Miracle-dz/UniFAR-FTUs huggingface dataset:
Autophagy, senescence and nitrogen remobilization in barley

Barley (Hordeum vulgare L.) is one of the most important cereals in the world. It was one of the first domesticated crops and was used for centuries for human food. As all plants, barley has a fundamental dependence of inorganic nitrogen and nitrogen remobilization efficiency is very important for grain filling and grain protein content. The aim of this work was then to give a picture of the leaf-senescence metabolism in barley leaves when plants are grown under low or high nitrate conditions. Biochemical, physiological and molecular analyses of barley leaf senescence were performed. Nitrogen management during leaf senescence was monitored measuring changes in the different nitrogen pools during leaf ageing. In addition a large metabolite profiling study was performed in order to determine the metabolic hallmarks of leaf senescence in barley. In parallel enzymes involved in nitrogen remobilization were studied measuring their activity and the transcript levels of their coding genes. There was a special focus on glutamine synthetase and asparagine synthetase enzymes and for autophagy machinery that are known to play a role in nitrogen remobilisation during leaf senescence.From all the sequences data available, cDNA, EST and genomic sequences, we could identified five genes coding for cytosolic glutamine synthetase (GS1), five genes coding for asparagine synthetase (AS) and 19 genes coding for autophagy machinery proteins. Transcript levels of all the genes identified were monitored during leaf senescence and depending on nitrate nutrition. Most of these genes were over-expressed in senescing leaves and differentially expressed depending on nitrate conditions. In addition to the characterization of autophagy, GS1 and ASN genes, phylogenic and gene structures were analysed. All the sequences data provided by this work will be helpful to further translational and genetic association studies.
Expression of endocannabinoid system components in human airway epithelial cells: impact of sex and chronic respiratory disease status

Cannabis smoking is the dominant route of delivery, with the airway epithelium functioning as the site of first contact. The endocannabinoid system is responsible for mediating the physiological effects of inhaled phytocannabinoids. The expression of the endocannabinoid system in the airway epithelium and contribution to normal physiological responses remains to be defined. To begin to address this knowledge gap, a curated dataset of 1090 unique human bronchial brushing gene expression profiles was created. The dataset included 616 healthy subjects, 136 subjects with asthma, and 338 subjects with COPD. A 32-gene endocannabinoid signature was analysed across all samples with sex and disease-specific analyses performed. Immunohistochemistry and immunoblots were performed to probe in situ and in vitro protein expression. CB1, CB2, and TRPV1 protein signal is detectable in human airway epithelial cells in situ and in vitro, justifying examining the downstream endocannabinoid pathway. Sex status was associated with differential expression of 7 of 32 genes. In contrast, disease status was associated with differential expression of 21 of 32 genes in people with asthma and 26 of 32 genes in people with COPD. We confirm at the protein level that TRPV1, the most differentially expressed candidate in our analyses, was upregulated in airway epithelial cells from people with asthma relative to healthy subjects. Our data demonstrate that the endocannabinoid system is expressed in human airway epithelial cells with expression impacted by disease status and minimally by sex. The data suggest that cannabis consumers may have differential physiological responses in the respiratory mucosa. The endocannabinoid system is differentially expressed in human airway epithelial cells from healthy subjects compared to those with asthma or COPD, which may be relevant for population-specific responses to inhaled cannabis smoke https://bit.ly/3cEWc2h
Assessing climate change effects on gladiola in Southern Brazil

: Gladiola ( Gladiolus × grandiflorus Hort.) is an important cut flower for small farmers in Brazil. While the El Niño Southern Oscillation, which causes interannual variability to air temperature in Southern Brazil, can shift the optimum planting window of gladiola, an increase in temperature due to climate change can accelerate gladiola flowering and cause injuries by heat. The objective of this study was to assess the potential climate change effects on gladiola optimum planting date for specific market dates and investigate injuries occurrence on spikes in the Rio Grande do Sul State, Brazil. Field experiments were conducted from 2016 to 2018 at four different locations across the Rio Grande do Sul State to evaluate the performance of the PhenoGlad model in simulating the developmental stages of gladiola. The PhenoGlad model was run on climate scenarios of the Coupled Model Intercomparison Project Phase 5 (CMIP5) named RCP2.6, RCP4.5 and RCP8.5 scenarios. The climate change scenarios caused a delay in the optimum planting date to harvest gladiola for All Souls’ Day across the Rio Grande do Sul State. For harvesting spikes for Mother’s Day, negative anomalies (earliest planting date) occurred in the warmest regions, because the very high temperature extended the crop development. Injuries by heat on spikes reached positive anomalies in 70 % of the years in the warmest regions for scenario RCP8.5. To harvest spikes for Mother’s Day, heat injury did not exceed 20 % of the years. Mitigation strategies for farmers to deal with climate change and keep their gladiola production include adjusting the optimum planting date.
Cell-free production of full-length ice nucleating protein InaZ

Unlike inorganic or other synthetic alternatives, ice nucleating proteins INPs remain the most efficient ice nuclei today. Their potential applications in cryo-preservation, biomedicine, food industry and in the modulation of climate are widespread. Nevertheless, due to multiple difficulties to express these proteins in full-length in necessary yields using cell-based recombinant methods, further applications are limited. As a result, our understanding of the structure and ice nucleation mechanism for this class of proteins is also incomplete. Using wheat-germ cell-free expression pipeline, we successfully expressed and purified full-length ice nucleating protein InaZ from Pseudomonas syringae, known as a model INP. High protein yield and solubility has been achieved using this cell-free platform, allowing us to confirm the heterogeneous nature of InaZ assembly using negative stain TEM. The cell-free produced InaZ protein was confirmed to be functional by conducting ice nucleation experiments inside a dynamic environmental scanning electron microscope (ESEM). We believe that the current platform will be suitable for expressing other INPs of interest and can be further employed for industrial and structural characterization needs as INP source.
Study of DNA Fragmentation in Gametes of Infertile Male by Using TUNEL Technique

Male factors leading to infertility account for at least half of all cases of infertility worldwide. In this study, we used Terminal desoxynucleotidyl transferase-mediated dUTP nick-end labeling (TUNEL) assay to evaluate DNA fragmentation in sperm cells. The study group included 12 males with infertility and oligoasthenoteratozoospermia (OATs). The mean DNA fragmentation index was significantly higher in patients compared to the control group. In conclusion the TUNEL may be considered as an additional assay for the evaluation of spermatozoa beside standard analysis, thus playing an important role during proper diagnosis and treatment of infertility. As in these days, for patients with OAT, intracytoplasmic sperm injection (ICSI) is frequently used.
DiagrammER: A Web Application to Support the Teaching-Learning Process of Database Courses Through the Creation of E-R Diagrams

This paper presents a web application to support the teaching-learning process of undergraduate database courses, which allows students to practice their knowledge on data modeling using Entity-Relationship (E-R) diagrams. The web application is oriented to teachers and students: teachers prepare examples and exercises, which can have associated E-R diagrams; on the other hand, students are able to design E-R diagrams, which they can review at any time, they also have the option of viewing and solve some of the exercises designed by the teacher. The development of the web application is explained; a comparison of similar existing E-R diagram systems is presented; and the operation of the web application is shown through the creation of an E-R diagram. The results of an instrument applied to students for the evaluation of the web application are provided.
Investigation and analysis on child rescue system from open bore well

In recent days, there are a lot of cases related to a child stuck in an open bore well. The actual methods involved in rescue are pulling the child using a rope with different knots or digging a parallel line beside the open bore using machines to the depth at which the child is stuck, the child is then pulled from the depth. But at deeper bore wells, these methods fail. This paper deals with a design to save a child who is stuck in manhole or open bore-well. Using this design the child can be easily rescued from the open bore wells, as this design includes hydraulic arm to hold the child with grips which won’t slip due to sweat or wet condition of the bore well, the locking mechanism to hold the rescue system in one place inside the pit once it reaches the depth at which the child is stuck. A live streaming video surveillance for monitoring the child motion, oxygen supply channel for the child and a communication system to have contact.
Regeneration of plantlets from immature explantsculture in [Glycine max (L.) Merrill]

For plant regeneration through somatic embryogenesis, immature cotyledonary nodes and embryonic axes explants of soybean cultivars JS 335 were cultured on six different medium fortified with MS salts, B5 vitamins and combinations of growth regulators. Between explants, immature embryonic axes demonstrated better regeneration potential as compared to cotyledonary node. For immature embryonic axes culture, better morphogenic callus induction, embryogenesis, organogenesis and plantlet regeneration was observed on MS with 4 B1.86N, MS 10N, MS . 1B1N and MS.2B1N as compared to other media formulations. Cotyledonary nodes exhibited higher callus induction, embryogenesis, organogenesis on media with MS4 B1.86N, MS . 1B1N, MS 3B6N and higher plantlet regeneration on media with MS.5B1N.
Ecology, seed dormancy and germination biology of Persoonia longifolia for use in land restoration and horticulture

summary. i Table of contents . iii Table of Figures . vi List of Tables . ix List of Appendices . x Acknowledgements . xi Statement of Candidate Contribution . xiv Chapter One An Introduction to a Peculiar Plant . 1 1.1 The plant and its habitat . 1 1.2 The importance of Persoonia longifolia . 3 1.3 The aims of this project . 5 1.4 The study environment . 5 1.5 Thesis structure . 8 Chapter Two Developmental Phenology of Persoonia longifolia and the Impact of Fire . 11 2.0 Abstract . 11 2.
Economic value for the trait tick count in Brangus cattle.

Profitability of a beef cattle system may be significantly reduced by the effects of tick (Rhipicephalus (Boophilus) microplus). Authors estimated significant losses due to decreased productivity by parasitism, and deaths of cattle from diseases that are transmitted by ticks. Our objective was to estimate the economic value (EV) for the trait tick count in Brangus cattle. A stochastic bio-economic simulation model was developed to study effects of tick load on treatment costs and death losses due to infestation (e.g., tick borne diseases). Parameters for the model were based on data collected in an experimental herd of 330 Brangus dams over a 3-year period. Average tick load was 71.4 ticks on one side of the body. Number of ticks was modeled as an exponential distribution with E(x)=1/λ, where λ is 0.0140056. Probability of mortality as a function of tick load were 0.1; 0.5; 1; 2; 5; 10; 30; 70; 80; 90 and 100% for animals with >20 and <=30; >30 and <=50; >50 and <=100; >100 and <=150; >150 and <=200; >200 and <=300; >300 and <=400; >401 and <=500; >500 and <=600; >600 and <=800 and >800 ticks, respectively. Simulated mortality of individual animals was calculated based on the uniform (0 to 1) distribution using the threshold as just described. Seven scenarios were analyzed varying only the number of dams in the herd (200; 400; 500; 600; 1,000; 2,000 and 4,000). Each scenario was replicated 10,000 times. The EV was the marginal cost per dam. The estimated marginal cost of ticks was, on average, -5.51±0.30, ranging between -5.86 and -5.00. To demonstrate the sensitivity of the system to tick load, a second series of simulations was conducted with the average tick count reduced to 51.4 (λ = 0.0194552). The estimated marginal cost of
Identification of gastrointestinal microflora in Hawaiian green turtles (Chelonia mydas Linnaeus), and effects of glyphosate herbicide on their gastrointestinal bacteria

30 INTRODUCTION . 31 METHODS . 32 RESULTS . 39 DISCUSSION . 41 TABLES . 43 v FIGURES . 53 REFERENCES . 62 Chapter 3: Glyphosate herbicide effects on gastrointestinal microflora of Hawaiian green turtles (Chelonia mydas Linnaeus) . 66 ABSTRACT . 66 INTRODUCTION . 68 METHODS . 70 RESULTS . 73 DISCUSSION . 74 FIGURES . 76 REFERENCES . 84.66 INTRODUCTION . 68 METHODS . 70 RESULTS . 73 DISCUSSION . 74 FIGURES . 76 REFERENCES . 84 Appendix I: Turtle Necropsy Reports . 90 Appendix II: Preliminary Collection Methods.104
Developing a goodness of fit test for a joint model of clustered survival and count data

Abstract Mixed responses within clusters are becoming an increasingly popular phenomenon. However, this scenario is a complex one. This research is based on survival and count response data which occur frequently in medical studies. In the literature, there is no satisfactory goodness of fit test for a joint model of these two responses within a cluster setting. Therefore, the main objective of this study is to develop a GOF test for this scenario. Simulation studies were used to examine the type I error rate and the power of the test. An example was used to display the practicality of the test.
AMOC fingerprints influence seasonal SST predictability in the North Atlantic

Abstract. We investigate the impact of the strength of the Atlantic Meridional Overturning Circulation (AMOC) at 26° N on the prediction of North Atlantic sea surface temperature anomalies (SSTA) a season ahead. We consider the physical mechanism proposed by Duchez et al. (2016a) and test the dependence of SST predictive skill in initialised hindcasts on the phase of AMOC at 26° N. We use initialised simulations with the MPI-ESM-MR seasonal prediction system. First, we use the assimilation experiment between 1979–2014 to confirm that the AMOC leads a SSTA dipole pattern in the tropical and subtropical North Atlantic, with strongest AMOC fingerprints after 2–4 months. Going beyond previous studies, we find that the AMOC fingerprint has a seasonal dependence, and is sensitive to the length of the observational window used, i.e. stronger over the last decade than for the entire time series back to 1979. We then use a set of ensemble hindcast simulations with 30 members, starting each February, May, August and November between 1982 and 2014. We compare the changes in skill between composites based on the AMOC phase a month prior to each start date to simulations without considering the AMOC phase. We find higher SST hindcast skill at 2–4 months lead time for SSTA composites based on the AMOC phase for February, May and November start dates. Our method shows major benefit for May start dates, where mean summer SST hindcast skill over the subtropics increase by a factor of 2, reaching up to 80 % agreement with ERA-Interim SST.
Bloom or Bust: Retrospective Analysis of the Giant Jellyfish, Nemopilema nomurai (Scyphozoa: Rhizostomeae), Ecology in the East Asian Marginal Seas

ii ACKNOWLEDGMENTS . iv TABLE OF CONTENTS . v LIST OF TABLES . 1 LIST OF ILLUSTRATIONS . 1 LIST OF ABBREVIATIONS . 1 CHAPTER I – INTRODUCTION . 1 Background . 7 Aquaculture in East Asia . 7 Benthic Structures . 9 Bottom Conditions . 9 Fisheries . 10 Hypoxia . 11 Objectives . 13 CHAPTER II – MATERIALS AND METHODS . 14 Study Area and Data Collection . 14 Data Analysis . 19 CHAPTER III – RESULTS . 21 Correlation Analysis . 21 vi GLM and GAM Analysis. 21 CHAPTER IV – DISCUSSION . 28 Aquaculture . 28 Fisheries . 30 Non-forage Fish . 30 Jellyfish . 30 Shellfish . 32 Benthic Structures . 37 Limitations . 39 CHAPTER V – CONCLUSIONS . 43 Recommendations . 46 APPENDIX A – Supplemental Data Tables . 48 APPENDIX B – Supplemental Generalized Additive Model (GAM) Figures . 56 APPENDIX C – Supplemental Linear Regression Figures . 67 WORKS CITED . 78
Improving Pointing Direction Estimation by Considering Hand- and Ocular-Dominance

This paper introduces a user study regarding the effects of handand ocular-dominances to pointing gestures. The result of this study is applicable for designing new gesture interfaces which are close to a user’s cognition, intuitive, and easy to use. The user study investigates the relationship between the participant’s dominances and pointing gestures. Four participant groups—right-handed right-eye dominant, righthanded left-eye dominant, left-handed right-eye dominant and left-handed left-eye dominant—were prepared, and participants were asked to point at the targets on a screen by their left and right hands. The pointing errors among the different participant groups are calculated and compared. The result of this user study shows that using dominant eyes produces better results than using non-dominant eyes and the accuracy increases when the targets are located at the same side of dominant eye. Based on these interesting properties, a method to find the dominant eye for pointing gestures is proposed. This method can find the dominant eye of an individual with more than 90% accuracy. key words: hand-dominance, ocular-dominance, pointing gesture interface
Family resilience and parenting stress in poor families

Abstract This quantitative and cross-sectional study aimed to describe and associate the levels of resilience, parenting stress and multidimensional poverty of poor families living in the city of Belém (PA). The probabilistic sample consisted of 429 caregivers, interviewed in Social Assistance Reference Centers, where the application of instruments to access socio-demographic information, family resilience, parenting stress and poverty was carried out, in order to investigateprotection and risk processes for development. The sample consisted of women (97%) between 20 and 39 years (69%). This study showed associations between low resilience, high parenting stress and higher level of poverty. None of the families had high resilience scores. These results point to aspects regulating family dynamics as crucial in the healthy development of these families in relation to risk exposure.
Global and Regional Implications of Biome Evolution on the Hydrologic Cycle and Climate in the NCAR Dynamic Vegetation Model

Vegetation influences climate by altering water and energy budgets. With intensifying threats from anthropogenic activities, both terrestrial biomes and climate are expected to change, and the need to understand land–atmosphere interactions will become increasingly crucial. We ran a climate model coupled with a Dynamic Global Vegetation Model (DGVM) to investigate the establishment of terrestrial biomes starting from a bareground scenario and how these biomes influence the climate throughout their evolution. Vegetation reaches quasi-equilibrium after ~350 years, and the vegetation establishment results in global increases in temperature (~2.5 °C), precipitation (~5.5%) and evapotranspiration as well as declines in albedo and sea ice volumes. In high latitude regions, vegetation establishment decreases albedo, causing an increase in global temperatures as well as a northward shift of the Intertropical Convergence Zone (ITCZ). Low latitude tropical afforestation results in greater evapotranspiration and precipitation, and an initial decrease in temperatures due to evaporative cooling.
Extending Hashing Towards Fast Re-Identification

Searching accuracy and efficiency are two challenges in person and vehicle Re-identification (Re-ID), which one focuses on robust representations learning which usually generating high-dimensional features while the other has not been fully explored. Hashing is a suitable solution to make REID efficient. However, directly extending the existing hashing methods to fast Re-ID faces two challenges: one is the non-overlap between training and testing set which need more discriminative hash codes, the other is the large identities in Re-ID tasks which will lead to slow convergence and hard optimization. In this work, we propose an attention pooling operator to exploit both local and global visual attributes which can break limited discriminative power in hash methods. To further make training procedure converge faster and optimize the network more easily, we substitute non-differentiable $l_{1^{-}}$ regularization with smooth l1-regularization. In experiments, our work outperforms state-of-the-art hashing and quantization methods on both person and vehicle Re-ID datasets. Besides, the results can serve as a strong baseline in the field of deep hashing for fast Re-ID.11Code is available at https://github.com/cynthia951031/Hashing ReID
Variability in Phytochemical Contents and Biological Potential of Pomegranate (Punica granatum) Peel Extracts: Toward a New Opportunity for Minced Beef Meat Preservation

Extraction of Tunisian pomegranate peels was employed with different solvents such as ethyl acetate, acetonitrile, and water. Total phenolic and flavonoids contents, antioxidant activity, and antibacterial capacity against five foodborne pathogenic bacteria were evaluated. The highest values of polyphenols (351 mg gallic acid equivalent/g), flavonoids (104 mg quercetin/g), and DPPH and ABTS inhibition were recorded in the ethyl acetate extract followed by the aqueous extract. The latter present the maximum antibacterial potential against S. enterica, P. aeruginosa, and E. coli. The potential use of the lyophilized aqueous extract (AE), used for safety reason and being rich in phenolic, as biopreservative in minced beef meat was described. AE was incorporated at 0.1, 0.5, and 1% and compared with 0.1% butylated hydroxytoluene (BHT). During 21 days at 4°C, AE at 1% could appreciably retard the microflora proliferation ( ), the accumulation of MetMb and the carbonyl group ( ), slowing down the loss of sulphydryl proteins ( ), and led to a decrease ( ) in primary (peroxide value and conjugated dienes) and secondary lipid oxidation (TBARS) in treated meat. By the 14th day, AE-treated minced meat obtained higher sensory scores than untreated and BHT samples. Based on these results, lipid and protein oxidation changes and sensorial attributes were useful in discriminating meat samples by overall acceptability prediction. Generally, AE at 1% presented the potent preservative effect that could be utilized as an application on meat-substituting synthetic antioxidant.
Meristotheca cylindrica sp. nov. (Solieriaceae, Rhodophyta) from the southern Gulf of Mexico

Abstract: Meristotheca cylindrica sp. nov. from the Gulf of Mexico is described on the basis of morphological and molecular evidence. Previously, all known species of Meristotheca were described as flattened or peltate in habit; the diagnostic character for M. cylindrica sp. nov. is a thallus with a cylindrical (or terete) axis and branches. rbcL sequences indicate an independent monophyletic group within the genus.