Miracle-dz/UniFAR-FTUs huggingface dataset:
Hypoxia-Inducible Ubiquitin Specific Peptidase 13 Contributes to Tumor Growth and Metastasis via Enhancing the Toll-Like Receptor 4/Myeloid Differentiation Primary Response Gene 88/Nuclear Factor-κB Pathway in Hepatocellular Carcinoma

Hepatocellular carcinoma (HCC) is one of the leading causes of cancer death worldwide. The activation of the toll-like receptor 4/myeloid differentiation primary response gene 88/nuclear factor-κB (TLR4/MyD88/NF-κB) pathway contributes to the development and progression of HCC. The ubiquitin–proteasome system regulates TLR4 expression. However, whether ubiquitin specific peptidase 13 (USP13) stabilizes TLR4 and facilitates HCC progression remains unclear. Here, quantitative real-time PCR (qRT-PCR) and immunohistochemistry analysis revealed that USP13 expression in HCC tissues was higher than in non-tumor liver tissues. Moreover, the elevated expression of USP13 was detected in HCC cells (SK-HEP-1, HepG2, Huh7, and Hep3B) compared to LO2 cells. Interestingly, the positive staining of USP13 was closely correlated with tumor size ≥ 5 cm and advanced tumor stage and conferred to significantly lower survival of HCC patients. Next, USP13 knockdown prominently reduced the proliferation, epithelial–mesenchymal transition (EMT), migration, and invasion of Hep3B and Huh7 cells, while USP13 overexpression enhanced these biological behaviors of HepG2 and LO2 cells. The silencing of USP13 significantly restrained the growth and lung metastasis of HCC cells in vivo. Mechanistically, the USP13 depletion markedly inhibited the TLR4/MyD88/NF-κB pathway in HCC cells. USP13 interacted with TLR4 and inhibited the ubiquitin-mediated degradation of TLR4. Significantly, TLR4 re-expression remarkably reversed the effects of USP13 knockdown on HCC cells. USP13 expression was markedly upregulated in HCC cells under hypoxia conditions. Notably, USP13 knockdown repressed hypoxia-induced activation of the TLR4/MyD88/NF-κB pathway in HCC cells. In conclusion, our study uncovered that hypoxia-induced USP13 facilitated HCC progression via enhancing TLR4 deubiquitination and subsequently activating the TLR4/MyD88/NF-κB pathway.
GAEAT: Graph Auto-Encoder Attention Networks for Knowledge Graph Completion

Knowledge graph embedding (KGE) encodes components of a KG including entities and relations into continuous low vector space. Most existing methods focus on treating entities and relations in triples independently and thus failing to capture the complex and hidden information that is inherently implicit inside the local neighborhood surrounding a triple. In this paper, we present a new approach for knowledge graph completion called GAEAT (Graph Auto-encoder Attention Network Embedding), which can encapsulate both entity and relation features. Specifically, we construct a triple-level auto-encoder by extending graph attention mechanisms to obtain latent representations of entities and relations simultaneously. To justify our proposed model, we evaluate GAEAT on two real-world datasets. The experimental results demonstrate that GAEAT can outperform state-of-the-art KGE models in knowledge graph completion task, which validates the effectiveness of GAEAT. The source code of this paper can be obtained from https://github.com/TomersHan/GAEAT.
Classification and Prediction of Disease Classes using Gene Microarray Data

- In the year 1999, when T. R Golub first presented an idea for classifying cancer at the molecular level, this boosted research in cancer diagnosis to a whole new level. The researchers began to analyze the disease at the genetic level with the help of microarray databases. Then there were many new algorithms designed by researchers to classify different types of cancer. The objective of this paper is to present a tool designed exclusively to predict and classify leukemia into its types. The leukemia dataset published by Golub is used for this purpose. The first step is to identify the most significant genes causing cancer from the training set. These selected genes then are used to build the classifier based on decision rules, and eventually to predict the type of leukamia. This classifier which is modeled based on decision rules is found to work with an accuracy of 94%. The algorithm is quite simple in terms of complexity. It is possible to use a minimum number of genes for classification purposes rather than using a large set of genes. The genes that are responsible for prognosis of cancer are mainly selected for designing the classifier.
Challenges and Future Directions of Big Data and Artificial Intelligence in Education

We discuss the new challenges and directions facing the use of big data and artificial intelligence (AI) in education research, policy-making, and industry. In recent years, applications of big data and AI in education have made significant headways. This highlights a novel trend in leading-edge educational research. The convenience and embeddedness of data collection within educational technologies, paired with computational techniques have made the analyses of big data a reality. We are moving beyond proof-of-concept demonstrations and applications of techniques, and are beginning to see substantial adoption in many areas of education. The key research trends in the domains of big data and AI are associated with assessment, individualized learning, and precision education. Model-driven data analytics approaches will grow quickly to guide the development, interpretation, and validation of the algorithms. However, conclusions from educational analytics should, of course, be applied with caution. At the education policy level, the government should be devoted to supporting lifelong learning, offering teacher education programs, and protecting personal data. With regard to the education industry, reciprocal and mutually beneficial relationships should be developed in order to enhance academia-industry collaboration. Furthermore, it is important to make sure that technologies are guided by relevant theoretical frameworks and are empirically tested. Lastly, in this paper we advocate an in-depth dialog between supporters of “cold” technology and “warm” humanity so that it can lead to greater understanding among teachers and students about how technology, and specifically, the big data explosion and AI revolution can bring new opportunities (and challenges) that can be best leveraged for pedagogical practices and learning.
The Stopping Power of Norms: Saturation Bombing, Civilian Immunity, and U.S. Attitudes toward the Laws of War

Abstract In “Hiroshima in Iran: What Americans Really Think about Using Nuclear Weapons and Killing Noncombatants,” a pathbreaking survey of attitudes toward the laws of war published in the summer 2017 issue of International Security, Scott Sagan and Benjamin Valentino found that Americans are relatively insensitive to the targeting of civilian populations and to international norms and taboos against the use of nuclear weapons. We replicated a key question of this study, where respondents were asked if they would support saturation bombing an Iranian city to end a war. We also introduced some variations into the experiment to directly measure any potential influence of international norms and laws. Overall, our quantitative and qualitative findings are more optimistic than those of Sagan and Valentino's study: Americans do strongly believe it is wrong to target civilians. And in a real-life scenario such as this, a majority would likely oppose such a bombing. These findings suggest, however, that much depends on how survey questions are structured in measuring those preferences and whether legal or ethical considerations are part of any national conversation about war policy.
Successful enhancement of Ridgway's Hawk populations through recruitment of translocated birds

ABSTRACT Survival and recruitment estimates are important for predicting population viability and the efficacy of translocations. This information requires intensive monitoring postrelease, which is often economically or logistically infeasible. Since 2009, juveniles of the critically endangered Ridgway's Hawk (Buteo ridgwayi) have been translocated from Los Haitises National Park to Punta Cana, Dominican Republic. Here, we use multistate capture–recapture models to estimate survival and recruitment of translocated Ridgway's Hawks. We further examine whether survival or recruitment differed between sexes or translocation status (translocated vs. wild-reared birds in Los Haitises). Survival was relatively high for breeders, nonbreeders, and juveniles, and did not differ by translocation status or sex. Translocated juveniles were recruited into the breeding population at Punta Cana at more than double the rate of wild-reared juveniles in Los Haitises—likely because more unoccupied territories were available in Punta Cana. Our results show that translocation does not reduce survival, but does increase recruitment, of Ridgway's Hawks when territories are available in suitable habitat. Future work should evaluate the reproductive performance of Ridgway's Hawks in Punta Cana and determine the effects of translocations on the population in Los Haitises. Although the types of data collected during postrelease monitoring are often determined by funding, feasibility, and research objectives, our results demonstrate the importance of continued monitoring of translocated animals.
Phosphoglucomutase : structural studies of the PGM1 gene and a search for PGM3 and PGM4.

Phosphoglucomutase is an enzyme central to glycolysis and gluconeogenesis. There are three well characterised forms: PGM1, PGM2 and PGM3. Genomic clones containing the 5' end of the PGM1 gene were Isolated and characterised. The exon/intron boundaries of the first exon (designated 1A) were determined. 15kb of intron 1 have been mapped and 2.8kb of the flanking regions sequenced. The proximal promoter shows features of a 'housekeeping' promoter. Features characteristic of a CpG island have been identified in this region. An alternative first exon has been identified (1B). The two exons show similarities indicating a gene duplication event. Exon IB is transcribed from a promoter in the first large intron of PGM 1.1 A. Expression studies of PGM 1.IB by RNA-PCR show a limited tissue expression, with predominate expression in striated muscle. Exons 1A and 1B were sequenced in DNA from eight individuals of known PGM1 protein phenotypes. No genetic variation in these sequences was encountered. The PGM1 cDNA was used as a probe in a search for the PGM3 gene. A human chromosome 6 library was screened. Positive cosmids were assigned to chromosome positions by fluorescent in situ hybridisation, restriction mapped and sequenced in part. These studies led to the identification of a novel PGM on chromosome 9. PGM3\Nas not isolated by this procedure, suggesting that the sequences of PGM1 and PGM3 have diverged significantly. Mammary gland cDNA libraries were screened using both anti-PGMI antibodies and PGM1 cDNA, to search for PGM4. Positive clones were all identified as PGM1. In addition the PGM1 type of DNA from recent mothers was compared to the typing of matched colostrum samples (by isoelectric focusing). Some similarities were seen between the colostrum and PGM1 isoform patterns. Together, these data suggest that PGM4 protein is a modified form of PGM1.
New Parasite Records for the Sunfish Mola mola in the Mediterranean Sea and Their Potential Use as Biological Tags for Long-Distance Host Migration

Studies describing the parasite fauna of sunfish species from the Mediterranean Sea are to date limited, despite information gained through parasitological examination may reveal unknown ecological and biological aspects of both hosts and parasites. Moreover, recent molecular studies on sunfish taxonomy revealed the presence of two species belonging to the genus Mola in the Mediterranean basin, namely M. mola and M. alexandrini. These two fish taxa have long been synonymized or confused among them, which implies that the majority of the studies carried out so far reported the parasites infecting both species under a single host species, generally referred to as M. mola. We hereby investigated the parasite fauna of a 43 cm long M. mola specimen from the Mediterranean Sea, whose identification was confirmed by molecular tool, and provided the first evidence of the occurrence of the nematode Anisakis simplex (s.s.) and of the cestode Gymnorhynchus isuri in Mola species anywhere. The use of helminth species as biological tags for the sunfish is also discussed.
Differential Screening in Immunodeficient Mice Reveals Bacterial Enzymes With Unexpected Roles in Host-Pathogen Interactions

1 Preface 2 The vertebrate immune system, and introduction 2 Classification of microbes 6 Chapter 1: Introduction 9 I. The Macrophage 9 Phagocytes and phagocytosis 9 Receptors for recognition of pathogens 10 Macrophage anti-microbial mechanisms 13 II. Macrophages and intracellular pathogens 21 Strategies for avoiding degradation in the lysosome 22 Strategies for coping with host production of RNI and ROI 28 III. Mycobacterium tuberculosis 31
The impact of terminal heat stress on yield and heat tolerance of bread wheat

In arid and semi-arid regions of the world bread wheat (Triticum aestivum L.) yield is highlylimited due to late season heat stress, mostly occurring during the reproductive phase. Hence thecurrent study was conducted to evaluate the effect of late season heat stress on grain yield andyield components of 20 spring bread wheat cultivars. For this purpose, a stripe block experimentincluding four sowing dates (6th of November, 6th of December, 5th of January and 4th ofFebruary) as vertical plots and 20 cultivars in horizontal plots was implemented with threereplicates in North-East of Ahwaz, Khuzestan, Iran during 2007-2008 and 2008-2009 growingseasons. The results indicated that the main effect of year, sowing date, cultivar and interactionbetween sowing date and cultivar were significant for all studied traits. However, no significantinteraction was found between year and other factors. Comparison of means showed that grainyield in the second year was higher than the first year. The maximum and minimum values(6.048 ton ha-1 and 1.754 ton ha-1) were obtained when seed sowing was performed on 6th ofNovember and 4th of February, respectively. The maximum grain yield (5.019 ton ha-1) wasrelated to Atila cultivar whereas the minimum yield (3.662 ton ha-1) was obtained from Inia 66cultivar. In general, the maximum and minimum grain yields were produced by Atila cultivarsown on 6th of December and Seri82 and Roshan sown on 4th of February, respectively. Theresults suggest that Arvand, Vee/Nac, Atila and Baiat cultivars as heat tolerant cultivars andRoshan, Hamoon, Seri82, Star, Inia66 and Darab2 as susceptible cultivars may be used in heattolerance studies.
Chloroplast structure and DNA methylation polymorphisms in an albino mutant of wheat (Triticum aestivum) cv. Xinong 1376

Abstract. DNA methylation plays an important role in regulating plant development, including organ and tissue differentiation, which may determine variations in agronomic traits. However, no reports exist for the regulation of leaf colour in wheat. The present study investigated the chloroplast structure and epigenetic mechanisms regulating leaf colour in an albino mutant of wheat (Triticum aestivum L.) cv. Xinong 1376. Structural analysis was performed by scanning and transmission electron microscopy, and epigenetic modifications were detected by methylation-sensitive amplification polymorphism (MSAP) analysis. Mesophyll cells of green leaves showed a well-ordered arrangement and they were filled with chloroplasts with intact lamellar structures and thylakoid membranes. By contrast, mesophyll cells of red and white leaves were disorganised and contained only a few plastids or chloroplasts with no lamellar structures or thylakoid membranes. Comparison of MSAP profiles revealed that white or red leaves had higher levels of cytosine methylation and showed changes in polymorphic loci compared with green leaves (4.35% and 4.10%, respectively). We sequenced 150 DNA fragments that were differentially displayed in MSAP patterns of white or red and green leaves of the Xinong 1376 albino mutant. A further BLAST search of 77 cloned sequences located them in coding regions. Most of these sequences were found to be involved in processes such as signal transduction, transcription regulation, post-transcriptional processing, DNA modification and repair, transport, biosynthesis of cellulose, photosynthesis, protein ubiquitination, stress responses, and retroposition. Expression analysis demonstrated a decrease in the transcription of two methylated genes, psaA and psbD, which are involved in the photosystem. Although the DNA methylation changes and leaf colour changes were not directly associated, these results may indicate that methylation of specific genes is an active and rapid epigenetic response to variation of leaf colour in the Xinong 1376 albino mutant, further elucidating the mechanism of variation in leaf colour.
Assessment of Cocoa Producers’ Children Nutritional Status in the Nawa Region, Côte d’Ivoire

Foods are important as they provide nutrients for human being. However, in the world and particularly in Africa, several people suffer of under nutrition due to a lack of proteins, energy and micronutrients. Malnutrition affects the agricultural sector unfortunately. A survey was conducted in 2015 among cocoa producers’ households from 11 localities in the Nawa region which is the largest cocoa production region of Cote d’Ivoire. Anthropometric measurements were collected on 218 children between 6 and 59 months old and the data were used to calculate the following indices used to assess nutritional status: weight-for-height, height-for-age and weight-for-age. The results showed that global acute malnutrition prevalence was 17.5% (95% Confidence interval (CI): 13.0, 23.1%), with 12.4% (95% CI: 8.7, 17.5%) for the moderate form and 5.1% (95% CI: 2.9, 8.8%) for the severe one. Global chronic malnutrition prevalence was about 39% (95% CI: 32.8, 45.6%) and the moderate and the severe forms were respectively 22% (95% CI: 17, 28%) and 17% (95% CI: 12.6, 22.5%). Underweight prevalence was 25.2% (95% CI: 19.9, 31.4%) with 17% (95% CI: 12.6, 22.5%) for moderate underweight and 8.3% (95% CI: 5.3, 12.7%) for severe underweight. There were any statistical difference between boys and girls. The distribution curves of index are offset from the reference curve for all malnutrition forms. Children among 6-17 months were generally affected by acute malnutrition while chronic malnutrition concerned children aged from 18 to 53 months. Cocoa producers’ children are affected by malnutrition and the prevalence is important, indicating a possible lack of food diversification.
Ethnobotanical study of antimalarial plants in the middle region of the Negro River, Amazonas, Brazil

ABSTRACT The middle Rio Negro region is an interesting place to seek novel antimalarial compounds because of the traditional knowledge of the Amazon population in conjunction with the high biodiversity of the region. The objective of this work was to study the use of antimalarial plants in Barcelos, state of Amazonas, Brazil. Fifty-two local specialists from eight different communities were interviewed over one year. The identified plants were collected with the assistance of local specialists, classified to species level and deposited in herbarium. In total, 55 antimalarial plants were identified in use in the region, of which 16 had not been previously reported in other published studies. Many factors could be involved with the use of antimalarial plants by the Barcelos population, such as the accessibility of these medicinal plants, efficiency and safety of using these plants, the accessibility to drugs or other medical treatments, plant bitterness, and the gender of the interviewees. Our results indicate that the population of Barcelos possesses an extensive knowledge on the use of a diverse array of antimalarial plants, and may contribute to the development of novel antimalarial compounds.
Experimental brood enlargement differentially influences the magnitude of the corticosterone stress response in closely related, co‐occurring songbirds

Funding information General Research Fund at Oregon State University; Margaret A. Cargill Foundation; North American Bluebird Society; New York State Bluebird Society; the Honor’s College at Oregon State University; the URISC Program at Oregon State University; E.R. Jackman Internship Support Program and the Golondrinas de las Americas programme at Cornell University, Grant/Award Number: NSF-PIRE and OISE-0730180
The effect of Psephodiplosis rubi (Diptera: Cecidomyiidae) leaf galls on the secondary metabolite profiles of two congeneric host plants

Galling insects have the unique ability to control the secondary chemistry of their host plants. Galled plant tissue often has higher concentrations of these secondary compounds compared with surrounding plant material. In this study, we used nuclear magnetic resonance (NMR) spectroscopy metabolomics techniques to investigate the effect of galls induced by Psephodiplosis rubi Kolesik, on the profiles of secondary metabolites in its two Rubus host plants in subtropical rainforest. We isolated four triterpenoid compounds from both Rubus species. Concentrations of individual triterpenes were not significantly different in galled and non‐galled leaves; however, the concentration of 2‐oxopolomic acid was significantly negatively correlated with gall abundance. At the interspecific level, non‐galled leaves from both Rubus species were chemically indistinguishable in principal component analysis analyses, while galled leaves showed slight chemical differences. Surprisingly, there was very little difference in metabolic profiles of galled and non‐galled leaves at the intraspecific level. Using NMR, we were able to detect slightly different chemical responses in two congeneric host plant species induced by P. rubi galls. We demonstrate how NMR can be used to detect interspecific chemical differences of plants in ecological studies.
Estimation of phylogenetic divergence times in Panagrolaimidae and other nematodes using relaxed molecular clocks calibrated with insect and crustacean fossils

This study presents the use of relaxed molecular clock methods to infer the dates of divergence between Panagrolaimus species. Autocorrelated relaxed tree methods, combined with well characterised fossil calibration dates, yield estimates of nematode divergence dates in accordance with the palaeontological age of fossil ascarid eggs and with the previously estimated date of 18 Ma (range 11.6 to 29.9 Ma) for the divergence of the Caenorhabditis lineage. Our data indicate that Panagrolaimus davidi from Antarctica separated ca 21.98 Ma from its currently known, most closely related strain. Thus, P. davidi may have existed in Antarctica prior to the Last Glacial Maximum, although this seems unlikely as it shares physiological and life history traits with closely related nematodes from temperate climates. These traits may have facilitated colonisation of Antarctica by P. davidi after the quaternary glaciation, analogous to the colonisation of Surtsey Island, Iceland, by P. superbus after its volcanic formation. This study demonstrates that autocorrelated relaxed tree methods combined with well characterised fossil calibration dates may be used as a method to estimate the divergence dates within nematodes in order to gain insight into their evolutionary history.