bluuebunny/crossref_metadata_2025_split huggingface dataset:
A magnetic levitation based low-gravity simulator with an unprecedented large functional volume
Authors: Sanavandi Hamid , Guo Wei 
Published: October 2021

AbstractLow-gravity environment can have a profound impact on the behaviors of biological systems, the dynamics of fluids, and the growth of materials. Systematic research on the effects of gravity is crucial for advancing our knowledge and for the success of space missions. Due to the high cost and the limitations in the payload size and mass in typical spaceflight missions, ground-based low-gravity simulators have become indispensable for preparing spaceflight experiments and for serving as stand-alone research platforms. Among various simulator systems, the magnetic levitation-based simulator (MLS) has received long-lasting interest due to its easily adjustable gravity and practically unlimited operation time. However, a recognized issue with MLSs is their highly non-uniform force field. For a solenoid MLS, the functional volume V1%, where the net force results in an acceleration <1% of the Earth’s gravity g, is typically a few microliters (μL) or less. In this work, we report an innovative MLS design that integrates a superconducting magnet with a gradient-field Maxwell coil. Through an optimization analysis, we show that an unprecedented V1% of over 4000 μL can be achieved in a compact coil with a diameter of 8 cm. We also discuss how such an MLS can be made using existing high-Tc-superconducting materials. When the current in this MLS is reduced to emulate the gravity on Mars (gM = 0.38g), a functional volume where the gravity varies within a few percent of gM can exceed 20,000 μL. Our design may break new ground for future low-gravity research.
Computing secure key rates for quantum cryptography with untrusted devices
Authors: Tan Ernest Y.-Z. , Schwonnek René , Goh Koon Tong , Primaatmaja Ignatius William , Lim Charles C.-W. 
Published: October 2021

AbstractDevice-independent quantum key distribution (DIQKD) provides the strongest form of secure key exchange, using only the input–output statistics of the devices to achieve information-theoretic security. Although the basic security principles of DIQKD are now well understood, it remains a technical challenge to derive reliable and robust security bounds for advanced DIQKD protocols that go beyond the previous results based on violations of the CHSH inequality. In this work, we present a framework based on semidefinite programming that gives reliable lower bounds on the asymptotic secret key rate of any QKD protocol using untrusted devices. In particular, our method can in principle be utilized to find achievable secret key rates for any DIQKD protocol, based on the full input–output probability distribution or any choice of Bell inequality. Our method also extends to other DI cryptographic tasks.
Salivary microbiome profiling reveals a dysbiotic schizophrenia-associated microbiota
Authors: Qing Ying , Xu Lihua , Cui Gaoping , Sun Liya , Hu Xiaowen , Yang Xuhan , Jiang Jie , Zhang Juan , Zhang Tianhong , Wang Tao , He Lin , Wang Jijun , Wan Chunling 
Published: October 2021

AbstractSchizophrenia is a debilitating mental disorder and often has a prodromal period, referred to as clinical high risk (CHR) for psychosis, prior to the first episode. The etiology and pathogenesis of schizophrenia remain unclear. Despite the human gut microbiome being associated with schizophrenia, the role of the oral microbiome, which is a vital player in the mouth–body connection, is not well understood. To address this, we performed 16S rRNA gene sequencing to investigate the salivary microbiome in 85 patients with drug-naïve first-episode schizophrenia (FES), 43 individuals at CHR, and 80 healthy controls (HCs). The salivary microbiome of FES patients was characterized by higher α-diversity and lower β-diversity heterogeneity than those of CHR subjects and HCs. Proteobacteria, the predominant phylum, was depleted, while Firmicutes and the Firmicutes/Proteobacteria ratio was enriched, in a stepwise manner from HC to CHR to FES. H2S-producing bacteria exhibited disease-stage-specific enrichment and could be potential diagnostic biomarkers for FES and CHR. Certain salivary microbiota exhibited disease-specific correlation patterns with symptomatic severities, peripheral pro-inflammatory cytokines, thioredoxin, and S100B in FES. Furthermore, the metabolic functions from inferred metagenomes of the salivary microbiome were disrupted in FES, especially amino acid metabolism, carbohydrate metabolism, and xenobiotic degradation. This study has established a link between salivary microbiome alterations and disease initiation and provided the hypothesis of how the oral microbiota could influence schizophrenia.
Deep learning and alignment of spatially resolved single-cell transcriptomes with Tangram
Authors: Biancalani Tommaso , Scalia Gabriele , Buffoni Lorenzo , Avasthi Raghav , Lu Ziqing , Sanger Aman , Tokcan Neriman , Vanderburg Charles R. , Segerstolpe Åsa , Zhang Meng , Avraham-Davidi Inbal , Vickovic Sanja , Nitzan Mor , Ma Sai , Subramanian Ayshwarya , Lipinski Michal , Buenrostro Jason , Brown Nik Bear , Fanelli Duccio , Zhuang Xiaowei , Macosko Evan Z. , Regev Aviv 
Published: October 2021

AbstractCharting an organs’ biological atlas requires us to spatially resolve the entire single-cell transcriptome, and to relate such cellular features to the anatomical scale. Single-cell and single-nucleus RNA-seq (sc/snRNA-seq) can profile cells comprehensively, but lose spatial information. Spatial transcriptomics allows for spatial measurements, but at lower resolution and with limited sensitivity. Targeted in situ technologies solve both issues, but are limited in gene throughput. To overcome these limitations we present Tangram, a method that aligns sc/snRNA-seq data to various forms of spatial data collected from the same region, including MERFISH, STARmap, smFISH, Spatial Transcriptomics (Visium) and histological images. Tangram can map any type of sc/snRNA-seq data, including multimodal data such as those from SHARE-seq, which we used to reveal spatial patterns of chromatin accessibility. We demonstrate Tangram on healthy mouse brain tissue, by reconstructing a genome-wide anatomically integrated spatial map at single-cell resolution of the visual and somatomotor areas.
A computed tomography vertebral segmentation dataset with anatomical variations and multi-vendor scanner data
Authors: Liebl Hans , Schinz David , Sekuboyina Anjany , Malagutti Luca , Löffler Maximilian T. , Bayat Amirhossein , El Husseini Malek , Tetteh Giles , Grau Katharina , Niederreiter Eva , Baum Thomas , Wiestler Benedikt , Menze Bjoern , Braren Rickmer , Zimmer Claus , Kirschke Jan S. 
Published: October 2021

AbstractWith the advent of deep learning algorithms, fully automated radiological image analysis is within reach. In spine imaging, several atlas- and shape-based as well as deep learning segmentation algorithms have been proposed, allowing for subsequent automated analysis of morphology and pathology. The first “Large Scale Vertebrae Segmentation Challenge” (VerSe 2019) showed that these perform well on normal anatomy, but fail in variants not frequently present in the training dataset. Building on that experience, we report on the largely increased VerSe 2020 dataset and results from the second iteration of the VerSe challenge (MICCAI 2020, Lima, Peru). VerSe 2020 comprises annotated spine computed tomography (CT) images from 300 subjects with 4142 fully visualized and annotated vertebrae, collected across multiple centres from four different scanner manufacturers, enriched with cases that exhibit anatomical variants such as enumeration abnormalities (n = 77) and transitional vertebrae (n = 161). Metadata includes vertebral labelling information, voxel-level segmentation masks obtained with a human-machine hybrid algorithm and anatomical ratings, to enable the development and benchmarking of robust and accurate segmentation algorithms.
Crop production and nitrogen use in European cropland and grassland 1961–2019
Authors: Einarsson Rasmus , Sanz-Cobena Alberto , Aguilera Eduardo , Billen Gilles , Garnier Josette , van Grinsven Hans J. M. , Lassaletta Luis 
Published: October 2021

AbstractThis paper presents EuropeAgriDB v1.0, a dataset of crop production and nitrogen (N) flows in European cropland 1961–2019. The dataset covers 26 present-day countries, detailing the cropland N harvests in 17 crop categories as well as cropland N inputs in synthetic fertilizers, manure, symbiotic fixation, and atmospheric deposition. The study builds on established methods but goes beyond previous research by combining data from FAOSTAT, Eurostat, and a range of national data sources. The result is a detailed, complete, and consistent dataset, intended as a basis for further analyses of past and present agricultural production patterns, as well as construction of scenarios for the future.
Annual dynamic dataset of global cropping intensity from 2001 to 2019
Authors: Liu Xiaoxuan , Zheng Juepeng , Yu Le , Hao Pengyu , Chen Bin , Xin Qinchuan , Fu Haohuan , Gong Peng 
Published: October 2021

AbstractThe cropping intensity has received growing concern in the agriculture field in applications such as harvest area research. Notwithstanding the significant amount of existing literature on local cropping intensities, research considering global datasets appears to be limited in spatial resolution and precision. In this paper, we present an annual dynamic global cropping intensity dataset covering the period from 2001 to 2019 at a 250-m resolution with an average overall accuracy of 89%, exceeding the accuracy of the current annual dynamic global cropping intensity data at a 500-m resolution. We used the enhanced vegetation index (EVI) of MOD13Q1 as the database via a sixth-order polynomial function to calculate the cropping intensity. The global cropping intensity dataset was packaged in the GeoTIFF file type, with the quality control band in the same format. The dataset fills the vacancy of medium-resolution, global-scale annual cropping intensity data and provides an improved map for further global yield estimations and food security analyses.
CLiP, catheter and line position dataset
Authors: Tang Jennifer S. N. , Seah Jarrel C. Y. , Zia Adil , Gajera Jay , Schlegel Richard N. , Wong Aaron J. N. , Gai Dayu , Su Shu , Bose Tony , Kok Marcus L. , Jarema Alex , Harisis George N. , Cheng Chris-Tin , Kavnoudias Helen , Wang Wayland , Stein Anouk , Shih George , Gaillard Frank , Dixon Andrew , Law Meng 
Published: October 2021

AbstractCorrect catheter position is crucial to ensuring appropriate function of the catheter and avoid complications. This paper describes a dataset consisting of 50,612 image level and 17,999 manually labelled annotations from 30,083 chest radiographs from the publicly available NIH ChestXRay14 dataset with manually annotated and segmented endotracheal tubes (ETT), nasoenteric tubes (NET) and central venous catheters (CVCs).
Modeling characterization of the vertical and temporal variability of environmental DNA in the mesopelagic ocean
Authors: Allan Elizabeth Andruszkiewicz , DiBenedetto Michelle H. , Lavery Andone C. , Govindarajan Annette F. , Zhang Weifeng G. 
Published: October 2021

AbstractIncreasingly, researchers are using innovative methods to census marine life, including identification of environmental DNA (eDNA) left behind by organisms in the water column. However, little is understood about how eDNA is distributed in the ocean, given that organisms are mobile and that physical and biological processes can transport eDNA after release from a host. Particularly in the vast mesopelagic ocean where many species vertically migrate hundreds of meters diurnally, it is important to link the location at which eDNA was shed by a host organism to the location at which eDNA was collected in a water sample. Here, we present a one-dimensional mechanistic model to simulate the eDNA vertical distribution after its release and to compare the impact of key biological and physical parameters on the eDNA vertical and temporal distribution. The modeled vertical eDNA profiles allow us to quantify spatial and temporal variability in eDNA concentration and to identify the most important parameters to consider when interpreting eDNA signals. We find that the vertical displacement by advection, dispersion, and settling has limited influence on the eDNA distribution, and the depth at which eDNA is found is generally within tens of meters of the depth at which the eDNA was originally shed from the organism. Thus, using information about representative vertical migration patterns, eDNA concentration variability can be used to answer ecological questions about migrating organisms such as what depths species can be found in the daytime and nighttime and what percentage of individuals within a species diurnally migrate. These findings are critical both to advance the understanding of the vertical distribution of eDNA in the water column and to link eDNA detection to organism presence in the mesopelagic ocean as well as other aquatic environments.
Design and SAR assessment of three compact 5G antenna arrays
Authors: Lak A. , Adelpour Z. , Oraizi H. , Parhizgar N. 
Published: October 2021

AbstractIn this paper three different multi stub antenna arrays at 27–29.5 GHz are designed. The proposed antenna arrays consist of eight single elements. The structure of feeding parts is the same but the radiation elements are different. The feeding network for array is an eight way Wilkinson power divider (WPD). To guarantee the simulation results, one of the proposed structures is fabricated and measured (namely the characteristics of S11, E-, and H-plane patterns) which shows acceptable consistency with measurement results. The simulation results by CST and HFSS show reasonable agreement for reflection coefficient and radiation patterns in the E- and H- planes. The overall size of the proposed antenna in maximum case is 29.5 mm × 52 mm ×  0.38 mm (2.8 $${{\varvec{\lambda}}}_{0}$$

λ

0

× 4.86$${{\varvec{\lambda}}}_{0}$$

λ

0

× 0.036$${{\varvec{\lambda}}}_{0}$$

λ

0

). Moreover, for Specific Absorption Rate (SAR) estimation, a three-layer spherical human head model (skin, skull, and the brain) is placed next to the arrays as the exposure source. The simulation results show that the performance of proposed antennas as low-SAR sources makes them ideal candidates for the safe usage and lack of impact of millimeter waves (mmW) on the human health. In all three cases of SAR simulations the value of SAR1g and SAR10g are below the standard limitations.
The giant panda is cryptic
Authors: Nokelainen Ossi , Scott-Samuel Nicholas E. , Nie Yonggang , Wei Fuwen , Caro Tim 
Published: October 2021

AbstractThe giant panda (Ailuropoda melanoleuca) is an iconic mammal, but the function of its black-and-white coloration is mysterious. Using photographs of giant pandas taken in the wild and state-of-the-art image analysis, we confirm the counterintuitive hypothesis that their coloration provides camouflage in their natural environment. The black fur blends into dark shades and tree trunks, whereas white fur matches foliage and snow when present, and intermediate pelage tones match rocks and ground. At longer viewing distances giant pandas show high edge disruption that breaks up their outline, and up close they rely more on background matching. The results are consistent across acuity-corrected canine, feline, and human vision models. We also show quantitatively that the species animal-to-background colour matching falls within the range of other species that are widely recognised as cryptic. Thus, their coloration is an adaptation to provide background matching in the visual environment in which they live and simultaneously to afford distance-dependent disruptive coloration, the latter of which constitutes the first computational evidence of this form of protective coloration in mammals.
Post-fire insect fauna explored by crown fermental traps in forests of the European Russia
Authors: Ruchin A. B. , Egorov L. V. , MacGowan I. , Makarkin V. N. , Antropov A. V. , Gornostaev N. G. , Khapugin A. A. , Dvořák L. , Esin M. N. 
Published: October 2021

AbstractWildfires considerably affect forest ecosystems. However, there is a lack of data on the post-fire status of insect communities in these ecosystems. This paper presents results of a study conducted in 2019 which considered the post-fire status of the insect fauna in a Protected Area, Mordovia State Nature Reserve (Republic of Mordovia, centre of European Russia), considered as regional hotspot of insect diversity in Mordovia. We sampled insects on intact (unburned, control) and fire-damaged (burnt in 2010) sites and compared the alpha-diversity between sites. In total, we sampled and analysed 16,861 specimens belonging to 11 insect orders, 51 families and 190 species. The largest orders represented in the samples were Coleoptera (95 species), Diptera (54 species), Hymenoptera (21 species), and Neuroptera (11 species). Other insect orders were represented by between one and four species. The largest four orders (Coleoptera, Lepidoptera, Diptera and Hymenoptera) represented 96.7% of all studied specimens. We found that in the ninth year after low intensity surface fire damage, the insect diversity had returned to a similar level to that of the control (unburned) sites. Sites damaged by crown wildfire differed considerably from other sites in terms of a negative impact on both species diversity and the number of specimens. This indicates the serious effect of the crown fires on the biodiversity and consequent long-term recovery of the damaged ecosystem.
Lipidomic profiling reveals biosynthetic relationships between phospholipids and diacylglycerol ethers in the deep-sea soft coral Paragorgia arborea
Authors: Imbs Andrey B. , Velansky Peter V. 
Published: October 2021

AbstractThe cold-water gorgonian coral Paragorgia arborea is considered as a foundation species of deep-sea ecosystems in the northern Atlantic and Pacific oceans. To advance lipidomic studies of deep-sea corals, molecular species compositions of diacylglycerol ethers (DAGE), which are specific storage lipids of corals, and structural glycerophospholipids (GPL) including ethanolamine, choline, inositol and serine GPL (PE, PC, PI, and PS, respectively) were analyzed in P. arborea by HPLC and tandem mass spectrometry. In DAGE molecules, alkyl groups (16:0, 14:0, and 18:1), polyunsaturated fatty acids (PUFA), and monounsaturated FA are mainly substituted the glycerol moiety at position sn-1, sn-2, and sn-3, respectively. The ether form (1-O-alkyl-2-acyl) predominates in PE and PC, while PI is comprised of the 1,2-diacyl form. Both ether and diacyl forms were observed in PS. At position sn-2, C20 PUFA are mainly attached to PC, but C24 PUFA, soft coral chemotaxonomic markers, concentrate in PS, PI, and PE. A comparison of non-polar parts of molecules has shown that DAGE, ether PE, and ether PC can originate from one set of 1-O-alkyl-2-acyl-sn-glycerols. Ether PE may be converted to ether PS by the base-exchange reaction. A diacylglycerol unit generated from phosphatidic acid can be a precursor for diacyl PS, PC, and PI. Thus, a lipidomic approach has confirmed the difference in biosynthetic origins between ether and diacyl lipids of deep-sea gorgonians.
Human influences shape the first spatially explicit national estimate of urban unowned cat abundance
Authors: McDonald Jennifer L. , Skillings Elizabeth 
Published: October 2021

AbstractGlobally, unowned cats are a common element of urban landscapes, and the focus of diverse fields of study due to welfare, conservation and public health concerns. However, their abundance and distribution are poorly understood at large spatial scales. Here, we use an Integrated Abundance Model to counter biases that are inherent in public records of unowned cat sightings to assess important drivers of their abundance from 162 sites across five urban towns and cities in England. We demonstrate that deprivation indices and human population densities contribute to the number of unowned cats. We provide the first spatially explicit estimates of expected distributions and abundance of unowned cats across a national scale and estimate the total UK urban unowned cat population to be 247,429 (95% credible interval: 157,153 to 365,793). Our results provide a new baseline and approach for studies on unowned cats and links to the importance of human-mediated effects.
Pharmacogenomics characterization of the MDM2 inhibitor MI-773 reveals candidate tumours and predictive biomarkers
Authors: Vuaroqueaux Vincent , Hendriks Hans R. , Al-Hasani Hoor , Peille Anne-Lise , Das Samayita , Fiebig Heinz-Herbert 
Published: October 2021

AbstractMI-773 is a recently developed small-molecule inhibitor of the mouse double minute 2 (MDM2) proto-oncogene. Preclinical data on the anti-tumour activity of MI-773 are limited and indicate that tumour cell lines (CLs) with mutatedTP53are more resistant to MI-773 than wild typeTP53. Here, we explored the compound’s therapeutic potential in vitro using a panel of 274 annotated CLs derived from a diversity of tumours. MI-773 exhibited a pronounced selectivity and moderate potency, with anti-tumour activity in the sub-micromolar range in about 15% of the CLs. The most sensitive tumour types were melanoma, sarcoma, renal and gastric cancers, leukaemia, and lymphoma. A COMPARE analysis showed that the profile of MI-773 was similar to that of Nutlin-3a, the first potent inhibitor of p53–MDM2 interactions, and, in addition, had a superior potency. In contrast, it poorly correlates with profiles of compounds targeting the p53 pathway with another mechanism of action. OMICS analyses confirmed that MI-773 was primarily active in CLs with wild typeTP53. In silico biomarker investigations revealed that theTP53mutation status plus the aggregated expression levels of 11 genes involved in the p53 signalling pathway predicted sensitivity or resistance of CLs to inhibitors of p53–MDM2 interactions reliably. The results obtained for MI-773 could help to refine the selection of cancer patients for therapy.
In vitro metabolic capacity of carbohydrate degradation by intestinal microbiota of adults and pre-frail elderly
Authors: An Ran , Wilms Ellen , Logtenberg Madelon J , van Trijp Mara P H , Schols Henk A , Masclee Ad A M , Smidt Hauke , Jonkers Daisy M A E , Zoetendal Erwin G 
Published: October 2021

Abstract
Globally increased life expectancy strongly triggered interest to delay the onset of frailty, which has been associated with alterations in compositional and functional characteristics of intestinal microbiota. In the current study, we used an in vitro batch incubation model to compare the metabolic capacity of the faecal microbiota of adults (n = 6) versus pre-frail elderly (n = 6) to degrade various glycosidic carbohydrates, including galacto-oligosaccharides, 2′-fucosyllactose, chicory fructo-oligosaccharides and inulin, and isomalto/malto-polysaccharides. The in vitro metabolic capacity was also compared with an in vivo GOS intervention study based on the same subjects. Analysis of 16S rRNA gene sequences and metabolites revealed distinct portions of variation in overall microbiota and metabolite composition during incubation being explained by individuality of the subjects and carbon source. In addition, the age group of the subjects also had significant impact on microbiota variation, carbohydrate degradation and metabolite production. This was accompanied by elevated increase in the relative abundance of Bifidobacterium in the microbiota of adults compared to that of pre-frail elderly and significantly decreased effectiveness to degrade galacto-oligosaccharides by the latter group. Altogether, the carbohydrate degradation in elderly was different compared to adults, with some carbohydrates showing decreased degradation rates. Longer interventions periods may be required to enhance bifidobacterial abundance in the microbiota of pre-frail elderly and thereby to obtain associated prebiotic health benefits.