bluuebunny/crossref_metadata_2025_split huggingface dataset:
Contribution of low population immunity to the severe Omicron BA.2 outbreak in Hong Kong
Authors: Chen Lin-Lei , Abdullah Syed Muhammad Umer , Chan Wan-Mui , Chan Brian Pui-Chun , Ip Jonathan Daniel , Chu Allen Wing-Ho , Lu Lu , Zhang Xiaojuan , Zhao Yan , Chuang Vivien Wai-Man , Au Albert Ka-Wing , Cheng Vincent Chi-Chung , Sridhar Siddharth , Yuen Kwok-Yung , Hung Ivan Fan-Ngai , Chan Kwok-Hung , To Kelvin Kai-Wang 
Published: June 2022

AbstractMonitoring population protective immunity against SARS-CoV-2 variants is critical for risk assessment. We hypothesize that Hong Kong’s explosive Omicron BA.2 outbreak in early 2022 could be explained by low herd immunity. Our seroprevalence study using sera collected from January to December 2021 shows a very low prevalence of neutralizing antibodies (NAb) against ancestral virus among older adults. The age group-specific prevalence of NAb generally correlates with the vaccination uptake rate, but older adults have a much lower NAb seropositive rate than vaccination uptake rate. For all age groups, the seroprevalence of NAb against Omicron variant is much lower than that against the ancestral virus. Our study suggests that this BA.2 outbreak and the exceptionally high case-fatality rate in the ≥80 year-old age group (9.2%) could be attributed to the lack of protective immunity in the population, especially among the vulnerable older adults, and that ongoing sero-surveillance is essential.
Phylogenomic characterization and signs of microevolution in the 2022 multi-country outbreak of monkeypox virus
Authors: Isidro Joana , Borges Vítor , Pinto Miguel , Sobral Daniel , Santos João Dourado , Nunes Alexandra , Mixão Verónica , Ferreira Rita , Santos Daniela , Duarte Silvia , Vieira Luís , Borrego Maria José , Núncio Sofia , de Carvalho Isabel Lopes , Pelerito Ana , Cordeiro Rita , Gomes João Paulo 
Published: June 2022

AbstractThe largest monkeypox virus (MPXV) outbreak described so far in non-endemic countries was identified in May 2022 (refs. 1–6). In this study, shotgun metagenomics allowed the rapid reconstruction and phylogenomic characterization of the first MPXV outbreak genome sequences, showing that this MPXV belongs to clade 3 and that the outbreak most likely has a single origin. Although 2022 MPXV (lineage B.1) clustered with 2018–2019 cases linked to an endemic country, it segregates in a divergent phylogenetic branch, likely reflecting continuous accelerated evolution. An in-depth mutational analysis suggests the action of host APOBEC3 in viral evolution as well as signs of potential MPXV human adaptation in ongoing microevolution. Our findings also indicate that genome sequencing may provide resolution to track the spread and transmission of this presumably slow-evolving double-stranded DNA virus.
NORA3-WP: A high-resolution offshore wind power dataset for the Baltic, North, Norwegian, and Barents Seas
Authors: Solbrekke Ida Marie , Sorteberg Asgeir 
Published: June 2022

AbstractWe present a new high resolution wind resource and wind power dataset named NORA3-WP. The dataset covers the North Sea, the Baltic Sea and parts of the Norwegian and Barents Seas. The 3-km Norwegian reanalysis (NORA3) forms the basis for the new dataset. NORA3-WP is an open access dataset intended for use in research, governmental management and for stakeholders to attain relevant wind resource and wind power information in the planning phase of a new wind farm project. The variables are available as monthly data, and provides a climatological overview of 25 wind resource and wind power related variables for three selected turbines for the ocean areas surrounding Norway. In addition, the underlying hourly wind speed data and hourly wind power generation for three selected turbines are also available for higher frequency analysis and case-studies.
Electric-field facilitated rapid and efficient dissociation of tissues Into viable single cells
Authors: Welch E. Celeste , Yu Harry , Barabino Gilda , Tapinos Nikos , Tripathi Anubhav 
Published: June 2022

AbstractSingle-Cell Analysis is a growing field that endeavors to obtain genetic profiles of individual cells. Disruption of cell–cell junctions and digestion of extracellular matrix in tissues requires tissue-specific mechanical and chemical dissociation protocols. Here, a new approach for dissociating tissues into constituent cells is described. Placing a tissue biopsy core within a liquid-filled cavity and applying an electric field between two parallel plate electrodes facilitates rapid dissociation of complex tissues into single cells. Different solution compositions, electric field strengths, and oscillation frequencies are investigated experimentally and with COMSOL Multiphysics. The method is compared with standard chemical and mechanical approaches for tissue dissociation. Treatment of tissue samples at 100 V/cm 1 kHz facilitated dissociation of 95 ± 4% of biopsy tissue sections in as little as 5 min, threefold faster than conventional chemical–mechanical techniques. The approach affords good dissociation of tissues into single cells while preserving cell viability, morphology, and cell cycle progression, suggesting utility for sample preparation of tissue specimens for direct Single-Cell Analysis.
Preparing for the next pandemic via transfer learning from existing diseases with hierarchical multi-modal BERT: a study on COVID-19 outcome prediction
Authors: Agarwal Khushbu , Choudhury Sutanay , Tipirneni Sindhu , Mukherjee Pritam , Ham Colby , Tamang Suzanne , Baker Matthew , Tang Siyi , Kocaman Veysel , Gevaert Olivier , Rallo Robert , Reddy Chandan K 
Published: June 2022

AbstractDeveloping prediction models for emerging infectious diseases from relatively small numbers of cases is a critical need for improving pandemic preparedness. Using COVID-19 as an exemplar, we propose a transfer learning methodology for developing predictive models from multi-modal electronic healthcare records by leveraging information from more prevalent diseases with shared clinical characteristics. Our novel hierarchical, multi-modal model ($${\textsc {TransMED}}$$

T

R
A
N
S
MED

) integrates baseline risk factors from the natural language processing of clinical notes at admission, time-series measurements of biomarkers obtained from laboratory tests, and discrete diagnostic, procedure and drug codes. We demonstrate the alignment of $${\textsc {TransMED}}$$

T

R
A
N
S
MED

’s predictions with well-established clinical knowledge about COVID-19 through univariate and multivariate risk factor driven sub-cohort analysis. $${\textsc {TransMED}}$$

T

R
A
N
S
MED

’s superior performance over state-of-the-art methods shows that leveraging patient data across modalities and transferring prior knowledge from similar disorders is critical for accurate prediction of patient outcomes, and this approach may serve as an important tool in the early response to future pandemics.
3pHLA-score improves structure-based peptide-HLA binding affinity prediction
Authors: Conev Anja , Devaurs Didier , Rigo Mauricio Menegatti , Antunes Dinler Amaral , Kavraki Lydia E. 
Published: June 2022

AbstractBinding of peptides to Human Leukocyte Antigen (HLA) receptors is a prerequisite for triggering immune response. Estimating peptide-HLA (pHLA) binding is crucial for peptide vaccine target identification and epitope discovery pipelines. Computational methods for binding affinity prediction can accelerate these pipelines. Currently, most of those computational methods rely exclusively on sequence-based data, which leads to inherent limitations. Recent studies have shown that structure-based data can address some of these limitations. In this work we propose a novel machine learning (ML) structure-based protocol to predict binding affinity of peptides to HLA receptors. For that, we engineer the input features for ML models by decoupling energy contributions at different residue positions in peptides, which leads to our novel per-peptide-position protocol. Using Rosetta’s ref2015 scoring function as a baseline we use this protocol to develop 3pHLA-score. Our per-peptide-position protocol outperforms the standard training protocol and leads to an increase from 0.82 to 0.99 of the area under the precision-recall curve. 3pHLA-score outperforms widely used scoring functions (AutoDock4, Vina, Dope, Vinardo, FoldX, GradDock) in a structural virtual screening task. Overall, this work brings structure-based methods one step closer to epitope discovery pipelines and could help advance the development of cancer and viral vaccines.
A novel approach for engineering efficient nanofluids by radiolysis
Authors: Maaza M. , Khamliche T. , Akbari M. , Kana N. , Tandjigora N. , Beukes P. , Genu A. , Kaviyarasu K. , K.Cloete J. , Lekala M. , Gibaud A. , Henini M. 
Published: June 2022

AbstractThis contribution reports for the first time the possibility of using radiolysis to engineer stable efficient nanofluids which exhibit an enhanced thermal conductivity. The validation was confirmed on Ag-H2O and Ag-C2H6O2nanofluids fabricated via g-radiolysis within the mild dose range of 0.95 × 103–2.45 × 103Gray. The enhanced thermal conductivity of Ag-H2O and Ag-C2H6O2nanofluids, was found to be g-radiations dose dependent. In the latter case of Ag-C2H6O2nanofluid, the relative enhancement in the temperature range of 25–50 °C was found to be 8.89%, 11.54%, 18.69%, 23.57% and 18.45% for D1 = 0.95 × 103Gray, D2 = 1.2 × 103Gray, D3 = 1.54 × 103Gray, D4 = 1.80 × 103Gray and D5 = 2.45 × 103Gray respectively. Yet not optimized, an enhancement of the effective thermal conductivity as much as 23.57% relatively to pure C2H6O2was observed in stable Ag-C2H6O2nanofluids. Equivalent results were obtained with Ag-H2O.
Human competition is not lower if competing is socially wasteful instead of socially beneficial
Authors: Otten Kasper 
Published: June 2022

AbstractHumans compete for jobs, promotions, income, status, and many other scarce goods. In some situations, allocating scarce goods via competition is socially beneficial. In other situations, competition is not necessary to allocate goods, and nevertheless engaging in competition creates inefficiencies and welfare loss. We use an incentivized lab experiment to study whether people compete differently depending on whether allocating scarce goods via competition is socially wasteful or socially beneficial. We find that competition behavior is strikingly similar in situations where competing is socially wasteful and socially beneficial. Accordingly, there is large excess competition in situations of wasteful competition, creating considerable efficiency losses. We find evidence of a social trap involved in this excess competition. People are considerably more likely to compete if they believe others compete, and their beliefs on others’ competition are similar in situations where competing is socially wasteful and socially beneficial. Interventions aimed at lowering beliefs on others’ competition may be an effective method of lowering excess competition to prevent inefficiencies and welfare loss.
Electromagnetic energy density in hyperbolic metamaterials
Authors: Moradi Afshin , Luan Pi-Gang 
Published: June 2022

AbstractWe present the theory of electromagnetic energy propagation through a dispersive and absorbing hyperbolic metamaterial (HMM). In this way, the permittivity tensor components of HMM (especially, nanowire HMM) may appear to be hopeless, but as a non-trivial step, we find that they can be cast into more transparent forms. We find under the influence of an electromagnetic wave, the responses of nanowire HMM (multilayer HMM) in the directions perpendicular to and parallel to the optical axis are similar to those of Lorentz (Drude) and Drude (Lorentz) media, respectively. We obtain simple expressions for the electromagnetic energy density formula of both typical structures of HMMs, i.e., nanowire and multilayer HMMs. Numerical examples reveal the general characteristics of the direction-dependent energy storage capacity of both nanowire and multilayer HMMs. The results of this study may shed more physical insight into the optical characteristics of HMMs.
Indecomposability of entanglement witnesses constructed from symmetric measurements
Authors: Siudzińska Katarzyna 
Published: June 2022

AbstractWe propose a family of positive maps constructed from a recently introduced class of symmetric measurements. These maps are used to define entanglement witnesses, which include other popular approaches with mutually unbiased bases and mutually unbiased measurements. A particular interest is given to indecomposable witnesses that can be used to detect entanglement of quantum states with positive partial transposition. We present several examples for different number of measurements.
GIS-based precise predictive model of mountain beacon sites in Wenzhou, China
Authors: Tan Lifeng , Wu Bei , Zhang Yukun , Zhao Shuaishuai 
Published: June 2022

AbstractIn ancient China, where was frequently troubled by invaders, the government set up many beacon towers for alerting and transmitting military information along the border and the coast. Many beacon sites still exist in some areas, which are generally located in dangerous places with high mountains and rough terrain, bringing great difficulties to archaeological discovery. Therefore, it is particularly important to develop a predictive model applicable to the distribution of mountain beacon sites. Taking 68 beacon sites found in Wenzhou as research samples, this study used the superimposed method of logistic regression and viewshed analysis, forming a high-precision, scientific and operational predictive model for the distribution of beacon sites, which was verified by the cross-validation method. The results showed that the beacon site predictive model simulated in this study could reduce the probability scope of site location by 90% compared with the common logistic regression predictive model, which greatly improved the accuracy and ability of site prediction. At the same time, it could also be used to understand the relationship between the known sites and their surroundings to assist in decision-making about conservation and management.
Social ties, fears and bias during the COVID-19 pandemic: Fragile and flexible mindsets
Authors: Tei Shisei , Fujino Junya 
Published: June 2022

AbstractFears and social ties have been frequently discussed during the COVID-19 pandemic; however, it is still insufficiently examined how people have developed or mitigated social ties, bias and inter-group conflicts caused by fear. This review examined relevant COVID-19 literature and the psychology of anxiety, distress and aggression to consider how these adverse behaviours might be neutralised by cognitive flexibility. The results showed that social ties function as both risk and protective factors. The importance of social ties was repeatedly described as alleviating loneliness; nevertheless, people also expressed stigma-related anxiety (fear of criticism via empathic distress) associated with peer pressures and hostile vigilantism. Social ties and empathy have strengthened human cohesion and helped reconcile relations, but they also reinforced unfavourable biased bonds, terror and rumours that benefited in-group members while discriminating against out-group individuals. Furthermore, cognitive flexibility may assuage these negative consequences through shifting attention and perspective. Context-adjusted viewpoints and reciprocal dialogues seem crucial. The subsequent mitigation of misunderstandings, fear-induced bias, and maladaptive distress appraisal may lead to more reasonable and flexible recognition of social ties. The significance of this conclusion is in its potential for implementing intervention programmes to reduce pandemic-induced fear, and it could help to address other relevant issues, such as refugee crises and displaced people, a phenomenon that is globally developing discrimination, stigma and polarised blaming. It is worth further investigating how flexibility and inter-group empathy help pursue humanitarianism.
Design of high-power arbitrary multi-way radial power dividers using periodic matching structure
Authors: Liu Haixia , Chen Liangping , Song Minsheng , Qin Yu , Meng Lin , Wang Bin , Li Hailong , Yin Yong 
Published: June 2022

An arbitrary multi-way radial power divider/combiner with high-power capacity based on the coaxial waveguide TE01-mode is presented in this paper. The study of the TE01-mode in the coaxial waveguide shows the radial power divider can operate in the base mode with a large diameter, which can allow arbitrary multi-way waveguides to be radially distributed along the circumference of the coaxial waveguide. An equivalent circuit model of the arbitrary multi-way radial power divider is used to analyze its design procedure including the matching section, which can improve the transmission coefficient and isolation between output ports. To verify these, a 4-way and a 20-way radial power divider/combiner with a matching section are designed; the simulation results show that the power capability is &gt;43 kW within 0.5 dB insertion loss for the four-way radial power divider. The average value of isolation between adjacent ports has improved by 11.1 dB after using the periodic matching structure as well as 2.78 dB between opposite ports in the frequency range of 34.08–36.32 GHz. The insertion loss of the 20-way radial power divider is less than 1 dB in the frequency range of 33.4–37.6 GHz, while the return loss is greater than 25 dB.
Selection criteria for frame score and its association with growth-, reproductive-, feed efficiency- and carcass-related traits in Nellore cattle
Authors: Negreiros M. P. , Peripolli E. , Espigolan R. , Londoño-Gil M. , Rodriguez J. D. , Brunes L. , Magnabosco C. U. , Guimarães N. C. , Sainz R. D. , Pereira A. S. C. , Lobo R. B. , Baldi F. 
Published: June 2022

Context A frame score prediction equation developed specifically for Nellore cattle could be an auxiliary tool to improve mating decisions on the basis of feed resources and production-system objectives. Aims Estimate genetic parameters for frame by using a prediction equation developed for Nellore cattle and genetic associations between frame score (FRAME) and growth-, reproductive-, carcass- and feed efficiency-related traits, and five bioeconomic indexes. Methods Birth weight (BW), adjusted weight at 120 (W120), 210 (W210) and 450 (W450) days of age, adult weight (AW), age at first calving (AFC), probability of precocious calving (PPC30), stayability (STAY), accumulated cow productivity (ACP), adjusted scrotal circumference at 365 (SC365) and 450 (SC450) days of age, rib eye area (REA), subcutaneous backfat thickness (BFT), rump fat thickness (RFT), intramuscular fat percentage (IMF), residual feed intake (RFI) and dry-matter intake (DMI) were included in the analyses. Frame score was calculated using the multiple linear regression (MLR) prediction method. The estimation of genetic parameters was performed using a linear animal model, except for PPC30 and STAY, which were estimated through a threshold animal model. The correlated response in FRAME considering selection for growth-, reproductive-, carcass- and feed efficiency-indicator traits were obtained in the context of single-trait selection and a multiple-trait context. Key results Heritability estimated for FRAME was moderate (0.30 ± 0.09). Frame score showed moderate genetic correlations with growth traits, BW (0.51 ± 0.08), W120 (0.41 ± 0.07), W210 (0.35 ± 0.07) and W450 (0.29 ± 0.08). The genetic correlation estimates between FRAME and RFT was high (−0.84 ± 0.02), but low with ACP (0.25 ± 0.08) and RFI (0.10 ± 0.13). In the single-trait and multi-trait contexts, there was a lower correlated gain for FRAME when the selection was applied for traits commonly measured in beef cattle breeding programs. Conclusion Selection to increase growth traits would lead to an increase in frame size and herd nutritional requirements, and it would reduce the carcass fatness level and early heifer sexual precocity. FRAME could be an alternative trait to monitor calf birth weight. Implications Selection for FRAME is feasible, and the most suitable frame score value depends on the production system objectives and feed resources.
Warm stratification and optimised temperatures improve conservation of the endangered orchid,
Authors: Janissen Brendan , Lawrie Ann C. , Huynh Tien 
Published: June 2022

Context Maximising seed germination and seedling development is critical for conservation of endangered plants around the world. Orchidaceae is one of the most threatened plant families and can be one of the most difficult to propagate ex situ. Three critical, but potentially limiting, factors are important for orchid germination, namely, conducive conditions, ‘ready-to-germinate’ seed and effective mycorrhizal fungi. Aims Our aim was to improve poor germination in vitro of a recalcitrant Australian endangered orchid, Caladenia robinsonii, and to predict the potential impacts of climate change on this species. Methods Three experiments were conducted to optimise germination in C. robinsonii, with a focus on temperature. In Experiment 1, on the basis of meteorological data, three constant temperatures (15°C, 20°C and 27°C) were tested. In Experiment 2, the optimal constant temperature was compared with diurnally varying temperatures of 22°C/18°C (12/12 h), with and without warm stratification at 30°C/27°C (12/12 h) for 1 week. In Experiment 3, the same diurnally varying temperature and warm stratification were tested using multiple orchid mycorrhizal fungal isolates cultured from wild and re-introduced populations of C. robinsonii. Key results Without warm stratification, germination was greatest at 20°C (21%), but only 4% of seedlings developed to the green-leaf stage, whereas fungal growth was greatest at 27°C. Stratification increased germination (79%) and development to the green-leaf stage (47%), but more so with subsequent incubation under constant 20°C than diurnal 22°C/18°C. Fungal isolate affected total germination (53–69%) and development to the green-leaf stage (26–41%); isolates from the wild population were less effective than were those from re-introductions. Conclusions Warm stratification and specific seasonal temperatures significantly improved germination, both factors being typical of seeds with physiological dormancy. Implications Mimicking in situ conditions can provide a strong basis for ex situ germination strategies and predicting future outcomes. Winter–spring flowering orchid seedlings are commonly observed in autumn, and warm stratification should be considered for improving germination of similar orchid species. However, future climate warming may reduce in situ seedling recruitment.
Invoking asymmetry of affiliation in couple and family therapists’ accounts
Authors: Pawelczyk Joanna , Janusz Bernadetta , Józefik Barbara 
Published: June 2022

AbstractIn this paper we examine how couple and family therapists, in accounting for the moments of their first therapeutic encounters identified asmeaningful, invoke asymmetric affiliations with their clients in the Interpersonal Process Recall (IPR) dialogues. Applying Conversation Analysis and drawing on Membership Categorization Analysis, we analyze how these invoked (dis)affiliations are constructed in the fine interactional details of the interview and in/through the categories mobilized by the participants. The findings show therapists’ explicit affiliation with one spouse and often concurrently disaffiliation with the other in yet another interactive format. Consequently, the asymmetric affiliations are further strengthened by remaining unrecognized, unaddressed and ultimately unreflected in the IPR dialogue. The interviewer’s key role in promoting or constraining the therapist’s recognition of the asymmetric relations is discussed.