bluuebunny/crossref_metadata_2025 huggingface dataset:
Leveraging multimodal microscopy to optimize deep learning models for cell segmentation
Authors: Cameron William D. , Bennett Alex M. , Bui Cindy V. , Chang Huntley H. , Rocheleau Jonathan V.
Published: January 2021

Deep learning provides an opportunity to automatically segment and extract cellular features from high-throughput microscopy images. Many labeling strategies have been developed for this purpose, ranging from the use of fluorescent markers to label-free approaches. However, differences in the channels available to each respective training dataset make it difficult to directly compare the effectiveness of these strategies across studies. Here, we explore training models using subimage stacks composed of channels sampled from larger, “hyper-labeled,” image stacks. This allows us to directly compare a variety of labeling strategies and training approaches on identical cells. This approach revealed that fluorescence-based strategies generally provide higher segmentation accuracies but were less accurate than label-free models when labeling was inconsistent. The relative strengths of label and label-free techniques could be combined through the use of merging fluorescence channels and using out-of-focus brightfield images. Beyond comparing labeling strategies, using subimage stacks for training was also found to provide a method of simulating a wide range of labeling conditions, increasing the ability of the final model to accommodate a greater range of candidate cell labeling strategies.
A hybrid interferometric system for velocity measurements in shock-wave experiments
Authors: Pavlenko A. V. , Mokrushin S. S. , Tyaktev A. A. , Anikin N. B.
Published: January 2021

This paper presents a hybrid interferometric system designed to measure the surface velocity of tested specimens in shock-wave experiments. The system integrates the All-Fiber Velocity Interferometer System for Any Reflector (AFVISAR) and the Photonic Doppler Velocimeter (PDV) interferometric channels using a single probing system to measure the velocity of one surface point of specimens under study. This design allows the same optical signal containing the Doppler frequency shift to be processed by the AFVISAR and PDV independent interferometric devices. The interferometric system has been tested in dynamic experiments and provides the velocity measurement accuracy of at least 1.5 m/s with a nanosecond time resolution.
Carbon-based nanomaterials for viral infection management
Authors: Yu Jinming , Kuwentrai Chaiyaporn , Huang Jian-Dong , Xu Chenjie
Published: January 2021

Carbon-based nanomaterials such as graphene and nanodiamonds have demonstrated impressive physical and chemical properties, such as remarkable strength, corrosion resistance, and excellent electrical and thermal conductivity, and stability. Because of these unique characteristics, carbon nanomaterials are explored in a wide range of fields, including the diagnosis and treatment of viruses. As there are emerging concerns about the control of virus including Middle East respiratory syndrome virus (MERS), severe acute respiratory syndrome coronavirus (SARS-CoV), and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), this review highlights the recent development of carbon based-nanomaterials for the management of viral infections.
Mid-infrared supercontinuum generation in a low-loss germanium-on-silicon waveguide
Authors: Della Torre Alberto , Sinobad Milan , Armand Remi , Luther-Davies Barry , Ma Pan , Madden Stephen , Mitchell Arnan , Moss David J. , Hartmann Jean-Michel , Reboud Vincent , Fedeli Jean-Marc , Monat Christelle , Grillet Christian
Published: January 2021

We experimentally demonstrate supercontinuum (SC) generation in a germanium-on-silicon waveguide. This waveguide exhibits propagation loss between 1.2 dB/cm and 1.35 dB/cm in the 3.6 µm–4.5 µm spectral region for both transverse electric (TE) and transverse magnetic (TM) polarizations. By pumping the waveguide with ∼200 fs pulses at 4.6 µm wavelength, we generate a mid-infrared (IR) SC spanning nearly an octave from 3.39 µm to 6.02 µm at the −40 dB level. Through numerical analysis of the evolution of the SC, we attribute the current limit to further extension into the mid-IR mainly to free-carrier absorption.
Externally driven bifurcation of current sheet: A particle-in-cell simulation
Authors: Jiang Luxiuyuan , Lu San
Published: January 2021

A current sheet is a confined layer of electric current in the presence of a strong magnetic gradient, which exists ubiquitously in space and the universe. Magnetic energy is stored in current sheets and then potentially released through processes such as magnetic reconnection. Spacecraft observations show that some current sheets in Earth’s magnetotail are bifurcated with a double-peak current density profile. The cause of this bifurcation, however, is still unclear. Here, using a particle-in-cell simulation, we show the bifurcation is formed when the current sheet is thinned by an external driver. In this process, an electron pressure anisotropy (pe⊥ > pe∥) is formed at the center of the current sheet, which decreases the current density at the center, leading to the bifurcated profile of the current density.
Performance and carcass composition of pigs from two sire lines are affected differently by ambient temperature
Authors: Sousa dos Santos Luan , Reis Furtado Campos Paulo Henrique , Cândido da Silva Welex , Veira Alini Mari , Fraga Alicia Zem , Caetano Raphael Perini , Hauschild Luciano
Published: January 2021

Context
Differences among breeds or lines of pigs in terms of growth and carcass characteristics may be affected by rearing environment (genetic × environment interaction).

Aims
The present study compared the growth performance and carcass composition of pigs from two sire lines reared under constant thermoneutral (22°C; TN) or high ambient temperature (33°C; HT) conditions.

Methods
Hampshire (HAM) and synthetic-cross (SYN) castrated male pigs (n = 12 per group; 32.0 ± 2.0 kg) were kept in individual pens at either 22°C (TN) or 33°C (HT) for 55 days (two experimental phases: 0–27 and 28–55 days) following an adaptation period of 7 days. Throughout the experimental period, growth performance and body composition (by dual-energy X-ray absorptiometry on Days 27 and 55) were assessed, and a range of other measurements (serum parameters and physiological responses), which were divided into four measurement groups, was taken on 9 days.

Key results
Irrespective of genetic line (G), the pigs in the HT treatment had lower average daily feed intake values (P < 0.001, by 29% and 41%) than did the pigs in the TN treatment during both experimental phases (0–27 and 28–55 days). During the second growth phase, the average daily gain of the SYN pigs in the HT treatment was reduced by 50%, whereas that of the HAM pigs was reduced by 24% (P < 0.05 for G × ambient temperature (AT)). On Days 27 and 55, pig bodyweight was lower (P < 0.05) in the HT treatment than in the TN treatment. On Day 27, a G × AT interaction was detected for backfat thickness (P < 0.05); among the SYN pigs, the value of this trait was lower (16%; P < 0.05) in the HT treatment than in the TN treatment, while for the HAM pigs, it was not influenced by treatment type.

Conclusion
Despite progeny from both genetic lines being affected negatively by high AT, the purebred HAM pigs were less affected by the high AT conditions than were the pigs from the synthetic line.

Implication
The present findings suggest that individual farm conditions and AT are among the most important factors to consider before implementing a G.
Hegemonic masculinity predicts 2016 and 2020 voting and candidate evaluations
Authors: Vescio Theresa K. , Schermerhorn Nathaniel E. C.
Published: January 2021

Significance

Donald J. Trump’s history-making ascension from nonpolitician to president of the United States has been attributed to the antiestablishment, antielitist, and nativist populism of Trump voters, as well as to sexism, racism, homophobia, and xenophobia. Based on the findings of seven studies involving 2,007 people, men’s and women’s endorsement of hegemonic masculinity predicted support for Trump over and beyond the aforementioned factors, even when controlling for political party affiliation. Results highlight the importance of looking beyond social identity–based conceptualizations of masculinity to fully consider how men’s and women’s endorsement of cultural ideologies about masculinity legitimate patriarchal forms of dominance and reify gender-, race-, and class-based hierarchies.
Prediction of elite athletes’ performance by analysis of peak‐performance age and age‐related performance progression
Authors: Gorzi Ali , Khantan Mina , Khademnoe Omid , Eston Roger
Published: January 2021

The aim of this study was to analyse age‐related performance progression and peak‐performance age (PPA) in elite track and field athletes and to use a model to predict peak performance. Best performances of world‐class athletes from ages 14 to 15 y up to and including the last Olympic year (n = 798), all‐time top lists (n = 444), and world record‐holders (n = 43) were considered in all 22 disciplines for men and 21 disciplines for women. A discipline/sex‐specified model was used by applying dynamic panel data methods to analyze the performance trends. Profile analysis showed that PPA of all‐time top list throwers was higher than middle‐distance runners (P < 0.001), distance runners (P < 0.05), and jumpers (P < 0.05) in men and higher (P < 0.05) than middle‐distance runners in women. Olympic year top list athletes showed that PPA of women throwers was higher than sprinters (P < 0.001) and middle‐distance runners (P < 0.05), and PPA of women distance runners was higher (P < 0.05) than sprinters. In both all‐time (P < 0.05) and Olympic year (P < 0.05) top lists, the PPA of men race walkers was higher than middle‐distance runners. Performance over the preceding 1–2 years (in all disciplines), height (in Long Jump Men; Long Jump Women; Triple Jump Men) and weight (in Discus Throwing Men) indices, respectively, are important (P < 0.05) for predicting future records with different coefficients in different disciplines. The models provide a useful tool for coaches to predict peak performance records and PPA of their athletes which may be of benefit with goal‐setting and evaluation of performance progression at different ages in track and field athletics.
Environmental Action Scale: psychometric properties of the Portuguese version (Escala de Acciones Ambientales: propiedades psicométricas de la versión portuguesa)
Authors: Carmona Beatriz , Loureiro Ana , Aguilar-Luzón M. Carmen
Published: January 2021

The Environmental Action Scale (EAS) is an 18-item questionnaire designed to assess the degree of involvement in collective actions in favour of the environment. This scale is of interest for research in environmental domains, particularly the recent study of environmental activism. The main objective of this study is to contribute to the adaptation and validation of the Portuguese version of the EAS. The EAS Portuguese version — following its adaptation — was administered to a total of 346 participants. Confirmatory factor analysis revealed the two dimensions considered by the authors of the original version: participatory actions and leadership actions. In addition, evidence of validity was obtained based on the relationship with other variables such as environmental identity. In conclusion, the Portuguese version maintains the 18 items and replicates the two-factor structure, showing good psychometric properties.
Morphologies of a spherical bimodal polyelectrolyte brush induced by polydispersity and solvent selectivity*
Authors: Hao Qing-Hai , Cheng Jie
Published: January 2021

It is commonly realized that polydispersity may significantly affect the surface modification properties of polymer brush systems. In light of this, we systematically study morphologies of bidisperse polyelectrolyte brush grafted onto a spherical nanocolloid in the presence of trivalent counterions using molecular dynamics simulations. Via varying polydispersity, grafting density, and solvent selectivity, the effects of electrostatic correlation and excluded volume are focused, and rich phase behaviors of binary mixed polyelectrolyte brush are predicted, including a variety of pinned-patch morphologies at low grafting density and micelle-like structures at high grafting density. To pinpoint the mechanism of surface structure formation, the shape factor of two species of polyelectrolyte chains and the pair correlation function between monomers from different polyelectrolyte ligands are analyzed carefully. Also, electrostatic correlations, manifested as the bridging through trivalent counterions, are examined by identifying four states of trivalent counterions. Our simulation results may be useful for designing smart stimuli-responsive materials based on mixed polyelectrolyte coated surfaces.
A modified analytical model of the alkali-metal atomic magnetometer employing longitudinal carrier field*
Authors: Chen Chang , Zhang Yi , Wang Zhi-Guo , Jiang Qi-Yuan , Luo Hui , Yang Kai-Yong
Published: January 2021

Alkali-metal atomic magnetometers employing longitudinal carrier magnetic field have ultrahigh sensitivity to measure transverse magnetic fields and have been applied in a variety of precise-measurement science and technologies. In practice, the magnetometer response is not rigorously proportional to the measured transverse magnetic fields and the existing fundamental analytical model of this magnetometer is effective only when the amplitudes of the measured fields are very small. In this paper, we present a modified analytical model to characterize the practical performance of the magnetometer more definitely. We find out how the longitudinal magnetization of the alkali metal atoms vary with larger transverse fields. The linear-response capacity of the magnetometer is determined by these factors: the amplitude and frequency of the longitudinal carrier field, longitudinal and transverse spin relaxation time of the alkali spins and rotation frequency of the transverse fields. We give a detailed and rigorous theoretical derivation by using the perturbation-iteration method and simulation experiments are conducted to verify the validity and correctness of the proposed modified model. This model can be helpful for measuring larger fields more accurately and configuring a desirable magnetometer with proper linear range.
Deterministic nondestructive state analysis for polarization-spatial-time-bin hyperentanglement with cross-Kerr nonlinearity*
Authors: Zhang Hui-Rong , Wang Peng , Yu Chang-Qi , Ren Bao-Cang
Published: January 2021

We present a deterministic nondestructive hyperentangled Bell state analysis protocol for photons entangled in three degrees of freedom (DOFs), including polarization, spatial-mode, and time-bin DOFs. The polarization Bell state analyzer and spatial-mode Bell state analyzer are constructed by polarization parity-check quantum nondemolition detector (P-QND) and spatial-mode parity-check quantum nondemolition detector (S-QND) using cross-Kerr nonlinearity, respectively. The time-bin Bell state analyzer is constructed by the swap gate for polarization state and time-bin state of a photon (P-T swap gate) and P-QND. The Bell states analyzer for one DOF will not destruct the Bell states of other two DOFs, so the polarization-spatial-time-bin hyperentangled Bell states can be determinately distinguished without destruction. This deterministic nondestructive state analysis method has useful applications in quantum information protocols.
Bilayer twisting as a mean to isolate connected flat bands in a kagome lattice throughWigner crystallization*
Authors: Wu Jing , Xie Yue-E , Chen Ming-Xing , Yuan Jia-Ren , Yan Xiao-Hong , Zhang Sheng-Bai , Chen Yuan-Ping
Published: January 2021

The physics of flat band is novel and rich but difficult to access. In this regard, recently twisting of bilayer van der Waals (vdW)-bounded two-dimensional (2D) materials has attracted much attention, because the reduction of Brillouin zone will eventually lead to a diminishing kinetic energy. Alternatively, one may start with a 2D kagome lattice, which already possesses flat bands at the Fermi level, but unfortunately these bands connect quadratically to other (dispersive) bands, leading to undesirable effects. Here, we propose, by first-principles calculation and tight-binding modeling, that the same bilayer twisting approach can be used to isolate the kagome flat bands. As the starting kinetic energy is already vanishingly small, the interlayer vdW potential is always sufficiently large irrespective of the twisting angle. As such the electronic states in the (connected) flat bands become unstable against a spontaneous Wigner crystallization, which is expected to have interesting interplays with other flat-band phenomena such as novel superconductivity and anomalous quantum Hall effect.
Superfluid phases and excitations in a cold gas of d-wave interacting bosonic atoms and molecules*
Authors: Li Zehan , Pan Jian-Song , Liu W Vincent
Published: January 2021

Motivated by recent advances in orbitally tuned Feshbach resonance experiments, we analyze the ground-state phase diagram and related low-energy excitation spectra of a d-wave interacting Bose gas. A two-channel model with d-wave symmetric interactions and background s-wave interactions is adopted to characterize the gas. The ground state is found to have three interesting superfluid phases: atomic, molecular, and atomic–molecular. In great contrast to what was previously known about the p-wave case, the atomic superfluid is found to be momentum-independent for the d-wave case discussed here. The Bogoliubov spectra above each superfluid phase are obtained both analytically and numerically.
Properties of B4C-TiB2 ceramics prepared by spark plasma sintering*
Authors: Fan Jingzhe , Shen Weixia , Zhang Zhuangfei , Fang Chao , Zhang Yuewen , Chen Liangchao , Wang Qianqian , Wan Biao , Jia Xiaopeng
Published: January 2021

By doping titanium hydride (TiH2) into boron carbide (B4C), a series of B4C + x wt% TiH2 (x = 0, 5, 10, 15, and 20) composite ceramics were obtained through spark plasma sintering (SPS). The effects of the sintering temperature and the amount of TiH2 additive on the microstructure, mechanical and electrical properties of the sintered B4C-TiB2 composite ceramics were investigated. Powder mixtures of B4C with 0–20 wt% TiH2 were heated from 1400 °C to 1800 °C for 20 min under 50 MPa. The results indicated that higher sintering temperatures contributed to greater ceramic density. With increasing TiH2 content, titanium diboride (TiB2) formed between the TiH2 and B4C matrix. This effectively improved Young’s modulus and fracture toughness of the composite ceramics, significantly improving their electrical properties: the electrical conductivity reached 114.9 S⋅cm−1 at 1800 °C when x = 20. Optimum mechanical properties were obtained for the B4C ceramics sintered with 20 wt% TiH2, which had a relative density of 99.9 ± 0.1%, Vickers hardness of 31.8 GPa, and fracture toughness of 8.5 MPa⋅m1 / 2. The results indicated that the doping of fine Ti particles into the B4C matrix increased the conductivity and the fracture toughness of B4C.
ℋ∞state estimation for Markov jump neural networks with transition probabilities subject to the persistent dwell-time switching rule*
Authors: Shen Hao , Wu Jia-Cheng , Xia Jian-Wei , Wang Zhen
Published: January 2021

We investigate the problem ofℋ∞state estimation for discrete-time Markov jump neural networks. The transition probabilities of the Markov chain are assumed to be piecewise time-varying, and the persistent dwell-time switching rule, as a more general switching rule, is adopted to describe this variation characteristic. Afterwards, based on the classical Lyapunov stability theory, a Lyapunov function is established, in which the information about the Markov jump feature of the system mode and the persistent dwell-time switching of the transition probabilities is considered simultaneously. Furthermore, via using the stochastic analysis method and some advanced matrix transformation techniques, some sufficient conditions are obtained such that the estimation error system is mean-square exponentially stable with anℋ∞performance level, from which the specific form of the estimator can be obtained. Finally, the rationality and effectiveness of the obtained results are verified by a numerical example.
Localized electric-field-enhanced low-light detection by a 2D SnS visible-light photodetector*
Authors: Wen Hao , Xiong Li , Tan Congbing , Zhu Kaimin , Tang Yong , Wang Jinbin , Zhong Xiangli
Published: January 2021

Due to their excellent carrier mobility, high absorption coefficient and narrow bandgap, most 2D IVA metal chalcogenide semiconductors (GIVMCs, metal = Ge, Sn, Pb; chalcogen = S, Se) are regarded as promising candidates for realizing high-performance photodetectors. We synthesized high-quality two-dimensional (2D) tin sulfide (SnS) nanosheets using the physical vapor deposition (PVD) method and fabricated a 2D SnS visible-light photodetector. The photodetector exhibits a high photoresponsivity of 161 A⋅W−1 and possesses an external quantum efficiency of 4.45 × 104%, as well as a detectivity of 1.15 × 109 Jones under 450 nm blue light illumination. Moreover, under poor illumination at optical densities down to 2 mW⋅cm−2, the responsivity of the device is higher than that at stronger optical densities. We suggest that a photogating effect in the 2D SnS photodetector is mainly responsible for its low-light responsivity. Defects and impurities in 2D SnS can trap carriers and form localized electric fields, which can delay the recombination process of electron-hole pairs, prolong carrier lifetimes, and thus improve the low-light responsivity. This work provides design strategies for detecting low levels of light using photodetectors made of 2D materials.
An SBT-memristor-based crossbar memory circuit*
Authors: Guo Mei , Liu Ren-Yuan , Dou Ming-Long , Dou Gang
Published: January 2021

Implementing memory using nonvolatile, low power, and nano-structure memristors has elicited widespread interest. In this paper, the SPICE model of Sr0.95Ba0.05TiO3 (SBT)-memristor was established and the corresponding characteristic was analyzed. Based on an SBT-memristor, the process of writing, reading, and rewriting of the binary and multi-value memory circuit was analyzed. Moreover, we verified the SBT-memristor-based 4 × 4 crossbar binary and multi-value memory circuits through comprehensive simulations, and analyzed the sneak-path current and memory density. Finally, we apply the 8 × 8 crossbar multi-value memory circuits to the images memory.
Electric-field-induced in-plane effective 90° magnetization rotation in Co2FeAl/PMN-PT structure*
Authors: Zhou Cai , Zhu Dengyu , Liu Fufu , Feng Cunfang , Zhang Mingfang , Ding Lei , Xu Mingyao , Wang Shengxiang
Published: January 2021

The in-plane effective 90° magnetization rotation of Co2FeAl thin film grown on PMN-PT substrate induced by the electric field is investigated at room temperature. The magnetic hysteresis loops under different positive and negative electric fields are obtained, which reveals remanent magnetization can be mediated by the electric field. Moreover, under positive electric fields, the obvious 90° magnetization rotation can be observed, while remanent magnetization is nearly unchanged under negative electric fields. The result is consistent with the electric field dependence of effective magnetic field, which can be attributed to the piezostrain effect in Co2FeAl/PMN-PT structure. In addition, the piezostrain-mediated 90° magnetization rotation can be demonstrated by the result of resonance field changing with electric field in the measurement of ferromagnetic resonance, which is promising for the design of future multiferroic devices.
Furi–Martelli–Vignoli spectrum and Feng spectrum of nonlinear block operator matrices*
Authors: Dong Xiao-Mei , Wu De-Yu , Chen Alatancang
Published: January 2021

We investigate the Furi–Martelli–Vignoli spectrum and the Feng spectrum of continuous nonlinear block operator matrices, and mainly describe the relationship between the Furi–Martelli–Vignoli spectrum (compared to the Feng spectrum) of the whole operator matrix and that of its entries. In addition, the connection between the Furi–Martelli–Vignoli spectrum of the whole operator matrix and that of its Schur complement is presented by means of Schur decomposition.
Bose–Einstein condensates under a non-Hermitian spin–orbit coupling*
Authors: Li Hao-Wei , Sun Jia-Zheng
Published: January 2021

We study the properties of Bose–Einstein condensates under a non-Hermitian spin–orbit coupling (SOC), induced by a dissipative two-photon Raman process. We focus on the dynamics of the condensate at short times, when the impact of decoherence induced by quantum jumps is negligible and the dynamics is coherently driven by a non-Hermitian Hamiltonian. Given the significantly modified single-particle physics by dissipative SOC, the interplay of non-Hermiticity and interaction leads to a quasi-steady-state phase diagram different from its Hermitian counterpart. In particular, we find that dissipation can induce a phase transition from the stripe phase to the plane-wave phase. We further map out the phase diagram with respect to the dissipation and interaction strengths, and finally investigate the stability of quasi-steady states through the time-dependent dissipative Gross–Pitaevskii equation. Our results are readily accessible based on standard experiments with synthetic spin–orbit couplings.
Surface plasmon polaritons induced reduced hacking
Authors: Bakhtawar  , Haneef Muhammad , Khan Humayun
Published: January 2021

There is always need for secure transmission of information and simultaneously compact-size photonic circuits. This can be achieved if surface plasmon-polaritons (SPPs) are used as source of information, and the reduced hacking as the transmission phenomenon. In this article, an SPP-based reduced hacking scheme is presented at interface between atomic medium and metallic conductor. The SPP propagation is manipulated with conductivity of the metal. The delay or advance of the SPP is found to create nanosecond time gap which can be used for storing and sending the information safely. The reduced hacking is further modified with conductivity of the metal and the control parameters of the atomic medium.
Sustained attention to response task-related beta oscillations relate to performance and provide a functional biomarker in ALS
Authors: McMackin Roisin , Dukic Stefan , Costello Emmet , Pinto-Grau Marta , Keenan Orla , Fasano Antonio , Buxo Teresa , Heverin Mark , Reilly Richard , Pender Niall , Hardiman Orla , Nasseroleslami Bahman
Published: January 2021

Objective. To characterize the cortical oscillations associated with performance of the sustained attention to response task (SART) and their disruptions in the neurodegenerative condition amyotrophic lateral sclerosis (ALS). Approach. A randomised SART was undertaken by 24 ALS patients and 33 healthy controls during 128-channel electroencephalography (EEG). Complex Morlet wavelet transform was used to quantify non-phase-locked oscillatory activity in event-related spectral perturbations associated with performing the SART. We investigated the relationships between these perturbations and task performance, and associated motor and cognitive changes in ALS. Main results. SART induced theta-band event-related synchronization (ERS) and alpha- and beta-band event-related desynchronization (ERD), followed by rebound beta ERS, in both Go and NoGo trials across the frontoparietal axis, with NoGo trials eliciting greater theta ERS and lesser beta ERS. Controls with greater Go trial beta ERS performed with greater speed and less accuracy. ALS patients exhibited increased anticipation compared to controls but similar reaction times and accuracy. Prefrontal (area under the receiver operating characteristic curve (AUROC) = 0.8, Cohen’s d = 0.97) and parietal (AUROC = 0.82, Cohen’s d = 1.12) beta-band ERD was significantly reduced in ALS but did not relate to performance, while patients with higher Edinburgh Cognitive and Behavioural ALS Screen (ECAS) ALS-specific scores demonstrated greater ERS in beta (rho = 0.72) upon successful withholding. Significance. EEG measurement of task-related oscillation changes reveals variation in cortical network engagement in relation to speed versus accuracy strategies. Such measures can also capture cognitive and motor network pathophysiology in the absence of task performance decline, which may facilitate development of more sensitive early neurodegenerative disease biomarkers.
An ongoing cooling in the eastern Pacific linked to eastward migrations of the Southeast Pacific Subtropical Anticyclone
Authors: Zou Youjia , Xi Xiangying
Published: January 2021

Previous studies demonstrate that recent global warming hiatuses are associated with an ongoing cooling in the eastern Pacific. However, the possible driver for this cooling remains vigorously debated. Present theories can be generally categorized into three different frameworks, the most prevailing theory considering the increased heat uptake in ocean interior as a direct trigger in cooling the eastern equatorial Pacific, the next regarding the prolonged solar minimum as a potential driver in producing weak radiative forcing over the Pacific, while another suggesting that changes in atmospheric water vapour and aerosols play an unnegligible role in absorbing and reflecting solar radiation. Most recently, some studies argue that the ongoing cooling in the eastern Pacific is induced by a strengthening of the easterly trade winds. Nevertheless, observational records coming from the monitoring buoys deployed along the equator by NOAA since 1992 indicate that an intensification of the trade winds is only confined to the central tropical Pacific (around 170° E–170° W) during hiatus decades, elsewhere along the equatorial Pacific the trade winds exhibit a stable condition even a slight weakening in the eastern equatorial Pacific, rendering it as a trigger of this cooling in the eastern Pacific unlikely. Here we use a model and long-term observational data to demonstrate that a persistent cooling in the eastern Pacific is directly linked to an eastward displacement of the Southeast Pacific Subtropical Anticyclone (SPSA). Interactions between the Andes and an eastward shift of the SPSA generate greater pressure gradients in the eastern flank, in turn, stronger alongshore winds and more intense upwelling, ultimately contributing to hiatus decades.
Demand side climate change mitigation actions and SDGs: literature review with systematic evidence search
Authors: Roy Joyashree , Some Shreya , Das Nandini , Pathak Minal
Published: January 2021

To strengthen current discourse on acceleration and scale up of the emissions mitigation actions by sector-specific demand side actions, information on the intersection of three dimensions becomes useful. First, what kind of actions help in avoiding, shifting and improving demand for activities/services and resultant emissions to help in deciding choices for actions; second, how these three categories of actions are linked to the wider impact on human wellbeing represented by the Sustainable Development Goals (SDGs) framework; and third, who are the actors associated with these mitigation actions. These three steps become important in the targeted scaling up of actions through policy interventions. This study undertakes a review of the literature between 2015 and 2020 with systematic evidence searching and screening. The literature search has been conducted in Scopus Database. From over 6887 literature in the initial search, 294 relevant literature were finally reviewed to link demand side interventions of avoid-shift-improve (ASI) categories to SDGs. It also maps these actions to actors who can lead the changes. Results show that a wide range of improvement actions are already helping in incremental steps to reduce demand and emissions in various services like mobility, shelter and industrial products. However, ASI categories provide more distinct mitigation actions. All actions need support of innovation, infrastructure development and industrialization. Actions that interact with several SDGs include active mode of transport, passive building design, cleaner cooking, and circular economy. Positive links of these actions to multiple SDGs are overall very strong; however, few trade-offs have been observed. These are mostly related to distributional impact across social groups which highlight the need for policy attention and hard infrastructure design changes. Mitigation and wider benefit outcomes cannot be achieved by individual or household level actions alone. They require the involvement of multiple actors, interconnected actions in sequence as well as in parallel, and support of hard infrastructure. Our results show that in mobility services, policy makers supported by spatial planners and service delivery providers are the major actors. In industry, major actors are policy makers followed by spatial planners and innovators. For buildings, key actors include spatial planners followed by policy makers. Besides these, strategic information sharing to enhance user awareness and education plays an important role in shaping behaviour. Digitalization, information and communication, and interactive technologies will play a significant role in understanding and modifying people’s choices; however, these would also require regulatory attention.
A thermodynamic description of the hysteresis in specific-heat curves in glass transitions
Authors: Shirai Koun
Published: January 2021

By refining the definition of thermodynamic equilibrium and state variables (thermodynamic coordinate, TC) for solids, it is determined that the state of a glass substance transforms into an equilibrium state after it is solidified. In contrast, the state of a glass substance during the glass transition is a nonequilibrium state. The specific-heat (C) versus temperature (T) curve exhibits hysteresis, which is traditionally believed to invalidate thermodynamic methods. However, the glass transition slowly occurs in a manner such that structural change is decoupled with the fast process of thermal relaxation of phonons, which enables us to describe the hysteresis by thermodynamic methods. The hysteresis is caused by the structural relaxation and the time of relaxation is determined by the energy barrier, which depends solely on the current value of TCs. Therefore, the state in hysteresis can be described by the information of the current structure alone: history-dependent response functions are unnecessary. On the basis of these conclusions, the behavior of the C-T curve with changing heating/cooling rate γ is simulated. The main features of the hysteresis, the shift of C to higher temperatures with increasing γ, the hump structure, and the memory effect are well reproduced from a structure-dependent energy barrier. In view of the structural dependence of the energy barrier, it is not surprising to observe deviations from the Arrhenius law. However, only the terms that are higher than linear in T are observed in Arrhenius plot as the deviation. An important finding of this study is that the apparent energy barrier obtained using the Arrhenius plot significantly overestimates the real value. The extraordinarily large values of the pre-exponential factor of the relaxation time can also be understood on this basis.
Why can deep convolutional neural networks improve protein fold recognition? A visual explanation by interpretation
Authors: Liu Yan , Zhu Yi-Heng , Song Xiaoning , Song Jiangning , Yu Dong-Jun
Published: January 2021

As an essential task in protein structure and function prediction, protein fold recognition has attracted increasing attention. The majority of the existing machine learning-based protein fold recognition approaches strongly rely on handcrafted features, which depict the characteristics of different protein folds; however, effective feature extraction methods still represent the bottleneck for further performance improvement of protein fold recognition. As a powerful feature extractor, deep convolutional neural network (DCNN) can automatically extract discriminative features for fold recognition without human intervention, which has demonstrated an impressive performance on protein fold recognition. Despite the encouraging progress, DCNN often acts as a black box, and as such, it is challenging for users to understand what really happens in DCNN and why it works well for protein fold recognition. In this study, we explore the intrinsic mechanism of DCNN and explain why it works for protein fold recognition using a visual explanation technique. More specifically, we first trained a VGGNet-based DCNN model, termed VGGNet-FE, which can extract fold-specific features from the predicted protein residue–residue contact map for protein fold recognition. Subsequently, based on the trained VGGNet-FE, we implemented a new contact-assisted predictor, termed VGGfold, for protein fold recognition; we then visualized what features were extracted by each of the convolutional layers in VGGNet-FE using a deconvolution technique. Furthermore, we visualized the high-level semantic information, termed fold-discriminative region, of a predicted contact map from the localization map obtained from the last convolutional layer of VGGNet-FE. It is visually confirmed that VGGNet-FE could effectively extract distinct fold-discriminative regions for different types of protein folds, thereby accounting for the improved performance of VGGfold for protein fold recognition. In summary, this study is of great significance for both understanding the working principle of DCNNs in protein fold recognition and exploring the relationship between the predicted protein contact map and protein tertiary structure. This proposed visualization method is flexible and applicable to address other DCNN-based bioinformatics and computational biology questions. The online web server of VGGfold is freely available at http://csbio.njust.edu.cn/bioinf/vggfold/.
Genome annotation of disease-causing microorganisms
Authors: Dong Yibo , Li Chang , Kim Kami , Cui Liwang , Liu Xiaoming
Published: January 2021

Humans have coexisted with pathogenic microorganisms throughout its history of evolution. We have never halted the exploration of pathogenic microorganisms. With the improvement of genome-sequencing technology and the continuous reduction of sequencing costs, an increasing number of complete genome sequences of pathogenic microorganisms have become available. Genome annotation of this massive sequence information has become a daunting task in biological research. This paper summarizes the approaches to the genome annotation of pathogenic microorganisms and the available popular genome annotation tools for prokaryotes, eukaryotes and viruses. Furthermore, real-world comparisons of different annotation tools using 12 genomes from prokaryotes, eukaryotes and viruses were conducted. Current challenges and problems were also discussed.
Bios2cor: an R package integrating dynamic and evolutionary correlations to identify functionally important residues in proteins
Authors: Taddese Bruck , Garnier Antoine , Deniaud Madeline , Henrion Daniel , Chabbert Marie
Published: January 2021

Both dynamic correlations in protein sidechain motions during molecular dynamics (MD) simulations and evolutionary correlations in multiple sequence alignments (MSAs) of homologous proteins may reveal functionally important residues. We developed the R package Bios2cor that provides a unique framework to investigate and, possibly, integrate both analyses. Bios2cor starts with an MSA or an MD trajectory and computes correlation/covariation scores between positions in the MSA or between sidechain dihedral angles or rotamers in the MD trajectory. In addition, Bios2cor provides a variety of tools for the analysis, the visualization and the interpretation of the data.

Availability and implementation

The R package Bios2cor is available from the Comprehensive R Archive Network, at https://CRAN.R-project.org/package=Bios2cor.
A transgenic DND1GFP fusion allele reports in vivo expression and RNA-binding targets in undifferentiated mouse germ cells
Authors: Ruthig Victor A , Yokonishi Tetsuhiro , Friedersdorf Matthew B , Batchvarova Sofia , Hardy Josiah , Garness Jason A , Keene Jack D , Capel Blanche
Published: January 2021

In vertebrates, the RNA-binding protein (RBP) dead end 1 (DND1) is essential for primordial germ cell (PGC) survival and maintenance of cell identity. In multiple species, Dnd1 loss or mutation leads to severe PGC loss soon after specification or, in some species, germ cell transformation to somatic lineages. Our investigations into the role of DND1 in PGC specification and differentiation have been limited by the absence of an available antibody. To address this problem, we used CRISPR/Cas9 gene editing to establish a transgenic mouse line carrying a DND1GFP fusion allele. We present imaging analysis of DND1GFP expression showing that DND1GFP expression is heterogeneous among male germ cells (MGCs) and female germ cells (FGCs). DND1GFP was detected in MGCs throughout fetal life but lost from FGCs at meiotic entry. In postnatal and adult testes, DND1GFP expression correlated with classic markers for the premeiotic spermatogonial population. Utilizing the GFP tag for RNA immunoprecipitation (RIP) analysis in MGCs validated this transgenic as a tool for identifying in vivo transcript targets of DND1. The DND1GFP mouse line is a novel tool for isolation and analysis of embryonic and fetal germ cells, and the spermatogonial population of the postnatal and adult testis.
Serum biomarkers in primary mitochondrial disorders
Authors: Varhaug Kristin N , Hikmat Omar , Nakkestad Hanne Linda , Vedeler Christian A , Bindoff Laurence A
Published: January 2021

The aim of this study was to explore the utility of the serum biomarkers neurofilament light chain, fibroblast growth factor 21 and growth and differentiation factor 15 in diagnosing primary mitochondrial disorders. We measured serum neurofilament light chain, fibroblast growth factor 21 and growth and differentiation factor 15 in 26 patients with a genetically proven mitochondrial disease. Fibroblast growth factor 21 and growth and differentiation factor 15 were measured by enzyme-linked immunosorbent assay and neurofilament light chain with the Simoa assay. Neurofilament light chain was highest in patients with multi-systemic involvement that included the central nervous system such as those with the m.3242A>G mutation. Mean neurofilament light chain was also highest in patients with epilepsy versus those without [49.74 pg/ml versus 19.7 pg/ml (P = 0.015)], whereas fibroblast growth factor 21 and growth and differentiation factor 15 levels were highest in patients with prominent myopathy, such as those with single-mitochondrial DNA deletion. Our results suggest that the combination of neurofilament light chain, fibroblast growth factor 21 and growth and differentiation factor 15 is useful in the diagnostic evaluation of mitochondrial disease. Growth and differentiation factor 15 and fibroblast growth factor 21 identify those with muscle involvement, whereas neurofilament light chain is a clear marker for central nervous system involvement independent of underlying mitochondrial pathology. Levels of neurofilament light chain appear to correlate with the degree of ongoing damage suggesting, therefore, that monitoring neurofilament light chain levels may provide prognostic information and a way of monitoring disease activity.
An update on the rod microglia variant in experimental and clinical brain injury and disease
Authors: Giordano Katherine R , Denman Charlotte R , Dubisch Phoebe S , Akhter Murtaza , Lifshitz Jonathan
Published: January 2021

Contemporary microglia morphologies include ramified, activated and amoeboid, with the morphology of microglia considered highly coupled to the cellular function. Rod microglia are an additional activated microglia variant observed in the ageing, injured and diseased brain. Rod microglia were reported frequently in the early 1900s by neuropathologists in post-mortem cases of general paresis, Alzheimer’s disease and encephalitis, and then remained largely ignored for almost 100 years. Recent reports have renewed interest in rod microglia, most notably after experimental traumatic brain injury. Rod microglia are formed by the narrowing of the soma and retraction of planar processes, which results in the appearance of an elongated, rod-shaped cell. Rod microglia are most commonly observed in the cortex, aligned perpendicular to the dural surface and adjacent to neuronal processes; in the hippocampus, they are aligned perpendicular to hippocampal layers. Furthermore, rod microglia form trains with one another, apical end to basal end. By replicating the process of sketching microscopic observation, rod microglia are re-defined by circumnutation around the long axis. In this update, we summarize the rod microglia variant in clinical and experimental literature and advocate for investigation into mechanisms of rod microglia origin and function.
Fumaric acid ester-induced renal Fanconi syndrome: evidence of mitochondrial toxicity
Authors: Wan Elizabeth R , Siew Keith , Heptinstall Lauren , Walsh Stephen B
Published: January 2021

Background

Fumaric acid esters (FAEs) are used to treat chronic plaque psoriasis. Fumarate is a crucial component of the Krebs cycle and mitochondrial function. Proximal tubule cells have high energy demands and rely on aerobic respiration. Proximal tubular dysfunction can cause renal Fanconi syndrome and acute kidney injury. We sought to better understand the mechanism for this in the context of FAE therapy.

Methods

We describe a case series of 10 patients with FAE-associated Fanconi syndrome. Patients were diagnosed and managed at a tertiary renal tubular disorder clinic, with examination of serum and urine biochemistry. Five patients had a renal biopsy with examination of the specimens by electron microscopy.

Results

The median age was 36.5 years [interquartile range (IQR) 32.25–54.25]. The median dose of FAE was 720 mg/day (IQR 390–720). There was low molecular weight proteinuria: the median urinary retinol-binding protein (RBP) at presentation was 8385 μg/mL (IQR 2793–14 600) and the RBP:creatinine ratio was 710 (IQR 390–2415). All patients had hyperphosphaturia [median fractional excretion of phosphate 24.2% (IQR 20.8–26.9), normal range <20%] as well as relative hypophosphataemia, with a median serum phosphate concentration of 0.93 mmol/L (IQR 0.83–0.97). Renal histology showed proximal tubular damage and abnormal mitochondrial morphology. Two patients had a favourable biochemical response to treatment with probenecid.

Conclusions

We document for the first time that FAE-associated renal Fanconi syndrome is associated with mitochondrial damage visible on electron microscopy. This effect may be ameliorated by antagonism of the organic anion transporter with probenecid.