bluuebunny/crossref_metadata_2025_split huggingface dataset:
The future of endangered crayfish in light of protected areas and habitat fragmentation
Authors: Pârvulescu Lucian , Iorgu Elena-Iulia , Zaharia Claudia , Ion Mihaela C. , Satmari Alina , Krapal Ana-Maria , Popa Oana-Paula , Miok Kristian , Petrescu Iorgu , Popa Luis-Ovidiu 
Published: September 2020

AbstractThe long-term survival of a species requires, among other things, gene flow between populations. Approaches for the evaluation of fragmentation in the frame of freshwater habitats consider only a small amount of the information that combined demography and geography are currently able to provide. This study addresses two species ofAustropotamobiuscrayfish in the light of population genetics, spatial ecology and protected areas of the Carpathians. Advancing the classical approaches, we defined ecological distances upon the rasterised river network as a surrogate of habitat resistance to migration, quantifying the deviations from the species´ suitability range for a set of relevant geospatial variables in each cell of the network. Molecular analyses revealed the populations of the twoAustropotamobiuscrayfish species are clearly distinct, lacking hybridisation. Comparing pairs of populations, we found, in some cases, a strong disagreement regarding genetic and ecological distances, potentially due to human-mediated translocations or the geophysical phenomena of regressive erosion, which may have led to unexpected colonisation routes. Protected areas were found to offer appropriate local habitat conditions but failed to ensure connectivity. The methodology applied in this study allowed us to quantify the contribution of each geospatial (environmental) variable to the overall effect of fragmentation, and we found that water quality was the most important variable. A multilevel approach proved to reveal a better understanding of drivers behind the distribution patterns, which can lead to more adequate conservation measures.
Automated detection of cribriform growth patterns in prostate histology images
Authors: Ambrosini Pierre , Hollemans Eva , Kweldam Charlotte F. , Leenders Geert J. L. H. van , Stallinga Sjoerd , Vos Frans 
Published: September 2020

AbstractCribriform growth patterns in prostate carcinoma are associated with poor prognosis. We aimed to introduce a deep learning method to detect such patterns automatically. To do so, convolutional neural network was trained to detect cribriform growth patterns on 128 prostate needle biopsies. Ensemble learning taking into account other tumor growth patterns during training was used to cope with heterogeneous and limited tumor tissue occurrences. ROC and FROC analyses were applied to assess network performance regarding detection of biopsies harboring cribriform growth pattern. The ROC analysis yielded a mean area under the curve up to 0.81. FROC analysis demonstrated a sensitivity of 0.9 for regions larger than $${0.0150}\,\hbox {mm}^{2}$$

0.0150

mm
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with on average 7.5 false positives. To benchmark method performance for intra-observer annotation variability, false positive and negative detections were re-evaluated by the pathologists. Pathologists considered 9% of the false positive regions as cribriform, and 11% as possibly cribriform; 44% of the false negative regions were not annotated as cribriform. As a final experiment, the network was also applied on a dataset of 60 biopsy regions annotated by 23 pathologists. With the cut-off reaching highest sensitivity, all images annotated as cribriform by at least 7/23 of the pathologists, were all detected as cribriform by the network and 9/60 of the images were detected as cribriform whereas no pathologist labelled them as such. In conclusion, the proposed deep learning method has high sensitivity for detecting cribriform growth patterns at the expense of a limited number of false positives. It can detect cribriform regions that are labelled as such by at least a minority of pathologists. Therefore, it could assist clinical decision making by suggesting suspicious regions.
Light and water treatment during the early grain filling stage regulates yield and aroma formation in aromatic rice
Authors: Li Yuzhan , Liang Luxin , Fu Xiaomeng , Gao Zifeng , Liu Hecheng , Tan Jiangtao , Potcho Mouloumdema Pouwedeou , Pan Shenggang , Tian Hua , Duan Meiyang , Tang Xiangru , Mo Zhaowen 
Published: September 2020

AbstractThe effect of light and water on aromatic rice remain largely unclear. A pot experiment was conducted to investigate the influences of light-water treatments (CK: natural light and well-watered conditions, WS: natural light and water-stressed conditions, LL: low light and well-watered conditions, LL-WS: low light and water-stressed treatment) on yield and 2-acetyl-1-pyrroline (2AP) formation in aromatic rice. Compared with CK, the light-water treatments decreased grain yield (10.32–39.19%) due to reductions in the filled grain percentage and total dry weight, in the regulation of biomass distribution, and in the attributes of gas exchange and antioxidant response parameters. The 2AP content in grains increased in the LL treatment (5.08–16.32%) but decreased in the WS treatment compared with that in CK. The changes in 2AP were associated with changes in 2AP formation-related traits and element content. Low light and water stress led to yield declines in aromatic rice, but low light alleviated the decrease in 2AP content caused by water stress.
The diel pattern in harbour porpoise clicking behaviour is not a response to prey activity
Authors: Osiecka Anna N. , Jones Owen , Wahlberg Magnus 
Published: September 2020

AbstractWild harbour porpoises (Phocoena phocoena) mainly forage during the night and, because they rely on echolocation to detect their prey, this is also when they are most acoustically active. It has been hypothesised that this activity pattern is a response to the diel behaviour of their major prey species. To test this hypothesis, we monitored the acoustic activity of two captive harbour porpoises held in a net pen continuously during a full year and fed by their human keepers during daylight hours, thus removing the influence of prey activity. The porpoises were exposed to similar temperature and ambient light conditions as free-ranging animals living in the same region. Throughout the year, there was a pronounced diel pattern in acoustic activity of the porpoises, with significantly greater activity at night, and a clear peak around sunrise and sunset throughout the year. Clicking activity was not dependent on lunar illumination or water level. Because the porpoises in the pen are fed and trained during daylight hours, the results indicate that factors other than fish behaviour are strongly influencing the diel clicking behaviour pattern of the species.
Paddy fields located in water storage zones could take over the wetland plant community
Authors: Osawa Takeshi , Nishida Takaaki , Oka Takashi 
Published: September 2020

AbstractLand use change could affect not only local species richness but also community assemblies. Essentially, the possible patterns of plant community assemblies are nonrandom species loss (nestedness) and species turnover. Plant community assemblies in human-mediated land use have a combination of both nestedness and turnover. This is because of historical effects that cause nonrandom species loss due to previous and/or original habitat quality and because of direct effects of human activities that cause species turnover. We investigated the complexity of the process of plant community assemblage in a paddy field, which is a typical agricultural land use in the monsoon season in central Japan. Using multi-temporal plant monitoring records, we tested the relationship between the ratio of species nestedness/turnover through multi-temporal and both the original habitat conditions and the extent of human modification. The findings revealed that paddy fields that originated from wetland habitat had a high nestedness ratio, whereas paddy fields that were largely consolidated had a high turnover ratio. Thus, we could divide the community assembly processes in human-mediated land use based on original habitat conditions and human activities. This concept could help land managers establish conservation and/or restoration plans that take into account community assembly.
An improved microwave assisted sequential extraction method followed by spectrometric analysis for metal distribution determination in South African coal samples
Authors: Mketo Nomvano , Nomngongo Philiswa N. 
Published: September 2020

AbstractSome metal pollutants are corrosive in nature, are associated with fouling and slagging challenges of the coal boilers, are highly volatile and might cause air pollution and are catalyst poisoners during Fischer–Tropsch catalytic reaction. Therefore, this work describes an improved microwave-assisted sequential extraction (MW-ASE) method followed by ICP-OES/MS analysis for metal distribution determination in South African coal samples. The multivariate optimum conditions for each sequential step were 0.1 g, 200 °C and 5 min for sample amount, microwave temperature and extraction time, respectively. Under the optimum conditions, Ga, Sr and Ba were the only metals that showed solubility towards water, therefore, these metals are classified as highly mobile and eco-toxic under wet environmental conditions. Additionally, all the investigated metals showed solubility towards acidic conditions (HCl and HNO3). These results suggest that, most metal ions are predominantly bonded to sulphate, sulphide, and carbonate coal minerals. Alternatively, Ce, Cr and Y showed total extraction recoveries of ≤ 90%, confirming their strong affinity towards quartz coal minerals. In overall, the proposed MW-ASE method reported short extraction time (0.34 h), environmentally friendly reagents (H2O and diluted H2O2) and rapid multivariate optimization with acceptable extraction efficiencies (79–98%) and reproducibility (RSD ≤ 5%).
Deposits from evaporating emulsion drops
Authors: Bittermann M. R. , Deblais A. , Lépinay S. , Bonn D. , Shahidzadeh N. 
Published: September 2020

AbstractThe processes in which droplets evaporate from solid surfaces, leaving behind distinct deposition patterns, have been studied extensively for variety of solutions. In this work, by combining different microscopy techniques (confocal fluorescence, video and Raman) we investigate pattern formation and evaporation-induced phase change in drying oil-in-water emulsion drops. This combination of techniques allows us to perform drop shape analysis while visualizing the internal emulsion structure simultaneously. We observe that drying of the continuous water phase of emulsion drops on hydrophilic surfaces favors the formation of ring-like zones depleted of oil droplets at the contact line, which originate from geometrical confinement of oil droplets by the meniscus. From such a depletion zone, a “coffee ring” composed of surfactant molecules forms as the water evaporates. On all surfaces drying induces emulsion destabilization by coalescence of oil droplets, commencing at the drop periphery. For hydrophobic surfaces, the coalescence of the oil droplets leads to a uniform oil film spreading out from the initial contact line. The evaporation dynamics of these composite drops indicate that the water in the continuous phase of the emulsion drops evaporates predominantly by diffusion through the vapor, showing no large differences to the evaporation of simple water drops.
The enhanced activity of Pt–Ce nanoalloy for oxygen electroreduction
Authors: Qin Juan , Zhang Yafeng , Leng Deying , Yin Feng 
Published: September 2020

AbstractThe widespread use of low-temperature polymer electrolyte membrane fuel cells for clean energy source require significant reductions in the amount of expensive electrocatalyst Pt for the oxygen reduction reaction (ORR). Pt based binary alloys are promising materials for more active and stable electrocatalysts. In this paper, we studied Pt–Ce nanoalloy, which was prepared by hydrogen reduction techniques as ORR electrocatalysts. Among all PtCe alloy catalysts, the PtCe/C-800 ℃ shows superior ORR activity, stability and durability compared to commercial Pt/C. The results presented in this paper will provide the future perspectives to research based on Pt-RE (RE = Ce, Dy, Gd, Er, Sm, and La) alloy as an novel electrocatalyst for various electrocatalytic reactions.
Foveated near-eye display using computational holography
Authors: Cem Ali , Hedili M. Kivanc , Ulusoy Erdem , Urey Hakan 
Published: September 2020

AbstractHolographic display is the only technology that can offer true 3D with all the required depth cues. Holographic head-worn displays (HWD) can provide continuous depth planes with the correct stereoscopic disparity for a comfortable 3D experience. Existing HWD approaches have small field-of-view (FOV) and small exit pupil size, which are limited by the spatial light modulator (SLM). Conventional holographic HWDs are limited to about 20° × 11° FOV using a 4 K SLM panel and have fixed FOV. We present a new optical architecture that can overcome those limitations and substantially extend the FOV supported by the SLM. Our architecture, which does not contain any moving parts, automatically follows the gaze of the viewer’s pupil. Moreover, it mimics human vision by providing varying resolution across the FOV resulting in better utilization of the available space-bandwidth product of the SLM. We propose a system that can provide 28° × 28° instantaneous FOV within an extended FOV (the field of view that is covered by steering the instantaneous FOV in space) of 60° × 40° using a 4 K SLM, effectively providing a total enhancement of > 3 × in instantaneous FOV area, > 10 × in extended FOV area and the space-bandwidth product. We demonstrated 20° × 20° instantaneous FOV and 40° × 20° extended FOV in the experiments.
Humoral immune response and delayed-type hypersensitivity in rabbits infected with Trypanosoma equiperdum
Authors: Di Febo Tiziana , Krasteva Ivanka , Bonfini Barbara , Tittarelli Manuela , Matteucci Osvaldo , Orsini Gianluca , Rossi Emanuela , Podaliri Vulpiani Michele , Rodomonti Diamante , Iannetti Luigi , Luciani Mirella 
Published: September 2020

AbstractTrypanosoma equiperdum is the causative agent of dourine, a parasitic venereal disease of equids. In this work, rabbits were infected with T. equiperdum strain OVI; serological tests (complement fixation test, ELISA and immunoblotting), used for the diagnosis of dourine in horses, were applied to study rabbit humoral immune response and to characterise T. equiperdum antigen pattern recognised by antibodies from infected rabbits. Moreover a protein extract of T. equiperdum strain OVI was produced and tested in skin tests on infected rabbits to detect the cell-mediated response induced by T. equiperdum, in order to evaluate its use in the field diagnosis of dourine. Sera of infected rabbits recognized in immunoblotting Trypanosoma protein bands with molecular weight below 37 kDa, providing a serological response comparable with that already observed in dourine infected horses. Moreover the trypanosome protein extract was capable to produce in vivo delayed-type hypersensitivity (DHT Type IV) in rabbits and proved itself to be non-toxic and non-sensitizing.
Investigating altered brain development in infants with congenital heart disease using tensor-based morphometry
Authors: Ng Isabel H. X. , Bonthrone Alexandra F. , Kelly Christopher J. , Cordero-Grande Lucilio , Hughes Emer J. , Price Anthony N. , Hutter Jana , Victor Suresh , Schuh Andreas , Rueckert Daniel , Hajnal Joseph V. , Simpson John , Edwards A. David , Rutherford Mary A. , Batalle Dafnis , Counsell Serena J. 
Published: September 2020

AbstractMagnetic resonance (MR) imaging studies have demonstrated reduced global and regional brain volumes in infants with congenital heart disease (CHD). This study aimed to provide a more detailed evaluation of altered structural brain development in newborn infants with CHD compared to healthy controls using tensor-based morphometry (TBM). We compared brain development in 64 infants with CHD to 192 age- and sex-matched healthy controls. T2-weighted MR images obtained prior to surgery were analysed to compare voxel-wise differences in structure across the whole brain between groups. Cerebral oxygen delivery (CDO2) was measured in infants with CHD (n = 49) using phase contrast MR imaging and the relationship between CDO2 and voxel-wise brain structure was assessed using TBM. After correcting for global scaling differences, clusters of significant volume reduction in infants with CHD were demonstrated bilaterally within the basal ganglia, thalami, corpus callosum, occipital, temporal, parietal and frontal lobes, and right hippocampus (p < 0.025 after family-wise error correction). Clusters of significant volume expansion in infants with CHD were identified in cerebrospinal fluid spaces (p < 0.025). After correcting for global brain size, there was no significant association between voxel-wise brain structure and CDO2. This study localizes abnormal brain development in infants with CHD, identifying areas of particular vulnerability.
A biocomposite-based rapid sampling assay for circulating cell-free DNA in liquid biopsy samples from human cancers
Authors: Koo Bonhan , Jun Eunsung , Liu Huifang , Kim Eo Jin , Park Yun-Yong , Lim Seok-Byung , Kim Song Cheol , Shin Yong 
Published: September 2020

AbstractCell-free nucleic acids (cfNAs) in liquid biopsy samples are emerging as important biomarkers for cancer diagnosis and monitoring, and for predicting treatment outcomes. Many cfNA isolation methods have been developed recently. However, most of these techniques are time-consuming, complex, require large equipment, and yield low-purity cfNAs because the genetic background of normal cells is amplified during cell lysis, which limits their clinical application. Here, we report a rapid and simple cfNA sampling platform that can overcome the limitations of conventional methods. We synthesised a biocomposite by combining amine-modified diatomaceous earth (DE) and cucurbituril (CB). The biocomposite platform showed high capture efficiency (86.78–90.26%) with genomic DNA and amplified DNA products (777, 525 and 150 bp). The biocomposite platform allowed the isolation of high purity and quantity cfDNAs from the plasma of 13 cancer patients (three colorectal cancer and ten pancreatic cancer samples) without requiring a lysis step or special equipment. The biocomposite platform may be useful to isolate cfNAs for the diagnosis and treatment of cancers in clinical applications.
Interaction dynamics and site-specific electronic recognition of DNA-nicks with 2D solid-state nanopores
Authors: Athreya Nagendra , Milenkovic Olgica , Leburton Jean-Pierre 
Published: September 2020

AbstractSingle-stranded breaks in the DNA backbone caused by many endogenous and exogenous agents often lead to double-stranded breaks that are known causes of chromosomal instabilities leading to copious diseases. We describe a label-free detection technique using two-dimensional (2D) solid-state nanopore field-effect transistors (FETs) to sense and map site-specific nicks in the DNA backbone. We use all-atom molecular dynamics simulations coupled with electronic transport modeling to illustrate the 2D membrane device capability to sense minute structural changes of any translocating biomolecules via their in-plane electronic sheet current signatures, whereas Van der Waals analyses explain the distinct hydrophobic interactions between various DNA-nick types with graphene and MoS2 nanopore membranes. Specifically, we describe the atypical unzipping behavior of DNA strands caused by the biomolecule sticking at nicked site in the graphene nanopore, under the influence of voltage-specific translocations.
CheXaid: deep learning assistance for physician diagnosis of tuberculosis using chest x-rays in patients with HIV
Authors: Rajpurkar Pranav , O’Connell Chloe , Schechter Amit , Asnani Nishit , Li Jason , Kiani Amirhossein , Ball Robyn L. , Mendelson Marc , Maartens Gary , van Hoving Daniël J. , Griesel Rulan , Ng Andrew Y. , Boyles Tom H. , Lungren Matthew P. 
Published: September 2020

AbstractTuberculosis (TB) is the leading cause of preventable death in HIV-positive patients, and yet often remains undiagnosed and untreated. Chest x-ray is often used to assist in diagnosis, yet this presents additional challenges due to atypical radiographic presentation and radiologist shortages in regions where co-infection is most common. We developed a deep learning algorithm to diagnose TB using clinical information and chest x-ray images from 677 HIV-positive patients with suspected TB from two hospitals in South Africa. We then sought to determine whether the algorithm could assist clinicians in the diagnosis of TB in HIV-positive patients as a web-based diagnostic assistant. Use of the algorithm resulted in a modest but statistically significant improvement in clinician accuracy (p = 0.002), increasing the mean clinician accuracy from 0.60 (95% CI 0.57, 0.63) without assistance to 0.65 (95% CI 0.60, 0.70) with assistance. However, the accuracy of assisted clinicians was significantly lower (p < 0.001) than that of the stand-alone algorithm, which had an accuracy of 0.79 (95% CI 0.77, 0.82) on the same unseen test cases. These results suggest that deep learning assistance may improve clinician accuracy in TB diagnosis using chest x-rays, which would be valuable in settings with a high burden of HIV/TB co-infection. Moreover, the high accuracy of the stand-alone algorithm suggests a potential value particularly in settings with a scarcity of radiological expertise.
Discovery of four Noggin genes in lampreys suggests two rounds of ancient genome duplication
Authors: Ermakova Galina V. , Kucheryavyy Alexander V. , Zaraisky Andrey G. , Bayramov Andrey V. 
Published: September 2020

AbstractThe secreted protein Noggin1 was the first discovered natural embryonic inducer produced by cells of the Spemann organizer. Thereafter, it was shown that vertebrates have a whole family of Noggin genes with different expression patterns and functional properties. For example, Noggin1 and Noggin2 inhibit the activity of BMP, Nodal/Activin and Wnt-beta-catenin signalling, while Noggin4 cannot suppress BMP but specifically modulates Wnt signalling. In this work, we described and investigated phylogeny and expression patterns of four Noggin genes in lampreys, which represent the most basally divergent group of extant vertebrates, the cyclostomes, belonging to the superclass Agnatha. Assuming that lampreys have Noggin homologues in all representatives of another superclass of vertebrates, the Gnathostomata, we propose a model for Noggin family evolution in vertebrates. This model is in agreement with the hypotheses suggesting two rounds of genome duplication in the ancestor of vertebrates before the divergence of Agnatha and Gnathostomata.