Miracle-dz/UniFAR-FTUs huggingface dataset:
Another string to the polo bow: a new mitotic role of PLK1 in centromere protection

ABSTRACT Polo-like kinase 1 (PLK1) plays a fundamental role in the spatiotemporal control of mitosis. Cells lacking PLK1 activity exhibit characteristic chromosome misalignment due to defects in microtubule-kinetochore organization and attachment. In our recently published paper, we uncover a new role for PLK1 in the preservation and maintenance of centromere integrity.
Mesoamerica is a cradle and the Brazilian Atlantic Forest is a museum of Neotropical butterfly diversity (Lepidoptera: Nymphalidae: Brassolini)

Regional species diversity is ultimately explained by speciation, extinction, and dispersal. Here we estimate dispersal and speciation rates in Neotropical rainforest biomes to propose an explanation for the distribution and diversity of extant butterfly species. We focus on the butterfly tribe Brassolini (Owl butterflies and allies): a Neotropical group that comprises 17 genera and 108 species, most of them endemic to rainforest biomes. We infer a total-evidence species tree of Brassolini using the multispecies coalescent framework. By applying biogeographical stochastic mapping, we infer ancestral ranges and estimate rates of butterfly dispersal and cladogenesis at the scale of millions of years. We suggest that speciation in Mesoamerica and the northwestern flank of the Andes has only increased within the past 2 million years. In contrast, speciation in the Brazilian Atlantic Forest has been constant throughout the past 10 million years. The disparate species diversification dynamics may be explained by the geological and environmental history of each bioregion: the Central American Arc was likely intermittently inundated by water for most of the Miocene (15 to 3 Ma), thus, reduced landmass area until the Plio-Pleistocene may have hindered species diversification; the Atlantic Forest, in turn, likely went through episodes of expansion and contraction and has probably been biologically connected with the Amazonian forest since at least the early Miocene until the Pliocene, about 5 Ma. Importantly, a longer time for speciation in the Atlantic Forest than in Mesoamerica plus NW Andes is ruled out because the dispersal rates into both regions increased simultaneously in the middle-Miocene. Our results reveal a mosaic of bioregion-specific evolutionary histories within the Neotropics, where species have diversified rapidly (cradles: e.g., Mesoamerica), have accumulated gradually (museums: e.g., Atlantic Forest), or have alternately diversified and accumulated (e.g., Amazonia).
Spatial whitening in the retina may be necessary for V1 to learn a sparse representation of natural scenes

Retinal ganglion cell outputs are less correlated across space than are natural scenes, and it has been suggested that this decorrelation is performed in the retina in order to improve efficiency and to benefit processing later in the visual system. However, sparse coding, a successful computational model of primary visual cortex, is achievable under some conditions with highly correlated inputs: most sparse coding algorithms learn the well-known sparse features of natural images and can output sparse, high-fidelity codes with or without a preceding decorrelation stage of processing. We propose that sparse coding with biologically plausible local learning rules does require decorrelated inputs, providing a possible explanation for why whitening may be necessary early in the visual system.
Hepatic Metabolism of some Breeds of Chickens

An experiment was conducted to study the differences in liver metabolism of some chicken breeds had different levels of domestication and production types. Hepatic oxygen consumption (HOC), liver weight percentage, liver glycogen, liver fat and Plasma lipids profiles of 180 birds of Dandarawi (D), Lohmann selected leghorn (L.S.L) and Cobb chicks were assayed. The experiment was terminated at 8 weeks of age. Breed had significant effect on hepatic oxygen consumption, liver weight percentage, liver glycogen, total cholesterol and high-density lipoprotein (HDL). The Dandarawi had significantly (P≤0.05) higher HOC and liver glycogen compared to L.S. L and Cobb chicks. Meanwhile, the Cobb chicks had significantly (P≤0.05) lower liver weight percentage and had significantly (P≤0.05) higher total cholesterol and HDL compared to D and L.S. L chicks. The effect of sex was also noticed in liver weight percentage, the female had significantly (P≤0.05) higher liver weight when compared to male chicks. The effect of interactions between breed and sex was also noticed in liver fat, the male Cobb had significantly (P≤0.05) higher liver fat when compared to female Cobb, male and female D and L.S. L. chicks. It can be concluded that domestication and intensive selection for growth rate and egg production has resulted in alterations in hepatic metabolism, liver glycogen, and, fat and plasma lipids profiles.
The importance of behavioral data to identify online fake reviews for tourism businesses: a systematic review

In the last several decades, electronic word of mouth (eWOM) has been widely used by consumers on different digital platforms to gather feedback about products and services from previous customer behavior. However, this useful information is getting blurred by fake reviews—i.e., reviews that were created artificially and are thus not representative of real customer opinions. The present study aims to thoroughly investigate the phenomenon of fake online reviews in the tourism sector on social networking and online reviews sites. To this end, we conducted a systematic review of the literature on fake reviews for tourism businesses. Our focus was on previous studies that addressed the following two main topics: (i) tourism (ii) fake reviews. Scientific databases were used to collect relevant literature. The search terms “tourism” and “fake reviews” were applied. The database of Web of Science produced a total of 124 articles and, after the application of different filters following the PRISMA 2009 Flow diagram, the process resulted in the selection of 17 studies. Our results demonstrate that (i) the analysis of fake reviews is interdisciplinary, ranging from Computer Science to Business and Management, (ii) the methods are based on algorithms and sentiment analysis, while other methodologies are rarely used; and (iii) the current and future state of fraudulent detection is based on emotional approaches, semantic analysis and new technologies such as Blockchain. This study also provides helpful strategies to counteract the ubiquity of fake reviews for tourism businesses.
A Review of GENETIC Polymorphism of GSTs (Glutathione –s Transferase) Genes in Breast Cancer

In this review article, several researchesabout genetic polymorphisms of Glutation –s transferase (GST) enzymes that may have an etiological role in breast cancer have been reviewed. Breast carcinoma is the most frequent malignancy in women and represents the second leading cause of cancer death among women and accounts for about one-fourth of female cancer cases all over the world. GSTs are a family of Phase II detoxification enzymes that catalyze the conjugation of glutathione (GSH) to a wide variety of xenobiotic The incorporation of glutathione increases the molecule’s water solubility. This detoxification ability to become Glutathione S-transferases play an important role in drug, carcinogen, and reactive oxygen species detoxication and act both as peroxidases and as catalysts of glutathione transfer to hydrophobic electrophiles.It is evaluated in Iran and other countries that the annual incidence of cancer in the world will increase to 25 million in 2030, of which more than 70 percent occurs in developing countries.It is the second cause of death among Iranian women and one million new cases diagnosed worldwide every year.
Sema3A Facilitates a Retrograde Death Signal via CRMP4-Dynein Complex Formation in ALS Motor Axons

Amyotrophic Lateral Sclerosis (ALS) is a fatal neurodegenerative disease with selective dysfunction; it causes the death of motor neurons (MNs). In spite of some progress, currently no effective treatment is available for ALS. Before such treatment can be developed, a more thorough understanding of ALS pathogenesis is required. Recently, we demonstrated that ALS-mutated muscles contribute to ALS pathology via secretion of destabilizing factors such as Sema3A; these factors trigger axon degeneration and Neuromuscular Junction (NMJ) disruption. Here, we focus on the molecular mechanism by which muscle contribute to MNs loss in ALS. We identified CRMP4 as part of a retrograde death signal generated in response to muscle-secreted Sema3A, in ALS-diseased MNs. Exposing distal axons to Sema3A induces CRMP4-dynein complex formation and MN loss in both mouse (SOD1G93A) and human-derived (C9orf72) ALS models. Introducing peptides that interfere with CRMP4-dynein interaction in MN axons profoundly reduces Sema3A-dependent MN loss. Thus, we discovered a novel retrograde death signal mechanism underlying MN loss in ALS. Summary Maimon et al. identify a novel retrograde death mechanism that contribute to MN loss in ALS, in which CRMP4-Dynein complex is form and retrogradely move along the axon.
Airgun blasts used in marine seismic surveys have limited effects on mortality, and no sublethal effects on behaviour or gene expression, in the copepod Calanus finmarchicus

Seismic surveys use airguns that emit low frequency high magnitude sound to detect subsea resources and to map seabed geology. The effect of seismic blasts on Calanus spp. , a key food source for commercially important fish, was assessed in field experiments. Immediate mortality of copepods was significantly different from controls at distances of 5 m or less from the airguns. Mortality 1 week after the airgun blast was significantly higher—by 9% relative to controls—in the copepods placed 10 m from the airgun blast but was not significantly different from the controls at a distance of 20 m from the airgun blast. The increase in mortality—relative to controls—did not exceed 30% at any distance from the airgun blast. Only two genes changed in response to the airgun blast; however, their function is unknown. There were no sublethal effects of the seismic blasts on the escape performance or the sensory threshold needed to initiate an escape response at any of the distances from the airgun blast that were tested. Results from these experiments suggest that seismic blasts have limited effects on the mortality or escape response of Calanus sp. within 10 m of the blast and no measurable impact at greater distances.
Exercise and angiotensin receptor blockade enhance recovery after orthopaedic trauma in mice by decreasing pain and improving muscle regeneration

Chronic pain and disability after limb injury are major public health problems. One key obstacle to addressing these adverse outcomes is that we do not know when exercise should be initiated or whether the beneficial effects of exercise can be reproduced using pharmacological tools. In these studies, we developed and used a murine model of orthopaedic trauma combining tibia fracture and pin fixation with tibialis anterior muscle damage. Behavioral measures included mechanical nociceptive thresholds and distances run on exercise wheels. Bone healing was quantified using microCT scanning, and muscle fiber size distribution as well as fibrosis were followed using immunohistochemistry. We found that the model provided robust mechanical allodynia, fibrosis and a shift to smaller average muscle fiber size lasting up to 5 weeks from injury. We also observed that allowing “late” (weeks 1-2) rather than “early” (weeks 0-1) wheel running after injury resulted in greater overall running activity and greater reversal of allodynia. In parallel, the late running paradigm was also associated with lower levels of muscle fibrosis and a return towards normal muscle fiber diameters. Providing the anti-fibrotic angiotensin receptor blocker losartan to mice in drinking water blocked TGFbeta production while reducing both allodynia and muscle fibrosis. Combining losartan and late exercise provided no additional benefit. We conclude that early healing after orthopaedic trauma must be allowed prior to the initiation of exercise to achieve optimal pain, functional and physiological outcomes. Losartan may provide many of the same pain, functional and physiological outcomes by its regulation of TGFbeta signaling and is a viable candidate for translational studies. Key points summary Our tibial fracture orthopaedic injury model in mice recapitulates the major manifestations of complex trauma including nociceptive sensitization, bone fracture, muscle fibrosis and muscle fiber loss. Delayed exercise after complex orthopaedic trauma results in decreased muscle fibrosis and improved pain Losartan, an angiotensin-receptor blocker with antifibrotic abilities, recapitulates the effect of exercise on post-injury recovery
Microarray Gene Expression Dataset Re-analysis Reveals Variability in Influenza Infection and Vaccination

Influenza, a communicable disease, affects thousands of people worldwide. Young children, elderly, immunocompromised individuals and pregnant women are at higher risk for being infected by the influenza virus. Our study aims to highlight differentially expressed genes in influenza disease compared to influenza vaccination. We also investigate genetic variation due to the age and sex of samples. To accomplish our goals, we conducted a meta-analysis using publicly available microarray expression data. Our inclusion criteria included subjects with influenza, subjects who received the influenza vaccine and healthy controls. We curated 18 microarray datasets for a total of 3,481 samples (1,277 controls, 297 influenza infection, 1,907 influenza vaccination). We pre-processed the raw microarray expression data in R using packages available to pre-process Affymetrix and Illumina microarray platforms. We used a Box-Cox power transformation of the data prior to our down-stream analysis to identify differentially expressed genes. Statistical analyses were based on linear mixed effects model with all study factors and successive likelihood ratio tests (LRT) to identify differentially-expressed genes. We filtered LRT results by disease (Bonferroni adjusted p-value < 0.05) and used a two-tailed 10% quantile cutoff to identify biologically significant genes. Furthermore, we assessed age and sex effects on the disease genes by filtering for genes with a statistically significant (Bonferroni adjusted p-value < 0.05) interaction between disease and age, and disease and sex. We identified 4,889 statistically significant genes when we filtered the LRT results by disease factor, and gene enrichment analysis (gene ontology and pathways) included innate immune response, viral process, defense response to virus, Hematopoietic cell lineage and NF-kappa B signaling pathway. Our quantile filtered gene lists comprised of 978 genes each associated with influenza infection and vaccination. We also identified 907 and 48 genes with statistically significant (Bonferroni adjusted p-value < 0.05) disease-age and disease-sex interactions respectively. Our meta-analysis approach highlights key gene signatures and their associated pathways for both influenza infection and vaccination. We also were able to identify genes with an age and sex effect. This gives potential for improving current vaccines and exploring genes that are expressed equally across ages when considering universal vaccinations for influenza.
A Recommendation System for Repetitively Purchasing Items in E-commerce Based on Collaborative Filtering and Association Rules

In this paper, we are to address the problem of item recommendations to users in shopping malls selling several different kinds of items, e.g., daily necessities such as cosmetics, detergent, and food ingredients. Most of current recommendation algorithms are developed for sites selling only one kind of items, e.g., music or movies. To devise efficient recommendation algorithms suitable for repetitively purchasing items, we give a method to implicitly assign ratings for these items by making use of repetitive purchase counts, and then use these ratings for the purpose of recommendation prediction with the help of user-based collaborative filtering and item-based collaborative filtering algorithms. We also propose associate item-based recommendation algorithm. Items are called associate items if they are frequently bought by users at the same time. If a user is to buy some item, it is reasonable to recommend some of its associate items. We implement user-based (item-based) collaborative filtering algorithm and associate item-based algorithm, and compare these three algorithms in view of the recommendation hit ratio, prediction performance, and recommendation coverage, along with computation time.
Construction of CRISPR/Cas9 vectors for directed mutagenesis of Fusarium graminearum

Fusarium graminearum causes the fungal disease known as scab or head blight in cereals, including barley. There is no known resistance in barley against scab disease. Generating mutations in the fungus is a promising strategy to reduce infection. Research has shown that CRISPR/Cas9 is a very powerful tool for gene mutation. In this study, CRISPR/Cas9 vectors containing guide RNA sequences were constructed to mutate one visual marker gene ( AUR1 ) and two genes essential for infection in F. graminearum ( Tri5 and MGV1 ). Plasmids pFC332 and pFC334 were used to create vectors with the target genes using the USER cloning kit. The vectors were cloned into E. coli sand confirmed the presence of guide RNA sequences and accompanying sequences (promoter, terminator, and tracrRNA) using PCR and sequencing. The vectors will be used to mutagenize AUR2, Tri5 , and MGV1 genes in F. graminearum in future studies. It is predicted that mutated F. graminearum would not be able to infect host barley ( Hordeum vulgare ) plants.
Étude de la résistance aux antibiotiques de souches de Vibrio parahaemolyticus isolées de produits de la pêche

La resistance aux antibiotiques chez les bacteries pathogenes est un enjeu de sante publique. Le milieu marin est peu etudie mais c’est un reservoir potentiel de bacteries et de genes de resistance. Vibrio parahaemolyticus est une bacterie pathogene naturellement presente dans le milieu marin, et pouvant echanger des genes avec les bacteries environnantes. L’objectif de ces travaux etait d’etudier la resistance aux antibiotiques de souches de Vibrio parahaemolyticus isolees de produits de la peche. Le panel de souches etudiees comprenait 225 souches isolees au laboratoire et 23 souches identifiees pendant l’etude par des tests biochimiques et de biologie moleculaire. Des antibiogrammes ont ete realises sur ce panel de souches. Sur les 248 souches etudiees, 39 possedaient 1 a 8 profils atypiques, dont une souche multi-resistante. Il semble donc que les souches de V. parahaemolyticus issues des produits de la peche soient majoritairement sensibles aux antibiotiques mais que des resistances apparaissent.
Can conservation tillage and residue management enhance energy use efficiency and sustainability of rice-pea system in the Eastern Himalayas?

ABSTRACT Low productivity and energy use efficiency (EUE) of rice farming are the major concerns for agricultural sustainability in the Eastern Himalayan region of India. A field experiment on rice (Oryza sativa L.)-pea (Pisum sativum L) system was conducted for three consecutive years during 2012–15 in lowland ecosystem to assess the direct and residual impact of tillage and residue management (RM) practises on productivity and sustainability. Significantly higher grain yield of rice was achieved under no-till (NT) than minimum tillage (MT) and conventional tillage (CT). Among RM practises, 50% NPK + green leaf manure, 50% NPK + weed biomass and 50% NPK + in-situ residue retention recorded significantly higher mean grain yields than application of 50% NPK and 100% NPK without residues. Residual effect of MT in preceding rice gave significantly higher green pod yield of succeeding pea than NT and CT. The system EUE was significantly higher under MT (rice)-NT (pea) compared to those of NT-NT and CT-NT systems. The sustainable yield index of rice and pea was maximum under MT-NT followed by NT-NT. Thus, NT/MT with suitable RM practises is a pertinent strategy for sustainable productivity of rice-pea system in the Eastern Himalayas and in similar adjoining regions.
Biochemical descriptors: importance of the genetic divergence study in peppers

ABSTRACT The genetic diversity of pepper genotypes is usually evaluated based on morphological and molecular descriptors. However, studies using biochemical descriptors of peppers are still incipient. Thus, the objective of this study was identify biochemical descriptors of Capsicum spp. with antioxidant action, most responsive to the selection of superior genotypes, and evaluate the correlation between concentrations of the parameters using principal components analysis. The experiment was conducted in the city of Cáceres, southwest Mato Grosso, Brazil. Seventy-eight pepper accessions from the Active Germplasm Bank of UNEMAT were planted in randomized block design. The harvested fruits were immersed in liquid nitrogen for two minutes, and the following biochemical analyses were performed: titratable acidity, ascorbic acid, total phenols, flavonoids, anthocyanins, carotenoids, chlorophyll a, chlorophyll b, and antioxidant activity. Biochemical descriptors that best estimated the genetic variability of the accessions were flavonoids, total phenols, chlorophyll a, and ascorbic acid. Chlorophyll a and chlorophyll b were the compounds that showed the highest degree of correlation. Except chlorophyll a with ascorbic acid, all other vectors showed correlation ranging from moderate to strong.
Cross‐taxon congruence of multiple diversity facets of freshwater assemblages is determined by large‐scale processes across China

An intensively debated issue in ecology is whether variability in the patterns of diversity of different groups of organisms is congruent in space, a phenomenon referred to as cross-taxon congruence. Whereas this has been previously mainly tested in terms of taxonomic dissimilarity, the role of ecological processes in determining the congruence of multiple diversity facets (i.e. alpha- and beta-diversity, taxonomic, and functional) remains poorly understood. We used a data set of observation records for 469 macrophyte and 543 fish taxa at the catchment-scale from the existing literature and data bases to test the existence of multi-faceted congruence patterns and investigate the variables driving them across 214 catchments covering the whole Chinese mainland. We found cross-taxon congruence of multiple diversity aspects between fish and macrophyte communities. The energy (i.e. diversity is limited by energy availability), area/environmental heterogeneity (i.e. diversity is higher in larger and more heterogeneous areas), and dispersal (i.e. diversity is driven by dispersal) hypotheses were all significantly attributed to the cross-taxon congruence, suggesting the existence of key repeated mechanisms underlying assemblage organisation. Our study provides new evidence that can further our understanding of the factors and underlying processes explaining cross-taxon congruence patterns at broad spatial scales in the freshwater realm, the studies of which significantly lag those in the marine and terrestrial realms. The present findings also provide important baseline information for freshwater conservation initiatives.