Miracle-dz/UniFAR-FTUs huggingface dataset:
Real Time Visualization of 13N-Translocation in Rice under Different Environmental Conditions Using Positron Emitting Tracer Imaging System

The ammonium ion is an indispensable nitrogen source for crops, especially paddy rice ( Oryza sativa L. cv Nipponbare). Until now, it has been impossible to measure ammonium uptake and nitrogen movement in plants in real time. Using the new technologies of PETIS (positron emitting tracer imaging system) and PMPS (positron multi-probe system), we were able to visualize the real time translocation of nitrogen and water in rice plants. We used positron-emitting 13 N-labeled ammonium ( 13 NH 4 + ) and 15 O-water to monitor the movement. In plants cultured under normal conditions, 13 NH 4 + supplied to roots was taken up, and a 13 N signal was detected at the discrimination center, the basal part of the shoots, within 2 minutes. This rapid translocation of 13 N was almost completely inhibited by a glutamine synthetase inhibitor, methionine sulfoximine. In general, nitrogen deficiency enhanced 13 N translocation to the discrimination center. In the dark, 13 N translocation to the discrimination center was suppressed to 40% of control levels, whereas 15 O-water flow from the root to the discrimination center stopped completely in the dark. In abscisic acid-treated rice, 13 N translocation to the discrimination center was doubled, whereas translocation to leaves decreased to 40% of control levels. Pretreatment with NO 3 − for 36 hours increased 13 N translocation from the roots to the discrimination center to 5 times of control levels. These results suggest that ammonium assimilation (from the roots to the discrimination center) depends passively on water flow, but actively on NH 4 + -transporter(s) or glutamine synthetase(s).
Diet and reproduction in the white-spotted eagle ray Aetobatus narinari from Queensland, Australia and the Penghu Islands, Taiwan

Aetobatus narinari, a circumglobal batoid, is subjected to increasing fishing pressures, especially throughout South-eastAsia.However,itsmanagementandprotectioniscomplicatedbythelackofrelevantlifehistoryinformation.It appears to be a late-maturing, long-lived stingray with a size-at-maturity of ,130 and4150cm in ventral disc width for males and females respectively. Like other myliobatids, A. narinari is a matrotrophic viviparous species exhibiting lipid histotrophy as indicated by trophonemata. Only the left ovary and uterus are functional. The presence of mature sperm in the testes, collecting ducts, epididymis and ductus deferens coincided with the estimated time of parturition and mating. Catches indicated an unbiased sex ratio. Aetobatus narinari is a hard-prey specialist that feeds mainly on gastropods, molluscs and hermit crabs (Diogenidae). Molluscs comprised numerically and gravimetrically the most important prey group(IndexofRelativeImportance(IRI):85.9%inAustralia,99.9%inTaiwan)andwereobservedin83.3%and100%of stomachs containing food from Australia and Taiwan respectively. Minor dietary shifts from a gastropod-crustacean to a more gastropod-bivalve based diet occurred as body size increased. This study provides vital biological data for the effective management and conservation of A. narinari.
Role of 70 kb plasmid of the Indian epidemic strain Shigella dysenteriae type 1 (Dt 66) in molecular pathogenesis

The aim of the present study is to characterize the role of the 70 kb plasmid in shigellosis. Curing of the plasmids of the Indian epidemic isolate Shigella dysenteriae type 1 (Dt 66) by acriflavine (AF) yielded 7 groups of derivatives. One group of derivatives containing 5 plasmids (70 - 2.5 kb) as against 6 (120 - 2.5 kb) in the wild type showed resistance to chloramphenicol, pivmecillinam, streptomycin and tetracycline (Cm r Piv r Sm r Tc r ) but sensitivity for ampicillin and nalidixic acid (Am s Nal s ). This derivative when used as donor in conjugation experiments with a plasmidless, nonpathogenic E. coli KL318 strain (Am s Cm s Piv s Sm r Tc s Nal r ) as recipient, transferred only its 70 kb plasmid into the recipient with concomitant transfer of the Cm r Piv r phenotype. Both the donor and transconjugant exhibited HeLa cell adherence and invasion, keratoconjunctivitis in guineapig’ s eye, a 42 kDa lipopolysaccharide band and congo red binding ability. A small fragment (0.564 kb) of this 70 kb - plasmid when cloned, the cloned transformant showed a 45 kDa Ipa-C protein, which was probed with the anti45 kDa (Ipa-C) monoclonal antibody. The result suggests the involvement of 70 kb plasmid in molecular pathogenesis of Shigella (Dt 66).
Detecting Signatures of Early-stage Dementia with Behavioural Models Derived from Sensor Data

There is a pressing need to automatically understand the state and progression of chronic neurological diseases such as dementia. The emergence of state-of-the-art sensing platforms offers unprecedented opportunities for indirect and automatic evaluation of disease state through the lens of behavioural monitoring. This paper specifically seeks to characterise behavioural signatures of mild cognitive impairment (MCI) and Alzheimer's disease (AD) in the \textit{early} stages of the disease. We introduce bespoke behavioural models and analyses of key symptoms and deploy these on a novel dataset of longitudinal sensor data from persons with MCI and AD. We present preliminary findings that show the relationship between levels of sleep quality and wandering can be subtly different between patients in the early stages of dementia and healthy cohabiting controls.
Laboratory Investigation ofAcanthamoeba Keratitis

Following thediagnosis ofAcanthamoeba keratitis ina contact lens wearer,theantimicrobial susceptibility oftheclinical isolate andtheenvironmental sourceoftheinfection were investigated. Contrary toprevious reports, invitro antimicrobial testing showedthattheinfecting strain was inherently resistant topropamidine isethionate. Restriction endonuclease digestion analysis ofAcanthamoeba whole-cell DNA ofstrains isolated fromthepatient's cornea,contact lens storage container, saline rinsing solution, andkitchen cold-water tap showed thattheisolates were identical. Thisimplicates, forthefirst time, domestic tapwaterasthesourceof Acanthamoeba sp.inthis infection. Itistherefore recommended thattheuseofhomemadesaline solutions and therinsing ofcontact lenses intapwaterbestrongly discouraged.
Determination of the most representative descriptor among a set of feature vectors for the same object

On an example of solution of the face recognition problem the approach for estimation of the most representative descriptor among a set of feature vectors for the same face is considered in present study. The estimation is based on robust calculation of the mode-median mixture vector for the set as the descriptor by means of Welsch/Leclerc loss function application in case of very sparse filling of the feature space with feature vectors
Equilibrium under uncertainty with fuzzy payoff

This paper studies n-player games where players beliefs about their opponents behaviour are capacities (fuzzy measures, non-additive probabilities). The concept of an equilibrium under uncertainty was introduced by J.Dow and S.Werlang (1994) for two players and was extended to n-player games by J.Eichberger and D.Kelsey (2000). Expected utility (payoff function) was expressed by Choquet integral. The concept of an equilibrium under uncertainty with expected utility expressed by Sugeno integral were considered by T.Radul (2018). We consider in this paper an equilibrium with expected utility expressed by fuzzy integral generated by a continuous t-norm which is a natural generalization of Sugeno integral.
MEASURING AERODYNAMIC INTERFERENCE DRAG BETWEEN A BIRD BODY AND THE MOUNTING STRUT OF A DRAG BALANCE

1.The drag of a bird body mounted on the strut of a drag balance in a wind tunnel is more than the sum of the drags of the isolated strut and the isolated body. The strut changes the air flow around the body and generates additional drag, known as interference drag. This paper describes practical methods for measuring the drag of bird bodies: a strain-gauge drag balance, dimensions for struts made with machine or hand tools, and a procedure for correcting drag measurements for interference drag. 2.Interference drag can be measured by extrapolating a relationship between the drag of isolated struts with different crosssectional sizes and shapes and the drag of a body mounted on those struts. The interference length the length of an isolated strut that produces drag equal to the interference drag is a usefulquantity for predicting interference drag. 3.The relationship mentioned above is a straight line for a model peregrine falcon (Falco peregrinus L.) body mounted on smooth struts struts with convex cross-sectional shapes ranging from streamlined to circular. This finding simplifies the determination of interference drag in three ways: (i) the line can be found from measurements with just two struts a standard strut with low drag and a calibration strut with high drag; (ii) the two struts need not have the same shape for example, the standard strut can be changed to a calibration strut by attaching a spoiler without disturbing the body mounted on the strut and (iii) a single value of interference length (33.1mm) describes smooth struts with a range of shapes and sizes. These struts had drag coefficients between 0.33 and 0.91 at Reynolds numbers between 2100 and 10800. 4.The interference length of a strut supporting the actual falcon body with a feathered surface is not significantly different from that of the strut supporting the model body with a rigid surface. 5.As a hypothesis, interference length (hI, in metres) of a smooth strut varieswith the size of the body mounted on it: hI=0.0365m0.333 where m is the body mass (in kg) of the intact bird.
Segmentation of Pulmonary Opacification in Chest CT Scans of COVID-19 Patients

The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has rapidly spread into a global pandemic. A form of pneumonia, presenting as opacities with in a patient's lungs, is the most common presentation associated with this virus, and great attention has gone into how these changes relate to patient morbidity and mortality. In this work we provide open source models for the segmentation of patterns of pulmonary opacification on chest Computed Tomography (CT) scans which have been correlated with various stages and severities of infection. We have collected 663 chest CT scans of COVID-19 patients from healthcare centers around the world, and created pixel wise segmentation labels for nearly 25,000 slices that segment 6 different patterns of pulmonary opacification. We provide open source implementations and pre-trained weights for multiple segmentation models trained on our dataset. Our best model achieves an opacity Intersection-Over-Union score of 0.76 on our test set, demonstrates successful domain adaptation, and predicts the volume of opacification within 1.7\% of expert radiologists. Additionally, we present an analysis of the inter-observer variability inherent to this task, and propose methods for appropriate probabilistic approaches.
Primer design for quantitative real-time PCR for the emerging Coronavirus SARS-CoV-2

In December 2019, a new coronavirus disease (COVID-19) outbreak occurred in Wuhan, China. Severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2), which is the seventh coronavirus known to infect humans, is highly contagious and has rapidly expanded worldwide since its discovery. Quantitative nucleic acid testing has become the gold standard for diagnosis and guiding clinical decisions regarding the use of antiviral therapy. However, the RT-qPCR assays targeting SARS-CoV-2 have a number of challenges, especially in terms of primer design. Primers are the pivotal components of a RT-qPCR assay. Once virus mutation and recombination occur, it is difficult to effectively diagnose viral infection by existing RT-qPCR primers. Some primers and probes have also been made available on the WHO website for reference. However, no previous review has systematically compared the previously reported primers and probes and described how to design new primers in the event of a new coronavirus infection. This review focuses on how primers and probes can be designed methodically and rationally, and how the sensitivity and specificity of the detection process can be improved. This brief review will be useful for the accurate diagnosis and timely treatment of the new coronavirus pneumonia.
An Evaluation of Publicly Available Deep Learning Based Commercial Information Retrieval Systems to search Biomedical Articles related to COVID-19

The COVID-19 pandemic has resulted in a tremendous need for access to the latest scientific information, primarily through the use of text mining and search tools. This has led to both corpora for biomedical articles related to COVID-19 (such as the CORD-19 corpus (Wang et al., 2020)) as well as search engines to query such data. While most research in search engines is performed in the academic field of information retrieval (IR), most academic search engines--though rigorously evaluated--are sparsely utilized, while major commercial web search engines (e.g., Google, Bing) dominate. This relates to COVID-19 because it can be expected that commercial search engines deployed for the pandemic will gain much higher traction than those produced in academic labs, and thus leads to questions about the empirical performance of these search tools. This paper seeks to empirically evaluate two such commercial search engines for COVID-19, produced by Google and Amazon, in comparison to the more academic prototypes evaluated in the context of the TREC-COVID track (Roberts et al., 2020). To ensure a fair comparison, we limit the number of documents in the retrieved runs and also annotate additional documents. We find that the top-performing system from TREC-COVID on bpref metric performed the best among the different systems evaluated in this study on all the metrics.
Chemical and morphological expression of the B and Asp seedcoat genes in Phaseolus vulgaris.

ADDITIONAL INDEX WORDS. common bean, flavonoids, anthocyanins, regulatory genes, phytoalexin, phaseollin ABSTRACT. Three common bean (Phaseolus vulgaris L.) seedcoat color (or glossiness) genotypes, differing from each other by a single substitution at a seedcoat locus, were analyzed for presence and concentration of three anthocyanins: delphinidin 3-O-glucoside, petunidin 3-O-glucoside, and malvidin 3-O-glucoside. The three anthocyanins were present in Florida common bean breeding line 5-593 (P C J G B V Asp), matte black (P C J G B V asp), and dark brown violet (P C J G b V Asp), but the amounts varied greatly depending on the genotype. Dark brown violet had 19% of the total anthocyanin content when compared to 5-593, whereas matte black had amounts intermediate between the two other genotypes. The B gene acts to regulate the production of precursors of anthocyanins in the seedcoat color pathway above the level of dihydrokaempferol formation, perhaps at the chalcone synthase or chalcone isomerase steps in the biosynthetic pathway. We hypothesize that B regulates simultaneously the flavonoid (color) and isoflavonoid (resistance) pathways. The I gene for resistance to bean common mosaic virus (BCMV) is known to be linked closely to B. It is therefore hypothesized that the I gene function may be to respond to BCMV infection by dramatically increasing (over a low constituitive level) production in the 5-dehydroxy isoflavonoid pathway, which leads to synthesis of the major phytoalexin, phaseollin, for resistance to BCMV. Alternatively, the B and I genes may be allelic. The Asp gene affects seedcoat glossiness by means of a structural change to the seedcoat. We demonstrate that Asp in the recessive condition (asp/asp) changes the size and shape of the palisade cells of the seedcoat epidermis, making them significantly smaller than either 5-593 or dark brown violet. Asp, therefore, limits the amounts of anthocyanins in the seedcoat by reducing the size of palisade cells.
Focused Ultrasound Hyperthermia Augments Release of Glioma-derived Extracellular Vesicles with Differential Immunomodulatory Capacity

Background: Increasing evidence points to the critical role of extracellular vesicles (EVs) as molecular parcels that carry a diverse array of bioactive payloads for coordination of complex intracellular signaling. Focused ultrasound (FUS) hyperthermia is a technique for non-invasive, non-ionizing sublethal heating of cells in a near-instantaneous manner; while it has been shown to improve drug delivery and immunological recognition of tumors, its impact on EVs has not been explored to date. The goal of this study was to determine whether FUS impacts the release, proteomic profile, and immune-activating properties of tumor-derived EVs. Methods: Monolayered murine glioma cells were seeded within acoustically transparent cell culture chambers, and FUS hyperthermia was applied to achieve complete coverage of the chamber. Glioma-derived EVs (GEVs) were isolated for characterization by Nanoparticle Tracking Analysis, cryo-electron microscopy and mass spectrometry. An in vitro experimental setup was designed to further dissect the impact of GEVs on innate inflammation; immortalized murine dendritic cells (DCs) were pulsed with GEVs (either naïve or FUS hyperthermia-exposed) and assayed for production of IL-12p70, an important regulator of DC maturation and T helper cell polarization toward the interferon-γ-producing type 1 phenotype. Results: We confirmed that FUS hyperthermia significantly augments GEV release (by ~46%) as well as shifts the proteomic profile of these GEVs. Such shifts included enrichment of common EV-associated markers, downregulation of markers associated with cancer progression and resistance and modulation of inflammation-associated markers. When DCs were pulsed with GEVs, we noted that naïve GEVs suppressed IL-12p70 production by DCs in a GEV dose-dependent manner. In contrast, GEVs from cells exposed to FUS hyperthermia promoted a significant upregulation in IL-12p70 production by DCs, consistent with a pro-inflammatory stimulus. Conclusion: FUS hyperthermia triggers release of proteomically distinct GEVs that are capable of facilitating an important component of innate immune activation, lending both to a potential mechanism by which FUS interfaces with the tumor-immune landscape and to a role for GEV-associated biomarkers in monitoring response to FUS.
Characteristics and Environmental Problems of a Eutrophic, Seasonally-stratified Lake, Wilgreen Lake, Madison County, Kentucky

Abstract Wilgreen Lake (Madison County, Kentucky) is listed as “nutrient impaired” by the United States Environmental Protection Agency and Commonwealth of Kentucky, and it also experiences high fecal microbe counts that restricts its use. The lake is a typical eutrophic lake, experiencing anoxia and dysoxia in its waters during summer stratification. Human activities in the watershed contribute additional nutrients to the lake that may exacerbate periods of anoxia, so knowing the sources of anthropogenic nutrient inputs to the lake would aid in developing best practices for development of lake shore areas and the watershed. Possible sources include residential fertilizers, cattle waste, and human sewage. High nutrient concentrations within surface waters generally occur only proximal to septic system clusters in the upper reaches of Taylor Fork. Bovine and human fecal microbes enter the lake causing periodic high fecal microbe counts, and are likewise restricted to shallow water areas especially after rain events. The areal distribution of high nutrient and fecal microbe values implicate septic systems as the most likely source of these pollutants, but runoff from pastureland must also contribute nutrients and fecal material. We plan to use additional tracing methods in the future to determine the main sources of nutrients and fecal microbes.
Genetic variation of Chilo suppressalis Walker (Lepidoptera: Pyralidae) populations in guilan and west of Mazandaran provinces analysed with RAPD markers.

studied in 2010 by means of RAPD markers. Collected 45 samples from 19 locations (representing 17 counties in Guilan province and 2 counties in Mazandaran province) were classified into four groups of populations: three population groups corresponding to the west, centre, and east of Guilan and one population group from the west of Mazandaran. RAPD PCR analysis showed that Chilo suppressalis populations in Mazandaran are genetically different from the Guilan populations while the western populations of Guilan are genetically separated from the two other populations. The central and the eastern populations of Guilan exhibit some similarities with those of Mazandaran and the similarities are more obvious between the eastern populations of Guilan and the western population of Mazandaran. The population from the centre of Guilan showed the highest level of intra-population genetic variation possibly due to wider rice cultivated area and/ or due to higher sample size. The results showed a high level of genetic variation in Chilo suppressalis populations in the two provinces in Iran. In spite of the model species is a widely distributed pest, the study indicated that the samples originated in populations with a different genetic make-up.
Sirt6 deficiency aggravates angiotensin II-induced cholesterol accumulation and injury in podocytes

Disturbed renal lipid metabolism, especially cholesterol dysregulation plays a crucial role in the pathogenesis of chronic kidney disease (CKD). We recently reported that angiotensin (Ang) II could induce cholesterol accumulation and injury in podocytes. However, the underlying mechanisms for these alterations remain unknown. Methods: Bioinformatics analysis of renal biopsy specimens from patients with hypertensive nephropathy (HN) suggests the involvement of Sirtuin 6 (Sirt6) in Ang II-induced dysregulation of glomerular cholesterol. Using a podocyte-specific Sirt6 knockout mouse model, the effects of Sirt6 on Ang II-induced cholesterol accumulation in podocytes and the therapeutic efficacies of cholesterol-lowering agents were evaluated. Results: Cholesterol accumulation was detected in the podocytes of Ang II-infused mice, whereas selective deletion of Sirt6 in podocytes not only increased cholesterol accumulation in these cells but also exacerbated Ang II-induced kidney injury. Deletion of Sirt6 also attenuated the protective effect of cyclodextrin (CD) on Ang II-induced urinary albumin excretion, glomerulosclerosis and podocyte injury. In addition, we demonstrated that Sirt6 affected cholesterol efflux in podocytes by regulating the expression of ATP-binding cassette transporter G1 (ABCG1). Conclusions: These findings provide evidence that Sirt6 is a potential target for renin-angiotensin system (RAS)-associated podocyte injury and provide a rationale for the application of cholesterol-lowering agents in patients with CKD.
Life history and host range of Oxydia vesulia transpeneus, an unsuitable biological control agent of Brazilian peppertree

ABSTRACT The suitability of Oxydia vesulia transpeneus (Cramer) (Lepidoptera: Geometridae) was assessed as a potential biological control agent of the invasive weed Brazilian Peppertree Schinus terebinthifolia Raddi. Larvae were collected in Brazil feeding on the plant in its native range and colonised in quarantine where life history and host range studies were conducted (27 ± 2°C; 50RH). Development time from neonate to adults when fed Brazilian peppertree leaves was 48.0 (±2.2) days for females and 51.0 (±1.3) days for males. Larvae generally required five (occasionally six) instars to reach the adult stage. Females had greater pupal weights 1004.1 (±45.9) mg compared with males 668.5 (±19.7) mg. Larvae were tested on seven non-target plant species from Florida natives, ornamentals, to economic species. Larvae completed development on all but one of these valued plant species. These results suggest that the host range of O. vesulia is not sufficiently specific for release as a biological control against Brazilian peppertree in the USA.