Miracle-dz/UniFAR-FTUs huggingface dataset:
Muscle function and homeostasis require macrophage-derived cytokine inhibition of AKT activity in Drosophila

Unpaired ligands are secreted signals that act via a GP130-like receptor, domeless, to activate JAK-STAT signaling in Drosophila. Like many mammalian cytokines, unpaireds can be activated by infection and other stresses and can promote insulin resistance in target tissues. However, the importance of this effect in non-inflammatory physiology is unknown. Here, we identify a requirement for unpaired-JAK signaling as a metabolic regulator in healthy adult Drosophila muscle. Adult muscles show basal JAK-STAT signaling activity in the absence of any immune challenge. Macrophages are the source of much of this tonic signal. Loss of the dome receptor on adult muscles significantly reduces lifespan and causes local and systemic metabolic pathology. These pathologies result from hyperactivation of AKT and consequent deregulation of metabolism. Thus, we identify a cytokine signal from macrophages to muscle that controls AKT activity and metabolic homeostasis.
Behavioral and health problems of poultry related to rearing systems

This review paper aims to give an overview of the literature data on common behavioral and health problems in broiler chickens and laying hens and to explain their interrelation and relation to the rearing system. In the initial part, the mechanism of arising of the most common forms of abnormal behavior and the way they affect the poultry are briefly described. Furthermore, the possibility of poultry to fulfill behavioral needs in different rearing systems and some of the consequences to the birds in the case of their inability to meet their needs are displayed. The influence of the main microclimate and space factors is also discussed, as well as the occurrence of some infectious, parasitic and production diseases in poultry rearing systems. The welfare problems of poultry are complexes and most often caused by the system design and its improper use. Continuous work on improving rearing systems is as important as better informing the producers and the public on poultry welfare problems.
The Effect of Estrogen on Hepatic Fat Accumulation during Early Phase of Liver Regeneration after Partial Hepatectomy in Rats

Fatty liver is common in men and post-menopausal women, suggesting that estrogen may be involved in liver lipid metabolism. The aim of this study is to be clear the role of estrogen and estrogen receptor alpha (ERα) in fat accumulation during liver regeneration using the 70% partial hepatectomy (PHX) model in male, female, ovariectomized (OVX) and E2-treated OVX (OVX-E2) rats. Liver tissues were sampled at 0–48 hr after PHX and fat accumulation, fatty acid translocase (FAT/CD36), sterol regulatory element-binding protein (SREBP1c), peroxisome proliferator-activated receptor α (PPARα), proliferative cell nuclear antigen (PCNA) and ERα were examined by Oil Red O, qRT-PCR and immunohistochemistry, respectively. Hepatic fat accumulation was abundant in female and OVX-E2 compared to male and OVX rats. FAT/CD36 expression was observed in female, OVX and OVX-E2 at 0–12 hr after PHX, but not in male rats. At 0 hr, SREBP1c and PPARα were elevated in female and male rats, respectively, but were decreased after PHX in all rats. The PCNA labeling index reached a maximum at 36 hr and 48 hr in OVX-E2 and OVX rats, respectively. ERα expression in OVX-E2 was higher than OVX at 0–36 hr after PHX. In conclusion, these results indicated that estrogen and ERα might play an important role in fat accumulation related to FAT/CD36 during early phase of rat liver regeneration.
In-silico endogenic substrate prediction study of Cytochrome P450 1B1 (CYP1B1)

Cytochrome P450 1B1 (CYP1B1) belongs to cytochrome P450 monooxygenases superfamily and is one of the CYP1 family isoforms, which actively take part in the metabolism of various xenobiotics in the body. CYP1B1 is highly expressed in multiple human tissues, implied in various types of human cancers, but its intracellular function and role in various human pathologies are yet to be understood entirely. In this regard, research in the past two decades has yielded sufficient information about its structure, amino acid sequence, and interaction with various xenobiotics, including pro-carcinogens. One aspect that remains hard to pin down is the information regarding the endogenic substrates of this protein. The scope of the present study is to predict the endogenic substrates (metabolic products of either arachidonic acid or cholesterol) of CYP1B1 with high binding affinity characteristics. We performed in-silico screening for these endogenic compounds with CYP1B1 protein modes to find best binding affinity, atomic contact energy (ACE) and score values. A total of thirteen compounds showed the highest binding affinity with CYP1B1. We found that leukotriene E4, leukotriene A4, Deoxycholic acid, tetrahydrocortisone showed highest ACE values and other substrate binding characteristics, making them excellent candidates for validation by laboratory experiments.
Disturbance of bioelectric transmission in carcinogenesis

Background: Despite significant financial resources invested in the field of cancer research, there has been a steady increase in the registration of new cases of malignant neoplasms. Modern technical capabilities for analyzing the molecular substrate of tumor genesis have revealed a large number of such factors. The latest studies point out the paramount importance of the integral bioelectric field as contrasted with molecular mechanisms in oncopathology. Clear evidence has emerged that the “decision” of a certain part of the body to develop a tumor depends on the bioelectric state of remote regions. In the light of these findings, it becomes obvious that the difficulties in solving the cancer problem are associated with a simplified approach focused only on molecular components. Conclusions: It can be assumed that the difficulties in solving the cancer problem are associated with a simplified approach, focused only on molecular components. It is difficult to identify clear differences between the blastomic and healthy cells, as they work according to the same biological principles, although differently expressed. Despite functioning with almost identical molecular components, tumor and healthy tissues diﬀer significantly in the dynamics of growth and pattern formation. The above data indicates that the “decision” of a certain part of the body to develop a tumor depends on the bioelectric state of remote regions. In this context, the prognosis and treatment of malignant neoplasms can most likely be achieved not by local, gene- targeting technology, but by methods for the detection of tumor signatures in the morphogenetic field of the organism.
Interhemispheric Communication and Lateralization in the Mouse Hippocampus

The left and right rodent hippocampi appear to exhibit striking lateralization in some of the very neural substrates considered to be critical for hippocampal cognitive function. Despite this, there is an overwhelming lack of consideration for hemispheric differences in studies of the rodent hippocampus. Asymmetries identified so far suggest that a bilateral model of the hippocampus will be essential for an understanding of this brain region, and perhaps of the brain more widely. Although models have been proposed to explain how the left and right hippocampus contribute to behavior and cognition, these models have either been refuted by more recent studies or have been limited in the scope of data they explain. Here, I will review data on human and rodent hippocampal lateralization and will propose a novel model of the hippocampus as a bilateral structure. This model proposes a lateralization of associative and working memory (LAW). The LAW model of bilateral hippocampal function postulates that the left hemisphere stores spatial information as discrete, salient locations and that the right hemisphere represents space continuously, contributing to route computation and flexible spatial navigation.
Contracaecum spp. (Nematoda: Anisakidae) and Eustrongylides spp. (Nematoda: Dioctophymatidae) nematode larvae with zoonotic potencial found in two fish species from Tramandaí river basin, southern Brazil

Parasitic nematodes can infect both wild and cultivated fish species and may be the source of many diseases. The consumption of raw fish meat in many countries has been the responsible of nematode related zoonosis. Knowing the risk of consumption of contaminated fish by the local communities, the main goal of this paper is to quantify and report the presence of larvae with zoonotic potential of Contracaecum spp. and Eustrongylides spp. found in two exotic fish species from the Tramandai River Basin in southern Brazil. The sample sites were two lagoons of the basin, the Itapeva lagoon and Palmital lagoon, sampled in the period of April 2018. Forty specimens of Acestrorhynchus pantaneiro and twenty specimens of Trachelyopterus lucenai were examined. A. pantaneiro presented a 58% and 4% prevalence and a mean intensity of 3.17 and 1 for Contracaecum spp. and Eustrongylides spp. , respectively. Meanwhile T. lucenai presented a prevalence of 70% and 5% and a mean intensity of 1.92 and 1 of Contracaecum spp. larvae and Eustrongylides spp. larvae, respectively. Although larvae of Contracaeucum spp. are reported only in the literature in experimental infections, they were able to complete their biological cycle in some mammals with certain pathogeneses. However, larvae of Eustrongylides spp. infect humans, as reported in the literature, causing severe damage to the intestinal tract. Knowing that local populations may be at risk, we recommend that all prophylactic measures be taken in relation to fish consumption. This study also contributes to the knowledge concerning the parasitic fauna of the host species studied.
Modeling the circadian dynamics of morning and evening oscillators and the role of circadian rhythm in learning and memory

Circadian rhythms (CR) are 24h endogenous oscillations seen in all organisms that control different biological processes including sleep-wake cycles, body temperature, cell division cycle, heartbeat, and metabolic rates. Light, the prime zeitgeber, accounts for the day-night changes and seasonal variation of the environment, and it modifies the endogenous (free running) period of the circadian rhythm, known as entrainment. In mammals, suprachiasmatic nucleus (SCN) is the main brain region that acts as a circadian master oscillator, which controls all the other peripheral oscillators. The circadian pacemaker in SCN plays an important role in encoding day length and seasonal changes. Identifying the molecular mechanism responsible for this encoding is an interesting problem that has attracted attention for a considerable period of time. A set of hypothesis has been proposed by Daan and his colleagues that the encoding is done by the circadian pacemaker that consists of two distinct oscillators of which one is the morning (M) oscillator that locks on to dawn and controls the morning activities, while the other is an evening (E) oscillator that locks on to the dusk and controls the evening activities. So far Daan’s hypotheses have neither been confirmed nor verified. The other problems that have attracted attention recently are the experimental generation of daily variation in firing patterns and the circadian modulation of synaptic plasticity, learning, and memory. However, molecular mechanisms responsible for the generation of daily varying firing patterns and the role of circadian rhythms in modulating learning and memory are not clearly delineated. Understanding of these problems requires careful construction of mathematical models with different time scales based on molecular mechanism of gene regulatory and signaling pathways. In this thesis, the following aspects of circadian rhythms are modelled and analyzed. (i) Construct and analyze the mathematical model of the circadian gene regulatory network (GRN) to verify the Daan’s hypothesis about ME oscillators. Modeling capture the differences in the variations in the period, phase response curves, entrainment in ME oscillators, and splitting. Our model largely supports the presence of ME oscillators in SCN.
The Kimberley, north‐western Australia, as a cradle of evolution and endemic biodiversity: An example using grunters (Terapontidae)

To test two prominent, alternate hypotheses that provide explanations for the great accumulation of endemic species in the Kimberley bioregion in north‐western Australia, using an extensively sampled, region wide phylogeny of northern Australia's most species‐rich freshwater fish family, Terapontidae. Specifically, we test whether the Kimberley may act as (1) a “museum” accumulating taxa and endemic species over time or (2) a “cradle” of more recent diversification and neoendemism.
Historical and contemporary climate legacy of the large-scale distributional patterns of plant richness across different taxonomic levels: An assessment of protected areas in China

<p align="left"><strong>Background: </strong>Historical and contemporary climates may shape the distributional patterns of plant species richness across different scales. However, few studies have focused on the effects of historical and contemporary climate changes on the distributional patterns of plant richness in Chinese protected areas across different taxonomic levels. </p><p align="left"><strong>Hypotheses: </strong>Historical and contemporary climates can have an important legacy effect on the large-scale distributional patterns of plant richness across different taxonomic levels. </p><p align="left"><strong>Studied species: </strong>Vascular plants. </p><p align="left"><strong>Study site: </strong>China. </p><p align="left"><strong>Method:</strong> We used data on plant richness at the family, genus, and species levels from Chinese protected areas and applied regression modelling to explore the relationships between climate change and plant richness among vascular, fern, seed, gymnosperm, and angiosperm plants based on paleoclimate (Last Glacial Maximum; LGM, ca. 22,000 years ago) and contemporary climate data. </p><p align="left"><strong>Results: </strong>The large-scale distributional patterns of plant richness could be predicted across different taxonomic levels on the basis of paleoclimate and contemporary climate data. Specifically, historical and contemporary climate variables were found to better correlate with fern plant richness than seed plant richness. For seed plants, the explanatory power of historical and contemporary climate variables was found to be stronger for the richness of gymnosperms than for the richness of angiosperms. </p><strong>Conclusions: </strong>The distributional pattern of plant richness could be predicted across different taxonomic levels after including paleoclimate (LGM, ca. 22,000 years ago) and contemporary climate data from China. Our study could support the effectiveness of the management of protected areas in China.
Disome-seq reveals sequence-mediated coupling of translational pauses and protein structures

The regulation of translation elongation plays a vital role in protein folding; an adequate translational pause provides time and cellular environments for the co-translational folding of nascent peptides. However, the genomic landscape, sequence determinants, and molecular consequences of translational pausing remain mostly unknown. In this study, we performed disome-seq that sequenced mRNA fragments protected by two consecutive ribosomes – a product of severe translational pauses during which the upstream ribosome collides into the paused one. We detected severe translational pauses on ∼75% of yeast genes. These pauses were often explained by one of the three mechanisms: 1) slow ribosome releasing at stop codons, 2) slow peptide formation from proline, glycine, asparagine, and cysteine, and 3) slow leaving of polylysine from the exit tunnel of ribosomes. Notably, these amino acids also terminate the α-helical conformation. Such dual roles of amino acids establish an inborn coupling between the synthetic completion of a structural motif and a translational pause. Furthermore, paused ribosomes often recruit chaperones to assist protein folding. As a consequence, emergent protein structures during evolution should be ready to be correctly folded. Collectively, our study shows widespread translational pauses and sheds lights on a better understanding of the regulation of co-translational protein folding.
Hierarchical network analysis of behavior and neuronal population activity

Recording of neuronal population activity in behaving animals is becoming increasingly popular. Computational markerless annotation tools allow for tracking of animal body-parts throughout the experiment. However, the question remains of how to cross-correlate the extracted behavioral data with the simultaneously acquired neuronal population activity, when both datasets are of high dimensionality. Here we propose a combined analysis, where the behavioral data is clustered into discrete states using a deep learning model and the occurrence of each state is correlated to clusters of neuronal activity. We then model the relationship between behavioral states as a network, where related states are hierarchically grouped while the similarity between their neuronal correlates is maximized. This type of analysis allows for hierarchical exploration of the bidirectional relationship between behavior and its neuronal correlates at different temporal scales.
Bayesian analysis of GWAS summary data reveals differential signatures of natural selection across human complex traits and functional genomic categories

Understanding how natural selection has shaped the genetic architecture of complex traits and diseases is of importance in medical and evolutionary genetics. Bayesian methods have been developed using individual-level data to estimate multiple features of genetic architecture, including signatures of natural selection. Here, we present an enhanced method (SBayesS) that only requires GWAS summary statistics and incorporates functional genomic annotations. We analysed GWAS data with large sample sizes for 155 complex traits and detected pervasive signatures of negative selection with diverse estimates of SNP-based heritability and polygenicity. Projecting these estimates onto a map of genetic architecture obtained from evolutionary simulations revealed relatively strong natural selection on genetic variants associated with cardiorespiratory and cognitive traits and relatively small number of mutational targets for diseases. Averaging across traits, the joint distribution of SNP effect size and MAF varied across functional genomic regions (likely to be a consequence of natural selection), with enrichment in both the number of associated variants and the magnitude of effect sizes in regions such as transcriptional start sites, coding regions and 5’- and 3’-UTRs.
Computational investigation of marine bioactive compounds reveals frigocyclinone as a potent inhibitor of Kaposi’s Sarcoma Associated Herpesvirus (KSHV) targets

In the present study, in silico analysis was employed to identify the action of marine bioactive compounds against KSHV targets. Virulence factor analysis of KSHV from literature review, three proteins LANA1, vIRF3/LANA2 and PF-8 were identified as putative drug targets. The quality of protein structures play a significant role in the experimental structure validation and prediction, where the predicted structures may contain considerable errors was checked by SAVES v5.0 servers. By virtual screening four potential bioactive compounds Ascorbic acid, Salicylihalamide A, Salicylihalamide B and Frigocyclinone were predicted. One of the potential compounds of Frigocyclinone has acting against KSHV proteins. Hence, determined as the good lead molecule against KSHV. Molecular dynamic simulation studies revealed the stability of LANA1- Frigocyclinone complex and it could be a futuristic perspective chemical compound for Kaposi’s sarcoma.
Loss of Cdc13 causes genome instability by a deficiency in replication-dependent telomere capping

In budding yeast, Cdc13, Stn1, and Ten1 form a telomere binding heterotrimer dubbed CST. Here we investigate the role of Cdc13/CST in maintaining genome stability, using a Chr VII disome system that can generate recombinants, loss, and enigmatic unstable chromosomes. In cells expressing a temperature sensitive CDC13 allele, cdc13F684S, unstable chromosomes frequently arise due to problems in or near a telomere. Hence, when Cdc13 is defective, passage through S phase causes Exo1-dependent ssDNA and unstable chromosomes, which then are the source for whole chromosome instability events (e.g. recombinants, chromosome truncations, dicentrics, and/or loss). Specifically, genome instability arises from a defect in Cdc13’s replication-dependent telomere capping function, not Cdc13s putative post-replication telomere capping function. Furthermore, the unstable chromosomes form without involvement of homologous recombination nor non-homologous end joining. Our data suggest that a Cdc13/CST defect in semi-conservative replication near the telomere leads to ssDNA and unstable chromosomes, which then are lost or subject to complex rearrangements. This system defines a links between replication-dependent chromosome capping and genome stability in the form of unstable chromosomes.
Genome Scans for Selection and Introgression based on k-nearest Neighbor Techniques

In recent years, genome-scan methods have been extensively used to detect local signatures of selection and introgression. Here, we introduce a series of versatile genome-scan methods that are based on non-parametric k-nearest neighbors (kNN) techniques, while incorporating pairwise Fixation Index (FST) estimates and pairwise nucleotide differences (dxy) as features. Simulations were performed for both positive directional selection and introgression, with varying parameters, such as recombination rates, population background histories, the proportion of introgression, and the time of gene flow. We find that kNN-based methods perform remarkably well while yielding stable results almost over the entire range of k. We provide a GitHub repository (pievos101/kNN-Genome-Scans) containing R source code to demonstrate how to apply the proposed methods to real-world genomic data using the population genomics R-package PopGenome.
Tourism and health : risks, research, and responses

Part 1 Overviews of travel and health: health and travel - historical perspectives, emerging problems, Jonathan Cossar the epidemiology of travel-related health problems, Robert Steffen important issues influencing the health of travellers, Ron Behrens current research on health and tourism issues and future directions, Douglas Frechtling. Part 2 Tourism and health risks - realities and representations: injuries and accidents among international tourists in Australasia - scale, causes and solutions, Stephen Page and Denny Meyer the Indian plague scare of 1994 - a case study, Peter Grabowski and Santanu Chatterjee British tourists in the Gambia - health precautions and malaria prophylaxis, Stephen Clift and Peter Grabowski. Part 3 Sexual behaviour and sun-seeking among tourists: New Zealand student tourists - risk behaviour and health, Chris Ryan and Emma Robertson who wants to be a "peely wally"? Glaswegian tourists' attitudes to sun tans and sun exposure, Simon Carter licensed for thrills - risk taking and tourism, Eugenia Wickens sexual behaviour and travel - quantitative and qualitative perspectives on the behaviour of genito-urinary medicine clinic attenders, Paula Black. Part 4 Travel and HIV/AIDS prevention initiatives: prostitution, intavenous drug use and travel - European HIV/AIDS prevention initiatives, Georg Broring the Europe against AIDS summer campaign 1995 - an evaluation of work in the United Kingdom, Lynette Thomas et al an HIV/AIDS prevention programme for Swiss travellers, Martin Buechi and Martin Werner.