bluuebunny/crossref_metadata_2025 huggingface dataset:
Spatio‐Temporal Pattern of Tuberculosis Distribution in Romania and Particulate Matter Pollution Associated With Risk of Infection
Authors: Peptenatu D. , Băloi A. M. , Andronic O. , Bolocan A. , Cioran N. , Gruia A. K. , Grecu A. , Panciu T. C. , Georgescu L. , Munteanu I. , Pistol A. , Furtunescu F. , Strâmbu I. R. , Ibrahim E. , Băiceanu D. , Popescu G. G. , Păduraru D. , Jinga V. , Mahler B.
Published: February 2024

The study proposes a dynamic spatio‐temporal profile of the distribution of tuberculosis incidence and air pollution in Romania, where this infectious disease induces more than 8,000 new cases annually. The descriptive analysis for the years 2012–2021 assumes an identification of the structuring patterns of mycobacterium tuberculosis risk in the Romanian population, according to gender and age, exploiting spatial modeling techniques of time series data. Through spatial autocorrelation, the degree of similarity between the analyzed territorial systems was highlighted and the relationships that are built between the analysis units in spatial proximity were investigated. By modeling the geographical distribution of tuberculosis, the spatial correlation with particulate matter (PM2.5) pollution was revealed. The identification of clusters of infected persons is an indispensable step in the construction of efficient tuberculosis management systems. The results highlight the link between the distribution of tuberculosis, air pollution and socio‐economic development, which requires a detailed analysis of the epidemiological data obtained in the national tuberculosis surveillance and control program from the perspective of geographical distribution.
Decadal‐Scale Influence of the Kuroshio and Oyashio Extension Fronts on Atmospheric Circulation and Storm Track
Authors: Li Xiang , Zhou Guidi , Cheng Xuhua
Published: February 2024

Recent findings showed that midlatitude oceanic fronts in the Kuroshio‐Oyashio Extension (KOE) region may significantly influence the overlying atmosphere on the decadal timescale. However, the exact mechanism and the combined effects of both the Kuroshio Extension Front (KEF) and the Oyashio Extension Front (OEF) are still largely unknown. Here we use front‐resolving ERA5 reanalysis data to investigate the characteristics and mechanisms of the atmospheric response to decadal fluctuations of the KEF and OEF in a consistent way. It is found that the atmospheric response is equivalent barotropic with upper‐level intensification in terms of both basic flow and storm track. The geopotential height and storm track responses over western subpolar North Pacific are of opposite signs driven by intensifying KEF and OEF. Diagnosis showed that eddy vorticity feedback is responsible for the basic flow response at upper levels, whereas direct linear response to surface thermal forcing dominates at lower levels. The upper‐level eddy response is realized by midlevel diabatic conversion which is forced by changes of near‐surface background baroclinicity. In total, the decadal modulation by the KEF and OEF explains 19% (12%) of the variance of geopotential height (storm track) variability at 250 hPa (500 hPa), which is much higher than found in previous studies, presumably due to the higher resolution and the consideration of both fronts.
Contribution of Anthropogenic Activities to the Intensification of Heat Index‐Based Spatiotemporally Contiguous Heatwave Events in China
Authors: Kong Dongdong , Xie Yuxuan , Gu Xihui , Slater Louise , Ci Hui , Song Heyang
Published: February 2024

In this study, we identified heat index‐based spatiotemporally contiguous heatwaves (HI‐STHWs) in China based on meteorological observations and Coupled Model Intercomparison Project Phase 6 global climate model simulations. We analyzed the spatiotemporal patterns of changes in HI‐STHWs in the past and future and quantitatively attributed these changes to anthropogenic activities. The results show that the duration, severity, average, maximum, and total impacted area of the annual strongest HI‐STHWs during the present period of 1991–2014 are 1.77, 2.0, 1.05, 1.14, and 1.89 times the historical period of 1961–1990, respectively. In the fingerprint results, the anthropogenic greenhouse gases (GHG) signal is significantly detected, while the aerosol (AER) and natural (NAT) signals are not. GHG is the primary factor driving the intensification of HI‐STHWs, which alone explains about 130%, 122%, 112%, 111%, and 114% of the above changes. The reason for GHG contribution exceeding 100% is that AER might have a negative contribution although nonsignificant. In the future warming climate, anthropogenic activities are projected to lead to more unprecedented HI‐STHWs. Under the high emissions scenario of SSP585, by 2100, the annual strongest HI‐STHW in China is projected to last almost the whole year and influence 96% regions of China in the most serious day. Meanwhile, its duration and total impacted area are 24.5 [17.2, 31.6] (90% confidence interval) and 107.2 [70, 129.9] times the preindustrial period. However, if the warming level could be limited to 2/1.5°C, those values would be 3.4/5.4 and 8.2/16.2 times smaller than that under the SSP585 scenario by 2100.
On the Choice of Training Data for Machine Learning of Geostrophic Mesoscale Turbulence
Authors: Yan F. E. , Mak J. , Wang Y.
Published: February 2024

Data plays a central role in data‐driven methods, but is not often the subject of focus in investigations of machine learning algorithms as applied to Earth System Modeling related problems. Here we consider the problem of eddy‐mean interaction in rotating stratified turbulence in the presence of lateral boundaries, where it is known that rotational components of the eddy flux plays no direct role in the sub‐grid forcing onto the mean state variables, and its presence is expected to affect the performance of the trained machine learning models. While an often utilized choice in the literature is to train a model from the divergence of the eddy fluxes, here we provide theoretical arguments and numerical evidence that learning from the eddy fluxes with the rotational component appropriately filtered out, achieved in this work by means of an object called the eddy force function, results in models with comparable or better skill, but substantially reduced sensitivity to the presence of small‐scale features. We argue that while the choice of data choice and/or quality may not be critical if we simply want a model to have predictive skill, it is highly desirable and perhaps even necessary if we want to leverage data‐driven methods to aid in discovering unknown or hidden physical processes within the data itself.
An Unsupervised Learning Approach for Predicting Wind Farm Power and Downstream Wakes Using Weather Patterns
Authors: Clare Mariana C. A. , Warder Simon C. , Neal Robert , Bhaskaran B. , Piggott Matthew D.
Published: February 2024

Wind energy resource assessment typically requires numerical modeling at fine resolutions, which is computationally expensive for multi‐year timescales. Increasingly, unsupervised machine learning techniques are used to identify representative weather patterns that can help simulate long‐term behavior. Here we develop a novel wind energy workflow that combines the weather patterns from unsupervised clustering with a numerical weather prediction model (WRF) to obtain efficient long‐term predictions of wind farm power and downstream wakes, which provide a good approximation to full WRF simulations at vastly reduced computational cost. We use ERA5 reanalysis data and compare clustering on low altitude pressure and wind velocity, a more relevant variable for wind resource assessment. We also compare varying domain sizes for the clustering. A WRF simulation is run at each cluster center and the results aggregated into a long‐term prediction using a novel post‐processing technique. We consider two case study regions and show that our long‐term predictions achieve good agreement with a year of WRF simulations in 2% of the computational time. Moreover, clustering over a Europe‐wide domain produces good agreement for predicting wind farm power output, but clustering over smaller domains is required for downstream wake predictions which agree with the year of WRF simulations. Our approach facilitates multi‐year predictions of power output and downstream farm wakes, by providing a fast, reliable, and flexible methodology applicable to any global region. Moreover, this constitutes the first tool to help mitigate effects of wind energy loss downstream of wind farms.
Tracking Rodinia Into the Neoproterozoic: New Paleomagnetic Constraints From the Jacobsville Formation
Authors: Zhang Yiming , Hodgin Eben B. , Alemu Tadesse , Pierce James , Fuentes Anthony , Swanson‐Hysell Nicholas L.
Published: February 2024

The paleogeography of Laurentia throughout the Neoproterozoic is critical for reconstructing global paleogeography due to its central position in the supercontinent Rodinia. We develop a new paleomagnetic pole from red siltstones and fine‐grained sandstones of the early Neoproterozoic Jacobsville Formation which is now constrained to be ca. 990 Ma in age. High‐resolution thermal demagnetization experiments resolve detrital remanent magnetizations held by hematite. These directions were reoriented within siltstone intraclasts and pass intraformational conglomerate tests—giving confidence that the magnetization is detrital and primary. An inclination‐corrected mean paleomagnetic pole position for the Jacobsville Formation indicates that Laurentia's motion slowed down significantly following the onset of the Grenvillian orogeny. Prior rapid plate motion associated with closure of the Unimos Ocean between 1,110 and 1,090 Ma transitioned to slow drift of Laurentia across the equator in the late Mesoproterozoic to early Neoproterozoic. We interpret the distinct position of this well‐dated pole from those in the Grenville orogen that have been assigned a similar age to indicate that the ages of the poles associated with the Grenville Loop likely need to be revised to be younger due to prolonged exhumation.
Exploring the Complex Effects of Wildfire on Stream Water Chemistry: Insights From Concentration‐Discharge Relationships
Authors: Richardson C. , Montalvo M. , Wagner S. , Barton R. , Paytan A. , Redmond M. , Zimmer M.
Published: February 2024

Wildfires are a worldwide disturbance with unclear implications for stream water quality. We examined stream water chemistry responses immediately (<1 month) following a wildfire by measuring over 40 constituents in four gauged coastal watersheds that burned at low to moderate severity. Three of the four watersheds also had pre‐fire concentration‐discharge data for 14 constituents: suspended sediment (SSfine), dissolved organic and inorganic carbon (DOC, DIC), specific UV absorbance (SUVA), major ions (Ca2+, K+, Mg2+, Na+, Cl−, , , F−), and select trace elements (total dissolved Mn, Fe). In all watersheds, post‐fire stream water concentrations of SSfine, DOC, Ca2+, Cl−, and changed when compared to pre‐fire data. Post‐fire changes in , K+, Na+, Mg2+, DIC, SUVA, and total dissolved Fe were also found for at least two of the three streams. For constituents with detectable responses to wildfire, post‐fire changes in the slopes of concentration‐discharge relationships commonly resulted in stronger enrichment trends or weaker dilution trends, suggesting that new contributing sources were surficial or near the surface. However, a few geogenic solutes, Ca2+, Mg2+, and DIC, displayed stronger dilution trends at nearly all sites post‐fire. Moreover, fire‐induced constituent concentration changes were highly discharge and site‐dependent. These similarities and differences in across‐site stream water chemistry responses to wildfire emphasize the need for a deeper understanding of landscape‐scale changes to solute sources and pathways. Our findings also highlight the importance of being explicit about reference points for both stream discharge and pre‐fire stream water chemistry in post‐fire assessment of concentration changes.
Synthetic Simulation of Spatially‐Correlated Streamflows: Weighted‐Modified Fractional Gaussian Noise
Authors: Chadwick Cristián , Babonneau Frederic , Homem‐de‐Mello Tito , Letelier Agustín
Published: February 2024

Stochastic methods have been typically used for the design and operations of hydraulic infrastructure. They allow decision makers to evaluate existing or new infrastructure under different possible scenarios, giving them the flexibility and tools needed in decision making. In this paper, we present a novel stochastic streamflow simulation approach able to replicate both temporal and spatial dependencies from the original data in a multi‐site basin context. The proposed model is a multi‐site extension of the modified Fractional Gaussian Noise (mFGN) model which is well‐known to be efficient to maintain periodic correlation for several time lags, but presents shortcomings in preserving the spatial correlation. Our method, called Weighted‐mFGN (WmFGN), incorporates spatial dependency into streamflows simulated with mFGN by relying on the Cholesky decomposition of the spatial correlation matrix of the historical streamflow records. As the order in which the decomposition steps are performed (temporal then spatial, or vice‐versa) affects the performance in terms of preserving the temporal and spatial correlation, our method searches for an optimal convex combination of the resulting correlation matrices. The result is a Pareto‐curve that indicates the optimal weights of the convex combination depending on the importance given by the user to spatial and temporal correlations. The model is applied to a number of river basins in Chile, where the results show that the WmFGN approach maintains the qualities of the single‐site mFGN, while significantly improving spatial correlation.
Sources of personal PM2.5 exposure during pregnancy in the MADRES cohort
Authors: Xu Yan , O’Sharkey Karl , Cabison Jane , Rosales Marisela , Chavez Thomas , Johnson Mark , Yang Tingyu , Cho Seung-Hyun , Chartier Ryan , Grubbs Brendan , Lurvey Nathana , Lerner Deborah , Lurmann Frederick , Farzan Shohreh , Bastain Theresa M. , Breton Carrie , Wilson John P. , Habre Rima
Published: February 2024

Background

Personal exposure to fine particulate matter (PM2.5) is impacted by different sources each with different chemical composition. Determining these sources is important for reducing personal exposure and its health risks especially during pregnancy.

Objective

Identify main sources and their contributions to the personal PM2.5 exposure in 213 women in the 3rd trimester of pregnancy in Los Angeles, CA.

Methods

We measured 48-hr integrated personal PM2.5 exposure and analyzed filters for PM2.5 mass, elemental composition, and optical carbon fractions. We used the EPA Positive Matrix Factorization (PMF) model to resolve and quantify the major sources of personal PM2.5 exposure. We then investigated bivariate relationships between sources, time-activity patterns, and environmental exposures in activity spaces and residential neighborhoods to further understand sources.

Results

Mean personal PM2.5 mass concentration was 22.3 (SD = 16.6) μg/m3. Twenty-five species and PM2.5 mass were used in PMF with a final R2 of 0.48. We identified six sources (with major species in profiles and % contribution to PM2.5 mass) as follows: secondhand smoking (SHS) (brown carbon, environmental tobacco smoke; 65.3%), fuel oil (nickel, vanadium; 11.7%), crustal (aluminum, calcium, silicon; 11.5%), fresh sea salt (sodium, chlorine; 4.7%), aged sea salt (sodium, magnesium, sulfur; 4.3%), and traffic (black carbon, zinc; 2.6%). SHS was significantly greater in apartments compared to houses. Crustal source was correlated with more occupants in the household. Aged sea salt increased with temperature and outdoor ozone, while fresh sea salt was highest on days with westerly winds from the Pacific Ocean. Traffic was positively correlated with ambient NO2 and traffic-related NOx at residence. Overall, 76.8% of personal PM2.5 mass came from indoor or personal compared to outdoor sources.

Impact

We conducted source apportionment of personal PM2.5 samples in pregnancy in Los Angeles, CA. Among identified sources, secondhand smoking contributed the most to the personal exposure. In addition, traffic, crustal, fuel oil, fresh and aged sea salt sources were also identified as main sources. Traffic sources contained markers of combustion and non-exhaust wear emissions. Crustal source was correlated with more occupants in the household. Aged sea salt source increased with temperature and outdoor ozone and fresh sea salt source was highest on days with westerly winds from the Pacific Ocean.
Lasting dynamic effects of the psychedelic 2,5-dimethoxy-4-iodoamphetamine ((±)-DOI) on cognitive flexibility
Authors: Šabanović Merima , Lazari Alberto , Blanco-Pozo Marta , Tisca Cristiana , Tachrount Mohamed , Martins-Bach Aurea B. , Lerch Jason P. , Walton Mark E. , Bannerman David M.
Published: February 2024

Psychedelic drugs can aid fast and lasting remission from various neuropsychiatric disorders, though the underlying mechanisms remain unclear. Preclinical studies suggest serotonergic psychedelics enhance neuronal plasticity, but whether neuroplastic changes can also be seen at cognitive and behavioural levels is unexplored. Here we show that a single dose of the psychedelic 2,5-dimethoxy-4-iodoamphetamine ((±)-DOI) affects structural brain plasticity and cognitive flexibility in young adult mice beyond the acute drug experience. Using ex vivo magnetic resonance imaging, we show increased volumes of several sensory and association areas one day after systemic administration of 2 mgkg−1 (±)-DOI. We then demonstrate lasting effects of (±)-DOI on cognitive flexibility in a two-step probabilistic reversal learning task where 2 mgkg−1 (±)-DOI improved the rate of adaptation to a novel reversal in task structure occurring one-week post-treatment. Strikingly, (±)-DOI-treated mice started learning from reward omissions, a unique strategy not typically seen in mice in this task, suggesting heightened sensitivity to previously overlooked cues. Crucially, further experiments revealed that (±)-DOI’s effects on cognitive flexibility were contingent on the timing between drug treatment and the novel reversal, as well as on the nature of the intervening experience. (±)-DOI’s facilitation of both cognitive adaptation and novel thinking strategies may contribute to the clinical benefits of psychedelic-assisted therapy, particularly in cases of perseverative behaviours and a resistance to change seen in depression, anxiety, or addiction. Furthermore, our findings highlight the crucial role of time-dependent neuroplasticity and the influence of experiential factors in shaping the therapeutic potential of psychedelic interventions for impaired cognitive flexibility.
Brain connectivity changes to fast versus slow dopamine increases
Authors: Manza Peter , Tomasi Dardo , Vines Leah , Sotelo Diana , Yonga Michele-Vera , Wang Gene-Jack , Volkow Nora D.
Published: February 2024

The rewarding effects of stimulant drugs such as methylphenidate (MP) depend crucially on how fast they raise dopamine in the brain. Yet how the rate of drug-induced dopamine increases impacts brain network communication remains unresolved. We manipulated route of MP administration to generate fast versus slow dopamine increases. We hypothesized that fast versus slow dopamine increases would result in a differential pattern of global brain connectivity (GBC) in association with regional levels of dopamine D1 receptors, which are critical for drug reward. Twenty healthy adults received MP intravenously (0.5 mg/kg; fast dopamine increases) and orally (60 mg; slow dopamine increases) during simultaneous [11C]raclopride PET-fMRI scans (double-blind, placebo-controlled). We tested how GBC was temporally associated with slow and fast dopamine increases on a minute-to-minute basis. Connectivity patterns were strikingly different for slow versus fast dopamine increases, and whole-brain spatial patterns were negatively correlated with one another (rho = −0.54, pspin < 0.001). GBC showed “fast>slow” associations in dorsal prefrontal cortex, insula, posterior thalamus and brainstem, caudate and precuneus; and “slow>fast” associations in ventral striatum, orbitofrontal cortex, and frontopolar cortex (pFDR < 0.05). “Fast>slow” GBC patterns showed significant spatial correspondence with D1 receptor availability (estimated via normative maps of [11C]SCH23390 binding; rho = 0.22, pspin < 0.05). Further, hippocampal GBC to fast dopamine increases was significantly negatively correlated with self-reported ‘high’ ratings to intravenous MP across individuals (r(19) = −0.68, pbonferroni = 0.015). Different routes of MP administration produce divergent patterns of brain connectivity. Fast dopamine increases are uniquely associated with connectivity patterns that have relevance for the subjective experience of drug reward.
Incidence of prostate cancer in transgender women in the US: a large database analysis
Authors: Loria Matthew , Gilbert David , Tabernacki Tomasz , Maravillas Mart Andrew , McNamara Megan , Gupta Shubham , Mishra Kirtishri
Published: February 2024

The risk of prostate cancer among transgender women undergoing medical and surgical gender-affirming interventions remains unclear, though up to a fivefold decreased risk has been reported in comparison to cisgender men. In this study, we conducted a comparative analysis of the risk of prostate cancer among transgender women (TW) using data from TriNetX, a large database, versus SEER. Our findings indicate that, overall, transgender women exhibited a 2.56-fold lower risk of prostate cancer compared to cisgender men. Specifically, among TW on hormone therapy between ages 50–64, we observed a 2.06-fold decrease in risk. Contrary to the previous perception of prostate cancer being rare in transgender women, our study suggests that it may not be as uncommon as previously believed.
DNA framework signal amplification platform-based high-throughput systemic immune monitoring
Authors: Chen Ye , Chen Xingyu , Zhang Bowen , Zhang Yuxin , Li Songhang , Liu Zhiqiang , Gao Yang , Zhao Yuxuan , Yan Lin , Li Yi , Tian Taoran , Lin Yunfeng
Published: February 2024

Systemic immune monitoring is a crucial clinical tool for disease early diagnosis, prognosis and treatment planning by quantitative analysis of immune cells. However, conventional immune monitoring using flow cytometry faces huge challenges in large-scale sample testing, especially in mass health screenings, because of time-consuming, technical-sensitive and high-cost features. However, the lack of high-performance detection platforms hinders the development of high-throughput immune monitoring technology. To address this bottleneck, we constructed a generally applicable DNA framework signal amplification platform (DSAP) based on post-systematic evolution of ligands by exponential enrichment and DNA tetrahedral framework-structured probe design to achieve high-sensitive detection for diverse immune cells, including CD4+, CD8+ T-lymphocytes, and monocytes (down to 1/100 μl). Based on this advanced detection platform, we present a novel high-throughput immune-cell phenotyping system, DSAP, achieving 30-min one-step immune-cell phenotyping without cell washing and subset analysis and showing comparable accuracy with flow cytometry while significantly reducing detection time and cost. As a proof-of-concept, DSAP demonstrates excellent diagnostic accuracy in immunodeficiency staging for 107 HIV patients (AUC > 0.97) within 30 min, which can be applied in HIV infection monitoring and screening. Therefore, we initially introduced promising DSAP to achieve high-throughput immune monitoring and open robust routes for point-of-care device development.
B cell-reactive triad of B cells, follicular helper and regulatory T cells at homeostasis
Authors: Lin Yihan , Wan Zurong , Liu Bo , Yao Jiacheng , Li Tianqi , Yang Fang , Sui Jianhua , Zhao Yongshan , Liu Wanli , Zhou Xuyu , Wang Jianbin , Qi Hai
Published: February 2024

Autoreactive B cells are silenced through receptor editing, clonal deletion and anergy induction. Additional autoreactive B cells are ignorant because of physical segregation from their cognate autoantigen. Unexpectedly, we find that follicular B cell-derived autoantigen, including cell surface molecules such as FcγRIIB, is a class of homeostatic autoantigen that can induce spontaneous germinal centers (GCs) and B cell-reactive autoantibodies in non-autoimmune animals with intact T and B cell repertoires. These B cell-reactive B cells form GCs in a manner dependent on spontaneous follicular helper T (TFH) cells, which preferentially recognize B cell-derived autoantigen, and in a manner constrained by spontaneous follicular regulatory T (TFR) cells, which also carry specificities for B cell-derived autoantigen. B cell-reactive GC cells are continuously generated and, following immunization or infection, become intermixed with foreign antigen-induced GCs. Production of plasma cells and antibodies derived from B cell-reactive GC cells are markedly enhanced by viral infection, potentially increasing the chance for autoimmunity. Consequently, immune homeostasis in healthy animals not only involves classical tolerance of silencing and ignoring autoreactive B cells but also entails a reactive equilibrium attained by a spontaneous B cell-reactive triad of B cells, TFH cells and TFR cells.
Sight impairment registration in Trinidad: trend in causes and population coverage in comparison to the National Eye Survey of Trinidad and Tobago
Authors: Ramsewak Shivaa , Deomansingh Frank , Winford Blaine , Bartholomew Debra , Maharaj Vedatta , Fraser Amandi , Singh Deo , Suratt Kenneth , Tripathi Vrijesh , McNally Kevin , Sharma Subash , Bascaran Covadonga , Ramsewak Samuel S. , Bourne Rupert R. A. , Braithwaite Tasanee
Published: February 2024

Background

Little was known about the population coverage and causes of sight impairment (SI) registration within the Caribbean, or the extent to which register studies offer insights into population eye health.

Methods

We compared causes of SI registration in the Trinidad and Tobago Blind Welfare Association (TTBWA) register with findings from the 2014 National Eye Survey of Trinidad and Tobago (NESTT), and estimated registration coverage. Cross-sectional validation studies of registered clients included interviews, visual function and cause ascertainment in July 2013, and interviews and visual function in July 2016.

Results

The TTBWA register included 863 people (all ages, 48.1%(n = 415) male) registered between 1951 and 2015. The NESTT identified 1.1%(75/7158) people aged ≥5years eligible for partial or severe SI registration, of whom 49.3%(n = 37) were male. Registration coverage was approximately 7% of the eligible population of Trinidad. Nevertheless, there was close agreement in the causes of SI comparing the register and population-representative survey. Glaucoma was the leading cause in both the register (26.1%,n = 225) and population-based survey (26.1%, 18/69 adults), followed by cataract and diabetic retinopathy. In the validation studies combined, 62.6%(93/151) clients had severe SI, 28.5%(43/151) had partial SI and 9.9%(15/151) did not meet SI eligibility criteria. SI was potentially avoidable in at least 58%(n = 36/62) adults and 50%(n = 7/14) children.

Conclusion

We report very low register coverage of the SI population, but close agreement in causes of SI to a contemporaneous national population-based eye survey, half of which resulted from preventable or treatable eye disease.
Antiviral fibrils of self-assembled peptides with tunable compositions
Authors: Dodd-o Joseph , Roy Abhishek , Siddiqui Zain , Jafari Roya , Coppola Francesco , Ramasamy Santhamani , Kolloli Afsal , Kumar Dilip , Kaundal Soni , Zhao Boyang , Kumar Ranjeet , Robang Alicia S. , Li Jeffrey , Azizogli Abdul-Rahman , Pai Varun , Acevedo-Jake Amanda , Heffernan Corey , Lucas Alexandra , McShan Andrew C. , Paravastu Anant K. , Prasad B. V. Venkataram , Subbian Selvakumar , Král Petr , Kumar Vivek
Published: February 2024

The lasting threat of viral pandemics necessitates the development of tailorable first-response antivirals with specific but adaptive architectures for treatment of novel viral infections. Here, such an antiviral platform has been developed based on a mixture of hetero-peptides self-assembled into functionalized β-sheets capable of specific multivalent binding to viral protein complexes. One domain of each hetero-peptide is designed to specifically bind to certain viral proteins, while another domain self-assembles into fibrils with epitope binding characteristics determined by the types of peptides and their molar fractions. The self-assembled fibrils maintain enhanced binding to viral protein complexes and retain high resilience to viral mutations. This method is experimentally and computationally tested using short peptides that specifically bind to Spike proteins of SARS-CoV-2. This platform is efficacious, inexpensive, and stable with excellent tolerability.
Inhibitory medial zona incerta pathway drives exploratory behavior by inhibiting glutamatergic cuneiform neurons
Authors: Sharma Sandeep , Badenhorst Cecilia A. , Ashby Donovan M. , Di Vito Stephanie A. , Tran Michelle A. , Ghavasieh Zahra , Grewal Gurleen K. , Belway Cole R. , McGirr Alexander , Whelan Patrick J.
Published: February 2024

The cuneiform nucleus (CnF) regulates locomotor activity, which is canonically viewed as being primarily involved in initiating locomotion and regulating speed. Recent research shows greater context dependency in the locomotor functions of this nucleus. Glutamatergic neurons, which contain vesicular glutamate transporter 2 (vGLUT2), regulate context-dependent locomotor speed in the CnF and play a role in defensive behavior. Here, we identify projections from the medial zona incerta (mZI) to CnF vGLUT2 neurons that promote exploratory behavior. Using fiber photometry recordings in male mice, we find that mZI gamma-aminobutyric acid (GABA) neurons increase activity during periods of exploration. Activation of mZI GABAergic neurons is associated with reduced spiking of CnF neurons. Additionally, activating both retrogradely labeled mZI-CnF GABAergic projection neurons and their terminals in the CnF increase exploratory behavior. Inhibiting CnF vGLUT2 neuronal activity also increases exploratory behavior. These findings provide evidence for the context-dependent dynamic regulation of CnF vGLUT2 neurons, with the mZI-CnF circuit shaping exploratory behavior.
Interfacial magnetic spin Hall effect in van der Waals Fe3GeTe2/MoTe2 heterostructure
Authors: Dai Yudi , Xiong Junlin , Ge Yanfeng , Cheng Bin , Wang Lizheng , Wang Pengfei , Liu Zenglin , Yan Shengnan , Zhang Cuiwei , Xu Xianghan , Shi Youguo , Cheong Sang-Wook , Xiao Cong , Yang Shengyuan A. , Liang Shi-Jun , Miao Feng
Published: February 2024

The spin Hall effect (SHE) allows efficient generation of spin polarization or spin current through charge current and plays a crucial role in the development of spintronics. While SHE typically occurs in non-magnetic materials and is time-reversal even, exploring time-reversal-odd (T-odd) SHE, which couples SHE to magnetization in ferromagnetic materials, offers a new charge-spin conversion mechanism with new functionalities. Here, we report the observation of giant T-odd SHE in Fe3GeTe2/MoTe2 van der Waals heterostructure, representing a previously unidentified interfacial magnetic spin Hall effect (interfacial-MSHE). Through rigorous symmetry analysis and theoretical calculations, we attribute the interfacial-MSHE to a symmetry-breaking induced spin current dipole at the vdW interface. Furthermore, we show that this linear effect can be used for implementing multiply-accumulate operations and binary convolutional neural networks with cascaded multi-terminal devices. Our findings uncover an interfacial T-odd charge-spin conversion mechanism with promising potential for energy-efficient in-memory computing.
Tuning the apparent hydrogen binding energy to achieve high-performance Ni-based hydrogen oxidation reaction catalyst
Authors: Wang Xingdong , Liu Xuerui , Fang Jinjie , Wang Houpeng , Liu Xianwei , Wang Haiyong , Chen Chengjin , Wang Yongsheng , Zhang Xuejiang , Zhu Wei , Zhuang Zhongbin
Published: February 2024

High-performance platinum-group-metal-free alkaline hydrogen oxidation reaction catalysts are essential for the hydroxide exchange membrane fuel cells, which generally require high Pt loadings on the anode. Herein, we report a highly active hydrogen oxidation reaction catalyst, NiCuCr, indicated by the hydroxide exchange membrane fuel cell with a high peak power density of 577 mW cm−2 (18 times as high as the Ni/C anode) and a stability of more than 150 h (a degradation rate slower by 7 times than the Ni/C anode). The spectroscopies demonstrate that the alloy effect from Cu weakens the hydrogen binding, and the surface Cr2O3 species enhance the interfacial water binding. Both effects bring an optimized apparent hydrogen binding energy and thus lead to the high hydrogen oxidation reaction performance of NiCuCr. These results suggest that the apparent hydrogen binding energy determines the hydrogen oxidation reaction performance and that its tuning is beneficial toward high electrocatalytic performance.
Sampling-accelerated prediction of phonon scattering rates for converged thermal conductivity and radiative properties
Authors: Guo Ziqi , Han Zherui , Feng Dudong , Lin Guang , Ruan Xiulin
Published: February 2024

The prediction of thermal conductivity and radiative properties is crucial. However, computing phonon scattering, especially for four-phonon scattering, could be prohibitively expensive, and the thermal conductivity for silicon after considering four-phonon scattering is significantly under-predicted and not converged in the literature. Here we propose a method to estimate scattering rates from a small sample of scattering processes using maximum likelihood estimation. The calculation of scattering rates and associated thermal conductivity and radiative properties are dramatically accelerated by three to four orders of magnitude. This allows us to use an unprecedented q-mesh (discretized grid in the reciprocal space) of 32 × 32 × 32 for calculating four-phonon scattering of silicon and achieve a converged thermal conductivity value that agrees much better with experiments. The accuracy and efficiency of our approach make it ideal for the high-throughput screening of materials for thermal and optical applications.
Generative adversarial network (GAN) enabled Statistically equivalent virtual microstructures (SEVM) for modeling cold spray formed bimodal polycrystals
Authors: Murgas Brayan , Stickel Joshua , Ghosh Somnath
Published: February 2024

Image-based micromechanical models, necessary for the development of structure-property-response relations, are far from mature for complex microstructures with multi-modal distributions of morphological and crystallographic features, such as those occurring with cold spray-formed (CSF) aluminum alloys. These materials have a bimodal polycrystalline microstructure composed of recrystallized ultra-fine grains (UFGs) and deformed coarse grains (CGs) within prior particles. A prime reason is the lack of robust approaches for generating statistically equivalent virtual microstructures (SEVM) capturing the statistics of characteristic morphological and crystallographic features, such as grain size, crystallographic orientations, and misorientations. This paper introduces an approach, strategically integrating Generative Adversarial Network-based approaches for producing bimodal CSF AA7050 alloy microstructures, with the synthetic microstructure builder Dream3D for packing prior particles with CGs having statistically equivalent morphological and crystallographic descriptors to electron backscatter diffraction (EBSD) maps. An efficient finite element (FE) simulation approach is developed for the SEVMs to generate local and overall response functions through the creation of sub-volume elements (SVEs).
Evidence of superconducting Fermi arcs
Authors: Kuibarov Andrii , Suvorov Oleksandr , Vocaturo Riccardo , Fedorov Alexander , Lou Rui , Merkwitz Luise , Voroshnin Vladimir , Facio Jorge I. , Koepernik Klaus , Yaresko Alexander , Shipunov Grigory , Aswartham Saicharan , Brink Jeroen van den , Büchner Bernd , Borisenko Sergey
Published: February 2024

An essential ingredient for the production of Majorana fermions for use in quantum computing is topological superconductivity1,2. As bulk topological superconductors remain elusive, the most promising approaches exploit proximity-induced superconductivity3, making systems fragile and difficult to realize4–7. Due to their intrinsic topology8, Weyl semimetals are also potential candidates1,2, but have always been connected with bulk superconductivity, leaving the possibility of intrinsic superconductivity of their topological surface states, the Fermi arcs, practically without attention, even from the theory side. Here, by means of angle-resolved photoemission spectroscopy and ab initio calculations, we identify topological Fermi arcs on two opposing surfaces of the non-centrosymmetric Weyl material trigonal PtBi2 (ref. 9). We show these states become superconducting at temperatures around 10 K. Remarkably, the corresponding coherence peaks appear as the strongest and sharpest excitations ever detected by photoemission from solids. Our findings indicate that superconductivity in PtBi2 can occur exclusively at the surface, rendering it a possible platform to host Majorana modes in intrinsically topological superconductor–normal metal–superconductor Josephson junctions.
Translation selectively destroys non-functional transcription complexes
Authors: Woodgate Jason , Mosaei Hamed , Brazda Pavel , Stevenson-Jones Flint , Zenkin Nikolay
Published: February 2024

Transcription elongation stalls at lesions in the DNA template1. For the DNA lesion to be repaired, the stalled transcription elongation complex (EC) has to be removed from the damaged site2. Here we show that translation, which is coupled to transcription in bacteria, actively dislodges stalled ECs from the damaged DNA template. By contrast, paused, but otherwise elongation-competent, ECs are not dislodged by the ribosome. Instead, they are helped back into processive elongation. We also show that the ribosome slows down when approaching paused, but not stalled, ECs. Our results indicate that coupled ribosomes functionally and kinetically discriminate between paused ECs and stalled ECs, ensuring the selective destruction of only the latter. This functional discrimination is controlled by the RNA polymerase’s catalytic domain, the Trigger Loop. We show that the transcription-coupled DNA repair helicase UvrD, proposed to cause backtracking of stalled ECs3, does not interfere with ribosome-mediated dislodging. By contrast, the transcription-coupled DNA repair translocase Mfd4 acts synergistically with translation, and dislodges stalled ECs that were not destroyed by the ribosome. We also show that a coupled ribosome efficiently destroys misincorporated ECs that can cause conflicts with replication5. We propose that coupling to translation is an ancient and one of the main mechanisms of clearing non-functional ECs from the genome.
Signatures of a surface spin–orbital chiral metal
Authors: Mazzola Federico , Brzezicki Wojciech , Mercaldo Maria Teresa , Guarino Anita , Bigi Chiara , Miwa Jill A. , De Fazio Domenico , Crepaldi Alberto , Fujii Jun , Rossi Giorgio , Orgiani Pasquale , Chaluvadi Sandeep Kumar , Chalil Shyni Punathum , Panaccione Giancarlo , Jana Anupam , Polewczyk Vincent , Vobornik Ivana , Kim Changyoung , Miletto-Granozio Fabio , Fittipaldi Rosalba , Ortix Carmine , Cuoco Mario , Vecchione Antonio
Published: February 2024

The relation between crystal symmetries, electron correlations and electronic structure steers the formation of a large array of unconventional phases of matter, including magneto-electric loop currents and chiral magnetism1–6. The detection of such hidden orders is an important goal in condensed-matter physics. However, until now, non-standard forms of magnetism with chiral electronic ordering have been difficult to detect experimentally7. Here we develop a theory for symmetry-broken chiral ground states and propose a methodology based on circularly polarized, spin-selective, angular-resolved photoelectron spectroscopy to study them. We use the archetypal quantum material Sr2RuO4 and reveal spectroscopic signatures that, despite being subtle, can be reconciled with the formation of spin–orbital chiral currents at the surface of the material8–10. As we shed light on these chiral regimes, our findings pave the way for a deeper understanding of ordering phenomena and unconventional magnetism.
CombFold: predicting structures of large protein assemblies using a combinatorial assembly algorithm and AlphaFold2
Authors: Shor Ben , Schneidman-Duhovny Dina
Published: February 2024

Deep learning models, such as AlphaFold2 and RosettaFold, enable high-accuracy protein structure prediction. However, large protein complexes are still challenging to predict due to their size and the complexity of interactions between multiple subunits. Here we present CombFold, a combinatorial and hierarchical assembly algorithm for predicting structures of large protein complexes utilizing pairwise interactions between subunits predicted by AlphaFold2. CombFold accurately predicted (TM-score >0.7) 72% of the complexes among the top-10 predictions in two datasets of 60 large, asymmetric assemblies. Moreover, the structural coverage of predicted complexes was 20% higher compared to corresponding Protein Data Bank entries. We applied the method on complexes from Complex Portal with known stoichiometry but without known structure and obtained high-confidence predictions. CombFold supports the integration of distance restraints based on crosslinking mass spectrometry and fast enumeration of possible complex stoichiometries. CombFold’s high accuracy makes it a promising tool for expanding structural coverage beyond monomeric proteins.
Naïve Bayes Classifiers and accompanying dataset for Pseudomonas syringae isolate characterization
Authors: Fautt Chad , Couradeau Estelle , Hockett Kevin L.
Published: February 2024

The Pseudomonas syringae species complex (PSSC) is a diverse group of plant pathogens with a collective host range encompassing almost every food crop grown today. As a threat to global food security, rapid detection and characterization of epidemic and emerging pathogenic lineages is essential. However, phylogenetic identification is often complicated by an unclarified and ever-changing taxonomy, making practical use of available databases and the proper training of classifiers difficult. As such, while amplicon sequencing is a common method for routine identification of PSSC isolates, there is no efficient method for accurate classification based on this data. Here we present a suite of five Naïve bayes classifiers for PCR primer sets widely used for PSSC identification, trained on in-silico amplicon data from 2,161 published PSSC genomes using the life identification number (LIN) hierarchical clustering algorithm in place of traditional Linnaean taxonomy. Additionally, we include a dataset for translating classification results back into traditional taxonomic nomenclature (i.e. species, phylogroup, pathovar), and for predicting virulence factor repertoires.
An open relaxation-diffusion MRI dataset in neurosurgical studies
Authors: Wu Ye , Liu Xiaoming , Huang Yunzhi , Zhou Tao , Zhang Fan
Published: February 2024

Diffusion MRI (dMRI) is a safe and noninvasive technique that provides insight into the microarchitecture of brain tissue. Relaxation-diffusion MRI (rdMRI) is an extension of traditional dMRI that captures diffusion imaging data at multiple TEs to detect tissue heterogeneity between relaxation and diffusivity. rdMRI has great potential in neurosurgical research including brain tumor grading and treatment response evaluation. However, the lack of available data has limited the exploration of rdMRI in clinical settings. To address this, we are sharing a high-quality rdMRI dataset from 18 neurosurgical patients with different types of lesions, as well as two healthy individuals as controls. The rdMRI data was acquired using 7 TEs, where at each TE multi-shell dMRI with high spatial and angular resolutions is obtained at each TE. Each rdMRI scan underwent thorough artifact and distortion corrections using a specially designed processing pipeline. The dataset’s quality was assessed using standard practices, including quality control and assurance. This resource is a valuable addition to neurosurgical studies, and all data are openly accessible.
An empirical assessment of whether urban green ecological networks have the capacity to store higher levels of carbon
Authors: Wan Yunshan , Wang Yilei , Gao Ming , Jin Lin
Published: February 2024

Carbon–neutral growth is a crucial long-term climatic aim in the context of global warming. This paper introduces complex network theory and explores its potential application to achieve this goal. Specifically, we investigate the spatial and temporal distribution of nodes and sources in the ecological network, and examine whether a relationship exists between the topological index of network nodes and the landscape pattern index of ecological source areas. We also determine the contribution of nodes to the carbon stock of the entire network by exploring the correlation between the carbon stock of nodes and sources to develop an optimization strategy based on the synergistic effect of node-source carbon enhancement. Finally, we test the effect of network optimization through robustness. Our results show that: (1) The correlation topological feature index analysis reveals that the degree distribution of the node network's topological characteristics becomes dispersed and modular, exhibiting the characteristics of small-world networks according to a large clustering coefficient. The heterogeneity and extent of ecological source landscapes have increased by modularity index but remain distributed and locally fragmented; (2) According to correlation analysis, by enhancing the eccentricity of the node topology, the patch cohesion index (COHESION) of the ecological source site can maximize the contribution of the node to the enhancement of the carbon stock benefits of the source site; (3) According to the tests on the robustness of nodes and edges and the robustness of network links, network stability is improved and carbon sink capacity is enhanced. Simultaneously, the restoration and rejuvenation of ecological space through national ecological construction projects can effectively improve the carbon sink within the organized region, contributing to the carbon neutrality aim. This research gives scientific and quantifiable references for potential ecological construction projects for sustainable cities and the optimization of urban ecological space structure.