bluuebunny/crossref_metadata_2025_split huggingface dataset:
Determinants of associations between codon and amino acid usage patterns of microbial communities and the environment inferred based on a cross-biome metagenomic analysis
Authors: Panda Arup , Tuller Tamir 
Published: January 2023

AbstractCodon and amino acid usage were associated with almost every aspect of microbial life. However, how the environment may impact the codon and amino acid choice of microbial communities at the habitat level is not clearly understood. Therefore, in this study, we analyzed codon and amino acid usage patterns of a large number of environmental samples collected from diverse ecological niches. Our results suggested that samples derived from similar environmental niches, in general, show overall similar codon and amino acid distribution as compared to samples from other habitats. To substantiate the relative impact of the environment, we considered several factors, such as their similarity in GC content, or in functional or taxonomic abundance. Our analysis demonstrated that none of these factors can fully explain the trends that we observed at the codon or amino acid level implying a direct environmental influence on them. Further, our analysis demonstrated different levels of selection on codon bias in different microbial communities with the highest bias in host-associated environments such as the digestive system or oral samples and the lowest level of selection in soil and water samples. Considering a large number of metagenomic samples here we showed that microorganisms collected from similar environmental backgrounds exhibit similar patterns of codon and amino acid usage irrespective of the location or time from where the samples were collected. Thus our study suggested a direct impact of the environment on codon and amino usage of microorganisms that cannot be explained considering the influence of other factors.
Steady-state Peierls transition in nanotube quantum simulator
Authors: Zhang Lin , Bhattacharya Utso , Bachtold Adrian , Forstner Stefan , Lewenstein Maciej , Pistolesi Fabio , Grass Tobias 
Published: January 2023

AbstractQuantum dots placed along a vibrating nanotube provide a quantum simulation platform that can directly address the electron-phonon interaction. This offers promising prospects for the search of new quantum materials and the study of strong correlation effects. As this platform is naturally operated by coupling the dots to an electronic reservoir, state preparation is straightforwardly achieved by driving into the steady state. Here we show that for intermediate electron-phonon coupling strength, the system with spin-polarized quantum dots undergoes a Peierls transition into an insulating regime which exhibits charge-density wave order in the steady state as a consequence of the competition between electronic Coulomb repulsive interactions and phonon-induced attractive interactions. The transport phenomena can be directly observed as fingerprints of electronic correlations. We also present powerful methods to numerically capture the physics of such an open electron-phonon system at large numbers of phonons. Our work paves the way to study and detect correlated electron-phonon physics in the nanotube quantum simulator with current experimentally accessible techniques.
A database of synthetic inelastic neutron scattering spectra from molecules and crystals
Authors: Cheng Yongqiang , Stone Matthew B. , Ramirez-Cuesta Anibal J. 
Published: January 2023

AbstractInelastic neutron scattering (INS) is a powerful tool to study the vibrational dynamics in a material. The analysis and interpretation of the INS spectra, however, are often nontrivial. Unlike diffraction, for which one can quickly calculate the scattering pattern from the structure, the calculation of INS spectra from the structure involves multiple steps requiring significant experience and computational resources. To overcome this barrier, a database of INS spectra consisting of commonly seen materials will be a valuable reference, and it will also lay the foundation of advanced data-driven analysis and interpretation of INS spectra. Here we report such a database compiled for over 20,000 organic molecules and over 10,000 inorganic crystals. The INS spectra are obtained from a streamlined workflow, and the synthetic INS spectra are also verified by available experimental data. The database is expected to greatly facilitate INS data analysis, and it can also enable the utilization of advanced analytics such as data mining and machine learning.Notice: This manuscript has been authored by UT-Battelle, LLC under Contract No. DE-AC05-00OR22725 with the U.S. Department of Energy. The United States Government retains and the publisher, by accepting the article for publication, acknowledges that the United States Government retains a non-exclusive, paid-up, irrevocable, world-wide license to publish or reproduce the published form of this manuscript, or allow others to do so, for United States Government purposes. The Department of Energy will provide public access to these results of federally sponsored research in accordance with the DOE Public Access Plan (http://energy.gov/downloads/doe-public-access-plan).
Geography shapes the genomics and antimicrobial resistance of Salmonella enterica Serovar Enteritidis isolated from humans
Authors: Cao Guojie , Zhao Shaohua , Kuang Dai , Hsu Chih-Hao , Yin Lanlan , Luo Yan , Chen Zhao , Xu Xuebin , Strain Errol , McDermott Patrick , Allard Marc , Brown Eric , Meng Jianghong , Zheng Jie 
Published: January 2023

AbstractMultidrug-resistant (MDR) Salmonella has been a long-standing challenge in public health and food safety. The prevalence of MDR S. Enteritidis, especially isolated from humans, in China is significantly higher than those from the U.S. and other countries. A dataset of 197 S. Enteritidis genomes, including 16 sequenced clinical isolates from China and 181 downloaded genomes of human isolates from the U.S., Europe, and Africa, was analyzed for genomic diversity, virulence potential, and antimicrobial resistance (AMR). Phylogenomic analyses identified four major well-supported clades (I–IV). While AMR genotype in the majority of isolates in clades I and IV displayed as pan-susceptible, 81.8% (9/11) and 22.4% (13/58) of isolates in clades III and II were MDR, respectively. It is noted that 77% (10/13) of MDR isolates in clade II were from China. The most common antimicrobial resistance genes (ARGs) carried by the Chinese isolates were aph(3′)-IIa, blaCTX-M-55, and blaTEM-1B, whereas blaTEM-1B, sul1, sul2, drfA7, aph(3")-Ib/strA, and aph(6)-Id/strB were most often identified in those from Africa (clade III). Among the 14 plasmid types identified, IncX1 and IncFII(pHN7A8) were found exclusively in the Chinese MDR isolates, while IncQ1 was highly associated with the African MDR isolates. The spvRABCD virulence operon was present in 94.9% (187/197) of isolates tested and was highly associated with both the IncF (IncFII and IncFIB) plasmids. In addition, phylogenetic differences in distribution of Salmonella pathogenicity islands (SPIs), prophages and other accessory genes were also noted. Taken together, these findings provide new insights into the molecular mechanisms underpinning diversification of MDR S. Enteritidis.
Stream instabilities in optical-field ionization of a monatomic dilute neutral gas in fully relativistic regime
Authors: Ghorbanalilu M. 
Published: January 2023

AbstractStream instabilities arising from anisotropic electron velocity distribution function (EVDF) are discussed in the optical-field ionization mechanism of a monatomic dilute gas by a circularly polarized laser beam in a fully relativistic regime. It is shown that a relativistically rotating electron beam is derived by a circularly polarized laser field with ($$p_z>p_\perp$$

p
z

>

p
⊥

). We show that the following ionization and before collisions thermalize the electrons, the plasma undergoes Buneman and Weibel instabilities. The Weibel and Buneman modes are co-propagating with k normal to the streaming direction. The theoretical results reveal that for the threshold of the relativistic regime ($$a_0\approx 1$$

a
0

≈
1

), instabilities are aperiodic and grow independently. However, by increasing the laser intensity for $$a_0>1$$

a
0

>
1

, two instabilities are coupled. The coupling process increased the growth rate of Weibel instability, while the Buneman instability experienced a decrement in its growth rate. For more intense laser radiation, both instabilities are broken into different oscillatory and aperiodic modes.
An energy-aware routing method using firefly algorithm for flying ad hoc networks
Authors: Lansky Jan , Rahmani Amir Masoud , Malik Mazhar Hussain , Yousefpoor Efat , Yousefpoor Mohammad Sadegh , Khan Muhammad Umair , Hosseinzadeh Mehdi 
Published: January 2023

AbstractFlying ad-hoc networks (FANETs) include a large number of drones, which communicate with each other based on an ad hoc model. These networks provide new opportunities for various applications such as military, industrial, and civilian applications. However, FANETs have faced with many challenges like high-speed nodes, low density, and rapid changes in the topology. As a result, routing is a challenging issue in these networks. In this paper, we propose an energy-aware routing scheme in FANETs. This scheme is inspired by the optimized link state routing (OLSR). In the proposed routing scheme, we estimate the connection quality between two flying nodes using a new technique, which utilizes two parameters, including ratio of sent/received of hello packets and connection time. Also, our proposed method selects multipoint relays (MPRs) using the firefly algorithm. It chooses a node with high residual energy, high connection quality, more neighborhood degree, and higher willingness as MPR. Finally, our proposed scheme creates routes between different nodes based on energy and connection quality. Our proposed routing scheme is simulated using the network simulator version 3 (NS3). We compare its simulation results with the greedy optimized link state routing (G-OLSR) and the optimized link state routing (OLSR). These results show that our method outperforms G-OLSR and OLSR in terms of delay, packet delivery rate, throughput, and energy consumption. However, our proposed routing scheme increases slightly routing overhead compared to G-OLSR.
Intrinsic fluctuations of reinforcement learning promote cooperation
Authors: Barfuss Wolfram , Meylahn Janusz M. 
Published: January 2023

AbstractIn this work, we ask for and answer what makes classical temporal-difference reinforcement learning with $$\epsilon$$
ϵ
-greedy strategies cooperative. Cooperating in social dilemma situations is vital for animals, humans, and machines. While evolutionary theory revealed a range of mechanisms promoting cooperation, the conditions under which agents learn to cooperate are contested. Here, we demonstrate which and how individual elements of the multi-agent learning setting lead to cooperation. We use the iterated Prisoner’s dilemma with one-period memory as a testbed. Each of the two learning agents learns a strategy that conditions the following action choices on both agents’ action choices of the last round. We find that next to a high caring for future rewards, a low exploration rate, and a small learning rate, it is primarily intrinsic stochastic fluctuations of the reinforcement learning process which double the final rate of cooperation to up to 80%. Thus, inherent noise is not a necessary evil of the iterative learning process. It is a critical asset for the learning of cooperation. However, we also point out the trade-off between a high likelihood of cooperative behavior and achieving this in a reasonable amount of time. Our findings are relevant for purposefully designing cooperative algorithms and regulating undesired collusive effects.
A denoising framework for 3D and 2D imaging techniques based on photon detection statistics
Authors: Dodda Vineela Chandra , Kuruguntla Lakshmi , Elumalai Karthikeyan , Chinnadurai Sunil , Sheridan John T , Muniraj Inbarasan 
Published: January 2023

AbstractA method to capture three-dimensional (3D) objects image data under extremely low light level conditions, also known as Photon Counting Imaging (PCI), was reported. It is demonstrated that by combining a PCI system with computational integral imaging algorithms, a 3D scene reconstruction and recognition is possible. The resulting reconstructed 3D images often look degraded (due to the limited number of photons detected in a scene) and they, therefore, require the application of superior image restoration techniques to improve object recognition. Recently, Deep Learning (DL) frameworks have been shown to perform well when used for denoising processes. In this paper, for the first time, a fully unsupervised network (i.e., U-Net) is proposed to denoise the photon counted 3D sectional images. In conjunction with classical U-Net architecture, a skip block is used to extract meaningful patterns from the photons counted 3D images. The encoder and decoder blocks in the U-Net are connected with skip blocks in a symmetric manner. It is demonstrated that the proposed DL network performs better, in terms of peak signal-to-noise ratio, in comparison with the classical TV denoising algorithm.
Hepatitis C and HIV detection by blood RNA-sequencing in cohort of smokers
Authors: Morrow Jarrett D. , Castaldi Peter J. , Chase Robert P. , Yun Jeong H. , Kinney Gregory L. , Silverman Edwin K. , Hersh Craig P. 
Published: January 2023

AbstractDetection of viruses by RNA and DNA sequencing has improved the understanding of the human virome. We sought to identify blood viral signatures through secondary use of RNA-sequencing (RNA-seq) data in a large study cohort. The ability to reveal undiagnosed infections with public health implications among study subjects with available sequencing data could enable epidemiologic surveys and may lead to diagnosis and therapeutic interventions, leveraging existing research data in a clinical context. We detected viral RNA in peripheral blood RNA-seq data from a COPD-enriched population of current and former smokers. Correlation between viral detection and both reported infections and relevant disease outcomes was evaluated. We identified Hepatitis C virus RNA in 228 subjects and HIV RNA in 30 subjects. Overall, we observed 31 viral species, including Epstein-Barr virus and Cytomegalovirus. We observed an enrichment of Hepatitis C and HIV infections among subjects reporting liver disease and HIV infections, respectively. Higher interferon expression scores were observed in the subjects with Hepatitis C and HIV infections. Through secondary use of RNA-seq from a cohort of current and former smokers, we detected peripheral blood viral signatures. We identified HIV and Hepatitis C virus (HCV), highlighting potential public health implications for the approach described this study. We observed correlations with reported infections, chronic infection outcomes and the host transcriptomic response, providing evidence to support the validity of the approach.
Efficient light transfer in coupled nonlinear triple waveguides using shortcuts to adiabaticity
Authors: Evangelakos Vasileios , Paspalakis Emmanuel , Stefanatos Dionisis 
Published: January 2023

AbstractWe use the method of shortcuts to adiabaticity to design the variable couplings in a three-waveguide directional coupler which may contain nonlinear elements, in order to accomplish efficient light transfer between the outer waveguides for shorter device lengths, despite the presence of nonlinearity. The shortcut couplings are obtained for the ideal case where all the waveguides are linear, for which a perfect transfer is guaranteed in theory, but are tested for various combinations of linear and nonlinear waveguides in the device. We show with numerical simulations that, in most configurations, high levels of transfer efficiency can be maintained even for large values of the input power, and for shorter lengths than those of conventional adiabatic devices. We also find that efficiency is improved for shortcut couplings with less spatial extent, since in this case the nonlinearity acts during a shorter range. The present work is expected to find application in research fields like optoelectronic computing and ultrafast light switching, where the fast and controlled light transmission inside a set of waveguides is a crucial task. Additionally, the reduction in the device size may be exploited for incorporating them in integrated optical systems, where a high density of waveguides is required.
Altered white matter connectivity in children with congenital heart disease with single ventricle physiology
Authors: Williamson Brady J. , Barnes-Davis Maria E. , Vannest Jennifer , Anixt Julia S. , Heydarian Haleh C. , Kuan Lisa , Laue Cameron S. , Pratap Jayant , Schapiro Mark , Tseng Stephanie Y. , Kadis Darren S. 
Published: January 2023

AbstractChildren born with congenital heart disease (CHD) have seen a dramatic decrease in mortality thanks to surgical innovations. However, there are numerous risk factors associated with CHD that can disrupt neurodevelopment. Recent studies have found that psychological deficits and structural brain abnormalities persist into adulthood. The goal of the current study was to investigate white matter connectivity in early school-age children (6–11 years), born with complex cyanotic CHD (single ventricle physiology), who have undergone Fontan palliation, compared to a group of heart-healthy, typically developing controls (TPC). Additionally, we investigated associations between white matter tract connectivity and measures on a comprehensive neuropsychological battery within each group. Our results suggest CHD patients exhibit widespread decreases in white matter connectivity, and the extent of these decreases is related to performance in several cognitive domains. Analysis of network topology showed that hub distribution was more extensive and bilateral in the TPC group. Our results are consistent with previous studies suggesting perinatal ischemia leads to white matter lesions and delayed maturation.
Clear Speech Variants: An Investigation of Intelligibility and Speaker Effort in Speakers With Parkinson's Disease
Authors: Stipancic Kaila L. , van Brenk Frits , Kain Alexander , Wilding Gregory , Tjaden Kris 
Published: January 2023

Purpose:
This study investigated the effects of three clear speech variants on sentence intelligibility and speaking effort for speakers with Parkinson's disease (PD) and age- and sex-matched neurologically healthy controls.

Method:
Fourteen speakers with PD and 14 neurologically healthy speakers participated. Each speaker was recorded reading 18 sentences from the Speech Intelligibility Test in their habitual speaking style and for three clear speech variants: clear (SC; given instructions to speak clearly), hearing impaired (HI; given instructions to speak with someone with a hearing impairment), and overenunciate (OE; given instructions to overenunciate each word). Speakers rated the amount of physical and mental effort exerted during each speaking condition using visual analog scales (averaged to yield a metric of overall speaking effort). Sentence productions were orthographically transcribed by 50 naive listeners. Linear mixed-effects models were used to compare intelligibility and speaking effort across the clear speech variants.

Results:
Intelligibility was reduced for the PD group in comparison to the control group only in the habitual condition. All clear speech variants significantly improved intelligibility above habitual levels for the PD group, with OE maximizing intelligibility, followed by the SC and HI conditions. Both groups rated speaking effort to be significantly higher for both the OE and HI conditions versus the SC and habitual conditions.

Discussion:
For speakers with PD, all clear speech variants increased intelligibility to a level comparable to that of healthy controls. All clear speech variants were also associated with higher levels of speaking effort than habitual speech for the speakers with PD. Clinically, findings suggest that clear speech training programs consider using the instruction “overenunciate” for maximizing intelligibility. Future research is needed to identify if high levels of speaking effort elicited by the clear speech variants affect long-term sustainability of the intelligibility benefit.
Understanding Training Needs in Pediatric Feeding for Allied Health Professionals: An Australian Perspective
Authors: Raatz Madeline , Marshall Jeanne , Ward Elizabeth C. , Dickinson Corrine , Frederiksen Nadine , Reilly Claire , Fernando Shenali 
Published: January 2023

Purpose:
Clinician experience and confidence can negatively impact pediatric feeding service availability, but limited research has investigated what training allied health professionals (AHPs) need to increase these factors. This study developed and distributed a survey investigating Australian AHPs' self-reported confidence and anxiousness, training needs, factors impacting training access, and training preferences.

Method:
This study was conducted over two phases. Phase 1 involved development and refinement of the survey, and Phase 2 involved distribution to Australian AHPs. Questions pertained to general demographics, feeding experience, feeding confidence and skills perception, and training needs. The questions were composed of multiple-choice, Likert scale, and short-response options.

Results:

Overall, 198 complete responses were received. Participants reported significantly lower confidence and higher anxiousness working with infants compared to older children (
p
< .01). Increased frequency of service provision predicted higher self-reported confidence and lower anxiousness (
p
< .01). Practical training opportunities including case discussion, videos, and clinical feedback were preferred. Access facilitators were online, on-demand training; however, respondents reported preferring hands-on training opportunities. Common barriers included cost, time, competing professional development priorities, and distance/travel.

Conclusions:
Findings have highlighted that recency and frequency of practice impact self-reported confidence and anxiousness, and that AHPs self-report lowest confidence and highest anxiety working with infants compared to older age groups. Overall, the findings highlight the need for flexible, practical, and remotely accessible training opportunities, as well as the need for access to regular clinical supervision and a pediatric feeding caseload.
Merkelzellkarzinom
Authors: Schultz Erwin 
Published: January 2023

ZusammenfassungDas Merkelzellkarzinom ist ein aggressiver neuroendokriner Tumor, welcher durch schnelles Wachstum und frühzeitige Metastasierung charakterisiert ist. Das mediane Erkrankungsalter liegt zwischen 75–80 Jahren. Mit Zunahme des durchschnittlichen Bevölkerungsalters tritt der einstmals seltene Tumor immer häufiger auf. Neben den klassischen Therapiesäulen Chirurgie, Strahlentherapie und Chemotherapie spielt die Immunonkologie auch beim Merkelzellkarzinom eine zunehmend wichtige Rolle.