (50 genes, i.e. PAM50). Furthermore, some of the genes identified have recently been proposed in the literature as new prognostic markers and may deserve more attention in current clinical trials to improve breast cancer risk prediction.

Availability and implementation

All data integrated and analyzed in this research will be available on GitHub (https://github.com/jdelasrivas-lab/breastcancersurvsign), including the R scripts and protocols used for the analyses.

Supplementary information

Supplementary data are available at Bioinformatics Advances online.
TB-ML—a framework for comparing machine learning approaches to predict drug resistance ofMycobacterium tuberculosis
Authors: Libiseller-Egger Julian , Wang Linfeng , Deelder Wouter , Campino Susana , Clark Taane G , Phelan Jody E
Published: March 2023

Motivation

Machine learning (ML) has shown impressive performance in predicting antimicrobial resistance (AMR) from sequence data, including for Mycobacterium tuberculosis, the causative agent of tuberculosis. However, current ML development and publication practices make it difficult for researchers and clinicians to use, test or reproduce published models.

Results

We packaged a number of published and unpublished ML models for predicting AMR of M.tuberculosis into Docker containers. Similarly, the pipelines required for pre-processing genomic data into the formats required by the models were also packaged into separate containers. By following a minimal container I/O standard, we ensured as much interoperability as possible. We also created a command-line application, TB-ML, which can be used to easily combine pre-processing and prediction containers into complete pipelines ready for predicting resistance from novel, raw data with a single command. As long as there is adherence to this minimal standard for the container interface, containers produced by researchers holding new models can likewise be included in these pipelines, making benchmark comparisons of different models simple and facilitating faster uptake in the clinic.

Availability and implementation

TB-ML contains a simple Docker API written in Python and is available at https://github.com/jodyphelan/tb-ml. Example Docker containers for resistance prediction and corresponding data pre-processing as well as a tutorial on how to create new containers for TB-ML are available at https://tb-ml.github.io/tb-ml-containers/.

Contact

jody.phelan@lshtm.ac.uk
A high-performance deep-learning-based pipeline for whole-brain vasculature segmentation at the capillary resolution
Authors: Li Yuxin , Liu Xuhua , Jia Xueyan , Jiang Tao , Wu Jianghao , Zhang Qianlong , Li Junhuai , Li Xiangning , Li Anan
Published: March 2023

Motivation

Reconstructing and analyzing all blood vessels throughout the brain is significant for understanding brain function, revealing the mechanisms of brain disease, and mapping the whole-brain vascular atlas. Vessel segmentation is a fundamental step in reconstruction and analysis. The whole-brain optical microscopic imaging method enables the acquisition of whole-brain vessel images at the capillary resolution. Due to the massive amount of data and the complex vascular features generated by high-resolution whole-brain imaging, achieving rapid and accurate segmentation of whole-brain vasculature becomes a challenge.

Results

We introduce HP-VSP, a high-performance vessel segmentation pipeline based on deep learning. The pipeline consists of three processes: data blocking, block prediction, and block fusion. We used parallel computing to parallelize this pipeline to improve the efficiency of whole-brain vessel segmentation. We also designed a lightweight deep neural network based on multi-resolution vessel feature extraction to segment vessels at different scales throughout the brain accurately. We validated our approach on whole-brain vascular data from three transgenic mice collected by HD-fMOST. The results show that our proposed segmentation network achieves the state-of-the-art level under various evaluation metrics. In contrast, the parameters of the network are only 1% of those of similar networks. The established segmentation pipeline could be used on various computing platforms and complete the whole-brain vessel segmentation in 3 h. We also demonstrated that our pipeline could be applied to the vascular analysis.

Availability and implementation

The dataset is available at http://atlas.brainsmatics.org/a/li2301. The source code is freely available at https://github.com/visionlyx/HP-VSP.
The transcriptomic response of bovine uterine tissue is altered in response to sperm from high- and low-fertility bulls
Authors: Donnellan Eimear M , Cormican Paul , Reid Colm , Duggan Gina , Stiavnicka Miriama , Meade Kieran G , Fair Sean
Published: March 2023

Despite stringent quality control checks, some bulls with apparently normal semen quality yield lower than expected pregnancy rates. This study profiled the transcriptome and performed histological analysis of the bovine uterus in response to sperm from high-fertility (HF) and low-fertility (LF) bulls. Postmortem uterine biopsies and uterine explants were collected from heifers 12 h after a fixed time artificial insemination (AI) to a synchronized estrus with frozen–thawed semen from five HF (fertility rate 4.01% ± 0.25) and five LF (fertility rate − 11.29% ± 1.11; mean ± SEM) bulls. Uterine biopsies were also collected from control (CTRL) heifers, which were not inseminated. RNA-sequencing and histological analysis were performed for differential gene expression and neutrophil quantification. In the HF treatment relative to CTRL heifers, there were 376 genes significantly differentially expressed in the endometrium with just one gene differentially expressed in the LF treatment relative to CTRL heifers. Comparing the HF and LF treatments directly, there were 40 significantly differentially expressed genes (P < 0.05). Transcriptomic analysis shows a predominant role for the inflammatory marker Interleukin-1 alpha, which was further confirmed by immunohistochemistry. Quantification of neutrophils in the endometrium showed a significant effect of sperm; however, there was no difference in neutrophil numbers between HF and LF groups. In conclusion, this novel study clearly shows a distinct inflammatory response to sperm in the endometrium and a divergent transcriptomic response to semen from HF and LF bulls.
Modeling Respiratory Syncytial Virus Adult Vaccination in the United States With a Dynamic Transmission Model
Authors: Van Effelterre T , Hens N , White L J , Gravenstein S , Bastian A R , Buyukkaramikli N , Cheng C Y , Hartnett J , Krishnarajah G , Weber K , Pastor L Hernandez
Published: March 2023

Background

Respiratory syncytial virus (RSV) is shown to cause substantial morbidity, hospitalization, and mortality in infants and older adults. Population-level modeling of RSV allows to estimate the full burden of disease and the potential epidemiological impact of novel prophylactics.

Methods

We modeled the RSV epidemiology in the United States across all ages using a deterministic compartmental transmission model. Population-level symptomatic RSV acute respiratory tract infection (ARI) cases were projected across different natural history scenarios with and without vaccination of adults aged ≥60 years. The impact of vaccine efficacy against ARIs, infectiousness and vaccine coverage on ARI incidence were assessed. The impact on medical attendance, hospitalization, complications, death, and other outcomes was also derived.

Results

Without a vaccine, we project 17.5–22.6 million symptomatic RSV ARI cases annually in adults aged ≥18 years in the US, with 3.6–4.8 million/year occurring in adults aged ≥60 years. Modeling indicates that up to 2.0 million symptomatic RSV-ARI cases could be prevented annually in ≥60-year-olds with a hypothetical vaccine (70% vaccine efficacy against symptomatic ARI and 60% vaccine coverage) and that up to 0.69 million/year could be prevented in the nonvaccinated population, assuming 50% vaccine impact on infectiousness.

Conclusions

The model provides estimated burden of RSV in the US across all age groups, with substantial burden projected specifically in older adults. Vaccination of adults aged ≥60 years could significantly reduce the burden of disease in this population, with additional indirect effect in adults aged <60 years due to reduced transmissibility.
Isolation and Quarantine for Coronavirus Disease 2019 in the United States, 2020–2022
Authors: Oeltmann John E , Vohra Divya , Matulewicz Holly H , DeLuca Nickolas , Smith Jonathan P , Couzens Chandra , Lash R Ryan , Harvey Barrington , Boyette Melissa , Edwards Alicia , Talboy Philip M , Dubose Odessa , Regan Paul , Loosier Penny , Caruso Elise , Katz Dolores J , Taylor Melanie M , Moonan Patrick K
Published: March 2023

Background

Public health programs varied in ability to reach people with coronavirus disease 2019 (COVID-19) and their contacts to encourage separation from others. For both adult case patients with COVID-19 and their contacts, we estimated the impact of contact tracing activities on separation behaviors from January 2020 until March 2022.

Methods

We used a probability-based panel survey of a nationally representative sample to gather data for estimates and comparisons.

Results

An estimated 64 255 351 adults reported a positive severe acute respiratory syndrome coronavirus 2 test result; 79.6% isolated for ≥5 days, 60.2% isolated for ≥10 days, and 79.2% self-notified contacts. A total of, 24 057 139 (37.7%) completed a case investigation, and 46.2% of them reported contacts to health officials. More adults who completed a case investigation isolated than those who did not complete a case investigation (≥5 days, 82.6% vs 78.2%, respectively; ≥10 days, 69.8% vs 54.8%; both P < .05). A total of 84 946 636 adults were contacts of a COVID-19 case patient. Of these, 73.1% learned of their exposure directly from a case patient; 49.4% quarantined for ≥5 days, 18.7% quarantined for ≥14 days, and 13.5% completed a contact tracing call. More quarantined among those who completed a contact tracing call than among those who did not complete a tracing call (≥5 days, 61.2% vs 48.5%, respectively; ≥14 days, 25.2% vs 18.0%; both P < .05).

Conclusions

Engagement in contact tracing was positively correlated with isolation and quarantine. However, most adults with COVID-19 isolated and self-notified contacts regardless of whether the public health workforce was able to reach them. Identifying and reaching contacts was challenging and limited the ability to promote quarantining, and testing.
Attainment of Target Antibiotic Levels by Oral Treatment of Left-Sided Infective Endocarditis: A POET Substudy
Authors: Bock Magnus , Theut Anna Marie , van Hasselt Johan G C , Wang Hengzhuang , Fuursted Kurt , Høiby Niels , Lerche Christian Johann , Ihlemann Nikolaj , Gill Sabine , Christiansen Ulrik , Nielsen Hans Linde , Lemming Lars , Elming Hanne , Povlsen Jonas A , Bruun Niels Eske , Høfsten Dan , Fosbøl Emil L , Køber Lars , Schultz Martin , Pries-Heje Mia M , Kristensen Jonas Henrik , Christensen Jens Jørgen , Rosenvinge Flemming S , Pedersen Christian Torp , Helweg-Larsen Jannik , Tønder Niels , Iversen Kasper , Bundgaard Henning , Moser Claus
Published: March 2023

Background

In the POET (Partial Oral Endocarditis Treatment) trial, oral step-down therapy was noninferior to full-length intravenous antibiotic administration. The aim of the present study was to perform pharmacokinetic/pharmacodynamic analyses for oral treatments of infective endocarditis to assess the probabilities of target attainment (PTAs).

Methods

Plasma concentrations of oral antibiotics were measured at day 1 and 5. Minimal inhibitory concentrations (MICs) were determined for the bacteria causing infective endocarditis (streptococci, staphylococci, or enterococci). Pharmacokinetic/pharmacodynamic targets were predefined according to literature using time above MIC or the ratio of area under the curve to MIC. Population pharmacokinetic modeling and pharmacokinetic/pharmacodynamic analyses were done for amoxicillin, dicloxacillin, linezolid, moxifloxacin, and rifampicin, and PTAs were calculated.

Results

A total of 236 patients participated in this POET substudy. For amoxicillin and linezolid, the PTAs were 88%–100%. For moxifloxacin and rifampicin, the PTAs were 71%–100%. Using a clinical breakpoint for staphylococci, the PTAs for dicloxacillin were 9%–17%.

Seventy-four patients at day 1 and 65 patients at day 5 had available pharmacokinetic and MIC data for 2 oral antibiotics. Of those, 13 patients at day 1 and 14 patients at day 5 did only reach the target for 1 antibiotic. One patient did not reach target for any of the 2 antibiotics.

Conclusions

For the individual orally administered antibiotic, the majority reached the target level. Patients with sub-target levels were compensated by the administration of 2 different antibiotics. The findings support the efficacy of oral step-down antibiotic treatment in patients with infective endocarditis.
Yield of diagnosis and risk of stroke with screening strategies for atrial fibrillation: a comprehensive review of current evidence
Authors: Corica Bernadette , Bonini Niccolò , Imberti Jacopo Francesco , Romiti Giulio Francesco , Vitolo Marco , Attanasio Lisa , Basili Stefania , Freedman Ben , Potpara Tatjana S , Boriani Giuseppe , Lip Gregory Y H , Proietti Marco
Published: March 2023

Atrial fibrillation (AF) is the most prevalent arrhythmia worldwide. The presence of AF is associated with increased risk of systemic thromboembolism, but with the uptake of oral anticoagulant (OAC) and implementation of a holistic and integrated care management, this risk is substantially reduced. The diagnosis of AF requires a 30-s-long electrocardiographic (ECG) trace, irrespective of the presence of symptoms, which may represent the main indication for an ECG tracing. However, almost half patients are asymptomatic at the time of incidental AF diagnosis, with similar risk of stroke of those with clinical AF. This has led to a crucial role of screening for AF, to increase the diagnosis of population at risk of clinical events. The aim of this review is to give a comprehensive overview about the epidemiology of asymptomatic AF, the different screening technologies, the yield of diagnosis in asymptomatic population, and the benefit derived from screening in terms of reduction of clinical adverse events, such as stroke, cardiovascular, and all-cause death. We aim to underline the importance of implementing AF screening programmes and reporting about the debate between scientific societies’ clinical guidelines recommendations and the concerns expressed by the regulatory authorities, which still do not recommend population-wide screening. This review summarizes data on the ongoing trials specifically designed to investigate the benefit of screening in terms of risk of adverse events which will further elucidate the importance of screening in reducing risk of outcomes and influence and inform clinical practice in the next future.
Factors associated with long-term outcomes in adult congenital heart disease patients with infective endocarditis: a 16-year tertiary single-centre experience
Authors: Verzelloni Sef Alessandra , Jaggar Siân I , Trkulja Vladimir , Alonso-Gonzalez Rafael , Sef Davorin , Turina Marko I
Published: March 2023

OBJECTIVES

Studies concerning factors associated with long-term outcomes in adult congenital heart disease (ACHD) patients after infective endocarditis (IE) are scarce, while IE-related mortality in these patients remains a burden. We evaluated the factors associated with long-term survival in ACHD patients admitted for IE.

METHODS

We performed a retrospective single-centre study of all ACHD patients admitted for IE to a tertiary cardiothoracic centre between 1999 and 2015. Underlying ACHD, detailed echocardiographic and clinical data, surgical treatment and long-term follow-up were analysed.

RESULTS

We identified 151 ACHD patients admitted due to 176 episodes IE with 30-day, 6-month and 1-, 5- and 10-year survival of 95.4%, 92.7%, 92.7%, 84.7% and 75.6%, respectively. In a multivariable analysis, adjusted estimated probability of death was consistently higher after an IE episode among patients with complex as compared to simple/moderate ACHD: 10.6% vs 2.4% at 30 days, 15.0% vs 3.4% at 6 months and 1 year, 30.4% vs 7.8% at 5 years and 44.9% vs 13.1% at 10 years. Risk of death was higher among patients with prosthetic valve in comparison with those without (risk ratios 1.73–1.92). Surgical treatment was required in 76 (43.2%) episodes with 30-day mortality of 3.9%. Risk of death appeared to be lower than in the conservatively treated subgroup (risk ratios 0.71–0.78).

CONCLUSIONS

We demonstrated satisfactory long-term survival in ACHD patients who were treated for IE in a tertiary cardiothoracic centre. Early mortality tended to be lower in the surgically treated subgroup. Factors negatively associated with long-term survival were complex ACHD and presence of prosthetic valve.
A case for ELF feito no Brasil
Authors: Jordão Clarissa Menezes
Published: March 2023

This article starts from a comment on my locus of enunciation (i.e., the context from which I speak), a key element of decoloniality as a means of resisting the idea of disembodied knowledge or neutrality promoted by modernity/coloniality. I then proceed to explain how I understand the entanglement of modernity and coloniality and why we need to break away from coloniality, both ontologically and epistemologically. It is in this entanglement where ELT is traditionally situated, and it is from such contexts that English teacher education in Brazil should be examined for its harm to local knowledges and knowers. I conclude by explaining what is meant by ELF feito no Brasil and why this may be a possibility to resist the coloniality of ELT.
Masters athlete screening study (MASS): incidence of cardiovascular disease and major adverse cardiac events and efficacy of screening over five years
Authors: Morrison Barbara N , Isserow Saul , Taunton Jack , Oxborough David , Moulson Nathaniel , Warburton Darren E R , McKinney James
Published: March 2023

Background

The efficacy of cardiovascular screening in Masters athletes (MAs) (≥35 y), and whether screening decreases their risk of major adverse cardiac events (MACEs) is unknown.

Purpose

To evaluate the effectiveness of yearly cardiovascular screening, and the incidence of cardiovascular disease (CVD) and MACE over five years.

Methods and results

MAs (≥35 y) without previous history of CVD underwent yearly cardiovascular screening. Participants with an abnormal screen underwent further evaluations. In the initial year, 798 MAs (62.7% male, 55 ± 10 y) were screened; 11.4% (n = 91) were diagnosed with CVD. Coronary artery disease (CAD) was the most common diagnosis (n = 64; 53%). During follow-up, there were an additional 89 CVD diagnoses with an incidence rate of 3.58/100, 4.14/100, 3.74/100, 1.19/100, for years one to four, respectively. The most common diagnoses during follow-up were arrhythmias (n = 33; 37%). Increasing age (OR = 1.047, 95% confidence interval (CI): 1.003–1.094; P = 0.0379), Framingham Risk Score (FRS) (OR = 1.092, 95% CI: 1.031–1.158; P = 0.003), and LDL cholesterol (OR = 1.709, 95% CI: 1.223–2.401; P = 0.002) were predictive of CAD, whereas moderate intensity activity (min/wk) (OR = 0.997, 95% CI: 0.996–0.999; P = 0.002) was protective. Ten MACE (2.8/1000 athlete-years) occurred. All of these MAs were male, and 90% had ≥10% FRS. All underwent further evaluations with only two identified to have obstructive CAD.

Conclusion

MACE occurred despite yearly screening. All MAs who had an event had an abnormal screen; however, cardiac functional tests failed to detect underlying CAD in most cases. It may be appropriate to offer computed coronary tomography angiography in MAs with ≥10% FRS to overcome the limitations of functional testing, and to assist with lifestyle and treatment modifications.
The difference in composition and nutritional potency of honey extracted by centrifugation and pressed processes
Authors: Hu Yueyang , Li Zhen , Wang Shoucheng , Wu Xiaobo
Published: March 2023

In traditional beekeeping, the two most important methods for extracting honey are centrifugation and honeycomb-pressing. In this study, the physicochemical composition of honey samples extracted using two distinct procedures was compared, as well as the impact of antioxidant capacity and nutritional potency on the lifespan and learning memory of worker bees. Honey samples were collected from ten colonies of Apis cerana: five samples via centrifugation and five via honeycomb-pressing. Our results showed that honey extraction methods influence the nutritional composition and potency of honey. Most parameters were superior in pressed honey, and the amylase activity in centrifuged honey was higher. The effects of antioxidant capacity and nutritional potency on worker bees’ lifespans and learning memory were also superior in pressed honey. Pressed honey had higher nutritional composition and potency. However, whether pressed honey, which is rich in pollen, spoils more easily requires further investigation.
Deletion of MEC1 suppresses the replicative senescence of the cdc13-2 mutant in Saccharomyces cerevisiae
Authors: Yao Yue , Fekete-Szücs Enikő , Rosas Bringas Fernando R , Chang Michael
Published: March 2023

In Saccharomyces cerevisiae, telomerase recruitment to telomeres depends on a direct interaction between Cdc13, a protein that binds single-stranded telomeric DNA, and the Est1 subunit of telomerase. The cdc13-2 allele disrupts telomerase association with telomeres, resulting in progressive telomere shortening and replicative senescence. The Mec1/ATR kinase is both a positive and a negative regulator of telomerase activity and is required for the cell cycle arrest in telomerase-deficient senescent cells. In this study, we find that the deletion of MEC1 suppresses the replicative senescence of cdc13-2. This suppression is dependent on telomerase, indicating that Mec1 antagonizes telomerase-mediated telomere extension in cdc13-2 cells to promote senescence.