bluuebunny/crossref_metadata_2025 huggingface dataset:
Design and validation of a novel online platform to support the usability evaluation of wearable robotic devices
Authors: Meyer Jan T. , Tanczak Natalie , Kanzler Christoph M. , Pelletier Colin , Gassert Roger , Lambercy Olivier
Published: January 2023

Wearable robotic devices (WRD) are still struggling to fulfill their vast potential. Inadequate daily life usability is one of the main hindrances to increased technology acceptance. Improving usability evaluation practices during the development of WRD could help address these limitations. In this work, we present the design and validation of a novel online platform aiming to fill this gap, the Interactive Usability Toolbox (IUT). This platform consists of a public website that offers an interactive, context-specific search within a database of 154 user research methods and educational information about usability. In a dedicated study, the effect of this platform to support usability evaluation was investigated. Twelve WRD experts were asked to complete the task of defining usability evaluation protocols for two specific use cases. The platform was provided to support one of the use cases. The quality and composition of the proposed protocols were assessed by (i) two blinded reviewers, (ii) the participants themselves, and (iii) the study coordinators. We showed that using the IUT significantly affected the proposed evaluation focus, shifting protocols from mainly effectiveness-oriented to more user-focused studies. The protocol quality, as rated by the external reviewers, remained equivalent to those designed with conventional strategies. A mixed-method usability evaluation of the platform yielded an overall positive image, with detailed suggestions for further improvements. The IUT is expected to positively affect the evaluation and development of WRD through its educational value, the context-specific recommendations supporting ongoing benchmarking endeavors, and highlighting the value of qualitative user research.
A Revised Estimate of Early Pliocene Global Mean Sea Level Using Geodynamic Models of the Patagonian Slab Window
Authors: Hollyday Andrew , Austermann Jacqueline , Lloyd Andrew , Hoggard Mark , Richards Fred , Rovere Alessio
Published: January 2023

Paleoshorelines serve as measures of ancient sea level and ice volume but are affected by solid Earth deformation including processes such as glacial isostatic adjustment (GIA) and mantle dynamic topography (DT). The early Pliocene Epoch is an important target for sea‐level reconstructions as it contains information about the stability of ice sheets during a climate warmer than today. Along the southeastern passive margin of Argentina, three paleoshorelines date to early Pliocene times (4.8–5.5 Ma), and their variable present‐day elevations (36–180 m) reflect a unique topographic deformation signature. We use a mantle convection model to back‐advect present‐day buoyancy variations, including those that correspond to the Patagonian slab window. Varying the viscosity and initial tomography‐derived mantle buoyancy structures allows us to compute a suite of predictions of DT change that, when compared to GIA‐corrected shoreline elevations, makes it possible to identify both the most likely convection parameters and the most likely DT change. Our simulations illuminate an interplay of upwelling asthenosphere through the Patagonian slab window and coincident downwelling of the subducted Nazca slab in the mantle transition zone. This flow leads to differential upwarping of the southern Patagonian foreland since early Pliocene times, in line with the observations. Using our most likely DT change leads to an estimate of global mean sea level of 17.5 ± 6.4 m (1σ) in the early Pliocene Epoch. This confirms that sea level was significantly higher than present and can be used to calibrate ice sheet models.
Seasonal Diversity of El Niño‐Induced Marine Heatwave Increases in the Bay of Bengal
Authors: Lin Xinyu , Qiu Yun , Wang Jianjun , Teng Hui , Ni Xutao , Liang Kunming
Published: January 2023

This study explored the characteristics of marine heatwaves (MHWs) and the related dynamics in Bay of Bengal (BOB) associated with El Niño events during 1982–2020. This showed that El Niño can induce more MHW days, which displays remarkable seasonality. The strong influences of El Niño were found in the southern BOB at its peak phase in winter and the following spring, characterized by an increase in MHW days by 106% in winter and 83% in spring. In the proceeding summer, its influences weakened and shifted to the central bay. The more MHW days during winter and spring are primarily caused by the enhanced solar radiation associated with El Niño and partly contributed by the thick barrier layer in winter. In contrast, besides atmospheric heating, the deepening thermocline in the central bay induced by equatorial and local winds also plays an important role in the increase in MHWs during summer.
Wintertime Supraglacial Lake Drainage Cascade Triggers Large‐Scale Ice Flow Response in Greenland
Authors: Maier Nathan , Andersen Jonas Kvist , Mouginot Jérémie , Gimbert Florent , Gagliardini Olivier
Published: January 2023

Surface melt forces summertime ice‐flow accelerations on glaciers and ice sheets. Here, we show that large meltwater‐forced accelerations also occur during wintertime in Greenland. We document supraglacial lakes (SGLs) draining in cascades at unusually high elevation, causing an expansive flow acceleration over a ∼5,200 km2 region during winter. The three‐component interferometric surface velocity field and decomposition modeling reveal the underlying flood propagation with unprecedented detail as it traveled over 160 km from the drainage site to the margin, providing novel constraints on subglacial water pathways, drainage morphology, and links with basal sliding. The triggering SGLs continuously grew over 40 years and suddenly released decades of stored meltwater, demonstrating surface melting can impact dynamics well beyond melt production. We show these events are likely common and thus their cumulative impact on dynamics should be further evaluated.
Ionospheric Pre‐Sunrise Uplift: Comparison of Sanya Incoherent Scatter Radar Observations and Numerical Simulations
Authors: Yue Xinan , Cai Yihui , Wang Junyi , Lei Jiuhou , Wang Zhongqiu , Wang Yonghui , Li Mingyuan , Zhang Ning , Ding Feng , Ning Baiqi
Published: January 2023

Using the high spatial‐temporal resolution electron density profiles observed by the newly built Sanya Incoherent Scatter Radar at Sanya (18.3°N, 109.6°E) in its first 1‐month‐long continuous run with Barker code, we identified a substantial ionospheric pre‐sunrise uplift at low latitudes associated with the upward movement of ions. The uplift mainly occurs during local solar time 01:00–06:00 and is ∼52–240 km with significant night‐to‐night variability. With increasing geomagnetic and/or interplanetary activity, the uplift can have a larger amplitude. Further TIEGCM simulations show that the pre‐sunrise ionospheric uplift is jointly determined by the net effect of ambipolar diffusion, neutral wind, and E × B drift. The neutral wind during 00:00–05:00 usually lifts the ionosphere through equatorward wind. After 02:00, the weakening and/or even the reversal of downward E × B drift, which is not sufficient to offset the net uplift effect of wind and diffusion combination, triggers uplifting.
Stochastic Watershed Model Ensembles for Long‐Range Planning: Verification and Validation
Authors: Shabestanipour Ghazal , Brodeur Zachary , Farmer William H. , Steinschneider Scott , Vogel Richard M. , Lamontagne Jonathan R.
Published: January 2023

Deterministic watershed models (DWMs) are used in nearly all hydrologic planning, design, and management activities, yet they cannot generate streamflow ensembles needed for hydrologic risk management (HRM). The stochastic component of DWMs is often ignored in practice, leading to a systematic bias in extreme events. Since traditional stochastic streamflow models used in HRM struggle to account for anthropogenic change, there is a need to convert DWMs into stochastic watershed models (SWMs) to generate ensembles for use in HRM. A DWM can be converted to an SWM using a post‐processing (pp) approach to add error to the DWM predictions. Many pp methods advanced in the area of flood forecasting are useful in HRM and for correcting extreme event biases. Selecting a suitable error model for pp is challenging due to nonnormality, skewness, heteroscedasticity, and autocorrelation. We develop a parsimonious pp method based on an autoregressive (AR) model of the logarithm of the ratio of the observations and simulations, which leads to AR model residuals that are approximately symmetric and independent. We document the value of pp for improving flood and low flow frequency analysis and we reintroduce the concepts of verification and validation of stochastic streamflow ensembles to ensure that the SWM can reproduce both statistics it was and was not designed to reproduce, respectively. These concepts are illustrated on a Massachusetts basin using the USGS Precipitation Runoff Modeling System, with an additional analysis indicating the approach may be applicable to 1,225 other sites across the United States.
Research progress of large size SiC single crystal materials and devices
Authors: Chen Xiufang , Yang Xianglong , Xie Xuejian , Peng Yan , Xiao Longfei , Shao Chen , Li Huadong , Hu Xiaobo , Xu Xiangang
Published: January 2023

SiC semiconductor is the focus of recent international research. It is also an important raw material for China to achieve carbon emission peak and carbon neutrality. After nearly 20 years of research and development, we focus on the three types SiC crystals, n-type, p-type and semi-insulating, indicating the development of Shandong University for crystal growth. And defects control, electrical property, atomic polishing, and corresponding device authentication all obtain great progress. Total dislocation density of 6-inch n-type substrates decreases to 2307 cm−2, where BPD (Basal Plane Dislocation) lowers to 333 cm−2 and TSD (Threading Screw Dislocation) 19 cm−2. The full width at half maximum (FWHM) (0004) rocking curves is only 14.4 arcsec. The resistivity reaches more than 1E + 12 Ω·cm for semi-insulating SiC and lower than 20 mΩ·cm for n-type SiC. The impurity concentrations in 6-inch high-purity semi-insulating (HPSI) SiC crystals reach extreme low levels. The devices made of various substrate materials have good performance.
Polygenic scores for psychiatric disorders in a diverse postmortem brain tissue cohort
Authors: Duncan Laramie , Shen Hanyang , Schulmann Anton , Li Tayden , Kolachana Bhaskar , Mandal Ajeet , Feng Ningping , Auluck Pavan , Marenco Stefano
Published: January 2023

A new era of human postmortem tissue research has emerged thanks to the development of ‘omics technologies that measure genes, proteins, and spatial parameters in unprecedented detail. Also newly possible is the ability to construct polygenic scores, individual-level metrics of genetic risk (also known as polygenic risk scores/PRS), based on genome-wide association studies, GWAS. Here, we report on clinical, educational, and brain gene expression correlates of polygenic scores in ancestrally diverse samples from the Human Brain Collection Core (HBCC). Genotypes from 1418 donors were subjected to quality control filters, imputed, and used to construct polygenic scores. Polygenic scores for schizophrenia predicted schizophrenia status in donors of European ancestry (p = 4.7 × 10−8, 17.2%) and in donors with African ancestry (p = 1.6 × 10−5, 10.4% of phenotypic variance explained). This pattern of higher variance explained among European ancestry samples was also observed for other psychiatric disorders (depression, bipolar disorder, substance use disorders, anxiety disorders) and for height, body mass index, and years of education. For a subset of 223 samples, gene expression from dorsolateral prefrontal cortex (DLPFC) was available through the CommonMind Consortium. In this subgroup, schizophrenia polygenic scores also predicted an aggregate gene expression score for schizophrenia (European ancestry: p = 0.0032, African ancestry: p = 0.15). Overall, polygenic scores performed as expected in ancestrally diverse samples, given historical biases toward use of European ancestry samples and variable predictive power of polygenic scores across phenotypes. The transcriptomic results reported here suggest that inherited schizophrenia genetic risk influences gene expression, even in adulthood. For future research, these and additional polygenic scores are being made available for analyses, and for selecting samples, using postmortem tissue from the Human Brain Collection Core.
HLTF promotes hepatocellular carcinoma progression by enhancing SRSF1 stability and activating ERK/MAPK pathway
Authors: Xu Yanan , Ke Shanjia , Lu Shounan , Wang Chaoqun , Li Zihao , Feng Zhigang , Yu Hongjun , Bai Miaoyu , Qian Baolin , Yin Bing , Li Xinglong , Hua Yongliang , Jiang Hongchi , Ma Yong
Published: January 2023

Helicase-like transcription factor (HLTF) has been found to be involved in the progression of several tumors, but the role of HLTF in hepatocellular carcinoma (HCC) progression has not been studied. Here, our study explored the underlying mechanism of HLTF in HCC progression for the first time. Database analysis and clinical sample examination indicated that HLTF was upregulated in HCC tissues and was related to poor clinicopathological features in patients. Upregulation of HLTF accelerated the growth and metastasis of HCC cells both in vitro and in vivo. Bioinformatics analysis and subsequent experiments revealed that ERK/MAPK signaling pathway activation was vital to HLTF-mediated proliferation and metastasis in HCC cells. Moreover, HLTF was demonstrated to interact with SRSF1 and contribute to its protein stability to activate the ERK/MAPK signaling pathway and enhance HCC growth and metastasis. In addition, miR-511-5p was expressed at a low level in HCC tissues, was negatively correlated HLTF, and regulated HLTF expression. Our study shows that HLTF plays an oncogenic role in HCC progression and provides a novel biomarker and therapeutic target for the diagnosis and treatment of HCC.
Cholinergic neurons in the basal forebrain are involved in behavioral abnormalities associated with Cul3 deficiency: Role of prefrontal cortex projections in cognitive deficits
Authors: Rapanelli Maximiliano , Wang Wei , Hurley Edward , Feltri Maria Laura , Pittenger Christopher , Frick Luciana Romina , Yan Zhen
Published: January 2023

Loss-of-function mutations of the gene Cul3 have been identified as a risk factor for autism-spectrum disorder (ASD), but the pathogenic mechanisms are not well understood. Conditional Cul3 ablation in cholinergic neurons of mice (ChatCRECul3F/+) recapitulated ASD-like social and sensory gating phenotypes and caused significant cognitive impairments, with diminished activity of cholinergic neurons in the basal forebrain (BF). Chemogenetic inhibition of BF cholinergic neurons in healthy mice induced similar social and cognitive deficits. Conversely, chemogenetic stimulation of BF cholinergic neurons in ChatCRECul3F/+ mice reversed abnormalities in sensory gating and cognition. Cortical hypofunction was also found after ChAT-specific Cul3 ablation and stimulation of cholinergic projections from the BF to the prefrontal cortex (PFC) mitigated cognitive deficits. Overall, we demonstrate that cholinergic dysfunction due to Cul3 deficiency is involved in ASD-like behavioral abnormalities, and that BF cholinergic neurons are particularly critical for cognitive component through their projections to the PFC.
The impact of COVID-19 on dental care in New York State and Georgia
Authors: Puskas Caroline , Morse Stephen S.
Published: January 2023

Introduction During the COVID-19 pandemic, there was an unprecedented and forced closure of dental offices worldwide. As American state recommendations differed considerably during this period, this research strives to better define the effects of this pause on dental care.

Materials and methods A 16-question Qualtrics survey was sent to the membership of the New York State Dental Association (NYSDA) and Georgia Dental Association (GDA). Licenced, actively practising dental members of the NYSDA and GDA (n = 680) answered questions about their practice demographics, appointment cancellations, reopening times and the volume of individual dental procedures performed from 1 March through to 1 August 2020, compared to the same five-month period in 2019.

Results Demographic characteristics of respondent NYSDA and GDA members were statistically similar. Nonetheless, NYSDA members reported significantly larger decreases in provision of all types of dental procedures, except for antibiotic prescription, including prophylaxis, elective care, emergency dental care and speciality procedures.

Discussion and conclusions All dental procedures declined significantly during the COVID-19 pandemic, with greater decrease in New York than in Georgia. This study raises concerns about the negative impact of the pandemic on oral public health and mandates both further research and clinical strategies to mitigate against this future risk.
Chromosome territory reorganization through artificial chromosome fusion is compatible with cell fate determination and mouse development
Authors: Wang Yuang , Qu Zhen , Fang Yi , Chen Yulong , Peng Jiayin , Song Jiawen , Li Jinsong , Shi Jiantao , Zhou Jin-Qiu , Zhao Yun
Published: January 2023

Chromosomes occupy discrete spaces in the interphase cell nucleus, called chromosome territory. The structural and functional relevance of chromosome territory remains elusive. We fused chromosome 15 and 17 in mouse haploid embryonic stem cells (haESCs), resulting in distinct changes of territories in the cognate chromosomes, but with little effect on gene expression, pluripotency and gamete functions of haESCs. The karyotype-engineered haESCs were successfully implemented in generating heterozygous (2n = 39) and homozygous (2n = 38) mouse models. Mice containing the fusion chromosome are fertile, and their representative tissues and organs display no phenotypic abnormalities, suggesting unscathed development. These results indicate that the mammalian chromosome architectures are highly resilient, and reorganization of chromosome territories can be readily tolerated during cell differentiation and mouse development.
Socioeconomic factors predict population changes of large carnivores better than climate change or habitat loss
Authors: Johnson Thomas F. , Isaac Nick J. B. , Paviolo Agustin , González-Suárez Manuela
Published: January 2023

Land-use and climate change have been linked to changes in wildlife populations, but the role of socioeconomic factors in driving declines, and promoting population recoveries, remains relatively unexplored. Here, we evaluate potential drivers of population changes observed in 50 species of some of the world’s most charismatic and functionally important fauna—large mammalian carnivores. Our results reveal that human socioeconomic development is more associated with carnivore population declines than habitat loss or climate change. Rapid increases in socioeconomic development are linked to sharp population declines, but, importantly, once development slows, carnivore populations have the potential to recover. The context- and threshold-dependent links between human development and wildlife population health are challenges to the achievement of the UN Sustainable development goals.
Long-term statins administration exacerbates diabetic nephropathy via ectopic fat deposition in diabetic mice
Authors: Huang Tong-sheng , Wu Teng , Wu Yan-di , Li Xing-hui , Tan Jing , Shen Cong-hui , Xiong Shi-jie , Feng Zi-qi , Gao Sai-fei , Li Hui , Cai Wei-bin
Published: January 2023

Statins play an important role in the treatment of diabetic nephropathy. Increasing attention has been given to the relationship between statins and insulin resistance, but many randomized controlled trials confirm that the therapeutic effects of statins on diabetic nephropathy are more beneficial than harmful. However, further confirmation of whether the beneficial effects of chronic statin administration on diabetic nephropathy outweigh the detrimental effects is urgently needed. Here, we find that long-term statin administration may increase insulin resistance, interfere with lipid metabolism, leads to inflammation and fibrosis, and ultimately fuel diabetic nephropathy progression in diabetic mice. Mechanistically, activation of insulin-regulated phosphatidylinositol 3-kinase/protein kinase B/mammalian target of rapamycin signaling pathway leads to increased fatty acid synthesis. Furthermore, statins administration increases lipid uptake and inhibits fatty acid oxidation, leading to lipid deposition. Here we show that long-term statins administration exacerbates diabetic nephropathy via ectopic fat deposition in diabetic mice.
Differential sensing with arrays of de novo designed peptide assemblies
Authors: Dawson William M. , Shelley Kathryn L. , Fletcher Jordan M. , Scott D. Arne , Lombardi Lucia , Rhys Guto G. , LaGambina Tania J. , Obst Ulrike , Burton Antony J. , Cross Jessica A. , Davies George , Martin Freddie J. O. , Wiseman Francis J. , Brady R. Leo , Tew David , Wood Christopher W. , Woolfson Derek N.
Published: January 2023

Differential sensing attempts to mimic the mammalian senses of smell and taste to identify analytes and complex mixtures. In place of hundreds of complex, membrane-bound G-protein coupled receptors, differential sensors employ arrays of small molecules. Here we show that arrays of computationally designed de novo peptides provide alternative synthetic receptors for differential sensing. We use self-assembling α-helical barrels (αHBs) with central channels that can be altered predictably to vary their sizes, shapes and chemistries. The channels accommodate environment-sensitive dyes that fluoresce upon binding. Challenging arrays of dye-loaded barrels with analytes causes differential fluorophore displacement. The resulting fluorimetric fingerprints are used to train machine-learning models that relate the patterns to the analytes. We show that this system discriminates between a range of biomolecules, drink, and diagnostically relevant biological samples. As αHBs are robust and chemically diverse, the system has potential to sense many analytes in various settings.
Rabphilin-3A undergoes phase separation to regulate GluN2A mobility and surface clustering
Authors: Yang Lei , Wei Mengping , Wang Yangzhen , Zhang Jingtao , Liu Sen , Liu Mengna , Wang Shanshan , Li Ke , Dong Zhaoqi , Zhang Chen
Published: January 2023

N-methyl-D-aspartate receptors (NMDARs) are essential for excitatory neurotransmission and synaptic plasticity. GluN2A and GluN2B, two predominant Glu2N subunits of NMDARs in the hippocampus and the cortex, display distinct clustered distribution patterns and mobility at synaptic and extrasynaptic sites. However, how GluN2A clusters are specifically organized and stabilized remains poorly understood. Here, we found that the previously reported GluN2A-specific binding partner Rabphilin-3A (Rph3A) has the ability to undergo phase separation, which relies on arginine residues in its N-terminal domain. Rph3A phase separation promotes GluN2A clustering by binding GluN2A’s C-terminal domain. A complex formed by Rph3A, GluN2A, and the scaffolding protein PSD95 promoted Rph3A phase separation. Disrupting Rph3A’s phase separation suppressed the synaptic and extrasynaptic surface clustering, synaptic localization, stability, and synaptic response of GluN2A in hippocampal neurons. Together, our results reveal the critical role of Rph3A phase separation in determining the organization and stability of GluN2A in the neuronal surface.
Structural insights into the elevator-type transport mechanism of a bacterial ZIP metal transporter
Authors: Zhang Yao , Jiang Yuhan , Gao Kaifu , Sui Dexin , Yu Peixuan , Su Min , Wei Guo-Wei , Hu Jian
Published: January 2023

The Zrt-/Irt-like protein (ZIP) family consists of ubiquitously expressed divalent metal transporters critically involved in maintaining systemic and cellular homeostasis of zinc, iron, and manganese. Here, we present a study on a prokaryotic ZIP from Bordetella bronchiseptica (BbZIP) by combining structural biology, evolutionary covariance, computational modeling, and a variety of biochemical assays to tackle the issue of the transport mechanism which has not been established for the ZIP family. The apo state structure in an inward-facing conformation revealed a disassembled transport site, altered inter-helical interactions, and importantly, a rigid body movement of a 4-transmembrane helix (TM) bundle relative to the other TMs. The computationally generated and biochemically validated outward-facing conformation model revealed a slide of the 4-TM bundle, which carries the transport site(s), by approximately 8 Å toward the extracellular side against the static TMs which mediate dimerization. These findings allow us to conclude that BbZIP is an elevator-type transporter.
Greenhouse warming and internal variability increase extreme and central Pacific El Niño frequency since 1980
Authors: Gan Ruyu , Liu Qi , Huang Gang , Hu Kaiming , Li Xichen
Published: January 2023

El Niño has been recorded to change its properties since the 1980s, characterized by more common extreme El Niño and Central Pacific (CP) El Niño events. However, it is still unclear whether such change is externally forced or part of the natural variability. Here, we find that the frequency of the extreme and CP El Niño events also increased during the period 1875–1905, when the anthropogenic CO2 concentration was relatively lower, but with a positive phase of the Atlantic Multidecadal Oscillation (AMO). Models and palaeoclimate proxies reveal that a positive AMO enhances the zonal sea surface temperature gradient in the CP, which strengthens zonal advective feedback, favoring extreme and CP El Niño development. Moreover, we estimate that internal variability contributed to ~65% of the increasingly extreme and CP El Niño events, while anthropogenic forcing has made our globe experience ~1 more extreme and ~2 more CP events over the past four decades.
A three-terminal magnetic thermal transistor
Authors: Castelli Lorenzo , Zhu Qing , Shimokusu Trevor J. , Wehmeyer Geoff
Published: January 2023

Three-terminal thermal analogies to electrical transistors have been proposed for use in thermal amplification, thermal switching, or thermal logic, but have not yet been demonstrated experimentally. Here, we design and fabricate a three-terminal magnetic thermal transistor in which the gate temperature controls the source-drain heat flow by toggling the source-drain thermal conductance from ON to OFF. The centimeter-scale thermal transistor uses gate-temperature dependent magnetic forces to actuate motion of a thermally conducting shuttle, providing thermal contact between source and drain in the ON state while breaking contact in the OFF state. We measure source-drain thermal switch ratios of 109 ± 44 in high vacuum with gate switching temperatures near 25 °C. Thermal measurements show that small heat flows into the gate can be used to drive larger heat flows from source to drain, and that the switching is reversible over >150 cycles. Proof-of-concept thermal circuit demonstrations show that magnetic thermal transistors can enable passive or active heat flow routing or can be combined to create Boolean thermal logic gates. This work will allow thermal researchers to explore the behavior of nonlinear thermal circuits using three-terminal transistors and will motivate further research developing thermal transistors for advanced thermal control.
Elevated temperature and CO2 strongly affect the growth strategies of soil bacteria
Authors: Ruan Yang , Kuzyakov Yakov , Liu Xiaoyu , Zhang Xuhui , Xu Qicheng , Guo Junjie , Guo Shiwei , Shen Qirong , Yang Yunfeng , Ling Ning
Published: January 2023

The trait-based strategies of microorganisms appear to be phylogenetically conserved, but acclimation to climate change may complicate the scenario. To study the roles of phylogeny and environment on bacterial responses to sudden moisture increases, we determine bacterial population-specific growth rates by 18O-DNA quantitative stable isotope probing (18O-qSIP) in soils subjected to a free-air CO2 enrichment (FACE) combined with warming. We find that three growth strategies of bacterial taxa – rapid, intermediate and slow responders, defined by the timing of the peak growth rates – are phylogenetically conserved, even at the sub-phylum level. For example, members of class Bacilli and Sphingobacteriia are mainly rapid responders. Climate regimes, however, modify the growth strategies of over 90% of species, partly confounding the initial phylogenetic pattern. The growth of rapid bacterial responders is more influenced by phylogeny, whereas the variance for slow responders is primarily explained by environmental conditions. Overall, these results highlight the role of phylogenetic and environmental constraints in understanding and predicting the growth strategies of soil microorganisms under global change scenarios.
Efficient stabilization of cyanonaphthalene by fast radiative cooling and implications for the resilience of small PAHs in interstellar clouds
Authors: Stockett Mark H. , Bull James N. , Cederquist Henrik , Indrajith Suvasthika , Ji MingChao , Navarro Navarrete José E. , Schmidt Henning T. , Zettergren Henning , Zhu Boxing
Published: January 2023

After decades of searching, astronomers have recently identified specific Polycyclic Aromatic Hydrocarbons (PAHs) in space. Remarkably, the observed abundance of cyanonaphthalene (CNN, C10H7CN) in the Taurus Molecular Cloud (TMC-1) is six orders of magnitude higher than expected from astrophysical modeling. Here, we report unimolecular dissociation and radiative cooling rate coefficients of the 1-CNN isomer in its cationic form. These results are based on measurements of the time-dependent neutral product emission rate and kinetic energy release distributions produced from an ensemble of internally excited 1-CNN+ studied in an environment similar to that in interstellar clouds. We find that Recurrent Fluorescence – radiative relaxation via thermally populated electronic excited states – efficiently stabilizes 1-CNN+, owing to a large enhancement of the electronic transition probability by vibronic coupling. Our results help explain the anomalous abundance of CNN in TMC-1 and challenge the widely accepted picture of rapid destruction of small PAHs in space.
3D RNA-scaffolded wireframe origami
Authors: Parsons Molly F. , Allan Matthew F. , Li Shanshan , Shepherd Tyson R. , Ratanalert Sakul , Zhang Kaiming , Pullen Krista M. , Chiu Wah , Rouskin Silvi , Bathe Mark
Published: January 2023

Hybrid RNA:DNA origami, in which a long RNA scaffold strand folds into a target nanostructure via thermal annealing with complementary DNA oligos, has only been explored to a limited extent despite its unique potential for biomedical delivery of mRNA, tertiary structure characterization of long RNAs, and fabrication of artificial ribozymes. Here, we investigate design principles of three-dimensional wireframe RNA-scaffolded origami rendered as polyhedra composed of dual-duplex edges. We computationally design, fabricate, and characterize tetrahedra folded from an EGFP-encoding messenger RNA and de Bruijn sequences, an octahedron folded with M13 transcript RNA, and an octahedron and pentagonal bipyramids folded with 23S ribosomal RNA, demonstrating the ability to make diverse polyhedral shapes with distinct structural and functional RNA scaffolds. We characterize secondary and tertiary structures using dimethyl sulfate mutational profiling and cryo-electron microscopy, revealing insight into both global and local, base-level structures of origami. Our top-down sequence design strategy enables the use of long RNAs as functional scaffolds for complex wireframe origami.
Brain Data Standards - A method for building data-driven cell-type ontologies
Authors: Tan Shawn Zheng Kai , Kir Huseyin , Aevermann Brian D. , Gillespie Tom , Harris Nomi , Hawrylycz Michael J. , Jorstad Nikolas L. , Lein Ed S. , Matentzoglu Nicolas , Miller Jeremy A. , Mollenkopf Tyler S. , Mungall Christopher J. , Ray Patrick L. , Sanchez Raymond E. A. , Staats Brian , Vermillion Jim , Yadav Ambika , Zhang Yun , Scheuermann Richard H. , Osumi-Sutherland David
Published: January 2023

Large-scale single-cell ‘omics profiling is being used to define a complete catalogue of brain cell types, something that traditional methods struggle with due to the diversity and complexity of the brain. But this poses a problem: How do we organise such a catalogue - providing a standard way to refer to the cell types discovered, linking their classification and properties to supporting data? Cell ontologies provide a partial solution to these problems, but no existing ontology schemas support the definition of cell types by direct reference to supporting data, classification of cell types using classifications derived directly from data, or links from cell types to marker sets along with confidence scores. Here we describe a generally applicable schema that solves these problems and its application in a semi-automated pipeline to build a data-linked extension to the Cell Ontology representing cell types in the Primary Motor Cortex of humans, mice and marmosets. The methods and resulting ontology are designed to be scalable and applicable to similar whole-brain atlases currently in preparation.
Optimization of tamoxifen solubility in carbon dioxide supercritical fluid and investigating other molecular targets using advanced artificial intelligence models
Authors: Alshahrani Saad M. , Alshetaili Abdullah S. , Alfadhel Munerah M. , Belal Amany , Abourehab Mohammad A. S. , Al Saqr Ahmed , Almutairy Bjad K. , Venkatesan Kumar , Alsubaiyel Amal M. , Pishnamazi Mahboubeh
Published: January 2023

Particle size, shape and morphology can be considered as the most significant functional parameters, their effects on increasing the performance of oral solid dosage formulation are indisputable. Supercritical Carbon dioxide fluid (SCCO2) technology is an effective approach to control the above-mentioned parameters in oral solid dosage formulation. In this study, drug solubility measuring is investigated based on artificial intelligence model using carbon dioxide as a common supercritical solvent, at different pressure and temperature, 120–400 bar, 308–338 K. The results indicate that pressure has a strong effect on drug solubility. In this investigation, Decision Tree (DT), Adaptive Boosted Decision Trees (ADA-DT), and Nu-SVR regression models are used for the first time as a novel model on the available data, which have two inputs, including pressure, X1 = P(bar) and temperature, X2 = T(K). Also, output is Y = solubility. With an R-squared score, DT, ADA-DT, and Nu-SVR showed results of 0.836, 0.921, and 0.813. Also, in terms of MAE, they showed error rates of 4.30E−06, 1.95E−06, and 3.45E−06. Another metric is RMSE, in which DT, ADA-DT, and Nu-SVR showed error rates of 4.96E−06, 2.34E−06, and 5.26E−06, respectively. Due to the analysis outputs, ADA-DT selected as the best and novel model and the find optimal outputs can be shown via vector: (x1 = 309, x2 = 317.39, Y1 = 7.03e−05).
Effect of climatic environment on immunological features of rheumatoid arthritis
Authors: Kondo Yuya , Abe Saori , Toko Hirofumi , Hirota Tomoya , Takahashi Hiroyuki , Shimizu Masaru , Noma Hisashi , Tsuboi Hiroto , Matsumoto Isao , Inaba Toshiro , Sumida Takayuki
Published: January 2023

The aim of this study was to clarify the effect of climatic environment on the immunological features of rheumatoid arthritis (RA). Blood samples were collected from patients with RA and healthy controls (HCs), matched by age and sex, living in two locations, Tsukuba and Karuizawa, which differ in their altitude and average air temperature and atmospheric pressure. Analysis of peripheral blood mononuclear cells (PBMCs) revealed that the proportion of T and B cell subpopulations in HCs and RA patients were significantly different between two sites. Inverse probability weighting adjustment with propensity scores was used to control for potential confounding factors. The results revealed that, in comparison with RA patients in Tsukuba, those in Karuizawa showed a significant increase in cTh1, cTfh1, and Tph cells, and significant decrease in cTh17, cTh17.1, and CD8+ Treg in T cell subpopulations, and a significant increase in DNB, DN1, DN2, and class-switched memory B cells, and a significant decrease in unswitched memory B, naïve B cells, and ABCs in B cell subpopulations. Our results suggest the possibility that climatic environment might have an effect on immune cell proportion and function, and be related to the pathogenic mechanism of RA.
EEG cortical activity and connectivity correlates of early sympathetic response during cold pressor test
Authors: Rho Gianluca , Callara Alejandro Luis , Bernardi Giulio , Scilingo Enzo Pasquale , Greco Alberto
Published: January 2023

Previous studies have identified several brain regions involved in the sympathetic response and its integration with pain, cognition, emotions and memory processes. However, little is known about how such regions dynamically interact during a sympathetic activation task. In this study, we analyzed EEG activity and effective connectivity during a cold pressor test (CPT). A source localization analysis identified a network of common active sources including the right precuneus (r-PCu), right and left precentral gyri (r-PCG, l-PCG), left premotor cortex (l-PMC) and left anterior cingulate cortex (l-ACC). We comprehensively analyzed the network dynamics by estimating power variation and causal interactions among the network regions through the direct directed transfer function (dDTF). A connectivity pattern dominated by interactions in $$\alpha$$
α
(8–12) Hz band was observed in the resting state, with r-PCu acting as the main hub of information flow. After the CPT onset, we observed an abrupt suppression of such $$\alpha$$
α
-band interactions, followed by a partial recovery towards the end of the task. On the other hand, an increase of $$\delta$$
δ
-band (1–4) Hz interactions characterized the first part of CPT task. These results provide novel information on the brain dynamics induced by sympathetic stimuli. Our findings suggest that the observed suppression of $$\alpha$$
α
and rise of $$\delta$$
δ
dynamical interactions could reflect non-pain-specific arousal and attention-related response linked to stimulus’ salience.
Analysis of oxidase activity and transcriptomic changes related to cutting propagation of hybrid larch
Authors: Qin Ruofan , Zhao Qingrong , Gu Chenrui , Wang Chen , Zhang Lei , Zhang Hanguo
Published: January 2023

Hybrid larch is the main timber and afforestation tree species in Northeast China. To solve the problem of rooting difficulties in larch cutting propagation, enzyme activity determination and transcriptome sequencing were carried out on the rooting tissues at five timepoints after cutting. peroxidase (POD), indole acetic acid oxidase (IAAO) and polyphenol oxidase (PPO) play important roles in the larch rooting process after cutting. A total of 101.20 Gb of clean data was obtained by transcriptome sequencing, and 43,246 unigenes were obtained after further screening and assembly. According to GO analysis and KEGG enrichment analysis, we think that plant hormones play an important role in the rooting process of larch stem cuttings. in the plant hormone signal transduction pathway, a larch gene c141104.graph_c0 that is homologous to the Arabidopsis AUX1 was found to be significantly up-regulated. We suggest that AUX1 may promote IAA transport in larch, thus affecting adventitious root development. According to the results of POD, PPO IAAO indexes and GO analysis, we think s1 and s2 periods may be important periods in the rooting process of larch stem cuttings, so we built a gene regulatory network, a total of 14genes, including LBD, NAC, AP2/ERF, bHLH and etc., may be important in different stages of cutting propagation. As the rooting rate after cutting inhibits the development of larch clone propagation, identifying the genes that regulate rooting could help us to preliminarily understand the molecular mechanism of adventitious root formation and select a better treatment method for cutting propagation.
Investigation of optimal convolutional neural network conditions for thyroid ultrasound image analysis
Authors: Lee Joon-Hyop , Kim Young-Gon , Ahn Youngbin , Park Seyeon , Kong Hyoun-Joong , Choi June Young , Kim Kwangsoon , Nam Inn-Chul , Lee Myung-Chul , Masuoka Hiroo , Miyauchi Akira , Kim Sungwan , Kim Young A. , Choe Eun Kyung , Chai Young Jun
Published: January 2023

Neural network models have been used to analyze thyroid ultrasound (US) images and stratify malignancy risk of the thyroid nodules. We investigated the optimal neural network condition for thyroid US image analysis. We compared scratch and transfer learning models, performed stress tests in 10% increments, and compared the performance of three threshold values. All validation results indicated superiority of the transfer learning model over the scratch model. Stress test indicated that training the algorithm using 3902 images (70%) resulted in a performance which was similar to the full dataset (5575). Threshold 0.3 yielded high sensitivity (1% false negative) and low specificity (72% false positive), while 0.7 gave low sensitivity (22% false negative) and high specificity (23% false positive). Here we showed that transfer learning was more effective than scratch learning in terms of area under curve, sensitivity, specificity and negative/positive predictive value, that about 3900 images were minimally required to demonstrate an acceptable performance, and that algorithm performance can be customized according to the population characteristics by adjusting threshold value.
Status does not predict stress among Hadza hunter-gatherer men
Authors: Fedurek Piotr , Lehmann Julia , Lacroix Laurent , Aktipis Athena , Cronk Lee , Makambi E. Jerryson , Mabulla Ibrahim , Berbesque J. Colette
Published: January 2023

In recent years there has been much research regarding the extent to which social status is related to long-term indices of health. The majority of studies looking at the interplay between social status and health have been conducted in industrialized societies. However, it has been argued that most of human evolution took place in small, mobile and egalitarian hunter-gatherer groups where individuals exhibited very little variation in terms of material wealth or possessions. In this study, we looked at the extent to which two domains of social status, hunting reputation (being perceived as a good hunter) and popularity (being perceived as a friend), are related to physiological stress levels among Hadza men, hunter-gatherers living in Northern Tanzania. The results of our study show that neither hunting reputation nor popularity is associated with stress levels. Overall, our data suggest that, in at least some traditional small-scale societies exhibiting an egalitarian social model, such as the Hadza, the variation in social status measures based on both popularity and hunting reputation does not translate into one of the commonly used indices of wellbeing.
Similarities in biomass and energy reserves among coral colonies from contrasting reef environments
Authors: Keister Elise F. , Gantt Shelby E. , Reich Hannah G. , Turnham Kira E. , Bateman Timothy G. , LaJeunesse Todd C. , Warner Mark E. , Kemp Dustin W.
Published: January 2023

Coral reefs are declining worldwide, yet some coral populations are better adapted to withstand reductions in pH and the rising frequency of marine heatwaves. The nearshore reef habitats of Palau, Micronesia are a proxy for a future of warmer, more acidic oceans. Coral populations in these habitats can resist, and recover from, episodes of thermal stress better than offshore conspecifics. To explore the physiological basis of this tolerance, we compared tissue biomass (ash-free dry weight cm−2), energy reserves (i.e., protein, total lipid, carbohydrate content), and several important lipid classes in six coral species living in both offshore and nearshore environments. In contrast to expectations, a trend emerged of many nearshore colonies exhibiting lower biomass and energy reserves than colonies from offshore sites, which may be explained by the increased metabolic demand of living in a warmer, acidic, environment. Despite hosting different dinoflagellate symbiont species and having access to contrasting prey abundances, total lipid and lipid class compositions were similar in colonies from each habitat. Ultimately, while the regulation of colony biomass and energy reserves may be influenced by factors, including the identity of the resident symbiont, kind of food consumed, and host genetic attributes, these independent processes converged to a similar homeostatic set point under different environmental conditions.
Resonant laser ionization and mass separation of 225Ac
Authors: Johnson Jake D. , Heines Michael , Bruchertseifer Frank , Chevallay Eric , Cocolios Thomas E. , Dockx Kristof , Duchemin Charlotte , Heinitz Stephan , Heinke Reinhard , Hurier Sophie , Lambert Laura , Leenders Benji , Skliarova Hanna , Stora Thierry , Wojtaczka Wiktoria
Published: January 2023

$$^{225}$$

225

Ac is a radio-isotope that can be linked to biological vector molecules to treat certain distributed cancers using targeted alpha therapy. However, developing $$^{225}$$

225

Ac-labelled radiopharmaceuticals remains a challenge due to the supply shortage of pure $$^{225}$$

225

Ac itself. Several techniques to obtain pure $$^{225}$$

225

Ac are being investigated, amongst which is the high-energy proton spallation of thorium or uranium combined with resonant laser ionization and mass separation. As a proof-of-principle, we perform off-line resonant ionization mass spectrometry on two samples of $$^{225}$$

225

Ac, each with a known activity, in different chemical environments. We report overall operational collection efficiencies of 10.1(2)% and 9.9(8)% for the cases in which the $$^{225}$$

225

Ac was deposited on a rhenium surface and a ThO$$_{2}$$

2

mimic target matrix respectively. The bottleneck of the technique was the laser ionization efficiency, which was deduced to be 15.1(6)%.