bluuebunny/crossref_metadata_2025 huggingface dataset:
A coupled thermal–hydrological–mechanical model for geothermal energy extraction in fractured reservoirs
Authors: Fang Tian , Feng Quanlin , Zhou Rui , Guo Chaobin , Wang Siqi , Gao Kun
Published: July 2023

Understanding fluid flow in fractured porous media under coupled thermal–hydrological–mechanical (THM) conditions is a fundamental aspect of geothermal energy extraction. In this study, we developed a fully coupled THM model, incorporating porosity and permeability variations, to scrutinize the process of geothermal energy extraction within fractured porous reservoirs. Moreover, we accentuated the significance of natural fracture orientation and hydraulic fracture permeability on fluid trajectories and heat extraction efficiency. Simulation results revealed that hydraulic fractures predominantly govern fluid channels and thermal exchange between injected water and the reservoir. Interconnected natural fractures bolster water migration into the reservoir, while detached fractures exert minimal influence on fluid dynamics, underscoring the crucial role of fracture connectivity in optimizing heat extraction efficiency. The sensitivity analysis indicated that larger fracture angles marginally hinder pressure and cool-water dispersion into the fractured reservoir, resulting in subtle enhancements in heat extraction rates and average production temperatures. An upsurge in hydraulic fracture permeability augments fluid velocity and thermal exchange, thereby fostering heat extraction efficiency. The THM model developed in this study offers a comprehensive insight into fluid flow within fractured porous media and its implications on geothermal energy extraction.
Intimate Relationship Between Stress and Human Alpha-Herpes Virus 1 (HSV-1) Reactivation from Latency
Authors: Jones Clinton
Published: July 2023

Purpose of Review

Numerous studies concluded stress (acute, episodic acute, or chronic) increases the incidence of human alpha-herpes virus 1 (HSV-1) reactivation from latency in neurons. This review will summarize how stress stimulates viral gene expression, replication, and reactivation from latency.

Recent Findings

Stress-mediated activation of the glucocorticoid receptor (GR) accelerates reactivation from latency, whereas a corticosteroid-specific antagonist impairs viral replication and reactivation from latency. GR and specific stress-induced cellular transcription factors also stimulate viral promoters that drive expression of key viral transcriptional regulators: infected cell protein 0 (ICP0), ICP4, ICP27 and viral tegument protein (VP16). Hence, GR is predicted to initially stimulate viral gene expression. GR-mediated immune-inhibitory functions are also predicted to enhance viral replication and viral spread.

Identifying cellular factors and viral regulatory proteins that trigger reactivation from latency in neurons may provide new therapeutic strategies designed to reduce the incidence of reactivation from latency.
Adaptive differential evolution with fitness-based crossover rate for global numerical optimization
Authors: Cheng Lianzheng , Zhou Jia-Xi , Hu Xing , Mohamed Ali Wagdy , Liu Yun
Published: July 2023

Differential evolution (DE) is one of the most efficient evolution algorithms (ES) for dealing with nonlinear, complicated and difficult global optimization problems. The main contribution of this paper can be summarized in three directions: Firstly, a novel crossover rate (CR) generation scheme based on the zscore value of fitness, named fcr, is introduced. For a minimization problem, the proposed CR generation strategy always assigns a smaller CR value to individual with smaller fitness value. Therefore, the parameters of individuals with better fitness are inherited by their offspring with high probability. In the second direction, the control parameters are adjusted by unused bimodal settings in which each parameter setting is selected according to the evolution status of individual. The third direction of our work is introducing the L1 norm distance as the weights for updating the mean value of crossover rate and scale factor. Theoretically, compared with L2 norm, L1-norm is more efficient to suppress outliers in the difference vector. These modifications are first integrated with the mutation strategy of JADE, then a modified version, named JADEfcr, is proposed. In addition, to improve the optimization ability further, another variant LJADEfcr by using a linear population reduction mechanism is considered. So as to confirm and examine the performance of JADEfcr and LJADEfcr, numerical experiments are conducted on 29 optimization problems defined by CEC2017 benchmark. For JADEfcr, its experimental results are made a comparison with twelve state-of-the-art algorithms. The comparative study demonstrates that in terms of robustness, stability and solution quality, JADEfcr are better and highly competitive with these well-known algorithms. For LJADEfcr, its results are compared with JADEfcr and other nine powerful algorithms including four recent algorithms and five top algorithms on CEC2017 competition. Experimental results indicate that LJADEfcr is superior and statistically competitive with these excellent algorithms in terms of robustness, stability and the quality of the obtained solutions.
Smart cities: the role of Internet of Things and machine learning in realizing a data-centric smart environment
Authors: Ullah Amin , Anwar Syed Myhammad , Li Jianqiang , Nadeem Lubna , Mahmood Tariq , Rehman Amjad , Saba Tanzila
Published: July 2023

This paper explores the concept of smart cities and the role of the Internet of Things (IoT) and machine learning (ML) in realizing a data-centric smart environment. Smart cities leverage technology and data to improve the quality of life for citizens and enhance the efficiency of urban services. IoT and machine learning have emerged as key technologies for enabling smart city solutions that rely on large-scale data collection, analysis, and decision-making. This paper presents an overview of smart cities’ various applications and discusses the challenges associated with implementing IoT and machine learning in urban environments. The paper also compares different case studies of successful smart city implementations utilizing IoT and machine learning technologies. The findings suggest that these technologies have the potential to transform urban environments and enable the creation of more livable, sustainable, and efficient cities. However, significant challenges remain regarding data privacy, security, and ethical considerations, which must be addressed to realize the full potential of smart cities.
Evolving deep gated recurrent unit using improved marine predator algorithm for profit prediction based on financial accounting information system
Authors: Li Xue , Khishe Mohammad , Qian Leren
Published: July 2023

This research proposes a hybrid improved marine predator algorithm (IMPA) and deep gated recurrent unit (DGRU) model for profit prediction in financial accounting information systems (FAIS). The study addresses the challenge of real-time processing performance caused by the increasing complexity of hybrid networks due to the growing size of datasets. To enable effective comparison, a new dataset is created using 15 input parameters from the original Chinese stock market Kaggle dataset. Additionally, five DGRU-based models are developed, including chaotic MPA (CMPA) and the nonlinear MPA (NMPA), as well as the best Levy-based variants, such as the dynamic Levy flight chimp optimization algorithm (DLFCHOA) and the Levy-base gray wolf optimization algorithm (LGWO). The results indicate that the most accurate model for profit forecasting among the tested algorithms is DGRU-IMPA, followed by DGRU-NMPA, DGRU-LGWO, DGRU-DLFCHOA, DGRU-CMPA, and traditional DGRU. The findings highlight the potential of the proposed hybrid model to improve profit prediction accuracy in FAIS, leading to enhanced decision-making and financial management.
Investigation on the effect of the gas-to-metal ratio on powder properties and PBF-LB/M processability
Authors: Cacace S. , Boccadoro M. , Semeraro Q.
Published: July 2023

Metal powders for the laser powder bed fusion process are usually produced via gas atomization. However, due to the tight particle size distribution required for this application, the yield of the atomization process is low, resulting in a high-powder cost. In this work, atomization process parameters were varied to increase the gas-to-metal ratio to reduce the particle size distribution produced, and therefore increase the yield of the process. As a result, eight powders were produced starting from scrap AISI 136L material at different gas-to-metal ratio values, and the atomization process yield was successfully increased by 50%. First, the eight powders were characterized in terms of powder size, shape distributions, and flowability. Later, all powders were used to produce tensile specimens. The powders produced at higher yield exhibited a larger number of fine particles but slightly lower circularity, particularly in the coarse fraction. Furthermore, powders produced at a high gas-to-metal ratio demonstrated enhanced flowing properties and higher packing density. Consequently, these powders exhibited superior tensile performance, with ultimate tensile strength (UTS) ranging from 651 to 673 MPa and elongation values between 63 and 66%.
Catalan generating functions for bounded operators
Authors: Miana Pedro J. , Romero Natalia
Published: July 2023

In this paper, we study the solution of the quadratic equation$$TY^2-Y+I=0$$TY2-Y+I=0whereTis a linear and bounded operator on a Banach spaceX. We describe the spectrum set and the resolvent operator ofYin terms of the ones ofT. In the case that 4Tis a power-bounded operator, we show that a solution (named Catalan generating function) of the above equation is given by the Taylor series$$\begin{aligned} C(T):=\sum _{n=0}^\infty C_nT^n, \end{aligned}$$C(T):=∑n=0∞CnTn,where the sequence$$(C_n)_{n\ge 0}$$(Cn)n≥0is the well-known Catalan numbers sequence. We expressC(T) by means of an integral representation which involves the resolvent operator$$(\lambda T)^{-1}$$(λT)-1. Some particular examples to illustrate our results are given, in particular an iterative method defined for square matricesTwhich involves Catalan numbers.
Bio-based alternatives to plastic drinking straws: are they more environmentally benign and consumer preferred?
Authors: Liang Yinglin , He Jiazhou , Zhuang Min , Chen Fayuan , Yang Kui , Ma Jinxing
Published: July 2023

The global production of nondegradable catering straws has skyrocketed due to their versatile properties, which results in significant CO2 emissions and pollution of the ecological system. While paper and polylactic acid straws have gained increasing popularity in the beverage industry, there needs to be more investigation of the vital product properties determining their hedonic differences. This study systematically compared the properties of paper, polylactic acid and plastic straws, and their impacts on the consumer experience and willingness. Results showed that the open structure of paper straws prompted water penetration and absorption, reaching a water absorption of 30% after 10-min wetting, which might affect the taste of the drink. In contrast, the compact polymer matrices of polylactic acid straws prevented mass exchange in their use for drinking but retarded product biodegradation under natural conditions. Results of consumer testing showed that while the participants had a comparable liking of paper and polylactic acid straws to insert into a drink (i.e., 4.16 and 4.47 out of 5, respectively), the intrinsic difference was covered up by the open-ended capping for beverages. For the “fully sealed on top” dataset, paper straws dropped to 3.46, while that for polylactic acid straws remained at 4.70. Furthermore, a biodegradable straw easily inserted into a drink without fracture may positively prompt merchants’ revenue. This study is expected to pave the way for the advancement and widespread use of bio-based products.

Graphical Abstract
Insights into Clinical Neurology
Authors: Laureno Robert
Published: July 2023

This illuminating book clarifies controversial topics in challenging and often confusing areas of neurology for all who are interested in clinical neuroscience. It provides an organized approach to neurological conditions such as amnesic syndrome, aphasia, agnosia and apraxia, it includes previously unpublished data on grasp reflex and Wernicke disease is presented. Written by an internationally renowned author, the book draws on his extensive personal experience to orient neurological clinicians to a variety of conditions by putting less accessible literature into context with recent advances and information from interviews undertaken throughout his career. This book will appeal to general and specialist neurologists, nurse practitioners, physician's assistants and those training to specialise in neurology.
The Creativity Advantage
Authors: Kaufman James C.
Published: July 2023

Creativity is usually seen as a good thing, but why? The Creativity Advantage first offers an overview of creativity studies with an emphasis on the little-discussed benefits of being creative. These include how creativity can lead to self-insight, help people heal, forge connections with others, inspire drive, and enable people to leave behind a meaningful legacy. Written in an engaging style and illustrated with interesting anecdotal material, this book offers a new perspective on creativity scholarship that can serve as an introduction to the field for newcomers or as a way to encourage new avenues for research.
Monody in Euripides
Authors: Catenaccio Claire
Published: July 2023

The solo singer takes center stage in Euripides' late tragedies. Solo song – what the Ancient Greeks called monody – is a true dramatic innovation, combining and transcending the traditional poetic forms of Greek tragedy. At the same time, Euripides uses solo song to explore the realm of the interior and the personal in an expanded expressive range. Contributing to the current scholarly debate on music, emotion, and characterization in Greek drama, this book presents a new vision for the role of monody in the musical design of Ion, Iphigenia among the Taurians, Phoenician Women, and Orestes. Drawing on her practical experience in the theater, Catenaccio establishes the central importance of monody in Euripides' art.
Vagabonds, Tramps, and Hobos
Authors: Clayton Owen
Published: July 2023

The most enduring version of the hobo that has come down from the so-called 'Golden Age of Tramping' (1890s to 1940s) is an American cultural icon, signifying freedom from restraint and rebellion to the established order while reinforcing conservative messages about American exceptionalism, individualism, race, and gender. Vagabonds, Tramps, and Hobos shows that this 'pioneer hobo' image is a misrepresentation by looking at works created by transient artists and thinkers, including travel literature, fiction, memoir, early feminist writing, poetry, sociology, political journalism, satire, and music. This book explores the diversity of meanings that accrue around 'the hobo' and 'the tramp'. It is the first analysis to frame transiency within a nineteenth-century literary tradition of the vagabond, a figure who attempts to travel without money. This book provide new ways for scholars to think about the activity and representation of US transiency.
Kilowatt-class high-energy frequency conversion to 95 J at 10 Hz at 515 nm
Authors: Divoky Martin , Phillips Jonathan , Pilar Jan , Hanus Martin , Navratil Petr , Denk Ondrej , Paliesek Tomas , Severova Patricie , Clarke Danielle , Smrz Martin , Butcher Thomas , Edwards Chris , Collier John , Mocek Tomas
Published: July 2023

We report on frequency doubling of high-energy, high repetition rate ns pulses from a cryogenically gas cooled multi-slab ytterbium-doped yttrium aluminum garnet laser system, Bivoj/DiPOLE, using a type-I phase matched lithium triborate crystal. We achieved conversion to 515 nm with energy of 95 J at repetition rate of 10 Hz and conversion efficiency of 79%. High conversion efficiency was achieved due to successful depolarization compensation of the fundamental input beam.
About the role of the Hanratty correction in the linear response of a turbulent flow bounded by a wavy wall
Authors: Chedevergne François , Stuck Maxime , Olazabal-Loumé Marina , Couzi Jacques
Published: July 2023

Scallop patterns forming on erodible surfaces were studied historically using a linear analysis of the inner region of a turbulent boundary layer growing on a corrugated wall. Experimental observations show a phase shift between the shear stress at the wall and the wall oscillation that depends on the wavenumber. Anad hoccorrection applied to the turbulent closure and due to Hanrattyet al.(Thorsnesset al.,Chem. Engng Sci., vol. 33, issue 5, 1978, pp. 579–592; Abrams & Hanratty,J. Fluid Mech., vol. 151, issue 1, 1985, p. 443; Frederick & Hanratty,Exp. Fluids, vol. 6, issue 7, 1988, pp. 477–486) was systematically used to recover the reference experimental results. In this study, Reynolds-averaged Navier–Stokes (RANS) and direct numerical simulations (DNS) were performed and revealed the role of the Boussinesq assumption in the results obtained. We show that the Hanratty correction acts as a palliative to the misrepresentation of Reynolds stresses due to the use of the Boussinesq hypothesis. The RANS calculations based on a turbulence model using a second-order moment closure recovered the expected results obtained in the reference DNS calculations, in particular with respect to wall heat transfer. The analysis of these results highlights the critical importance of the anisotropy of the diagonal Reynolds stresses on the prediction of wall transfer under these conditions and their implication in the occurrence of scalloping.
EXPERIMENTAL STUDY ON THE CHARGE-EXCHANGE CROSS-SECTIONS OF LOW-ENERGY CARBON IONS IN HELIUM AT GXNU
Authors: Zhang Guofeng , Shen Hongtao , Zhao Zhenchi , Tang Junsen , Wang Li , Chen Dingxiong , Qi Linjie , Wu Kaiyong , Han Xinyi , Ouyang He , Wang Ning , Sun Xiaojun , He Ming , Sasa Kimikazu , Jiang Shan
Published: July 2023

Compared with nitrogen and argon, helium is lighter and can better reduce the beam loss caused by angular scattering during beam transmission. The molecular dissociation cross-section in helium is high and stable at low energies, which makes helium the prevalent stripping gas in low-energy accelerator mass spectrometry (AMS). To study the stripping behavior of 14C ions in helium at low energies, the charge state distributions of carbon ion beams with −1, +1, +2, +3, and +4 charge states were measured at energies of 70–220 keV with a compact 14C-AMS at Guangxi Normal University (GXNU). The experimental data were used to analyze the stripping characteristics of C-He in the energy range of 70–220 keV, and new charge state yields and exchange cross-sections in C-He were obtained at energies of 70–220 keV.
The prevailing infection of Schistosoma japonicum and other zoonotic parasites in bubaline reservoir hosts in the ricefield of lake ecosystem: the case of Lake Mainit, Philippines
Authors: Estaño Leonardo A. , Jumawan Joycelyn C.
Published: July 2023

Bovines are important reservoir hosts of schistosomiasis, placing humans and animals in rice fields areas at risk of infection. This study reported the prevailing infection of zoonotic parasites from bovine feces in the rice fields adjacent to Lake Mainit, Philippines. Formalin Ethyl Acetate Sedimentation was performed on 124 bovine fecal samples from rice fields and documented eggs and cysts from seven parasites: Schistosoma japonicum, Fasciola gigantica, Ascaris sp., Strongyloides sp., Balantidium coli, coccidian oocyst and a hookworm species. Among these parasites, F. gigantica harboured the highest infection with a 100% prevalence rate, followed by hookworms (51.61%), B. coli (30.64%) and S. japonicum (12.09%), respectively. The intensity of infection of S. japonicum eggs per gram (MPEG = 4.19) among bovines is categorized as ‘light.’ Bovine contamination index (BCI) calculations revealed that, on average, infected bovines in rice fields excrete 104 750 S. japonicum eggs daily. However, across all ricefield stations, bovines were heavily infected with fascioliasis with BCI at 162 700 F. gigantica eggs per day. The study reports that apart from the persistent cases of schistosomiasis in the area, bovines in these rice fields are also heavily infected with fascioliasis. The study confirms the critical role of bovines as a reservoir host for continued infection of schistosomiasis, fascioliasis and other diseases in the rice fields of Lake Mainit. Immediate intervention to manage the spread of these diseases in bovines is recommended.
Whose open science are we talking about? From open science in psychology to open science in applied linguistics
Authors: Liu Meng
Published: July 2023

“An extremely timely, thoughtful, and well-informed discussion in applied linguistics and beyond concerning open science. The essay seeks to engage with a broad audience and to dispel some of the persisting myths around open science and would be read fruitfully by many in the field”.
Brain Model Technology and Its Implications
Authors: Muotri Alysson R.
Published: July 2023

The complexity of the human brain creates a spectrum of sophisticated behavioral repertoires, such as language, tool use, self-awareness, symbolic thought, cultural learning, and consciousness. Understanding how the human brain achieves that has been a longstanding challenge for neuroscientists and may bring insights into the evolution of human cognition and disease states. Human pluripotent stem cells could differentiate into specialized cell types and tissues in vitro. From this pluripotent state, it is possible to generate models of the human brain, such as brain organoids. The recent observation that brain organoids can spontaneously develop complex neural network activity in a dish can help one understand how neural network oscillations evolve and vary between normal and disease states. Moreover, this finding can be leveraged to other applications outside medicine, including engineering and artificial intelligence. However, as the brain model technology becomes more complex, it raises a series of ethical and moral dilemmas. This article discusses the status of this technology, some of its current limitations, and a vision of the future.
‘Differences within a range of similarity’: mapping Australian urban history
Authors: Lesh James
Published: July 2023

In 1964, Australian writer Donald Horne observed that ‘whatever differences there are between the Australian cities are differences within a range of similarity’. He proposed that Australia had 11 major cities and yet, in general, there existed a singular national urban culture, a one-city Australia. Unpacking the story of Australian urban history, its national trends and local nuances, has been an ongoing project ever since. What follows is an analysis of the field, which suggests how historians might begin to unpack Horne’s assertion. The final section of the article explores the contribution of Australian urban history in the national and global contexts.
Black-grass (Alopecurus myosuroides) in cereal multispectral detection by UAV
Authors: Cox Jonathan , Li Xiaodong , Fox Charles , Coutts Shaun
Published: July 2023

Site-specific weed management (on the scale of a few meters or less) has the potential to greatly reduce pesticide use and its associated environmental and economic costs. A prerequisite for site-specific weed management is the availability of accurate maps of the weed population that can be generated quickly and cheaply. Improvements and cost reductions in unmanned aerial vehicles (UAVs) and camera technology mean these tools are now readily available for agricultural use. We used UAVs to collect aerial images captured in both RGB and multispectral formats of 12 cereal fields (wheat [Triticum aestivumL.] and barley [Hordeum vulgareL.]) across eastern England. These data were used to train machine learning models to generate prediction maps of locations of black-grass (Alopecurus myosuroidesHuds.), a prolific weed in UK cereal fields. We tested machine learning and data set resampling methods to obtain the most accurate system for predicting the presence and absence of weeds in new out-of-sample fields. The accuracy of the system in predicting the absence ofA. myosuroidesis 69% and its presence above 5 g in weight with 77% accuracy in new out-of-sample fields. This system generates prediction maps that can be used by either agricultural machinery or autonomous robotic platforms for precision weed management. Improvements to the accuracy can be made by increasing the number of fields and samples in the data set and the length of time over which data are collected to gather data across the entire growing season.
Pillars of Cloud‐Based Earth Observation Science Education
Authors: Crowley Morgan A. , Stuhlmacher Michelle , Trochim Erin D. , Van Den Hoek Jamon , Pasquarella Valerie J. , Szeto Sabrina H. , Howarth Jeffrey T. , Platt Rud , Roy Samapriya , Tellman Beth , Chakraborty T. C. , Ignatius Amber , Cherrington Emil , Markert Kel , Wu Qiusheng , Madhusudan M. D. , Mayer Timothy , Cardille Jeffrey A. , Erickson Tyler , Moore Rebecca , Clinton Nicholas E. , Saah David
Published: July 2023

Earth observation (EO) is undergoing a paradigm shift with the development of cloud‐based analytical platforms supporting EO data collection and access, parallel processing, easier communication of results, and expanded accessibility. As the global community of users and the diversity of applications grow, there is a clear need for expanded educational capacity to leverage these developments and increase the impact of EO research and teaching. Drawing upon extensive conversations between educators, practitioners, and researchers, we propose three pillars that must be prioritized to prepare students, researchers, and professionals to take full advantage of the cloud‐based EO paradigm and guide future growth.
Impacts of air pollution and meteorological conditions on dry eye disease among residents in a northeastern Chinese metropolis: a six-year crossover study in a cold region
Authors: Lu Cheng-Wei , Fu Jing , Liu Xiu-Fen , Cui Zhi-Hua , Chen Wei-Wei , Guo Li , Li Xiao-Lan , Ren Yu , Shao Fei , Chen Li-Na , Hao Ji-Long
Published: July 2023

The purpose of this study is to explore the associations among dry eye disease (DED), air pollution, and meteorological conditions in the cold region of a northeastern Chinese metropolis (i.e., Changchun). Data on ambient air pollutants and meteorological parameters as well as diagnosed DED outpatients during 2015–2021 were collected. The associations between DED and environmental factors were analysed at multiple time scales using various statistical methods (i.e., correlation, regression and machine learning). Among the 10,809 DED patients (21,617 eyes) studied, 64.60% were female and 35.40% were male. A higher frequency of DED was observed in March and April, followed by January, August and October. Individual and multiple factor models showed the positive importance of particles with aerodynamic diameters <10 μm (PM10), carbon monoxide (CO), and ozone (O3) among normal air pollutants and air pressure (AP), air temperature (AT) and wind speed (WS) among normal meteorological parameters. Air pollutants (PM10, nitrogen dioxide: NO2) and meteorological parameters (AT, AP) have combined impacts on DED occurrence. For the first time, we further explored the associations of detailed components of atmospheric particles and DED, suggesting potential emission sources, including spring dust from bare soil and roads and precursor pollutants of summer O3 formation from vehicles and industry in Northeast China. Our results revealed the quantitative associations among air pollutants, meteorological conditions and DED outpatients in cold regions, highlighting the importance of coordinated policies in air pollution control and climate change mitigation.
Trans-ancestry meta-analysis of genome wide association studies of inhibitory control
Authors: Arnatkeviciute Aurina , Lemire Mathieu , Morrison Claire , Mooney Michael , Ryabinin Peter , Roslin Nicole M. , Nikolas Molly , Coxon James , Tiego Jeggan , Hawi Ziarih , Fornito Alex , Henrik Walter , Martinot Jean-Luc , Martinot Marie-Laure Paillère , Artiges Eric , Garavan Hugh , Nigg Joel , Friedman Naomi P. , Burton Christie , Schachar Russell , Crosbie Jennifer , Bellgrove Mark A.
Published: July 2023

Deficits in effective executive function, including inhibitory control are associated with risk for a number of psychiatric disorders and significantly impact everyday functioning. These complex traits have been proposed to serve as endophenotypes, however, their genetic architecture is not yet well understood. To identify the common genetic variation associated with inhibitory control in the general population we performed the first trans-ancestry genome wide association study (GWAS) combining data across 8 sites and four ancestries (N = 14,877) using cognitive traits derived from the stop-signal task, namely – go reaction time (GoRT), go reaction time variability (GoRT SD) and stop signal reaction time (SSRT). Although we did not identify genome wide significant associations for any of the three traits, GoRT SD and SSRT demonstrated significant and similar SNP heritability of 8.2%, indicative of an influence of genetic factors. Power analyses demonstrated that the number of common causal variants contributing to the heritability of these phenotypes is relatively high and larger sample sizes are necessary to robustly identify associations. In Europeans, the polygenic risk for ADHD was significantly associated with GoRT SD and the polygenic risk for schizophrenia was associated with GoRT, while in East Asians polygenic risk for schizophrenia was associated with SSRT. These results support the potential of executive function measures as endophenotypes of neuropsychiatric disorders. Together these findings provide the first evidence indicating the influence of common genetic variation in the genetic architecture of inhibitory control quantified using objective behavioural traits derived from the stop-signal task.
The spatiotemporal dynamics of spatially variable genes in developing mouse brain revealed by a novel computational scheme
Authors: Hong Yingzhou , Song Kai , Zhang Zongbo , Deng Yuxia , Zhang Xue , Zhao Jinqian , Jiang Jun , Zhang Qing , Guo Chunming , Peng Cheng
Published: July 2023

To understand how brain regions form and work, it is important to explore the spatially variable genes (SVGs) enriched in specific brain regions during development. Spatial transcriptomics techniques provide opportunity to select SVGs in the high-throughput way. However, previous methods neglected the ranking order and combinatorial effect of SVGs, making them difficult to automatically select the high-priority SVGs from spatial transcriptomics data. Here, we proposed a novel computational pipeline, called SVGbit, to rank the individual and combinatorial SVGs for marker selection in various brain regions, which was tested in different kinds of public datasets for both human and mouse brains. We then generated the spatial transcriptomics and immunohistochemistry data from mouse brain at critical embryonic and neonatal stages. The results show that our ranking and clustering scheme captures the key SVGs which coincide with known anatomic regions in the developing mouse brain. More importantly, SVGbit can facilitate the identification of multiple gene combination sets in different brain regions. We identified three dynamical sub-regions which can be segregated by the staining of Sox2 and Calb2 in thalamus, and we also found that Nr4a2 expression gradually segregates the neocortex and hippocampus during the development. In summary, our work not only reveals the spatiotemporal dynamics of individual and combinatorial SVGs in developing mouse brain, but also provides a novel computational pipeline to facilitate the selection of marker genes from spatial transcriptomics data.
A BAHD-type acyltransferase concludes the biosynthetic pathway of non-bitter glycoalkaloids in ripe tomato fruit
Authors: Sonawane Prashant D. , Gharat Sachin A. , Jozwiak Adam , Barbole Ranjit , Heinicke Sarah , Almekias-Siegl Efrat , Meir Sagit , Rogachev Ilana , Connor Sarah E. O’ , Giri Ashok P. , Aharoni Asaph
Published: July 2023

Tomato is the highest value fruit and vegetable crop worldwide, yet produces α-tomatine, a renowned toxic and bitter-tasting anti-nutritional steroidal glycoalkaloid (SGA) involved in plant defense. A suite of modifications during tomato fruit maturation and ripening converts α-tomatine to the non-bitter and less toxic Esculeoside A. This important metabolic shift prevents bitterness and toxicity in ripe tomato fruit. While the enzymes catalyzing glycosylation and hydroxylation reactions in the Esculeoside A pathway have been resolved, the proposed acetylating step remains, to date, elusive. Here, we discovered that GAME36 (GLYCOALKALOID METABOLISM36), a BAHD-type acyltransferase catalyzes SGA-acetylation in cultivated and wild tomatoes. This finding completes the elucidation of the core Esculeoside A biosynthetic pathway in ripe tomato, allowing reconstitution of Esculeoside A production in heterologous microbial and plant hosts. The involvement of GAME36 in bitter SGA detoxification pathway points to a key role in the evolution of sweet-tasting tomato as well as in the domestication and breeding of modern cultivated tomato fruit.
Locomotion modulates olfactory learning through proprioception in C. elegans
Authors: Zhan Xu , Chen Chao , Niu Longgang , Du Xinran , Lei Ying , Dan Rui , Wang Zhao-Wen , Liu Ping
Published: July 2023

Locomotor activities can enhance learning, but the underlying circuit and synaptic mechanisms are largely unknown. Here we show that locomotion facilitates aversive olfactory learning in C. elegans by activating mechanoreceptors in motor neurons, and transmitting the proprioceptive information thus generated to locomotion interneurons through antidromic-rectifying gap junctions. The proprioceptive information serves to regulate experience-dependent activities and functional coupling of interneurons that process olfactory sensory information to produce the learning behavior. Genetic destruction of either the mechanoreceptors in motor neurons, the rectifying gap junctions between the motor neurons and locomotion interneurons, or specific inhibitory synapses among the interneurons impairs the aversive olfactory learning. We have thus uncovered an unexpected role of proprioception in a specific learning behavior as well as the circuit, synaptic, and gene bases for this function.
Neuroprotective role for RORA in Parkinson’s disease revealed by analysis of post-mortem brain and a dopaminergic cell line
Authors: Al-Zaid Felwah S. , Hurley Michael J. , Dexter David T. , Gillies Glenda E.
Published: July 2023

Parkinson’s disease (PD) is almost twice as prevalent in men, which has largely been attributed to neuroprotective effect of oestradiol in women. RORA (retinoic acid receptor-related orphan receptor alpha) regulates the transcription of central aromatase, the enzyme responsible for local oestradiol synthesis, simultaneously, RORA expression is regulated by sex hormones. Moreover, RORA protects neurones against oxidative stress, a key mechanism contributing to the loss of dopaminergic neurones in PD. Therefore, we hypothesized that there would be sex differences in RORA expression in the substantia nigra pars compacta (SNpc), which could contribute to sex differences observed in PD prevalence and pathogenesis. In a case control study, qPCR and western blot analyses were used to quantify gene and protein expression in the SNpc of post-mortem brains (n = 14 late-stage PD and 11 age and sex matched controls). The neuroprotective properties of a RORA agonist were then investigated directly using a cell culture toxin-based model of PD coupled with measures of viability, mitochondrial function and apoptosis. RORA was expressed at significantly higher levels in the SNpc from control females’ brains compared to males. In PD, we found a significant increase in SNpc RORA expression in male PD compared to female PD. Treatment with a RORA agonist showed a significant neuroprotection in our cell culture model of PD and revealed significant effects on intracellular factors involved in neuronal survival and demise. This study is the first to demonstrate a sex specific pattern of RORA protein and gene expression in the SNpc of controls post-mortem human brains, and to show that this is differentially altered in male and female PD subjects, thus supporting a role for RORA in sex-specific aspects of PD. Furthermore, our in vitro PD model indicates mechanisms whereby a RORA agonist exerts its neuroprotective effect, thereby highlighting the translational potential for RORA ligands in PD.
Exact electronic states with shallow quantum circuits from global optimisation
Authors: Burton Hugh G. A. , Marti-Dafcik Daniel , Tew David P. , Wales David J.
Published: July 2023

Quantum computers promise to revolutionise molecular electronic simulations by overcoming the exponential memory scaling. While electronic wave functions can be represented using a product of fermionic unitary operators, the best ansatz for strongly correlated electronic systems is far from clear. In this contribution, we construct universal wave functions from gate-efficient, spin symmetry-preserving fermionic operators by introducing an algorithm that globally optimises the wave function in the discrete ansatz design and continuous parameter spaces. Our approach maximises the accuracy that can be obtained with near-term quantum circuits and provides a practical route for designing ansätze in the future. Numerical simulations for strongly correlated molecules, including water and molecular nitrogen, and the condensed-matter Hubbard model, demonstrate the improved accuracy of gate-efficient quantum circuits for simulating strongly correlated chemistry.
Influence of inter-stimulus interval on 40-Hz auditory steady-state response in patients with schizophrenia
Authors: Choi Kang-Min , Im Chang-Hwan , Yang Chaeyeon , Lee Hyun Seo , Kim Sungkean , Lee Seung-Hwan
Published: July 2023

Decreased 40-Hz auditory steady-state response (ASSR) is believed to reflect abnormal gamma oscillation in patients with schizophrenia (SZ). However, previous studies have reported conflicting results due to variations in inter-stimulus interval (ISI) used. In this study, we aimed to investigate the influence of varying ISI on the 40-Hz ASSR, particularly for patients with SZ and healthy controls (HCs). Twenty-four SZ patients (aged 40.8 ± 13.9 years, male: n = 11) and 21 HCs (aged 33.3 ± 11.3 years, male: n = 8) were recruited. For every participant, 40-Hz ASSRs were acquired for three different stimulus types: 500, 2000, and 3500 ms of ISIs. Two conventional ASSR measures (total power and inter-trial coherence, ITC) were calculated. Several additional ASSR measures were also analyzed: (i) ISI-dependent power; (ii) power onset slope; (iii) power centroid latency; (iv) ISI-dependent ITC; (v) ITC onset slope (500, 2000, 3500 ms); (vi) ITC centroid latency (500, 2000, 3500 ms). As ISI increased, total power and ITC increased in patients with SZ but decreased in HCs. In addition, patients with SZ showed higher ISI-dependent ITC, which was positively correlated with the psychotic symptom severity. The abnormal ITC onset slope and centroid latency for the ISI-500 ms condition were associated with cognitive speed decline in patients with SZ. Our study confirmed that the 40-Hz ASSR could be severely influenced by ISI. Furthermore, our results showed that the additional ASSR measures (ISI-dependent ITC, ITC onset slope, ITC centroid latency) could represent psychotic symptom severity or impairment in cognitive function in patients with SZ.
Exposure of iPSC-derived human microglia to brain substrates enables the generation and manipulation of diverse transcriptional states in vitro
Authors: Dolan Michael-John , Therrien Martine , Jereb Saša , Kamath Tushar , Gazestani Vahid , Atkeson Trevor , Marsh Samuel E. , Goeva Aleksandrina , Lojek Neal M. , Murphy Sarah , White Cassandra M. , Joung Julia , Liu Bingxu , Limone Francesco , Eggan Kevin , Hacohen Nir , Bernstein Bradley E. , Glass Christopher K. , Leinonen Ville , Blurton-Jones Mathew , Zhang Feng , Epstein Charles B. , Macosko Evan Z. , Stevens Beth
Published: July 2023

Microglia, the macrophages of the brain parenchyma, are key players in neurodegenerative diseases such as Alzheimer’s disease. These cells adopt distinct transcriptional subtypes known as states. Understanding state function, especially in human microglia, has been elusive owing to a lack of tools to model and manipulate these cells. Here, we developed a platform for modeling human microglia transcriptional states in vitro. We found that exposure of human stem-cell-differentiated microglia to synaptosomes, myelin debris, apoptotic neurons or synthetic amyloid-beta fibrils generated transcriptional diversity that mapped to gene signatures identified in human brain microglia, including disease-associated microglia, a state enriched in neurodegenerative diseases. Using a new lentiviral approach, we demonstrated that the transcription factor MITF drives a disease-associated transcriptional signature and a highly phagocytic state. Together, these tools enable the manipulation and functional interrogation of human microglial states in both homeostatic and disease-relevant contexts.
Genome-wide identification of accessible chromatin regions by ATAC-seq upon induction of the transcription factor bZIP11 in Arabidopsis
Authors: Hellens Alicia M. , Humphreys Jazmine L. , Fichtner Franziska , Tanurdžić Miloš , Beveridge Christine A. , Barbier François F.
Published: July 2023

Basic leucine zipper 11 (bZIP11) is a transcription factor that is activated under low energy conditions in plants and plays a crucial role in enabling plants to adapt to starvation situations. Although previous results indicate that bZIP11 regulates chromatin accessibility based on evidence obtained from single genomic loci, to what extent this transcription factor regulates the chromatin landscape at the whole genome level remains unknown. Here we addressed this by performing an ATAC-seq (Assay for Transposase-Accessible Chromatin with high-throughput sequencing) on Arabidopsis thaliana (Arabidopsis) leaf protoplasts to obtain a profile of chromatin patterning in response upon bZIP11 induction. We identified, on average, 10,000 differentially accessible regions upon bZIP11 induction, corresponding to over 8,420 different genes out of the 25,000 genes present in the Arabidopsis genome. Our study provides a resource for understanding how bZIP11 regulates the genome at the chromatin level and provides an example of the impact of a single transcription factor on a whole plant genome.
A multi-predator trophic database for the California Current Large Marine Ecosystem
Authors: Bizzarro Joseph J. , Dewitt Lynn , Wells Brian K. , Curtis K. Alexandra , Santora Jarrod A. , Field John C.
Published: July 2023

The California Current Trophic Database (CCTD) was developed at NOAA Southwest Fisheries Science Center in collaboration with numerous diet data contributors. We compiled the CCTD from twenty-four data sets, representing both systematic collections and directed trophic studies. Diet composition data, including stomach and scat samples, were obtained from 105,694 individual predators among 143 taxa collected throughout the California Current Large Marine Ecosystem (CCLME) from 1967–2019. Predator taxa consist of squids (n = 5), elasmobranchs (n = 13), bony fishes (n = 118), and marine mammals (n = 7). Extensive time series are available for some predators (e.g., California Sea Lion, Pacific Hake, Chinook Salmon). The CCTD represents the largest compilation of raw trophic data within the CCLME, allowing for more refined analyses and modeling studies within this region. Our intention is to further augment and periodically update the dataset as additional historical or contemporary data become available to increase its utility and impact.
A paired dataset of T1- and T2-weighted MRI at 3 Tesla and 7 Tesla
Authors: Chen Xiaoyang , Qu Liangqiong , Xie Yifang , Ahmad Sahar , Yap Pew-Thian
Published: July 2023

Brain magnetic resonance imaging (MRI) provides detailed soft tissue contrasts that are critical for disease diagnosis and neuroscience research. Higher MRI resolution typically comes at the cost of signal-to-noise ratio (SNR) and tissue contrast, particularly for more common 3 Tesla (3T) MRI scanners. At ultra-high magnetic field strength, 7 Tesla (7T) MRI allows for higher resolution with greater tissue contrast and SNR. However, the prohibitively high costs of 7T MRI scanners deter their widespread adoption in clinical and research centers. To obtain higher-quality images without 7T MRI scanners, algorithms that can synthesize 7T MR images from 3T MR images are under active development. Here, we make available a dataset of paired T1-weighted and T2-weighted MR images at 3T and 7T of 10 healthy subjects to facilitate the development and evaluation of 3T-to-7T MR image synthesis models. The quality of the dataset is assessed using image quality metrics implemented in MRIQC.
Towards automated long-term acoustic monitoring of endangered river dolphins: a case study in the Brazilian Amazon floodplains
Authors: Erbs Florence , Gaona Marina , van der Schaar Mike , Zaugg Serge , Ramalho Emiliano , Houser Dorian , André Michel
Published: July 2023

Using passive acoustic monitoring (PAM) and convolutional neural networks (CNN), we monitored the movements of the two endangered Amazon River dolphin species, the boto (Inia geoffrensis) and the tucuxi (Sotalia fluviatilis) from main rivers to floodplain habitats (várzea) in the Mamirauá Reserve (Amazonas, Brazil). We detected dolphin presence in four main areas based on the classification of their echolocation clicks. Using the same method, we automatically detected boat passages to estimate a possible interaction between boat and dolphin presence. Performance of the CNN classifier was high with an average precision of 0.95 and 0.92 for echolocation clicks and boats, respectively. Peaks of acoustic activity were detected synchronously at the river entrance and channel, corresponding to dolphins seasonally entering the várzea. Additionally, the river dolphins were regularly detected inside the flooded forest, suggesting a wide dispersion of their populations inside this large area, traditionally understudied and particularly important for boto females and calves. Boats overlapped with dolphin presence 9% of the time. PAM and recent advances in classification methods bring a new insight of the river dolphins’ use of várzea habitats, which will contribute to conservation strategies of these species.