bluuebunny/crossref_metadata_2025 huggingface dataset:
Application of seismic stratigraphy in reservoir characterisation: a case study of the passive margin deposits of the northern Orange Basin, South Africa
Authors: Samakinde Chris Adesola , Van Bever Donker Jan Marinus , Durrheim Ray , Manzi Musa
Published: December 2020

The Barremian-Cenozoic depositional sequences in the northern Orange Basin, SW, South Africa, were investigated using the principles of seismic stratigraphy to understand the interplay of tectonics and sedimentary processes in the distribution of potential hydrocarbon reservoirs. A seismic stratigraphic workflow (seismic sequence, seismic facies and lithofacies analysis) was completed by utilising three seismic lines (L1, L2 and L3) tied to Wireline data (gamma, checkshots and sonic) in two exploration wells (A1 and A2). Seven depositional sequences were mapped followed by the creation of lithofacies log interpreted from the gamma-ray log (GR) by setting maximum GR value at 60 API for Sandstone, 60–100 API for Siltstone and above 100 API for Shale. Six seismic facies units are recognised based on internal geometry and configurations of the seismic reflectors; Tangential-Oblique (SF1), Hummocky (SF2), Wavy-Parallel (SF3), Chaotic (SF4), Sub-parallel/parallel (SF5) and Divergent (SF6). SF4 is dominant within the Barremian-Aptian sequence and expressed in an incised valley fill, suggesting mass transport deposition accompanied by strong hydrodynamic conditions. Evidence of sedimentary basins progradation is seen within the Late-Albian-Turonian sequences, because of the occurrences of SF2, SF6 and SF 4 facies. SF5 facies is prominent in the Maastrichtian/Campanian sequence, indicating that the deposition of sediments may have been accompanied by uniform margin subsidence after the Late-Cretaceous uplift of the Africa margin. The occurrence of SF1 and SF4 facies within the Cenozoic sequence indicates terrigenous pro-deltaic deposits and mass transport deposits, respectively. Further results from seismic-lithofacies modelling reveal that sand deposits of Barremian-Aptian (SF4 facies unit) and Albian sequences (SF2 and SF6 facies units) are potential stratigraphic reservoirs in this part of the basin.
The modern tontine
Authors: Weinert Jan-Hendrik , Gründl Helmut
Published: December 2020

We investigate whether a historical pension concept, the tontine, yields enough innovative potential to extend and improve the prevailing privately funded pension solutions in a modern way. The tontine basically generates an age-increasing cash flow, which can help to match the increasing financing needs at old ages. In contrast to traditional pension products, however, the tontine generates volatile cash flows, which means that the insurance character of the tontine cannot be guaranteed in every situation. By employing Multi Cumulative Prospect Theory (MCPT) we answer the question to what extent tontines can be a complement to or a substitute for traditional annuities. We find that it is only optimal to invest in tontines for a certain range of initial wealth. In addition, we investigate in how far the tontine size, the volatility of individual liquidity needs and expected mortality rates contribute to the demand for tontines.
Using electronic AKI alerts to define the epidemiology of acute kidney injury in renal transplants
Authors: Jones Aled , Holmes Jennifer , Stephens Michael , Geen John , Williams John , Donovan Kieron , Phillips Aled O.
Published: December 2020

Background

Little is known regarding the impact of acute kidney injury (AKI) on renal transplant outcome. Our aim was to define the incidence and outcome of AKI in renal transplant patients using data collected from a national AKI electronic alert system

Methods

The study represents a prospective national cohort study collecting data on 1224 renal transplants recipients with a functioning renal transplant, between April 2015 and March 2019.

Results

Four hundred forty patients experienced at least one episode of AKI giving an incidence rate of 35.4%. Sixty-four point seven% of episodes were AKI stage 1, 7.3% AKI stage 2 and 28% AKI stage 3. Only 6.2% of episodes occurred in the context of rejection. Forty-three point five% of AKI episodes were associated with sepsis. AKI was associated with pre-existing renal dysfunction, and a primary renal diagnosis of diabetic nephropathy. AKI was more prevalent in recipients from a donor after cardiac death (26.4% vs. 21.4%, p < 0.05) compared to the non-AKI cohort. Following AKI, 30-day mortality was 19.8% and overall mortality was 34.8%, compared to 8.4% in the non AKI cohort (RR 4.06, 95% CI 3.1–5.3, p < 0.001). Graft survival (GS), and death censored graft survival (DCGS) censored at 4 years, in the AKI cohort were significantly lower than in the non AKI group (p < 0.0001 for GS and DCGS).

Conclusion

The study provides a detailed characterisation of AKI in renal transplant recipients highlighting its significant negative impact on patient and graft survival.
Trends and influencing factors of plasma folate levels in Chinese women at mid-pregnancy, late pregnancy and lactation periods
Authors: Zhou Yu-Bo , Si Ke-Yi , Li Hong-Tian , Li Xiu-Cui , Meng Ying , Liu Jian-Meng
Published: December 2020

Folate status for women during early pregnancy has been investigated, but data for women during mid-pregnancy, late pregnancy or lactation are sparse or lacking. Between May and July 2014, we conducted a cross-sectional study in 1211 pregnant and lactating women from three representative regions in China. Approximately 135 women were enrolled in each stratum by physiological periods (mid-pregnancy, late pregnancy or lactation) and regions (south, central or north). Plasma folate concentrations were measured by microbiological assay. The adjusted medians of folate concentration decreased from 28·8 (interquartile range (IQR) 19·9, 38·2) nmol/l in mid-pregnancy to 18·6 (IQR 13·2, 26·4) nmol/l in late pregnancy, and to 17·0 (IQR 12·3, 22·5) nmol/l in lactation (Pfor trend < 0·001). Overall, lower folate concentrations were more likely to be observed in women residing in the northern region, with younger age, higher pre-pregnancy BMI, lower education or multiparity, and in lactating women who had undergone a Caesarean delivery or who were breastfeeding exclusively. In total, 380 (31·4 %) women had a suboptimal folate status (folate concentration <13·5 nmol/l). Women in late pregnancy and lactating, residing in the northern region, having multiparity and low education level had a higher risk of suboptimal folate status, while those with older age had a lower risk. In conclusion, maternal plasma folate concentrations decreased as pregnancy progressed, and were influenced by geographic region and maternal socio-demographic characteristics. Future studies are warranted to assess the necessity of folic acid supplementation during later pregnancy and lactation especially for women at a higher risk of folate depletion.
Differences in native and introduced chalcid parasitoid communities recruited by the invasive chestnut pest Dryocosmus kuriphilus in two Iberian territories
Authors: Gil-Tapetado D. , Cabrero-Sañudo F.J. , Gómez J.F. , Askew R.R. , Nieves-Aldrey J.L.
Published: December 2020

Dryocosmus kuriphilus (Hymenoptera: Cynipidae) is a global invasive gall wasp and a pest of chestnuts (Castanea spp.). A study of the Chalcidoidea parasitoid community of D. kuriphilus was undertaken over two years, from March 2017 to March 2019, at 15 sites in south and northwest Spain (Málaga and Galicia regions). More than 18,000 galls were collected, and 1153 parasitoids belonging to 22 species of seven chalcidoid families, plus two individuals of an inquiline Cynipidae, Synergus facialis, emerged. Richness was higher in the Málaga region, with 20 species, while 17 parasitoids and one inquiline were identified in Galicia. The parasitism rate of native chalcid parasitoid species in both regions was low. Eupelmus urozonus and Mesopolobus lichtensteini were the most abundant native species. Mesopolobus tibialis was a dominant species in south Spain, while Ormyrus pomaceus was a dominant species in northwest Spain. Our results revealed the existence of a sub-community of univoltine, probably host specialized, parasitoids in south Spain, which overwinter in galls, exhibiting a similar life cycle to Torymus sinensis. These species were Torymus notatus, Aulogymnus bicolor, Aulogymnus obscuripes and Aulogymnus balani. Data on the recovery of T. sinensis after release in the south Spain region show it to be well established, but its numbers are still low in northwest Spain.
Transmission networks and ectoparasite mite burdens in Oecomys paricola (Rodentia: Cricetidae)
Authors: Fernandes Fernanda Rodrigues , da Silva Abreu Somayra , Cruz Leonardo Dominici
Published: December 2020

The host contact network structure results from the movement and behaviour of hosts (e.g. degree of sociability; vagility and greater or lesser fidelity of shelters), which can generate heterogeneity in the transmission of parasites and influence the parasitic burden of individual hosts. In the current study, we tested the hypothesis that the burdens of Gigantolaelaps oudemansi mites are related to the characteristics of the transmission networks of individuals of Oecomys paricola, a solitary rodent. The study was carried out in a savannah habitat in north-eastern Brazil. In the dry season, the rodent network presented sub-groups of rodent individuals interacting with each other, whereas in the wet season, no modules were formed in the network. Mite burden was positively related to the number of connections that an individual host had with other host individuals in the dry season. The pairwise absolute difference between the mean mite burdens among individual rodents was negatively correlated with the similarities of node interactions. No relationships were observed during the wet season. There was a higher heterogeneity of mite burden among hosts in the dry season compare to that in the wet season. In solitary species, spatial organization may show seasonal variation, causing a change in the opportunities of host contacts, thereby influencing the transmission and dispersion of their ectoparasite burdens.
Harnessing Erebus volcano's thermal energy to power year-round monitoring
Authors: Peters Nial J. , Oppenheimer Clive , Jones Bryn , Rose Michael , Kyle Philip
Published: December 2020

Year-round monitoring of Erebus volcano (Ross Island) has proved challenging due to the difficulties of maintaining continuous power for scientific instruments, especially through the Antarctic winter. We sought a potential solution involving the harvesting of thermal energy dissipated close to the summit crater of the volcano in a zone of diffuse hot gas emissions. We designed, constructed and tested a power generator based on the Seebeck effect, converting thermal energy to electrical power, which could, in principle, be used to run monitoring devices year round. We report here on the design of the generator and the results of an 11 day trial deployment on Erebus volcano in December 2014. The generator produced a mean output power of 270 mW, although we identified some technical issues that had impaired its efficiency. Nevertheless, this is already sufficient power for some monitoring equipment and, with design improvements, such a generator could provide a viable solution to powering a larger suite of instrumentation.
The Atmospheric Drivers of the Major Saharan Dust Storm in June 2020
Authors: Francis Diana , Fonseca Ricardo , Nelli Narendra , Cuesta Juan , Weston Michael , Evan Amato , Temimi Marouane
Published: December 2020

This study investigates the atmospheric dynamics of the major dust storm that occurred in June 2020 over the Sahara and during which dust clouds associated with the highest‐on‐record aerosol optical depths were transported toward the America. An anomalous atmospheric circulation pattern in the mid‐latitudes, linked to a circumglobal wavetrain, resulted in the development of a subtropical high‐pressure system to the west of the Saharan heat low. This created a pressure dipole and generated anomalously strong northeasterlies over the Sahara, which caused continuous dust emissions over 4 days. Occurring along the northern fringes of the intertropical discontinuity, the dust was transported to higher altitudes (6 km) by the strong updraft in this region. This injected the dust at the African Easterly Jet (AEJ) altitudes and favored a rapid westward long‐range transport. The AEJ was also anomalously strong, being strengthened by the anticyclonic circulation associated with the anomalous high.
Testing the Organization of Lower‐Band Whistler‐Mode Chorus Wave Properties by Plasmapause Location
Authors: Malaspina David M. , Jaynes Allison N. , Elkington Scot , Chan Anthony , Hospodarsky George , Wygant John
Published: December 2020

Lower‐band whistler‐mode chorus waves are important to the dynamics of Earth's radiation belts, playing a key role in accelerating seed population electrons (hundreds of keV) to relativistic (>1 MeV) energies, and in scattering electrons such that they precipitate into the atmosphere. When constructing and using statistical models of lower‐band whistler‐mode chorus wave power, it is commonly assumed that wave power is spatially distributed with respect to magnetic L‐shell. At the same time, these waves are known to drop in power at the plasmapause, a cold plasma boundary which is dynamic in time and space relative to L‐shell. This study organizes wave power and propagation direction data with respect to distance from the plasmapause location to evaluate what role the location of the plasmapause may play in defining the spatial distribution of lower‐band whistler‐mode chorus wave power. It is found that characteristics of the statistical spatial distribution of equatorial lower‐band whistler‐mode chorus are determined by L‐shell and are largely independent of plasmapause location. The primary physical importance of the plasmapause is to act as an Earthward boundary to lower‐band whistler‐mode chorus wave activity. This behavior is consistent with an equatorial lower‐band whistler‐mode chorus wave power spatial distribution that follows the L‐shell organization of the particles driving wave growth.
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

The 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

The 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

Lobularia 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

Freezing 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

Clarifying 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

Cross-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

Skin 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

Although 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

Tumor 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

1-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

Advances 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

Alteration 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

Mechanistic 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

To 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.
Structural insights into the bypass of the major deaminated purines by translesion synthesis DNA polymerase
Authors: Jung Hunmin , Hawkins Michael A. , Lee Seongmin
Published: December 2020

The exocyclic amines of nucleobases can undergo deamination by various DNA damaging agents such as reactive oxygen species, nitric oxide, and water. The deamination of guanine and adenine generates the promutagenic xanthine and hypoxanthine, respectively. The exocyclic amines of bases in DNA are hydrogen bond donors, while the carbonyl moiety generated by the base deamination acts as hydrogen bond acceptors, which can alter base pairing properties of the purines. Xanthine is known to base pair with both cytosine and thymine, while hypoxanthine predominantly pairs with cytosine to promote A to G mutations. Despite the known promutagenicity of the major deaminated purines, structures of DNA polymerase bypassing these lesions have not been reported. To gain insights into the deaminated-induced mutagenesis, we solved crystal structures of human DNA polymerase η (polη) catalyzing across xanthine and hypoxanthine. In the catalytic site of polη, the deaminated guanine (i.e. xanthine) forms three Watson–Crick-like hydrogen bonds with an incoming dCTP, indicating the O2-enol tautomer of xanthine involves in the base pairing. The formation of the enol tautomer appears to be promoted by the minor groove contact by Gln38 of polη. When hypoxanthine is at the templating position, the deaminated adenine uses its O6-keto tautomer to form two Watson–Crick hydrogen bonds with an incoming dCTP, providing the structural basis for the high promutagenicity of hypoxanthine.
Varicella-zoster virus: molecular controls of cell fusion-dependent pathogenesis
Authors: Oliver Stefan L. , Zhou Momei , Arvin Ann M.
Published: December 2020

Varicella–zoster virus (VZV) is the causative agent of chicken pox (varicella) and shingles (zoster). Although considered benign diseases, both varicella and zoster can cause complications. Zoster is painful and can lead to post herpetic neuralgia. VZV has also been linked to stroke, related to giant cell arteritis in some cases. Vaccines are available but the attenuated vaccine is not recommended in immunocompromised individuals and the efficacy of the glycoprotein E (gE) based subunit vaccine has not been evaluated for the prevention of varicella. A hallmark of VZV pathology is the formation of multinucleated cells termed polykaryocytes in skin lesions. This cell–cell fusion (abbreviated as cell fusion) is mediated by the VZV glycoproteins gB, gH and gL, which constitute the fusion complex of VZV, also needed for virion entry. Expression of gB, gH and gL during VZV infection and trafficking to the cell surface enables cell fusion. Recent evidence supports the concept that cellular processes are required for regulating cell fusion induced by gB/gH–gL. Mutations within the carboxyl domains of either gB or gH have profound effects on fusion regulation and dramatically restrict the ability of VZV to replicate in human skin. This loss of regulation modifies the transcriptome of VZV infected cells. Furthermore, cellular proteins have significant effects on the regulation of gB/gH–gL-mediated cell fusion and the replication of VZV, exemplified by the cellular phosphatase, calcineurin. This review provides the current state-of-the-art knowledge about the molecular controls of cell fusion-dependent pathogenesis caused by VZV.
End‐to‐end feature fusion Siamese network for adaptive visual tracking
Authors: Guo Dongyan , Wang Jun , Zhao Weixuan , Cui Ying , Wang Zhenhua , Chen Shengyong
Published: December 2020

According to observations, different visual objects have different salient features in different scenarios. Even for the same object, its salient shape and appearance features may change greatly from time to time in a long‐term tracking task. Motivated by them, an end‐to‐end feature fusion framework was proposed based on the Siamese network, named FF‐Siam, which can effectively fuse different features for adaptive visual tracking. The framework consists of four layers. A feature extraction layer is designed to extract the different features of the target region and search region. The extracted features are then put into a weight generation layer to obtain the channel weights, which indicate the importance of different feature channels. Both features and the channel weights are utilised in a template generation layer to generate a discriminative template. Finally, the corresponding response maps created by the convolution of the search region features and the template are applied with a fusion layer to obtain the final response map for locating the target. Experimental results demonstrate that the proposed framework achieves state‐of‐the‐art performance on the popular Temple‐Colour, OTB50 and UAV123 benchmarks.
An innovate approach for retinal blood vessel segmentation using mixture of supervised and unsupervised methods
Authors: Sayed Md. Abu , Saha Sajib , Rahaman G. M. Atiqur , Ghosh Tanmai K. , Kanagasingam Yogesan
Published: December 2020

Segmentation of retinal blood vessels is a very important diagnostic procedure in ophthalmology. Segmenting blood vessels in the presence of pathological lesions is a major challenge. In this paper, an innovative approach to segment the retinal blood vessel in the presence of pathology is proposed. The method combines both supervised and unsupervised approaches in the retinal imaging context. Two innovative descriptors named local Haar pattern and modified speeded up robust features are also proposed. Experiments are conducted on three publicly available datasets named: DRIVE, STARE and CHASE DB1, and the proposed method has been compared against the state‐of‐the‐art methods. The proposed method is found about 1% more accurate than the best performing supervised method and 2% more accurate than the state‐of‐the‐art Nguyen et al.’s method.
Gender discrimination, age group classification and carried object recognition from gait energy image using fusion of parallel convolutional neural network
Authors: Russel Newlin Shebiah , Selvaraj Arivazhagan
Published: December 2020

Age and gender are the two key attributes for healthy social interactions, access control, intelligence marketing etc. Likewise, carried object recognition helps in identifying owner of the baggage being abandoned or the person littering in the public places. The above‐mentioned surveillance task displays discriminative characteristics in gait. Primates can accomplish scene context understanding and reacting to different circumstances with varying reflexes with ease. Human beings achieve this by recollecting prior experiences and adapting to new situations quickly. Modelling the human behaviour, this research work has combined customized and learnable filters so that knowledge database can always be kept up to date, as well as, provides flexibility in learning new contexts. Thus, a specialized parallel deep convolutional neural network architecture with customized filters that extracts intrinsic characteristics and data driven learnable filters are fused to enhance the performance of single convolutional neural network is proposed. From the experimentation it is observed that, the learning is augmented when customized filters and learnable filters are fused together. Results show that the proposed system achieves better performance for CASIA B datAQ2abase and OU‐ISIR gait database‐large population dataset with age and real‐life carried object.
Parameter‐space‐based robust control of event‐triggered heterogene‐ous platoon
Authors: Ma Fangwu , Wang Jiawei , Yu Yang , Wu Liang , Liu Zhenze , Aksun‐Guvenc Bilin , Guvenc Levent
Published: December 2020

A parameter‐space‐based robust platooning controller for the event‐triggered heterogeneous platoon is presented. The novel heterogeneous platoon is established with different longitudinal vehicle dynamic and driving preferences and the event‐triggered communication scheme is designed to reduce the utilization of communication resources. To handle the stricter demand of the heterogeneous system and the disturbance caused by event‐triggered communication scheme, the parameter space approach is adopted to optimize the gains of a robust controller. The feasible region where internal stability and string stability are satisfied is then visualized in the parameters space, by extending the parameter space approach to the D‐stability and frequency response magnitude specifications. Subsequently, the robust controller, which combines the feedforward loop and feedback loop, is developed by selecting the gain from the feasible solution area. The simulation results of the event‐triggered heterogeneous platoon are presented and evaluated to verify the efficiency of this control algorithm. It is seen that the internal stability and string stability of the event‐triggered heterogeneous platoon are guaranteed by this robust controller. Furthermore, 89.7% of communication resources are saved by the application of event‐triggered communication scheme, while the following performance is also favourable during the highway fuel economy cycle.