bluuebunny/crossref_metadata_2025_split huggingface dataset:
Measurement of oxygen consumption rates of human renal proximal tubule cells in an array of organ-on-chip devices to monitor drug-induced metabolic shifts
Authors: Kann Samuel H. , Shaughnessey Erin M. , Coppeta Jonathan R. , Azizgolshani Hesham , Isenberg Brett C. , Vedula Else M. , Zhang Xin , Charest Joseph L. 
Published: September 2022

AbstractMeasurement of cell metabolism in moderate-throughput to high-throughput organ-on-chip (OOC) systems would expand the range of data collected for studying drug effects or disease in physiologically relevant tissue models. However, current measurement approaches rely on fluorescent imaging or colorimetric assays that are focused on endpoints, require labels or added substrates, and lack real-time data. Here, we integrated optical-based oxygen sensors in a high-throughput OOC platform and developed an approach for monitoring cell metabolic activity in an array of membrane bilayer devices. Each membrane bilayer device supported a culture of human renal proximal tubule epithelial cells on a porous membrane suspended between two microchannels and exposed to controlled, unidirectional perfusion and physiologically relevant shear stress for several days. For the first time, we measured changes in oxygen in a membrane bilayer format and used a finite element analysis model to estimate cell oxygen consumption rates (OCRs), allowing comparison with OCRs from other cell culture systems. Finally, we demonstrated label-free detection of metabolic shifts in human renal proximal tubule cells following exposure to FCCP, a drug known for increasing cell oxygen consumption, as well as oligomycin and antimycin A, drugs known for decreasing cell oxygen consumption. The capability to measure cell OCRs and detect metabolic shifts in an array of membrane bilayer devices contained within an industry standard microtiter plate format will be valuable for analyzing flow-responsive and physiologically complex tissues during drug development and disease research.
A Japanese patient with neonatal biotin-responsive basal ganglia disease
Authors: Kobayashi Mizuki , Suzuki Yuichi , Nodera Maki , Matsunaga Ayako , Kohda Masakazu , Okazaki Yasushi , Murayama Kei , Yamagata Takanori , Osaka Hitoshi 
Published: September 2022

AbstractBiotin-responsive basal ganglia disease (BBGD) with SLC19A3 mutation was first reported in 1998, and over 30 mutations have been reported. We report a neonatal BBGD case with sudden-onset feeding difficulty and impaired consciousness. Encephalopathy resolved after the initiation of biotin and thiamine treatment. Genetic testing revealed a novel heterozygous mutation [c.384_387del, p.Tyr128fs];[c.265 A > C, p.Ser89Arg] in SLC19A3. Early treatment for BBGD is essential, especially with onset in the neonatal or early infancy period.
The macroeconomic effects of adapting to high-end sea-level rise via protection and migration
Authors: Bachner Gabriel , Lincke Daniel , Hinkel Jochen 
Published: September 2022

AbstractClimate change-induced sea level rise (SLR) is projected to be substantial, triggering human adaptation responses, including increasing protection and out-migration from coastlines. Yet, in macroeconomic assessments of SLR the latter option has been given little attention. We fill this gap by providing a global analysis of the macroeconomic effects of adaptation to SLR, including coastal migration, focusing on the higher end of SLR projections until 2050. We find that when adapting simultaneously via protection and coastal migration, macroeconomic costs can be lower than with protection alone. For some developing regions coastal migration is even less costly (in GDP) than protection. Additionally, we find that future macroeconomic costs are dominated by accumulated macroeconomic effects over time, rather than by future direct damages, implying the need for immediate adaptation. Finally, we demonstrate the importance of including autonomous adaptation in the reference scenario of economic assessment studies to avoid overestimation of adaptation benefits.
Control of electronic topology in a strongly correlated electron system
Authors: Dzsaber Sami , Zocco Diego A. , McCollam Alix , Weickert Franziska , McDonald Ross , Taupin Mathieu , Eguchi Gaku , Yan Xinlin , Prokofiev Andrey , Tang Lucas M. K. , Vlaar Bryan , Winter Laurel E. , Jaime Marcelo , Si Qimiao , Paschen Silke 
Published: September 2022

AbstractIt is becoming increasingly clear that breakthrough in quantum applications necessitates materials innovation. In high demand are conductors with robust topological states that can be manipulated at will. This is what we demonstrate in the present work. We discover that the pronounced topological response of a strongly correlated “Weyl-Kondo” semimetal can be genuinely manipulated—and ultimately fully suppressed—by magnetic fields. We understand this behavior as a Zeeman-driven motion of Weyl nodes in momentum space, up to the point where the nodes meet and annihilate in a topological quantum phase transition. The topologically trivial but correlated background remains unaffected across this transition, as is shown by our investigations up to much larger fields. Our work lays the ground for systematic explorations of electronic topology, and boosts the prospect for topological quantum devices.
A deeper understanding of system interactions can explain contradictory field results on pesticide impact on honey bees
Authors: Breda Dimitri , Frizzera Davide , Giordano Giulia , Seffin Elisa , Zanni Virginia , Annoscia Desiderato , Topping Christopher J. , Blanchini Franco , Nazzi Francesco 
Published: September 2022

AbstractWhile there is widespread concern regarding the impact of pesticides on honey bees, well-replicated field experiments, to date, have failed to provide clear insights on pesticide effects. Here, we adopt a systems biology approach to gain insights into the web of interactions amongst the factors influencing honey bee health. We put the focus on the properties of the system that depend upon its architecture and not on the strength, often unknown, of each single interaction. Then we test in vivo, on caged honey bees, the predictions derived from this modelling analysis. We show that the impact of toxic compounds on honey bee health can be shaped by the concurrent stressors affecting bees. We demonstrate that the immune-suppressive capacity of the widespread pathogen of bees, deformed wing virus, can introduce a critical positive feed-back loop in the system causing bistability, i.e., two stable equilibria. Therefore, honey bees under similar initial conditions can experience different consequences when exposed to the same stressor, including prolonged survival or premature death. The latter can generate an increased vulnerability of the hive to dwindling and collapse. Our conclusions reconcile contrasting field-testing outcomes and have important implications for the application of field studies to complex systems.
Building up libraries and production line for single atom catalysts with precursor-atomization strategy
Authors: He Xiaohui , Zhang Hao , Zhang Xingcong , Zhang Ying , He Qian , Chen Hongyu , Cheng Yujie , Peng Mi , Qin Xuetao , Ji Hongbing , Ma Ding 
Published: September 2022

AbstractHaving the excellent catalytic performance, single atom catalysts (SACs) arouse extensive research interest. However, the application of SACs is hindered by the lack of versatile and scalable preparation approaches. Here, we show a precursor-atomization strategy to produce SACs, involving the spray of droplets of solutions containing metal precursors onto support surface through ultrasonic atomization and the subsequent calcination. This approach is versatile to successful synthesis of a series of catalysts, including 19 SACs with different metal sites and supports and 3 derivatives of SACs (single atom alloys, double atom catalysts and bi-metallic SACs). Furthermore, it can be scaled up by a homemade production line with productivity over 1 kg day−1, and the well-controlled catalyst uniformity is evidenced by the identical characterization results and catalytic properties in Suzuki-Miyaura cross-coupling. This strategy lays a foundation for further investigation and may accelerate the trend from basic research to industrial applications of SACs.
Synchronous quantitative analysis of chiral mesostructured inorganic crystals by 3D electron diffraction tomography
Authors: Ai Jing , Zhang Xueliang , Bai Te , Shen Qing , Oleynikov Peter , Duan Yingying , Terasaki Osamu , Che Shunai , Han Lu 
Published: September 2022

AbstractChiral mesostructures exhibit distinctive twisting and helical hierarchical stacking ranging from atomic to micrometre scales with fascinating structural-chiral anisotropy properties. However, the detailed determination of their multilevel chirality remains challenging due to the limited information from spectroscopy, diffraction techniques, scanning electron microscopy and the two-dimensional projections in transmission electron microscopy. Herein, we report a general approach to determine chiral hierarchical mesostructures based on three-dimensional electron diffraction tomography (3D EDT), by which the structure can be solved synchronously according to the quantitative measurement of diffraction spot deformations and their arrangement in reciprocal space. This method was verified on two samples—chiral mesostructured nickel molybdate and chiral mesostructured tin dioxide—revealing hierarchical chiral structures that cannot be determined by conventional techniques. This approach provides more precise and comprehensive identification of the hierarchical mesostructures, which is expected to advance our understanding of structural–chiral anisotropy at the fundamental level.
Genomic analyses of rice bean landraces reveal adaptation and yield related loci to accelerate breeding
Authors: Guan Jiantao , Zhang Jintao , Gong Dan , Zhang Zhengquan , Yu Yang , Luo Gaoling , Somta Prakit , Hu Zheng , Wang Suhua , Yuan Xingxing , Zhang Yaowen , Wang Yanlan , Chen Yanhua , Laosatit Kularb , Chen Xin , Chen Honglin , Sha Aihua , Cheng Xuzhen , Xie Hua , Wang Lixia 
Published: September 2022

AbstractRice bean (Vigna umbellata) is an underexploited domesticated legume crop consumed for dietary protein in Asia, yet little is known about the genetic diversity of this species. Here, we present a high-quality reference genome for a rice bean landrace (FF25) built using PacBio long-read data and a Hi-C chromatin interaction map, and assess the phylogenetic position and speciation time of rice bean within the Vigna genus. We sequence 440 landraces (two core collections), and GWAS based on data for growth sites at three widely divergent latitudes reveal loci associated with flowering and yield. Loci harboring orthologs of FUL (FRUITFULL), FT (FLOWERING LOCUS T), and PRR3 (PSEUDO-RESPONSE REGULATOR 3) contribute to the adaptation of rice bean from its low latitude center of origin towards higher latitudes, and the landraces which pyramid early-flowering alleles for these loci display maximally short flowering times. We also demonstrate that copy-number-variation for VumCYP78A6 can regulate seed-yield traits. Intriguingly, 32 landraces collected from a mountainous region in South-Central China harbor a recently acquired InDel in TFL1 (TERMINAL FLOWER1) affecting stem determinacy; these materials also have exceptionally high values for multiple human-desired traits and could therefore substantially advance breeding efforts to improve rice bean.
Emergent topological states via digital (001) oxide superlattices
Authors: Liu Zhiwei , Liu Hongquan , Ma Jiaji , Wang Xiaoxuan , Li Gang , Chen Hanghui 
Published: September 2022

AbstractOxide heterostructures exhibit many intriguing properties. Here we provide design principles for inducing multiple topological states in (001) (AMO3)1/($$AM^{\prime}$$

A

M

′

O3)1 oxide superlattices. Aided by first-principles calculations and model analysis, we show that a (SrMO3)1/(Sr$$M^{\prime}$$

M

′

O3)1 superlattice (M = Nb, Ta and $$M^{\prime}$$

M

′

= Rh, Ir) is a strong topological insulator with Z2 index (1;001). More remarkably, a (SrMoO3)1/(SrIrO3)1 superlattice exhibits multiple coexisting topological insulator (TI) and topological Dirac semi-metal (TDS) states. The TDS state has a pair of type-II Dirac points near the Fermi level and symmetry-protected Dirac node lines. The surface TDS Dirac cone is sandwiched by two surface TI Dirac cones in the energy-momentum space. The non-trivial topological properties arise from the band inversion between d orbitals of two dissimilar transition metal atoms and a particular parity property of (001) superlattice geometry. Our work demonstrates how to induce non-trivial topological states in (001) perovskite oxide heterostructures by rational design.
Nigral glucose metabolism as a diagnostic marker of neurodegenerative parkinsonian syndromes
Authors: Schröter Nils , Blazhenets Ganna , Frings Lars , Jost Wolfgang H. , Weiller Cornelius , Rijntjes Michel , Meyer Philipp T. , Brumberg Joachim 
Published: September 2022

AbstractParkinson’s disease (PD), multiple system atrophy (MSA), and progressive supranuclear palsy (PSP) are characterized by nigrostriatal degeneration. We used [18F]FDG PET to assess glucose metabolism of the substantia nigra (SN) in patients with these diseases and evaluated its ability to discriminate neurodegenerative parkinsonian syndromes (NP) from controls. We retrospectively evaluated [18F]FDG PET scans of 171 patients with NP (n = 115 PD, n = 35 MSA, n = 21 PSP) and 48 controls (13 healthy controls [HC] and 35 control patients). Mean normalized bilateral [18F]FDG uptake in the SN was calculated and compared between groups with covariance and receiver operating characteristic (ROC) analyses (selection of the optimal cut-off required a minimum specificity of 90% to meet the clinical need of a confirmatory test). PD patients were additionally stratified by the expression of the well-established PD-related metabolic pattern (PDRP; elevated expression defined as 2 standard deviations above the mean value of HC). [18F]FDG uptake was significantly lower in NP (Cohen’s d = 1.09, p < 0.001) and its subgroups (PD, d = 1.10, p < 0.001; MSA, d = 0.97, p < 0.001; PSP, d = 1.79, p < 0.001) than in controls. ROC analysis for discriminating NP vs. controls revealed an area under the curve of 0.81 and a sensitivity and specificity of 56 and 92%. Moreover, nigral metabolism was below the cut-off in 60% of PD patients without elevated PDRP expression. Glucose metabolism of the SN can distinguish patients with NP from controls with good diagnostic accuracy and can be used as a marker of nigral degeneration. Its evaluation is particularly valuable in PD patients without elevated PDRP expression and may thus help to narrow the diagnostic gap of [18F]FDG PET in neurodegenerative parkinsonism (i.e., identification of patients with PD without cortical involvement).
Spironolactone alleviates schizophrenia-related reversal learning in Tcf4 transgenic mice subjected to social defeat
Authors: Stephan Marius , Schoeller Jonathan , Raabe Florian J. , Schmitt Andrea , Hasan Alkomiet , Falkai Peter , Jensen Niels , Rossner Moritz J. 
Published: September 2022

AbstractCognitive deficits are a hallmark of schizophrenia, for which no convincing pharmacological treatment option is currently available. Here, we tested spironolactone as a repurposed compound in Tcf4 transgenic mice subjected to psychosocial stress. In this ‘2-hit’ gene by environment mouse (GxE) model, the animals showed schizophrenia-related cognitive deficits. We had previously shown that spironolactone ameliorates working memory deficits and hyperactivity in a mouse model of cortical excitatory/inhibitory (E/I) dysbalance caused by an overactive NRG1-ERBB4 signaling pathway. In an add-on clinical study design, we used spironolactone as adjuvant medication to the standard antipsychotic drug aripiprazole. We characterized the compound effects using our previously established Platform for Systematic Semi-Automated Behavioral and Cognitive Profiling (PsyCoP). PsyCoP is a widely applicable analysis pipeline based on the Research Domain Criteria (RDoC) framework aiming at facilitating translation into the clinic. In addition, we use dimensional reduction to analyze and visualize overall treatment effect profiles. We found that spironolactone and aripiprazole improve deficits of several cognitive domains in Tcf4tg x SD mice but partially interfere with each other’s effect in the combination therapy. A similar interaction was detected for the modulation of novelty-induced activity. In addition to its strong activity-dampening effects, we found an increase in negative valence measures as a side effect of aripiprazole treatment in mice. We suggest that repurposed drug candidates should first be tested in an adequate preclinical setting before initiating clinical trials. In addition, a more specific and effective NRG1-ERBB4 pathway inhibitor or more potent E/I balancing drug might enhance the ameliorating effect on cognition even further.
Optical emissivity dataset of multi-material heterogeneous designs generated with automated figure extraction
Authors: Baibakova Viktoriia , Elzouka Mahmoud , Lubner Sean , Prasher Ravi , Jain Anubhav 
Published: September 2022

AbstractOptical device design is typically an iterative optimization process based on a good initial guess from prior reports. Optical properties databases are useful in this process but difficult to compile because their parsing requires finding relevant papers and manually converting graphical emissivity curves to data tables. Here, we present two contributions: one is a dataset of thermal emissivity records with design-related parameters, and the other is a software tool for automated colored curve data extraction from scientific plots. We manually collected 64 papers with 176 figures reporting thermal emissivity and automatically retrieved 153 colored curve data records. The automated figure analysis software pipeline uses Faster R-CNN for axes and legend object detection, EasyOCR for axes numbering recognition, and k-means clustering for colored curve retrieval. Additionally, we manually extracted geometry, materials, and method information from the text to add necessary metadata to each emissivity curve. Finally, we analyzed the dataset to determine the dominant classes of emissivity curves and determine the underlying design parameters leading to a type of emissivity profile.
The dual neural effects of oxytocin in autistic youth: results from a randomized trial
Authors: Korisky Adi , Goldstein Abraham , Gordon Ilanit 
Published: September 2022

AbstractRecent discoveries have highlighted the effects of oxytocin (OT) on social behavior and perception among autistic individuals. However, a gap persists in the literature regarding the potential effects of OT and the neural temporal dynamics due to OT administration. We explored the effect of OT on autistic individuals using magnetoencephalography (MEG), focusing on M100, M170, and M250, social perception-related components that tend to show atypical patterns in autistic individuals. Twenty-five autistic adolescents participated in this randomized, double-blind MEG study. Autistic individuals arrived at the lab twice and received an acute dose of intranasal OT or placebo in each session. During the scans, participants were asked to identify pictures of social and non-social stimuli. Additionally, 23 typically developing (TD) adolescents performed the same task in the MEG as a benchmark that allowed us to better characterize neural regions of interest and behavioral results for this age group in this task. A source-model beamformer analysis revealed that OT enhanced neural activity for social stimuli in frontal regions during M170. Additionally, in each of the preselected time windows, OT increased activation in the left hemisphere, regardless of the content of the presented stimuli. We suggest that OT increased the processing of social stimuli through two separate mechanisms. First, OT increased neural activity in a nonspecific manner, allowing increased allocation of attention toward the stimuli. Second, OT enhanced M170 activity in frontal regions only in response to social stimuli. These results reveal the temporal dynamics of the effects of OT on the early stages of social and non-social perception in autistic adolescents.Trial registration: This study was a part of a project registered as clinical trial October 27th, 2021. ClinicalTrials.gov Identifier: NCT05096676.
A tree-based scan statistic for zero-inflated count data in post-market drug safety surveillance
Authors: Park Goeun , Jung Inkyung 
Published: September 2022

AbstractAfter new drugs enter the market, adverse events (AE) induced by their use must be tracked; rare AEs may not be detected during clinical trials. Some organizations have been collecting information on suspected drugs and AEs via a spontaneous reporting system to conduct post-market drug safety surveillance. These organizations use the information to detect a signal representing potential causality between drugs and AEs. The drug and AE data are often hierarchically structured. Accordingly, the tree-based scan statistic can be used as a statistical data mining method for signal detection. Most of the AE databases contain a large number of zero-count cells. Notably, not only an observational zero from the Poisson distribution, but also a true zero exists in zero-count cells. True zeros represent theoretically impossible observations or possible but unreported observations. The existing tree-based scan statistic assumes that all zeros are zero-valued observations from the Poisson distribution. Therefore, true zeros are not considered in the modeling, which can lead to bias in the inferences. In this study, we propose a tree-based scan statistic for zero-inflated count data in a hierarchical structure. According to our simulation study, in the presence of excess zeros, our proposed tree-based scan statistic provides better performance than the existing tree-based scan statistic. The two methods were illustrated using Korea Adverse Event Reporting System data from the Korea Institute of Drug Safety and Risk Management.
Spontaneous activity in whisker-innervating region of neonatal mouse trigeminal ganglion
Authors: Banerjee Piu , Kubo Fumi , Nakaoka Hirofumi , Ajima Rieko , Sato Takuya , Hirata Tatsumi , Iwasato Takuji 
Published: September 2022

AbstractSpontaneous activity during the early postnatal period is thought to be crucial for the establishment of mature neural circuits. It remains unclear if the peripheral structure of the developing somatosensory system exhibits spontaneous activity, similar to that observed in the retina and cochlea of developing mammals. By establishing an ex vivo calcium imaging system, here we found that neurons in the whisker-innervating region of the trigeminal ganglion (TG) of neonatal mice generate spontaneous activity. A small percentage of neurons showed some obvious correlated activity, and these neurons were mostly located close to one another. TG spontaneous activity was majorly exhibited by medium-to-large diameter neurons, a characteristic of mechanosensory neurons, and was blocked by chelation of extracellular calcium. Moreover, this activity was diminished by the adult stage. Spontaneous activity in the TG during the first postnatal week could be a source of spontaneous activity observed in the neonatal mouse barrel cortex.