bluuebunny/crossref_metadata_2025 huggingface dataset:
DECAF perks up plasma forecasting
Authors: Patrick Chris
Published: March 2023

Physics-based approach accurately predicts plasma disruption events in tokamaks producing fusion energy
Molecular size dependence on achievable resolution from XFEL single-particle 3D reconstruction
Authors: Nakano Miki , Miyashita Osamu , Tama Florence
Published: March 2023

Single-particle analysis using x-ray free-electron lasers (XFELs) is a novel method for obtaining structural information of samples in a state close to nature. In particular, it is suitable for observing the inner structure of large biomolecules by taking advantage of the high transmittance of x-rays. However, systematic studies on the resolution achievable for large molecules are lacking. In this study, the molecular size dependence of the resolution of a three-dimensional (3D) structure resulting from XFEL single-particle reconstruction is evaluated using synthetic data. Evidently, 3D structures of larger molecules can be restored with higher detail (defined relative to the molecular sizes) than smaller ones; however, reconstruction with high absolute resolution (defined in nm−1) is challenging. Our results provide useful information for the experimental design of 3D structure reconstruction using coherent x-ray diffraction patterns of single-particles.
Dynamics of a stochastic epidemic-like rumor propagation model with generalized nonlinear incidence and time delay
Authors: Zhang Yuhuai , Zhu Jianjun , Din Anwarud , Ma Xinsheng
Published: March 2023

Rumors are abnormal children of public opinion, they usually arise with environmental crisis and have serious negative functions. Hence, how to control rumor propagation has become an urgent topic for the government. Since the communication between people in the real world is inevitably interfered by random factors, and time delay exists in the process of rumor propagation not only influence rumor-forwarding individuals by rumor-hesitant individuals but also in government decision-making. Based on these premises, we propose a stochastic delayed rumor propagation model with generalized incidence function. By setting the suitable Lyapunov functions, we show that the asymptotic behavior of stochastic rumor spreading model is constrained by some conditions. Finally, our analytical results are supported by numerical simulations. The results show that (1) the increase of noise intensity in social environment will reduce rumor propagation; (2) time delay has an impact on rumor propagation to a certain extent. Extending the thinking time may reduce the number of rumor-forwarding individuals and even lead to the disappearance of rumors; (3) improve scientific literacy and accelerate rumor refutation (i.e. reduce the value of β), strengthen rumor suppression (i.e. increase the value of γ) can effectively control rumor transmission.
Performance improvement factors in quantum radar/illumination
Authors: Hosseiny Seyed Mohammad , Norouzi Milad , Seyed-Yazdi Jamileh , Irannezhad Fatemeh
Published: March 2023

In this study, we exploit quantum information processing, the research field focusing on quantum two-mode squeezed (QTMS) radar and quantum illumination (QI), to investigate the qualitative behaviors of entanglement, the entropy of formation, and squeezing in these protocols. We use logarithmic negativity to investigate entanglement between the signal and idler and propose strategies to maintain entanglement at room temperature in both protocols. We also calculate the entanglement, squeezing, and entropy for the QTMS radar when the target is present and the signal is transmitted to the target. In addition, by controlling the squeezing parameter which is a tool to control entanglement, entropy, and squeezing, the performance of the QTMS radar can be improved, so this work shows how it is implemented in practice. In both protocols, entanglement is maintained by considering conditions. Since the squeezing parameter controls both signal and idler power and the correlation between them, therefore, the qualitative behavior of squeezing in the QTMS radar and QI is also studied in this research. The significant result obtained from the QI is that the entanglement maintains at high power, low temperature, and high correlation between signal and idler. In contrast, in the QTMS, the entanglement survives when the correlation and power are low, even at room temperature.
Quantum-enhanced optical precision measurement assisted by low-frequency squeezed vacuum states
Authors: Kang 康 Guohui 国辉 , Feng 冯 Jinxia 晋霞 , Cheng 程 Lin 琳 , Li 李 Yuanji 渊骥 , Zhang 张 Kuanshou 宽收
Published: March 2023

Stable low-frequency squeezed vacuum states at a wavelength of 1550 nm were generated. By controlling the squeezing angle of the squeezed vacuum states, two types of low-frequency quadrature-phase squeezed vacuum states and quadrature-amplitude squeezed vacuum states were obtained using one setup respectively. A quantum-enhanced fiber Mach–Zehnder interferometer (FMZI) was demonstrated for low-frequency phase measurement using the generated quadrature-phase squeezed vacuum states that were injected. When phase modulation was measured with the quantum-enhanced FMZI, there were above 3 dB quantum improvements beyond the shot-noise limit (SNL) from 40 kHz to 200 kHz, and 2.3 dB quantum improvement beyond the SNL at 20 kHz was obtained. The generated quadrature-amplitude squeezed vacuum state was applied to perform low-frequency amplitude modulation measurement for sensitivity beyond the SNL based on optical fiber construction. There were about 2 dB quantum improvements beyond the SNL from 60 kHz to 200 kHz. The current scheme proves that quantum-enhanced fiber-based sensors are feasible and have potential applications in high-precision measurements based on fiber, particularly in the low-frequency range.
Energy shift and subharmonics induced by nonlinearity in a quantum dot system
Authors: Zhou Yuan , Cao Gang , Li Hai-Ou , Guo Guo-Ping
Published: March 2023

The presence of anticrossings induced by coupling between two states causes curvature in energy levels, yielding a nonlinearity in the quantum system. When the system is driven back and forth along the bending energy levels, subharmonic transitions and energy shifts can be observed, which would cause a significant influence as the system is applied to quantum computing. In this paper, we study a longitudinally driven singlet-triplet (ST) system in a double quantum dot (DQD) system, and illustrate the consequences of nonlinearity by driving the system close to the anticrossings. We provide a straightforward theory to quantitatively describe the energy shift and subharmonics caused by nonlinearity, and find good agreement between our theoretical result and the numerical simulation. Our results reveal the existence of nonlinearity in the vicinity of anticrossings and provide a direct way of analytically assessing its impact, which can be applied to other quantum systems without excessive labor.
Current status of the end-of-substructure (EoS) card project for the ATLAS strip tracker upgrade using final ASICs
Authors: Boebel A.L. , Ceslik H. , Dam M. , Diez S. , Garvey C. , Göttlicher P. , Gregor I.M. , Keaveney J.M. , Van der Merwe M.N. , Oechsle J. , Schmitt S. , Stanitzki M. , Strom L.R. , Wyngaard J.R.
Published: March 2023

In the context of the high-luminosity upgrade of the LHC and ATLAS, the microstrip-tracking detector will be redesigned. The main building blocks are substructures with multiple sensors and their electronics. Each substructure will have a single interface to the off-detector system, the so-called End-of-Substructure (EoS) card. Its physical realisation is a set of printed circuit boards (PCBs). The PCB integrates ASICs and hybrids, which multiplex or demultipex the data and transmit with a rate up to 10 Gb/s or receive with a rate up to 2.5 Gb/s on optical fibres. These active parts are developed at CERN and are known as lpGBT and VTRx+. The EoS card integrates the active parts with the required electronics for the specified operation and within the mechanical constraints of the detector. In this paper critical design aspects such as the low-impedance powering scheme and the PCB setup are described. The EoS card has reached its final state for a series production, including the required setups for quality control. The achieved transmission quality on the 10 Gb/s links is presented.
Timespot1: a 28 nm CMOS Pixel Read-Out ASIC for 4D Tracking at High Rates
Authors: Cadeddu Sandro , Frontini Luca , Lai Adriano , Liberali Valentino , Piccolo Lorenzo , Rivetti Angelo , Shojaii Jafar , Stabile Alberto
Published: March 2023

We present the first characterization results of Timespot1,
an ASIC designed in CMOS 28 nm technology, featuring a
32 × 32 pixel matrix with a pitch of 35 μm. Timespot1
is the first small-size prototype, conceived to readout fine-pitch
pixels with single-hit time resolution below
50 psrms and input rates of several hundreds of
kilohertz per pixel. Such experimental conditions will be typical of
the next generation of high-luminosity collider experiments, from
the LHC run5 and beyond. Each pixel of the ASIC includes a charge
amplifier, a discriminator, and a Time-to-Digital Converter with a
time resolution indicatively of 22.6 psrms and
maximum readout rates (per pixel) of 3 MHz. To respect system-level
constraints, the timing performance has been obtained keeping the
power budget per pixel below 40 mW. The ASIC has been tested and
characterised in the laboratory concerning its performance in terms
of time resolution, power budget and sustainable rates. The ASIC
will be hybridized on a matched 32 × 32 pixel sensor matrix
and will be tested under laser beam and Minimum Ionizing Particles
in the laboratory and at test beams. In this paper we present a
description of the ASIC operation and the first results obtained
from characterization tests concerning its performance.
Bone formation beyond the skeletal envelope using calcium phosphate granules packed into a collagen pouch—a pilot study
Authors: Guillet Claire , Birgersson Ulrik , Engstrand Thomas , Åberg Jonas , Lopes Viviana R , Thor Andreas , Engqvist Håkan , Forterre Franck
Published: March 2023

In this proof-of-concept, bone neoformation beyond the skeletal envelope is explored by using a collagen pouch (n = 6) packed with calcium phosphate (CaP) granules placed over the frontal bone in sheep (n = 3). At 13 weeks, macroscopic examination showed specimens covered by an adherent fibrinous envelope with slight vascularization. Histology revealed colonization of the implant by newly formed woven bone and fibrous connective tissue. Surface osteoblasts as well as material-filled macrophages, lymphocytes, polymorphonuclear cells and giant cells were also found in large quantities surrounding the newly formed bone tissue inside the collagen pouch. On the side facing the recipient bone, the collagen membrane had to a large extent been resorbed and bridging bone formation was clearly visible between the test article and recipient bone. On the other side facing soft tissue, the collagen pouch remained intact with a visible fibrous capsule. This study demonstrated that the use of a collagen sleeve as a container for CaP granules allows for good neoformation beyond the skeletal envelope with bridging bone formation clearly visible between the test article and recipient bone. Additionally, in this model, macrophages rather than osteoclasts appear to modulate CaP granule resorption and remodeling into new bone. This construct opens new perspectives for treatment methods that could be used for bone augmentation and restoration of cranio-maxillofacial defects and malformations.
On the capabilities of the SWOT satellite to monitor the lake level change over the Third Pole
Authors: Xiong Jinghua , Jiang Liguang , Qiu Yuanlin , Wongchuig Sly , Abhishek  , Guo Shenglian , Chen Jie
Published: March 2023

The lake level dynamics of the Qinghai–Tibetan Plateau (QTP, also called the ‘Third Pole’) are a crucial indicator of climate change and human activities; however, they remain poorly measured due to extremely high elevation and cold climate. The existing satellite altimeters also suffer from relatively coarse temporal resolution or low spatial coverage, preventing effective monitoring of lake level change at such a large spatial scale. The recently launched surface water and ocean topography (SWOT) mission is expected to greatly enhance the current lake level monitoring capabilities. However, a systematic evaluation is still lacking in the region. To elucidate this potential, here, we generated SWOT-like lake products for 38 major lakes (>150 km2) over the QTP during 2000–2018 using a large-scale SWOT hydrology simulator with the input of satellite altimetry and water mask databases. The comparative assessments between the satellite altimetry data and SWOT simulations using various statistical metrics and decomposed time series components demonstrate that SWOT can successfully monitor both short-term dynamics and long-term trends. Extended experiments to derive SWOT-like data of 783 lakes (>1 km2) based on the synthetic lake level series present the spatial pattern of SWOT performance that tends to improve with the increasing lake area. Our findings provide comprehensive inferences and confidence for lake level monitoring in the Third Pole in the early period of the SWOT satellite.
Seasonal variation in near-surface seasonally thawed active layer and permafrost soil microbial communities
Authors: Baker Christopher C M , Barker Amanda J , Douglas Thomas A , Doherty Stacey J , Barbato Robyn A
Published: March 2023

Understanding how soil microbes respond to permafrost thaw is critical to predicting the implications of climate change for soil processes. However, our knowledge of microbial responses to warming is mainly based on laboratory thaw experiments, and field sampling in warmer months when sites are more accessible. In this study, we sampled a depth profile through seasonally thawed active layer and permafrost in the Imnavait Creek Watershed, Alaska, USA over the growing season from summer to late fall. Amplicon sequencing showed that bacterial and fungal communities differed in composition across both sampling depths and sampling months. Surface communities were most variable while those from the deepest samples, which remained frozen throughout our sampling period, showed little to no variation over time. However, community variation was not explained by trace metal concentrations, soil nutrient content, pH, or soil condition (frozen/thawed), except insofar as those measurements were correlated with depth. Our results highlight the importance of collecting samples at multiple times throughout the year to capture temporal variation, and suggest that data from across the annual freeze-thaw cycle might help predict microbial responses to permafrost thaw.
Climate mitigation sustains agricultural research and development expenditure returns for maize yield improvement in developing countries
Authors: Yoshida Ryuhei , Iizumi Toshichika
Published: March 2023

Governmental expenditure on agricultural research and development (R&D) has played a substantial role in increasing crop yields in recent decades. However, studies suggest that annual yield growth rates would decline in a warming climate compared to that in a non-warming climate. Here, we present how projected climate could alter maize yield gain owing to a US$ 1 billion increase in agricultural R&D expenditure (referred to as yield response) for 71 maize-producing countries using global gridded crop model simulations with socioeconomic and climate scenarios as inputs. For the middle of this century (2041–2060) under the low warming scenario (shared socioeconomic pathways: SSP126), the median yield response between countries is estimated to be the highest at 27.2% in the low-income group, followed by 6.6% in the lower-middle-income group, 1.0% in the high-income group, and 0.1% in upper-middle-income group. The projected median yield response for lower (the low- and lower-middle)-income groups under the high warming scenario (SSP585) was approximately half than that under the low warming scenario: 27.2% → 15.6% for the low-income, 6.6% → 1.7% for the lower-middle-income, and 1.0% → 0.6% for the high-income groups. For the upper-middle-income group, where there is limited room for adopting high-yielding technology and management already being used in higher (the high- and higher-middle)-income groups, the negative impacts of climate change cannot be offset and yields are projected to decline, even with continued R&D investments (0.1% → –0.2%). Even if the R&D expenditures increase at the same value, expected yield gains will depend on future warming levels. This finding suggests that climate mitigation is a prerequisite for maintaining the yield returns from agricultural R&D investments in developing countries.
Integrability of two-species partially asymmetric exclusion processes
Authors: Lobaskin Ivan , Evans Martin R , Mallick Kirone
Published: March 2023

We work towards the classification of all one-dimensional exclusion processes with two species of particles that can be solved by a nested coordinate Bethe ansatz (BA). Using the Yang–Baxter equations, we obtain conditions on the model parameters that ensure that the underlying system is integrable. Three classes of integrable models are thus found. Of these, two classes are well known in literature, but the third has not been studied until recently, and never in the context of the BA. The Bethe equations are derived for the latter model as well as for the associated dynamics encoding the large deviation of the currents.
Performance of green concrete paving block imbibed with industrial scrap steel mill scale for sustainable construction
Authors: Parvathikumar Ganeshprabhu , Balachandran Gurukarthik Babu , Sahadevan Brintha
Published: March 2023

The utilization of industrial waste materials in concrete compensates the shortage of natural resources by not only solving the problem due to disposal of wastes but also by developing alternative solutions to protect the environment as well as reduction in the area requirement for landfill. The concrete made with such wastages using less energy during its production and eco-friendly is called as Green Concrete. Variety of industrial wastes is employed as whole or partial substitution for coarse or fine aggregate. Steel mill scale is one such kind of waste materials produced as a result of hot process of rolling of steel in steel companies with rich source of iron content with least impurities. This research study investigates the viability of adopting steel mill scale as a partial substitute material for fine aggregate (M-sand). The current study investigates the influence on fresh and hardened concrete paving blocks and its properties, when M-sand is replaced at 0%, 20%, 40%, 60%, 80%, and 100% with steel mill scale using a mix ratio of 1:1.6:2.1 at sustained water-cement ratio value of 0.5 and target strength at 28 days of 30 Mega Pascal. Physical and chemical characterisation of the materials, concrete compressive strength, concrete split tensile strength, water absorption, and also micro-structural examination of hardened paving blocks are experimentally investigated. Results suggest that 60% of the replacements outperformed the originals. The research findings point towards the feasibility of producing paving blocks from scrap steel mill scale for enhancing environmentally friendly construction practices and sustainable pavement infrastructure.
Defects in WS2 monolayer calculated with a nonlocal functional: any difference from GGA?
Authors: Kieczka Daria , Durrant Thomas , Milton Katherine , Goh Kuan Eng Johnson , Bosman Michel , Shluger Alexander
Published: March 2023

Density functional theory (DFT) with generalised gradient approximation (GGA) functionals is commonly used to predict defect properties in 2D transition metal dichalcogenides (TMDs). Since GGA functionals often underestimate band gaps of semiconductors and incorrectly describe the character of electron localisation in defects and their level positions within the band gap, it is important to assess the accuracy of these predictions. To this end, we used the non-local density functional Perdew—Burke—Ernzerhof (PBE)0-TC-LRC to calculate the properties of a wide range of intrinsic defects in monolayer WS2. The properties, such as geometry, in-gap states, charge transition levels, electronic structure and the electron/hole localisation of the lowest formation energy defects are discussed in detail. They are broadly similar to those predicted by the GGA PBE functional, but exhibit numerous quantitative differences caused by the degree of electron and hole localisation in charged states. For some anti-site defects, more significant differences are seen, with both changes in defect geometries (differences of up to 0.5 Å) as well as defect level positions within the band gap of WS2. This work provides an insight into the performance of functionals chosen for future DFT calculations of TMDs with respect to the desired defect properties.
Deep learning representations for quantum many-body systems on heterogeneous hardware
Authors: Liang Xiao , Li Mingfan , Xiao Qian , Chen Junshi , Yang Chao , An Hong , He Lixin
Published: March 2023

The quantum many-body problems are important for condensed matter physics, however solving the problems are challenging because the Hilbert space grows exponentially with the size of the problem. The recently developed deep learning methods provide a promising new route to solve long-standing quantum many-body problems. We report that a deep learning based simulation can achieve solutions with competitive precision for the spin

J
1

–

J
2

model and fermionic t-J model, on rectangular lattices within periodic boundary conditions. The optimizations of the deep neural networks are performed on the heterogeneous platforms, such as the new generation Sunway supercomputer and the multi graphical-processing-unit clusters. Both high scalability and high performance are achieved within an AI-HPC hybrid framework. The accomplishment of this work opens the door to simulate spin and fermionic lattice models with state-of-the-art lattice size and precision.
Protein Deficient Diets: Cascade Effects on a Lepidopteran Pest and Its Parasitoid Wasp
Authors: Hervet V A D , Laird R A , Floate K D
Published: March 2023

The nutritional quality of herbivorous insects’ food can not only directly affect the herbivorous insects themselves, but can also indirectly affect their parasitoids. To investigate these cascading, multi-trophic effects, we reared cabbage looper, Trichoplusia ni (Hübner) (Lepidoptera: Noctuidae), on artificial diets (8.1, 11.5, 16.75, 25.5, 34.25, and 43 g protein/liter diet) to assess how diet protein content affected the development of this common pest and its suitability as a host for the gregarious parasitoid, Cotesia vanessae (Reinhard) (Hymenoptera: Braconidae). Nonparasitized caterpillars experienced increased mortality when reared on 8.1 g protein/liter diet, and slower development and reduced pupal mass when reared on ≤16.75 g protein/liter diet. Host diet did not affect the percentage of hosts with parasitoid emergence nor the mass of individual parasitoids. However, parasitoid broods emerging from caterpillars reared on ≤25.5 g protein/liter diet were smaller and those reared on ≤16.75 g protein/liter diet exhibited prolonged development. The consequences of host diet on these latter F1 parasitoids did not affect their reproductive fitness. Caterpillars compensated for nutrient stress, induced by either low quality diet or parasitism, by increasing the amount of diet that they consumed. These collective results demonstrate the plasticity of host-parasitoid systems. Compensatory feeding allows the host caterpillar to moderate the consequences of low quality diets, which may subsequently affect the F1 parasitoids developing within the host, but not necessarily affect the F2 parasitoid generation.
Availability and quality of assessment instruments on patient-centredness in older adults with multimorbidity: a systematic review
Authors: Glattacker Manuela , Giesler Juergen M , Bablok Isabella , Kivelitz Laura , Schaefer Jonas , Kanat Manuela , Mohr Jil , Motschall Edith , Voigt-Radloff Sebastian , Kienbaum Thomas , Dirmaier Joerg
Published: March 2023

Objective

Patient-centredness (PC) is central to the health care of older adults with multimorbidity, but knowledge about the psychometric quality of instruments measuring it in this group is scarce. Based on an integrative model of PC, we aimed to identify assessment instruments of PC for this particular group and evaluate their psychometric properties.

Methods

We systematically searched six electronic databases (MEDLINE, CINAHL, EMBASE, PsycINFO, Web of Science and PSYNDEX), initially covering research published up to 2018 and updated later to include work up to July 2022. In evaluating the psychometric properties of identified instruments, we followed the COSMIN methodology.

Results

We identified 12 studies reporting on 10 instruments measuring PC in the health care of older adults with multimorbidity. For these instruments, structural validity and internal consistency were the psychometric properties reported most often. Based on the COSMIN criteria, eight instruments received favourable ratings for internal consistency with respect to methodological quality (‘very good’), measurement property (‘sufficient’) and overall quality of evidence (‘moderate’). Ratings of structural validity varied more largely, with three to seven instruments showing at least adequate methodological quality, sufficient structural validity or moderate quality of evidence.

Conclusions

Similar to comparable previous reviews, evidence on the psychometric properties of instruments assessing PC in the health care of older adults with multimorbidity was rather limited. Informed by comprehensive models of PC, further research should aim at developing measures of PC that stand out on a broader range of psychometric properties.
Different Responses to Social Capital Among Black People and White People: What Racial Differential Item Functioning Reveals for Racial Health Equity
Authors: Villalonga-Olives Ester , Majercak Kayleigh R , Wang Weimeng , Dean Lorraine T , Ransome Yusuf
Published: March 2023

Social capital has been conceptualized as features of social organization, such as networks, and norms that facilitate coordination and cooperation for mutual benefit. Because of long-standing anti-Black structural oppression in the United States, social capital may be associated with health differently for Black people than for other racial/ethnic groups. Our aim was to examine the psychometric properties of social capital indicators, comparing responses from Black and White people to identify whether there is differential item functioning (DIF) in social capital according to race. DIF examines how items are related to a latent construct and whether this relationship differs across groups such as different racial groups. We used data from respondents to the Southeastern Pennsylvania Household Health Survey in 2004, who lived in Philadelphia (n = 2,048), a city with a large Black population. We used item response theory analysis to test for racial DIF. We found DIF across the items, indicating measurement error, which could be related to the way these items were developed (i.e., based on cultural assumptions tested in mainstream White America). Hence, our findings underscore the need to interrogate the assumptions that underly existing social capital items through an equity-based lens, and to take corrective action when developing new items to ensure that they are racially and culturally congruent.
DaDL-SChlo: protein subchloroplast localization prediction based on generative adversarial networks and pre-trained protein language model
Authors: Wang Xiao , Han Lijun , Wang Rong , Chen Haoran
Published: March 2023

Chloroplast is a crucial site for photosynthesis in plants. Determining the location and distribution of proteins in subchloroplasts is significant for studying the energy conversion of chloroplasts and regulating the utilization of light energy in crop production. However, the prediction accuracy of the currently developed protein subcellular site predictors is still limited due to the complex protein sequence features and the scarcity of labeled samples. We propose DaDL-SChlo, a multi-location protein subchloroplast localization predictor, which addresses the above problems by fusing pre-trained protein language model deep learning features with traditional handcrafted features and using generative adversarial networks for data augmentation. The experimental results of cross-validation and independent testing show that DaDL-SChlo has greatly improved the prediction performance of protein subchloroplast compared with the state-of-the-art predictors. Specifically, the overall actual accuracy outperforms the state-of-the-art predictors by 10.7% on 10-fold cross-validation and 12.6% on independent testing. DaDL-SChlo is a promising and efficient predictor for protein subchloroplast localization. The datasets and codes of DaDL-SChlo are available at https://github.com/xwanggroup/DaDL-SChlo.
miProBERT: identification of microRNA promoters based on the pre-trained model BERT
Authors: Wang Xin , Gao Xin , Wang Guohua , Li Dan
Published: March 2023

Accurate prediction of promoter regions driving miRNA gene expression has become a major challenge due to the lack of annotation information for pri-miRNA transcripts. This defect hinders our understanding of miRNA-mediated regulatory networks. Some algorithms have been designed during the past decade to detect miRNA promoters. However, these methods rely on biosignal data such as CpG islands and still need to be improved. Here, we propose miProBERT, a BERT-based model for predicting promoters directly from gene sequences without using any structural or biological signals. According to our information, it is the first time a BERT-based model has been employed to identify miRNA promoters. We use the pre-trained model DNABERT, fine-tune the pre-trained model on the gene promoter dataset so that the model includes information about the richer biological properties of promoter sequences in its representation, and then systematically scan the upstream regions of each intergenic miRNA using the fine-tuned model. About, 665 miRNA promoters are found. The innovative use of a random substitution strategy to construct a negative dataset improves the discriminative ability of the model and further reduces the false positive rate (FPR) to as low as 0.0421. On independent datasets, miProBERT outperformed other gene promoter prediction methods. With comparison on 33 experimentally validated miRNA promoter datasets, miProBERT significantly outperformed previously developed miRNA promoter prediction programs with 78.13% precision and 75.76% recall. We further verify the predicted promoter regions by analyzing conservation, CpG content and histone marks. The effectiveness and robustness of miProBERT are highlighted.
scMCs: a framework for single-cell multi-omics data integration and multiple clusterings
Authors: Ren Liangrui , Wang Jun , Li Zhao , Li Qingzhong , Yu Guoxian
Published: March 2023

Motivation

The integration of single-cell multi-omics data can uncover the underlying regulatory basis of diverse cell types and states. However, contemporary methods disregard the omics individuality, and the high noise, sparsity, and heterogeneity of single-cell data also impact the fusion effect. Furthermore, available single-cell clustering methods only focus on the cell type clustering, which cannot mine the alternative clustering to comprehensively analyze cells.

Results

We propose a single-cell data fusion based multiple clustering (scMCs) approach that can jointly model single-cell transcriptomics and epigenetic data, and explore multiple different clusterings. scMCs first mines the omics-specific and cross-omics consistent representations, then fuses them into a co-embedding representation, which can dissect cellular heterogeneity and impute data. To discover the potential alternative clustering embedded in multi-omics, scMCs projects the co-embedding representation into different salient subspaces. Meanwhile, it reduces the redundancy between subspaces to enhance the diversity of alternative clusterings and optimizes the cluster centers in each subspace to boost the quality of corresponding clustering. Unlike single clustering, these alternative clusterings provide additional perspectives for understanding complex genetic information, such as cell types and states. Experimental results show that scMCs can effectively identify subcellular types, impute dropout events, and uncover diverse cell characteristics by giving different but meaningful clusterings.

Availability and implementation

The code is available at www.sdu-idea.cn/codes.php?name=scMCs.
Attitudes Toward Engagement in Citizen Science Increase Self-Related, Ecology-Related, and Motivation-Related Outcomes in an Urban Wildlife Project
Authors: Greving Hannah , Bruckermann Till , Schumann Anke , Stillfried Milena , Börner Konstantin , Hagen Robert , Kimmig Sophia E , Brandt Miriam , Kimmerle Joachim
Published: March 2023

Citizen science projects are crucial for engaging citizens in conservation efforts. Although attitudes toward engagement in citizen science were mostly considered an outcome of citizen science participation, citizens may also have a certain attitude toward engagement in citizen science when starting with a citizen science project. Moreover, there is a lack of citizen science studies that consider changes over longer periods of time. Therefore, in this research, we present two-wave data from four field studies of a citizen science project about urban wildlife ecology using cross-lagged panel analyses. We investigated the influence of attitudes toward engagement in citizen science on self-related, ecology-related, and motivation-related outcomes. We found that positive attitudes toward engagement in citizen science at the beginning of the project had positive influences on the participants’ psychological ownership and pride in their participation, their attitudes toward and enthusiasm about wildlife, and their internal and external motivation 2 months later. We discuss the implications for citizen science research and practice.
Beyond Content, Understanding What Makes Test Questions Most Challenging
Authors: Marion Sarah B , Reynolds Julie A , Schmid Lorrie , Carter B Elijah , Willis John H , Mauger Laurie , Thompson Robert J
Published: March 2023

When students answer test questions incorrectly, we often assume they don't understand the content; instead, they may struggle with certain cognitive skills or with how questions are asked. Our goal was to look beyond content to understand what makes assessment questions most challenging. On the basis of more than 76,000 answers to multiple-choice questions in a large, introductory biology course, we examined three question components—cognitive skills, procedural knowledge, and question forms—and their interactions. We found that the most challenging questions require the students to organize information and make meaning from it—skills that are essential in science. For example, some of the most challenging questions are presented as unstructured word problems and require interpretation; to answer correctly, the students must identify and extract the important information and construct their understanding from it. Our results highlight the importance of teaching students to organize and make meaning from the content we teach.
A multivariate view of the speciation continuum
Authors: Bolnick Daniel I , Hund Amanda K , Nosil Patrik , Peng Foen , Ravinet Mark , Stankowski Sean , Subramanian Swapna , Wolf Jochen B W , Yukilevich Roman
Published: March 2023

The concept of a “speciation continuum” has gained popularity in recent decades. It emphasizes speciation as a continuous process that may be studied by comparing contemporary population pairs that show differing levels of divergence. In their recent perspective article in Evolution, Stankowski and Ravinet provided a valuable service by formally defining the speciation continuum as a continuum of reproductive isolation, based on opinions gathered from a survey of speciation researchers. While we agree that the speciation continuum has been a useful concept to advance the understanding of the speciation process, some intrinsic limitations exist. Here, we advocate for a multivariate extension, the speciation hypercube, first proposed by Dieckmann et al. in 2004, but rarely used since. We extend the idea of the speciation cube and suggest it has strong conceptual and practical advantages over a one-dimensional model. We illustrate how the speciation hypercube can be used to visualize and compare different speciation trajectories, providing new insights into the processes and mechanisms of speciation. A key strength of the speciation hypercube is that it provides a unifying framework for speciation research, as it allows questions from apparently disparate subfields to be addressed in a single conceptual model.
Asexual male production by ZW recombination inArtemia parthenogenetica
Authors: Boyer Loreleï , Jabbour-Zahab Roula , Joncour Pauline , Glémin Sylvain , Haag Christoph R , Lenormand Thomas
Published: March 2023

In some asexual species, parthenogenetic females occasionally produce males, which may strongly affect the evolution and maintenance of asexuality if they cross with related sexuals and transmit genes causing asexuality to their offspring (“contagious parthenogenesis”). How these males arise in the first place has remained enigmatic, especially in species with sex chromosomes. Here, we test the hypothesis that rare, asexually produced males of the crustacean Artemia parthenogenetica are produced by recombination between the Z and W sex chromosomes during non-clonal parthenogenesis, resulting in ZZ males through loss of heterozygosity at the sex determination locus. We used RAD-sequencing to compare asexual mothers with their male and female offspring. Markers on several sex-chromosome scaffolds indeed lost heterozygosity in all male but no female offspring, suggesting that they correspond to the sex-determining region. Other sex-chromosome scaffolds lost heterozygosity in only a part of the male offspring, consistent with recombination occurring at a variable location. Alternative hypotheses for the production of these males (such as partial or total hemizygosity of the Z) could be excluded. Rare males are thus produced because recombination is not entirely suppressed during parthenogenesis in A. parthenogenetica. This finding may contribute to explaining the maintenance of recombination in these asexuals.
The efficacy of selection may increase or decrease with selfing depending upon the recombination environment
Authors: Sianta Shelley A , Peischl Stephan , Moeller David A , Brandvain Yaniv
Published: March 2023

Much theory has focused on how a population’s selfing rate affects the ability of natural selection to remove deleterious mutations from a population. However, most such theory has focused on mutations of a given dominance and fitness effect in isolation. It remains unclear how selfing affects the purging of deleterious mutations in a genome-wide context where mutations with different selection and dominance coefficients co-segregate. Here, we use individual-based forward simulations and analytical models to investigate how mutation, selection and recombination interact with selfing rate to shape genome-wide patterns of mutation accumulation and fitness. In addition to recovering previously described results for how selfing affects the efficacy of selection against mutations of a given dominance class, we find that the interaction of purifying selection against mutations of different dominance classes changes with selfing and recombination rates. In particular, when recombination is low and recessive deleterious mutations are common, outcrossing populations transition from purifying selection to pseudo-overdominance, dramatically reducing the efficacy of selection. At these parameter combinations, the efficacy of selection remains low until populations hit a threshold selfing rate, above which it increases. In contrast, selection is more effective in outcrossing than (partial) selfing populations when recombination rates are moderate to high and recessive deleterious mutations are rare.
Technical comment on “Negative-assortative mating for color in wolves”
Authors: Muir Christopher D
Published: March 2023

Hedrick et al. (2016) (Negative-assortative mating for color in wolves. Evolution, 70, 757–766) reported on “negative-assortative mating for color in wolves” from Yellowstone National Park, the "first documented case of significant negative-assortative mating in mammals." Here I report a logical inconsistency in their population genetic model that effectively imposes selection against some assortatively mating genotype. After pointing out this inconsistency, I derive new expressions for the frequency of different matings and the equilibrium allele frequencies. Compared to Hedrick et al. (2016) (Negative-assortative mating for color in wolves. Evolution, 70, 757–766), the system rapidly approaches an equilibrium based on observed levels of negative-assortative mating in this population. Hence, the revised model may strengthen the case that assortative mating can maintain polymorphism and provides logically consistent results to inform the study of nonrandom mating in other organisms.
Remating opportunities and low costs underlie maternal desertion
Authors: McDonald Grant C , Cuthill Innes C , Székely Tamás , Kosztolányi András
Published: March 2023

Parental care can enhance offspring survival but may impose significant costs to parents. The costs and benefits of care are key to understanding patterns of parental care, where parents can benefit by having their partner increase investment in care, while reducing their own effort. However, investigating the costs and benefits of parental care in wild populations is challenging. Here we use highly detailed behavioral observations in families of a small shorebird, where one parent frequently deserts its offspring, to explore the potential costs and benefits of desertion in a wild population. We first show that females desert their broods more frequently than males. Second, we investigate the benefits of this frequent female desertion in terms of additional mating opportunities, and the costs of desertion to females in terms of the growth and survival of deserted offspring. Our results indicate that female desertion is favored by a combination of remating benefits and a lack of costs to brood growth and survival, as abandoned male parents continue to provide care after desertion. Our results shed light on the costs and benefits underlying natural desertion strategies and suggest that female desertion is a fine-tuned behavior that responds to seasonally changing benefits of desertion.
Sex matters: predator presence induces sexual dimorphism in a monomorphic prey, from stress genes to morphological defences
Authors: Vinterstare Jerker , Brönmark Christer , Nilsson P Anders , Langerhans R Brian , Chauhan Pallavi , Hansson Bengt , Hulthén Kaj
Published: March 2023

Inducible defences allow prey to increase survival chances when predators are present while avoiding unnecessary costs in their absence. Many studies report considerable inter-individual variation in inducible defence expression, yet what underlies this variation is poorly understood. A classic vertebrate example of a predator-induced morphological defence is the increased body depth in crucian carp (Carassius carassius), which reduces the risk of predation from gape-size limited predators. Here, we report that among-individual variation in morphological defence expression can be linked to sex. We documented sexual dimorphism in lakes in which crucian carp coexisted with predators, where females showed shallower relative body depths than males, but not in a predator-free lake. When exposing crucian carp from a population without predators to perceived predation risk in a laboratory environment (presence/absence of pike, Esox lucius), we found that males expressed significantly greater morphological defence than females, causing sexual dimorphism only in the presence of predators. We uncovered a correlative link between the sex-specific inducible phenotypic response and gene expression patterns in major stress-related genes (POMC, MC3R, and MC4R). Together, our results highlight that sex-specific responses may be an important, yet underappreciated, component underlying inter-individual differences in the expression of inducible defences, even in species without pronounced sexual dimorphism.
Sex, amitosis, and evolvability in the ciliate Tetrahymena thermophila
Authors: Tarkington Jason , Zhang Hao , Azevedo Ricardo B R , Zufall Rebecca A
Published: March 2023

Understanding the mechanisms that generate genetic variation, and thus contribute to the process of adaptation, is a major goal of evolutionary biology. Mutation and genetic exchange have been well studied as mechanisms to generate genetic variation. However, there are additional factors, such as genome architecture, that may also impact the amount of genetic variation in some populations, and the extent to which these variation generating mechanisms are themselves shaped by natural selection is still an open question. To test the effect of genome architecture on the generation of genetic variation, and hence evolvability, we studied Tetrahymena thermophila, a ciliate with an unusual genome structure and mechanism of nuclear division, called amitosis, whereby homologous chromosomes are randomly distributed to daughter cells. Amitosis leads to genetic variation among the asexual descendants of a newly produced sexual progeny because different progeny cells will contain different combinations of parental alleles. We hypothesize that amitosis thus increases the evolvability of newly produced sexual progeny relative to their unmated parents and species that undergo mitosis. To test this hypothesis, we used experimental evolution and simulations to compare the rate of adaptation in T. thermophila populations founded by a single sexual progeny to parental populations that had not had sex in many generations. The populations founded by a sexual progeny adapted more quickly than parental populations in both laboratory populations and simulated populations. This suggests that the additional genetic variation generated by amitosis of a heterozygote can increase the rate of adaptation following sex and may help explain the evolutionary success of the unusual genetic architecture of Tetrahymena and ciliates more generally.