Miracle-dz/UniFAR-FTUs huggingface dataset:
‘Master switch’ genes for disease resistance in rice: lessons learnt and lessons to learn

Evolving disease resistance rice variety has become a continuous encounter from plant pathologists’ point of view, against the changing scenario in the severity of various fungal, bacterial and viral diseases. Although we are successful to some extent in developing some varieties through conventional and molecular breeding, the recent genome level data indicate that we have only disclosed the tip of an iceberg. The strategy of introducing single foreign gene for every disease crop plants like rice, suffers not only from regulatory issues of genetically modified rice but also lack of sustainability under field tests. This is attributed to the fact that pathogen resistance is mediated by complex networking of genes and their protein products. Transcription factors that control expression of hundreds of other genes offer themselves as valid candidate for key gene transgenics. Rice transcription factors like Osmyb4 is observed to regulate many PR protein genes and genes involved in post infection defense. Hence, over-expressing these gene(s) in cultivated variety(s) would result in transgenic rice resistant to multiple diseases. The level of constitutive expression of these genes should however be evaluated in major cultivated varieties of rice and a correlation of their native level of resistance/susceptibility to diseases may complement the approach.
FOSSIL LAND SNAIL FAUNAS OF PORTO SANTO, MADEIRAN ARCHIPELAGO: CHANGE AND STASIS IN PLEISTOCENE TO RECENT TIMES

Samples of fossil land snails were made at 14 sites on the island of Porto Santo, Madeiran archipelago. Material in stratigraphical sequences could be dated by A/I racemization calibrated against radiocarbon dating, and against Uranium/Thorium estimates based on Madeiran material. Although errors associated with the oldest samples are large, it is clear that the oldest shell-bearing deposits are at least 300 ka old, and probably much older. Some taxonomic difficulties have been resolved by morphometric studies. The geographical pattern in the fossils (in both faunal composition and morphometrics) resembles closely that seen today, the southwest of the island being particularly distinctive. Of 58 native taxa found in the deposits, 22 are extinct on the island, though four still survive on Madeira. Extinction has been greater in the southwest than elsewhere, and early fossil faunas there are richer than later ones. As on Madeira, more than half of this extinction seems likely to be the consequence of human disturbance, which has also reduced and fragmented the ranges of other species. The overall pattern is of distributional stasis in many species, reduction of range or extinction in many others, but very few cases of range expansion. Neither extinctions nor changes in apparent abundance can be related to known changes in global climate over the period involved. This relative stasis is in marked contrast to the situation on Madeira, only 40 km away, where there are temporal shifts in the fauna, and evidence of colonization events. Possible reasons for this difference are discussed.
A new species of Wyeomyia ( Hystatomyia ) (Diptera: Culicidae) from Colombia and a redescription of Wy . ( Hystatomyia ) intonca Dyar & Knab

Species within the Wyeomyia subgenus Hystatomyia represent one of the dominant mosquito groups utilizing tank bromeliads as larval development sites in mangrove and adjacent forest habitats on the northern Pacific Coast of Colombia. Surveys of phytotelm plants in this region found larval stages of Wy. intonca Dyar & Knab frequently associated with large tank bromeliads, especially of the genus Werauhia, growing in mangrove. Wyeomyia intonca was originally described in 1910 on the basis of a male from the Canal Zone, Panama, and the larval stage was partial described in the 1920s. These incomplete descriptions have led to confusion over its identity and differentiation from Wy. circumcincta Dyar & Knab. Consequently, Wy. intonca is redescribed here. In addition, Wy. chocoensis sp.n. is described from specimens reared from tank bromeliads in the same region where Wy. intonca occurred. The descriptions of these two species, accompanied with relevant illustrations, are of adult males and females and of the pupal and larval stages.
Biallelic loss‐of‐function variants in TBC1D2B cause a neurodevelopmental disorder with seizures and gingival overgrowth

The family of Tre2‐Bub2‐Cdc16 (TBC)‐domain containing GTPase activating proteins (RABGAPs) is not only known as key regulatorof RAB GTPase activity but also has GAP‐independent functions. Rab GTPases are implicated in membrane trafficking pathways, such as vesicular trafficking. We report biallelic loss‐of‐function variants in TBC1D2B, encoding a member of the TBC/RABGAP family with yet unknown function, as the underlying cause of cognitive impairment, seizures, and/or gingival overgrowth in three individuals from unrelated families. TBC1D2B messenger RNA amount was drastically reduced, and the protein was absent in fibroblasts of two patients. In immunofluorescence analysis, ectopically expressed TBC1D2B colocalized with vesicles positive for RAB5, a small GTPase orchestrating early endocytic vesicle trafficking. In two independent TBC1D2B CRISPR/Cas9 knockout HeLa cell lines that serve as cellular model of TBC1D2B deficiency, epidermal growth factor internalization was significantly reduced compared with the parental HeLa cell line suggesting a role of TBC1D2B in early endocytosis. Serum deprivation of TBC1D2B‐deficient HeLa cell lines caused a decrease in cell viability and an increase in apoptosis. Our data reveal that loss of TBC1D2B causes a neurodevelopmental disorder with gingival overgrowth, possibly by deficits in vesicle trafficking and/or cell survival.
Predicting outcomes of pelvic exenteration using machine learning

We aim to compare machine learning with neural network performance in predicting R0 resection (R0), length of stay > 14 days (LOS), major complication rates at 30 days postoperatively (COMP) and survival greater than 1 year (SURV) for patients having pelvic exenteration for locally advanced and recurrent rectal cancer.
Simultaneous Three-Dimensional Vascular and Tubular Imaging of Whole Mouse Kidneys With X-ray μCT

Abstract Concurrent three-dimensional imaging of the renal vascular and tubular systems on the whole-kidney scale with capillary level resolution is labor-intensive and technically difficult. Approaches based on vascular corrosion casting and X-ray micro computed tomography (μCT), for example, suffer from vascular filling artifacts and necessitate imaging with an additional modality to acquire tubules. In this work, we report on a new sample preparation, image acquisition, and quantification protocol for simultaneous vascular and tubular μCT imaging of whole, uncorroded mouse kidneys. The protocol consists of vascular perfusion with the water-soluble, aldehyde-fixable, polymeric X-ray contrast agent XlinCA, followed by laboratory-source μCT imaging and structural analysis using the freely available Fiji/ImageJ software. We achieved consistent filling of the entire capillary bed and staining of the tubules in the cortex and outer medulla. After imaging at isotropic voxel sizes of 3.3 and 4.4 μm, we segmented vascular and tubular systems and quantified luminal volumes, surface areas, diffusion distances, and vessel path lengths. This protocol permits the analysis of vascular and tubular parameters with higher reliability than vascular corrosion casting, less labor than serial sectioning and leaves tissue intact for subsequent histological examination with light and electron microscopy.
Food-Based Dietary Guidelines – development of a conceptual framework for future Food-Based Dietary Guidelines in Europe: report of a Federation of European Nutrition Societies Task-Force Workshop in Copenhagen, 12–13 March 2018

Abstract Identifying a need for developing a conceptual framework for the future development of Food-Based Dietary Guidelines (FBDG) in Europe, The Federation of European Nutrition Sciences established a Task Force for this purpose. A workshop was held with the specific objective to discuss the various dimensions considered as particularly relevant. Existing frameworks for FBDG were discussed, and presentations from various countries illustrated not only several commonalities but also a high degree of heterogeneity in the guidelines from different countries. Environmental aspects were considered in several countries, and dimensions like food safety, dietary habits and preparation were included in others. The workshop provided an overview of the use of FBDG – both in developing front-of-pack nutrition labels and for reformulation and innovation. The European FBDG dimensions were described with examples from the close connection between FBDG and European Union (EU) policies and activities and from the compilation of a database of national FBDG. Also, the challenges with communication of FBDG were discussed. Considering the current scientific basis and the experiences from several countries, the Task Force discussed the various dimensions of developing FBDG and concluded that environmental aspects should be included in the future conceptual framework for FBDG. A change in terminology to sustainable FDBG (SFBDG) could reflect this. The Task Force concluded that further work needs to be done exploring current practice, existing methodologies and the future prospects for incorporating other relevant dimensions into a future Federation of European Nutrition Societies conceptual framework for SFBDG in Europe and working groups were formed to address that.
Design and simulation of a photonic crystal resonator as a biosensor for point-of-care applications

Abstract Point-of-care (POC) devices are essential for rapid testing of samples for early diagnosis of diseases. The accuracy and the sensitivity of the POC device depend mainly on the biosensors. The currently used POC devices require specialized operating personnel, long sample preparation time and high equipment costs. We aim to explain a bio-sensing concept using a photonic crystal (PC) resonator that would mitigate the drawbacks of the present sensing techniques. Photonic crystals consist of spatially arranged dielectric materials presenting a band gap that prevents electromagnetic waves of certain frequency range to propagate through it. PC resonators have shown to have very high sensitivities for bio-sensing applications at THz frequencies. A PC resonator with a high Q-factor is designed and simulated to detect the changes in the surrounding dielectric permittivity. As an application for detecting specific biomolecules, a protocol for surface functionalization has been explained. This will enable the selective binding of biomolecules from the sample. Shift in resonant frequency and attenuation in magnitude at the peak resonant frequency can be observed from the simulation results. These changes in the resonator properties can be indicative of the presence of a particular biomolecule or pathogen and its concentration within the sample.
Phylogeographic relationships of the southern green stink bug Nezara viridula (Hemiptera: Pentatomidae)

Abstract The sequences of 16S rDNA, cytochrome oxidase subunit I (COI) and cytochrome b (Cyt b) genes from nine field collections (seven provinces in China: Guangxi, Hubei, Guangdong, Guizhou, Zhejiang, Hunan, Jiangxi, and also southern and northern part of Iran), plus the sequences of Africa, Europe, Americas and Japan obtained form GenBank were used to re‐analyse the genetic variation in the southern green stink bug Nezara viridula (Linnaeus). The phylogeographic re‐analysis by using four algorithms (NJ, MP, ML and Bayesian) showed three main lineages. The Iranian haplotypes fell into lineage II formed from Europe and America, rather than in lineage III from Asia; the Chinese haplotypes fell into the Asian clade. Our results suggested that African and non‐African gene pools have been isolated since the Miocene era with the molecular clock calibrations for Heteroptera mtDNA, and not since the Pliocene as mentioned previously. The corresponding age of the separation of the eastern and western Asia clades is estimated to be 4.0–1.6 million years ago, coinciding with the Pliocene–Pleistocene epoch and with acute rising events in the Tibet Plateau locates in the western China, which may have formed the barriers observed today.
3D Printed Compressible Quasi-Solid-State Nickel-Iron Battery.

The design of a compressible battery with stable electrochemical performance is extremely important in compression-tolerant and flexible electronics. While this remains challenging with the current battery manufacturing method, the field of 3D printing offers unique possibility to produce free-standing 3D printed electrodes with various structural configurations. Through the simple and scalable strategy, various structural configurations can be produced. Herein, we demonstrate, for the first time, a 3D printed quasi-solid-state Ni-Fe battery (QSS-NFB) that shows excellent compressibility, ultra-high energy density and superior long-term cycling durability. Through a rational design and adjustment of chemical components, two electrodes consisting of ultrathin Ni(OH)2 nanosheet array cathode and holey α-Fe2O3 nanorod array anode are achieved with a ultrahigh active material loading over 130 mg cm-3 and excellent compressibility up to 60%. Remarkably, the compressible QSS-NFB demonstrated an extremely high cycling stability (~91.3% capacity retentions after 10000 cycles) and ultra-high energy densities (28.1 mWh cm-3 at a power of 10.6 mW cm-3). Our work opens a new method for producing compression-tolerant energy-storage devices, which are expected to have promising applications in new generation stretchable/wearable electronics.
Competitiveness of Nigerian Cashew Nuts in the Global Market (1961 – 2016): An Application of Vector Error Correction Model (VECM)

Cashew grows almost everywhere in Nigeria. Cashew is a major cash crop with high potential to generate foreign exchange and to create employment, as well as curb desertification in Nigeria. The continuous increase in cashew production will depend on the international competitiveness and the effects of policy intervention. This paper analysed the competitiveness of Nigeria’s cashew nuts in the global market. Secondary data were used for this study; national annual aggregates from 1961-2016. The aggregates were obtained from the Food and Agriculture Organization (FAO) website, Annual Abstract of Statistics of the National Bureau of Statistics (NBS), and Annual Reports of the Central Bank of Nigeria (CBN). Descriptive statistics such as line graphs were used to examine the trends in cashew nuts production, export and competitiveness. Also, Phillips Perron co-integration test and vector error correction model (VECM) were used to determine the drivers of competitiveness of Nigerian cashew nuts in the global market. From the results, the total quantity of cashew nuts export from Nigeria was 704,221 metric tons and the average volume was 12,575.37 metric tons from 1961-2016. The lowest comparative advantage (RCA) of 0.7% was recorded in 1968, while the highest comparative advantage of 209.7% was recorded in 1989, which can be attributed to the structural adjustment policy in 1985. The lowest coefficient of variation was 0% in the 1971-1980 sub-period and the highest was 92.82% in the 1991-2000 sub-period, showing high instability in the production of cashew nuts in Nigeria. Annual growth rate in cashew nuts export quantity was highest (114.15%) in the 1981-1990 sub-period while it was lowest (-7.66%) in the 1991-2000 sub-period. The revealed comparative advantage (RCA) from 1961-2016 was 182.77 percent, showing high instability in RCA as shown by coefficients of variation, ranging from 102.59 percent to 21.2 percent. Results of vector error correction analysis showed that world price of Nigeria’s cashew (p ≤ 0.05), inflation rate (p ≤ 0.05), export quantity (p ≤ 0.05) and production quantity (p ≤ 0.05) significantly influence Nigeria’s cashew competitiveness in the world market. It was concluded that world price of Nigeria’s cashew and inflation rate impede competitiveness while export quantity and production quantity improve it. Policies to sustain and improve the observed production and export quantities and lower inflation rates will improve competitiveness of Nigeria cashew nuts.
Evaluation of Protein Solubility as an Indicator of Underprocessing of Soybean Meal

Abstract Three experiments were conducted to compare urease activity (UA), orange G-binding capacity (OGBC), and protein solubility (PS) in a potassium-hydroxide solution of soybean meal (SBM) as indicators of overprocessing. In two additional experiments, amino-acid supplementation was employed in an attempt to overcome the growth depression associated with overheating SBM. Subsamples of commercially prepared lots of dehulled SBM were heated for varying periods of time in an autoclave at 121 C. In Experiments 1, 2, and 3, UA dropped to zero (pH change) after approximately 10 min of cooking. The assay was unable to differentiate between meals that were heated for longer periods. The OGBC of SBM was decreased by autoclaving. However, the narrow range of the orange G values that corresponded to degrees of heat treatment indicated that this test may be of limited value in identifying overprocessed SBM. By contrast, PS values decreased with each increase of autoclaving time, and did not approach zero even with 80 min of heating. Adding . 2 % lysine either singly or in combination with . 2% arginine or. 1% methionine, or both, totally overcame the growth depression due to overprocessing. The weight gains and feed conversions of broiler chicks were negatively correlated with autoclaving times in excess of 10 minutes. In all experiments, PS values more closely reflected the impaired chick performance from overheated SBM than UA or OGBC. The PS values below 70% suggested overprocessed SBM.
Personalized Persuasive Technology for Maternal Healthcare in Nigeria

This study employs four social influence strategies including social learning, social comparison, normative influence and recognition, to personalize a persuasive system aimed at regular and timely ante-natal, intra-partum and post-partum care amongst women in developing nations such as Nigeria. This new persuasive system will take the privacy into consideration while presenting a customized display of relevant and up-to-date maternal health information to the potential users. It will provide avenues for expectant mothers to observe and learn appropriate maternal health behaviors, compare their performances with similar others’ performances, imbibe healthier and safer maternal lifestyles and receive some form of recognition for performing target maternal health behaviors. Via the operationalization of these socially-oriented persuasive strategies, we hope to investigate how the new intervention will be able to support expectant mothers to change, improve and/or reinforce a positive attitude to their health and that of their unborn and suckling children. We contribute to research by demonstrating how socially-oriented strategies can be tailored in a persuasive technology for maternal healthcare to promote information and healthseeking behaviors amongst local women.
Design and screening of FAK, CDK 4/6 dual inhibitors by pharmacophore model, molecular docking, and molecular dynamics simulation

Abstract Focal adhesion kinase (FAK) is one kind of tyrosine kinases that modulates integrin and growth factor signaling pathways, which is a promising therapeutic target because of involving in the migration, proliferation and survival of cancer cell. Overexpression and amplification of cyclin-dependent kinase 4/6 (CDK4/6) occur in many cancers and may be the cause of resistance to CDK4/6 inhibitors in preclinical models. The latest research shows that the combination of FAK and CDK4/6 can be dually targeted to enhance the antitumor effects. In this study, FAK and CDK4/6 dual target inhibitors were designed by computer-aided drug design. Seven million molecules were screened by the pharmacophore model and molecular docking. Finally, 6 compounds were obtained. Molecular dynamics simulation of compound 1, 2 and 3 showed that it has good binding stability to both receptors. According to the binding modes of compound 1 with two receptors, corresponding modifications were made, and 7 novel designed compounds were obtained. The docking energy of these novel designed compounds were lower than that of compound 1, and they can be tested in future. Communicated by Ramaswamy H. Sarma
Genetic Diversity in Faba Bean (Vicia faba L.) Using Inter-Simple Sequence Repeat (ISSR) Markers and Protein Analysis

The present study aims to assess the genetic diversity among 10 varied faba bean cultivars, collected from two wide-ranging geographical locations of Egypt. Variability based on the DNA level was inspected through nine ISSR-PCR screening, which showed obvious differences among the various Vicia faba (V. faba) cvs. A total of 576 ISSR loci were detected and 398 (69.10%) of them were polymorphic, which represent a relatively high polymorphism level. Cluster analysis via ISSR markers separated three green large-seeded cvs. (V. faba var. major) from dry small-seeded cvs. (V. faba var. minor). The small-seeded cvs. were further classified into two sub-clusters according to two geographic locations. The first sub-cluster included dry small-seeded cvs. grown under clay soil conditions (Abies location). However, the second sub-cluster integrated the similar dry small-seeded cvs. but were grown under calcareous soil conditions (Fuka location). SDS-PAGE analysis of various faba bean leaf proteins reflected some variations among studied V. faba populations. The results clarified that ISSR markers and protein analysis were helpful to recognize genetic variation among faba bean cultivars. (H. S. Abdel-Razzak, A. M. Alfrmawy, H. M. Ibrahim and Amr. A. El-Hanafy. Genetic Diversity in Faba Bean (Vicia faba L.) Using Inter-Simple Sequence Repeat (ISSR) Markers and Protein Analysis. Life Sci J 2012;9(2):497-503). (ISSN:1097-8135). http://www.lifesciencesite. com . 74
Developmental divergence among hatchery strains of rainbow trout (Salmo gairdneri). I. Pure strains

We compare the developmental rate of six closely related hatchery strains of rainbow trout. Hatching time, morphological analysis, and the pattern of ontogenetic change in lactate dehydrogenase, malate dehydrogenase, glucosephosphate isomerase, and phosphoglucomutase activities indicate significant differences in developmental rate between strains. There is close concordance among the different measures of developmental rate. Strains with higher levels of heterozygosity, as estimated from electrophoretic analysis of 42 loci, developed faster than less heterozygous strains. The variation in developmental rate in these closely related strains indicates that there is substantial genetic variation affecting the developmental process in rainbow trout.Key words: development rate, intraspecific variation, rainbow trout.