bluuebunny/crossref_metadata_2025 huggingface dataset:
Single-trajectory map equation
Authors: Kawamoto Tatsuro
Published: April 2023

Community detection, the process of identifying module structures in complex systems represented on networks, is an effective tool in various fields of science. The map equation, which is an information-theoretic framework based on the random walk on a network, is a particularly popular community detection method. Despite its outstanding performance in many applications, the inner workings of the map equation have not been thoroughly studied. Herein, we revisit the original formulation of the map equation and address the existence of its “raw form,” which we refer to as the single-trajectory map equation. This raw form sheds light on many details behind the principle of the map equation that are hidden in the steady-state limit of the random walk. Most importantly, the single-trajectory map equation provides a more balanced community structure, naturally reducing the tendency of the overfitting phenomenon in the map equation.
Potential utility of risk stratification for multicancer screening with liquid biopsy tests
Authors: Kim Elle S. , Scharpf Robert B. , Garcia-Closas Montserrat , Visvanathan Kala , Velculescu Victor E. , Chatterjee Nilanjan
Published: April 2023

Our proof-of-concept study reveals the potential of risk stratification by the combined effects of age, polygenic risk scores (PRS), and non-genetic risk factors in increasing the risk-benefit balance of rapidly emerging non-invasive multicancer early detection (MCED) liquid biopsy tests. We develop and validate sex-specific pan-cancer risk scores (PCRSs), defined by the combination of body mass index, smoking, family history of cancers, and cancer-specific polygenic risk scores (PRSs), to predict the absolute risk of developing at least one of the many common cancer types. We demonstrate the added value of PRSs in improving the predictive performance of the risk factors only model and project the positive and negative predictive values for two promising multicancer screening tests across risk strata defined by age and PCRS.
HaploCoV: unsupervised classification and rapid detection of novel emerging variants of SARS-CoV-2
Authors: Chiara Matteo , Horner David S. , Ferrandi Erika , Gissi Carmela , Pesole Graziano
Published: April 2023

Accurate and timely monitoring of the evolution of SARS-CoV-2 is crucial for identifying and tracking potentially more transmissible/virulent viral variants, and implement mitigation strategies to limit their spread. Here we introduce HaploCoV, a novel software framework that enables the exploration of SARS-CoV-2 genomic diversity through space and time, to identify novel emerging viral variants and prioritize variants of potential epidemiological interest in a rapid and unsupervised manner. HaploCoV can integrate with any classification/nomenclature and incorporates an effective scoring system for the prioritization of SARS-CoV-2 variants. By performing retrospective analyses of more than 11.5 M genome sequences we show that HaploCoV demonstrates high levels of accuracy and reproducibility and identifies the large majority of epidemiologically relevant viral variants - as flagged by international health authorities – automatically and with rapid turn-around times.

Our results highlight the importance of the application of strategies based on the systematic analysis and integration of regional data for rapid identification of novel, emerging variants of SARS-CoV-2. We believe that the approach outlined in this study will contribute to relevant advances to current and future genomic surveillance methods.
NF-κB/p52 augments ETS1 binding genome-wide to promote glioma progression
Authors: Sim Nicholas , Li Yinghui
Published: April 2023

Gliomas are highly invasive and chemoresistant cancers, making them challenging to treat. Chronic inflammation is a key driver of glioma progression as it promotes aberrant activation of inflammatory pathways such as NF-κB signalling, which drives cancer cell invasion and angiogenesis. NF-κB factors typically dimerise with its own family members, but emerging evidence of their promiscuous interactions with other oncogenic factors has been reported to promote transcription of new target genes and function. Here, we show that non-canonical NF-κB activation directly regulates p52 at the ETS1 promoter, activating its expression. This impacts the genomic and transcriptional landscape of ETS1 in a glioma-specific manner. We further show that enhanced non-canonical NF-κB signalling promotes the co-localisation of p52 and ETS1, resulting in transcriptional activation of non-κB and/or non-ETS glioma-promoting genes. We conclude that p52-induced ETS1 overexpression in glioma cells remodels the genome-wide regulatory network of p52 and ETS1 to transcriptionally drive cancer progression.
Spontaneous tumor regression mediated by human T cells in a humanized immune system mouse model
Authors: Patel A. K. , Dhanik Ankur , Lim Wei Keat , Adler Christina , Ni Min , Wei Yi , Zhong Maggie , Nguyen Cindy , Zhong Jun , Lu Yi-Fen , Thurston Gavin , Macdonald Lynn , Murphy Andrew , Gurer Cagan , Frleta Davor
Published: April 2023

Immunodeficient mice reconstituted with a human immune system (HIS mice) give rise to human T cells, which make them an attractive system to study human immune responses to tumors. However, such HIS mice typically exhibit sub-optimal responses to immune challenges as well as fail to develop antigen-specific B or T cell memory. Here we report HIS mice mediate spontaneous regression of human B cell lymphoma Raji. Tumor regression was dependent on CD4+ and CD8+ T cell responses and resulted in T cell memory. The T cell memory elicited was mainly Raji-specific, however some level of cross-protection was also elicited to a related B cell lymphoma cell line Ramos. Single-cell RNAseq analysis indicated activation of CD8+ T cells in regressing Raji tumors as well as clonal expansion of specific T cell receptors (TCRs). Cloning of TCRs from Raji-infiltrating T cells into a Jurkat reporter cell line showed reactivity specific for Raji tumor cells. Overall, we report a platform for studying in vivo human T cell tumor immunity by highlighting spontaneous Raji tumor regression, clonal TCR expansion, and T cell memory in HIS mice.
Search for a Grotthuss mechanism through the observation of proton transfer
Authors: Popov Ivan , Zhu Zhenghao , Young-Gonzales Amanda R. , Sacci Robert L. , Mamontov Eugene , Gainaru Catalin , Paddison Stephen J. , Sokolov Alexei P.
Published: April 2023

The transport of protons is critical in a variety of bio- and electro-chemical processes and technologies. The Grotthuss mechanism is considered to be the most efficient proton transport mechanism, generally implying a transfer of protons between ‘chains’ of host molecules via elementary reactions within the hydrogen bonds. Although Grotthuss proposed this concept more than 200 years ago, only indirect experimental evidence of the mechanism has been observed. Here we report the first experimental observation of proton transfer between the molecules in pure and 85% aqueous phosphoric acid. Employing dielectric spectroscopy, quasielastic neutron, and light scattering, and ab initio molecular dynamic simulations we determined that protons move by surprisingly short jumps of only ~0.5–0.7 Å, much smaller than the typical ion jump length in ionic liquids. Our analysis confirms the existence of correlations in these proton jumps. However, these correlations actually reduce the conductivity, in contrast to a desirable enhancement, as is usually assumed by a Grotthuss mechanism. Furthermore, our analysis suggests that the expected Grotthuss-like enhancement of conductivity cannot be realized in bulk liquids where ionic correlations always decrease conductivity.
Electric vehicle fleet penetration helps address inequalities in air quality and improves environmental justice
Authors: Chang Shih Ying , Huang Jiaoyan , Chaveste Melissa R. , Lurmann Frederick W. , Eisinger Douglas S. , Mukherjee Anondo D. , Erdakos Garnet B. , Alexander Marcus , Knipping Eladio
Published: April 2023

Accelerated penetration of on-road electric vehicles offers regional and community-scale air quality benefits; however, such benefits have not been previously quantified regarding environmental justice communities near major roads. This study evaluated six 2040 electric vehicle scenarios and quantified concentration reductions of nitrogen dioxide and fine particulate matter (diameter less than 2.5 µm) for southern California environmental justice communities near Interstate 710. Findings showed that aggressive electric vehicle penetration (85% electric vehicle share) reduced nitrogen dioxide and fine particulate matter concentrations more in communities with more people of color (1.9 ppb and 1.1 μg m−3) than in communities with more White residents (1.6 ppb and 0.94 μg m−3). Aggressive electric vehicle penetration reduced pollution exposure disparity by 30% for nitrogen dioxide and 14% for fine particulate matter. Disparity reductions were also found based on educational attainment. Results suggest policies that encourage accelerated electric vehicle penetration will address inequalities in air pollution and help achieve environmental justice.
Microscopic charcoals in ocean sediments off Africa track past fire intensity from the continent
Authors: Haliuc Aritina , Daniau Anne-Laure , Mouillot Florent , Chen Wentao , Leys Bérangère , David Valérie , Hanquiez Vincent , Dennielou Bernard , Schefuß Enno , Bayon Germain , Crosta Xavier
Published: April 2023

Fires in Africa account for more than half of global fire-carbon emissions but the long-term evolution of fire activity and its link to global climate change remains elusive. Paleofire records provide descriptive information about fire changes through time, going beyond the range of satellite observations, although fire regime characteristics are challenging to reconstruct. To address this conceptual gap, we report here the abundance and morphometric data for a large set of microscopic charcoal samples (n = 128) recovered from surface ocean sediments offshore Africa. We show that in subtropical Southern Africa, large and intense fires prevailing in open savanna-grassland ecosystems produce a high abundance of small and elongated microcharcoal particles. In contrast, in the forest ecosystems of equatorial and tropical regions of western and central Africa, low-intensity fires dominate, producing low amounts of squared microcharcoal particles. Microcharcoal concentration and morphotype in marine sediment records off Africa are thus indicative of fire regime characteristics. Applied to down-core marine charcoal records, these findings reveal that at orbital time-scale intense and large, open grassland-savanna fires occurred during wet periods in the sub-tropical areas. A strong contribution of fire carbon emissions during periods of precession and summer insolation maxima in the geological record is thus expected.
Global mining footprint mapped from high-resolution satellite imagery
Authors: Tang Liang , Werner Tim T.
Published: April 2023

Mining is of major economic, environmental and societal consequence, yet knowledge and understanding of its global footprint is still limited. Here, we produce a global mining land use dataset via remote sensing analysis of high-resolution, publicly available satellite imagery. The dataset comprises 74,548 polygons, covering ~66,000 km2 of features like waste rock dumps, pits, water ponds, tailings dams, heap leach pads and processing/milling infrastructure. Our polygons finely contour the edges of mine features and do not include the space between them. This distinguishes our dataset from others that employ broader definitions of mining lands. Hence, despite our database being the largest to date by number of polygons, comparisons show relatively lower global land use. Our database is made freely available to support future studies of global mining impacts. A series of spatial analyses are also presented that highlight global mine distribution patterns and broader environmental risks.
Recent advances in the synthesis of cyclic sulfinic acid derivatives (sultines and cyclic sulfinamides)
Authors: Zhang Yongxin , Li Helian , Yang Xiaoxiao , Zhou Pan , Shu Chao
Published: April 2023

This feature article discusses the state-of-play of cyclic sulfinic acid derivative (sultines and cyclic sulfinamides) formation.
Advances in organic semiconductors for photocatalytic hydrogen evolution reaction
Authors: Guo Yan , Zhou Qixin , Zhu Bowen , Tang Chuyang Y. , Zhu Yongfa
Published: April 2023

This article reviews organic photocatalyst hydrogen evolution reaction (HER), discussing the excitonic behaviour and improvement strategies. It also covers progress in organic photocatalysts, and assesses HER efficiency and stability.
Indian traditional rice variety “Gathuwan” suppresses T-cell-mediated immune responsesviaactivation of ERK/Nrf2/HO-1 signalling pathway
Authors: Chauhan Anjali , Checker Rahul , Nair Sunil , Sahu Parmeshwar K. , Sharma Deepak , Sharma Deepak , Das Bikram K.
Published: April 2023

Gathuwan brown rice extract inhibited T-cell mediated immune responses, bothin vitroandin vivo, through Nrf2 dependent mechanisms. The putative compound classes conferring these properties were identified through enrichment analysis of UHPLC-MS/MS data.
Emerging trends in mesoporous silica nanoparticle-based catalysts for CO2utilization reactions
Authors: Mohan Anandhu , Jaison Augustine , Lee Young-Chul
Published: April 2023

Mesoporous silica nanoparticles (MSNs) have modifiable porous surfaces, can be easily modified/functionalized, and have good chemical/thermal stability; thus, they are promising candidates in the field of CO2conversion/reduction reactions.
CeO2 stabilized by tourmaline as a novel inorganic filler to simultaneously increase the conductivity and durability of proton exchange membranes
Authors: Pei Supeng , Xu Kangwei , Xu Xiaojun , Liu Guipeng , Ma Jialu , Zhang Yingge , Zou Yecheng , Liu Feng , Zhang Yongming , Zhou Yongfeng
Published: April 2023

Optimized PFSA/TM-CeO2 (1 wt%) showed enhanced fuel cell power density while maintaining outstanding chemical stability compared to pristine PFSA.
Hypoxic tumor therapy based on free radicals
Authors: Zheng Jingtao , Pan Yanyan , Chen Yubin , Li Junyan , Li Weishuo
Published: April 2023

This review summarizes the physicochemical and biological characteristics of hypoxic tumor tissues. And then, the construction principles of different atom-centered free-radical based hypoxic tumor therapies are discussed in detail.
Flower-like Cu9S8nanocatalysts with highly active sites for synergistic NIR-II photothermal therapy and chemodynamic therapy
Authors: Zou Quan , Pan Haiyan , Zhang Xuening , Zhang Cai
Published: April 2023

One-pot biomineralization fabricated protamine-stabilized flower-like Cu9S8nanocatalysts possessing high surface area and superior photothermal ability for successful synergistic photothermal therapy and chemodynamic therapy of tumors.
Two kinds of average approximation accuracy
Authors: Kong Qingzhao , Wang Wanting , Zhang Dongxiao , Zhang Wenbin
Published: April 2023

Rough set theory places great importance on approximation accuracy, which is used to gauge how well a rough set model describes a target concept. However, traditional approximation accuracy has limitations since it varies with changes in the target concept and cannot evaluate the overall descriptive ability of a rough set model. To overcome this, two types of average approximation accuracy that objectively assess a rough set model’s ability to approximate all information granules is proposed. The first is the relative average approximation accuracy, which is based on all sets in the universe and has several basic properties. The second is the absolute average approximation accuracy, which is based on undefinable sets and has yielded significant conclusions. We also explore the relationship between these two types of average approximation accuracy. Finally, the average approximation accuracy has practical applications in addressing missing attribute values in incomplete information tables.
A small‐area and low‐power all‐digital duty cycle corrector with de‐skew circuit
Authors: Hai Ya , Liu Fei , Wang Yongshan , Kang Jing
Published: April 2023

This paper proposes a small‐area and low‐power all‐digital duty cycle corrector with de‐skew circuit. By adopting the proposed delay unit containing a pre‐charge transistor, half cycle delay line can accurately generate half‐cycle delay, thus ensuring that the circuit can achieve duty cycle correction with small area and low power. To achieve high‐precision clock synchronization, the proposed de‐skew circuit utilizes a high‐resolution two‐stage digital control delay line to eliminate the additional clock skew between the input clock and output clock of the circuit. The test chip is fabricated in 130 nm CMOS process and the area only occupies 0.009 mm2. The chip testing results show that duty cycle correction error is within 3.2% and phase error is less than 16 ps when input duty cycle from 20% to 80% at the frequency range from 380 MHz to 1.25 GHz. And the proposed circuit only consumes 3 mW when supply voltage is 1.2 V and clock frequency is 1 GHz.
A novel miniaturized sext‐band bandstop filter based on tree‐shaped branches loaded asymmetric multimode resonators
Authors: Luo Jie , Zhao Guangxu , Sheng Zhongxi , Gao Shanshan
Published: April 2023

The working mechanism of suggested tunable bandstop filtered with asymmetrical multiple‐mode resonator equipped with tree‐shape branches is described in this letter. Because of the established degree of freedom, the suggested bandstop filters’ (BSFs) centre frequencies may be modified based on the design approach. Meanwhile, the suggested BSFs have small dimensions and abrupt roll‐off skirts for transition bands. A technology demonstration filter with six stopbands placed at 1.91/2.38/3.54/5.19/5.79/6.85 GHz was constructed to verify the design and analyses. It is found that the measurement of a filter is consistent with the comparison of simulation data, which indicates that the proposed structure is an optional approach for BSF design. The filter proposed can be applied in the field of communication, information and coal mine automation.
A single‐source switched‐capacitor based 13‐level sextuple boost inverter with reduced component count and low THD
Authors: Hussan Md Reyaz , Sarwar Adil , Tayyab Mohammad , Tariq Mohd , Bakhsh Farhad Ilahi , Ahmad Akbar
Published: April 2023

A switched‐capacitor‐based 13‐level inverter with a lesser number of components is presented in this article. The 13‐level single‐phase AC output voltage is achieved with a voltage gain of 6 by including a single DC source, 11 switches, 4 capacitors, and 3 diodes in the proposed converter. The self‐voltage balancing is achieved for various types of load without the need for complex control schemes and auxiliary circuits. The proposed topology does not require a back‐end H‐bridge to generate negative polarity. This leads to a reduction in voltage stresses across the switches. Thus, total standing voltage (TSV) and the overall cost of the proposed topology are reduced as compared to the state‐of‐the‐art topologies reported in the literature. Furthermore, an Improved Nearest Level Modulation (INLM) scheme is used to improve the power quality of the output voltage. Using the proposed scheme, the Total Harmonic Distortion (THD) of the output voltage is reduced to 5.08%. The power loss analysis for various elements of the proposed converter is also included. A comparison with recent topologies in reference to various performance parameters is carried out. In addition to the simulation study, a laboratory prototype is prepared to validate the efficacy of the proposed converter.
HEAT: Incorporating hierarchical enhanced attention transformation into urban road detection
Authors: Han Ting , Li Chuanmu , Chen Siyu , Wang Zongyue , Su Jinhe , Wu Yundong , Cai Guorong
Published: April 2023

Road detection plays a vital role in automated driving and advanced driver assistance systems. In recent years, mainstream frameworks have suffered from the restrictions of a receptive field and the limitation of modelling long‐range relations. Previous methods fail to segment precise road boundaries when urban roads with similar surface textures are presented. Moreover, road regions are perceived as non‐road areas due to the shadow effect, which affects the completeness of the road in the traffic environment. To this end, for urban road detection, a hierarchical enhanced attention transformation (HEAT) architecture, which holds both fine details (road edges) and global contextual information (road structure) is proposed. The symmetrical data‐fusion residual network fuses visual semantic and spatial structure information. The attention consolidation units model global contextual information at different layers to realize the feature enhancement from coarse to fine. In addition, corresponding local and global features are fused hierarchically in the progressive up‐sampling modules. Comprehensive empirical studies are conducted to compare other mainstream methods in the KITTI and the Cityscapes dataset. HEAT shows highly competitive performance in that confusable areas are correctly distinguished in the presence of obstacles, shadows, and similar road textures. HEAT outperforms state‐of‐the‐art methods in urban road detection.
Globular clusters in the Galactic center region: Expected behavior within the infall and merger scenario
Authors: Navarro Maria Gabriela , Capuzzo-Dolcetta Roberto , Arca-Sedda Manuel , Minniti Dante
Published: April 2023

In this work, we reexamine the infall and merger scenario of massive clusters in the Milky Way’s potential well as a plausible Milky Way formation mechanism. We aim to understand how the stars of the merging clusters are redistributed during and after the merger process. We used, for the first time, high-resolution simulations with concentrated in the 300 pc around the Galactic center. We adopted simulations developed in the framework of the Modelling the Evolution of Galactic Nuclei (MEGaN) project. We compared the evolution of representative clusters in the mass and concentration basis in the vicinity of a supermassive black hole. We used the spatial distribution, density profile, and the 50% Lagrange radius (half mass radius) as indicators along the complete simulation to study the evolutionary shape in physical and velocity space and the final fate of these representative clusters. We find that the least massive clusters are quickly (< 10 Myr) destroyed. On the other hand, the most massive clusters have a long evolution, showing variations in the morphology, especially after each passage close to the supermassive black hole. The deformation of the clusters depends on the concentration, with general deformations for the least concentrated clusters and outer strains for the more concentrated ones. At the end of the simulation, a dense concentration of stars belonging to the clusters was formed. The particles that belong to the most massive and most concentrated clusters are concentrated in the innermost regions, meaning that the most massive and concentrated clusters contribute a more significant fraction of particles to the final concentration. This finding suggests that the population of stars of the nuclear star cluster formed through this mechanism comes from massive clusters rather than low-mass globular clusters.
A validation of the Pseudoscience Endorsement Scale and assessment of the cognitive correlates of pseudoscientific beliefs
Authors: Torres Marta N. , Barberia Itxaso , Rodríguez-Ferreiro Javier
Published: April 2023

Pseudoscientific beliefs are widespread and have potentially harmful consequences. Being able to identify their presence and recognize the factors characterizing their endorsement is crucial to understanding their prevalence. In this preregistered study, we validated the English version of the Pseudoscience Endorsement Scale and investigated its correlates. A group of volunteers (n = 510), representative of the U.S. population, responded to this scale and to questionnaires measuring the presence of paranormal, denialist, and conspiracist beliefs. The validation resulted in a shorter version of the scale, the sPES. Participants also completed a scientific literacy questionnaire as well as bullshit detection and cognitive reflection tests. Scores obtained on the questionnaires corresponding to different unwarranted beliefs correlated with each other, suggesting a possible common basis. Scientific knowledge, cognitive reflection scores, and bullshit sensitivity were negatively associated with scores on the pseudoscience scale. Of note, bullshit receptivity was the main contributor in a model predicting pseudoscience endorsement.
Associations between attachment-related variables in fifth and sixth graders and their mothers in Japan
Authors: Inagawa Michiyo , Nakao Tatsuma
Published: April 2023

Obtaining data from non-Western cultural contexts is essential for enhancing the cross-cultural validity of attachment theory. This study investigated the associations among maternal attachment style, maternal willingness to serve as an attachment figure, and children’s attachment security in middle childhood in Japan. Sample 1 included a nationwide web survey of 104 dyads of fifth and sixth graders and their mothers. Sample 2 included 53 dyads in an in-person questionnaire survey conducted in Kyoto. In both Samples 1 and 2, the results revealed (1) negative Spearman’s rank correlation coefficients between maternal attachment anxiety and children’s attachment security, (2) positive Pearson’s product-moment correlation coefficients between maternal willingness to serve as an attachment figure and children’s attachment security, and (3) negative Pearson’s product-moment correlation coefficients between maternal attachment anxiety and maternal willingness to serve as an attachment figure. Our data could enhance the cross-cultural validity of attachment in fifth and sixth graders, and suggest that the influence of maternal attachment styles on parental responsiveness changes in middle childhood.
Floquet dynamical quantum phase transitions in transverse XY spin chains under periodic kickings
Authors: Luan Li-Na , Zhang Mei-Yu , Wang Lin-Cheng
Published: April 2023

Floquet dynamical quantum phase transitions (DQPTs), which are nonanalytic phenomena recuring periodically in time-periodic driven quantum many-body systems, have been widely studied in recent years. In this article, the Floquet DQPTs in transverse XY spin chains under the modulation of δ-function periodic kickings are investigated. We analytically solve the system, and by considering the eigenstate as well as the ground state as the initial state of the Floquet dynamics, we study the corresponding multiple Floquet DQPTs emerged in the micromotion with different kicking moments. The rate function of return amplitude, the Pancharatnam geometric phase and the dynamical topological order parameter are calculated, which consistently verify the emergence of Floquet DQPTs in the system.
β-Ga2O3 junction barrier Schottky diode with NiO p-well floating field rings
Authors: He 何 Qiming 启鸣 , Hao 郝 Weibing 伟兵 , Li 李 Qiuyan 秋艳 , Han 韩 Zhao 照 , He 贺 Song 松 , Liu 刘 Qi 琦 , Zhou 周 Xuanze 选择 , Xu 徐 Guangwei 光伟 , Long 龙 Shibing 世兵
Published: April 2023

Recently, β-Ga2O3, an ultra-wide bandgap semiconductor, has shown great potential to be used in power devices blessed with its unique material properties. For instance, the measured average critical field of the vertical Schottky barrier diode (SBD) based on β-Ga2O3 has reached 5.45 MV/cm, and no device in any material has measured a greater before. However, the high electric field of the β-Ga2O3 SBD makes it challenging to manage the electric field distribution and leakage current. Here, we show β-Ga2O3 junction barrier Schottky diode with NiO p-well floating field rings (FFRs). For the central anode, we filled a circular trench array with NiO to reduce the surface field under the Schottky contact between them to reduce the leakage current of the device. For the anode edge, experimental results have demonstrated that the produced NiO/β-Ga2O3 heterojunction FFRs enable the spreading of the depletion region, thereby mitigating the crowding effect of electric fields at the anode edge. Additionally, simulation results indicated that the p-NiO field plate structure designed at the edges of the rings and central anode can further reduce the electric field. This work verified the feasibility of the heterojunction FFRs in β-Ga2O3 devices based on the experimental findings and provided ideas for managing the electric field of β-Ga2O3 SBD.
Self-generated vortex flows in a tokamak magnetic island with a background flow
Authors: Choi G.J.
Published: April 2023

We present a gyrokinetic theory of self-generated E × B vortex flows in a magnetic island in a collisionless tokamak plasma with a background vortex flow. We find that the long-term evolution of the self-generated vortex flows can be classified into two regimes by the background vortex flow potential Φ, with an asymptotic criterion given by

e

Φ

c
r

/

T
=
ϵ
w

/

r

, where T is temperature, ε is the inverse aspect ratio and r is the radial coordinate. We find that the background vortex flow above the criterion significantly weakens the toroidal precession-induced long-term damping and structure change of the self-generated vortex flows. That is, the finite background vortex flow is beneficial to maintain the self-generated vortex flows, favorable to an internal transport barrier formation. Our result indicates that the island boundary region is a prominent location for triggering the transition to an enhanced confinement state of the magnetic island.
Characterization method of the Joule heating efficiency of electric textiles and influence of boundary conditions
Authors: Shuvo Ikra Iftekhar , Decaens Justine , Dolez Patricia I
Published: April 2023

Joule heating textiles are available on the market for a variety of applications. However, their market growth is limited by challenges in terms of quality, for instance with the need to provide a reliable account of the heating to be expected, prevent the occurrence of overheating leading to burns and fires, and ensure the long-term performance when exposed to use conditions such as abrasion and laundering. Standard test methods are a key component to solve these issues of efficiency, safety, and durability. Yet, they mostly remain to be established. In this research, a test method was developed for the characterization of the Joule heating efficiency of electric textiles. It involves measuring the temperature of a heating textile using a thermocouple affixed to its surface while it is powered for an hour. The value of the surface temperature that would ultimately be reached by the heating textile after an infinite heating time and the time for the temperature to enter a slow increase regime are determined by fitting an equation to the temperature-time data. These two parameters provide a quantitative mean of comparison between different heating textiles/conditions. This test method was used to analyze the effect of different experimental conditions on the heating efficiency of four heaters corresponding to different technologies of Joule heating textiles and make recommendations in terms of conditions for a standardized test protocol. These results give some insights towards the development of a robust and universal test method for the quantitative assessment of the Joule heating efficiency of electrical textiles that will ultimately be proposed for standardization to help support the growth of the e-textile industry.
Voting Decisions and Racialized Fluidity in South Africa’s Metropolitan Municipalities
Authors: Paret Marcel , Runciman Carin
Published: April 2023

Do racial identities determine voting behaviour in post-apartheid South Africa? To address this question, we draw from a representative sample of 3,905 registered voters in five metropolitan municipalities: Johannesburg, Tshwane, Durban, Cape Town, and Nelson Mandela Bay. Our findings are mixed. On the one hand, Black voters were significantly more likely to vote for the African National Congress, whereas Coloured, Indian, and especially white voters were more likely to vote for the Democratic Alliance. This contrast comes into particular focus when we examine how voters acted over the course of a three-election period. On the other hand, race was far from a guaranteed predictor, not the least because many chose to abstain from voting—a trend that extended, though unevenly, to all racial groups. Importantly, though, the electorate did not split between party loyalists and consistent abstainers. Instead, fluidity predominated: About half of the electorate changed positions between elections, either by switching between parties or between voting and abstaining. Our findings thus demonstrate what we call ‘racialized fluidity’: Many voters are changing their voting decision from one election to the next, but in the aggregate, racial identity remains correlated with voting decisions.
Peer Counselor Intervention for Reducing Mortality and/or Hospitalization in Adults With Hypertensive Urgency in Tanzania: A Pilot Study
Authors: Kisigo Godfrey A , Mgeta Frank , Mcharo Onike , Okello Elialilia , Wajanga Bahati , Kalokola Fredrick , Mtui Graham , Sundararajan Radhika , Peck Robert N
Published: April 2023

BACKGROUND

Worldwide, people with hypertensive urgency experience high rates of hospitalization and death due to medication non-adherence. Interventions to improve medication adherence and health outcomes after hypertensive urgency are urgently needed.

METHODS

This prospective cohort assessed the effect of a peer counselor intervention—named Rafiki mwenye msaada—on the 1-year incidence of hospitalization and/or death among adults with hypertensive urgency in Mwanza, Tanzania. We enrolled 50 patients who presented with hypertensive urgency to 2 hospitals in Mwanza, Tanzania. All 50 patients received a Rafiki mwenye msaada an individual-level, time-limited case management intervention. Rafiki mwenye msaada aims to empower adult patients with hypertensive urgency to manage their high blood pressure. It consists of 5 sessions delivered over 3 months by a peer counselor. Outcomes were compared to historical controls.

RESULTS

Of the 50 patients (median age, 61 years), 34 (68%) were female, and 19 (38%) were overweight. In comparison to the historical controls, the intervention cohort had a significantly lower proportion of patients with a secondary level of education (22% vs. 35%) and health insurance (40% vs. 87%). Nonetheless, the 1-year cumulative incidence of hospitalization and/or death was 18% in the intervention cohort vs. 35% in the control cohort (adjusted Hazard Ratio, 0.48, 95% CI 0.24–0.97; P = 0.041). Compared to historical controls, intervention participants maintained higher rates of medication use and clinic attendance at both 3- and 6-months but not at 12 months. Of intervention participants who survived and remained in follow-up, >90% reported good medication adherence at all follow-up time points.

CONCLUSION

Our findings support the hypothesis that a peer counselor intervention may improve health outcomes among adults living with hypertensive urgency. A randomized clinical trial is needed to evaluate the intervention’s effectiveness.
RBAtools: a programming interface for Resource Balance Analysis models
Authors: Bodeit Oliver , Ben Samir Inès , Karr Jonathan R , Goelzer Anne , Liebermeister Wolfram
Published: April 2023

Motivation

Efficient resource allocation can contribute to an organism’s fitness and can improve evolutionary success. Resource Balance Analysis (RBA) is a computational framework that models an organism’s growth-optimal proteome configurations in various environments. RBA software enables the construction of RBA models on genome scale and the calculation of medium-specific, growth-optimal cell states including metabolic fluxes and the abundance of macromolecular machines. However, existing software lacks a simple programming interface for non-expert users, easy to use and interoperable with other software.

Results

The python package RBAtools provides convenient access to RBA models. As a flexible programming interface, it enables the implementation of custom workflows and the modification of existing genome-scale RBA models. Its high-level functions comprise simulation, model fitting, parameter screens, sensitivity analysis, variability analysis and the construction of Pareto fronts. Models and data are represented as structured tables and can be exported to common data formats for fluxomics and proteomics visualization.

Availability and implementation

RBAtools documentation, installation instructions and tutorials are available at https://sysbioinra.github.io/rbatools/. General information about RBA and related software can be found at rba.inrae.fr.
Digital PCR cluster predictor: a universal R-package and shiny app for the automated analysis of multiplex digital PCR data
Authors: De Falco Alfonso , Olinger Christophe M , Klink Barbara , Mittelbronn Michel , Stieber Daniel
Published: April 2023

Digital polymerase chain reaction (dPCR) is an emerging technology that enables accurate and sensitive quantification of nucleic acids. Most available dPCR systems have two channel optics, with ad hoc software limited to the analysis of single and duplex assays. Although multiplexing strategies were developed, variable assay designs, dPCR systems, and the analysis of low DNA input data restricted the ability for a universal automated clustering approach. To overcome these issues, we developed dPCR Cluster Predictor (dPCP), an R package and a Shiny app for automated analysis of up to 4-plex dPCR data. dPCP can analyse and visualize data generated by multiple dPCR systems carrying out accurate and fast clustering not influenced by the amount and integrity of input of nucleic acids. With the companion Shiny app, the functionalities of dPCP can be accessed through a web browser.
HOTSPOT: hierarchical host prediction for assembled plasmid contigs with transformer
Authors: Ji Yongxin , Shang Jiayu , Tang Xubo , Sun Yanni
Published: April 2023

Motivation

As prevalent extrachromosomal replicons in many bacteria, plasmids play an essential role in their hosts’ evolution and adaptation. The host range of a plasmid refers to the taxonomic range of bacteria in which it can replicate and thrive. Understanding host ranges of plasmids sheds light on studying the roles of plasmids in bacterial evolution and adaptation. Metagenomic sequencing has become a major means to obtain new plasmids and derive their hosts. However, host prediction for assembled plasmid contigs still needs to tackle several challenges: different sequence compositions and copy numbers between plasmids and the hosts, high diversity in plasmids, and limited plasmid annotations. Existing tools have not yet achieved an ideal tradeoff between sensitivity and precision on metagenomic assembled contigs.

Results

In this work, we construct a hierarchical classification tool named HOTSPOT, whose backbone is a phylogenetic tree of the bacterial hosts from phylum to species. By incorporating the state-of-the-art language model, Transformer, in each node’s taxon classifier, the top-down tree search achieves an accurate host taxonomy prediction for the input plasmid contigs. We rigorously tested HOTSPOT on multiple datasets, including RefSeq complete plasmids, artificial contigs, simulated metagenomic data, mock metagenomic data, the Hi-C dataset, and the CAMI2 marine dataset. All experiments show that HOTSPOT outperforms other popular methods.

Availability and implementation

The source code of HOTSPOT is available via: https://github.com/Orin-beep/HOTSPOT
DIGGER-Bac: prediction of seed regions for high-fidelity construction of synthetic small RNAs in bacteria
Authors: Philipp Niklas , Brinkmann Cedric K , Georg Jens , Schindler Daniel , Berghoff Bork A
Published: April 2023

Synthetic small RNAs (sRNAs) are gaining increasing attention in the field of synthetic biology and bioengineering for efficient post-transcriptional regulation of gene expression. However, the optimal design of synthetic sRNAs is challenging because alterations may impair functions or off-target effects can arise. Here, we introduce DIGGER-Bac, a toolbox for Design and Identification of seed regions for Golden Gate assembly and Expression of synthetic sRNAs in Bacteria. The SEEDling tool predicts optimal sRNA seed regions in combination with user-defined sRNA scaffolds for efficient regulation of specified mRNA targets. Results are passed on to the G-GArden tool, which assists with primer design for high-fidelity Golden Gate assembly of the desired synthetic sRNA constructs.
Smoking is a predictor of complications in all types of surgery: a machine learning-based big data study
Authors: Gräsbeck Helene L , Reito Aleksi R P , Ekroos Heikki J , Aakko Juhani A , Hölsä Olivia , Vasankari Tuula M
Published: April 2023

Background

Machine learning algorithms are promising tools for smoking status classification in big patient data sets. Smoking is a risk factor for postoperative complications in major surgery. Whether this applies to all surgery is unknown. The aims of this retrospective cohort study were to develop a machine learning algorithm for clinical record-based smoking status classification and to determine whether smoking and former smoking predict complications in all surgery types.

Methods

All surgeries performed in a Finnish hospital district from 1 January 2015 to 31 December 2019 were analysed. Exclusion criteria were age below 16 years, unknown smoking status, and unknown ASA class. A machine learning algorithm was developed for smoking status classification. The primary outcome was 90-day overall postoperative complications in all surgeries. Secondary outcomes were 90-day overall complications in specialties with over 10 000 surgeries and critical complications in all surgeries.

Results

The machine learning algorithm had precisions of 0.958 for current smokers, 0.974 for ex-smokers, and 0.95 for never-smokers. The sample included 158 638 surgeries. In adjusted logistic regression analyses, smokers had increased odds of overall complications (odds ratio 1.17; 95 per cent c.i. 1.14 to 1.20) and critical complications (odds ratio 1.21; 95 per cent c.i. 1.14 to 1.29). Corresponding odds ratios of ex-smokers were 1.09 (95 per cent c.i. 1.06 to 1.13) and 1.09 (95 per cent c.i. 1.02 to 1.17). Smokers had increased odds of overall complications in all specialties with over 10 000 surgeries. ASA class was the most important complication predictor.

Conclusion

Machine learning algorithms are feasible for smoking status classification in big surgical data sets. Current and former smoking predict complications in all surgery types.
Cholinergic system correlates of postural control changes in Parkinson’s disease freezers
Authors: Roytman Stiven , Paalanen Rebecca , Griggs Alexis , David Simon , Pongmala Chatkaew , Koeppe Robert A , Scott Peter J H , Marusic Uros , Kanel Prabesh , Bohnen Nicolaas I
Published: April 2023

Postural instability and freezing of gait are the most debilitating dopamine-refractory motor impairments in advanced stages of Parkinson’s disease because of increased risk of falls and poorer quality of life. Recent findings suggest an inability to efficaciously utilize vestibular information during static posturography among people with Parkinson’s disease who exhibit freezing of gait, with associated changes in cholinergic system integrity as assessed by vesicular acetylcholine transporter PET. There is a lack of adequate understanding of how postural control varies as a function of available sensory information in patients with Parkinson’s disease with freezing of gait. The goal of this cross-sectional study was to examine cerebral cholinergic system changes that associate with inter-sensory postural control processing features as assessed by dynamic computerized posturography and acetylcholinesterase PET.

Seventy-five participants with Parkinson’s disease, 16 of whom exhibited freezing of gait, underwent computerized posturography on the NeuroCom© Equitest sensory organization test platform, striatal dopamine, and acetylcholinesterase PET scanning. Findings demonstrated that patients with Parkinson’s disease with freezing of gait have greater difficulty maintaining balance in the absence of reliable proprioceptive cues as compared to those without freezing of gait [β = 0.28 (0.021, 0.54), P = 0.034], an effect that was independent of disease severity [β = 0.16 (0.062, 0.26), P < 0.01] and age [β = 0.092 (−0.005, 0.19), P = 0.062]. Exploratory voxel-based analysis revealed an association between postural control and right hemispheric cholinergic network related to visual-vestibular integration and self-motion perception. High anti-cholinergic burden predicted postural control impairment in a manner dependent on right hemispheric cortical cholinergic integrity [β = 0.34 (0.065, 0.61), P < 0.01].

Our findings advance the perspective that cortical cholinergic system might play a role in supporting postural control after nigro-striatal dopaminergic losses in Parkinson’s disease. Failure of cortex-dependent visual-vestibular integration may impair detection of postural instability in absence of reliable proprioceptive cues. Better understanding of how the cholinergic system plays a role in this process may augur novel treatments and therapeutic interventions to ameliorate debilitating symptoms in patients with advanced Parkinson’s disease.
SARM1 deletion delays cerebellar but not spinal cord degeneration in an enhanced mouse model of SPG7 deficiency
Authors: Montoro-Gámez Carolina , Nolte Hendrik , Molinié Thibaut , Evangelista Giovanna , Tröder Simon E , Barth Esther , Popovic Milica , Trifunovic Aleksandra , Zevnik Branko , Langer Thomas , Rugarli Elena I
Published: April 2023

Hereditary spastic paraplegia is a neurological condition characterized by predominant axonal degeneration in long spinal tracts, leading to weakness and spasticity in the lower limbs. The nicotinamide adenine dinucleotide (NAD+)-consuming enzyme SARM1 has emerged as a key executioner of axonal degeneration upon nerve transection and in some neuropathies. An increase in the nicotinamide mononucleotide/NAD+ ratio activates SARM1, causing catastrophic NAD+ depletion and axonal degeneration. However, the role of SARM1 in the pathogenesis of hereditary spastic paraplegia has not been investigated.

Here, we report an enhanced mouse model for hereditary spastic paraplegia caused by mutations in SPG7. The eSpg7 knockout mouse carries a deletion in both Spg7 and Afg3l1, a redundant homologue expressed in mice but not in humans. The eSpg7 knockout mice recapitulate the phenotypic features of human patients, showing progressive symptoms of spastic-ataxia and degeneration of axons in the spinal cord as well as the cerebellum. We show that the lack of SPG7 rewires the mitochondrial proteome in both tissues, leading to an early onset decrease in mito-ribosomal subunits and a remodelling of mitochondrial solute carriers and transporters.

To interrogate mechanisms leading to axonal degeneration in this mouse model, we explored the involvement of SARM1. Deletion of SARM1 delays the appearance of ataxic signs, rescues mitochondrial swelling and axonal degeneration of cerebellar granule cells and dampens neuroinflammation in the cerebellum. The loss of SARM1 also prevents endoplasmic reticulum abnormalities in long spinal cord axons, but does not halt the degeneration of these axons. Our data thus reveal a neuron-specific interplay between SARM1 and mitochondrial dysfunction caused by lack of SPG7 in hereditary spastic paraplegia.