bluuebunny/crossref_metadata_2025_split huggingface dataset:
Investigation of plasmon relaxation mechanisms using nonadiabatic molecular dynamics
Authors: Wu Xiaoyan , Liu Baopi , Frauenheim Thomas , Tretiak Sergei , Yam ChiYung , Zhang Yu 
Published: December 2022

Hot carriers generated from the decay of plasmon excitation can be harvested to drive a wide range of physical or chemical processes. However, their generation efficiency is limited by the concomitant phonon-induced relaxation processes by which the energy in excited carriers is transformed into heat. However, simulations of dynamics of nanoscale clusters are challenging due to the computational complexity involved. Here, we adopt our newly developed Trajectory Surface Hopping (TSH) nonadiabatic molecular dynamics algorithm to simulate plasmon relaxation in Au20 clusters, taking the atomistic details into account. The electronic properties are treated within the Linear Response Time-Dependent Tight-binding Density Functional Theory (LR-TDDFTB) framework. The relaxation of plasmon due to coupling to phonon modes in Au20 beyond the Born–Oppenheimer approximation is described by the TSH algorithm. The numerically efficient LR-TDDFTB method allows us to address a dense manifold of excited states to ensure the inclusion of plasmon excitation. Starting from the photoexcited plasmon states in Au20 cluster, we find that the time constant for relaxation from plasmon excited states to the lowest excited states is about 2.7 ps, mainly resulting from a stepwise decay process caused by low-frequency phonons of the Au20 cluster. Furthermore, our simulations show that the lifetime of the phonon-induced plasmon dephasing process is ∼10.4 fs and that such a swift process can be attributed to the strong nonadiabatic effect in small clusters. Our simulations demonstrate a detailed description of the dynamic processes in nanoclusters, including plasmon excitation, hot carrier generation from plasmon excitation dephasing, and the subsequent phonon-induced relaxation process.
Maternal care and juvenile development of captive-bred short-beaked echidnas (
Authors: Ferguson Arthur , Laming Belinda 
Published: December 2022

Successful breeding of short-beaked echidnas (Tachyglossus aculeatus acanthion) occurred at Perth Zoo on eight occasions between 2007 and 2012. Here we report the methods used for monitoring and managing breeding females and their young from hatching through to weaning. Growth and development of the young during burrow-life was quantified through regular weighing and maternal care was monitored using video camera surveillance. All young hatched between early August and mid-September and were deposited in nursery burrows in October–November at 58–63 days of age at an average mass of 295 ± 64.3 g. Mothers suckled their young, on average, every 3.3 ± 1.1 days. Young first emerged from their nursery burrow from mid-January into February at an average 169 ± 21 days of age and weighing 1674 ± 511 g, and reached 3 kg in mass at 348 ± 97 days of age. Sexual maturity of two female offspring was attained at 4 years of age. Our observations of maternal care and development of the captive-bred young are consistent with published observations made on wild echidnas. We suggest that important factors for the successful rearing of captive-bred echidnas are enclosure set-up, daily monitoring, combined with a suitably designed and managed nursery burrow that provides a suitable substrate and microenvironment.
Kawa and the variable stopping of obstruents in Ende
Authors: Strong Katherine , Lindsey Kate L. , Drager Katie 
Published: December 2022

Abstract
This paper details a study investigating sociophonetic variation in Ende, a language spoken in Papua New Guinea.
The study examines speech produced by 30 individuals, investigating what social and linguistic factors are linked with the
variable alternation between stopped and affricated realizations of Ende retroflex obstruents [ʈ͡ʂ~ʈ] and [ɖ͡ʐ~ɖ].
Our analysis provides evidence that the obstruents in question are more likely to be realized as stops when they
are voiced and when the speakers are orators. Orators are people who practice kawa, a long-standing practice
whereby select individuals perform regular public orations. Among orators, the speaker’s age also appears to play a role in
retroflex stopping. The link between the stop variant and social factors can be understood within the context of the distribution
of power in the community, even in the absence of any explicit standard.
Quantum traps for coupling of fluorofullerene molecules
Authors: Oreshkin A I , Muzychenko D A , Oreshkin S I , Panov V I , Surov V O , Maslova N S , Petukhov M N 
Published: December 2022

Abstract
The interaction of fluorine atoms with Cu(111) surface has been analyzed by means of scanning tunneling microscopy and x-ray photoelectron spectroscopy (XPS). A submonolayer coverage of fluorinated fullerene C60F18 has been chosen to provide a well controllable arrival of fluorine atoms on copper surface. The appearance of F-induced surface structures on the Cu(111) surface caused by defluorination of C60F18 molecules adsorbed on the surface was shown. XPS measurements unambiguously indicate the existence of chemical state of fluorine not typical for CuF2 formation. Superstructure of well ordered metastable clusters consisting of fluorofullerene molecules are formed on the Cu(111) surface as a result of the balance of two interactions: the dipole-dipole interaction between fluorofullerene molecules and the interaction of C60F18 molecules with the two-dimensional gas phase, emerging above the copper surface. Regular surface structure formed by fullerene molecules interacting through collective vibrational mode can be used for entanglement formation between two qubits each associated with ground and excited electronic states of the molecule by applying two coherent laser pulses.
Group Outcomes for Time-Weighted Averaging in WBGT-Based Heat Stress Exposure Assessment
Authors: Bernard Thomas E , Flach John W , Ashley Candi D 
Published: December 2022

AbstractThe wet bulb globe temperature (WBGT)-based occupational exposure limits (OELs) were developed from steady exposures to heat stress at constant WBGT and metabolic rate (M). The exposure limits were based on compensable heat stress exposures at the upper limit of the prescriptive zone for most healthy people. Professional practice allows for using time-weighted averages (TWAs) of WBGT and M to account for heterogeneous heat stress exposures. The purpose of the current paper was to report on the effectiveness of time-weighted averaging to assess occupational heat stress using published studies. Our hypothesis was using TWA-WBGT and TWA-M was as protective as the recommended OELs for steady exposures. The current paper reports on 62 observations of work that alternate between at least two heat stress conditions (usually work and recovery) reported in 16 papers. The TWA-WBGT and TWA-M were determined for all observations. ΔLimit was the observed TWA-WBGT minus the exposure limit at the TWA-M based on acclimatization state. The observations were then classified as above or below ΔLimit = 0. Each observation was also classified as uncompensable if the mean core temperature for the group was greater than 38°C or a less tolerant individual was above 38.5°C. When comparing exposure classifications to outcome classifications using 2 × 2 tables, the sensitivity and specificity for all observations were 0.72 and 0.73, respectively. The sensitivity was much less than the expected value near 1.0, and the large difference called into question the ability of TWAs to represent actual heat stress. There was some suspicion that there were differences between acclimatized and unacclimatized observations. Before any of these findings are embedded in policy or practice, a more careful evaluation of TWAs is required. In conclusion, we believe that the use of TWAs for heat stress analysis was not fully evaluated, and we proposed a framework for evaluation.
Transitioning between ‘Outside’ and ‘Inside’ Knowledge in an Online University EMI Chemistry Course
Authors: Bozbiyik Merve , Morton Tom 
Published: December 2022

AbstractRecent studies in applied linguistics research have focused on how teachers draw on ‘outside’ knowledge relating to students’ everyday life for the purpose of teaching subject matter content. This study focuses on such practices in the context of English-medium instruction (EMI) higher education in an online undergraduate chemistry module. Adopting an interdisciplinary perspective, the study combines multimodal Conversation Analysis (CA) and the Autonomy dimension of Legitimation Code Theory (LCT) to examine how one lecturer shifts between ‘inside’ knowledge of chemistry and ‘outside’ knowledge for a range of different purposes. Multimodal CA is used to carry out micro-analyses of epistemics and identity-related positioning in interaction, while LCT ‘autonomy codes’ are used to trace knowledge-building trajectories in which knowledge is positioned inside or outside the target topic and is used for different purposes. The analyses highlight how the lecturer skilfully deployed a range of semiotic resources in transitioning between ‘inside’ and ‘outside’ knowledge, and how these resources were leveraged for the building of disciplinary knowledge. Implications of this interdisciplinary approach for research and practice in university EMI contexts are discussed.
A realist approach to understanding alliancing within Local Government public health and social care service provision
Authors: Redgate S , Spencer L , Adams E A , Arnott B , Brown H , Christie A , Hardy C , Harrison H , Kaner E , Mawson C , McGovern W , Phillips P , Rankin J , McGovern R 
Published: December 2022

Abstract

Background
Within the current context of continued austerity and post-pandemic recovery, it remains important that Local Government services address the increasing needs of residents as cost-effectively as possible. Alliancing, whereby services work collaboratively focusing on the ‘whole-system’, has gained popularity as a tool with the potential to support collaborative whole systems approaches. This synthesis aims to identify how alliancing can be successfully operationalised in the commissioning of public health, wider National Health Service (NHS) and social care-related services.

Methods
A realist literature synthesis was undertaken in order to identify underlying generative mechanisms associated with alliancing, the contextual conditions surrounding the implementation and operationalisation of the alliancing approach mechanisms, and the outcomes produced as a result. An iterative approach was taken, using a recent systematic review of the effectiveness of Alliancing, online database searches, and grey literature searches.

Results
Three mechanistic components were identified within the data as being core to the successful implementation of alliances in public health and social care-related services within Local Government: (i) Achieving a system-level approach; (ii) placing local populations at the heart of the system; and (iii) creating a cultural shift. Programme theories were postulated within these components.

Conclusions
The alliancing approach offers an opportunity to achieve system-level change with the potential to benefit local populations. The realist synthesis approach taken within this study has provided insights into the necessary contextual and mechanistic factors of the Alliancing approach, above and beyond effectiveness outcomes typically collected through more conventional evaluation methodologies.
Development and applications of a CRISPR activation system for facile genetic overexpression in Candida albicans
Authors: Gervais Nicholas C , La Bella Alyssa A , Wensing Lauren F , Sharma Jehoshua , Acquaviva Victoria , Best Madison , Cadena López Ricardo Omar , Fogal Meea , Uthayakumar Deeva , Chavez Alejandro , Santiago-Tirado Felipe , Flores-Mireles Ana L , Shapiro Rebecca S 
Published: December 2022

Abstract
For the fungal pathogen Candida albicans, genetic overexpression readily occurs via a diversity of genomic alterations, such as aneuploidy and gain-of-function mutations, with important consequences for host adaptation, virulence, and evolution of antifungal drug resistance. Given the important role of overexpression on C. albicans biology, it is critical to develop and harness tools that enable the analysis of genes expressed at high levels in the fungal cell. Here, we describe the development, optimization, and application of a novel, single-plasmid-based CRISPR activation (CRISPRa) platform for targeted genetic overexpression in C. albicans, which employs a guide RNA to target an activator complex to the promoter region of a gene of interest, thus driving transcriptional expression of that gene. Using this system, we demonstrate the ability of CRISPRa to drive high levels of gene expression in C. albicans, and we assess optimal guide RNA targeting for robust and constitutive overexpression. We further demonstrate the specificity of the system via RNA sequencing. We highlight the application of CRISPR activation to overexpress genes involved in pathogenesis and drug susceptibility, and contribute toward the identification of novel phenotypes. Consequently, this tool will facilitate a broad range of applications for the study of C. albicans genetic overexpression.
Genetics of tibia bone properties of crossbred commercial laying hens in different housing systems
Authors: Johnsson Martin , Wall Helena , Lopes Pinto Fernando A , Fleming Robert H , McCormack Heather A , Benavides-Reyes Cristina , Dominguez-Gasca Nazaret , Sanchez-Rodriguez Estefania , Dunn Ian C , Rodriguez-Navarro Alejandro B , Kindmark Andreas , de Koning Dirk-Jan 
Published: December 2022

Abstract
Osteoporosis and bone fractures are a severe problem for the welfare of laying hens, with genetics and environment, such as housing system, each making substantial contributions to bone strength. In this work, we performed genetic analyses of bone strength, bone mineral density, and bone composition, as well as body weight, in 860 commercial crossbred laying hens from 2 different companies, kept in either furnished cages or floor pens. We compared bone traits between housing systems and crossbreds and performed a genome-wide association study of bone properties and body weight. As expected, the 2 housing systems produced a large difference in bone strength, with layers housed in floor pens having stronger bones. These differences were accompanied by differences in bone geometry, mineralization, and chemical composition. Genome scans either combining or independently analyzing the 2 housing systems revealed no genome-wide significant loci for bone breaking strength. We detected 3 loci for body weight that were shared between the housing systems on chromosomes 4, 6, and 27 (either genome-wide significant or suggestive) and these coincide with associations for bone length. In summary, we found substantial differences in bone strength, content, and composition between hens kept in floor pens and furnished cages that could be attributed to greater physical activity in pen housing. We found little evidence for large-effect loci for bone strength in commercial crossbred hens, consistent with a highly polygenic architecture for bone strength in the production environment. The lack of consistent genetic associations between housing systems in combination with the differences in bone phenotypes could be due to gene-by-environment interactions with housing system or a lack of power to detect shared associations for bone strength.
Differences in homologous recombination and maintenance of heteropolyploidy between Haloferax volcanii and Haloferax mediterranei
Authors: Dattani Ambika , Sharon Itai , Shtifman-Segal Ella , Robinzon Shachar , Gophna Uri , Allers Thorsten , Altman-Price Neta 
Published: December 2022

Abstract
Polyploidy, the phenomenon of having more than one copy of the genome in an organism, is common among haloarchaea. While providing short-term benefits for DNA repair, polyploidy is generally regarded as an “evolutionary trap” that by the notion of the Muller's ratchet will inevitably conclude in the species' decline or even extinction due to a gradual reduction in fitness. In most reported cases of polyploidy in archaea, the genetic state of the organism is considered as homoploidy i.e. all copies of the genome are identical. Here we demonstrate that while this is indeed the prevalent genetic status in the halophilic archaeon Haloferax volcanii, its close relative H. mediterranei maintains a prolonged heteroploidy state in a nonselective environment once a second allele is introduced. Moreover, a strong genetic linkage was observed between two distant loci in H. mediterranei indicating a low rate of homologous recombination while almost no such linkage was shown in H. volcanii indicating a high rate of recombination in the latter species. We suggest that H. volcanii escapes Muller's ratchet by means of an effective chromosome-equalizing gene-conversion mechanism facilitated by highly active homologous recombination, whereas H. mediterranei must elude the ratchet via a different, yet to be elucidated mechanism.
Pleiotropic fitness effects of a Drosophila odorant-binding protein
Authors: Mokashi Sneha S , Shankar Vijay , Johnstun Joel A , Mackay Trudy F C , Anholt Robert R H 
Published: December 2022

Abstract
Insect odorant-binding proteins (OBPs) are members of a rapidly evolving multigene family traditionally thought to facilitate chemosensation. However, studies on Drosophila have shown that members of this family have evolved functions beyond chemosensation, as evident from their expression in reproductive tissues and the brain. Previous studies implicated diverse functions of Obp56h, a member of the largest gene cluster of the D. melanogaster Obp repertoire. Here, we examined the effect of CRISPR/Cas9-mediated deletion of Obp56h on 2 fitness phenotypes, on resistance to starvation stress and heat stress, and on locomotion and sleep phenotypes. Obp56h−/− mutants show a strong sexually dimorphic effect on starvation stress survival, with females being more resistant to starvation stress than the control. In contrast, Obp56h−/− females, but not males, are highly sensitive to heat stress. Both sexes show changes in locomotion and sleep patterns. Transcriptional profiling of RNA from heads of Obp56h−/− flies and the wildtype control reveals differentially expressed genes, including gene products associated with antimicrobial immune responses and members of the Turandot family of stress-induced secreted peptides. In addition, differentially expressed genes of unknown function were identified in both sexes. Genes encoding components of the mitochondrial electron transport chain, cuticular proteins, gene products associated with regulation of feeding behavior (Lst and CCHa2), ribosomal proteins, lncRNAs, snoRNAs, tRNAs, and snRNAs show changes in transcript abundances in Obp56h−/− females. These differentially expressed genes are likely to contribute to Obp56h-mediated effects on the diverse phenotypes that arise upon deletion of this OBP.
The Gossypium herbaceum L. Wagad genome as a resource for understanding cotton domestication
Authors: Ramaraj Thiruvarangan , Grover Corrinne E , Mendoza Azalea C , Arick Mark A , Jareczek Josef J , Leach Alexis G , Peterson Daniel G , Wendel Jonathan F , Udall Joshua A 
Published: December 2022

Abstract
Gossypium herbaceum is a species of cotton native to Africa and Asia that is one of the 2 domesticated diploids. Together with its sister-species G. arboreum, these A-genome taxa represent models of the extinct A-genome donor of modern polyploid cotton, which provide about 95% of cotton grown worldwide. As part of a larger effort to characterize variation and improve resources among diverse diploid and polyploid cotton genomes, we sequenced and assembled the genome of G. herbaceum cultivar (cv.) Wagad, representing the first domesticated accession for this species. This chromosome-level genome was generated using a combination of PacBio long-read technology, HiC, and Bionano optical mapping and compared to existing genome sequences in cotton. We compare the genome of this cultivar to the existing genome of wild G. herbaceum subspecies africanum to elucidate changes in the G. herbaceum genome concomitant with domestication and extend these analyses to gene expression using available RNA-seq. Our results demonstrate the utility of the G. herbaceum cv. Wagad genome in understanding domestication in the diploid species, which could inform modern breeding programs.
Growth condition-dependent differences in methylation imply transiently differentiated DNA methylation states in Escherichia coli
Authors: Breckell Georgia L , Silander Olin K 
Published: December 2022

Abstract
DNA methylation in bacteria frequently serves as a simple immune system, allowing recognition of DNA from foreign sources, such as phages or selfish genetic elements. However, DNA methylation also affects other cell phenotypes in a heritable manner (i.e. epigenetically). While there are several examples of methylation affecting transcription in an epigenetic manner in highly localized contexts, it is not well-established how frequently methylation serves a more general epigenetic function over larger genomic scales. To address this question, here we use Oxford Nanopore sequencing to profile DNA modification marks in three natural isolates of Escherichia coli. We first identify the DNA sequence motifs targeted by the methyltransferases in each strain. We then quantify the frequency of methylation at each of these motifs across the entire genome in different growth conditions. We find that motifs in specific regions of the genome consistently exhibit high or low levels of methylation. Furthermore, we show that there are replicable and consistent differences in methylated regions across different growth conditions. This suggests that during growth, E. coli transiently differentiate into distinct methylation states that depend on the growth state, raising the possibility that measuring DNA methylation alone can be used to infer bacterial growth states without additional information such as transcriptome or proteome data. These results show the utility of using Oxford Nanopore sequencing as an economic means to infer DNA methylation status. They also provide new insights into the dynamics of methylation during bacterial growth and provide evidence of differentiated cell states, a transient analog to what is observed in the differentiation of cell types in multicellular organisms.