bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effectiveness of Urban Hydrological Processes in Mitigating Urban Heat Island and Human Thermal Stress During a Heat Wave Event in Nanjing, China
Authors: Wang Xueyuan , Liu Hongnian , Miao Shiguang , Wu Qigang , Zhang Ning , Qiao Fengxue 
Published: December 2020

AbstractThe effectiveness of urban hydrological processes in mitigating the urban heat island (UHI) effect and human thermal stress in the megacity of Nanjing during an extreme heat wave event (6th–10th August 2013) was assessed using Weather Research and Forecasting Single‐Layer Urban Canopy Models. The inclusion of urban hydrological processes improved model performance, with more reasonable diurnal cycles and smaller mean errors, root mean square errors, and normalized root mean square errors for meteorological variables. Through evaporative cooling, urban hydrological processes can greatly increase specific and relative humidity, while reducing near‐surface and surface temperatures, wind speed, and planetary boundary layer (PBL) height, and the cooling and wetting effects could affect the entire PBL, especially in low‐intensity residential areas. Urban hydrological processes can effectively mitigate both the near‐surface and surface UHI effect. The city‐wide mitigation effectiveness of near‐surface UHI ranged between 0.9°C and 1.1°C throughout the day, while the city‐wide mitigation effectiveness of surface UHI at noon reached ∼5°C. The maximum reduction of near‐surface and surface UHI in low‐intensity residential areas reached 1.3°C and 10.0°C, respectively. Changes in heat stress indices indicate that the cooling effect improves human thermal comfort at night, while the increased humidity outweighs the cooling effect and exacerbates human thermal discomfort during daytime. The city‐wide thermal stress increased by up to 0.4°C, 0.2°C, and 0.5°C during daytime and decreased by up to 0.4°C, 0.3°C, and 0.6°C at night for wet‐bulb globe temperature, apparent temperature, and humidity index, respectively.
Trends and challenges in modeling glioma using 3D human brain organoids
Authors: Mariappan Aruljothi , Goranci-Buzhala Gladiola , Ricci-Vitiani Lucia , Pallini Roberto , Gopalakrishnan Jay 
Published: December 2020

AbstractThe human brain organoids derived from pluripotent cells are a new class of three-dimensional tissue systems that recapitulates several neural epithelial aspects. Brain organoids have already helped efficient modeling of crucial elements of brain development and disorders. Brain organoids’ suitability in modeling glioma has started to emerge, offering another usefulness of brain organoids in disease modeling. Although the current state-of-the organoids mostly reflect the immature state of the brain, with their vast cell diversity, human brain-like cytoarchitecture, feasibility in culturing, handling, imaging, and tractability can offer enormous potential in reflecting the glioma invasion, integration, and interaction with different neuronal cell types. Here, we summarize the current trend of employing brain organoids in glioma modeling and discuss the immediate challenges. Solving them might lay a foundation for using brain organoids as a pre-clinical 3D substrate to dissect the glioma invasion mechanisms in detail.
A chromosome-scale reference genome of Lobularia maritima, an ornamental plant with high stress tolerance
Authors: Huang Li , Ma Yazhen , Jiang Jiebei , Li Ting , Yang Wenjie , Zhang Lei , Wu Lei , Feng Landi , Xi Zhenxiang , Xu Xiaoting , Liu Jianquan , Hu Quanjun 
Published: December 2020

AbstractLobularia maritima (L.) Desv. is an ornamental plant cultivated across the world. It belongs to the family Brassicaceae and can tolerate dry, poor and contaminated habitats. Here, we present a chromosome-scale, high-quality genome assembly of L. maritima based on integrated approaches combining Illumina short reads and Hi–C chromosome conformation data. The genome was assembled into 12 pseudochromosomes with a 197.70 Mb length, and it includes 25,813 protein-coding genes. Approximately 41.94% of the genome consists of repetitive sequences, with abundant long terminal repeat transposable elements. Comparative genomic analysis confirmed that L. maritima underwent a species-specific whole-genome duplication (WGD) event ~22.99 million years ago. We identified ~1900 species-specific genes, 25 expanded gene families, and 50 positively selected genes in L. maritima. Functional annotations of these genes indicated that they are mainly related to stress tolerance. These results provide new insights into the stress tolerance of L. maritima, and this genomic resource will be valuable for further genetic improvement of this important ornamental plant.
Transcriptional regulation of bark freezing tolerance in apple (Malus domestica Borkh.)
Authors: Liang Yinghai , Wang Shanshan , Zhao Chenhui , Ma Xinwei , Zhao Yiyong , Shao Jing , Li Yuebo , Li Honglian , Song Hongwei , Ma Hong , Li Hao , Zhang Bingbing , Zhang Liangsheng 
Published: December 2020

AbstractFreezing tolerance is a significant trait in plants that grow in cold environments and survive through the winter. Apple (Malus domestica Borkh.) is a cold-tolerant fruit tree, and the cold tolerance of its bark is important for its survival at low temperatures. However, little is known about the gene activity related to its freezing tolerance. To better understand the gene expression and regulation properties of freezing tolerance in dormant apple trees, we analyzed the transcriptomic divergences in the bark from 1-year-old branches of two apple cultivars, “Golden Delicious” (G) and “Jinhong” (H), which have different levels of cold resistance, under chilling and freezing treatments. “H” can safely overwinter below −30 °C in extremely low-temperature regions, whereas “G” experiences severe freezing damage and death in similar environments. Based on 28 bark transcriptomes (from the epidermis, phloem, and cambium) from 1-year-old branches under seven temperature treatments (from 4 to −29 °C), we identified 4173 and 7734 differentially expressed genes (DEGs) in “G” and “H”, respectively, between the chilling and freezing treatments. A gene coexpression network was constructed according to this expression information using weighted gene correlation network analysis (WGCNA), and seven biologically meaningful coexpression modules were identified from the network. The expression profiles of the genes from these modules suggested the gene regulatory pathways that are responsible for the chilling and freezing stress responses of “G” and/or “H.” Module 7 was probably related to freezing acclimation and freezing damage in “H” at the lower temperatures. This module contained more interconnected hub transcription factors (TFs) and cold-responsive genes (CORs). Modules 6 and 7 contained C-repeat binding factor (CBF) TFs, and many CBF-dependent homologs were identified as hub genes. We also found that some hub TFs had higher intramodular connectivity (KME) and gene significance (GS) than CBFs. Specifically, most hub TFs in modules 6 and 7 were activated at the beginning of the early freezing stress phase and maintained upregulated expression during the whole freezing stress period in “G” and “H”. The upregulation of DEGs related to methionine and carbohydrate biosynthetic processes in “H” under more severe freezing stress supported the maintenance of homeostasis in the cellular membrane. This study improves our understanding of the transcriptional regulation patterns underlying freezing tolerance in the bark of apple branches.
Dual role of MdSND1 in the biosynthesis of lignin and in signal transduction in response to salt and osmotic stress in apple
Authors: Chen Keqin , Guo Yunna , Song Mengru , Liu Lifu , Xue Hao , Dai Hongyan , Zhang Zhihong 
Published: December 2020

AbstractClarifying the stress signal transduction pathway would be helpful for understanding the abiotic stress resistance mechanism in apple (Malus × domestica Borkh.) and could assist in the development of new varieties with high stress tolerance by genetic engineering. The key NAC transcription factor SND1, which is involved in the lignin biosynthesis process in apple, was functionally analyzed. The results of the stress treatments indicated that MdSND1 could be induced by salt, mannitol and ABA. Compared with wild-type GL-3 plants, MdSND1-overexpressing apple plants with greater antioxidant capacity and lignin were more resistant to salt and simulated osmotic stress, while RNAi plants were more vulnerable. Additionally, molecular experiments confirmed that MdSND1 could regulate the biosynthesis of lignin by activating the transcription of MdMYB46/83. Moreover, genes known to be involved in the stress signal transduction pathway (MdAREB1A, MdAREB1B, MdDREB2A, MdRD29A, and MdRD22) were screened for their close correlations with the expression of MdSND1 and the response to salt and osmotic stress. Multiple verification tests further demonstrated that MdSND1 could directly bind to these gene promoters and activate their transcription. The above results revealed that MdSND1 is directly involved in the regulation of lignin biosynthesis and the signal transduction pathway involved in the response to both salt and osmotic stress in apple.
Low threshold lasing emissions from a single upconversion nanocrystal
Authors: Shang Yunfei , Zhou Jiajia , Cai Yangjian , Wang Fan , Fernandez-Bravo Angel , Yang Chunhui , Jiang Lei , Jin Dayong 
Published: December 2020

AbstractCross-relaxation among neighboring emitters normally causes self-quenching and limits the brightness of luminescence. However, in nanomaterials, cross-relaxation could be well-controlled and employed for increasing the luminescence efficiency at specific wavelengths. Here we report that cross-relaxation can modulate both the brightness of single upconversion nanoparticles and the threshold to reach population inversion, and both are critical factors in producing the ultra-low threshold lasing emissions in a micro cavity laser. By homogenously coating a 5-μm cavity with a single layer of nanoparticles, we demonstrate that doping Tm3+ ions at 2% can facilitate the electron accumulation at the intermediate state of 3H4 level and efficiently decrease the lasing threshold by more than one order of magnitude. As a result, we demonstrate up-converted lasing emissions with an ultralow threshold of continuous-wave excitation of ~150 W/cm2 achieved at room temperature. A single nanoparticle can lase with a full width at half-maximum as narrow as ~0.45 nm.
HuskinDB, a database for skin permeation of xenobiotics
Authors: Stepanov Dmitri , Canipa Steven , Wolber Gerhard 
Published: December 2020

AbstractSkin permeation is an essential biological property of small organic compounds our body is exposed to, such as drugs in topic formulations, cosmetics, and environmental toxins. Despite the limited availability of experimental data, there is a lack of systematic analysis and structure. We present a novel resource on skin permeation data that collects all measurements available in the literature and systematically structures experimental conditions. Besides the skin permeation value kp, it includes experimental protocols such as skin source site, skin layer used, preparation technique, storage conditions, as well as test conditions such as temperature, pH as well as the type of donor and acceptor solution. It is important to include these parameters in the assessment of the skin permeation data. In addition, we provide an analysis of physicochemical properties and chemical space coverage, laying the basis for applicability domain determination of insights drawn from the collected data points. The database is freely accessible under https://huskindb.drug-design.de or https://doi.org/10.7303/syn21998881.
Exposure to acute normobaric hypoxia results in adaptions of both the macro- and microcirculatory system
Authors: Mirna Moritz , Bimpong-Buta Nana-Yaw , Hoffmann Fabian , Abusamrah Thaer , Knost Thorben , Sander Oliver , Hew Yayu Monica , Lichtenauer Michael , Muessig Johanna M. , Bruno Raphael Romano , Kelm Malte , Zange Jochen , Wilhelm Jilada , Limper Ulrich , Jordan Jens , Tank Jens , Jung Christian 
Published: December 2020

AbstractAlthough acute hypoxia is of utmost pathophysiologic relevance in health and disease, studies on its effects on both the macro- and microcirculation are scarce. Herein, we provide a comprehensive analysis of the effects of acute normobaric hypoxia on human macro- and microcirculation. 20 healthy participants were enrolled in this study. Hypoxia was induced in a normobaric hypoxia chamber by decreasing the partial pressure of oxygen in inhaled air stepwisely (pO2; 21.25 kPa (0 k), 16.42 kPa (2 k), 12.63 kPa (4 k) and 9.64 kPa (6 k)). Macrocirculatory effects were assessed by cardiac output measurements, microcirculatory changes were investigated by sidestream dark-field imaging in the sublingual capillary bed and videocapillaroscopy at the nailfold. Exposure to hypoxia resulted in a decrease of systemic vascular resistance (p < 0.0001) and diastolic blood pressure (p = 0.014). Concomitantly, we observed an increase in heart rate (p < 0.0001) and an increase of cardiac output (p < 0.0001). In the sublingual microcirculation, exposure to hypoxia resulted in an increase of total vessel density, proportion of perfused vessels and perfused vessel density. Furthermore, we observed an increase in peripheral capillary density. Exposure to acute hypoxia results in vasodilatation of resistance arteries, as well as recruitment of microvessels of the central and peripheral microcirculation. The observed macro- and microcirculatory effects are most likely a result from compensatory mechanisms to ensure adequate tissue oxygenation.
Identification of potential TNF-α inhibitors: from in silico to in vitro studies
Authors: Zia Komal , Ashraf Sajda , Jabeen Almas , Saeed Maria , Nur-e-Alam Mohammad , Ahmed Sarfaraz , Al-Rehaily Adnan J. , Ul-Haq Zaheer 
Published: December 2020

AbstractTumor Necrosis Factor Alpha (TNF-α) is a pleiotropic pro-inflammatory cytokine. It act as central biological regulator in critical immune functions, but its dysregulation has been linked with a number of diseases. Inhibition of TNF-α has considerable therapeutic potential for diseases such as cancer, diabetes, and especially autoimmune diseases. Despite the fact that many small molecule inhibitors have been identified against TNF-α, no orally active drug has been reported yet which demand an urgent need of a small molecule drug against TNF-α. This study focuses on the development of ligand-based selective pharmacophore model to perform virtual screening of plant origin natural product database for the identification of potential inhibitors against TNF-α. The resultant hits, identified as actives were evaluated by molecular docking studies to get insight into their potential binding interaction with the target protein. Based on pharmacophore matching, interacting residues, docking score, more affinity towards TNF-α with diverse scaffolds five compounds were selected for in vitro activity study. Experimental validation led to the identification of three chemically diverse potential compounds with the IC50 32.5 ± 4.5 µM, 6.5 ± 0.8 µM and 27.4 ± 1.7 µM, respectively.
Evaluation of Pseudomonas sp. for its multifarious plant growth promoting potential and its ability to alleviate biotic and abiotic stress in tomato (Solanum lycopersicum) plants
Authors: Pandey Sangeeta , Gupta Shikha 
Published: December 2020

Abstract1-Aminocyclopropane-1-carboxylate (ACC) deaminase activity is one of the most beneficial traits of plant growth promoting (PGP) rhizobacteria responsible for protecting the plants from detrimental effects of abiotic and biotic stress. The strain S3 with ACC deaminase activity (724.56 nmol α-ketobutyrate mg−1protein hr−1) was isolated from rhizospheric soil of turmeric (Curcuma longa), a medicinal plant, growing in Motihari district of Indian state, Bihar. The halotolerant strain S3, exhibited optimum growth at 8% (w/v) NaCl. It also exhibited multiple PGP traits such as indole acetic acid production (37.71 μg mL−1), phosphate solubilization (69.68 mg L−1), siderophore, hydrocyanic acid (HCN) and ammonia production as well as revealed antagonism againstRhizoctonia solani. The potential of isolated strain to alleviate salinity stress in tomato plants was investigated through pots trials by inoculating strain S3 through-seed bacterization, soil drenching, root dipping as well as seed treatment + soil drenching. The strain S3 inoculated through seed treatment and soil drenching method led to improved morphological attributes (root/shoot length, root/shoot fresh weight and root/shoot dry weight), photosynthetic pigment content, increased accumulation of osmolytes (proline and total soluble sugar), enhanced activities of antioxidants (Catalase and Peroxidase) and phenolic content in salt stressed tomato plants. The biochemical characterisation, FAMEs analysis and 16S rRNA gene sequencing revealed that strain S3 belongs to the genusPseudomonas. The overall findings of the study revealed thatPseudomonassp. strain S3 can be explored as an effective plant growth promoter which stimulate growth and improve resilience in tomato plants under saline condition.
Assessing the sociability of former pet and entertainment chimpanzees by using multiplex networks
Authors: Crailsheim Dietmar , Romani Toni , Llorente Miquel , Kalcher-Sommersguter Elfriede 
Published: December 2020

AbstractAdvances in the field of social network analysis facilitate the creation of multiplex networks where several interaction types can be analysed simultaneously. In order to test the potential benefits of this approach, we investigated the sociability of atypically raised chimpanzees by constructing and analysing 4-layered multiplex networks of two groups of former pet and entertainment chimpanzees (Pan troglodytes). These networks are based on four social interaction types (stationary vicinity, affiliative behaviour, allogrooming, passive close proximity) representing low- to high-level interaction types in terms of sociability. Using the tools provided by the MuxViz software, we could assess and compare the similarity and information gain of each these social interaction types. We found some social interaction types to be more similar than other ones. However, each social interaction type imparted different information. We also tested for a possible impact of the chimpanzees’ biographical background on the social interaction types and found affiliative behaviour as well as allogrooming to be affected by adverse early life experiences. We conclude that this multiplex approach provides a more realistic framework giving detailed insight into the sociability of these chimpanzees and can function as a tool to support captive care management decisions.
Fossil microbial shark tooth decay documents in situ metabolism of enameloid proteins as nutrition source in deep water environments
Authors: Feichtinger Iris , Lukeneder Alexander , Topa Dan , Kriwet Jürgen , Libowitzky Eugen , Westall Frances 
Published: December 2020

AbstractAlteration of organic remains during the transition from the bio- to lithosphere is affected strongly by biotic processes of microbes influencing the potential of dead matter to become fossilized or vanish ultimately. If fossilized, bones, cartilage, and tooth dentine often display traces of bioerosion caused by destructive microbes. The causal agents, however, usually remain ambiguous. Here we present a new type of tissue alteration in fossil deep-sea shark teeth with in situ preservation of the responsible organisms embedded in a delicate filmy substance identified as extrapolymeric matter. The invading microorganisms are arranged in nest- or chain-like patterns between fluorapatite bundles of the superficial enameloid. Chemical analysis of the bacteriomorph structures indicates replacement by a phyllosilicate, which enabled in situ preservation. Our results imply that bacteria invaded the hypermineralized tissue for harvesting intra-crystalline bound organic matter, which provided nutrient supply in a nutrient depleted deep-marine environment they inhabited. We document here for the first time in situ bacteria preservation in tooth enameloid, one of the hardest mineralized tissues developed by animals. This unambiguously verifies that microbes also colonize highly mineralized dental capping tissues with only minor organic content when nutrients are scarce as in deep-marine environments.
VISTA: VIsual Semantic Tissue Analysis for pancreatic disease quantification in murine cohorts
Authors: Ternes Luke , Huang Ge , Lanciault Christian , Thibault Guillaume , Riggers Rachelle , Gray Joe W. , Muschler John , Chang Young Hwan 
Published: December 2020

AbstractMechanistic disease progression studies using animal models require objective and quantifiable assessment of tissue pathology. Currently quantification relies heavily on staining methods which can be expensive, labor/time-intensive, inconsistent across laboratories and batch, and produce uneven staining that is prone to misinterpretation and investigator bias. We developed an automated semantic segmentation tool utilizing deep learning for rapid and objective quantification of histologic features relying solely on hematoxylin and eosin stained pancreatic tissue sections. The tool segments normal acinar structures, the ductal phenotype of acinar-to-ductal metaplasia (ADM), and dysplasia with Dice coefficients of 0.79, 0.70, and 0.79, respectively. To deal with inaccurate pixelwise manual annotations, prediction accuracy was also evaluated against biological truth using immunostaining mean structural similarity indexes (SSIM) of 0.925 and 0.920 for amylase and pan-keratin respectively. Our tool’s disease area quantifications were correlated to the quantifications of immunostaining markers (DAPI, amylase, and cytokeratins; Spearman correlation score = 0.86, 0.97, and 0.92) in unseen dataset (n = 25). Moreover, our tool distinguishes ADM from dysplasia, which are not reliably distinguished with immunostaining, and demonstrates generalizability across murine cohorts with pancreatic disease. We quantified the changes in histologic feature abundance for murine cohorts with oncogenic Kras-driven disease, and the predictions fit biological expectations, showing stromal expansion, a reduction of normal acinar tissue, and an increase in both ADM and dysplasia as disease progresses. Our tool promises to accelerate and improve the quantification of pancreatic disease in animal studies and become a unifying quantification tool across laboratories.
Plasmodium falciparum sexual parasites regulate infected erythrocyte permeability
Authors: Bouyer Guillaume , Barbieri Daniela , Dupuy Florian , Marteau Anthony , Sissoko Abdoulaye , N’Dri Marie-Esther , Neveu Gaelle , Bedault Laurianne , Khodabux Nabiha , Roman Diana , Houzé Sandrine , Siciliano Giulia , Alano Pietro , Martins Rafael M. , Lopez-Rubio Jose-Juan , Clain Jérome , Duval Romain , Egée Stéphane , Lavazec Catherine 
Published: December 2020

AbstractTo ensure the transport of nutrients necessary for their survival, Plasmodium falciparum parasites increase erythrocyte permeability to diverse solutes. These new permeation pathways (NPPs) have been extensively characterized in the pathogenic asexual parasite stages, however the existence of NPPs has never been investigated in gametocytes, the sexual stages responsible for transmission to mosquitoes. Here, we show that NPPs are still active in erythrocytes infected with immature gametocytes and that this activity declines along gametocyte maturation. Our results indicate that NPPs are regulated by cyclic AMP (cAMP) signaling cascade, and that the decrease in cAMP levels in mature stages results in a slowdown of NPP activity. We also show that NPPs facilitate the uptake of artemisinin derivatives and that phosphodiesterase (PDE) inhibitors can reactivate NPPs and increase drug uptake in mature gametocytes. These processes are predicted to play a key role in P. falciparum gametocyte biology and susceptibility to antimalarials.