Miracle-dz/UniFAR-FTUs huggingface dataset:
Physiological and Biochemical Responses in Cucurbita pepo Leaves Associated with Some Elicitors-Induced Systemic Resistance against Zucchhini yellow mosaic virus

In a greenhouse experiment, four treatments (Salix alba water extract, Mannitol solution, Pomegranate peel water extract andSpirulina sp. filtrate), were tested as seeds soaking for induction systemic resistance in Cucurbita pepo cv. Eskandarani plants against Zucchhini yellow mosaic virus (ZYMV). The results demonstrated that ZYMV challenged plants emerged from Salix-soaked seeds and Spirulina-soaked seeds not only showed a pronounced and significant reduction in percent disease severity (DS) but also a significant reduction in the virus concentration (ELISA), compared to challenged control plants. Results from analysis of physiological parameters indicated that viral infection and seeds soaked treatments affected metabolism. Viral infection decreased photosynthetic pigments, carbohydrate and protein levels. An alleviation of ZYMV severe infection effects was evidenced by alteration in the photosynthetic pigments, the carbohydrate and protein contents in challenged treatments (Salix+V, Mannitol+V, Pomegranate peel+V and Spirulina+V). Moreover, the other biochemical parameters showed variable alterations, where the proline content and antioxidant enzymes activities were induced by both viral infection and treatments compared to absolute control plants. On the other hand, IAA and GA3 were significantly decreased, while ABA, JA and SA contents were significantly increased due to the viral infection. Significantly, higher IAA GA3, JA and SA, levels were observed in leaves of non-challenged treatments (Salix and Spirulina) and challenging treatments (Salix+V and Spirulina+V), while the ABA content was significantly decreased compared to absolute control (AC) and challenged control (ChC). In addition, protein patterns using SDS-PAGE represent two newly synthesized polypeptides (46 and 41 KDa) which reflect formation of pathogenesis related proteins in challenged treatments (Salix+V and Spirulina+V), respectively. Also, Salix and Spirulina increased the density and number of peroxidase and polyphenoloxidase isozymes. It can be concluded thatSalix and Spirulina treatments increase the Cucurbita pepo cv. Eskandarani plants resistance against ZYMV.
Differences in TLR2 pattern recognition receptor expression on blood mononuclear cells with and without ligand stimulation among dairy cattle classified by estimated breeding value (EBV) of adaptive immune response

NSERC (I2I and Discovery Grants), OMAFRA (KTT Grant) and CDN (NSERC-CRD grant). Graduate training was supported by an Ontario Graduate Scholarship, an OVC Graduate Program Scholarship, an award from the Canadian Agri-Food Policy Institute (CAPI), and stipends provided by Dr. B. Mallard.
Effects of dietary spent pink guava mesocarp on egg quality of caged and free-range layers

Pink guava is known to contain high levels of lycopene, a carotenoid that have one of the highest antioxidant activities. Lycopene was also indicated to produce good pigmentation in egg yolk. Feeding studies on laboratory animals using spent pink guava mesocarp (SPGM), which contains lycopene, indicated that SPGM has high antioxidant properties, has lipid–lowering effect and prevented obesity. There is no information regarding the effect of dietary SPGM on other animals such as laying hens. Therefore two studies were conducted to evaluate the SPGM product and its effect on the performance and egg quality of the layer chicken. In the first study, nutrient profiles and lycopene content of three batches of SPGM from different fruit harvesting dates were evaluated and were found to be consistent among batches. The second study was a 9-week feeding trial using a total of 90 ISA Brown layer chicken aged 30 weeks under two management systems. Treatment diets consisted of (i) control diet (without SPGM); (ii) diet with 2.5% SPGM, (iii) diet with 5% SPGM; (iv) diet with 7.5% SPGM, and (v) diet with 10% SPGM. The SPGM used were in dried form. Inclusion of 5% to10% SPGM in layer chicken diet significantly (p<0.05) improved feed intake, Feed Conversion Ratio (FCR), egg production, egg weight, eggshell weight, eggshell thickness, Haugh unit, egg mass, and egg yolk color, regardless of the cage system or free-range system. Yolk color score (based on DSM Yolk Color Fan) improved with SPGM inclusion. The SPGM dietary inclusion from 5% to 10% of SPGM registered yolk color score of up to 6 and 8 for cage rearing and free-ranging, respectively. Lycopene content in egg yolk increased linearly with increased in SPGM inclusion in the diet. Eggs from hens fed with SPGM had a significant lower cholesterol (p<0.05) content compared to the control group. It is concluded that feeding layer hens with SPGM enriched the eggs with lycopene besides improving the yolk color score. These eggs are also lower in cholesterol and SPGM-based eggs can become an alternative health product.
Extraction, Isolation and Identification of Antimicrobial Substances from Bacillus amyloliquefaciens CMN1308

Four separation methods of antimicrobial substances produced by CMN1308 ( Bacillus amyloliquefaciens ) were evaluated and selected according to number of antimicrobial substances and its activity in vitro . The results showed that extraction by acid precipitation of the fermentation supernatant of CMN1308 was the best with a diameter of inhibition zone of pathogen fungi P. expansum of 12.3 mm in a laboratory bioassay. Applying a silica thin layer chromatography (TLC), SDS-PAGE and other separation technologies we isolate antimicrobial substances, and the separated band were cut off for mass spectrometry analysis. The TLC of crude extract of CMN1308 show a topical band corresponding with the surfactin standard (Rf value =0.75), proved that the strain CMN1308 can produce this surface active compound. The mycoprotein extracted from CMN1308 was separated by Tricine-SDS-PAGE modified with the addition of urea in the separation gel. After mass spectrometric analysis and protein characterization, the isolated mycoprotein showed a maximum ion peak at M/Z of 2679 and molecular weight of 29.5 kDa, matching with protein flagellin. The extracellular antimicrobial protein of strain CMN1308 display four bands after urea-Tricine-SDS-PAGE, but after mass spectrometry analysis only two bands were identified. Band “A” with a maximum ion peak at M/Z of 1926 and molecular weight of 49.8 kDa, aligned with NCBI database, matching with DLDH (dihydrolipoamide dehydrogenase enzyme). Band “D” show the maximum ion peak at M/Z of 2936 and molecular weight of 22.4 kD, matching with a chitin binding protein. Thus, the strain CMN1308 has the potential to be developed as a commercial biological control agent for chestnut common pathogenic fungi.
Serial quantification of brain oxygenation in acute stroke using streamlined-qBOLD

It has been proposed that metabolic markers of baseline brain oxygenation have a role to play in the early identification of the ischemic penumbra. Streamlined-qBOLD is a magnetic resonance imaging technique that does not require exogenous contrast. It is a refinement of the quantitative BOLD methodology that provides a simplified approach to mapping and quantifying baseline brain oxygenation related parameters (reversible transverse relaxation rate (R2′), deoxygenated blood volume (DBV) and deoxyhaemoglobin concentration ([dHb])) in a clinically relevant manner. Streamlined-qBOLD was applied to an exploratory cohort of acute stroke patients in a serial imaging study. Detailed voxel-level analysis was used to quantify the metabolic profile of ischaemic tissue on presentation and investigate these metrics in relation to tissue outcome. Individual patient examples illustrate the appropriate interpretation of R2′, DBV and [dHb] in acute stroke and demonstrate the ability of this method to deliver regional information related to oxygen metabolism in the ischaemic tissue. Regional analysis confirms that R2′, DBV and [dHb] vary between regions of ischaemia with different tissue outcomes.
A theory of participation: what makes stakeholder and public engagement in environmental management work?

This article differentiates between descriptive and explanatory factors to develop a typology and a theory of stakeholder and public engagement. The typology describes different types of public and stakeholder engagement, and the theory comprises four factors that explain much of the variation in outcomes (for the natural environment and/or for participants) between different types of engagement. First, we use a narrative literature search to develop a new typology of stakeholder and public engagement based on agency (who initiates and leads engagement) and mode of engagement (from communication to coproduction). We then propose a theory to explain the variation in outcomes from different types of engagement: (1) a number of socioeconomic, cultural, and institutional contextual factors influence the outcomes of engagement; (2) there are a number of process design factors that can increase the likelihood that engagement leads to desired outcomes, across a wide range of sociocultural, political, economic, and biophysical contexts; (3) the effectiveness of engagement is significantly influenced by power dynamics, the values of participants, and their epistemologies, that is, the way they construct knowledge and which types of knowledge they consider valid; and (4) engagement processes work differently and can lead to different outcomes when they operate over different spatial and temporal scales. We use the theoretical framework to provide practical guidance for those designing engagement processes, arguing that a theoretically informed approach to stakeholder and public engagement has the potential to markedly improve the outcomes of environmental decision‐making processes.
Glia to glioma: A wrathful journey

Glial cells, unlike neurons in the brain, can undergo cellular division to maintain their functional continuity. However, sometimes this divisional attribute gets uncontrolled, which breaches tissue organization and transforms tissues into neoplasm. The proliferative abnormality of neuroglia results in one of the most dreaded neoplasm amounting to 30% of all brain tumors—the glioma. The abnormal proliferation, high level of progression and invasive potential makes glioma one of the most lethal killers in its class. The pathological scenario becomes more moribund owing to poor prognosis and high mortality rate of the menace. Conventional onco-therapies yield dismal results compared to other soft tissue tumors. In time, with the advent of newer trends of prognosis and treatment modalities in the field of oncology, a hope for betterment is expected, but not yet achieved. These advancements would fetch some better results with proper and minute understanding of the biology of glioma, both at physiological as well as molecular level. In the present context, we have tried to document an insight to glioma biology that can serve as a primer to understand this lethal killer and its killing spree, with some approaches to combat its carnage.
China's desertification deconstructed: towards a scientists' model based on long‐term perceptions of grassland restoration (1995–2011)

There is considerable debate about the causes of grassland degradation and desertification in China. The discussion is rekindled by recent studies that claim restoration. The reversal in degradation is attributed to policies, which include the grazing ban and the pasture contract system. Contrarily, this article maintains that these studies disregard the complexity and multilayered nature of grassland degradation, and questions whether aforementioned policies have had this effect. In this context, we report on one of the first long‐term surveys (1995 and 2011) of herders' perceptions. The survey (492 valid responses) represents two ecoregions: the semiarid desert/steppe and Loess Plateau pasture. Based on the data, we adopted a renewed analytical model for scientists, termed the CCC‐Framework. The model calls for caution in proposing certain restoration measures when uncertainties are identified around a “triple C”: (1) condition of vegetation; (2) causality of degradation; and (3) costs of implementation. According to this framework, we establish uncertainty about the condition of allegedly restored vegetation, with particular reference to herders' perceived rise in nonpalatable grass species. Moreover, causality between grassland restoration and effect is difficult to ascertain due the short time frame in which most studies have been conducted. Lastly, it is doubtful whether to date undetermined ecological benefits outweigh implementation costs, especially as the survey pinpointed herders' loss of livelihood without alternative income, illegal grazing, low legal understanding, and limited access to grassland rights.
Factors Affecting Human T Cell Engraftment, Trafficking and Associated Xenogeneic Graft-Versus-Host Disease in NOD/SCID

Objective—Graft-versus-host disease (GVHD) is the major cause of morbidity and mortality following allogeneic hematopoietic stem cell transplantation. Models of immunodeficient mice that consistently and efficiently reconstitute with xenoreactive human T cells would be a valuable tool for the in vivo study of GVHD, as well as other human immune responses. Materials and Methods—We developed a consistent and sensitive model of human GVHD by retro-orbitally injecting purified human T cells into sublethally irradiated NOD/SCID-β2m null recipients. In addition, we characterized for the first time the trafficking patterns and expansion profiles of xenoreactive human T cells in NOD/SCID-β2m null recipients using in vivo bioluminescence imaging. Results—All NOD/SCID-β2m null mice conditioned with 300 cGy of total body irradiation and injected with 1 × 10 7 human T cells exhibited human T cell engraftment, activation, and expansion, with infiltration of multiple target tissues and a subsequent greater than 20% loss of pretransplant body weight. Importantly, histological examination of the GVHD target tissues revealed changes consistent with human GVHD. Furthermore, we also showed by in vivo bioluminescence imaging that the development of lethal GVHD in the NOD/SCID-β2m null recipients was dependent upon the initial retention and early expansion of human T cells in the retroorbital sinus cavity. Conclusion—Our NOD/SCID-β2m null mouse model provides a system to study the pathophysiology of acute GVHD induced by human T cells and aids in the development of more effective therapies for human GVHD.
The Hip-twist Jump: A Unique Mechanism for Jumping in Lungless Salamanders

Abstract Many terrestrial and aquatic animals jump to escape predators. Most terrestrial animals use robust hindlimbs to produce the power needed to lift their bodies off the ground. This paper explores an alternative jump mechanism used by the lungless salamander, Desmognathus ochrophaeus. Previous work on this jump mechanism suggested that lungless salamanders invoke rapid torso flexion to hurl themselves into the air with minimal hindlimb contribution. The current study was designed to investigate how salamanders pushed off the ground to jump and to determine whether elastic structures contribute to jump power amplification. Specifically, we focused on trunk action, hip rotation, limb placement, and jump power production. We used high speed cameras to film salamander jumps and used these videos to conduct a subsequent motion analysis. Our results demonstrate that prior to jumping, the trunk flexes laterally into a C-shape while the hindlimb (inside of the bend) is planted in front of the hips. Next, the salamander rapidly undulates, rotating the pelvic girdle toward the planted hindfoot. At this point, the planted hindlimb acts like a strut that allows the salamander to pole-vault over the planted hindfoot and into the air. We estimate that the trunk axial muscles are the main contributors to jump power, but they must be aided by elastic structures that amplify jump power output. Future studies should focus on identifying the elastic structures responsible for power amplification as well as possible neurological connections between the salamander jump and the C-start escape strategy of fishes.
Evaluation of cell sheet application on one wall bone defect in Macaca nemestrina through periostin expression

Chronic periodontitis is an oral disease in which the destruction of periodontal tissue leads to tooth loss. Regenerative therapy for attachment cannot be applied to one wall bone defects owing to the minimal existing healthy bone. Tissue engineering in the form of cell sheets has been developed to overcome this limitation. In a previous study, cell sheet application to a one wall bone defect in Macaca nemestrina showed good clinical results. To evaluate the effectiveness of cell sheet application histologically, the level of periostin expression in the gingival crevicular fluid (GCF) of M. nemestrina was determined. Periostin is a 90-kDa protein that regulates coordination and interaction for regeneration and tissue repair. A laboratory observation study was performed to see the differences in periostin levels in samples collected from M. nemestrina’s GCF, where a cell sheet was applied to the bone defect. Gel electrophoresis with SDS-PAGE was performed to detect periostin expression based on its molecular weight and to compare the expression band between the cell sheet and the control at 1, 2, and 3 weeks after treatment. The gel electrophoresis result shows different thicknesses of the protein band around the molecular weight of periostin between the cell sheet groups.
A craniometric and genetic approach to the systematics of the genus Dasymys PETERS, 1875 and the description of three new taxa (Rodentia, Muridae, Africa)

In an attempt to properly identify Dasymys specimens that were collected during the last decennia in the East-African region (Rwanda-Tanzania) we undertook a revision, of this genus. Although we initially limited our study area to central and eastern Africa, we were forced to include specimens for comparison from other areas, including western Africa, Angola and Zimbabwe-Zambia. This revision was realized using craniometric data of nearly 1000 skulls grouped in 20 operational taxonomical units (OTU's) mainly occurring in the central and eastern part of the African continent. The observation that differences in age and sex composition of the OTU's are of no or little consequence for the branching of the obtained phenetic trees, allowed us to undertake the screening of the genus Dasymys of the central and eastern African region. This approach enabled us to evaluate already described taxa, to select a neotype for D. nudipes and to describe three new taxa. Subsequent genetic analysis (cytochrome b) allowed us to provide a genetical characterization of two of the new species and several other taxa. Our phylogenetic analysis suggests that the genus Dasymys originated in the west African forest block betore spreading in a first step to the forest of the central African region and then in a second step to the savannahs of southern, eastern and possibly also western Africa.
Assessment of M. longissimus fibre types and metabolic enzymes in Bama miniature pigs and Landrace swine

Abstract Overt differences exist between Chinese local pigs and exotic pig breeds, especially in muscle growth rate and meat quality. However, the underlying molecular mechanisms remain unclear. This study aimed to assess muscle fibre types and metabolic enzymes in Bama miniature pigs and Landrace swine. Meat quality traits, including intramuscular fat content, and muscle colour, conductivity, and tenderness, were assessed in these pig breeds. Then, muscle fibre types were classified, and mRNA amounts and activities of lactate dehydrogenase (LDH), succinate dehydrogenase (SDH), and malate dehydrogenase (MDH) assessed, in M. longissimus from the two pig breeds, at various ages. Our data showed significantly higher back fat thickness, muscle conductivity, and intramuscular fat content in samples from Bama miniature pigs compared with the values obtained for Landrace pigs (p < .05). In addition, SDH activity was significantly higher, and LDH activity overtly lower in Bama pigs compared with Landrace swine (p < .05). Furthermore, myosin heavy-chain (MyHC) II A, II B, and II X mRNA levels in Bama miniature pigs at 180 were significantly higher than values obtained for Landrace pigs of the same age. Although MyHC I gene expression levels were similar in Bama miniature and Landrace pigs at 180 days of age, significantly higher amounts were obtained in 300 day old Bama miniature pigs compared with 180 day old Landrace pigs (p < .05). Collectively, these preliminary findings indicated that skeletal muscles from Bama miniature pigs may contain more oxidative fibres compared with those from Landrace pigs, which might explain the meat quality differences between the two pig breeds.
Isolation and Structure Elucidation of Bioactive Secondary Metabolites from Marine Sponges

Summary 139 5. Summary Natural products isolated from marine organism such as sponges, fungi and bacteria show a unique structural diversity which may lead to new metabolites which can be used for medicinal purposes. This study involved the isolation, structural elucidation and biological screening of the active constituents of some marine sponges collected from both the Red Sea and Indonesia using different chromatographic techniques and various tools of spectral analysis. Four sponges have been used in this study and the number of compounds which have been isolated and structurally elucidated are concluded in the next table [Table 5.1). 5.1. The Red Sea sponge Erylus lendenfeldi The sponge Erylus lendenfeldi was successively extracted with MeOH and acetone respectively. The combined extracts were concentrated to dryness and partitioned between Petroleum ether, EtOAc, n-BuOH and H 2 O, respectively. EtOAc and n-BuOH fractions were pooled since the two fractions were similar to each other. The combined n-BuOH and EtOAc fraction (1.79 g) was subjected to medium pressure column chromatography (MPLC) using normal silica gel as stationary phase and eluted with CH
A comprehensive toolkit to enable MinION sequencing in any laboratory

Long-read sequencing technologies are transforming our ability to assemble highly complex genomes. Realising their full potential relies crucially on extracting high quality, high molecular weight (HMW) DNA from the organisms of interest. This is especially the case for the portable MinION sequencer which potentiates all laboratories to undertake their own genome sequencing projects, due to its low entry cost and minimal spatial footprint. One challenge of the MinION is that each group has to independently establish effective protocols for using the instrument, which can be time consuming and costly. Here we present a workflow and protocols that enabled us to establish MinION sequencing in our own laboratories, based on optimising DNA extractions from a challenging plant tissue as a case study. Following the workflow illustrated we were able to reliably and repeatedly obtain > 8.5 Gb of long read sequencing data with a mean read length of 13 kb and an N50 of 26 kb. Our protocols are open-source and can be performed in any laboratory without special equipment. We also illustrate some more elaborate workflows which can increase mean and average read lengths if this is desired. We envision that our workflow for establishing MinION sequencing, including the illustration of potential pitfalls, will be useful to others who plan to establish long-read sequencing in their own laboratories.