Miracle-dz/UniFAR-FTUs huggingface dataset:
Squamous differentiation portends poor prognosis in low and intermediate-risk endometrioid endometrial cancer

Background Endometrial cancer presents well-defined risk factors (myometrial invasion, histological subtype, tumor grade, lymphovascular space invasion (LVSI)). Some low and intermediate-risk endometrioid endometrial cancer patients exhibited unexpected outcomes. The aim of this study was to investigate other clinical-pathological factors that might influence the recurrence rates of patients diagnosed with low and intermediate-risk endometrioid endometrial cancer. Methods A case-control study from a cohort retrospective of 196 patients diagnosed with low and intermediate-risk endometrioid endometrial cancer at a single institution between 2009 and 2014 was conducted. Medical records were reviewed to compare clinical (race, smoking, menopause age, body mass index) and pathological (histological characteristics (endometrioid vs endometrioid with squamous differentiation), tumor differentiation grade, tumor location, endocervical invasion, LVSI) features of patients with recurrence (case) and without recurrence (control) of disease. Three controls for each case were matched for age and staging. Results Twenty-one patients with recurrence were found (10.7%), of which 14 were stage IA, and 7 were stage IB. In accordance, 63 patients without recurrence were selected as controls. There were no significant differences in any clinical characteristics between cases and controls. Among pathological variables, presence of squamous differentiation (28.6% vs. 4.8%, p=0.007), tumor differentiation grade 2 or 3 (57.1% vs. 30.2%, p=0.037) and presence of endocervical invasion (28.6% vs. 12.7%, p=0.103) were associated with disease recurrence on univariate analysis. On multivariable analysis, only squamous differentiation was a significant risk factor for recurrence (p=0.031). Conclusion Our data suggest that squamous differentiation may be an adverse prognostic factor in patients with low and intermediate-risk endometrioid endometrial cancer, that showed a 5.6-fold increased risk for recurrence.
Single-gene resolution of locally adaptive genetic variation in Mexican maize

Threats to crop production due to climate change are one of the greatest challenges facing plant breeders today. While considerable adaptive variation exists in traditional landraces, natural populations of crop wild relatives, and ex situ germplasm collections, separating adaptive alleles from linked deleterious variants that impact agronomic traits is challenging and has limited the utility of these diverse germplasm resources. Modern genome editing techniques such as CRISPR offer a potential solution by targeting specific alleles for transfer to new backgrounds, but such methods require a higher degree of precision than traditional mapping approaches can achieve. Here we present a high-resolution genome-wide association analysis to identify loci exhibiting adaptive patterns in a large panel of more than 4500 traditional maize landraces representing the breadth of genetic diversity of maize in Mexico. We evaluate associations between genotype and plant performance in 13 common gardens across a range of environments, identifying hundreds of candidate genes underlying genotype by environment interaction. We further identify genetic associations with environment across Mexico and show that such loci are associated with variation in yield and flowering time in our field trials and predict performance in independent drought trials. Our results indicate that the variation necessary to adapt crops to changing climate exists in traditional landraces that have been subject to ongoing environmental adaptation and can be identified by both phenotypic and environmental association.
QUALITY DIFFERENCES OF BOER LIQUID SEMEN DURING STORAGE WITH ADDITION SWEETORANGEESSENTIAL OIL IN TRIS YOLK AND GENTAMICIN EXTENDER

Abstract The purpose of this study was to know the quality of Boer liquid semen during storage by adding sweet orange essential oil and gentamicin into the tris yolkextender.The semenlongevity test was carried out by storing semen in a closed tube at room temperature and refrigerator, and evaluated motility and Viability every 3 hours at room temperature and 12 hours in refrigerator. The results showed that the characteristics of the liquid semen, with the addition of 1% of essential oils showed percentage of motility and Viability significantly higher than 0.5% and without the addition of essential oil, either stored at room temperature or in the refrigerator. This may be related to the content of essential oils of sweet orange peel containing flavonoids and antibacterials that are capable of maintaining liquid semen quality of Boer Goat.In addition, gentamicin contains antibacterials capable of suppressing the growth of bacteria which can damage and durabilitythe spermatozoa. Keywords: Boer Goat,Gentamicin, Liquid semen, Sweet orange
The mitochondrial genome of Hilara sp. (Diptera: Empididae)

Abstract The dance fly Hilara sp. belongs to the subfamily Empidinae of Empididae. The mitogenome (GenBank accession number: MN064659) of Hilara sp. was sequenced, the new representative of the mitogenome of the subfamily. The nearly complete mitogenome is 14,927 bp totally, consisting of 13 protein-coding genes, 2 rRNAs, and 22 transfer RNAs. All genes have the similar locations and strands with that of other published species of Empididae. The nucleotide composition biases towards A and T, which together made up 75.7％of the entirety. Bayesian inference analysis strongly supported the monophyly of Empidoidea, Empididae, and Dolichopodidae. It is clear that the phylogenetic relationship within Empidoidea: Dolichopodinae was the sister group to Neurigoninae, and Empidinae was the sister group to Trichopezinae, and the clade that contains Dolichopodinae and Neurigoninae was assigned to the sister group to the clade that contains Empidinae and Trichopezinae.
An Investigation of Healthy Food Consumption in Low-Income Families

The highest obesity rates were associated with the lowest incomes and low educational levels. Little is currently known about low-income families’ perceptions about healthy food and their decision-making processes when selecting food items. The purpose of this project was to assess perceptions, determinants, and decision-making processes regarding healthy food choices among low-income families in the U.S. Study participants were recruited from a local food pantry in Ruston, Louisiana in the US from February 2016 to May 2016. Researchers set up a table inside of the food pantry, and participants were asked to complete a written survey during their food pantry visits. A total 153 participants completed the survey. The survey instrument was composed of three sections. The first part consisted of items assessing participants’ attitude, subjective norm, perceived behavioral control, and intention toward healthy food consumption. The second section included measurement items designed to assess salient beliefs and referents regarding healthy food consumption. The last section consisted of questions related to participants’ social demographic information, including gender, age, race, income level, education level, and self-reported height (feet and inches) and weight (pounds). Descriptive analysis, exploratory factor analysis, confirmatory factor analysis, and multi-group structural equation modeling were used in the study. Most of the low-income families participating in the study hold positive attitude and high intention towards consuming healthy food (β = 0.730, p < 0.01). For normal-weight, low-income individuals, intention to consume healthy food was only influenced by cost and environmental constraints (β = 0.552, p < 0.01), while perceptions of family members, friends, and health practitioners (β = 0.757, p < 0.01) significantly influenced overweight participants’ intention. Nutrition and health monitoring and assistance are very important for the well-being of overweight low-income residents.
Lack of Renal Tubular Glucocorticoid Receptor Decreases the Thiazide-Sensitive Na+/Cl– Cotransporter NCC and Transiently Affects Sodium Handling

Chronic glucocorticoid infusion impairs NCC activity and induces a non-dipping profile in mice, suggesting that glucocorticoids are essential for daily blood pressure variations. In this paper, we studied mice lacking the renal tubular glucocorticoid receptor (GR) in adulthood (GR knockouts, Nr3c1Pax8/LC1). Upon standard salt diet, Nr3c1Pax8/LC1 mice grow normally, but show reduced NCC activity despite normal plasma aldosterone levels. Following diet switch to low sodium, Nr3c1Pax8/LC1 mice exhibit a transient but significant reduction in the activity of NCC and expression of NHE3 and NKCC2 accompanied by significant increased Spak activity. This is followed by transiently increased urinary sodium excretion and higher plasma aldosterone concentrations. Plasma corticosterone levels and 11βHSD2 mRNA expression and activity in the whole kidney remain unchanged. High salt diet does not affect whole body Na+ and/or K+ balance and NCC activity is not reduced, but leads to a significant increase in diastolic blood pressure dipping in Nr3c1Pax8/LC1 mice. When high sodium treatment is followed by 48 h of darkness, NCC abundance is reduced in knockout mice although activity is not different. Our data show that upon Na+ restriction renal tubular GR-deficiency transiently affects Na+ handling and transport pathways. Overall, upon standard, low Na+ and high Na+ diet exposure Na+ and K+ balance is maintained as evidenced by normal plasma and urinary Na+ and K+ and aldosterone concentrations.
Immunology going wild : genetic variation and immunocompetence in the mallard (Anas platyrhynchos)

21 1. Background . 22 2. RNA analysis of birds before NGS, a brief history . 24 3. Ornithology in the age of *omics . 26 3.1 RNA-seq, a brief introduction . 28 4. Applications of transcriptomics for non-model bird species . 28 4.1 Characterisation of transcriptomes . 29 4.2 Functional studies (gene expression) . 32 4.3 Gene interactions and function . 36 4.4 Genetic marker discovery . 37 4.5 Genetic variation . 40 4.6 Alternative splicing / transcriptome isoforms . 42 5. Planning of an RNA-seq study quick guide . 48 5.1 Sample collection . 48 5.2 RNA-isolation and library preparation . 50 5.3 Sequencing . 53 5.4 Transcriptome assembly or alignment . 56 5.5 Analysis . 57 6. Challenges with RNA-seq and its utility for non-model ornithology . 59 6.1 Library preparation, we might be introducing bias in the data . 59 6.2. Working with large datasets (“Big Data”), a new era for biology . 59 6.3 Transcriptomics, from the lab to the field . 60 6.4 Experimental proof as a last step to ascribe biological function . 60 7. Future . 61 7.1 Single Cell Sequencing . 61 7.2 Spatially resolved *omics . 62 7.3 On-site sequencing platforms . 62 Acknowledgements . 63 Chapter 2 . 65 Abstract . 65 Introduction . 66 Methods . 69 Birds and housing . 69. 65 Introduction . 66 Methods . 69 Birds and housing . 69 Treatments . 70 Experimental setup . 70 Analysis of body temperature, heart rate and activity data . 72 Leukocyte counting and differentiation . 73 Genome wide gene expression profiling . 74 Gene expression of target genes . 77 Results . 78 Body temperature, heart rate and activity . 78 Genome wide gene expression profiling . 83 Gene expression of target genes . 92 Discussion . 92 Body temperature, heart rate and activity . 92 Leukocyte counting and differentiation . 93 Gene expression profiling . 94 Acknowledgements . 97 Chapter 3 . 99 Abstract . 99 Introduction . 101 Materials and Methods . 103 Birds . 103. 99 Introduction . 101 Materials and Methods . 103 Birds . 103 Bait design . 103 Library preparation and enrichment . 103 Reference-based assembly and retrieval of immune genes . 104 Genetic variation in immune genes in mallards . 104 Evidence of Natural Selection . 105 Immune pathway function . 107 Results and Discussion . 107 Reference-based assembly and retrieval of immune genes . 107 Genetic variation in immune genes in mallards . 108 Evidence of Natural Selection . 110 Immune pathway function . 117 Conclusion .
The microbiome wants what it wants: microbial evolution overtakes experimental host-mediated indirect selection

Microbes ubiquitously inhabit animals and plants, often affecting their host’s phenotype. As a result, even in a constant genetic background, the host’s phenotype may evolve through indirect selection on the microbiome. ‘Microbiome engineering’ offers a promising novel approach for attaining desired host traits but has been attempted only a few times. Building on the known role of the microbiome on development in fruit flies, we attempted to evolve earlier eclosing flies by selecting on microbes in the growth media. We carried out parallel evolution experiments in no- and high-sugar diets by transferring media associated with fast-developing fly lines over the course of four rounds of selection. In each round, we used sterile eggs from the same inbred population, and assayed fly mean eclosion times. Ultimately, flies eclosed seven to twelve hours earlier, depending on the diet, but selection had no effect. 16S sequencing showed that the microbiome did evolve, particularly in the no sugar diet, with an increase in alpha diversity over time. Thus, while microbiome evolution did affect host eclosion times, these effects were incidental. Instead, any experimentally enforced selection effects were swamped by independent microbial evolution. These results imply that selection on host phenotypes must be strong enough to overcome other selection pressures simultaneously operating on the microbiome. The independent evolutionary trajectories of the host and the microbiome may limit the extent to which indirect selection on the microbiome can ultimately affect host phenotype. Random-selection lines accounting for independent microbial evolution are essential for experimental microbiome engineering studies.
Population structure determined by comparative amplicon gene sequencing in biofilm and planktonic bacterial communities from pesticide-contaminated water

Molecular and bioinformatics tools for research are very important for biodiversity characterization in contaminated environments due the presence of a high percentage of nonculturable microorganisms. The wide use of pesticides in agriculture exposes microbiomes to stressful and selective conditions that demand survival strategies such as biofilm formation. The purpose of this work was to evaluate the bacterial population structure in planktonic and biofilm communities of water that was used for washing the packaging of herbicides and stored for six months in tanks. This substance is highly contaminated waste. Samples of water and biofilms from tanks and biofilms developed for short times in flasks were used for DNA isolation and 16S rRNA gene sequencing. The physicochemical conditions imposed by water used for washing the containers were inadequate for killing the bacterial genera identified according to water and wastewater standards. The variation in population structure and diversity was lower in the planktonic samples than in the biofilm samples, indicating a possible combination of genetic drift and subsequent selection of individuals surviving under stressful water conditions, such as heating and contact with agrochemicals, over a six-month period. The biofilm formation in water tanks contaminated with pesticides enabled the survival of bacterial genera harboring the essential processes for adaptation to these environments; the presence of these processes was determined according to descriptions obtained from the genomic databases. This study suggests the potential of bacterial genera identified in biofilms obtained from tanks to adapt to contaminated environments through their metabolic complexity. Thus, herbicide biodegradation kinetics can be accessed through a culturable collection obtained from these communities.
Chromosomal condensation leads to a preference for peripheral heterochromatin

A layer of dense heterochromatin is found at the periphery of the nucleus. Because this peripheral heterochromatin functions as a repressive phase, mechanisms that relocate genes to the periphery play an important role in regulating transcription. Using Monte-Carlo simulations, we show that an interaction between chromatin and the nuclear boundary need not be specific to heterochromatin in order to preferentially locate heterochromatin to the nuclear periphery. This observation considerably broadens the class of possible interactions that result in peripheral positioning to include boundary interactions that either weakly attract all chromatin or strongly bind to a randomly chosen small subset of loci. The key distinguishing feature of heterochromatin is its high chromatin density with respect to euchromatin. In our model this densification is caused by HP1’s preferential binding to H3K9me3 marked histone tails. We conclude that factors that are themselves unrelated to the nuclear periphery can determine which genomic regions condense to form heterochromatin and thereby control which regions are relocated to the periphery.
Plasticity of High-Density Neutrophils in Multiple Myeloma is Associated with Increased Autophagy Via STAT3

In both monoclonal gammopathy of uncertain significance (MGUS) and multiple myeloma (MM) patients, immune functions are variably impaired, and there is a high risk of bacterial infections. Neutrophils are the most abundant circulating leukocytes and constitute the first line of host defense. Since little is known about the contribution of autophagy in the neutrophil function of MGUS and MM patients, we investigated the basal autophagy flux in freshly sorted neutrophils of patients and tested the plastic response of healthy neutrophils to soluble factors of MM. In freshly sorted high-density neutrophils obtained from patients with MGUS and MM or healthy subjects, we found a progressive autophagy trigger associated with soluble factors circulating in both peripheral blood and bone marrow, associated with increased IFNγ and pSTAT3S727. In normal high-density neutrophils, the formation of acidic vesicular organelles, a morphological characteristic of autophagy, could be induced after exposure for three hours with myeloma conditioned media or MM sera, an effect associated with increased phosphorylation of STAT3-pS727 and reverted by treatment with pan-JAK2 inhibitor ruxolitinib. Taken together, our data suggest that soluble factors in MM can trigger contemporary JAK2 signaling and autophagy in neutrophils, targetable with ruxolitinib.
Evidence of coral bleaching avoidance, resistance and recovery in the Maldives during the 2016 mass-bleaching event

During the third global coral bleaching event in 2016, the Maldives experienced elevated water temperatures, inducing coral bleaching. We recorded the bleaching intensity and mortality of coral communities in different habitats, depths and wave exposure conditions around North Ari Atoll in the central Maldives to investigate the effect of physical and biological factors that may contribute to bleaching avoidance, resistance and recovery. Approximately 50% of coral cover bleached and ~20% died, with significant variation with wave exposure and depth. Deeper wave-exposed reefs were dominated by bleaching resistant massive and encrusting growth forms and experienced less thermal stress than shallow sheltered reefs. Shallow sheltered reefs showed rapid recovery from the previous mass-bleaching event in 1998, regaining high coral cover dominated by branching and tabular growth forms by 2015. However, these bleaching-sensitive growth forms experienced high bleaching and mortality in 2016, causing greater coral loss. Several of the reefs in central Ari Atoll simultaneously experienced a crown-of-thorn starfish (COTS) outbreak, resulting in very degraded reefs that lacked any apparent resilience in 2017. Our findings demonstrate the complex interactions between different components of resilience. In this case, wave exposure and depth appeared to promote avoidance and resistance of corals to bleaching, but reduced their recovery potential, while the reverse was true for shallow sheltered reefs. The resilience of reefs in the Maldives to date appears to be the result of low thermal and anthropogenic stress; therefore, their future condition will depend on the frequency and intensity of bleaching events and the level of human pressures such as construction and fishing.
A novel lineage of candidate pheromone receptors for sex communication in moths

Sex pheromone receptors (PRs) are key players in chemical communication between mating partners in insects. In the highly diversified insect order Lepidoptera, male PRs tuned to female-emitted type I pheromones (which make up the vast majority of pheromones identified) form a dedicated subfamily of odorant receptors (ORs). Here, using a combination of heterologous expression and in vivo genome editing methods, we bring functional evidence that at least one moth PR does not belong to this subfamily but to a distantly related OR lineage. This PR, identified in the cotton leafworm Spodoptera littoralis, is over-expressed in male antennae and is specifically tuned to the major sex pheromone component emitted by females. Together with a comprehensive phylogenetic analysis of moth ORs, our functional data suggest two independent apparitions of PRs tuned to type I pheromones in Lepidoptera, opening up a new path for studying the evolution of moth pheromone communication.
High sampling effectiveness for non‐bee flower visitors using vane traps in both open and wooded habitats

Many non‐bee insects are important for pollination, yet few studies have assessed the effectiveness of sampling these taxa using low‐cost techniques, such as coloured vane traps, among different habitat types. This study sampled 192 sites – 108 in wooded and 84 in open habitats – within an agricultural region of southern Australia. Pairs of blue and yellow vane traps were placed at each site for a period of seven days during the austral spring. Overall, 3114 flies (Diptera) from 19 families and 528 wasps (non‐bee and non‐formicid Hymenoptera) from 16 families were collected during the study. This sampling was representative of the region, with vane traps equally or more likely to collect as many families from both taxa as those reported on the Atlas of Living Australia (ALA) database for the sampling area. Blue vane traps (BVTs) had greater average richness of both flies and wasps and greater activity density (abundance per 7‐day sampling period) of individuals than yellow vane traps (YVTs). BVTs were particularly favoured by fly and wasp families known to pollinate flowers (e.g. Syrphidae, Bombyliidae and Scoliidae), whilst YVTs sampled flower visitors that also provide additional ecosystem services, such as pest control and nutrient cycling. Here, vane traps were an effective sampling technique to capture non‐bee flower visitors, such as flies and wasps. This study supports the use of vane traps as a component of the sampling protocol for ecological census and population monitoring within multiple habitat types, where colour attraction will more effectively sample a comprehensive pollinator community.