bluuebunny/crossref_metadata_2025 huggingface dataset:
Remote Sensing‐Based Modeling of the Bathymetry and Water Storage for Channel‐Type Reservoirs Worldwide
Authors: Liu Kai , Song Chunqiao , Wang Jida , Ke Linghong , Zhu Yunqiang , Zhu Jingying , Ma Ronghua , Luo Zhu
Published: October 2020

Estimations of reservoir bathymetry and storage are of great significance due to their substantial impacts on hydrological processes and water resource management. However, existing approaches for reservoir bathymetry construction often rely on field measurements, which restricts their application at regional and global scales. This study proposes a novel Approach for Determining the BAthymetry and water storage of channel‐type Reservoirs, hereafter referred to as ADBAR, for which only open‐access digital elevation model (DEM) and satellite images are required. The basic idea of ADBAR is to utilize the geomorphological similarity and topographical continuity of the reservoir inundation area with its lateral valleys and upstream/downstream regions to predict underwater bathymetry. Forty‐eight reservoirs with different topographic and geometric characteristics were selected for method validation. The selected reservoirs were all impounded after the year 2000, so the modeled reservoir bathymetry can be validated by the “reference” reservoir storage calculated using the exposed topography in SRTM DEM and the mapped water extents from spectral images. The difference between the estimated and reference storages is about 13% on average. Furthermore, the modeled results in two selected basins with dense reservoir distributions, the Upper Yellow River Basin in China and the Tocantins River Basin in Brazil, are comparable with the documented effective storage capacities. The validations for both individual reservoirs and the two large basins demonstrate that ADBAR is a robust tool for estimating reservoir bathymetries and storage capacities and thus facilitates the modeling of reservoir impacts on water budgets at large and global scales.
Influence of Capillarity on Relative Permeability in Fractional Flows
Authors: Zou Shuangmei , Liu Yang , Cai Jianchao , Armstrong Ryan T.
Published: October 2020

The effect of capillary pressure on multiphase flow is described by the capillary pressure gradient term in the fractional flow equation. This term is typically neglected during core‐flooding experiments, as it is not easily accessible. However, the capillary pressure is not constant during core flooding owing to a capillary pressure discontinuity at the core outlet. By imaging spatial fluid distributions under two‐phase steady‐state flow, we determine in situ phase saturations and capillary pressures from interfacial curvature measurements along an entire core, thus achieving the assessment of the capillary pressure gradient and its influence on multiphase flow. We demonstrate how the pore‐scale capillary pressure gradient affects multiphase flow and, in turn, the core‐scale relative permeability measurements. Further, an alternative approach to determining relative permeability from a single fractional flow experiment is proposed. The approach provides a range of relative permeabilities for a single fractional flow experiment and does not require capillary‐end correction, as the formulation directly accounts for the effect of capillary pressure on the flow.
Quantifying the Effect of Subcritical Water Repellency on Sorptivity: A Physically Based Model
Authors: Shillito R. M. , Berli M. , Ghezzehei T. A.
Published: October 2020

Soil water wettability or water repellency is a phenomenon that can affect infiltration and, ultimately, runoff. Thus, there is a need to develop a model that can quantitatively capture the influence of water repellency on infiltration in a physically meaningful way and within the framework of existing infiltration theory. The analytical model developed in this study relates soil sorptivity (an infiltration parameter) with contact angle (a direct measure of water repellency) for variably saturated media. The model was validated with laboratory experiments using a silica sand of known properties treated to produce controlled degrees of water repellency. The measured contact angle and sorptivity values closely matched the model‐predicted values. Further, the relationship between the frequently used water drop penetration time test (used to assess water repellency) and sorptivity was illustrated. Finally, the direct impact of water repellency on saturated hydraulic conductivity was investigated due to its role in infiltration equations and to shed light on inconsistent field observations. It was found that water repellency had minimal effect on the saturated hydraulic conductivity of structureless sand. A quantitative model for infiltration incorporating the effect of water repellency is particularly important for post‐fire hydrologic modeling of burned areas exhibiting water repellent soils.
Charting Pathways Toward Sustainability for Aquifers Supporting Irrigated Agriculture
Authors: Butler J. J. , Bohling G. C. , Whittemore D. O. , Wilson B. B.
Published: October 2020

The question of how much longer groundwater can support large‐scale agricultural production is one of global significance. Many of the world's regional aquifers supporting irrigated agriculture are on a trajectory toward resource depletion. In the absence of alternative water supplies, the only viable near‐term (few to several decades) option for redirecting these heavily stressed systems on to more sustainable paths is to reduce pumping. The key issues therefore become how much should pumping be reduced to significantly extend an aquifer's lifetime and what is the likelihood of attaining a sustainable condition. We have developed a water‐balance approach to glean insights into these issues and chart pathways toward more sustainable states. An aquifer's response to pumping reductions heavily depends on the net inflow component of an aquifer's water budget, both in terms of its magnitude and how it decreases with time in response to reductions. If a reduction leads to a pumping rate that is above net inflow, the aquifer lifespan can often be extended by a factor of two or more, but depletion will be the final outcome. In contrast, if a reduction results in a pumping rate more than 10% below net inflow, a lengthy period of apparent sustainability will result. In that case, the aquifer lifespan may be extended long enough so that other options, such as large‐scale water transfers or development of more sustainable crop mixes, become viable. These concepts are demonstrated using examples based on an ongoing experiment in pumping reductions in the High Plains aquifer.
A microfluidic platform for cultivating ovarian cancer spheroids and testing their responses to chemotherapies
Authors: Dadgar Neda , Gonzalez-Suarez Alan M. , Fattahi Pouria , Hou Xiaonan , Weroha John S. , Gaspar-Maia Alexandre , Stybayeva Gulnaz , Revzin Alexander
Published: October 2020

There is increasing interest in utilizing in vitro cultures as patient avatars to develop personalized treatment for cancer. Typical cultures utilize Matrigel-coated plates and media to promote the proliferation of cancer cells as spheroids or tumor explants. However, standard culture conditions operate in large volumes and require a high concentration of cancer cells to initiate this process. Other limitations include variability in the ability to successfully establish a stable line and inconsistency in the dimensions of these microcancers for in vivo drug response measurements. This paper explored the utility of microfluidics in the cultivation of cancer cell spheroids. Six patient-derived xenograft (PDX) tumors of high-grade serous ovarian cancer were used as the source material to demonstrate that viability and epithelial marker expression in the microfluidic cultures was superior to that of Matrigel or large volume 3D cultures. To further demonstrate the potential for miniaturization and multiplexing, we fabricated multichamber microfluidic devices with integrated microvalves to enable serial seeding of several chambers followed by parallel testing of several drug concentrations. These valve-enabled microfluidic devices permitted the formation of spheroids and testing of seven drug concentrations with as few as 100,000 cancer cells per device. Overall, we demonstrate the feasibility of maintaining difficul-to-culture primary cancer cells and testing drugs in a microfluidic device. This microfluidic platform may be ideal for drug testing and personalized therapy when tumor material is limited, such as following the acquisition of biopsy specimens obtained by fine-needle aspiration.
Exosome-mediated metabolic reprogramming: the emerging role in tumor microenvironment remodeling and its influence on cancer progression
Authors: Yang Enli , Wang Xuan , Gong Zhiyuan , Yu Miao , Wu Haiwei , Zhang Dongsheng
Published: October 2020

Metabolic reprogramming is reported to be one of the hallmarks of cancer, which is an adaptive mechanism by which fast-growing cancer cells adapt to their increasing energy demands. Recently, extracellular vesicles (EVs) known as exosomes have been recognized as crucial signaling mediators in regulating the tumor microenvironment (TME). Meanwhile, the TME is a highly heterogeneous ecosystem incorporating cancer cells, fibroblasts, adipocytes, endothelial cells, mesenchymal stem cells, and extracellular matrix. Accumulated evidence indicates that exosomes may transfer biologically functional molecules to the recipient cells, which facilitate cancer progression, angiogenesis, metastasis, drug resistance, and immunosuppression by reprogramming the metabolism of cancer cells and their surrounding stromal cells. In this review, we present the role of exosomes in the TME and the underlying mechanism of how exosomes exacerbate tumor development through metabolic reprogramming. In addition, we will also discuss the potential role of exosomes targeting metabolic process as biomarkers for tumor diagnosis and prognosis, and exosomes-mediated metabolic reprogramming as potential targets for cancer therapy. Furthermore, a better understanding of the link between exosomes and metabolic reprogramming, and their impact on cancer progression, would provide novel insights for cancer prevention and treatment in the future.
Niche differentiation and evolution of the wood decay machinery in the invasive fungus Serpula lacrymans
Authors: Hess Jaqueline , Balasundaram Sudhagar V , Bakkemo Renee I , Drula Elodie , Henrissat Bernard , Högberg Nils , Eastwood Daniel , Skrede Inger
Published: October 2020

Ecological niche breadth and the mechanisms facilitating its evolution are fundamental to understanding adaptation to changing environments, persistence of generalist and specialist lineages and the formation of new species. Woody substrates are structurally complex resources utilized by organisms with specialized decay machinery. Wood-decaying fungi represent ideal model systems to study evolution of niche breadth, as they vary greatly in their host range and preferred decay stage of the substrate. In order to dissect the genetic basis for niche specialization in the invasive brown rot fungus Serpula lacrymans, we used phenotyping and integrative analysis of phylogenomic and transcriptomic data to compare this species to wild relatives in the Serpulaceae with a range of specialist to generalist decay strategies. Our results indicate specialist species have rewired regulatory networks active during wood decay towards decreased reliance on enzymatic machinery, and therefore nitrogen-intensive decay components. This shift was likely accompanied with adaptation to a narrow tree line habitat and switch to a pioneer decomposer strategy, both requiring rapid colonization of a nitrogen-limited substrate. Among substrate specialists with narrow niches, we also found evidence for pathways facilitating reversal to generalism, highlighting how evolution may move along different axes of niche space.
Epigenetic perspective on the role of brain-derived neurotrophic factor in burnout
Authors: Bakusic Jelena , Ghosh Manosij , Polli Andrea , Bekaert Bram , Schaufeli Wilmar , Claes Stephan , Godderis Lode
Published: October 2020

Brain-derived neurotrophic factor (BDNF) plays a potential role in the neurobiology of burnout, but there are no studies investigating the underlying genetic and epigenetic mechanisms. Our aim is to further explore the role of BDNF in burnout, by focusing on the Val66Met polymorphism and methylation patterns of the BDNF gene and serum BDNF (sBDNF) protein expression. We conducted a cross-sectional study by recruiting 129 individuals (59 with burnout and 70 healthy controls). Participants underwent a clinical interview, psychological assessment and blood sample collection. Polymorphism and DNA methylation were measured on DNA from whole blood, using pyrosequencing and sBDNF levels were measured using ELISA. We found significantly increased methylation of promoter I and IV in the burnout group, which also correlated with burnout symptoms. In addition, DNA methylation of promoter I had a significant negative effect on sBDNF. For DNA methylation of exon IX, we did not find a significant difference between the groups, nor associations with sBDNF. The Val66Met polymorphism neither differed between groups, nor was it associated with sBDNF levels. Finally, we did not observe differences in sBDNF level between the groups. Interestingly, we observed a significant negative association between depressive symptoms and sBDNF levels. The current study is the first to show that BDNF DNA methylation changes might play an important role in downregulation of the BDNF protein levels in burnout. The presence of depressive symptoms might have an additional impact on these changes.
Solution-processable integrated CMOS circuits based on colloidal CuInSe2 quantum dots
Authors: Yun Hyeong Jin , Lim Jaehoon , Roh Jeongkyun , Neo Darren Chi Jin , Law Matt , Klimov Victor I.
Published: October 2020

The emerging technology of colloidal quantum dot electronics provides an opportunity for combining the advantages of well-understood inorganic semiconductors with the chemical processability of molecular systems. So far, most research on quantum dot electronic devices has focused on materials based on Pb- and Cd chalcogenides. In addition to environmental concerns associated with the presence of toxic metals, these quantum dots are not well suited for applications in CMOS circuits due to difficulties in integrating complementary n- and p-channel transistors in a common quantum dot active layer. Here, we demonstrate that by using heavy-metal-free CuInSe2 quantum dots, we can address the problem of toxicity and simultaneously achieve straightforward integration of complimentary devices to prepare functional CMOS circuits. Specifically, utilizing the same spin-coated layer of CuInSe2 quantum dots, we realize both p- and n-channel transistors and demonstrate well-behaved integrated logic circuits with low switching voltages compatible with standard CMOS electronics.
Hsc70/Stub1 promotes the removal of individual oxidatively stressed peroxisomes
Authors: Chen Bo-Hua , Chang Yao-Jen , Lin Steven , Yang Wei Yuan
Published: October 2020

Peroxisomes perform beta-oxidation of branched and very-long chain fatty acids, which leads to the formation of reactive oxygen species (ROS) within the peroxisomal lumen. Peroxisomes are therefore prone to ROS-mediated damages. Here, using light to specifically and acutely induce ROS formation within the peroxisomal lumen, we find that cells individually remove ROS-stressed peroxisomes through ubiquitin-dependent pexophagy. Heat shock protein 70 s mediates the translocation of the ubiquitin E3 ligase Stub1 (STIP1 Homology and U-Box Containing Protein 1) onto oxidatively-stressed peroxisomes to promote their selective ubiquitination and autophagic degradation. Artificially targeting Stub1 to healthy peroxisomes is sufficient to trigger pexophagy, suggesting a key role Stub1 plays in regulating peroxisome quality. We further determine that Stub1 mutants found in Ataxia patients are defective in pexophagy induction. Dysfunctional peroxisomal quality control may therefore contribute to the development of Ataxia.
Direct C(sp2)–H alkylation of unactivated arenes enabled by photoinduced Pd catalysis
Authors: Kim Daeun , Lee Geun Seok , Kim Dongwook , Hong Soon Hyeok
Published: October 2020

Despite the fundamental importance of efficient and selective synthesis of widely useful alkylarenes, the direct catalytic C(sp2)–H alkylation of unactivated arenes with a readily available alkyl halide remains elusive. Here, we report the catalytic C(sp2)–H alkylation reactions of unactivated arenes with alkyl bromides via visible-light induced Pd catalysis. The reaction proceeds smoothly under mild conditions without any skeletal rearrangement of the alkyl groups. The direct syntheses of structurally diverse linear and branched alkylarenes, including the late-stage phenylation of biologically active molecules and an orthogonal one-pot sequential Pd-catalyzed C–C bond-forming reaction, are achieved with exclusive chemoselectivity and exceptional functional group tolerance. Comprehensive mechanistic investigations through a combination of experimental and computational methods reveal a distinguishable Pd(0)/Pd(I) redox catalytic cycle and the origin of the counter-intuitive reactivity differences among alkyl halides.
Automated microfluidic platform for dynamic and combinatorial drug screening of tumor organoids
Authors: Schuster Brooke , Junkin Michael , Kashaf Sara Saheb , Romero-Calvo Isabel , Kirby Kori , Matthews Jonathan , Weber Christopher R. , Rzhetsky Andrey , White Kevin P. , Tay Savaş
Published: October 2020

Three-dimensional (3D) cell culture technologies, such as organoids, are physiologically relevant models for basic and clinical applications. Automated microfluidics offers advantages in high-throughput and precision analysis of cells but is not yet compatible with organoids. Here, we present an automated, high-throughput, microfluidic 3D organoid culture and analysis system to facilitate preclinical research and personalized therapies. Our system provides combinatorial and dynamic drug treatments to hundreds of cultures and enables real-time analysis of organoids. We validate our system by performing individual, combinatorial, and sequential drug screens on human-derived pancreatic tumor organoids. We observe significant differences in the response of individual patient-based organoids to drug treatments and find that temporally-modified drug treatments can be more effective than constant-dose monotherapy or combination therapy in vitro. This integrated platform advances organoids models to screen and mirror real patient treatment courses with potential to facilitate treatment decisions for personalized therapy.
Author Correction: In-vivo vascular application via ultra-fast bioprinting for future 5D personalised nanomedicine
Authors: Foresti Ruben , Rossi Stefano , Pinelli Silvana , Alinovi Rossella , Sciancalepore Corrado , Delmonte Nicola , Selleri Stefano , Caffarra Cristina , Raposio Edoardo , Macaluso Guido , Macaluso Claudio , Freyrie Antonio , Miragoli Michele , Perini Paolo
Published: October 2020

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Geometric morphometric wing analysis represents a robust tool to identify female mosquitoes (Diptera: Culicidae) in Germany
Authors: Sauer F. G. , Jaworski L. , Erdbeer L. , Heitmann A. , Schmidt-Chanasit J. , Kiel E. , Lühken R.
Published: October 2020

Accurate species identification is the prerequisite to assess the relevance of mosquito specimens, but is often hindered by missing or damaged morphological features. The present study analyses the applicability of wing geometric morphometrics as a low-cost and practical alternative to identify native mosquitoes in Germany. Wing pictures were collected for 502 female mosquitoes of five genera and 19 species from 80 sampling sites. The reliable species identification based on interspecific wing geometry of 18 landmarks per specimen was tested. Leave-one-out cross validation revealed an overall accuracy of 99% for the genus and 90% for the species identification. Misidentifications were mainly due to three pairings ofAedesspecies:Aedes annulipesvs.Aedes cantans,Aedes cinereusvs.Aedes rossicusandAedes communisvs.Aedes punctor.Cytochrome oxidase subunit I (COI) gene region was sequenced to validate the morphological and morphometric identification. Similar to the results of the morphometric analysis, the same problematic threeAedes-pairs clustered, but most other species could be well separated. Overall, our study underpins that morphometric wing analysis is a robust tool for reliable mosquito identification, which reach the accuracy of COI barcoding.
Split-cube-resonator-based metamaterials for polarization-selective asymmetric perfect absorption
Authors: Tsilipakos Odysseas , Xomalis Angelos , Kenanakis George , Farsari Maria , Soukoulis Costas M. , Economou Eleftherios N. , Kafesaki Maria
Published: October 2020

A split-cube-resonator-based metamaterial structure that can act as a polarization- and direction-selective perfect absorber for the infrared region is theoretically and experimentally demonstrated. The structure, fabricated by direct laser writing and electroless silver plating, is comprised of four layers of conductively-coupled split-cube magnetic resonators, appropriately rotated to each other to bestow the desired electromagnetic properties. We show narrowband polarization-selective perfect absorption when the structure is illuminated from one side; the situation is reversed when illuminating from the other side, with the orthogonal linear polarization being absorbed. The absorption peak can be tuned in a wide frequency range by a sparser or denser arrangement of the split cube resonators, allowing to cover the entire atmospheric transparency window. The proposed metamaterial structure can find applications in polarization-selective thermal emission at the IR atmospheric transparency window for radiative cooling, in cost-effective infrared sensing devices, and in narrowband filters and linear polarizers in reflection mode.
Selenium and silica nanostructure-based recovery of strawberry plants subjected to drought stress
Authors: Zahedi Seyed Morteza , Moharrami Faezeh , Sarikhani Saadat , Padervand Mohsen
Published: October 2020

Drought is an important environmental stress that has negative effects on plant growth leading to a reduction in yield. In this study, the positive role of nanoparticles of SiO2, Se, and Se/SiO2 (SiO2-NPs, Se-NPs and Se/SiO2-NPs) has been investigated in modulating negative effects of drought on the growth and yield of strawberry plants. Spraying of solutions containing nanoparticles of SiO2, Se, and Se/SiO2 (50 and 100 mg L−1) improved the growth and yield parameters of strawberry plants grown under normal and drought stress conditions (30, 60, and 100%FC). Plants treated with Se/SiO2 (100 mg L−1) preserved more of their photosynthetic pigments compared with other treated plants and presented higher levels of key osmolytes such as carbohydrate and proline. This treatment also increased relative water content (RWC), membrane stability index (MSI) and water use efficiency (WUE). In addition, exogenous spraying of Se/SiO2 increased drought tolerance through increasing the activity of antioxidant enzymes including catalase (CAT), ascorbate peroxidase (APX), guaiacol peroxidase (GPX) and superoxide dismutase (SOD) as well as decreasing lipid peroxidation and hydrogen peroxide (H2O2) content. Increase in biochemical parameters of fruits such as anthocyanin, total phenolic compounds (TPC), vitamin C and antioxidant activity (DPPH) in strawberry plants treated with Se/SiO2 under drought stress revealed the positive effects of these nanoparticles in improving fruit quality and nutritional value. In general, our results supported the positive effect of the application of selenium and silicon nanoparticles, especially the absolute role of Se/SiO2 (100 mg L−1), on the management of harmful effects of soil drought stress not only in strawberry plants, but also in other agricultural crops.
Determinants favoring weight regain after weight-loss therapy among postmenopausal women
Authors: Bajerska Joanna , Chmurzynska Agata , Muzsik-Kazimierska Agata , Mądry Edyta , Pięta Beata , Sobkowski Maciej , Walkowiak Jarosław
Published: October 2020

Little is known about the factors affecting body weight-loss maintenance among postmenopausal women. We thus performed an analysis to identify some sociodemographic, physiological, and behavioral predictors of weight regain in a targeted subpopulation of women who had lost weight 1 year earlier. We also measured how eating behaviors and habits as well as physical activity pattern differ among successful and unsuccessful weight-loss maintainers over the trial. Sixty-four postmenopausal women were followed up for a year after dieting, and the successful and unsuccessful maintainers were identified. The regainers had regained an average of 4.9 kg of their lost body weight, while the maintainers had regained only 1.5 kg. Regainers had fewer years of education and lower initial body weight loss than maintainers. They also showed poor dietary adherence during dieting, and had unhealthy patterns of eating involving the avoidance of breakfast and a lower intake of nuts, seeds, and pulses, and a higher intake of sweets, biscuits, cakes, and pastries over time (excluding the dieting period). All the significant sociodemographic, physiological and behavioral variables differentiating regainers and maintainers before and after dieting were then examined as independent variables in a logistic regression model. The model showed that less weight reduction during dieting, higher disinhibition scores after dieting, and avoidance of breakfast before dieting were significant predictors of body weight regain in postmenopausal women. From a practical point of view, early identification of postmenopausal women who are at risk of regaining lost weight can allow health professionals to create behavioral and dietary supports to help prevent this. A regular schedule of follow-ups over at least the first year should be considered for them—including psychological and dietary intervention, if necessary. Since this sample study included only postmenopausal women, our findings are not generalizable to other populations.
Winter movement patterns of a globally endangered avian scavenger in south-western Europe
Authors: Morant Jon , Abad-Gómez José María , Álvarez Toribio , Sánchez Ángel , Zuberogoitia Iñigo , López-López Pascual
Published: October 2020

Partial migration, whereby some individuals migrate and some do not, is relatively common and widespread among animals. Switching between migration tactics (from migratory to resident or vice versa) occurs at individual and population levels. Here, we describe for the first time the movement ecology of the largest wintering population of Egyptian Vultures (Neophron percnopterus) in south-west Europe. We combined field surveys and GPS tracking data from December to February during four wintering seasons (2014–2018). The wintering population consisted on average of 85 individuals (range 58–121; 76% adults and 24% subadults). Individuals were counted at five different roosting sites located near farms, unauthorized carcass deposition sites and authorized carcass deposition sites. Our results show that vultures tend to remain close to the roosting site. Moreover, we observed that females exhibited smaller home range sizes than males, which suggests a possible differential use of food sources. Overall, birds relied more on farms than other available food resources, particularly subadult individuals which exploited more intensively these sites. Our results showed that Egyptian Vultures congregate in significant numbers at specific sites throughout the winter period in south-west Spain and that these roosting and feeding sites should be given some level of legal protection and regular monitoring. Furthermore, predictable food sources might be driving the apparent increase in the non-migratory population of Egyptian Vultures, as observed in other avian species which are also changing their migratory behavior.
RNA-sequencing of the Nyssomyia neivai sialome: a sand fly-vector from a Brazilian endemic area for tegumentary leishmaniasis and pemphigus foliaceus
Authors: Vernal Sebastian , Oliveira Fabiano , Oliveira Wanderson H. C. , Goulart Thais M. , Oristian James , Calvo Eric , Pinto Mara C. , Roselino Ana Maria , Ribeiro José M. C.
Published: October 2020

Leishmaniasis encompasses a spectrum of diseases caused by a protozoan belonging to the genusLeishmania. The parasite is transmitted by the bite of sand flies, which inoculate the promastigote forms into the host’s skin while acquiring a blood meal.Nyssomyia neivaiis one of the main vectors of tegumentary leishmaniasis (TL) in Brazil. Southeastern Brazil is an endemic region for TL but also overlaps with an endemic focus for pemphigus foliaceus (PF), also known asFogo Selvagem. Salivary proteins of sand flies, specifically maxadilan and LJM11, have been related to pemphigus etiopathogenesis in the New World, being proposed as an environmental trigger for autoimmunity. We present a comprehensive description of the salivary transcriptome of theN. neivai, using deep sequencing achieved by the Illumina protocol. In addition, we highlight the abundances of severalN. neivaisalivary proteins and use phylogenetic analysis to compare with Old- and New-World sand fly salivary proteins. The collection of protein sequences associated with the salivary glands ofN. neivaican be useful for monitoring vector control strategies as biomarkers ofN. neivai, as well as driving vector-vaccine design for leishmaniasis. Additionally, this catalog will serve as reference to screen for possible antigenic peptide candidates triggering anti-Desmoglein-1 autoantibodies.
Large seasonal and spatial variation in nano- and microphytoplankton diversity along a Baltic Sea—North Sea salinity gradient
Authors: Olofsson Malin , Hagan James G. , Karlson Bengt , Gamfeldt Lars
Published: October 2020

Aquatic phytoplankton experience large fluctuations in environmental conditions during seasonal succession and across salinity gradients, but the impact of this variation on their diversity is poorly understood. We examined spatio-temporal variation in nano- and microphytoplankton (> 2 µm) community structure using almost two decades of light-microscope based monitoring data. The dataset encompasses 19 stations that span a salinity gradient from 2.8 to 35 along the Swedish coastline. Spatially, both regional and local phytoplankton diversity increased with broad-scale salinity variation. Diatoms dominated at high salinity and the proportion of cyanobacteria increased with decreasing salinity. Temporally, cell abundance peaked in winter-spring at high salinity but in summer at low salinity. This was likely due to large filamentous cyanobacteria blooms that occur in summer in low salinity areas, but which are absent in higher salinities. In contrast, phytoplankton local diversity peaked in spring at low salinity but in fall and winter at high salinity. Whilst differences in seasonal variation in cell abundance were reasonably well-explained by variation in salinity and nutrient availability, variation in local-scale phytoplankton diversity was poorly predicted by environmental variables. Overall, we provide insights into the causes of spatio-temporal variation in coastal phytoplankton community structure while also identifying knowledge gaps.
Impacts of discriminated PM2.5 on global under-five and maternal mortality
Authors: Owili Patrick Opiyo , Lin Tang-Huang , Muga Miriam Adoyo , Lien Wei-Hung
Published: October 2020

Globally, it was estimated that maternal and under-five deaths were high in low-income countries than that of high-income countries. Most studies, however, have focused only on the clinical causes of maternal and under-five deaths, and yet there could be other factors such as ambient particulate matter (PM). The current global estimates indicate that exposure to ambient PM2.5 (with ≤ 2.5 microns aerodynamic diameter) has caused about 7 million deaths and over 100 million disability-adjusted life-years. There are also several health risks that have been linked PM2.5, including mortality, both regionally and globally; however, PM2.5 is a mixture of many compounds from various sources. Globally, there is little evidence of the health effects of various types of PM2.5, which may uniquely contribute to the global burden of disease. Currently, only two studies had estimated the effects of discriminated ambient PM2.5, that is, anthropogenic, biomass and dust, on under-five and maternal mortality using satellite measurements, and this study found a positive association in Africa and Asia. However, the study area was conducted in only one region and may not reflect the spatial variations throughout the world. Therefore, in this study, we discriminated different ambient PM2.5 and estimated the effects on a global scale. Using the generalized linear mixed-effects model (GLMM) with a random-effects model, we found that biomass PM2.5 was associated with an 8.9% (95% confidence interval [CI] 4.1–13.9%) increased risk of under-five deaths, while dust PM2.5 was marginally associated with 9.5% of under-five deaths. Nevertheless, our study found no association between PM2.5 type and global maternal deaths. This result may be because the majority of maternal deaths could be associated with preventable deaths that would require clinical interventions. Identification of the mortality-related types of ambient PM2.5 can enable the development of a focused intervention strategy of placing appropriate preventive measures for reducing the generation of source-specific PM2.5 and subsequently diminishing PM2.5-related mortality.
Controlling the behaviour of Drosophila melanogaster via smartphone optogenetics
Authors: Meloni Ilenia , Sachidanandan Divya , Thum Andreas S. , Kittel Robert J. , Murawski Caroline
Published: October 2020

Invertebrates such asDrosophila melanogasterhave proven to be a valuable model organism for studies of the nervous system. In order to control neuronal activity, optogenetics has evolved as a powerful technique enabling non-invasive stimulation using light. This requires light sources that can deliver patterns of light with high temporal and spatial precision. Currently employed light sources for stimulation of small invertebrates, however, are either limited in spatial resolution or require sophisticated and bulky equipment. In this work, we used smartphone displays for optogenetic control ofDrosophila melanogaster. We developed an open-source smartphone app that allows time-dependent display of light patterns and used this to activate and inhibit different neuronal populations in both larvae and adult flies. Characteristic behavioural responses were observed depending on the displayed colour and brightness and in agreement with the activation spectra and light sensitivity of the used channelrhodopsins. By displaying patterns of light, we constrained larval movement and were able to guide larvae on the display. Our method serves as a low-cost high-resolution testbench for optogenetic experiments using small invertebrate species and is particularly appealing to application in neuroscience teaching labs.
Rational approach toward COVID-19 main protease inhibitors via molecular docking, molecular dynamics simulation and free energy calculation
Authors: Keretsu Seketoulie , Bhujbal Swapnil P. , Cho Seung Joo
Published: October 2020

In the rapidly evolving coronavirus disease (COVID-19) pandemic, repurposing existing drugs and evaluating commercially available inhibitors against druggable targets of the virus could be an effective strategy to accelerate the drug discovery process. The 3C-Like proteinase (3CLpro) of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been identified as an important drug target due to its role in viral replication. The lack of a potent 3CLproinhibitor and the availability of the X-ray crystal structure of 3CLpro(PDB-ID 6LU7) motivated us to perform computational studies to identify commercially available potential inhibitors. A combination of modeling studies was performed to identify potential 3CLproinhibitors from the protease inhibitor database MEROPS (https://www.ebi.ac.uk/merops/index.shtml). Binding energy evaluation identified key residues for inhibitor design. We found 15 potential 3CLproinhibitors with higher binding affinity than that of an α-ketoamide inhibitor determined via X-ray structure. Among them, saquinavir and three other investigational drugs aclarubicin, TMC-310911, and faldaprevir could be suggested as potential 3CLproinhibitors. We recommend further experimental investigation of these compounds.
Free-standing spider silk webs of the thomisid Saccodomus formivorus are made of composites comprising micro- and submicron fibers
Authors: Haynl Christian , Vongsvivut Jitraporn , Mayer Kai R. H. , Bargel Hendrik , Neubauer Vanessa J. , Tobin Mark J. , Elgar Mark A. , Scheibel Thomas
Published: October 2020

Our understanding of the extraordinary mechanical and physico-chemical properties of spider silk is largely confined to the fibers produced by orb-weaving spiders, despite the diversity of foraging webs that occur across numerous spider families. Crab spiders (Thomisidae) are described as ambush predators that do not build webs, but nevertheless use silk for draglines, egg cases and assembling leaf-nests. A little-known exception is the Australian thomisid Saccodomus formivorus, which constructs a basket-like silk web of extraordinary dimensional stability and structural integrity that facilitates the capture of its ant prey. We examined the physical and chemical properties of this unusual web and revealed that the web threads comprise microfibers that are embedded within a biopolymeric matrix containing additionally longitudinally-oriented submicron fibers. We showed that the micro- and submicron fibers differ in their chemical composition and that the web threads show a remarkable lateral resilience compared with that of the major ampullate silk of a well-investigated orb weaver. Our novel analyses of these unusual web and silk characteristics highlight how investigations of non-model species can broaden our understanding of silks and the evolution of foraging webs.
Novel carbon film induces precocious calcium oscillation to promote neuronal cell maturation
Authors: Ludwig Anastasia , Kesaf Sebnem , Heikkinen Joonas J. , Sukhanova Tatiana , Khakipoor Shokoufeh , Molinari Florence , Pellegrino Christophe , Kim Sung I. , Han Jeon G. , Huttunen Henri J. , Lauri Sari E. , Franssila Sami , Jokinen Ville , Rivera Claudio
Published: October 2020

Different types of carbon materials are biocompatible with neural cells and can promote maturation. The mechanism of this effect is not clear. Here we have tested the capacity of a carbon material composed of amorphous sp3 carbon backbone, embedded with a percolating network of sp2 carbon domains to sustain neuronal cultures. We found that cortical neurons survive and develop faster on this novel carbon material. After 3 days in culture, there is a precocious increase in the frequency of neuronal activity and in the expression of maturation marker KCC2 on carbon films as compared to a commonly used glass surface. Accelerated development is accompanied by a dramatic increase in neuronal dendrite arborization. The mechanism for the precocious maturation involves the activation of intracellular calcium oscillations by the carbon material already after 1 day in culture. Carbon-induced oscillations are independent of network activity and reflect intrinsic spontaneous activation of developing neurons. Thus, these results reveal a novel mechanism for carbon material-induced neuronal survival and maturation.
A trophic latitudinal gradient revealed in anchovy and sardine from the Western Mediterranean Sea using a multi-proxy approach
Authors: Bachiller Eneko , Albo-Puigserver Marta , Giménez Joan , Pennino Maria Grazia , Marí-Mena Neus , Esteban Antonio , Lloret-Lloret Elena , Jadaud Angelique , Carro Belén , Bellido José María , Coll Marta
Published: October 2020

This work combines state-of-the-art methods (DNA metabarcoding) with classic approaches (visual stomach content characterization and stable isotope analyses of nitrogen (δ15N) and carbon (δ13C)) to investigate the trophic ecology of anchovy (Engraulis encrasicolus) and sardine (Sardina pilchardus) at high taxonomic and spatial resolution in the Western Mediterranean Sea. Gut contents observed are in accordance with the dietary plasticity generally described for anchovy and sardine, suggesting a diet related to the opportunistic ingestion of available prey in a certain area and/or time. Genetic tools also showed modest inter-specific differences regarding ingested species. However, inter-specific and intra-specific differences in ingested prey frequencies and prey biomass reflected a latitudinal signal that could indicate a more effective predation on large prey like krill by anchovy versus sardine, as well as a generalized higher large prey ingestion by both species southwards. In fact, both species presented lowerδ15N in the northernmost area. This latitudinal gradient indicates changes in the trophic ecology of anchovy and sardine that coincide with previously described better biological conditions for fish in the southern part of the study area as well as higher landings of both species in recent years.
HIF1α is not a target of 14q deletion in clear cell renal cancer
Authors: Shenoy Niraj
Published: October 2020

HIF1α has been termed a tumor-suppressor in clear cell renal cell carcinoma (ccRCC), primarily based on functional proliferation studies in cell lines (in vitro and in vivo) with genetic manipulation, and the adverse prognosis of 14q-deleted ccRCC patients. In other malignancies, however, HIF1α has an established tumor-promoting role. Therefore, this study sought to further examine the role of HIF1α in ccRCC using bioinformatic analyses of 530 ccRCC patients from The Cancer Genome Atlas (TCGA) and The Cancer Proteome Atlas (TCPA) registries. Although lower copy numbers of HIF1A (encoding HIF1α, located at 14q23.2) was associated with worse survival, there was no survival difference based on either HIF1A mRNA or HIF1α protein expression. Interestingly, L2HGDH (L-2-Hydroxyglutarate Dehydrogenase), a recently characterized epigenetic modulating ccRCC tumor-suppressor with a marked impact on survival, was found to be located only ~ 11.5Mbp from HIF1A on 14q (at 14q21.3). L2HGDH was therefore co-deleted in ~ 95% of 14q deletions involving HIF1A locus. Remarkably, HIF1A CNV had a markedly stronger correlation with L2HGDH expression (Rho = 0.55) than its own gene expression (Rho = 0.27), indicating high preserved-allele compensation of HIF1A. Genetic loss of HIF1A was therefore associated with a much greater reduction of L2HGDH gene expression than its own gene expression, providing a possible explanation for survival differences based on HIF1A CNV and mRNA expression. Furthermore, in 14q-deleted ccRCC patients with complete (uncensored) survival data, in the relatively rare cases where genetic loss of HIF1A occurred without genetic loss of L2HGDH (n = 5), the survival was significantly greater than where there was simultaneous genetic loss of both (n = 87) (mean survival 1670.8 ± 183.5 days vs 885.1 ± 78.4 days; p = 0.007). In addition, there was no correlation between HIF1A mRNA and HIF1α protein expression in ccRCC (R = 0.02), reflecting the primarily post-translational regulation of HIF1α. Lastly, even between L2HGDH and HIF1A loci, 14q was found to have several other yet-to-be-characterized potential ccRCC tumor-suppressors. Taken together, the data indicate that HIF1α is not a target of 14q deletion in ccRCC and that it is not a tumor-suppressor in this malignancy.
Evaluating the effect of rice (Oryza sativa L.: SRNC05053-6-2) crude extract on psoriasis using in vitro and in vivo models
Authors: Ampawong Sumate , Kengkoom Kanchana , Sukphopetch Passanesh , Aramwit Pornanong , Muangkaew Watcharamat , Kanjanapruthipong Tapanee , Buaban Theerapong
Published: October 2020

Psoriasis is mainly caused because of inappropriate immune responses in the epidermis. Rice (Oryza sativa L.: SRNC05053-6-2) consists of anthocyanin, which exhibits strong antioxidative and anti-inflammatory properties. This study aimed to evaluate the role of this black-coloured rice crude extract in alleviating the symptoms of psoriasis using human psoriatic artificial skin and an imiquimod-induced rat psoriasis model. Psoriasis-related genes, cytokines and chemokines were examined; in addition, the antioxidative and anti-inflammatory properties and the immunohistopathological features of this condition were studied. The results showed that the rice extract reduced the severity of psoriasis by (1) decreasing the epidermal thickness, acanthosis, hyperkeratosis, epidermal inflammation and degree of apoptosis induction via caspase-3, (2) increasing the expression levels of anti-inflammatory cytokines (IL-10 and TGF-β), (3) reducing the levels of pro-inflammatory cytokines (IL-6, IL-8, IL-20, IL-22 and TNF-α), chemokines (CCL-20) and anti-microbial peptides (psoriasin and β-defensin), (4) enhancing the antioxidative property (Nrf-2), (5) downregulating the levels of psoriasis-associated genes (psoriasin, β-defensin, koebnerisin 15L and koebnerisin 15S) and (6) upregulating the levels of psoriasis-improving genes (caspase-14, involucrin and filaggrin). Thus, the extract appears to exert therapeutic effects on psoriasis through its antioxidative and immunomodulatory properties.
A pioneer calf foetus microbiome
Authors: Guzman Cesar E. , Wood Jennifer L. , Egidi Eleonora , White-Monsant Alison C. , Semenec Lucie , Grommen Sylvia V. H. , Hill-Yardin Elisa L. , De Groef Bert , Franks Ashley E.
Published: October 2020

Foetus sterility until parturition is under debate due to reports of microorganisms in the foetal environment and meconium. Sufficient controls to overcome sample contamination and provide direct evidence of microorganism viability in the pre-rectal gastrointestinal tract (GIT) have been lacking. We conducted molecular and culture-based analyses to investigate the presence of a microbiome in the foetal GIT of calves at 5, 6 and 7 months gestation, while controlling for contamination. The 5 components of the GIT (ruminal fluid, ruminal tissue, caecal fluid, caecal tissue and meconium) and amniotic fluid were found to contain a pioneer microbiome of distinct bacterial and archaeal communities. Bacterial and archaeal richness varied between GIT components. The dominant bacterial phyla in amniotic fluid differed to those in ruminal and caecal fluids and meconium. The lowest bacterial and archaeal abundances were associated with ruminal tissues. Viable bacteria unique to the ruminal fluids, which were not found in the controls from 5, 6 and 7 months gestation, were cultured, subcultured, sequenced and identified. We report that the foetal GIT is not sterile but is spatially colonised before birth by a pioneer microbiome.