bluuebunny/crossref_metadata_2025 huggingface dataset:
Investigating the reliability of metapodials as taxonomic Indicators for Beringian horses
Authors: Landry Zoe , Roloson Mathew J. , Fraser Danielle
Published: September 2022

The metapodials of extinct horses have long been regarded as one of the most useful skeletal elements to determine taxonomic identity. However, recent research on both extant and extinct horses has revealed the possibility for plasticity in metapodial morphology, leading to notable variability within taxa. This calls into question the reliability of metapodials in species identification, particularly for species identified from fragmentary remains. Here, we use ten measurements of metapodials from 203 specimens of four Pleistocene horse species from eastern Beringia to test whether there are significant differences in metapodial morphology that support the presence of multiple species. We then reconstruct the body masses for every specimen to assess the range in body size within each species and determine whether species differ significantly from one another in mean body mass. We find that that taxonomic groups are based largely on the overall size of the metapodial, and that all metapodial measurements are highly autocorrelated. We also find that mean body mass differs significantly among most, but not all, species. We suggest that metapodial measurements are unreliable taxonomic indicators for Beringian horses given evidence for plasticity in metapodial morphology and their clear reflection of differences in body mass. We recommend future studies use more reliable indicators of taxonomy to identify Beringian horse species, particularly from localities from which fossils of several species have been recovered.
Two-sided Bogoliubov inequality to estimate finite size effects in quantum molecular simulations
Authors: Reible Benedikt , Hartmann Carsten , Delle Site Luigi
Published: September 2022

We generalise the two-sided Bogoliubov inequality for classical particles (Delle Site et al. in J Stat Mech Theory Exp 083201, 2017 to systems of quantum particles. As in the classical set-up, the inequality leads to upper and lower bounds for the free energy difference associated with the partitioning of a large system into smaller, independent subsystems. From a thermodynamic modelling point of view, the free energy difference determines the finite size correction needed to consistently treat a small system as a representation of a large system. Applications of the bounds to quantify finite size effects are ubiquitous in physics, chemistry, material science, or biology, to name just a few; in particular, it is relevant for molecular dynamics simulations in which a small portion of a system is usually taken as representative of the idealized large system.
Unusual “Asian-origin” 2c to 2b point mutant canine parvovirus (Parvoviridae) and canine astrovirus (Astroviridae) co-infection detected in vaccinated dogs with an outbreak of severe haemorrhagic gastroenteritis with high mortality rate in Hungary
Authors: Boros Ákos , Albert Mihály , Urbán Péter , Herczeg Róbert , Gáspár Gábor , Balázs Benigna , Cságola Attila , Pankovics Péter , Gyenesei Attila , Reuter Gábor
Published: September 2022

In this study, the aetiological background of an outbreak of severe haemorrhagic gastroenteritis (HGE) in a colony of purebred Jack Russell Terriers vaccinated against CPV-2 in Hungary was investigated. Canine parvovirus 2 (CPV-2, Parvoviridae) and canine astrovirus (CaAstV, Astroviridae) co-infection was identified by viral metagenomics and next-generation sequencing (VM-NGS) methods from a rectal swab of an affected 7-week-old puppy. The complete coding sequence of CPV-2 strain FR1/CPV2-2021-HUN (ON733252) and the complete genome of CaAstV strain FR1/CaAstV-2021-HUN (ON733251) were determined by VM-NGS and PCR methods. Results of sequence and phylogenetic analyses showed that CPV-2 strain FR1/CPV2-2021-HUN was different from the applied vaccine strains and previously identified strains from Hungary but showed high sequence identity (> 99.8%) and close phylogenetic relationship to recently described “Asian-origin” CPV-2c strains from Italy. But, based on the single amino acid difference on position 426 of VP2 (Glu/Asp) between the study strain and the closest relatives, FR1/CPV2-2021-HUN belonged to the 2b antigenic type rather than 2c. The CaAstV strain FR1/CaAstV-2021-HUN showed close relationship with a CaAstV strain identified previously from a diarrhoeic dog in Hungary. Both viruses were continuously detectable by PCR in additional enteric samples, and the CPV-2 could also be detected in several (n = 32) tissue samples from 9 affected deceased puppies. Further comparative studies are necessary to confirm the role of the point mutation causing the change in the antigenic type of this “Asian-origin” CPV-2 and/or the role of CaAstV co-infection in the development and/or severity of (haemorrhagic) gastroenteritis among dogs vaccinated against CPV-2.
Schooling upheaval during COVID-19: troubling consequences for students’ return to school
Authors: Fray Leanne , Jaremus Felicia , Gore Jennifer , Harris Jess
Published: September 2022

Efforts to contain the COVID-19 virus resulted in various stay-at-home orders and school closures around the globe, causing unprecedented disruption to the lives of children and generating grave concern for their well-being. This study draws on phone interviews with 12 teachers and 6 school leaders from 13 government schools in New South Wales, Australia, to provide insight into how students fared on their return to school after the first wave of COVID-19 in 2020. The interviews highlighted negative consequences for many students including increased stress and anxiety and decreased engagement. This evidence suggests that even a comparatively short period of school closure can drive troubling changes in students’ well-being and behaviour following their return to school. Given far more challenging conditions arising from the pandemic, both elsewhere in Australia and globally, we argue that attending to student well-being is as important as ensuring academic achievement and must be a key focus of policy makers and education systems moving forward.
The global integrative network: integration of signaling and metabolic pathways
Authors: Lin Yuying , Yan Shen , Chang Xiao , Qi Xiaoquan , Chi Xu
Published: September 2022

The crosstalk between signaling and metabolic pathways has been known to play key roles in human diseases and plant biological processes. The integration of signaling and metabolic pathways can provide an essential reference framework for crosstalk analysis. However, current databases use distinct structures to present signaling and metabolic pathways, which leads to the chaos in the integrated networks. Moreover, for the metabolic pathways, the metabolic enzymes and the reactions are disconnected by the current widely accepted layout of edges and nodes, which hinders the topological analysis of the integrated networks. Here, we propose a novel “meta-pathway” structure, which uses the uniformed structure to display the signaling and metabolic pathways, and resolves the difficulty in linking the metabolic enzymes to the reactions topologically. We compiled a comprehensive collection of global integrative networks (GINs) by merging the meta-pathways of 7077 species. We demonstrated the assembly of the signaling and metabolic pathways using the GINs of four species—human, mouse, Arabidopsis, and rice. Almost all of the nodes were assembled into one major network for each of the four species, which provided opportunities for robust crosstalk and topological analysis, and knowledge graph construction.
Computing growth rates of random matrix products via generating functions
Authors: Bao Naranmandula , Lu Junbiao , Cai Ruobing , Lan Yueheng
Published: September 2022

Random matrix products arise in many science and engineering problems. An efficient evaluation of its growth rate is of great interest to researchers in diverse fields. In the current paper, we reformulate this problem with a generating function approach, based on which two analytic methods are proposed to compute the growth rate. The new formalism is demonstrated in a series of examples including an Ising model subject to on-site random magnetic fields, which seems very efficient and easy to implement. Through an extensive comparison with numerical computation, we see that the analytic results are valid in a region of considerable size.The formulation could be conveniently applied to stochastic processes with more complex structures.
Early versus late intubation on the outcome of intensive care unit-admitted COVID-19 patients at Addis Ababa COVID-19 treatment centers, Addis Ababa, Ethiopia: A multicenter retrospective cohort study
Authors: Birhanu Tsehay , Gemeda Leulayehu Akalu , Fekede Mulualem Sitot , Hirbo Hirbo Samuel
Published: September 2022

Abstract

Background

Coronavirus disease 2019 (COVID-19) has resulted in severe acute respiratory failure, requiring intubation and an invasive mechanical ventilation. However, the time for initiation of intubation remains debatable. Therefore, this study aimed to compare early and late intubation on the outcome of COVID-19 patients admitted to the intensive care unit (ICU) of selected Addis Ababa COVID-19 treatment centers, Ethiopia.

Methods

A multicenter retrospective cohort study was conducted on 94 early and late intubated ICU-admitted COVID-19 patients from October 1, 2020, to October 31, 2021, in three selected COVID-19 treatment centers in Addis Ababa, Ethiopia. A simple random sampling technique was used to select study participants. An independent t-test, Mann Whitney U test and Fisher’s exact test were used for statistical analysis, as appropriate. A P value < 0.05 was used to declare a statistical significance.

Results

A total of 94 patients participated, for a response rate of 94.68%. There was a statistically insignificant difference in the rates of death between the early intubated (47.2%) and the late intubated (46.1%) groups (P = 0.678). There was no difference in the median length of stay on a mechanical ventilator (in days) between the groups (P = 0.11). However, the maximum length of stay in the ICU to discharge was significantly shorter in the early intubated (33.1 days) than late intubated groups (63.79 days) (P < 0.001).

Conclusion

Outcomes (death or survival) were similar whether early or late intubation was used. Early intubation did appear to improve length of ICU stay in ICU-admitted COVID-19 patients.

Highlights
Decentering European History from the Margins
Authors: Werner Michael , Deller Joanne
Published: September 2022

The article considers the global historiography of Europe from two angles. First it outlines the difficulties, both historical and epistemological, that Europe poses as an object of study, especially after the historiographical transformations prompted by the events of 1989, the rise of postcolonial studies, the growing critique of Eurocentrism, and, most recently, the “global turn.” The conceptions of Europe that emerge from these currents have often been based on a rather homogenized vision of the continent, centered on the great nation-states of western Europe and their imperial policies. They also perpetuate, even as they criticize it, the legacy of a conception of modernity that positions Europe as both its historical center and the agent of its expansion on a global scale. The second part of the paper proposes to limit the blind spots inherent in this kind of vision by shifting our gaze to the eastern and Balkan margins of Europe, where the Austro-Hungarian, Ottoman, and Russian empires intersected over the “long” nineteenth century. This change of perspective displaces the history of Europe’s connection to modernity, revealing the great diversity of local actors, the importance of multicultural and pluriethnic societies, and the particular role of transnational populations such as Jews, who, while negotiating their own relationship to a European modernity, escaped the grip of national movements.
Timing of energy intake and BMI in children: differential impacts by age and sex
Authors: Mahdi Sundus , Dickerson Andrew , Infield Solar Gisele , Caton Samantha J.
Published: September 2022

Body weight regulation may be influenced by the timing of food intake. The relationship between children’s BMI and their daily pattern of energy consumption was investigated using data from the UK National Diet and Nutrition Survey 2008–2019. The sample included 6281 children aged 4–18 years. Linear and logistic regression models investigated the timing of energy intake (103kJ) as a predictor of BMI (kg/m2) and healthy weight status. The models showed that children aged 4–10 years who consume more energy content after 20:00, in comparison with less energy content, had a significantly higher BMI (young girls:β= 0·159; 95 % CI 0·003, 0·315;P= 0·05; young boys:β= 0·166; 95 % CI 0·028, 0·304;P= 0·02). Similar findings were also present for boys aged 11–18 years (β= 0·091; 95 % CI 0·003, 0·180;P= 0·04), though logistic regression findings were contradictory (OR = 0·9566; 95 % CI 0·926, 0·989;P =0·009). However, older girls who consumed more energy content in the morning had a significantly lower BMI (β =–0·464; 95 % CI –0·655, –0·273;P< 0·001) and a lower probability of non-healthy weight (OR = 0·901; 95 % CI 0·826, 0·982;P= 0·02). Physical activity reduced the likelihood of unhealthy weight status. The data suggest that food consumption later in the day in childhood and into adolescence may increase the risk of a higher BMI, especially for less active children. Developing guidance on appropriate meal timings and recommended energy distribution throughout the day could promote healthier lifestyles. Doing so may help increase parental awareness of timing of food intake and its potential impact on BMI.
A before−after assessment of the response of mammals to tourism in a Brazilian national park
Authors: Barcelos Daniele , Vieira Emerson M. , Pinheiro Marcell Soares , Ferreira Guilherme Braga
Published: September 2022

Worldwide, nature-based tourism is becoming more popular and important economically. However, there is still debate regarding its impact on wildlife in protected areas. We conducted a quasi-experimental study to investigate the effects of tourism on the mammal community of Cavernas do Peruaçu National Park, a priority area for conservation in Brazil. We used camera traps to survey tourist and non-tourist trails during 2011–2017, encompassing periods before and after tourism started in the Park. We used four metrics for assessment: species richness, probability of using trails, activity levels and daily activity patterns. After tourism began in the Park there was no significant change in species richness and the probability of using tourist trails either increased or remained stable for five of the six species assessed. The rock cavyKerodon rupestriswas the only species to be displaced from tourist areas and to show reduced overall activity on tourist trails after tourism began. The ocelotLeopardus pardalisshowed reduced diurnal activity on tourist trails, an indication of temporal adjustment. Overall, our results show that the initial years of visitation at the Park had limited negative impacts on the target mammal species, supporting the possibility of accommodating tourism activity and effective conservation of wildlife in the region. However, it is essential to continue monitoring in the Park because of the expected growth in tourism and potential time lags in responses of species.
Ephemeral by design
Authors: Chattopadhyay Swati
Published: September 2022

Between the months of September and October, Kolkata celebrates the Hindu religious festival of Durgapuja on a grand scale. Organised by local clubs and neighbourhood voluntary associations, approximately 2,500 temporary structures – pandals – are built for the worship or puja of the goddess Durga and her entourage. Of these about two thousand occupy the city’s public spaces: streets, parks, green islands, and vacant lots. A large number of the pandals are finely engineered structures that are fabulously decorated and attract hundreds of thousands of visitors each day of the festivities. It takes anywhere between three months to three days to build these pavilions. After five days of festivities the pandals are dismantled and the clay deities destroyed by immersing them in the Hooghly River or another nearby body of water.
Living (in) the archive
Authors: Inglis Megha Chand
Published: September 2022

Let us sit down here on this seat. We had it made as a sample for a temple in Junagadh. Now it has a place here at home. We call its back the kakshasan. Do you know why? Because the backrest supports the kaksh or the armpit, when you lean against it while sitting, just like this.
Rethinking ‘architect’ and ‘architecture’
Authors: Chatterjee Jaideep
Published: September 2022

My fellow architects, let me begin this piece with a provocative, even blasphemous, proposition: it is time to do away with the twin terms ‘architect’ and ‘architecture’ as signs that stand in for what we are, what we do or as a ‘thing’ in the world.
Architectural knowledge and the ‘Dravidian’ temple in colonial Madras Presidency
Authors: Branfoot Crispin
Published: September 2022

In around 1912 Gabriel Jouveau-Dubreuil, a young science teacher from French colonial Pondicherry in South India, visited the nearby town of Cuddalore in order to inspect the construction of a new Hindu temple. Since arriving in South India in 1909 he had been travelling to many temples and archaeological sites in order to understand the history of South Indian art. The modern temple that he visited in a suburb of Cuddalore at Tiruppappuliyur was not in fact new but a wholesale renovation of a nine-hundred-year-old shrine on a site sacred to Tamil Shaivas. This was just one of the many temples substantially rebuilt from the 1890s to the 1930s under the patronage of a wealthy merchant community, the Nattukkottai Chettiars, at a time of religious revival and growing Tamil cultural nationalism. The Nattukkottai Chettiars came from the villages and towns of Chettinadu, an arid region in southern Madras Presidency. This region was significant not only for being the provenance of the most prolific patrons of South Indian temple architecture in colonial Madras Presidency but also their builders, for many of the architects and craftsmen working on the temple at Tiruppappuliyur were from villages in Chettinadu. One of these men, M. S. Swaminathan of Pillaiyarpatti, was Jouveau-Dubreuil’s chief informant, one of the many ‘natives’ who were a critical and inextricable element of colonial knowledge production. The understanding of formal composition and terminology that Jouveau-Dubreuil learnt from contemporary architects and craftsmen and his observations of the evolution of architectural design contributed towards the first study of the Tamil temple for both a scholarly and wider public audience from the very earliest monuments of the seventh century through to those currently under construction. This article explores this architectural ‘renaissance’ in colonial Madras Presidency under Chettiar patronage and evaluates modern temple design through the pioneering scholarship of Jouveau-Dubreuil and his contemporaries.
Sacred architectures as monuments: a study of the Kalkaji Mandir, Delhi
Authors: Sutton Deborah
Published: September 2022

This article considers the relationship between architecture, bodies, and custodies in the making of Indian urban monuments. Monuments are created through a combination of design and designation. In this article I explore a religious architecture that is dynamic and iterative and at which monumental designation was attempted and quickly abandoned. I align three issues: what a monument looks like, what a monument does, and how both design and function connect to the custodian regimes at monumental, or potentially monumental, sites. In particular, I am concerned with architectures of divinity, and devotion, as both quotidian and monumental aspects of a city.
Virtual Reality als Trainingstool in der Klinischen und Gesundheitspsychologie
Authors: Schuster Laura , Friedrich Amos-Silvio , Kothgassner Oswald D. , Zemp Martina
Published: September 2022

Zusammenfassung. Hintergrund: Virtual Reality (VR) wird zunehmend als Hilfsmittel für psychologische Interventionen eingesetzt. Auch für sozial-emotionale Fähigkeiten kann VR realitätsnahe Übungsszenarien kreieren. Fragestellung: Dieses systematische Review gibt einen Überblick über den aktuellen Forschungsstand zu VR-Trainings sozial-emotionaler Fähigkeiten. Methode: Die systematische Literaturrecherche erfolgte in PSYNDEX, PsycINFO, Scopus, PubMed und Web of Science und orientierte sich an den PRISMA-Richtlinien. Eingeschlossen wurden deutsch- und englischsprachige empirische Studien zu VR-basierten Trainings sozial-emotionaler Fähigkeiten für gesunde oder psychisch beeinträchtigte Personen aller Altersstufen. Ergebnisse: Elf Studien wurden eingeschlossen. Die Mehrheit untersuchte klinische Stichproben. Die methodische Qualität wurde bei zehn Studien positiv beurteilt. Schlussfolgerungen: Insgesamt spricht das Review für die Nützlichkeit VR-basierter Trainings sozial-emotionaler Fähigkeiten, aber der aktuelle Forschungsstand erlaubt noch keine eindeutigen Schlussfolgerungen bezüglich ihrer Wirksamkeit.
Thin Current Sheet Formation and Reconnection at X ∼ −10 RE During the Main Phase of a Magnetic Storm
Authors: Runov A. , Angelopoulos V. , Weygand J. M. , Artemyev A. V. , Beyene F. , Sergeev V. , Kubyshkina M. , Henderson M. G.
Published: September 2022

The main question addressed in this study is whether particles with relativistic energy can be injected directly into the inner magnetosphere by very near‐Earth reconnection during magnetic storms. We study a sequence of events observed in the solar wind, in the magnetotail, at geosynchronous orbit (GEO), in the inner magnetosphere, and in the ionosphere during the main phase of a geomagnetic storm on 16 June 2012–17 June 2012. The storm was caused by a magnetic cloud with a high dynamic pressure and a strong southward IMF lasting about 10 hr. These conditions caused an extreme compression of the magnetosphere (SymH reached ∼150 nT) and an enhancement of the lobe magnetic field strength to ∼90 nT at R ∼ 10 Earth radii (RE). We focus on an hour‐long interval between 1050 and 1150 UT on 17 June 2012 when the Time History of Events and Macroscale Interactions during Substorms (THEMIS) satellites were at apogee at geocentric distances R ≈ 12 RE near midnight. At that time a thin current sheet formed between cis‐GEO distances and THEMIS. This thin current sheet reconnected between GEO and THEMIS. A strong lobe magnetic field enabled ion and electron energization to energies E ≈ 600 keV. Fluxes of high energy (up to relativistic) particles at GEO increased within ≈20 s after reconnection onset detected by THEMIS. Fluxes of relativistic electrons at L ∼ 4 in the morning sector increased within about 600 s after reconnection onset. We interpret these observations as signatures of direct injection of reconnected particles into the inner magnetosphere.
Variability in Sea Surface pCO2 and Controlling Factors in the Bay of Bengal Based on buoy Observations at 15°N, 90°E
Authors: Ye Haijun , Tang Shilin , Morozov Evgeny
Published: September 2022

Diurnal variability of the CO2 partial pressure (pCO2) at the sea surface (pCO2sea) and its impact on air‐sea CO2 flux estimations are currently poorly understood. In this work, diurnal variations in pCO2sea were examined in the Bay of Bengal (BoB) based on 3‐hourly observations collected at the BoB Ocean Acidification moored buoy between November 2013 and November 2018 by a moored autonomous pCO2 system. Significant mean diurnal pCO2sea cycles and a mean diurnal amplitude of 11 ± 9 μatm were observed based on 1215 complete diurnal cycles. One‐dimensional mass budget model calculations suggest that temperature was responsible for these mean diurnal variations in pCO2sea and that these variations were intensified by biological activity. The effects of air‐sea gas fluxes and mixing on the mean diurnal pCO2sea variability were very low. A weak annual net source of 12.1 mmol m−2 year−1 was estimated at this site. The sampling frequency greatly impacted the annual air‐sea CO2 flux estimations. Compared to the 3‐hr sampling frequency, random daily sampling resulted in a bias of ±7.7 mmol m−2 year−1 or 64%, and regular daily sampling resulted in a maximum bias of 400%. Factorial experiments showed that wind speed had the largest impact on the air‐sea CO2 flux estimations, followed by pCO2sea and atmospheric pCO2 (pCO2air). These findings indicate the importance of obtaining continuous pCO2 measurements to accurately estimate air‐sea CO2 flux; additionally, pCO2 and wind speed measurements should be obtained at frequencies higher than 6 hr.
Evaluation of Soil Moisture in CMIP6 Multimodel Simulations Over Conterminous China
Authors: Wang Aihui , Kong Xianghui , Chen Yue , Ma Xin
Published: September 2022

The Sixth Phase of the Coupled Model Intercomparison Project (CMIP6) provides the long‐term soil moisture (SM) products and this study conducts a comprehensive assessment of SM products of multiple CMIP6 model simulations over conterminous China. Both near‐surface (0–10 cm) SM simulations from 40 models and root‐zone (0–100 cm) SM from 25 models are compared with a set of in situ and a satellite‐based data set in the growing season for 1992–2013. The long‐term trend and interannual variability of near‐surface SM for 1961–2014 are further evaluated with an offline land surface modeling data set. Simulations from most models broadly capture the spatial characteristics of observation, and the multimodel mean (MME) well reproduces seasonal variations over the majority of regions, regardless of the large spread across models. SM from CMIP6 models from the same institution likely manifests similar performances, which indicates that the land‐surface scheme plays a dominant role in the CMIP6 SM reproduction. The majority of CMIP6 models well simulate the overall drying trend in China as a whole and the signs of a SM trend are highly consistent across different models, but the areas with significant wetting/drying trends vary with models. The spatial patterns of SM interannual variability are model‐dependent. MME is overall superior to the simulation of individual model and may have potential applications in future research. The heterogeneity of SM performances across CMIP6 models reveals the complexity and uncertainty in modeling land surface variables, suggesting the need for improving representations of land surface processes in the coupled models.
Heritability of REM sleep neurophysiology in adolescence
Authors: Markovic Andjela , Kaess Michael , Tarokh Leila
Published: September 2022

Alterations of rapid eye movement (REM) sleep have long been observed in patients with psychiatric disorders and proposed as an endophenotype—a link between behavior and genes. Recent experimental work has shown that REM sleep plays an important role in the emotional processing of memories, emotion regulation, and is altered in the presence of stress, suggesting a mechanism by which REM sleep may impact psychiatric illness. REM sleep shows a developmental progression and increases during adolescence—a period of rapid maturation of the emotional centers of the brain. This study uses a behavioral genetics approach to understand the relative contribution of genes, shared environmental and unique environmental factors to REM sleep neurophysiology in adolescents. Eighteen monozygotic (MZ; n = 36; 18 females) and 12 dizygotic (DZ; n = 24; 12 females) same-sex twin pairs (mean age = 12.46; SD = 1.36) underwent whole-night high-density sleep EEG recordings. We find a significant genetic contribution to REM sleep EEG power across frequency bands, explaining, on average, between 75 to 88% of the variance in power, dependent on the frequency band. In the lower frequency bands between delta and sigma, however, we find an additional impact of shared environmental factors over prescribed regions. We hypothesize that these regions may reflect the contribution of familial and environmental stress shared amongst the twins. The observed strong genetic contribution to REM sleep EEG power in early adolescence establish REM sleep neurophysiology as a potentially strong endophenotype, even in adolescence—a period marked by significant brain maturation.
From concepts to treatment: a dialog between a preclinical researcher and a clinician in addiction medicine
Authors: Vandaele Youna , Daeppen Jean-Bernard
Published: September 2022

The debate surrounding the brain disease model and the associated questioning of the relevance of animal models is polarizing the field of addiction, and tends to widen the gap between preclinical research and addiction medicine. Here, we aimed at bridging this gap by establishing a dialog between a preclinical researcher and a clinician in addiction medicine. Our objective was to evaluate animal models and the neuroscientific conceptualization of addiction in light of alcohol or drug dependence and treatment in patients struggling with an addiction. We sought to determine how preclinical research influenced addiction medicine over past decades, and reciprocally, what can preclinical researchers learn from addiction medicine that could lead to more effective approaches. In this dialog, we talk about the co-evolution of addiction concepts and treatments from neuroscientific and medical perspectives. This dialog illustrates the reciprocal influences and mutual enrichment between the two disciplines and reveals that, although preclinical research might not produce new pharmacotherapies, it does shape the theoretical conceptualization of addiction and could thereby contribute to the implementation of therapeutic approaches.
Intrinsic bias estimation for improved analysis of bulk and single-cell chromatin accessibility profiles using SELMA
Authors: Hu Shengen Shawn , Liu Lin , Li Qi , Ma Wenjing , Guertin Michael J. , Meyer Clifford A. , Deng Ke , Zhang Tingting , Zang Chongzhi
Published: September 2022

Genome-wide profiling of chromatin accessibility by DNase-seq or ATAC-seq has been widely used to identify regulatory DNA elements and transcription factor binding sites. However, enzymatic DNA cleavage exhibits intrinsic sequence biases that confound chromatin accessibility profiling data analysis. Existing computational tools are limited in their ability to account for such intrinsic biases and not designed for analyzing single-cell data. Here, we present Simplex Encoded Linear Model for Accessible Chromatin (SELMA), a computational method for systematic estimation of intrinsic cleavage biases from genomic chromatin accessibility profiling data. We demonstrate that SELMA yields accurate and robust bias estimation from both bulk and single-cell DNase-seq and ATAC-seq data. SELMA can utilize internal mitochondrial DNA data to improve bias estimation. We show that transcription factor binding inference from DNase footprints can be improved by incorporating estimated biases using SELMA. Furthermore, we show strong effects of intrinsic biases in single-cell ATAC-seq data, and develop the first single-cell ATAC-seq intrinsic bias correction model to improve cell clustering. SELMA can enhance the performance of existing bioinformatics tools and improve the analysis of both bulk and single-cell chromatin accessibility sequencing data.
Observation of spin-glass-like characteristics in ferrimagnetic TbCo through energy-level-selective approach
Authors: Park Ji-Ho , Kim Won Tae , Won Woonjae , Kang Jun-Ho , Lee Soogil , Park Byong-Guk , Ham Byoung S. , Jo Younghun , Rotermund Fabian , Kim Kab-Jin
Published: September 2022

Rare earth (RE)–transition metal (TM) ferrimagnetic alloys are gaining increasing attention because of their potential use in the field of antiferromagnetic spintronics. The moment from RE sub-lattice primarily originates from the 4f-electrons located far below the Fermi level (EF), and the moment from TM sub-lattice arises from the 3d-electrons across the EF. Therefore, the individual magnetic moment configurations at different energy levels must be explored to clarify the microscopic mechanism of antiferromagnetic spin dynamics. Considering these issues, here we investigate the energy-level-selective magnetic moment configuration in ferrimagnetic TbCo alloy. We reveal that magnetic moments at deeper energy levels are more easily altered by the external magnetic field than those near the EF. More importantly, we find that the magnetic moments at deeper energy levels exhibit a spin-glass-like characteristics such as slow dynamics and magnetic moment freezing whereas those at EF do not. These unique energy-level-dependent characteristics of RE-TM ferrimagnet may provide a better understanding of ferrimagnet, which could be useful in spintronic applications as well as in spin-glass studies.
Atomistic deformation mechanism of silicon under laser-driven shock compression
Authors: Pandolfi Silvia , Brown S. Brennan , Stubley P. G. , Higginbotham Andrew , Bolme C. A. , Lee H. J. , Nagler B. , Galtier E. , Sandberg R. L. , Yang W. , Mao W. L. , Wark J. S. , Gleason A. E.
Published: September 2022

Silicon (Si) is one of the most abundant elements on Earth, and it is the most widely used semiconductor. Despite extensive study, some properties of Si, such as its behaviour under dynamic compression, remain elusive. A detailed understanding of Si deformation is crucial for various fields, ranging from planetary science to materials design. Simulations suggest that in Si the shear stress generated during shock compression is released via a high-pressure phase transition, challenging the classical picture of relaxation via defect-mediated plasticity. However, direct evidence supporting either deformation mechanism remains elusive. Here, we use sub-picosecond, highly-monochromatic x-ray diffraction to study (100)-oriented single-crystal Si under laser-driven shock compression. We provide the first unambiguous, time-resolved picture of Si deformation at ultra-high strain rates, demonstrating the predicted shear release via phase transition. Our results resolve the longstanding controversy on silicon deformation and provide direct proof of strain rate-dependent deformation mechanisms in a non-metallic system.
Metabolic pathway assembly using docking domains from type I cis-AT polyketide synthases
Authors: Sun Xixi , Yuan Yujie , Chen Qitong , Nie Shiqi , Guo Jiaxuan , Ou Zutian , Huang Min , Deng Zixin , Liu Tiangang , Ma Tian
Published: September 2022

Engineered metabolic pathways in microbial cell factories often have no natural organization and have challenging flux imbalances, leading to low biocatalytic efficiency. Modular polyketide synthases (PKSs) are multienzyme complexes that synthesize polyketide products via an assembly line thiotemplate mechanism. Here, we develop a strategy named mimic PKS enzyme assembly line (mPKSeal) that assembles key cascade enzymes to enhance biocatalytic efficiency and increase target production by recruiting cascade enzymes tagged with docking domains from type I cis-AT PKS. We apply this strategy to the astaxanthin biosynthetic pathway in engineered Escherichia coli for multienzyme assembly to increase astaxanthin production by 2.4-fold. The docking pairs, from the same PKSs or those from different cis-AT PKSs evidently belonging to distinct classes, are effective enzyme assembly tools for increasing astaxanthin production. This study addresses the challenge of cascade catalytic efficiency and highlights the potential for engineering enzyme assembly.
Physics-embedded graph network for accelerating phase-field simulation of microstructure evolution in additive manufacturing
Authors: Xue Tianju , Gan Zhengtao , Liao Shuheng , Cao Jian
Published: September 2022

The phase-field (PF) method is a physics-based computational approach for simulating interfacial morphology. It has been used to model powder melting, rapid solidification, and grain structure evolution in metal additive manufacturing (AM). However, traditional direct numerical simulation (DNS) of the PF method is computationally expensive due to sufficiently small mesh size. Here, a physics-embedded graph network (PEGN) is proposed to leverage an elegant graph representation of the grain structure and embed the classic PF theory into the graph network. By reformulating the classic PF problem as an unsupervised machine learning task on a graph network, PEGN efficiently solves temperature field, liquid/solid phase fraction, and grain orientation variables to minimize a physics-based loss/energy function. The approach is at least 50 times faster than DNS in both CPU and GPU implementation while still capturing key physical features. Hence, PEGN allows to simulate large-scale multi-layer and multi-track AM build effectively.
Tracking SARS-COV-2 variants using Nanopore sequencing in Ukraine in 2021
Authors: Yakovleva Anna , Kovalenko Ganna , Redlinger Matthew , Liulchuk Mariia G. , Bortz Eric , Zadorozhna Viktoria I. , Scherbinska Alla M. , Wertheim Joel O. , Goodfellow Ian , Meredith Luke , Vasylyeva Tetyana I.
Published: September 2022

The use of real-time genomic epidemiology has enabled the tracking of the global spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), informing evidence-based public health decision making. Ukraine has experienced four waves of the Coronavirus Disease 2019 (COVID-19) between spring 2020 and spring 2022. However, insufficient capacity for local genetic sequencing limited the potential application of SARS-CoV-2 genomic surveillance for public health response in the country. Herein, we report local sequencing of 103 SARS-CoV-2 genomes from patient samples collected in Kyiv in July-December 2021 using Oxford Nanopore technology. Together with other published Ukrainian SARS-CoV-2 genomes, our data suggest that the third wave of the epidemic in Ukraine (June-December 2021) was dominated by the Delta Variant of Concern (VOC). Our phylogeographic analysis revealed that in summer 2021 Delta VOC was introduced into Ukraine from multiple locations worldwide, with most introductions coming from Central and Eastern European countries. The wide geographic range of Delta introductions coincides with increased volume of travel to Ukraine particularly from locations outside of Europe in summer 2021. This study highlights the need to urgently integrate affordable and easily scaled pathogen sequencing technologies in locations with less developed genomic infrastructure, in order to support local public health decision making.
Depression and bipolar disorder subtypes differ in their genetic correlations with biological rhythms
Authors: Sirignano Lea , Streit Fabian , Frank Josef , Zillich Lea , Witt Stephanie H. , Rietschel Marcella , Foo Jerome C.
Published: September 2022

Major Depression and Bipolar Disorder Type I (BIP-I) and Type II (BIP-II), are characterized by depressed, manic, and hypomanic episodes in which specific changes of physical activity, circadian rhythm, and sleep are observed. It is known that genetic factors contribute to variation in mood disorders and biological rhythms, but unclear to what extent there is an overlap between their underlying genetics. In the present study, data from genome-wide association studies were used to examine the genetic relationship between mood disorders and biological rhythms. We tested the genetic correlation of depression, BIP-I, and BIP-II with physical activity (overall physical activity, moderate activity, sedentary behaviour), circadian rhythm (relative amplitude), and sleep features (sleep duration, daytime sleepiness). Genetic correlations of depression, BIP-I, and BIP-II with biological rhythms were compared to discover commonalities and differences. A gene-based analysis tested for associations of single genes and common circadian genes with mood disorders. Depression was negatively correlated with overall physical activity and positively with sedentary behaviour, while BIP-I showed associations in the opposite direction. Depression and BIP-II had negative correlations with relative amplitude. All mood disorders were positively correlated with daytime sleepiness. Overall, we observed both genetic commonalities and differences across mood disorders in their relationships with biological rhythms: depression and BIP-I differed the most, while BIP-II was in an intermediate position. Gene-based analysis suggested potential targets for further investigation. The present results suggest shared genetic underpinnings for the clinically observed associations between mood disorders and biological rhythms. Research considering possible joint mechanisms may offer avenues for improving disease detection and treatment.
China’s LNG import risk assessment based on the perspective of global governance
Authors: Zeng Weijing , Zhang Xianfeng , Li Na , Wang Xiaobo , Wang Xiaolin
Published: September 2022

The uncertainty of LNG import risks will have a significant impact on China's energy security. This paper establishes a multi-agent game model based on the current LNG transportation network and global LNG supply and demand pattern, evaluates the LNG import risks faced by China under the global governance model, and simulates and predicts the optimal LNG import strategy of China in 2030. The research results show that between 2007 and 2020, China’s LNG import risks increased rapidly compared with political risks and national risks. From the perspective of risk identification, the comprehensive risk of China's imports from Southeast Asia and Australia is lower. However, due to the increasing demand gap for LNG, the Middle East, and Africa are still necessary supply sources. It is estimated that by 2030, the future LNG market will be oversupplied, and the United States is expected to become the world's top LNG supplier. China will reduce its dependence on Africa and the Middle East, and import a large amount of natural gas from the United States, Australia, Qatar, and Russia to reduce supply risks. From the perspective of import market competition, the new analysis model proposed in this article provides an effective tool for exploring the optimal strategy for LNG import.
Novel method for detecting complement C3 deposition on Staphylococcus aureus
Authors: Wonfor Toska , Li Shuxian , Dunphy Rhys W. , Macpherson Alex , van den Elsen Jean , Laabei Maisem
Published: September 2022

The primary host response to Staphylococcus aureus infection occurs via complement. Complement is an elegant evolutionarily conserved system, playing essential roles in early defences by working in concert with immune cells to survey, label and destroy microbial intruders and coordinate inflammation. Currently the exact mechanisms employed by S. aureus to manipulate and evade complement is not clear and is hindered by the lack of accurate molecular tools that can report on complement deposition on the bacterial surface. Current gold-standard detection methods employ labelled complement-specific antibodies and flow cytometry to determine complement deposited on bacteria. These methods are restricted by virtue of the expression of the S. aureus immunoglobulin binding proteins, Protein A and Sbi. In this study we describe the use of a novel antibody-independent C3 probe derived from the staphylococcal Sbi protein, specifically Sbi-IV domain. Here we show that biotin-labelled Sbi-IV interacts specifically with deposited C3 products on the staphylococcal surface and thus can be used to measure complement fixation on wild-type cells expressing a full repertoire of immune evasion proteins. Lastly, our data indicates that genetically diverse S. aureus strains restrict complement to different degrees suggesting that complement evasion is a variable virulence trait among S. aureus isolates.
Updated reference ranges for aminotransferase levels of Korean children and young adolescents based on the risk factors for metabolic syndrome
Authors: Seo Young-Jun , Shim Young Suk , Lee Hae Sang , Hwang Jin Soon
Published: September 2022

We investigated the reference values of liver enzymes based on cardiometabolic risks among children and adolescents using the Korea National Health and Nutrition Examination Survey. A total of 8091 subjects aged 10–18 years were included from the data from 2007–2017. Overall, aspartate aminotransferase (AST), alanine aminotransferase (ALT), and the AST/ALT ratio varied with sex and age. AST levels tended to decrease with age, but ALT levels had a U-shaped curve, which resulted in a gradual increase in the AST/ALT ratio after age 13. The prevalence of MetS was strongly associated with elevated AST or ALT and a decreased AST/ALT ratio. The prevalence ratios of the development of MetS were also elevated in groups with high levels of AST and ALT and a low AST/ALT ratio. Particularly in the combined ALT and AST/ALT analyses, borderline-high levels also showed a high prevalence ratio of MetS. Liver enzymes were also involved in the increase in the adjusted mean values for each risk factor for MetS. Here, we provided updated reference values for liver enzymes based on the analysis between population-based data and cardiometabolic risk factors; AST, ALT and the AST/ALT ratio might be useful in the early diagnosis and treatment of MetS.
Deep RNA sequencing of intensive care unit patients with COVID-19
Authors: Fredericks Alger M. , Jentzsch Maximilian S. , Cioffi William G. , Cohen Maya , Fairbrother William G. , Gandhi Shivam J. , Harrington Elizabeth O. , Nau Gerard J. , Reichner Jonathan S. , Ventetuolo Corey E. , Levy Mitchell M. , Ayala Alfred , Monaghan Sean F.
Published: September 2022

COVID-19 has impacted millions of patients across the world. Molecular testing occurring now identifies the presence of the virus at the sampling site: nasopharynx, nares, or oral cavity. RNA sequencing has the potential to establish both the presence of the virus and define the host’s response in COVID-19. Single center, prospective study of patients with COVID-19 admitted to the intensive care unit where deep RNA sequencing (> 100 million reads) of peripheral blood with computational biology analysis was done. All patients had positive SARS-CoV-2 PCR. Clinical data was prospectively collected. We enrolled fifteen patients at a single hospital. Patients were critically ill with a mortality of 47% and 67% were on a ventilator. All the patients had the SARS-CoV-2 RNA identified in the blood in addition to RNA from other viruses, bacteria, and archaea. The expression of many immune modulating genes, including PD-L1 and PD-L2, were significantly different in patients who died from COVID-19. Some proteins were influenced by alternative transcription and splicing events, as seen in HLA-C, HLA-E, NRP1 and NRP2. Entropy calculated from alternative RNA splicing and transcription start/end predicted mortality in these patients. Current upper respiratory tract testing for COVID-19 only determines if the virus is present. Deep RNA sequencing with appropriate computational biology may provide important prognostic information and point to therapeutic foci to be precisely targeted in future studies.