REVIEW | doi:10.20944/preprints201807.0378.v1
Subject: Life Sciences, Virology Keywords: Yellow fever virus; flavivirus; vector-borne transmission, emergence
Online: 20 July 2018 (05:54:00 CEST)
As revealed by the recent resurgence of yellow fever virus (YFV) activity in the tropical regions of Africa and South America, YFV control measures need urgent rethinking. Over the last decade, most reported outbreaks occurred in, or eventually reached, areas of low vaccination coverage but suitable for virus transmission, with an unprecedented risk of expansion to densely populated territories in Africa, South America and Asia. As reflected in the World Health Organization’s initiative launched in 2017, it is high time to strengthen epidemiological surveillance to monitor accurately, viral dissemination and redefine vaccination recommendation areas. Vector-control and immunisation measures need to be adapted and vaccine manufacturing must be reconciled with an increasing demand. We will have to face more YF cases in the upcoming years hence, improving disease management through the development of efficient treatments will prove most beneficial. Undoubtedly, these developments will require in-depth descriptions of YFV biology at molecular, physiological and ecological levels. This second section of the two-part review describes the current state of knowledge and gaps regarding the molecular biology of YFV, along with an overview of the tools that can be used to manage the disease at the individual, local and global levels.
REVIEW | doi:10.20944/preprints201805.0099.v1
Subject: Life Sciences, Virology Keywords: yellow fever virus; Flavivirus; vector-borne transmission, emergence
Online: 7 May 2018 (05:19:50 CEST)
The recent resurgence of yellow fever virus (YFV) activity in the tropical regions of Africa and South America has sparked renewed interest in this infamous arboviral disease. YFV had been a human plague for centuries prior to the identification of its urban transmission vector, the Aedes aegypti mosquito species, and the development of an efficient live-attenuated vaccine, the YF-17D strain. The combination of vector-control measures and vaccination campaigns drastically reduced YFV incidence in humans on many occasions, but the virus never ceased to circulate in the forest, through its sylvatic invertebrate vector(s) and vertebrate host(s). Outbreaks recently reported in Central Africa (2015-2016) and Brazil (since late 2016), reached considerable proportions in terms of spatial distribution and total numbers of cases, with multiple exports, including to China. In turn, questions regarding the likeliness of occurrence of large urban YFV outbreaks in the Americas or of a successful import of YFV to Asia are currently resurfacing. This two-part review describes the current state of knowledge and gaps regarding the molecular biology and transmission dynamics of YFV, along with an overview of the tools that can be used to manage the disease at the individual, local and global levels.
ARTICLE | doi:10.20944/preprints202005.0390.v1
Subject: Life Sciences, Virology Keywords: Zika; Yellow fever; cross reactive; flavivirus; congenital infection; enhancement
Online: 24 May 2020 (17:12:58 CEST)
Zika virus (ZIKV) is a flavivirus that originated in Africa but emerged in Latin America in 2015. In this region, other flaviviruses such as Dengue (DENV), West Nile, and Yellow Fever Virus (YFV) also circulate, allowing for possible antigenic cross-reactivity to impact viral infections and immune responses. Studies have found antibody mediated enhancement between DENV and ZIKV, but the impact of YFV antibodies on ZIKV infection has not been fully explored. ZIKV infections cause congenital syndromes, such as microcephaly, necessitating further research into ZIKV vertical transmission through the placental barrier. Recent advancements in biomedical engineering have generated co-culture methods that allow for in vitro recapitulation of the maternal: fetal interface. This study utilized a transwell assay, which is a co-culture model utilizing human placental syncytiotrophoblasts, fetal umbilical cells, and a differentiating embryoid body to replicate the maternal: fetal axis. To determine if cross reactive YFV vaccine antibodies impact the pathogenesis of ZIKV across the maternal fetal axis, maternal syncytiotrophoblasts were inoculated with ZIKV or ZIKV incubated with YFV vaccine anti-sera, and viral load was measured 72 hours post inoculation. The data show that the impact of YFV on ZIKV replication is cell line dependent. In differentiating embryoids, the presence of YFV antibodies enhanced ZIKV infection. Since viral pathogenesis, and the impact of antigenic cross-reactive antibodies, is cell line specific at the maternal-fetal axis, this suggests there may be discreet mechanisms that impact congenital ZIKV infections.
COMMUNICATION | doi:10.20944/preprints202112.0406.v1
Subject: Life Sciences, Virology Keywords: Yellow fever; Liver; Vascular endothelium; Adhesion molecule.
Online: 24 December 2021 (11:41:19 CET)
Yellow fever (YF) is a pansystemic disease caused by the yellow fever virus (YFV), the prototype species of the family Flaviviridae and genus Flavivirus, and has a highly complex host-pathogen relationship, in which endothelial dysfunction reflects viral disease tropism. In this study, the in situ endothelial response was evaluated. Liver tissue samples were collected from 21 YFV-positive patients who died due to the disease and five flavivirus-negative controls who died of other causes and whose hepatic parenchyma architecture was preserved. Immunohistochemical analysis of tissues in the hepatic parenchyma of YF cases showed significantly higher expression of E-selectin, P-selectin, intercellular adhesion molecule-1, vascular cell adhesion molecule-1, and very late antigen-4 in YFV-positive cases than in flavivirus-negative controls. These results indicate that endothelium activation aggravates the inflammatory response by inducing the expression of adhesion molecules that contribute to the rolling, recruitment, migration, and construction of the inflammatory process in the hepatic parenchyma in fatal YF cases.
ARTICLE | doi:10.20944/preprints202007.0105.v1
Subject: Life Sciences, Virology Keywords: Zika virus; yellow fever virus; cross-reactivity; neutralization; enhancement; zika congenital syndrome; stem cells
Online: 7 July 2020 (02:29:39 CEST)
Zika virus (ZIKV) is a flavivirus that originated in Africa but emerged in Latin America in 2015. In this region, other flaviviruses such as Dengue (DENV), West Nile, and Yellow Fever Virus (YFV) also circulate, allowing for possible antigenic cross-reactivity to impact viral infections and immune responses. Studies have found antibody mediated enhancement between DENV and ZIKV, but the impact of YFV antibodies on ZIKV infection has not been fully explored. ZIKV infections cause congenital syndromes, such as microcephaly, necessitating further research into ZIKV vertical transmission through the placental barrier. Recent advancements in biomedical engineering have generated co-culture methods that allow for in vitro recapitulation of the maternal: fetal interface. This study utilized a transwell assay, which is a co-culture model utilizing human placental syncytiotrophoblasts, fetal umbilical cells, and a differentiating embryoid body to replicate the maternal: fetal axis. To determine if cross reactive YFV vaccine antibodies impact the pathogenesis of ZIKV across the maternal fetal axis, maternal syncytiotrophoblasts were inoculated with ZIKV or ZIKV incubated with YFV vaccine anti-sera, and viral load was measured 72 hours post inoculation. Here we report that BeWo and HUVEC cells are permissive to ZIKV and that the impact of YFV post-vaccination antibodies on ZIKV replication is cell line dependent. Embryoid bodies are also permissive to ZIKV and the presence of YFV antibodies collected 1 to 6 months post vaccination enhances ZIKV infection. Our data show that each of the cell lines and EBs have a unique response to ZIKV complexed with post-vaccination serum suggesting there may be cell-specific mechanisms that impact congenital ZIKV infections. Since ZIKV infections can cause severe congenital syndromes, it is crucial to understand any potential enhancement or protection offered from cross-reactive, post-vaccination antibodies.
ARTICLE | doi:10.20944/preprints202211.0315.v1
Subject: Biology, Other Keywords: Tick-borne encephalitis virus; Yellow fever virus; vaccine strain; chimeric virus; infectious subgenomic amplicons; candidate vaccines
Online: 16 November 2022 (16:35:12 CET)
Tick-borne encephalitis virus (TBEV) is one of the most threatening pathogens which affects the human central nervous system (CNS). TBEV circulates widely in Northern Eurasia. According to ECDC the number of TBE cases increase annually. There is no specific treatment for the TBEV infection, thus vaccination is the main preventive measure. Despite the existence of several inactivated vaccines currently being licensed, the development of new TBEV vaccines remains a leading priority in countries endemic to this pathogen. Here we report new recombinant virus made by infectious subgenomic amplicon (ISA) approach using TBEV and yellow fever virus vaccine strain (YF17DD-UN) as a genetic backbone. The recombinant virus is capable of effective replication in mammalian cells and induce TBEV-neutralizing antibodies in mice. Unlike the original vector based on the yellow fever vaccine strain chimeric virus became neuroinvasive in doses of 107-106 PFU and can be used as a model of Flavivirus neuroinvasiveness, neurotropism and neurovirulence. These properties of hybrid structures are the main factors limiting their practical use as vaccines platforms.
ARTICLE | doi:10.20944/preprints202106.0022.v1
Subject: Life Sciences, Virology Keywords: Zika; Dengue; Yellow fever; Antivirals; Adamantanes; Amantadine; Rimantadine
Online: 1 June 2021 (10:45:01 CEST)
Zika virus (ZIKV) is a mosquito-born flavivirus which human infection became relevant dur-ing recent outbreaks in Latin America, due to its unrecognized association with fetal neurologi-cal disorders. Currently there are no approved effective antivirals or vaccines for treatment or prevention of ZIKV infections. Amantadine and rimantadine are approved antivirals used against susceptible influenza A virus infections, that have been shown to have antiviral activity against other viruses, such as dengue virus (DENV). Here, we report the in vitro effectiveness of both amantadine and rimantadine hydrochlorides against ZIKV replication, resulting in a dose-dependent reduction in viral titers of a ZIKV clinical isolate and two different ZIKV refer-ence strains. Additionally, we demonstrate similar in vitro antiviral activity of these drugs against DENV-1 and yellow fever virus (YFV), although at higher drug concentrations for the later. ZIKV replication was inhibited at drug concentrations well below cytotoxic levels of both compounds, as denoted by the high selectivity indexes obtained with the tested strains. Further work is absolutely needed to determine a potential clinical use of these antivirals against ZIKV infections, but our results suggest the existence of a highly conserved mechanism across fla-vivirus, susceptible to be blocked by modified more specific adamantane compounds.
ARTICLE | doi:10.20944/preprints202006.0089.v1
Subject: Life Sciences, Genetics Keywords: Wuhua yellow chicken; whole genome resequencing; heritable variation; selection signal
Online: 7 June 2020 (14:42:23 CEST)
Chickens have extensive phenotypic variation. The Wuhua yellow chicken (WHYC) is an important traditional yellow-feathered chicken in China, characterized by white tail feathers, white flight feathers, and strong disease resistance. However, the genomic basis of traits associated with WHYC is still poorly understood. In this study, whole genome resequencing was performed with an average coverage of 20.77-fold to investigate heritable variation and identify selection signals in WHYC. Reads were mapped onto the chicken reference genome (Galgal5) with a coverage of 85.95%. After quality control, 11,953,471 SNPs and 1,069,574 InDels were obtained. In addition, 41,408 structural variants and 33,278 copy number variants were found. A comparative genomic analysis of WHYC and other yellow-feathered chicken showed that selected regions were enriched in genes involved in transport and catabolism, immune system, infectious diseases, signal transduction, and signaling molecules and interaction. Several genes associated with disease resistance were identified, including IFNA, IFNB, CD86, IL18, IL11RA, VEGFC, and ATG10. Furthermore, PMEL and TYRP1 may contribute to the coloring of white feathers in WHYC. These findings improve our understanding of the genetic characteristics of WHYC and may contribute to future breed improvement.
REVIEW | doi:10.20944/preprints202205.0041.v1
Subject: Biology, Plant Sciences Keywords: Amaryllidaceae alkaloids; Biological activities; Traditional medicines; Yellow rain lily; Zephyranthes citrine
Online: 5 May 2022 (12:41:44 CEST)
Zephyranthes citrina Baker is a bulbous herb, commonly known as yellow rain lily belongs to the family Amaryllidaceae. It is a native of tropical and subtropical America but nowadays it is cultivated as a popular ornamental herb in several parts of the world including India. This herb represents one of the richest sources of phytochemicals, especially alkaloids and possesses great potential for pharmaceutical applications. It shows remarkable antiprotozoal, antimicrobial, anti-Alzheimer, cytotoxic, antioxidant, anti-inflammatory, analgesic, and dye removal activities. This review is an effort to give a detailed study of the literature on the biological activities of Zephyranthes citrina. This review concludes that Zephyranthes citrina has a great potential to treat various diseases and could be used as a source for novel healthcare products in the near future, which requires further experimentation.
ARTICLE | doi:10.20944/preprints201809.0465.v1
Subject: Life Sciences, Other Keywords: Phaseolus vulgaris L., yellow beans, Manteca, cooking time, iron, bioavailability, polyphenols
Online: 24 September 2018 (15:24:38 CEST)
The common dry bean (Phaseolus vulgaris L.) is a nutrient dense food produced globally as a major pulse crop for direct human consumption, and is an important source of protein and micronutrients for hundreds of millions of people across Latin America, the Caribbean and Sub-Saharan Africa. Beans require large amounts of heat energy and time to cook, deterring consumers worldwide from purchasing beans. In regions where consumers rely on expensive fuelwood for food preparation, the yellow bean is often marketed as fast cooking. A Yellow Bean Panel (YBP) was assembled to explore the cooking time and health benefits of the five major seed types within the yellow bean market class (Amarillo, Canary, Manteca, Mayocoba, Njano) over two field seasons. This study shows how the Manteca yellow bean possess a fast cooking phenotype, which could serve a genetic resource for introducing fast cooking properties into a new generation of dry beans with cooking times < 20 minutes when pre-soaked and < 80 minutes unsoaked. Nutritional evaluation revealed fast cooking yellow beans have high iron retention (>80%) after boiling. An in vitro digestion/Caco-2 cell culture bioassay revealed a strong negative association between cooking time and iron bioavailability in the YBP (r values > -0.73). When either pre-soaked or left unsoaked the highest iron bioavailability scores were measured in the fast cooking Manteca genotypes providing evidence that this yellow market class is worthy of germplasm enhancement through the added benefit of improved iron quality after cooking.
ARTICLE | doi:10.20944/preprints201805.0384.v1
Subject: Engineering, Civil Engineering Keywords: fracture grouting; cement-silicate grout; geophysical prospecting; seepage; Yellow River Embankment
Online: 28 May 2018 (05:45:00 CEST)
Fracture grouting has been a widely used mitigation measure against seepage in the Yellow River Embankment. However, there is currently a lack of systematic investigation for evaluating the anti-seepage effectiveness of fracture grouting employed in this longest river embankment in China. Therefore, in this work, laboratory and in-situ experiments are carried out for investigating the reinforcement effect of fracture grouting in the Jinan Section of the Yellow River Embankment. In particular, firstly, the laboratory tests concentrate on studying the optimum strength improvement for cement-silicate grout by varying the content of backfilled fly ash and bentonite as admixtures. Flexural strength and Scanning Electron Microscope photographs are investigated for assessing the strength and compactness improvement. Subsequently, based on the obtained optimum admixtures content, in-situ grouting tests are carried out in the Jinan Section of the Yellow River Embankment to evaluate the anti-seepage effectiveness of fracture grouting, where geophysical prospecting and pit prospecting methods are employed. Laboratory results show that, compared with pure cement-silicate grouts, the gelation time of the improved slurry is longer and gelation time increases as fly ash content increases. The optimum mixing proportion of the compound cement-silicate grout is 70% cement, 25% fly ash and 5% bentonite, and the best volume ratio is 2 for the investigated cases. Geophysical prospecting using the Ground Penetrating Radar and High Density Resistivity methods can reflect the anti-seepage effectiveness of fracture grouting on site. It shows that the grouting material mainly flows along the axial direction of the embankment. The treatment that is used to generate directional fracture is proved to be effective. The injection hole interval distance is suggested to be 1.2 m, where the lapping effect of the grouting veins is relatively significant. For the investigated cases, the average thickness of the grouting veins is approximately 6.0 cm and the corresponding permeability coefficient is averagely 1.6 × 10−6 cm/s, which meets the anti-seepage criterion in practice.
ARTICLE | doi:10.20944/preprints202301.0154.v1
Subject: Engineering, Biomedical & Chemical Engineering Keywords: Amine functionalized MWCNTs; Reactive yellow 2; Adsorption; Rapid removal; Ionic strength; Reusability
Online: 9 January 2023 (09:02:49 CET)
This research intended to report amine-functionalized multiwall carbon nanotubes (MWCNTs) prepared by a simple method for efficient and rapid removal of Reactive Yellow 2 (RY2) from water. EDS analysis showed that the N content increased from 0 to 2.42% and from 2.42 to 8.66% after modification by APTES and PEI, respectively. BET analysis displayed that the specific surface area, average pore size, and total pore volume were reduced from 405.22 to 176.16 m2/g, 39.67 to 6.30 nm, and 4.02 to 0.28 cm3/g, respectively. These results proved that the PEI/APTES-MWCNTs were successfully prepared. pH edge experiment indicated that pH 2 was optimal for RY2 removal. At pH 2 and 25 °C, the time required for adsorption equilibrium was 10, 15, and 180 min at initial concentrations of 50, 100, and 200 mg/L, respectively; and the maximum RY2 uptake calculated by the Langmuir model was 714.29 mg/g. Thermodynamic studies revealed that the adsorption process was spontaneous and endothermic. 0-0.1 mol/L of NaCl showed negligible effect on RY2 removal by PEI/APTES-MWCNTs. Five adsorption/desorption cycles confirmed the good reusability of PEI/APTES-MWCNTs in RY2 removal. Overall, the PEI/APTES-MWCNTs are a potential and efficient adsorbent for reactive dye wastewater treatment.
ARTICLE | doi:10.20944/preprints201610.0023.v1
Subject: Earth Sciences, Geophysics Keywords: climate change; water cycle; downscaling; hydrological model; Yangtze River; Yellow River; Tibetan Plateau
Online: 8 October 2016 (11:29:05 CEST)
Climate change is a global issue that draws widespread attention from the international society. As an important component of the climate system, the water cycle is directly affected by climate change. Thus, it is very important to study the influences of climate change on the basin water cycle with respect to maintenance of healthy rivers, sustainable use of water resources, and sustainable socioeconomic development in the basin. In this study, by assessing the suitability of multiple General Circulation Models (GCMs) recommended by the Intergovernmental Panel on Climate Change, Statistical Downscaling Model (SDSM) and Automated Statistical Downscaling model (ASD) were used to generate future climate change scenarios. These were then used to drive distributed hydrologic models (Variable Infiltration Capacity, Soil and Water Assessment Tool) for hydrological simulation of the Yangtze River and Yellow River basins, thereby quantifying the effects of climate change on the basin water cycle. The results showed that suitability assessment adopted in this study could effectively reduce the uncertainty of GCMs, and that statistical downscaling was able to greatly improve precipitation and temperature outputs in global climate mode. Compared to a baseline period (1961–1990), projected future periods (2046–2065 and 2081–2100) had a slightly decreasing tendency of runoff in the lower reaches of the Yangtze River basin. In particular, a significant increase in runoff was observed during flood seasons in the southeast part. However, runoff of the upper Yellow River basin decreased continuously. The results provide a reference for studying climate change in major river basins of China.
ARTICLE | doi:10.20944/preprints201903.0021.v1
Subject: Engineering, Industrial & Manufacturing Engineering Keywords: White rot fungus; Co-immobilization; Dye wastewater treatment; Dye decolorisation; Acid golden yellow dye
Online: 4 March 2019 (09:04:40 CET)
The dye effluent is usually difficult to be degraded by conventional wastewater treatment in leather industry. In order to develop efficient and cost-effective treatment methods, we evaluate the effect of white-rot fungus immobilization for dye decolorisation in this paper. The Phanerochaete chrysosporium BKM-F-1767 was used for immobilization. This research found that the white-rot fungus immobilization had an obviously decolorisation effect in dye wastewater treatment, and plant carriers such as sorghum stalk and corn cob were helpful to the growth of Phanerochaete chrysosporium in white-rot fungus immobilization. Due to the stability and recyclability, the white-rot fungus co-immobilization was considered as the most suitable treatment for decolorisation of dye effluent which enjoyed the advantages of both adsorption immobilization and entrapment immobilization. Furthermore, the dye decolorisation evaluation was carried out to find the most suitable carrier for co-immobilization, and it found that sorghum stalk - calcium-alginate gel spherical particle (SS-CGPB) has better decolorisation effect than corn cobs - calcium-alginate gel spherical particle (CC-CGPB), and the dye decolorisation rate was 86.77%. After 5 cycles, the dye decolorisation rate was 85.87% which indicated the SS-CGPB preserved functional integrity successfully. By further analyzing the biodegradation process with white-rot fungus immobilization, the intermediate products were observed and the degradation pathway of acid golden yellow dye molecular was proposed. The results showed that the C-N single bonds attached to the central benzene in the dye molecule were attacked and destroyed in white-rot fungus co-immobilization treatment, thus the structure of dye molecule could be successfully degraded into small molecules which would be more easily treated by conventional treatment methods. Therefore, the white rot fungus co-immobilization might be appropriate for pre-treatment as an important biotechnology for the advanced treatment of dye effluent.
ARTICLE | doi:10.20944/preprints202109.0240.v1
Subject: Biology, Agricultural Sciences & Agronomy Keywords: Gene Silencing; Host–Virus Interaction; RNA Interference; Saccharum officinarum; Sugarcane Yellow Leaf Virus and Target Prediction
Online: 14 September 2021 (12:43:22 CEST)
The Sugarcane yellow leaf virus (SCYLV) is associated with sugarcane yellow leaf disease (SCYLD) and is considered to be the most economically deleterious emerging pathogen that represents a potential threat and danger to sugarcane cultivation in China. Over the last two decades, high genetic diversity in the SCYLV genotypes was observed worldwide, with a greater chance of YLD incidence for sugarcane injury. SCYLV infection has significantly damaged its economic traits and is responsible for substantial losses in biomass production in sugarcane cultivars. This study aims to identify and comprehensively analyze sugarcane microRNAs (miRNAs) as therapeutic targets against SCYLV using plant miRNA prediction tools. Mature sugarcane miRNAs are retrieved and are used for hybridization of the SCYLV. A total of seven common sugarcane miRNAs were selected based on consensus genomic positions. The biologically significant, top ranked ssp-miR528 was consensually predicted to have a potentially unique hybridization site at nucleotide position 4162 for targeting the ORF5 of the SCYLV genome; this was predicted by all the algorithms used in this study. Then, the miRNA–mRNA regulatory network was generated using the Circos algorithm, which was used to predict novel targets. There are no acceptable commercial SCYLV-resistant sugarcane varieties available at present. Therefore, the predicted biological data offer valuable evidence for the generation of SCYLV-resistant sugarcane plants.
ARTICLE | doi:10.20944/preprints202011.0400.v1
Subject: Biology, Anatomy & Morphology Keywords: Geminivirus; bipartite begomovirus; transcriptional trans-activation; abscisic acid; promoter motifs; AC2; BV1; mungbean yellow mosaic virus
Online: 16 November 2020 (08:44:26 CET)
Geminiviruses possess single-stranded, circular DNA genomes, and control the transcription of their late genes, including BV1 of many bipartite begomoviruses, through transcriptional activation by the early expressing AC2 protein. DNA binding by AC2 is not sequence-specific, hence the specificity of AC2 activation is thought to be conferred by plant transcription factors (TFs) recruited by AC2 in infected cells. However, the exact TFs AC2 recruits are not known for most viruses. Here we report a systematic examination of the BV1 promoter (PBV1) of mungbean yellow mosaic virus (MYMV) for conserved promoter motifs. We found that MYMV PBV1 contains three abscisic acid (ABA)-responsive elements (ABREs) within its first 70 nucleotides. Deleting these ABREs, or mutating them all via site-directed mutagenesis, abolished the capacity of PBV1 to respond to AC2-mediated transcriptional activation. Furthermore, ABRE and other related ABA-responsive elements were prevalent in more than a dozen Old World begomoviruses we inspected. Together these findings suggest that ABA-responsive TFs may be recruited by AC2 to BV1 promoters of these viruses to confer specificity to AC2 activation. These observations are expected to guide the search for the actual TF(s), furthering our understanding of the mechanism of AC2 action.
ARTICLE | doi:10.20944/preprints201910.0173.v1
Subject: Biology, Animal Sciences & Zoology Keywords: UAV remote sensing; large wild herbivore populations; grazing pressure; functional zones; Yellow-River-Source National Park
Online: 16 October 2019 (04:30:27 CEST)
Using the Yellow-River-Source National Park (YRSNP) as a study site, an unmanned aerial vehicle (UAV) remote sensing and line transect method was used to investigate the number of wild herbivorous animals and livestock, including the kiang (Equus kiang) and Tibetan gazelle (Procapra picticaudata). A downscaling algorithm was used to generate the forage yield data in YRSNP based on 30 m spatial resolution. On this basis, we estimated the forage–livestock balance, which included both wild animals and livestock, and analyzed the effects of functional zone planning in national parks on the forage–livestock balance in YRSNP. The results showed that the estimates of large herbivore population numbers in YRSNP based on population density in the aerial sample strips, which were compared and validated with statistical data and warm season survey results, indicated that the number of kiangs and Tibetan gazelles in the 2017 cold season was 12900 and 12100, respectively. The number of domestic yaks, Tibetan sheep, and horses was 53400, 76800, and 800, respectively, and the total number of sheep units was 353200. The ratio of the number of large wild herbivores and livestock sheep units was 1:5; Large wild herbivores have different preferences for functional zones, preferring ecological restoration areas consisting mainly of degraded grassland; The grazing pressure indices of the core reserve areas and ecological restoration areas were 0.168 and 0.276, respectively, indicating that these two regions still have high grazing potential. However, the grazing pressure index of the traditional utilization areas was 1.754, indicating that these grasslands are severely overloaded; After the planning and implementation of functional zones, the grazing pressure index of YRSNP was 1.967. Under this measure, the number of livestock was not reduced and the grazing pressure nearly doubled, indicating that forage–livestock conflict has become more severe.
ARTICLE | doi:10.20944/preprints202007.0081.v1
Subject: Biology, Animal Sciences & Zoology Keywords: Dryophytes immaculatus; Dryophytes suweonensis; Dryophytes flaviventris; Yellow sea; North East Asia; threat; amphibian; recommendation IUCN Red List
Online: 5 July 2020 (15:17:27 CEST)
Threat assessment is important to prioritize species conservation projects and planning. The taxonomic resolution regarding the status of the “Dryophytes immaculatus group” and the description of a new species in the Republic of Korea resulted in a shift in ranges and population sizes. Thus, reviewing the IUCN Red List status of the three species from the group: D. immaculatus, D. suweonensis and D. flaviventris and recommending an update is needed. While the three species have similar ecological requirements and are distributed around the Yellow sea, they are under contrasting anthropological pressure and threats. Here, based on the literature available, I have applied all IUCN Red List criteria and tested the fit of each species in each criteria to recommend listing under the adequate threat level. This resulted in the recommendation of the following categories: Near Threatened for D. immaculatus, Endangered following the criteria C2a(i)b for D. suweonensis and Critically Endangered following the criteria E for D. flaviventris. All three species are declining, mostly because of landscape changes as a result of human activities, but the differences in range, population dynamics and already extirpated sub-populations result in different threat levels for each species. Dryophytes flaviventris is under the highest threat category mostly because of its limited range, segregated into two sub-populations and several known historical sub-populations are now extirpated. Immediate actions for the conservation of this species are required. Dryophytes suweonensis is present in both the Republic of Korea and the Democratic Republic of Korea and is under lower ecological pressure in DPR Korea. Dryophytes immaculatus is present in the People’s Republic of China, on a very large range despite a marked decline. I recommend joint efforts for the conservation of these species.
ARTICLE | doi:10.20944/preprints202212.0249.v1
Subject: Biology, Entomology Keywords: tan; Drosophila; Drosophila guttifera; CRM; cis-regulatory; evo-devo; yellow; transcription factor; cis-regulatory module; cis-regulatory element
Online: 14 December 2022 (06:48:07 CET)
How complex morphological patterns form is an intriguing question in developmental biology. However, the mechanisms that generate complex patterns remain largely unknown. Here we sought to identify the genetic mechanisms that regulate the tan (t) gene in a multi-spotted pigmentation pattern on the abdomen and wings of Drosophila guttifera. Previously, we showed that yellow (y) gene expression completely prefigures the abdominal  and wing  pigment patterns of this species. In the current study, we demonstrate that the t gene is co-expressed with the y gene in nearly identical patterns, both transcripts foreshadowing the adult abdominal and wing melanin spot patterns. We identified cis-regulatory modules (CRMs) of t, one of which drives reporter expression in six longitudinal rows of spots on the developing pupal abdomen, while the second CRM activates the reporter gene in a spotted wing pattern. Comparing the abdominal spot CRMs of y and t, we found a similar composition of putative transcription factor binding sites that are thought to regulate the complex expression patterns of both terminal pigmentation genes y and t. In contrast, the y and t wing spots appear to be regulated by distinct upstream factors. Our results suggest that the D. guttifera abdominal and wing melanin spot patterns have been established through the co-regulation of y and t, shedding light on how complex morphological traits may be regulated through the parallel coordination of downstream target genes.
ARTICLE | doi:10.20944/preprints202209.0258.v1
Subject: Engineering, Energy & Fuel Technology Keywords: Sedimentary; Heterogeneous porous carbonate reservoirs; Isotope analysis; Carboniferous-Early Permian; Central Uplift of the South Yellow Sea Basin
Online: 19 September 2022 (04:45:33 CEST)
Mesozoic-Palaeozoic marine carbonate rocks are important hydrocarbon reservoirs in the Central Uplift area of the South Yellow Sea Basin (SYSB). Due to the lack of boreholes and the great heterogeneity of carbonate reservoirs, the distribution of porous carbonate reservoirs and their related key controlling factors remain unclear. Based on seismic inversion and isotope analysis, this study explores the factors affecting the distribution of porous Carboniferous-Early Permian carbonate reservoirs in the SYSB. In this study, the log-seismic characteristics of porous carbonate reservoirs, sensitive lithology parameters, and physical property parameters are extracted and analyzed. The pre-stack simultaneous inversion technique is applied to predict the lithology properties and physical properties of the porous carbonate reservoirs. Moreover, the sedimentary of carbonate is analyzed using isotopes of carbon, oxygen, and strontium. The results indicate that porous carbonate reservoirs with porosities of 3%~5% mainly occur at the paleo-highland (Huanglong Formation and Chuanshan Formation) and the slope of paleo-highland (Hezhou Formation). The porous carbonate reservoirs of the Qixia Formation are only locally developed. In addition, the study area was dominated by a warm and humid tropical climate from the Carboniferous to Early Permian, with four sea-level eustatic fluctuation indicated by the negative and positive δ13C excursions. When the sea level fell, the study area was exposed and denuded, and the supply of terrigenous detrital was dominated, which significantly influenced the carbonate deposit and diagenesis. This study highlights that sedimentation was a key factor in controlling the quality of Carboniferous-Early Permian carbonate reservoirs. The methods proposed in this study can be used in other carbonate-dominated strata worldwide.
ARTICLE | doi:10.20944/preprints202104.0755.v1
Subject: Life Sciences, Biochemistry Keywords: wheat; leaf rust; powdery mildew; septoria; stem rust; yellow rust; image recognition; deep learning; convolutional neural network; phenotyping
Online: 28 April 2021 (15:35:37 CEST)
Diseases of cereals caused by pathogenic fungi can significantly reduce crop yields. Many cultures are exposed to them. The disease is difficult to control on a large scale, thus one of the relevant approaches is the crop field monitoring, which helps to identify the disease at an early stage and take measures to prevent its spread. One of the effective control methods is disease identification based on the analysis of digital images with the possibility of obtaining them in field conditions using mobile devices. In this work, we propose a method for the recognition of five fungal diseases of wheat shoots (leaf rust, stem rust, yellow rust, powdery mildew, and septoria), both separately and in combination, with the possibility of identifying the stage of plant development. A set of 2414 images of wheat fungi diseases (WFD2020) was generated, for which expert labeling was performed by the type of disease. WFD2020 data are available freely at http://wfd.sysbio.ru/. In the process of creating this set, a method was applied to reduce the degeneracy of the training data based on the image hashing algorithm. The disease recognition algorithm is based on the convolutional neural network with the EfficientNet architecture. The best accuracy (0.942) was shown by a network with a training strategy based on augmentation and transfer of image styles. The recognition method was implemented by the authors as a bot on the Telegram platform, which allows assessing plants by lesions in the field conditions.
ARTICLE | doi:10.20944/preprints201811.0476.v1
Subject: Earth Sciences, Geoinformatics Keywords: remotely sensed drought indices (RSDIs); Standardized Precipitation Evapotranspiration Index (SPEI); meteorological drought; Skill Score (SS); Yellow River basin (YRB)
Online: 19 November 2018 (17:26:37 CET)
Due to the advantages of wide coverage and continuity, remotely sensed data are widely used for large-scale drought monitoring to compensate the deficiency and discontinuity of meteorological data. However, few researches have focused on the capability of various remotely sensed drought indices (RSDIs) for representing the spatio-temporal variations of the meteorological droughts. In this study, five RSDIs, namely Vegetation Condition Index (VCI), Temperature Condition Index (TCI), Vegetation Health Index (VHI), Modified Temperature Vegetation Dryness Index (MTVDI) and Normalized Vegetation Supply Water Index (NVSWI) were calculated using Moderate Resolution Imaging Spectroradiometer (MODIS) monthly NDVI and LST. The monthly NDVI and LST data were filtered by Savitzky-Golay (S-G) filtering method. Meteorological station-based drought index represented by Standardized Precipitation Evapotranspiration Index (SPEI) was compared with RSDIs. And the dimensionless Skill Score (SS) method was adopted to identify the spatiotemporally optimal RSDIs for presenting the meteorological droughts in the Yellow River basin (YRB) from 2000 to 2015. The results indicated that (1) RSDIs revealed a decreasing trend to the overall YRB consistent with SPEI except for in winter, and different variations of seasonal trends spatially; (2) the optimal RSDIs in spring, summer, autumn and winter were VHI, TCI, MTVDI and VCI, respectively, and the average correlation coefficient between the RSDIs and SPEI was 0.577 (=0.05); (3) different RSDIs have a 0–3 months’ time-lags compared with meteorological drought index.
ARTICLE | doi:10.20944/preprints202106.0020.v1
Subject: Life Sciences, Virology Keywords: Vesicular Stomatitis; Herpes Simplex; Yellow Fever; Animal Viruses; Plaque Assay; Real-time; Live Cell Imaging, Automated Image Analysis; DNA Fluorescent Dyes, Antiviral Screening
Online: 1 June 2021 (10:40:37 CEST)
Conventional plaque assays rely on the use of overlays to restrict viral infection allowing the formation of distinct foci that grow in time as the replication cycle continues leading to counta-ble plaques that are visualized with standard techniques such as crystal violet, neutral red or immunolabeling. This classical approach takes several days until large enough plaques can be visualized and counted with some variation due to subjectivity in plaque recognition. Since plaques are clonal lesions produced by virus-induced cytopathic effect, we applied DNA fluores-cent dyes with differential cell permeability to visualize them by live cell imaging. We could observe different stages of that cytopathic effect corresponding to an early wave of cells with chromatin-condensation followed by a wave of dead cells with membrane permeabilization within plaques generated by different animal viruses. This approach enables an automated plaque identification using image analysis to increase single plaque resolution compared to crystal violet counterstaining and allows its application to plaque tracking and plaque reduction assays to test compounds for both antiviral and cytotoxic activities. This fluorescent real-time plaque assay sums to those next-generation technologies by combining this robust classical method with modern fluorescence microscopy and image analysis approaches for future applica-tions in virology.
ARTICLE | doi:10.20944/preprints202211.0005.v1
Subject: Life Sciences, Other Keywords: Epidemics; Twitter; Natural Language Processing; Topic Modelling; Sentiment Analysis; ARI; Cholera; Ebola; HIV/AIDS; Influenza; Malaria; Spanish influenza; Swine flu; Tuberculosis; Typhus; Yellow fever; and Zika
Online: 1 November 2022 (01:17:14 CET)
At the end of 2019, while the world was being hit by the COVID-19 virus and, consequently, was living a global health crisis, many other pandemics were putting humankind in danger. The role of social media is of paramount importance in these kinds of contexts since they help health systems to cope with emergencies by contributing to conducting some activities such as the identification of public concerns, the detection of infections’ symptoms, and the traceability of the virus diffusion. In this paper, we have analyzed comments on events related to cholera, ebola, HIV/AIDS, influenza, malaria, Spanish influenza, swine flu, tuberculosis, typhus, yellow fever, and zika, collecting 369,472 tweets from the 3rd of March to the 15th of September, 2022. Our analysis has started with the collection of comments composed of unstructured texts on which we have applied natural language processing solutions. Afterward, we have employed topic modelling and sentiment analysis techniques to obtain a collection of people’s concerns and attitudes toward these pandemics. According to our findings, people's discussions were mostly about malaria, influenza, and tuberculosis and the focus was on the diseases themselves. As regards emotions, the most popular were fear, trust, and disgust where trust is mainly regarding HIV/AIDS tweets.