Miracle-dz/UniFAR-FTUs huggingface dataset:
Bursting on a two state stochastic model for gene transcription in Drosophila embryos

Recent experimental data on the transcription dynamics of eve gene stripe two formation of Drosophila melanogaster embryos occurs in bursts of multiple sizes and durations. That has motivated the proposition of a transcription model having multiple ON states for the promoter of the eve gene each of them characterized by different synthesis rate. To understand the role of multiple ON states on gene transcription we approach the exact solutions for a two state stochastic model for gene transcription in D. melanogaster embryos and derive its bursting limit. Simulations based on the Gillespie algorithm at the bursting limit show the occurrence of bursts of multiple sizes and durations. Based on our theoretical approach, we interpret the aforementioned experimental data as a demonstration of the intrinsic stochasticity of the transcriptional processes in fruit fly embryos. Then, we conceive the experimental arrangement to determine when gene transcription has multiple ON promoter state in a noisy environment.
SOLOv2: Dynamic and Fast Instance Segmentation

In this work, we aim at building a simple, direct, and fast instance segmentation framework with strong performance. We follow the principle of the SOLO method of Wang et al. "SOLO: segmenting objects by locations". Importantly, we take one step further by dynamically learning the mask head of the object segmenter such that the mask head is conditioned on the location. Specifically, the mask branch is decoupled into a mask kernel branch and mask feature branch, which are responsible for learning the convolution kernel and the convolved features respectively. Moreover, we propose Matrix NMS (non maximum suppression) to significantly reduce the inference time overhead due to NMS of masks. Our Matrix NMS performs NMS with parallel matrix operations in one shot, and yields better results. We demonstrate a simple direct instance segmentation system, outperforming a few state-of-the-art methods in both speed and accuracy. A light-weight version of SOLOv2 executes at 31.3 FPS and yields 37.1% AP. Moreover, our state-of-the-art results in object detection (from our mask byproduct) and panoptic segmentation show the potential to serve as a new strong baseline for many instance-level recognition tasks besides instance segmentation. Code is available at: this https URL
Transcriptome sequencing reveals abundant olfactory genes in the antennae of the rice leaffolder, Cnaphalocrocis medinalis (Lepidoptera: Pyralidae)

The rice leaffolder, Cnaphalocrocis medinalis Guenée, is an important lepidopteran pest of rice in Asia. Insect olfactory proteins, including olfactory receptors (ORs), ionotropic receptors (IRs), odorant‐binding proteins (OBPs), chemosensory proteins (CSPs) and sensory neuron membrane proteins (SNMPs), are responsible for perception of sex pheromones and host plant volatiles, and thus regulate insect behavior. In the present study, transcriptome sequencing was conducted for C. medinalis antennae to identify genes involved in olfaction. A total of 45800 unigenes were assembled from the transcriptome dataset. Of these, 19696 (43.0%) unigenes were annotated by searching against the NCBI non‐redundant database. Functional classification of these unigenes were also conducted by using the Gene Ontology (GO) and Cluster of Orthologous Groups (COG) databases. We identified 90 putative olfactory genes (including 37 novel ones): 46 ORs, 15 IRs, 12 OBPs, 15 CSPs and two SNMPs. BLASTX best hit results indicated that these genes were most identical to their respective orthologs from other lepidopteran insects. Quantitative reverse transcription‐PCR (qRT‐PCR) assays were performed to investigate the expression profiles of newly identified OR genes. All of the OR genes were antennae‐specific or antennae‐enriched. Of these, CmedOR28 and CmedOR31 were mainly expressed in male antennae, while CmedOR27 and CmedOR32 were enriched in female antennae. Our results establish a solid foundation for future functional studies of these genes.
Inference of metabolic flux distributions from transcriptomic data

OF THE DISSERTATION . ii DEDICATION . iv ACKNOWLEDGEMENT . v NOTES . vii TABLE OF CONTENTS . ix CHAPTER 1: Introduction . 1 1.1 13 C-Metabolic Flux Analysis . 1 1.2 Flux Balance Analysis for predicting system-level metabolic flux distributions . 2 1.3 Integration of transcriptomic data for predicting condition-specific metabolic flux distributions . 4 1.4 Summary of existing methods for inferring metabolic flux distributions from transcriptomic data based on four grouping criteria . 8 1.4. 1 Grouping criterion 1: Requirement for multiple gene expression datasets as input . 9 1.4. 2 Grouping criterion 2: Requirement for a threshold to define a gene's high/low expression . 13 1.4. 3 Grouping criterion 3: Requirement for a priori assumption of an appropriate objective function . 16 1.4. 4 Grouping criterion 4: Validation of predicted fluxes directly against measured intracellular fluxes . 17 1.4. 5 Summary and outlook . 18 1.5 Objective of this study . 20 CHAPTER 2: Development of E-Flux2 and SPOT. 22 2.1 Background . 22 2.2 Materials and Methods . 27
Could ecologists be more random? Straightforward alternatives to haphazard spatial sampling

When conducting field studies, it is common for ecologists to choose the locations of sampling units arbitrarily at the time sampling occurs, rather than using a properly randomised sampling design. Unfortunately, this ‘haphazard’ sampling approach cannot provide formal statistical inference from the sample to the population without making untestable assumptions. Here, we argue that two recent technological developments remove the need for haphazard sampling in many situations. A general approach to simple randomised sampling designs is outlined, and some examples demonstrate that even complicated designs can be implemented easily using software that is widely used among ecologists. We consider that more rigorous, randomised sampling designs would strengthen the validity of the conclusions drawn from ecological studies, to the benefit of the discipline as a whole. This article is protected by copyright. All rights reserved.
Cascading effects of changes in land use on the invasion of the walnut Juglans regia in forest ecosystems

Plant invasions are affected by many factors that must be favourable in order for invasions to occur. Factors can be grouped into three major categories: propagule pressure, biotic factors and abiotic characteristics; all may be moderated by human activity. However, studies examining all factors simultaneously are rare, and most are limited to a single factor. This hampers our understanding of the mechanisms driving invasions. In recent decades, an alien walnut (Juglans regia) has become invasive in Central Europe due to an increase in the populations of native dispersers, rooks (Corvus frugilegus) and political changes that have resulted in the abandonment of farmland. Here, we test whether increased propagule pressure resulting from the presence of seed‐bearing walnuts in abandoned fields interacts with native forest seed‐dispersing animals (biotic factors), landscape structure and management, and passive secondary dispersal by gravity (abiotic factors) to facilitate the further invasion of walnuts into forests. Seed‐dispersing animals were observed visiting walnuts growing in abandoned fields and in human settlements. Walnuts and seed dispersers were surveyed in 102 forest patches. Forest characteristics were examined, and field experiments examining passive dispersal were conducted. Walnut seeds were carried into forests by native birds, jays (Garrulus glandarius). Jays harvested seeds from both wild walnuts growing in abandoned fields and walnuts planted in human settlements. The density of walnuts in forest patches was correlated with jay density. Forest occupancy by walnuts and walnut densities were correlated with the cover of abandoned fields and human settlements containing seed‐bearing walnuts. Secondary seed dispersal also affected forest colonization. Walnut seeds hidden by native rooks in sloping, arable fields may be transported passively to forest edges. Synthesis. Our results show that this invasion is a multifaceted process in which human‐related alterations to propagule pressure and biotic and abiotic factors have led to the spread of alien walnuts from human settlements and abandoned fields into forest ecosystems. Thus, politically related land use changes can create an invasion debt that causes unexpected linkages among the invasive plant, native dispersers, land management and topography that together can cause cascading changes in ecosystems.
Length–weight relationships of four fish species from the Niulan River, China

Summary This study provides the length–weight relationships (LWRs) for four fish species [Leptobotia rubrilabris (Dabry de Thiersant, 1872); Opsariichthys bidens Gunther, 1873; Xenocypris yunnanensis Nichols, 1925; and Sinogastromyzon sichangensis Chang, 1944] collected from the Niulan River, China. Samples were obtained between April 2008 and June 2011 using various types of fishing gear [drift gill nets (mesh: 5 × 5 cm), hook and electro fishing]. A total of 136 specimens belonging to four fish species were analyzed. For each species the sample size, length range, weight range, LWR, 95% confidence intervals of a and b, and coefficient of correlation were determined. Prior to this study, the LWRs for S. sichangensis and X. yunnanensis were unknown. New maximum sizes for S. sichangensis and X. yunnanensis are also provided.
Effect of Six Sessions of High Intensity Interval Training on Levels of Hypoxanthine, Xanthine, Hypoxanthine-Guanine phosphoribosyltransferase (HGPRT) and Serum Uric Acid in active young men

Abstract Introduction and objectives: long-term sport and physical activity results in compatibility in maintaining purine derivatives but the compatibility achieved within a few sessions is not well investigated. This study aimed to investigate the effect of a 30-seconds high intensity interval training on Hypoxanthine, xanthine, hypoxanthine-guanine phosphoribosyltransferase (HGPRT) and serum uric acid in young college men. Methods: In this study, 18 untrained healthy men were divided into two control and training groups after homogenization based on their personal characteristics. Training included six sessions (every other day for two weeks) with different intervals (4, 7, 6, 6, 5 & 4, respectively) with a fixed four-minute rest between each interval, and with a constant load of . 6 on the cycle-ergometer. Blood samples were taken before and 48 hours after the last training session, and were used to analyze hypoxanthine, xanthine, uric acid, and serum HGPRT. Statistical analysis was performed using analysis of covariance (ANCOVA). Results: The results showed that high-intensity interval training for two weeks did not cause significant changes in serum HGPRT (P = .73); likewise, the increase in serum hypoxanthine (P = .170) and serum xanthine (P = .170) was not statistically significant but significant reduction was observed in serum uric acid (P = .025). Discussion and conclusion: The results of this study indicated that two-week HIIT training is likely to enhance athletic performance and recovery of purine nucleotide cycle.
The cellular and humoral immune response against primary infection with Coxiella burnetii

Coxiella burnetii is an obligate intracellular pathogen that causes the zoonotic disease Q fever in humans. Previous studies have found important roles for CD4+ and CD8+ T cells in the immune response to primary infection with this pathogen. However, the precise role for these cells in infection is still unknown. In the present study, we examined the role of CD4+ and CD8+ T cells in primary infection using MHC I and MHC II knockout mice. Our data indicates that mice lacking MHC I and CD8+ T cells have more severe disease than wild-type mice, and these mice have persistent infections. CD4+ T cells and MHC II also play a role in primary infection protection, and this pathway also plays a role in vaccine protection. Our results utilizing Tap1 knockout mice suggest that the MHC Ia pathway is involved in the protective response against primary infection. In terms of CD8+ T cell function, we found that IFNγ production by these cells may help reduce bacterial burden, but that other cells are producing this proinflammatory cytokine during infection. We also utilized granzyme B and perforin knockout mice and discovered that CD8+ T cell cytotoxic T cell lysis (CTL) is critical in the primary immune response to C. burnetii infection. This data indicates that MHC I and CD8+ T cell CTL are important during primary infection and that MHC II and CD4+ T cells are important during both primary infection and during the vaccine response against C. burnetii.
Yield and Yield Attributes Responses of Soybean (Glycine max L. Merrill) to Elevated CO2 and Arbuscular Mycorrhizal Fungi Inoculation in the Humid Transitory Rainforest

Variations in yield components and grain yield of arbuscular mycorrhizal fungi (AMF) inoculated soybean varieties ( Glycine max L. Merrill) grown in CO 2 enriched environment in the humid rainforest were tested. A screen house trial was established with soybean varieties (‘TGx 1448-2E’, ‘TGx 1440-1E’ and ‘TGx 1740-2F’), AMF inoculation (with and without) and CO 2 enrichment (350±50 ppm and 550±50 ppm) in open top chamber, arranged in completely randomised design, replicated three times. A field trial was also conducted; the treatments were arranged in a split-split plot configuration fitted into randomised complete block design. In the main plot the variant was CO 2 enrichment, the sub-plot consisted of AMF inoculation (with and without), while the sub-sub plot consisted of soybean varieties, replicated three times. Both trials had significantly higher grain yield at elevated CO 2 than ambient. This could be attributed to improved yield attributes, more spore count and root colonisation. In both trials, inoculated soybean had significantly higher dry pod weight than un-inoculated, which could suggest the increased grain yield observed on the field. AMF inoculated soybean varieties outperformed un-inoculated in both CO 2 enriched and ambient concentrations. AMF inoculated soybean variety ‘TGx 1740-2F’ is most preferable in CO 2 enriched environment, while variety ‘TGx 1448-2E’ had the most stable grain yield in all growth environments.
WORKING CONDITIONS

MISCELLANEOUS MATTERS EXPERIMENTAL PROCEDURE No "experiment" was planned in advance. Good books must seem good, thought the writer, to the people whose experience has been right. Inarticulate in her feelings about leisure, she approached a class of juniors to find out what they really wished to do as leisure reading. Then it was natural that the plan which they worked out and found successful should be tried in the tenth grade, with modifications and improvements. What a class with this background would do as juniors was a problem which could be considered another experiment and what they could do the next year as seniors, still another. For the benefits of rightness are cumulative. One experiment when successful creates new ones. In the composition as well as the literature course, one works backward and forward, in succession. Having developed power in a given year, one tries the same work in the previous grade, and, finding that it can be done, is able to build on that foundation more advanced work which would otherwise wait until later. After many such pragmatic experiences, analysis of successes suggests controlling principles. Approximate xpression of these has been attempted in this book, to simplify the interpretation of complexities; complete description, however, is impossible. The success of strikingly different individualities in the tenth and eleventh-grade t aching has demonstrated the fact that procedures have not been contingent on personality, unless by that word is meant integrity, versatility, humor, and industry.
How climatic variability is linked to the spatial distribution of range sizes: seasonality versus climate change velocity in sphingid moths

To map the spatial variation of range sizes within sphingid moths, and to test hypotheses on its environmental control. In particular, we investigate effects of climate change velocity since the Pleistocene and the mid‐Holocene, temperature and precipitation seasonality, topography, Pleistocene ice cover, and available land area.
Phylogeny and Molecular Evolution of the Voltage-gated Sodium Channel Gene scn4aa in the Electric Fish Genus Gymnotus

Analyses of the evolution and function of voltage-gated sodium channel proteins (Navs) have largely been limited to mutations from individual people with diagnosed neuromuscular disease. This project investigates the carboxyl-terminus of the Nav paralog (locus scn4aa 3’) that is preferentially expressed in electric organs of Neotropical weakly-electric fishes (Order Gymnotiformes). As a model system, I used the genus Gymnotus, a diverse clade of fishes that produce species-specific electric organ discharges (EODs). I clarified evolutionary relationships among Gymnotus species using mitochondrial (cytochrome b, and 16S ribosome) and nuclear (rag2, and scn4aa) gene sequences (3739 nucleotide positions from 28 Gymnotus species). I analyzed the molecular evolution of scn4aa 3’, and detected evidence for positive selection at eight amino acid sites in seven Gymnotus lineages. These eight amino acid sites are located in motifs that may be important for modulation of EOD frequencies.
Uptake of dissolved organic and inorganic nitrogen in microalgae-dominated sediment: comparing dark and light in situ and ex situ additions of 15N

: Microbial communities within bare intertidal sediment have an active role in uptake of inorganic and organic nitrogen as it is transported through estuaries. 15 N-labeled dissolved inorganic nitrogen (DIN, NH 4+ ; 250 µmol l −1 , 500 µmol l −1 ) and dissolved organic nitrogen (DON, algal-derived; 125 µmol l −1 , 250 µmol l −1 ) were applied to diatom-dominated sandy intertidal sediment under light and dark conditions to investigate short-term N uptake (24 h). Two experiments compared uptake in intact sediments (in situ) and homogenized slurries (ex situ) . In both experiments, N uptake was similar in light and dark conditions, and benthic microalgae (BMA) dominated both biomass and DIN and DON uptake over heterotrophic bacteria. Substantially lower uptake of DON than DIN occurred for both experiments, likely because organic molecules require extra cellular processing before uptake by BMA. Compared to intact sediments, sediment slurries had higher N uptake into sediment organic matter (3−36×), lower bacterial biomass (13.6 ± 3.5% versus 41.1 ± 7.6% intact) and low bacterial contribution to 15 N uptake (14 ± 0.8% versus 14 ± 3.0%). Differences are likely due to shifts within the microbial community and sediment environment caused by sediment homogenization or incubation effects. Consistently, uptake rates within slurries were greater than within intact sediments, and patterns of significant differences among treatments were different. Slurry incubations are therefore not reliable for quantification or comparison of in situ uptake rates across different N substrates, but biomarkers appear robust between the 2 methods, indicating low bacterial contribution to N uptake in BMA-dominated sediment.
The Effect Of Mycorrhiza And Vermicompost Bio-fertilizers On Some Physiological Characteristics Of Sweet Basil Plant (ocimum Basilicum L.) Under The Stress Condition Caused By Water Deficit

One of the main limiting factors in crop production in different regions of Iran is water deficit stress. Mycorrhiza and vermicompost fertilizer may be help plants to uptake more water. Therefore, a greenhouse experiment was carried out in factorial design that was carried out to evaluate the effect of Mycorrhiza, vermicompost fertilizer and water deficit stress on some physiological traits of sweet basil ( Ocimum basilicum L.). Factors included Mycorrhiza (inoculation and non-inoculation), Vermicompost fertilizer (0, 30, 50, and 70 percentage of pod volume), and water deficit stress factor included irrigating up to 60% of F.C as water deficit stress treatment, up to 75% of F.C as mild water deficit stress treatment and up to 90% of F.C as well irrigated treatment. The results showed that sugars and proline increased with increasing water deficit stress, while higher vermicompost consumption decreased the severity of the increase. Merging vermicompost, and mycorrhiza, had a synergistic effect on the catalase enzyme and chlorophyl a+b. Significant negative and positive relationships were found between shoot dry weight and proline with water deficit stress. In addition, basil plant physiological responses to drought stress showed that this stress-sensitive plants, tried to adjust to stress, through osmotic adjustment and increasing antioxidant activity. The results totally showed that merging mycorrhizal inoculation and vermicompost mitigate the effects of drought stress in Basil.
A Response to ‘Comment to Wetzeliella and Its Allies - the ‘Hole’ Story: A Taxonomic Revision of the Paleogene Dinoflagellate Subfamily Wetzelielloideae by Williams et al. (2015)’

ABSTRACT The paper by Williams et al. (2015) concerning a proposed taxonomic revision of the subfamily Wetzelielloideae has led to a comment by Bijl et al. (2016) that questions the validity of our assumptions regarding recognition of the equiepeliform, latiepeliform, hyperepeliform and soleiform archaeopyle types and their significance at the generic level. In this response we address the points that they raise, which are: the introduction of taxonomic criteria allegedly not followed in other fossil subfamilies; the erection of too many taxa; the unworkable nature of the proposed classification; and the reduction of stratigraphic applicability of many significant marker species. We have organised our response under the following topics: pragmatism versus theory; generic criteria: intergroup consistency; the genus Apectodinium and operculum attachment; stratigraphic utility; the number of taxa; and recognition problems. We also discuss specimens illustrated in the two plates included with the comment. The variations in archaeopyle shapes and types of attachment of the operculum (the latter concept has been modified following more recent research) that we have used in part to separate the genera within the Wetzelielloideae have been previously applied to other peridiniacean subfamilies, most notably the Deflandreoideae. As with that subfamily, we consider that our focus on archaeopyle shape and operculum attachment for differentiating wetzelielloidean genera introduces an approach that may help refine the stratigraphic ranges of individual species. While it is a fundamental truth that there are no ‘correct’ taxonomic ideas, we consider that new approaches should be tested with usage over time, not rejected out of hand prior to careful study.