bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dynamic CT Reconstruction With Improved Temporal Resolution for Scanning of Fluid Flow in Porous Media
Authors: Goethals Wannes , Bultreys Tom , Manigrasso Zaira , Mascini Arjen , Aelterman Jan , Boone Matthieu N. 
Published: March 2022

AbstractLab‐based high‐resolution Computed Tomography (μCT) is an important tool to investigate multiphase fluid flow through porous media. Rapid and continuous μCT acquisition can be used to resolve the dynamics of the 3D fluid distribution in the pores over time while the flow processes occur. However, the temporal resolution of this technique remains limited due to a trade‐off between acquisition time and image quality. This work presents a method to improve the temporal resolution of multiphase flow imaging experiments by limiting the angular range of radiographs used to reconstruct each time step, while compensating for this loss of information by including a temporal total variation term in the reconstruction algorithm. This addition penalizes improper temporal fluctuations in the reconstructed images, but not those dynamic events that are consistent with the radiographs. We perform a thorough evaluation of the resulting gain in temporal resolution at the single‐pore level. The method is validated on both simulated and experimental data representing multiphase flow in porous media. We find that this method improved the temporal resolution up to a factor 3 compared to reconstructions that use full 360° rotations for each time step.
Capillaric field effect transistors
Authors: Meffan Claude , Menges Julian , Dolamore Fabian , Mak Daniel , Fee Conan , Dobson Renwick C. J. , Nock Volker 
Published: March 2022

AbstractControlling fluid flow in capillaric circuits is a key requirement to increase their uptake for assay applications. Capillary action off-valves provide such functionality by pushing an occluding bubble into the channel using a difference in capillary pressure. Previously, we utilized the binary switching mode of this structure to develop a powerful set of fundamental fluidic valving operations. In this work, we study the transistor-like qualities of the off-valve and provide evidence that these structures are in fact functionally complementary to electronic junction field effect transistors. In view of this, we propose the new term capillaric field effect transistor to describe these types of valves. To support this conclusion, we present a theoretical description, experimental characterization, and practical application of analog flow resistance control. In addition, we demonstrate that the valves can also be reopened. We show modulation of the flow resistance from fully open to pinch-off, determine the flow rate–trigger channel volume relationship and demonstrate that the latter can be modeled using Shockley’s equation for electronic transistors. Finally, we provide a first example of how the valves can be opened and closed repeatedly.
The DNMT1-PAS1-PH20 axis drives breast cancer growth and metastasis
Authors: Fu Yenan , Zhang Xi , Liu Xiao , Wang Peng , Chu Wenhui , Zhao Wei , Wang Yunling , Zhou Guangbiao , Yu Yu , Zhang Hongquan 
Published: March 2022

AbstractPH20 is a member of the human hyaluronidase family that degrades hyaluronan in the extracellular matrix and controls tumor progression. Inhibition of DNA methyltransferases (DNMTs) leads to elevated hyaluronan levels; however, whether DNMT inhibitors control PH20 remains unclear. Here, we report that the DNMT1 inhibitor, decitabine, suppresses PH20 expression by activating the long non-coding RNA PHACTR2-AS1 (PAS1). PAS1 forms a tripartite complex with the RNA-binding protein vigilin and histone methyltransferase SUV39H1. The interaction between PAS1 and vigilin maintains the stability of PAS1. Meanwhile, PAS1 recruits SUV39H1 to trigger the H3K9 methylation of PH20, resulting in its silencing. Functionally, PAS1 inhibits breast cancer growth and metastasis, at least partially, by suppressing PH20. Combination therapy of decitabine and PAS1-30nt-RNA, which directly binds to SUV39H1, effectively blocked breast cancer growth and metastasis in mice. Taken together, DNMT1, PAS1, and PH20 comprise a regulatory axis to control breast cancer growth and metastasis. These findings reveal that the DNMT1-PAS1-PH20 axis is a potential therapeutic target for breast cancer.
BMP-7 ameliorates partial epithelial-mesenchymal transition by restoring SnoN protein level via Smad1/5 pathway in diabetic kidney disease
Authors: Peng Wei , Zhou Xingcheng , Xu Tingting , Mao Yanwen , Zhang Xiaohuan , Liu Huiming , Liang Luqun , Liu Lingling , Liu Lirong , Xiao Ying , Zhang Fan , Li Shuang , Shi Mingjun , Zhou Yuxia , Tang Lei , Wang Yuanyuan , Guo Bing 
Published: March 2022

AbstractTubulointerstitial fibrosis (TIF) is involved in the development of diabetic kidney disease (DKD). Transforming growth factor β1 (TGF-β1) is involved in the extensive fibrosis of renal tissue by facilitating the partial epithelial-mesenchymal transition (EMT), increasing the synthesis of extracellular matrix (ECM), inhibiting degradation, inducing apoptosis of renal parenchyma cells, and activating renal interstitial fibroblasts and inflammatory cells. Recent studies indicated that bone morphogenetic protein-7 (BMP-7) upregulated the expression of endogenous SnoN against renal TIF induced by TGF-β1 or hyperglycemia. Nevertheless, the mechanisms underlying the BMP-7-mediated restoration of SnoN protein level remains elusive. The present study demonstrated the increased expression of BMP-7 in diabetic mellitus (DM) mice by hydrodynamic tail vein injection of overexpressed BMP-7 plasmid, which attenuated the effects of DM on kidney in mice. Partial tubular EMT and the accumulation of Collagen-III were resisted in DM mice that received overexpressed BMP-7 plasmid. Similar in vivo results showed that BMP-7 was competent to alleviate NRK-52E cells undergoing partial EMT in a high-glucose milieu. Furthermore, exogenous BMP-7 activated the Smad1/5 pathway to promote gene transcription of SnoN and intervened ubiquitination of SnoN; both effects repaired the SnoN protein level in renal tubular cells and kidney tissues of DM mice. Therefore, these findings suggested that BMP-7 could upregulate SnoN mRNA and protein levels by activating the classical Smad1/5 pathway to refrain from the partial EMT of renal tubular epithelial cells and the deposition of ECM in DKD-induced renal fibrosis.
Ultra-processed foods: how functional is the NOVA system?
Authors: Braesco Véronique , Souchon Isabelle , Sauvant Patrick , Haurogné Typhaine , Maillot Matthieu , Féart Catherine , Darmon Nicole 
Published: March 2022

Abstract
Background
In the NOVA classification system, descriptive criteria are used to assign foods to one of four groups based on processing-related criteria. Although NOVA is widely used, its robustness and functionality remain largely unexplored. We determined whether this system leads to consistent food assignments by users.

Methods
French food and nutrition specialists completed an online survey in which they assigned foods to NOVA groups. The survey comprised two lists: one with 120 marketed food products with ingredient information and one with 111 generic food items without ingredient information. We quantified assignment consistency among evaluators using Fleiss’ κ (range: 0–1, where 1 = 100% agreement). Hierarchical clustering on principal components identified clusters of foods with similar distributions of NOVA assignments.

Results
Fleiss’ κ was 0.32 and 0.34 for the marketed foods (n = 159 evaluators) and generic foods (n = 177 evaluators), respectively. There were three clusters within the marketed foods: one contained 90 foods largely assigned to NOVA4 (91% of assignments), while the two others displayed greater assignment heterogeneity. There were four clusters within the generic foods: three clusters contained foods mostly assigned to a single NOVA group (69–79% of assignments), and the fourth cluster comprised 28 foods whose assignments were more evenly distributed across the four NOVA groups.

Conclusions
Although assignments were more consistent for some foods than others, overall consistency among evaluators was low, even when ingredient information was available. These results suggest current NOVA criteria do not allow for robust and functional food assignments.
Contrasting genetic trajectories of endangered and expanding red fox populations in the western U.S
Authors: Quinn Cate B. , Preckler-Quisquater Sophie , Akins Jocelyn R. , Cross Patrick R. , Alden Preston B. , Vanderzwan Stevi L. , Stephenson John A. , Figura Pete J. , Green Gregory A. , Hiller Tim L. , Sacks Benjamin N. 
Published: March 2022

AbstractAs anthropogenic disturbances continue to drive habitat loss and range contractions, the maintenance of evolutionary processes will increasingly require targeting measures to the population level, even for common and widespread species. Doing so requires detailed knowledge of population genetic structure, both to identify populations of conservation need and value, as well as to evaluate suitability of potential donor populations. We conducted a range-wide analysis of the genetic structure of red foxes in the contiguous western U.S., including a federally endangered distinct population segment of the Sierra Nevada subspecies, with the objectives of contextualizing field observations of relative scarcity in the Pacific mountains and increasing abundance in the cold desert basins of the Intermountain West. Using 31 autosomal microsatellites, along with mitochondrial and Y-chromosome markers, we found that populations of the Pacific mountains were isolated from one another and genetically depauperate (e.g., estimated Ne range = 3–9). In contrast, red foxes in the Intermountain regions showed relatively high connectivity and genetic diversity. Although most Intermountain red foxes carried indigenous western matrilines (78%) and patrilines (85%), the presence of nonindigenous haplotypes at lower elevations indicated admixture with fur-farm foxes and possibly expanding midcontinent populations as well. Our findings suggest that some Pacific mountain populations could likely benefit from increased connectivity (i.e., genetic rescue) but that nonnative admixture makes expanding populations in the Intermountain basins a non-ideal source. However, our results also suggest contact between Pacific mountain and Intermountain basin populations is likely to increase regardless, warranting consideration of risks and benefits of proactive measures to mitigate against unwanted effects of Intermountain gene flow.
A phase II trial of an alternative schedule of palbociclib and embedded serum TK1 analysis
Authors: Krishnamurthy Jairam , Luo Jingqin , Suresh Rama , Ademuyiwa Foluso , Rigden Caron , Rearden Timothy , Clifton Katherine , Weilbaecher Katherine , Frith Ashley , Roshal Anna , Tandra Pavan K. , Cherian Mathew , Summa Tracy , Haas Brittney , Thomas Shana , Hernandez-Aya Leonel , Bergqvist Mattias , Peterson Lindsey , Ma Cynthia X. 
Published: March 2022

AbstractPalbociclib 3-weeks-on/1-week-off, combined with hormonal therapy, is approved for hormone receptor positive (HR+)/HER2-negative (HER2−) advanced/metastatic breast cancer (MBC). Neutropenia is the most frequent adverse event (AE). We aim to determine whether an alternative 5-days-on/2-days-off weekly schedule reduces grade 3 and above neutropenia (G3 + ANC) incidence. In this single-arm phase II trial, patients with HR+/HER2− MBC received palbociclib 125 mg, 5-days-on/2-days-off, plus letrozole or fulvestrant per physician, on a 28-day cycle (C), as their first- or second-line treatment. The primary endpoint was G3 + ANC in the first 29 days (C1). Secondary endpoints included AEs, efficacy, and serum thymidine kinase 1 (sTK1) activity. At data-cutoff, fifty-four patients received a median of 13 cycles (range 2.6–43.5). The rate of G3 + ANC was 21.3% (95% CI: 11.2–36.1%) without G4 in C1, and 40.7% (95% CI: 27.9–54.9%), including 38.9% G3 and 1.8% G4, in all cycles. The clinical benefit rate was 80.4% (95% CI: 66.5–89.7%). The median progression-free survival (mPFS) (95% CI) was 19.75 (12.11–34.89), 33.5 (17.25–not reached [NR]), and 11.96 (10.43–NR) months, in the overall, endocrine sensitive or resistant population, respectively. High sTK1 at baseline, C1 day 15 (C1D15), and C2D1 were independently prognostic for shorter PFS (p = 9.91 × 10−4, 0.001, 0.007, respectively). sTK1 decreased on C1D15 (p = 4.03 × 10−7), indicating target inhibition. Rise in sTK1 predicted progression, with the median lead time of 59.5 (inter-quartile range: −206.25–0) days. Palbociclib, 5-days-on/2-days-off weekly, met its primary endpoint with reduced G3 + ANC, without compromising efficacy. sTK1 is prognostic and shows promise in monitoring the palbociclib response. ClinicalTrials.gov#: NCT3007979.
Comprehensive analysis of recessive carrier status using exome and genome sequencing data in 1543 Southern Chinese
Authors: Chau Jeffrey Fong Ting , Yu Mullin Ho Chung , Chui Martin Man Chun , Yeung Cyrus Chun Wing , Kwok Aaron Wing Cheung , Zhuang Xuehan , Lee Ryan , Fung Jasmine Lee Fong , Lee Mianne , Mak Christopher Chun Yu , Ng Nicole Ying Ting , Chung Claudia Ching Yan , Chan Marcus Chun Yin , Tsang Mandy Ho Yin , Chan Joshua Chun Ki , Chan Kelvin Yuen Kwong , Kan Anita Sik Yau , Chung Patrick Ho Yu , Yang Wanling , Lee So Lun , Chan Godfrey Chi Fung , Tam Paul Kwong Hang , Lau Yu Lung , Yeung Kit San , Chung Brian Hon Yin , Tang Clara Sze Man 
Published: March 2022

AbstractTraditional carrier screening has been utilized for the detection of carriers of genetic disorders. Since a comprehensive assessment of the carrier frequencies of recessive conditions in the Southern Chinese population is not yet available, we performed a secondary analysis on the spectrum and carrier status for 315 genes causing autosomal recessive disorders in 1543 Southern Chinese individuals with next-generation sequencing data, 1116 with exome sequencing and 427 with genome sequencing data. Our data revealed that 1 in 2 people (47.8% of the population) was a carrier for one or more recessive conditions, and 1 in 12 individuals (8.30% of the population) was a carrier for treatable inherited conditions. In alignment with current American College of Obstetricians and Gynecologists (ACOG) pan-ethnic carrier recommendations, 1 in 26 individuals were identified as carriers of cystic fibrosis, thalassemia, and spinal muscular atrophy in the Southern Chinese population. When the >1% expanded carrier screening rate recommendation by ACOG was used, 11 diseases were found to meet the criteria in the Southern Chinese population. Approximately 1 in 3 individuals (35.5% of the population) were carriers of these 11 conditions. If the 1 in 200 carrier frequency threshold is used, and additional seven genes would meet the criteria, and 2 in 5 individuals (38.7% of the population) would be detected as a carrier. This study provides a comprehensive catalogue of the carrier spectrum and frequency in the Southern Chinese population and can serve as a reference for careful evaluation of the conditions to be included in expanded carrier screening for Southern Chinese people.
Resonant inelastic X-ray scattering as a probe of Jeff = 1/2 state in 3d transition-metal oxide
Authors: Huang H. Y. , Singh A. , Wu C. I. , Xie J. D. , Okamoto J. , Belik A. A. , Kurmaev E. , Fujimori A. , Chen C. T. , Streltsov S. V. , Huang D. J. 
Published: March 2022

AbstractThe state with effective total moment Jeff = 1/2 stabilized by the spin-orbit coupling is known to suppress Jahn-Teller distortions and may induce a strong exchange anisotropy. This in turn may lead to the formation of an elusive spin-liquid state in real materials. While recent studies have demonstrated that such a situation can be realized in 3d transition-metal compounds such as those based on Co2+ and Cu2+, diagnosis of Jeff = 1/2 state remains challenging. We show that resonant inelastic X-ray scattering is an effective tool to probe this state and apply it to CuAl2O4, material where Cu2+ ions were previously proposed to be in the Jeff = 1/2 state. Our results unambiguously demonstrate that, contrary to previous expectations, a competitive (to Jeff = 1/2) Jahn-Teller state realizes in this compound.
Early-stage visual perception impairment in schizophrenia, bottom-up and back again
Authors: Adámek Petr , Langová Veronika , Horáček Jiří 
Published: March 2022

AbstractVisual perception is one of the basic tools for exploring the world. However, in schizophrenia, this modality is disrupted. So far, there has been no clear answer as to whether the disruption occurs primarily within the brain or in the precortical areas of visual perception (the retina, visual pathways, and lateral geniculate nucleus [LGN]). A web-based comprehensive search of peer-reviewed journals was conducted based on various keyword combinations including schizophrenia, saliency, visual cognition, visual pathways, retina, and LGN. Articles were chosen with respect to topic relevance. Searched databases included Google Scholar, PubMed, and Web of Science. This review describes the precortical circuit and the key changes in biochemistry and pathophysiology that affect the creation and characteristics of the retinal signal as well as its subsequent modulation and processing in other parts of this circuit. Changes in the characteristics of the signal and the misinterpretation of visual stimuli associated with them may, as a result, contribute to the development of schizophrenic disease.
Band transport by large Fröhlich polarons in MXenes
Authors: Zheng Wenhao , Sun Boya , Li Dongqi , Gali Sai Manoj , Zhang Heng , Fu Shuai , Di Virgilio Lucia , Li Zichao , Yang Sheng , Zhou Shengqiang , Beljonne David , Yu Minghao , Feng Xinliang , Wang Hai I. , Bonn Mischa 
Published: March 2022

AbstractMXenes are emerging layered materials that are promising for electrochemical energy storage and (opto-)electronic applications. A fundamental understanding of charge transport in MXenes is essential for such applications, but has remained under debate. While theoretical studies pointed to efficient band transport, device measurements have revealed thermally activated, hopping-type transport. Here we present a unifying picture of charge transport in two model MXenes by combining ultrafast terahertz and static electrical transport measurements to distinguish the short- and long-range transport characteristics. We find that band-like transport dominates short-range, intra-flake charge conduction in MXenes, whereas long-range, inter-flake transport occurs through thermally activated hopping, and limits charge percolation across the MXene flakes. Our analysis of the intra-flake charge carrier scattering rate shows that it is dominated by scattering from longitudinal optical phonons with a small coupling constant (α ≈ 1), for both semiconducting and metallic MXenes. This indicates the formation of large polarons in MXenes. Our work therefore provides insight into the polaronic nature of free charges in MXenes, and unveils intra- and inter-flake transport mechanisms in the MXene materials, which are relevant for both fundamental studies and applications.
Development of spirulina for the manufacture and oral delivery of protein therapeutics
Authors: Jester Benjamin W. , Zhao Hui , Gewe Mesfin , Adame Thomas , Perruzza Lisa , Bolick David T. , Agosti Jan , Khuong Nhi , Kuestner Rolf , Gamble Caitlin , Cruickshank Kendra , Ferrara Jeremy , Lim Rachelle , Paddock Troy , Brady Colin , Ertel Stacey , Zhang Miaohua , Pollock Alex , Lee Jamie , Xiong Jian , Tasch Michael , Saveria Tracy , Doughty David , Marshall Jacob , Carrieri Damian , Goetsch Lauren , Dang Jason , Sanjaya Nathaniel , Fletcher David , Martinez Anissa , Kadis Bryce , Sigmar Kristjan , Afreen Esha , Nguyen Tammy , Randolph Amanda , Taber Alexandria , Krzeszowski Ashley , Robinett Brittney , Volkin David B. , Grassi Fabio , Guerrant Richard , Takeuchi Ryo , Finrow Brian , Behnke Craig , Roberts James 
Published: March 2022

AbstractThe use of the edible photosynthetic cyanobacterium Arthrospira platensis (spirulina) as a biomanufacturing platform has been limited by a lack of genetic tools. Here we report genetic engineering methods for stable, high-level expression of bioactive proteins in spirulina, including large-scale, indoor cultivation and downstream processing methods. Following targeted integration of exogenous genes into the spirulina chromosome (chr), encoded protein biopharmaceuticals can represent as much as 15% of total biomass, require no purification before oral delivery and are stable without refrigeration and protected during gastric transit when encapsulated within dry spirulina. Oral delivery of a spirulina-expressed antibody targeting campylobacter—a major cause of infant mortality in the developing world—prevents disease in mice, and a phase 1 clinical trial demonstrated safety for human administration. Spirulina provides an advantageous system for the manufacture of orally delivered therapeutic proteins by combining the safety of a food-based production host with the accessible genetic manipulation and high productivity of microbial platforms.
DaXi—high-resolution, large imaging volume and multi-view single-objective light-sheet microscopy
Authors: Yang Bin , Lange Merlin , Millett-Sikking Alfred , Zhao Xiang , Bragantini Jordão , VijayKumar Shruthi , Kamb Mason , Gómez-Sjöberg Rafael , Solak Ahmet Can , Wang Wanpeng , Kobayashi Hirofumi , McCarroll Matthew N. , Whitehead Lachlan W. , Fiolka Reto P. , Kornberg Thomas B. , York Andrew G. , Royer Loic A. 
Published: March 2022

AbstractThe promise of single-objective light-sheet microscopy is to combine the convenience of standard single-objective microscopes with the speed, coverage, resolution and gentleness of light-sheet microscopes. We present DaXi, a single-objective light-sheet microscope design based on oblique plane illumination that achieves: (1) a wider field of view and high-resolution imaging via a custom remote focusing objective; (2) fast volumetric imaging over larger volumes without compromising image quality or necessitating tiled acquisition; (3) fuller image coverage for large samples via multi-view imaging and (4) higher throughput multi-well imaging via remote coverslip placement. Our instrument achieves a resolution of 450 nm laterally and 2 μm axially over an imaging volume of 3,000 × 800 × 300 μm. We demonstrate the speed, field of view, resolution and versatility of our instrument by imaging various systems, including Drosophila egg chamber development, zebrafish whole-brain activity and zebrafish embryonic development – up to nine embryos at a time.
Analysis of metabolic dynamics during drought stress in Arabidopsis plants
Authors: Lozano-Elena Fidel , Fàbregas Norma , Coleto-Alcudia Veredas , Caño-Delgado Ana I. 
Published: March 2022

AbstractDrought is a major cause of agricultural losses worldwide. Climate change will intensify drought episodes threatening agricultural sustainability. Gaining insights into drought response mechanisms is vital for crop adaptation to climate emergency. To date, only few studies report comprehensive analyses of plant metabolic adaptation to drought. Here, we present a multifactorial metabolomic study of early-mid drought stages in the model plant Arabidopsis thaliana. We sampled root and shoot tissues of plants subjected to water withholding over a six-day time course, including brassinosteroids receptor mutants previously reported to show drought tolerance phenotypes. Furthermore, we sequenced the root transcriptome at basal and after 5 days drought, allowing direct correlation between metabolic and transcriptomic changes and the multi-omics integration. Significant abiotic stress signatures were already activated at basal conditions in a vascular-specific receptor overexpression (BRL3ox). These were also rapidly mobilized under drought, revealing a systemic adaptation strategy driven from inner tissues of the plant. Overall, this dataset provides a significant asset to study drought metabolic adaptation and allows its analysis from multiple perspectives.