bluuebunny/crossref_metadata_2025_split huggingface dataset:
Diagnostic accuracy of digital breast tomosynthesis in combination with 2D mammography for the characterisation of mammographic abnormalities
Authors: Sanmugasiva Vithya Visalatchi , Ramli Hamid Marlina Tanty , Fadzli Farhana , Rozalli Faizatul Izza , Yeong Chai Hong , Ab Mumin Nazimah , Rahmat Kartini 
Published: November 2020

AbstractThis study aims to assess the diagnostic accuracy of digital breast tomosynthesis in combination with full field digital mammography (DBT + FFDM) in the charaterisation of Breast Imaging-reporting and Data System (BI-RADS) category 3, 4 and 5 lesions. Retrospective cross-sectional study of 390 patients with BI-RADS 3, 4 and 5 mammography with available histopathology examination results were recruited from in a single center of a multi-ethnic Asian population. 2 readers independently reported the FFDM and DBT images and classified lesions detected (mass, calcifications, asymmetric density and architectural distortion) based on American College of Radiology-BI-RADS lexicon. Of the 390 patients recruited, 182 malignancies were reported. Positive predictive value (PPV) of cancer was 46.7%. The PPV in BI-RADS 4a, 4b, 4c and 5 were 6.0%, 38.3%, 68.9%, and 93.1%, respectively. Among all the cancers, 76% presented as masses, 4% as calcifications and 20% as asymmetry. An additional of 4% of cancers were detected on ultrasound. The sensitivity, specificity, PPV and NPV of mass lesions detected on DBT + FFDM were 93.8%, 85.1%, 88.8% and 91.5%, respectively. The PPV for calcification is 61.6% and asymmetry is 60.7%. 81.6% of cancer detected were invasive and 13.3% were in-situ type. Our study showed that DBT is proven to be an effective tool in the diagnosis and characterization of breast lesions and supports the current body of literature that states that integrating DBT to FFDM allows good characterization of breast lesions and accurate diagnosis of cancer.
A physical unclonable neutron sensor for nuclear arms control inspections
Authors: Philippe Sébastien , d’Errico Francesco 
Published: November 2020

AbstractClassical sensor security relies on cryptographic algorithms executed on trusted hardware. This approach has significant shortcomings, however. Hardware can be manipulated, including below transistor level, and cryptographic keys are at risk of extraction attacks. A further weakness is that sensor media themselves are assumed to be trusted, and any authentication and encryption is done ex situ and a posteriori. Here we propose and demonstrate a different approach to sensor security that does not rely on classical cryptography and trusted electronics. We designed passive sensor media that inherently produce secure and trustworthy data, and whose honest and non-malicious nature can be easily established. As a proof-of-concept, we manufactured and characterized the properties of non-electronic, physical unclonable, optically complex media sensitive to neutrons for use in a high-security scenario: the inspection of a military facility to confirm the absence or presence of nuclear weapons and fissile materials.
A new method for isolating and analysing coccospheres within sediment
Authors: Langley Beth , Halloran Paul R. , Power Ann , Rickaby Rosalind E. M. , Chana Prabhjoat , Diver Poppy , Thornalley David , Hacker Christian , Love John 
Published: November 2020

AbstractSize is a fundamental cellular trait that is important in determining phytoplankton physiological and ecological processes. Fossil coccospheres, the external calcite structure produced by the excretion of interlocking plates by the phytoplankton coccolithophores, can provide a rare window into cell size in the past. Coccospheres are delicate however and are therefore poorly preserved in sediment. We demonstrate a novel technique combining imaging flow cytometry and cross-polarised light (ISX+PL) to rapidly and reliably visually isolate and quantify the morphological characteristics of coccospheres from marine sediment by exploiting their unique optical and morphological properties. Imaging flow cytometry combines the morphological information provided by microscopy with high sample numbers associated with flow cytometry. High throughput imaging overcomes the constraints of labour-intensive manual microscopy and allows statistically robust analysis of morphological features and coccosphere concentration despite low coccosphere concentrations in sediments. Applying this technique to the fine-fraction of sediments, hundreds of coccospheres can be visually isolated quickly with minimal sample preparation. This approach has the potential to enable rapid processing of down-core sediment records and/or high spatial coverage from surface sediments and may prove valuable in investigating the interplay between climate change and coccolithophore physiological/ecological response.
Deep eutectic solvents for solid pesticide dosage forms
Authors: Phillips Justin , Focke Walter W. , du Toit Elizabeth L. , Wesley-Smith James 
Published: November 2020

AbstractDeep eutectic solvents aid the formulation of solid pesticide dosage forms for water-insoluble actives. This was demonstrated by encapsulating Amitraz powder in a low-melting matrix based on the eutectic mixture of urea (32 wt%) and 1,3-dimethylurea. Dissolution in water of melt-cast discs, containing 20 wt% active, led to the rapid release of Amitraz in a finely dispersed form. The order of magnitude reduction in particle size, after dissolution, is ascribed to the solubilization of Amitraz in the hot deep eutectic solvent and its subsequent precipitation as a separate phase on crystallization of the matrix.
Depthwise microbiome and isotopic profiling of a moderately saline microbial mat in a solar saltern
Authors: Paul Varun , Banerjee Yogaraj , Ghosh Prosenjit , Busi Susheel Bhanu 
Published: November 2020

AbstractThe solar salterns in Tuticorin, India, are man-made, saline to hypersaline systems hosting some uniquely adapted populations of microorganisms and eukaryotic algae that have not been fully characterized. Two visually different microbial mats (termed ‘white’ and ‘green’) developing on the reservoir ponds (53 PSU) were isolated from the salterns. Firstly, archaeal and bacterial diversity in different vertical layers of the mats were analyzed. Culture-independent 16S rRNA gene analysis revealed that both bacteria and archaea were rich in their diversity. The top layers had a higher representation of halophilic archaea Halobacteriaceae, phylum Chloroflexi, and classes Anaerolineae, Delta- and Gamma- Proteobacteria than the deeper sections, indicating that a salinity gradient exists within the mats. Limited presence of Cyanobacteria and detection of algae-associated bacteria, such as Phycisphaerae, Phaeodactylibacter and Oceanicaulis likely implied that eukaryotic algae and other phototrophs could be the primary producers within the mat ecosystem. Secondly, predictive metabolic pathway analysis using the 16S rRNA gene data revealed that in addition to the regulatory microbial functions, methane and nitrogen metabolisms were prevalent. Finally, stable carbon and nitrogen isotopic compositions determined from both mat samples showed that the δ13Corg and δ15Norg values increased slightly with depth, ranging from − 16.42 to − 14.73‰, and 11.17 to 13.55‰, respectively. The isotopic signature along the microbial mat profile followed a pattern that is distinctive to the community composition and net metabolic activities, and comparable to saline mats in other salterns. The results and discussions presented here by merging culture-independent studies, predictive metabolic analyses and isotopic characterization, provide a collective strategy to understand the compositional and functional characteristics of microbial mats in saline environments.
Geological CO2 quantified by high-temporal resolution stable isotope monitoring in a salt mine
Authors: Frank Alexander H. , van Geldern Robert , Myrttinen Anssi , Zimmer Martin , Barth Johannes A. C. , Strauch Bettina 
Published: November 2020

AbstractThe relevance of CO2 emissions from geological sources to the atmospheric carbon budget is becoming increasingly recognized. Although geogenic gas migration along faults and in volcanic zones is generally well studied, short-term dynamics of diffusive geogenic CO2 emissions are mostly unknown. While geogenic CO2 is considered a challenging threat for underground mining operations, mines provide an extraordinary opportunity to observe geogenic degassing and dynamics close to its source. Stable carbon isotope monitoring of CO2 allows partitioning geogenic from anthropogenic contributions. High temporal-resolution enables the recognition of temporal and interdependent dynamics, easily missed by discrete sampling. Here, data is presented from an active underground salt mine in central Germany, collected on-site utilizing a field-deployed laser isotope spectrometer. Throughout the 34-day measurement period, total CO2 concentrations varied between 805 ppmV (5th percentile) and 1370 ppmV (95th percentile). With a 400-ppm atmospheric background concentration, an isotope mixing model allows the separation of geogenic (16–27%) from highly dynamic anthropogenic combustion-related contributions (21–54%). The geogenic fraction is inversely correlated to established CO2 concentrations that were driven by anthropogenic CO2 emissions within the mine. The described approach is applicable to other environments, including different types of underground mines, natural caves, and soils.
A calibrated measure to compare fluctuations of different entities across timescales
Authors: Chołoniewski Jan , Sienkiewicz Julian , Dretnik Naum , Leban Gregor , Thelwall Mike , Hołyst Janusz A. 
Published: November 2020

AbstractA common way to learn about a system’s properties is to analyze temporal fluctuations in associated variables. However, conclusions based on fluctuations from a single entity can be misleading when used without proper reference to other comparable entities or when examined only on one timescale. Here we introduce a method that uses predictions from a fluctuation scaling law as a benchmark for the observed standard deviations. Differences from the benchmark (residuals) are aggregated across multiple timescales using Principal Component Analysis to reduce data dimensionality. The first component score is a calibrated measure of fluctuations—the reactivityRA of a given entity. We apply our method to activity records from the media industry using data from the Event Registry news aggregator—over 32M articles on selected topics published by over 8000 news outlets. Our approach distinguishes between different news outlet reporting styles: high reactivity points to activity fluctuations larger than expected, reflecting a bursty reporting style, whereas low reactivity suggests a relatively stable reporting style. Combining our method with the political bias detector Media Bias/Fact Check we quantify the relative reporting styles for different topics of mainly US media sources grouped by political orientation. The results suggest that news outlets with a liberal bias tended to be the least reactive while conservative news outlets were the most reactive.
Diffusion tensor imaging and arterial tissue: establishing the influence of arterial tissue microstructure on fractional anisotropy, mean diffusivity and tractography
Authors: Tornifoglio B. , Stone A. J. , Johnston R. D. , Shahid S. S. , Kerskens C. , Lally C. 
Published: November 2020

AbstractThis study investigates diffusion tensor imaging (DTI) for providing microstructural insight into changes in arterial tissue by exploring how cell, collagen and elastin content effect fractional anisotropy (FA), mean diffusivity (MD) and tractography. Five ex vivo porcine carotid artery models (n = 6 each) were compared—native, fixed native, collagen degraded, elastin degraded and decellularised. Vessels were imaged at 7 T using a DTI protocol with b = 0 and 800 s/mm2and 10 isotopically distributed directions. FA and MD were evaluated in the vessel media and compared across models. FA values measured in native (p < 0.0001), fixed native (p < 0.0001) and collagen degraded (p = 0.0018, p = 0.0016, respectively) were significantly higher than those in elastin degraded and decellularised arteries. Native and fixed native had significantly lower MD values than elastin degraded (p < 0.0001) and decellularised tissue (p = 0.0032, p = 0.0003, respectively). Significantly lower MD was measured in collagen degraded compared with the elastin degraded model (p = 0.0001). Tractography yielded helically arranged tracts for native and collagen degraded vessels only. FA, MD and tractography were found to be highly sensitive to changes in the microstructural composition of arterial tissue, specifically pointing to cell, not collagen, content as the dominant source of the measured anisotropy in the vessel wall.
Natural selection on sleep duration in Drosophila melanogaster
Authors: Souto-Maior Caetano , Serrano Negron Yazmin L. , Harbison Susan T. 
Published: November 2020

AbstractSleep is ubiquitous across animal species, but why it persists is not well understood. Here we observe natural selection act on Drosophila sleep by relaxing bi-directional artificial selection for extreme sleep duration for 62 generations. When artificial selection was suspended, sleep increased in populations previously selected for short sleep. Likewise, sleep decreased in populations previously selected for long sleep when artificial selection was relaxed. We measured the corresponding changes in the allele frequencies of genomic variants responding to artificial selection. The allele frequencies of these variants reversed course in response to relaxed selection, and for short sleepers, the changes exceeded allele frequency changes that would be expected under random genetic drift. These observations suggest that the variants are causal polymorphisms for sleep duration responding to natural selection pressure. These polymorphisms may therefore pinpoint the most important regions of the genome maintaining variation in sleep duration.
Activity-dependent interdomain dynamics of matrix metalloprotease-1 on fibrin
Authors: Kumar Lokender , Planas-Iglesias Joan , Harms Chase , Kamboj Sumaer , Wright Derek , Klein-Seetharaman Judith , Sarkar Susanta K. 
Published: November 2020

AbstractThe roles of protein conformational dynamics and allostery in function are well-known. However, the roles that interdomain dynamics have in function are not entirely understood. We used matrix metalloprotease-1 (MMP1) as a model system to study the relationship between interdomain dynamics and activity because MMP1 has diverse substrates. Here we focus on fibrin, the primary component of a blood clot. Water-soluble fibrinogen, following cleavage by thrombin, self-polymerize to form water-insoluble fibrin. We studied the interdomain dynamics of MMP1 on fibrin without crosslinks using single-molecule Forster Resonance Energy Transfer (smFRET). We observed that the distance between the catalytic and hemopexin domains of MMP1 increases or decreases as the MMP1 activity increases or decreases, respectively. We modulated the activity using (1) an active site mutant (E219Q) of MMP1, (2) MMP9, another member of the MMP family that increases the activity of MMP1, and (3) tetracycline, an inhibitor of MMP1. We fitted the histograms of smFRET values to a sum of two Gaussians and the autocorrelations to an exponential and power law. We modeled the dynamics as a two-state Poisson process and calculated the kinetic rates from the histograms and autocorrelations. Activity-dependent interdomain dynamics may enable allosteric control of the MMP1 function.
Sleep, 24-h activity rhythms, and plasma markers of neurodegenerative disease
Authors: Lysen Thom S. , Ikram M. Arfan , Ghanbari Mohsen , Luik Annemarie I. 
Published: November 2020

AbstractSleep and 24-h activity rhythm disturbances are associated with development of neurodegenerative diseases and related pathophysiological processes in the brain. We determined the cross-sectional relation of sleep and 24-h activity rhythm disturbances with plasma-based biomarkers that might signal neurodegenerative disease, in 4712 middle-aged and elderly non-demented persons. Sleep and activity rhythms were measured using the Pittsburgh Sleep Quality Index and actigraphy. Simoa assays were used to measure plasma levels of neurofilament light chain, and additionally β-amyloid 40, β-amyloid 42, and total-tau. We used linear regression, adjusting for relevant confounders, and corrected for multiple testing. We found no associations of self-rated sleep, actigraphy-estimated sleep and 24-h activity rhythms with neurofilament light chain after confounder adjustment and correction for multiple testing, except for a non-linear association of self-rated time in bed with neurofilament light chain (P = 2.5*10−4). Similarly, we observed no significant associations with β-amyloid 40, β-amyloid 42, and total-tau after multiple testing correction. We conclude that sleep and 24-h activity rhythm disturbances were not consistently associated with neuronal damage as indicated by plasma neurofilament light chain in this population-based sample middle-aged and elderly non-demented persons. Further studies are needed to determine the associations of sleep and 24-h activity rhythm disturbances with NfL-related neuronal damage.
Pedagogical questions promote causal learning in preschoolers
Authors: Daubert Emily N. , Yu Yue , Grados Milagros , Shafto Patrick , Bonawitz Elizabeth 
Published: November 2020

AbstractWhat maximizes instructional impact in early childhood? We propose a simple intervention employing “Pedagogical Questions”. We explore whether swapping some instructional language with questions in psychosomatic storybooks improves preschoolers’ memory, learning, and generalization. Seventy-two preschoolers were randomly assigned to one of three conditions and were read storybooks employing either Direct Instruction, Pedagogical Questions, or Control content. Posttest measures of psychosomatic understanding, judgments about the possibility of psychosomatic events, and memory for storybook details showed that children in the Pedagogical Questions condition demonstrated greater memory for relevant storybook details and improved psychosomatic understanding. Our results suggest that pedagogical questions are a relatively simple educational manipulation to improve memory, learning, and transfer of theory-rich content.
Cerebellar and hepatic alterations in ACBD5-deficient mice are associated with unexpected, distinct alterations in cellular lipid homeostasis
Authors: Darwisch Warda , von Spangenberg Marino , Lehmann Jana , Singin Öznur , Deubert Geralt , Kühl Sandra , Roos Johannes , Horstmann Heinz , Körber Christoph , Hoppe Simone , Zheng Hongwei , Kuner Thomas , Pras-Raves Mia L. , van Kampen Antoine H. C. , Waterham Hans R. , Schwarz Kathrin V. , Okun Jürgen G. , Schultz Christian , Vaz Frédéric M. , Islinger Markus 
Published: November 2020

AbstractACBD5 deficiency is a novel peroxisome disorder with a largely uncharacterized pathology. ACBD5 was recently identified in a tethering complex mediating membrane contacts between peroxisomes and the endoplasmic reticulum (ER). An ACBD5-deficient mouse was analyzed to correlate ACBD5 tethering functions with the disease phenotype. ACBD5-deficient mice exhibit elevated very long-chain fatty acid levels and a progressive cerebellar pathology. Liver did not exhibit pathologic changes but increased peroxisome abundance and drastically reduced peroxisome-ER contacts. Lipidomics of liver and cerebellum revealed tissue-specific alterations in distinct lipid classes and subspecies. In line with the neurological pathology, unusual ultra-long chain fatty acids (C > 32) were elevated in phosphocholines from cerebelli but not liver indicating an organ-specific imbalance in fatty acid degradation and elongation pathways. By contrast, ether lipid formation was perturbed in liver towards an accumulation of alkyldiacylglycerols. The alterations in several lipid classes suggest that ACBD5, in addition to its acyl-CoA binding function, might maintain peroxisome-ER contacts in order to contribute to the regulation of anabolic and catabolic cellular lipid pathways.
Carnosine alleviates diabetic nephropathy by targeting GNMT, a key enzyme mediating renal inflammation and fibrosis
Authors: Liu Xue-qi , Jiang Ling , Lei Lei , Nie Zhen-yong , Zhu Wei , Wang Sheng , Zeng Han-xu , Zhang Shi-qi , Zhang Qiu , Yard Benito , Wu Yong-gui 
Published: November 2020

Abstract
Diabetic nephropathy (DN) is a common microvascular complication of diabetes and the main cause of end-stage nephropathy (ESRD). Inflammation and fibrosis play key roles in the development and progression of diabetic nephropathy. By using in vivo and in vitro DN models, our laboratory has identified the protective role of carnosine (CAR) on renal tubules. Our results showed that carnosine restored the onset and clinical symptoms as well as renal tubular injury in DN. Furthermore, carnosine decreased kidney inflammation and fibrosis in DN mice. These results were consistent with high glucose (HG)-treated mice tubular epithelial cells (MTECs). Using web-prediction algorithms, cellular thermal shift assay (CETSA) and molecular docking, we identified glycine N-methyltransferase (GNMT) as a carnosine target. Importantly, we found that GNMT, a multiple functional protein that regulates the cellular pool of methyl groups by controlling the ratio of S-adenosylmethionine (SAM) to S-adenosylhomocysteine (SAH), was down-regulated significantly in the serum of Type 1 DM patients and renal tissues of DN mice. Moreover, using cultured TECs, we confirmed that the increased GNMT expression by transient transfection mimicked the protective role of carnosine in reducing inflammation and fibrosis. Conversely, the inhibition of GNMT expression abolished the protective effects of carnosine. In conclusion, carnosine might serve as a promising therapeutic agent for DN and GNMT might be a potential therapeutic target for DN.
Identification and analysis of circRNA–miRNA–mRNA regulatory network in hepatocellular carcinoma
Authors: Zhou Daxiang , Dong Ling , Yang Lishan , Ma Qiang , Liu Feng , Li Yanjie , Xiong Shu 
Published: November 2020

This study was to identify important circRNA–miRNA–mRNA (ceRNAs) regulatory mechanisms in hepatocellular carcinoma (HCC). The circRNA dataset GSE97332 and miRNA dataset GSE57555 were used for analyses. Functional enrichment analysis for miRNA and target gene was conducted using cluster Profiler. Survival analysis was conducted through R package Survival. The ceRNAs and drug–gene interaction networks were constructed. The ceRNAs network contained five miRNAs including hsa‐miR‐25‐3p, hsa‐miR‐3692‐5p, hsa‐miR‐4270, hsa‐miR‐331‐3p, and hsa‐miR‐125a‐3p. Among the network, hsa‐miR‐25‐3p targeted the most genes, hsa‐miR‐3692‐5p and hsa‐miR‐4270 were targeted by more circRNAs than other miRNAs, hsa‐circ‐0034326 and hsa‐circ‐0011950 interacted with three miRNAs. Furthermore, target genes, including NRAS, ITGA5, SLC7A1, SEC14L2, SLC12A5, and SMAD2 were obtained in drug–gene interaction network. Survival analysis showed NRAS, ITGA5, SLC7A1, SEC14L2, SLC12A5, and SMAD2 were significantly associated with prognosis of HCC. NRAS, ITGA5, and SMAD2 were significantly enriched in proteoglycans in cancer. Moreover, hsa‐circ‐0034326 and hsa‐circ‐0011950 might function as ceRNAs to play key roles in HCC. Furthermore, miR‐25‐3p, miR‐3692‐5p, and miR‐4270 might be significant for HCC development. NRAS, ITGA5, SEC14L2, SLC12A5, and SMAD2 might be prognostic factors for HCC patients via proteoglycans in cancer pathway. Taken together, the findings will provide novel insight into pathogenesis, selection of therapeutic targets and prognostic factors for HCC.