bluuebunny/crossref_metadata_2025_split huggingface dataset:
Performance optimization of annealing salp swarm algorithm: frameworks and applications for engineering design
Authors: Song Jiuman , Chen Chengcheng , Heidari Ali Asghar , Liu Jiawen , Yu Helong , Chen Huiling 
Published: February 2022

AbstractSwarm salp algorithm is a swarm intelligence optimization algorithm enlightened by the movement and foraging behaviors of the salp population. The salp swarm algorithm (SSA) has a simple structure and fast processing speed and can gain significant results on objective functions with fewer local optima. However, it has poor exploration ability and is easy to suffer from the local optimal solutions, so it performs poorly on multimodal objective functions. Besides, its unfair balance of exploration and exploitation is another notable shortcoming. To ameliorate these shortcomings and enhance the algorithm’s performance on multimodal functions, this research proposes simulated annealing (SA) improved salp swarm algorithm (SASSA). SASSA embeds the SA strategy into the followers’ position updating method of SSA, performs a certain number of iterations of the SA strategy, and uses Lévy flight to realize the random walk in the SA strategy. SASSA and 23 original and improved competitive algorithms are compared on 30 IEEE CEC2017 benchmark functions. SASSA ranked first in the Friedman test. Compared with SSA, SASSA can obtain better solutions on 27 benchmark functions. The balance and diversity experiment and analysis of SSA and SASSA are carried out. SASSA’s practicability is verified by solving five engineering problems and the fertilizer effect function problem. Experimental and statistical results reveal that the proposed SASSA has strong competitiveness and outperforms all the competitors. SASSA has excellent exploration ability, suitable for solving composition functions with multiple peaks. Meanwhile, SASSA brings about a good balance of exploration and exploitation and dramatically improves the quality of the solutions.
A Framework for Equitable Partnerships to Promote Cancer Prevention and Control in Rural Settings
Authors: Ko Linda K , Scarinci Isabel C , Bouchard Elizabeth G , Drake Bettina F , Rodriguez Elisa M , Chen Moon S , Kepka Deanna , Kruse-Diehr Aaron J , Befort Christie , Shannon Jackilen , Farris Paige E , Trentham-Dietz Amy , Onega Tracy 
Published: February 2022

Abstract
Rural populations continue to experience persistent cancer disparities compared with urban populations particularly in cancers that can be prevented or detected early through screening and vaccination. Although the National Cancer Institute and the larger cancer research community have identified rural community partnerships as the foundation for reducing the disparities, we have identified limited application of community-based participatory research in cancer prevention and control research. Guided by the Community-Based Participatory Research Conceptual Model and our collective experience, we provide a framework for a community–cancer center partnership that focuses on promoting health equity. In this commentary, we articulate that the partnership process must foster capacity for communities and cancer centers, strive for rural representation in clinical trials and biobanking, build a pipeline for dissemination and implementation research, and create a bidirectional flow of knowledge between communities and academic institutions. Authentic partnerships with rural communities should be the ultimate goal of cancer centers, and the process described in this commentary can serve as an initial platform to build capacity and continue to strive toward that goal.
Accretion mode versus radio morphology in the LOFAR Deep Fields
Authors: Mingo B , Croston J H , Best P N , Duncan K J , Hardcastle M J , Kondapally R , Prandoni I , Sabater J , Shimwell T W , Williams W L , Baldi R D , Bonato M , Bondi M , Dabhade P , Gürkan G , Ineson J , Magliocchetti M , Miley G , Pierce J C S , Röttgering H J A 
Published: February 2022

ABSTRACT
Radio-loud active galaxies have two accretion modes [radiatively inefficient (RI) and radiatively efficient (RE)], with distinct optical and infrared signatures, and two jet dynamical behaviours, which in arcsec- to arcmin-resolution radio surveys manifest primarily as centre- or edge-brightened structures [Fanaroff–Riley (FR) class I and II]. The nature of the relationship between accretion mode and radio morphology (FR class) has been the subject of long debate. We present a comprehensive investigation of this relationship for a sample of 286 well-resolved radio galaxies in the LOFAR Two-metre Sky Survey Deep Fields (LoTSS-Deep) first data release, for which robust morphological and accretion mode classifications have been made. We find that two-thirds of luminous FRII radio galaxies are RI, and identify no significant differences in the visual appearance or source dynamic range (peak/mean surface brightness) of the RI and RE FRIIs, demonstrating that both RI and RE systems can produce FRII structures. We also find a significant population of low-luminosity FRIIs (predominantly RI), supporting our earlier conclusion that FRII radio structures can be produced at all radio luminosities. We demonstrate that in the luminosity range where both morphologies are present, the probability of producing FRI or FRII radio morphology is directly linked to stellar mass, while across all morphologies and luminosities, RE accretion occurs in systems with high specific star formation rate, presumably because this traces fuel availability. In summary, the relationship between accretion mode and radio morphology is very indirect, with host-galaxy environment controlling these two key parameters in different ways.
A multiwavelength-motivated X-ray model for the Circinus Galaxy
Authors: Andonie Carolina , Ricci Claudio , Paltani Stéphane , Arévalo Patricia , Treister Ezequiel , Bauer Franz , Stalevski Marko 
Published: February 2022

ABSTRACT
Reprocessed X-ray emission in active galactic nuclei can provide fundamental information about the circumnuclear environments of supermassive black holes. Recent mid-infrared studies have shown evidence of an extended dusty structure perpendicular to the torus plane. In this work, we build a self-consistent X-ray model for the Circinus Galaxy including the different physical components observed at different wavelengths and needed to reproduce both the morphological and spectral properties of this object in the mid-infrared. The model consists of four components: the accretion disc, the broad-line region (BLR), a flared disc in the equatorial plane, and a hollow cone in the polar direction. Our final model reproduces well the 3–70 keV Chandra and NuSTAR spectra of Circinus, including the complex Fe Kα zone and the spectral curvature, although several additional Gaussian lines, associated with either ionized iron or broadened Fe Kα/Kβ lines, are needed. We find that the flared disc is Compton-thick ($N_{\rm H,d}= \rm 1.01^{+0.03}_{-0.24}\times 10^{25}\, cm^{-2}$) and geometrically thick ($\mathrm{ CF}=0.55^{+0.01}_{-0.05}$), and that the hollow cone has a Compton-thin column density ($N_{\rm H,c}= \rm 2.18^{+0.47}_{-0.43}\times 10^{23}\, cm^{-2}$), which is consistent with the values inferred by mid-infrared studies. Including also the BLR, the effective line-of-sight column density is $N_{\rm H}= \rm 1.47^{+0.03}_{-0.24}\times 10^{25}\, cm^{-2}$. This approach to X-ray modelling, i.e. including all the different reprocessing structures, will be very important to fully exploit data from future X-ray missions.
Shot noise and scatter in the star formation efficiency as a source of 21-cm fluctuations
Authors: Reis Itamar , Barkana Rennan , Fialkov Anastasia 
Published: February 2022

ABSTRACT
The 21-cm signal from cosmic dawn and the epoch of reionization probes the characteristics of the high redshift galaxy population. Many of the astrophysical properties of galaxies at high redshifts are currently unconstrained due to the lack of observations. This creates a vast space of possible astrophysical scenarios where the 21-cm signal needs to be modeled in order to plan for, and eventually fit, future observations. This is done with fast numerical methods which make simplifying approximations for the underlying physical processes. In this work, we quantify the effect of Poisson fluctuations and scatter in the star formation efficiency; while Poisson fluctuations are included in some works and not in others, scatter in the star formation efficiency is usually neglected, and all galaxies of a given mass are assumed to have the same properties. We show that both features can have a significant effect on the 21-cm power spectrum, most importantly in scenarios where the signal is dominated by massive galaxies. Scatter in the star formation efficiency does not simply enhance the effect of Poisson fluctuations; for example, we show that the power spectrum shape at cosmic dawn has a feature corresponding to the width of the galaxy brightness distribution. We also discuss some of the consequences for 21-cm imaging, and the signature of reduced correlation between the density and radiation fields.
TransposonUltimate: software for transposon classification, annotation and detection
Authors: Riehl Kevin , Riccio Cristian , Miska Eric A , Hemberg Martin 
Published: February 2022

AbstractMost genomes harbor a large number of transposons, and they play an important role in evolution and gene regulation. They are also of interest to clinicians as they are involved in several diseases, including cancer and neurodegeneration. Although several methods for transposon identification are available, they are often highly specialised towards specific tasks or classes of transposons, and they lack common standards such as a unified taxonomy scheme and output file format. We present TransposonUltimate, a powerful bundle of three modules for transposon classification, annotation, and detection of transposition events. TransposonUltimate comes as a Conda package under the GPL-3.0 licence, is well documented and it is easy to install through https://github.com/DerKevinRiehl/TransposonUltimate. We benchmark the classification module on the large TransposonDB covering 891,051 sequences to demonstrate that it outperforms the currently best existing solutions. The annotation and detection modules combine sixteen existing softwares, and we illustrate its use by annotating Caenorhabditis elegans, Rhizophagus irregularis and Oryza sativa subs. japonica genomes. Finally, we use the detection module to discover 29 554 transposition events in the genomes of 20 wild type strains of C. elegans. Databases, assemblies, annotations and further findings can be downloaded from (https://doi.org/10.5281/zenodo.5518085).
Bridging: Accelerating Regulatory Acceptance of Reduced-Risk Tobacco and Nicotine Products
Authors: Gaca Marianna , Williamson Justine , Digard Helena , Adams Louise , Hawkridge Lauren , Proctor Christopher 
Published: February 2022

Abstract

Introduction
The number and variety of alternative tobacco and nicotine products that can potentially provide reduced-risk choices for cigarette smokers who switch completely to such products instead of continued smoking have grown substantially in the past decade. Innovation and choice are likely to improve the prospects of smokers making the switch, but this provides challenges to regulators and manufacturers to ensure that changes to regulations and products promote and do not hinder contributions to tobacco harm reduction.

Aims and Methods
This paper looks at where bridging data sets for tobacco heating products, closed system vaping products, and oral nicotine products might enable innovation while protecting the interests of consumers.

Results
We review product data from chemical studies and a toxicological study showing how bridging can be applied and consider what product development changes might allow bridging from existing datasets or trigger the need for new ones.

Conclusions
Bridging across specific product ranges can increase the speed of innovation, foster competition, and limit the burden of assessment for regulators while maintaining product safety and quality.

Implications
Bridging partial data sets is an established practice within other industries, that aims to improve efficiency with regulatory approvals, accepts natural product variation, and supports product innovation. We review product data from chemical studies and a toxicological study showing how bridging can be applied and consider what product development changes might allow bridging from existing datasets or trigger the need for new ones. This in turn can increase the speed of innovation, foster competition, and limit the burden of assessment for regulators while maintaining product safety and quality.
The Impact of the 13-Valent Pneumococcal Conjugate Vaccine on Otitis Media–Related Antibiotic Use Among Young Children in Tennessee, USA
Authors: Griffith Hannah , Wiese Andrew D , Mitchel Edward F , Grijalva Carlos G 
Published: February 2022

Abstract
Otitis media (OM) is a leading cause of pediatric antibiotic use. Introduction of the 13-valent pneumococcal conjugate vaccine (PCV13) led to reductions in OM among US children, though its impact on OM-related antibiotic use remains unclear. Among 499 683 Tennessee children &lt;2 years of age, the OM-related antibiotic fill rate was stable after PCV13 introduction.
A Prospective Randomized Study Comparing Ceftolozane/Tazobactam to Standard of Care in the Management of Neutropenia and Fever in Patients With Hematological Malignancies
Authors: Chaftari Anne-Marie , Hachem Ray , Malek Alexandre E , Mulanovich Victor E , Szvalb Ariel D , Jiang Ying , Yuan Ying , Ali Shahnoor , Deeba Rita , Chaftari Patrick , Raad Issam 
Published: February 2022

Abstract

Background
With increased use of antibiotics in high-risk patients, the investigation of new antibiotics to cover potentially resistant pathogens is warranted. In this prospective randomized trial, we compared ceftolozane/tazobactam (C/T), a new cephalosporin/β-lactamase inhibitor, to the standard of care (SOC) for the empiric treatment of neutropenia and fever in patients with hematological malignancies.

Methods
We enrolled 100 patients to receive intravenous (IV) C/T or SOC antibiotics (cefepime, piperacillin/tazobactam, or meropenem) in combination with gram-positive antibacterial agents. We evaluated responses at the end of IV therapy (EOIV), test of cure (TOC; days 21–28), and late follow-up (LFU; days 35–42).

Results
We analyzed 47 C/T patients and 50 SOC patients. C/T patients had a higher rate of favorable clinical response at EOIV (87% vs 72%). A 1-sided noninferiority analysis indicated that C/T was at least not inferior to the SOC for favorable clinical response at EOIV (P = .002), TOC (P = .004), and LFU (P = .002). Superiority tests showed that C/T led to significantly lower rates of clinical failure at TOC (6% vs 30%; P = .003) and LFU (9% vs 30%; P = .008). C/T and SOC patients with documented infections had similar rates of favorable microbiological response. Serious adverse events leading to drug discontinuation (2% vs 0%; P = .48) and overall mortality (6% vs 4%; P = .67) were similar in both groups.

Conclusions
The empiric use of C/T in high-risk patients with hematological malignancies and febrile neutropenia is safe and associated with better clinical outcomes than SOC antimicrobial agents.

Clinical Trials Registration
NCT03485950.
Translational Landscape of a C4 Plant, Sorghum bicolor, Under Normal and Sulfur-Deficient Conditions
Authors: Sotta Naoyuki , Chiba Yukako , Aoyama Haruka , Takamatsu Seidai , Suzuki Takamasa , Miwa Kyoko , Yamashita Yui , Naito Satoshi , Fujiwara Toru 
Published: February 2022

Abstract
Recent accumulation of genomic and transcriptomic information has facilitated genetic studies. Increasing evidence has demonstrated that translation is an important regulatory step, and the transcriptome does not necessarily reflect the profile of functional protein production. Deep sequencing of ribosome-protected mRNA fragments (ribosome profiling or Ribo-seq) has enabled genome-wide analysis of translation. Sorghum is a C4 cereal important not only as food but also as forage and a bioenergy resource. Its resistance to harsh environments has made it an agriculturally important research subject. Yet genome-wide translational profiles in sorghum are still missing. In this study, we took advantage of Ribo-seq and identified actively translated reading frames throughout the genome. We detected translation of 4,843 main open reading frames (ORFs) annotated in the sorghum reference genome version 3.1 and revealed a number of unannotated translational events. A comparison of the transcriptome and translatome between sorghums grown under normal and sulfur-deficient conditions revealed that gene expression is modulated independently at transcript and translation levels. Our study revealed the translational landscape of sorghum’s response to sulfur and provides datasets that could serve as a fundamental resource to extend genetic research on sorghum, including studies on translational regulation.
Genetic analysis for type 1 diabetes genes in juvenile dermatomyositis unveils genetic disease overlap
Authors: Qu Hui-Qi , Qu Jingchun , Vaccaro Courtney , Chang Xiao , Mentch Frank , Li Jin , Mafra Fernanda , Nguyen Kenny , Gonzalez Michael , March Michael , Pellegrino Renata , Glessner Joseph , Sleiman Patrick , Kao Charlly , Hakonarson Hakon 
Published: February 2022

Abstract

Objectives
JDM is a serious autoimmune and complex genetic disease. Another autoimmune genetic disease, type 1 diabetes (T1D), has been observed for significantly increased prevalence in families with JDM, while increased JDM risk has also been observed in T1D cases. This study aimed to study whether these two autoimmune diseases, JDM and T1D, share common genetic susceptibility.

Methods
From 169 JDM families, 121 unrelated cases with European ancestry (EA) were identified by genome-wide genotyping, principal component analysis and identical-by-descent (IBD) analysis. T1D genetic risk score (GRS) were calculated in these cases and were compared with 361 EA T1D cases and 1943 non-diabetes EA controls. A total of 113 cases of the 121 unrelated European cases were sequenced by whole exome sequencing.

Results
We observed increased T1D GRS in JDM cases (P = 9.42E-05). Using whole exome sequencing, we uncovered the T1D genes, phospholipase B1, cystic fibrosis transmembrane conductance regulator, tyrosine hydroxylase, CD6 molecule, perforin 1 and dynein axonemal heavy chain 2, potentially associated with JDM by the burden test of rare functional coding variants.

Conclusion
Novel mechanisms of JDM related to these T1D genes are suggested by this study, which may imply novel therapeutic targets for JDM and warrant further study.
Time-modulated excitation for enhanced single-molecule localization microscopy
Authors: Jouchet Pierre , Poüs Christian , Fort Emmanuel , Lévêque-Fort Sandrine 
Published: February 2022

Structured illumination in single-molecule localization microscopy provides new information on the position of molecules and thus improves the localization precision compared to standard localization methods. Here, we used a time-shifted sinusoidal excitation pattern to modulate the fluorescence signal of the molecules whose position information is carried by the phase and recovered by synchronous demodulation. We designed two flexible fast demodulation systems located upstream of the camera, allowing us to overcome the limiting camera acquisition frequency and thus to maximize the collection of photons in the demodulation process. The temporally modulated fluorescence signal was then sampled synchronously on the same image, repeatedly during acquisition. This microscopy, called ModLoc, allows us to experimentally improve the localization precision by a factor of 2.4 in one direction, compared to classical Gaussian fitting methods. A temporal study and an experimental demonstration both show that the short lifetimes of the molecules in blinking regimes impose a modulation frequency in the kilohertz range, which is beyond the reach of current cameras. A demodulation system operating at these frequencies would thus be necessary to take full advantage of this new localization approach.
This article is part of the Theo Murphy meeting issue 'Super-resolution structured illumination microscopy (part 2)'.
Polarized illumination coded structured illumination microscopy (picoSIM): experimental results
Authors: Appelt Daniel , Ehler Elisabeth , Shukla Mukherjee Sapna , Heintzmann Rainer , Wicker Kai 
Published: February 2022

The need for acquiring at least three images to reconstruct an optical section of a sample limits the acquisition rate in structured illumination microscopy (SIM) for optical sectioning. In polarized illumination coded structured illumination microscopy (picoSIM) the three individual light patterns are encoded in a single polarized illumination light distribution, enabling the acquisition of the complete SIM data in a single exposure. Here, we describe our experimental set-up and show experimental results acquired with sequential and single-shot picoSIM.
This article is part of the Theo Murphy meeting issue ‘Super-resolution structured illumination microscopy (part 2)’.
Quantifying political influence on COVID-19 fatality in Brazil
Authors: de Almeida Leandro , Carelli Pedro V. , Cavalcanti Nara G. , Nascimento José-Dias do , Felinto Daniel 
Published: February 2022

AbstractThe COVID-19 pandemic was severely aggravated in Brazil due to its politicization by the country’s central government. However, the impact of diffuse political forces on the fatality of an epidemic is commonly hard to quantify. Here we introduce a method to measure this effect in the Brazilian case, based on the inhomogeneous distribution throughout the national territory of political support to the central government. The correlation between fatality rate and political support grows as the government’s misinformation campaign is developed, leading to the dominance of such political factor for the pandemic impact in Brazil in 2021. Once this dominance is established, this correlation allows for an estimation of the total number of deaths due to political influence as 350 ± 70 thousands up to the end of 2021.
“Investigating the effect of obesity on adipose-derived stem cells (ASCs) using Göttingen Minipigs”
Authors: Meyhoff-Madsen Maria , Østrup Esben , Fredholm Merete , Cirera Susanna 
Published: February 2022

AbstractObesity is associated with low grade inflammation, which may adversely impact the biological functions of adipose tissue and consequently of adipose-derived stem cells (ASCs). Studies in humans and rodents have described that obesity alters ASC properties and functionality, compromising their therapeutic prospects. The Göttingen Minipig (GM) is a commonly used obesity model. Nevertheless, there are no studies investigating the effect of obesity on ASCs from GM, which could constitute a valuable addition to both obesity modelling and adult stem cells investigations.In this study, we isolated subcutaneous ASCs from lean and obese GM to investigate the effect of obesity on cell behavior and differentiation capacity. During culturing, we observed an inherent difference in cell morphology between lean and obese ASCs. Upon adipogenic induction, obese-ASCs readily differentiated, developing significantly larger amounts of adipocytes than corresponding lean-ASCs, hinting at a predisposition towards adipogenic differentiation. Expression profiling of obesity-related genes in cell cultures, before and after adipogenic differentiation, revealed a tendency towards up-regulation in differentiated obese-cultures. Altogether, our results indicate that stem cells from obese donors could display different therapeutic properties. In summary, our results point towards GM as a valuable model for future ASCs investigations in healthy and obese states.