Miracle-dz/UniFAR-FTUs huggingface dataset:
Effects of methyl jasmonate and salicylic acid on the production of camphor and phenolic compounds in cell suspension culture of endemic Turkish yarrow(Achilleagypsicola) species

Elicitors have been widely used as biotic and abiotic stimulants in triggering the production of secondary metabolites in plant cell culture. The present study aimed to enhance the production of camphor and phenolic compounds and cell growth using methyl jasmonate (MeJA) and salicylic acid (SA) in the cell suspension culture of Turkish endemic species Achillea gypsicola. Various concentrations (0, 10, 50, and 100 μM) of MeJA and SA were applied to 8-day-old cell cultures. The camphor and phenolic compound contents were determined using a headspace gas chromatographic-mass spectrometer device and spectrophotometer. Increasing doses of MeJA and SA significantly enhanced the accumulation of the camphor and phenolic compounds in general. The highest amount of camphor accumulation occurred in cells treated with 100 μM MeJA (0.3449 μg/g) and 50 μM SA (0.3816 μg/g). Increasing concentrations of MeJA resulted in a significant decrease in the total anthocyanin when compared to the initial culture. The present study showed that MeJA and SA could effectively be used as potent elicitors to enhance the production of camphor and phenolic compounds, along with cell growth, in cell suspension cultures of the endemic Turkish yarrow species Achillea gypsicola.
LIN28 selectively modulates a subclass of let-7 microRNAs

LIN28 is a bipartite RNA-binding protein that post-transcriptionally inhibits let-7 microRNAs to regulate development and influence disease states. However, the mechanisms of let-7 suppression remains poorly understood, because LIN28 recognition depends on coordinated targeting by both the zinc knuckle domain (ZKD)—which binds a GGAG-like element in the precursor—and the cold shock domain (CSD), whose binding sites have not been systematically characterized. By leveraging single-nucleotide-resolution mapping of LIN28 binding sites in vivo, we determined that the CSD recognizes a (U)GAU motif. This motif partitions the let-7 family into Class I precursors with both CSD and ZKD binding sites and Class II precursors with ZKD but no CSD binding sites. LIN28 in vivo recognition—and subsequent 3′ uridylation and degradation—of Class I precursors is more efficient, leading to their stronger suppression in LIN28-activated cells and cancers. Thus, CSD binding sites amplify the effects of the LIN28 activation with potential implication in development and cancer.
Combination of MCM2 With Ki67 and p16 Immunohistochemistry Can Distinguish Uterine Leiomyosarcomas

Our objective was to evaluate the diagnostic utility of 2 new proliferation markers, cyclin D1 and minichromosome maintenance complex component 2 (MCM2), in comparison with p16, p53, and Ki67 in differentiating the spectrum of smooth muscle tumors. An institutional database search from 2009 to 2017 identified 10 cases of uterine leiomyoma with bizarre nuclei (LBN), 12 smooth muscle tumors of uncertain malignant potential, and 13 leiomyosarcomas (LMS). Ten resected leiomyomas (LM) were included as controls. Immunohistochemistry was performed on the befitting representative block from each case. Ki67 was <10% in all LMs and LBNs, whereas >10% in all LMSs. Although wild-type in majority of cases, p53 was overexpressed in 38% of LMSs. Cyclin D1 nuclear positivity in LMs, LBNs, and smooth muscle tumors of uncertain malignant potentials ranged from 0% to 65% of neoplastic cells with mostly weak to moderate staining intensity. Instead, cyclin D1 expression was <5% in all LMSs. The ratio of MCM2 positivity exhibited a similar wide range (<1%–80%) in LMs, LBNs, and smooth muscle tumors of uncertain malignant potentials but interestingly, 92% (12/13) of LMSs were diffusely and strongly positive for MCM2 (>80% cell positivity). Overall, for diagnosis of LMS, the sensitivity for diffuse intense MCM2 staining was higher (92%) compared with diffuse staining for p16 (77%); however, specificity of MCM2 and p16 was comparable (94% and 97%, respectively). Herein, we describe the immunohistochemical profile of 2 new proliferation markers, cyclin D1 and MCM2 in uterine smooth muscle tumors. A combination of diffuse strong MCM2 and p16 reactivity with increased Ki67 index can reliably distinguish LMSs from benign histologic mimics.
Captive breeding programmes for nocturnal prosimians

Due to the nocturnal and arboreal nature of nocturnal prosimians field research on these species is limited. Maintaining populations in zoos provides an opportunity to increase our knowledge of these elusive species. This study aimed to update and contribute to the limited research on captive populations of nocturnal prosimians. The study consists of two parts. Part one aimed to identify the current European captive population of six nocturnal prosimian species (aye-aye, fat-tailed dwarf lemur, Goodman’s mouse lemur, grey mouse lemur, grey slender loris and pygmy slow loris) and determine their demographic self-sustainability. To achieve this aim studbook data was analysed. The difference between birth and death rates, infant mortality rates, age structure and sex composition were investigated. The study concludes populations of aye-aye, fat-tailed dwarf lemur, grey slender loris and pygmy slow loris were not self-sustaining whereas Goodman’s mouse lemur are self-sustaining and grey mouse lemur were found to have an increasing population trend. Part two focussed on the European captive population of pygmy slow loris and grey slender loris. This section sort to determine if husbandry methods affect breeding success. This involved conducting a survey of the current husbandry methods used in 20 European zoos. Statistical tests were carried out to determine if there was a correlation between institution breeding success and the husbandry methods used. The study concludes that there was a significant correlation between institution breeding success and the interval duration between cleaning the fixed enclosure furniture (P=0.030). Results also strongly suggested pygmy slow lorises housed with another species have a higher breeding success than those housed as a single-species exhibit. Part 1 – The sustainability of nocturnal prosimian captive breeding programmes in European zoos
The Role of fosA in Challenges with Fosfomycin Susceptibility Testing of Multispecies Klebsiella pneumoniae Carbapenemase-Producing Clinical Isolates

With multidrug-resistant (MDR) Enterobacterales on the rise, a nontoxic antimicrobial agent with a unique mechanism of action such as fosfomycin seems attractive. However, establishing accurate fosfomycin susceptibility testing for non-Escherichia coli isolates in a clinical microbiology laboratory remains problematic. We evaluated fosfomycin susceptibility by multiple methods with 96 KPC-producing clinical isolates of multiple strains and species collected at a single center between 2008 and 2016. ABSTRACT With multidrug-resistant (MDR) Enterobacterales on the rise, a nontoxic antimicrobial agent with a unique mechanism of action such as fosfomycin seems attractive. However, establishing accurate fosfomycin susceptibility testing for non-Escherichia coli isolates in a clinical microbiology laboratory remains problematic. We evaluated fosfomycin susceptibility by multiple methods with 96 KPC-producing clinical isolates of multiple strains and species collected at a single center between 2008 and 2016. In addition, we assessed the presence of fosfomycin resistance genes from whole-genome sequencing (WGS) data using NCBI’s AMRFinder and custom HMM search. Susceptibility testing was performed using a glucose-6-phosphate-supplemented fosfomycin Etest and Kirby-Bauer disk diffusion (DD) assays, and the results were compared to those obtained by agar dilution. Clinical Laboratory and Standards Institute (CLSI) breakpoints for E. coli were applied for interpretation. Overall, 63% (60/96) of isolates were susceptible by Etest, 70% (67/96) by DD, and 88% (84/96) by agar dilution. fosA was detected in 80% (70/88) of previously sequenced isolates, with species-specific associations and alleles, and fosA-positive isolates were associated with higher MIC distributions. Disk potentiation testing was performed using sodium phosphonoformate to inhibit fosA and showed significant increases in the zone diameter of DD testing for isolates that were fosA positive compared to those that were fosA negative. The addition of sodium phosphonoformate (PPF) corrected 10/14 (71%) major errors in categorical agreement with agar dilution. Our results indicate that fosA influences the inaccuracy of susceptibility testing by methods readily available in a clinical laboratory compared to agar dilution. Further research is needed to determine the impact of fosA on clinical outcomes.
Fundamental Toxicological Sciences

Discarded scallop internal organs, especially the hepatopancreas, are rich in n-3 polyunsaturated fatty acids such as eicosapentaenoic acid and docosahexaenoic acid. However, they have not been utilized because of their contamination with toxic substances, such as cadmium (Cd), and the occurrence of diarrheic shellfish toxins (DST). We have successfully prepared a high-quality scallop oil (SCO) from the internal organs of the Japanese giant scallop (Patinopecten yessoensis), including the hepatopancreas without Cd and DST. These pollutants were removed by liquid-liquid partitioning followed by adsorption to active carbon of fine particle size with high pore surface volume. In this study, we prepared SCO from scallop internal organs obtained from two different processing areas (Mutsu and Uchiura bays, Japan), and referred to them as SCO-M and SCO-U, respectively. Genotoxicity of SCO-M and SCO-U was evaluated by the in vitro bacterial reverse mutation test (Ames test) and in vivo micronucleus test in accordance with the Organisation for Economic Co-operation and Development guidelines. SCO-M and SCO-U showed negative results in the Ames test in the presence or absence of metabolic activation with S9 mix. In addition, no genotoxic effects of SCO-M and SCO-U were observed at all tested doses in the micronucleus test. Based on the results of the present study, it can be concluded that SCO-M and SCO-U are safe products in terms of genotoxicity under these experimental conditions.
Absence of general rules governing molluscan body-size response to climatic fluctuation during the Cenozoic

ABSTRACT Body size is a key factor in predicting the outcome of organisms’ interaction with their environment. A negative temperature–size relationship (TSR) is claimed to be one of the universal responses to climatic warming. Studies on extant biota also predicted that groups with narrow latitudinal range, tropical affinity, and higher body size would show higher sensitivity to climatic fluctuation. To confirm the generality of these relationships among marine ectotherms, we compiled the data on body size and global temperature over the Cenozoic using a global database of marine molluscs of Class Gastropoda and Bivalvia. Molluscan species do not show any signature of TSR for any taxonomic, regional, or ecological category during the Cenozoic. We did not find any evidence supporting heightened response in groups with limited latitudinal spread or with large body size. The body-size response of tropical species is not different from those of temperate species. Response of infauna and epifauna does not show any difference either and hence, refutes the predicted variation due to difference in their thermal-specialisation. Our results highlight the limited validity of ‘universal rules’ in explaining the climate-induced morphological response of marine communities in deep time and underscore the complexity in generalising the biotic outcome of climatic fluctuation.
Towards empirical evaluation of test-driven development in a university environment

Test driven development (TDD) is an agile software development technique and it is one of the core development practices of Extreme programming (XP). In TDD, developers write automatically executable tests prior to writing the code they test. We ran a set of experiments to empirically assess different parameters of the TDD. We compared TDD to a more "traditionally" oriented iterative test-last development process (ITL). Our preliminary results show that TDD is not substantially different from ITL and our qualitative findings about a development process are different from results obtained from other researches.
THE EFFECT OF OSMOCOTE FERTILISERS ON GROWTH AND NUTRIENT STATUS OF ANEMANTHELE LESSONIANA (STEUD). VELDKAMP. AND BOUTELOUA GRACILIS (KUNTH). LAG. EX GRIFFITHS

HenscHke, M. , st. szczepaniak and e. WojciecHoWska, 2015. The effect of osmocote fertilisers on growth and nutrient status of Anemanthele lessoniana (steud). Veldkamp. and Bouteloua gracilis (kunth). Lag. ex Griffiths. Bulg. J. Agric. Sci., 21: 605–610 The increasing importance of ornamental grasses in horticultural cultures results in the need to determine their cultivation requirements. A particularly essential role is played by the selection of fertilisers and specification of nutrient requirements. an experiment on the effect of osmocote fertilisers on growth and nutrient status of Anemanthele lessoniana (steud). Veldkamp. and Bouteloua gracilis (kunth). Lag. ex Griffiths was conducted in the years 2008 – 2009. The differentiating factors included the type of fertiliser, i.e. osmocote exact standard 16:11:11 and osmocote exact High start 11:11:19, and fertiliser doses of 2 and 4 g·dm-3. in the culture of Anemanthele lessoniana and Bouteloua gracilis it is recommended to apply osmocote 11:11:19 at a dose of 4 g·dm-3. The best quality plants in their aboveground parts contained the following amounts of macronutrients and sodium [%]: Anemanthele lessoniana – n 1.54, p – 0.35, k – 2.10, ca – 0.61, Mg – 0.14, na – 0.10, while in Bouteloua gracilis it was – n – 1.75, p – 0.59, k – 2.31, ca – 0.91, Mg – 0.36 and na – 0.05, respectively.
N-Substituted Analogs of 2β-Carbomethoxy-3β-(4‘-iodophenyl)tropane (β-CIT) with Selective Affinity to Dopamine or Serotonin Transporters in Rat Forebrain

: This report concerns the synthesis and chemical characterization of novel series of N-substituted 2 beta-carbomethoxy-3 beta-(4'-iodophenyl)tropane (beta-CIT, 2) analogs and their neuropharmacological evaluation for affinity at dopamine (DAT), serotonin (5-HTT), and norepinephrine membrane transporters in rat brain tissue. N-Substituted analogs of beta-CIT with a 2 beta-carbomethoxy ester moiety showed lower DAT affinity than beta-CIT for the DAT, and some were more selective for the 5-HTT over the DAT. 2 beta-Carbomethoxy(iodophenyl)nortropane analogs of beta-CIT with the N-substituents difluoroethyl, mesoxypropyl, iodopropyl, and methylpropionyl all yielded > 10-fold lower DAT affinity than beta-CIT itself, whereas the N-(fluoropropyl)-2 beta- isopropyl ester analog (1) of beta-CIT exceeded beta-CIT (2, an N-methyl-2 beta-carbomethoxy ester) in DAT affinity. Several N-haloalkyl-substituted beta-CIT analogs yielded high 5-HTT affinity (Ki N-chloropropyl (4) > or = N-bromopropyl (3) > beta-CIT (2) > N-3'-phtalimidopropyl (11), with particularly high (ca. 30-fold) 5-HTT-over-DAT selectivity found in the N-fluoropropyl (5) and N-fluoroethyl (6) compounds, compared to only 3.o-fold 5-HTT selectivity in beta-CIT itself. Highly 5-HTT selective agents such as 5 and 6 may be useful as brain-imaging ligands for serotonin neurons or as mood-elevating drugs, while the high affinity and selectivity for the DA transporter found in N-(fluoropropyl)-2 beta-(carboxyisopropyl)-3 beta-(4'-iodophenyl)-nortropane (1) and N-(fluoropropyl)-2 beta-carboxymethoxy-3 bet-(4'-iodophenyl)nortropane (FP-beta-CIT, 5) support their use as improved markers for DA neurons.
Transcriptomic response to aquaculture intensification in Nile tilapia

To meet future global demand for fish protein, more fish will need to be farmed using fewer resources, and this will require the selection of nonaggressive individuals that perform well at high densities. Yet, the genetic changes underlying loss of aggression and adaptation to crowding during aquaculture intensification are largely unknown. We examined the transcriptomic response to aggression and crowding in Nile tilapia, one of the oldest and most widespread farmed fish, whose social structure shifts from social hierarchies to shoaling with increasing density. A mirror test was used to quantify aggression and skin darkening (a proxy for stress) of fish reared at low and high densities, and gene expression in the hypothalamus was analysed among the most and least aggressive fish at each density. Fish reared at high density were darker, had larger brains, were less active and less aggressive than those reared at low density and had differentially expressed genes consistent with a reactive stress‐coping style and activation of the hypothalamus–pituitary–interrenal (HPI) axis. Differences in gene expression among aggressive fish were accounted for by density and the interaction between density and aggression levels, whereas for nonaggressive fish differences in gene expression were associated with individual variation in skin brightness and social stress. Thus, the response to crowding in Nile tilapia is context dependent and involves different neuroendocrine pathways, depending on social status. Knowledge of genes associated with the response to crowding may pave the way for more efficient fish domestication, based on the selection of nonaggressive individuals with increasing tolerance to chronic stress necessary for aquaculture intensification.
Resizing Lisowicia bojani: volumetric body mass estimate and 3D reconstruction of the giant Late Triassic dicynodont

ABSTRACT Body size is one of the most crucial biological properties, with a major influence on ecology, metabolism and several physiological aspects. Recently the exceptionally large dicynodont Lisowicia bojani from the Late Triassic of Poland has been described. Using a regression formula based on long bone circumferences, an impressive body mass of 9.33 tons was reconstructed in the original description for this new and largest member of dicynodonts. The taxon is characterized by particularly robust long bones with very massive and stout shafts, thus raising the theoretical possibility that the regression formulae may have led to a substantial overestimate of the body mass. Here we present a new body mass estimate for Lisowicia based on 3D digital volumetric models, aiming to provide a more reliable and conservative estimate. The new body mass ranges from 4.87 tons to 7.02 tons for the adult taxon, with an average body mass of 5.88 tons; thus, the original value of 9.33 tons overestimates the weight of about 60%. Our study confirms empirically that volumetric methods for body mass estimates should be preferred and implemented whenever possible. Synapsids still had to wait until the Eocene to reach the enormous body mass of 9 tons.
Understanding the functional and structural differences across excitatory and inhibitory neurons

One of the most fundamental organizational principles of the brain is the separation of excitatory (E) and inhibitory (I) neurons. In addition to their opposing effects on post-synaptic neurons, E and I cells tend to differ in their selectivity and connectivity. Although many such differences have been characterized experimentally, it is not clear why they exist in the first place. We studied this question in an artificial neural network equipped with multiple E and I cell types. We found that a deep convolutional recurrent network trained to perform an object classification task was able to capture salient distinctions between E and I neurons. We explored the necessary conditions for the network to develop distinct selectivity and connectivity across cell types. We found that neurons that project to higher-order areas will have greater stimulus selectivity, regardless of whether they are excitatory or not. Sparser connectivity is required for higher selectivity, but only when the recurrent connections are excitatory. These findings demonstrate that the differences observed across E and I neurons are not independent, and can be explained using a smaller number of factors.
Environmental toxicology and chemistry (1 November 2017–31 October 2018)

Laboratory testing of sediments frequently involves manipulation by amendment with contaminants and homogenization, which changes the physicochemical structure of sediments. These changes can influence the bioavailability of divalent metals, and field and mesocosm experiments have shown that laboratory‐derived thresholds are often overly conservative. We assessed the mechanisms that lead to divergence between laboratory‐ and field‐derived thresholds; specifically, we assessed the importance of slow equilibration to solid‐phase ligands and vertical stratification. To mimic natural physicochemical conditions, we uniquely aged sediment with a flow‐through exposure system. These sediments were then homogenized and compared, toxicologically, with freshly metal‐amended sediments in a 28‐d chronic toxicity bioassay with the amphipod Hyalella azteca. We assessed concentration–response relationships for 3 metals (copper, nickel, and zinc) and 5 geochemically distinct sediments. We observed minimal differences in growth and survival of H. azteca between aged and freshly spiked sediments across all sediments and metals. These trends suggest that a loss of toxicity observed during long‐term sediment aging is reversed after sediment homogenization. By comparison with mesocosm experiments, we demonstrate that homogenizing sediment immediately before toxicity assays may produce artificially high toxicity thresholds. We suggest that toxicity assays with sediments that maintain vertical redox gradients are needed to generate field‐ relevant sediment metal toxicity thresholds. Environ Toxicol Chem 2019;38:1995–2007. © 2019 SETAC
Antimicrobial Activity of Cinnamon Barks (Aqueous and Ethanolic Extracts) and some Antifungals against Candida albicans Isolated from Oral Candidiasis in Leukemia Patients

Oral pharyngeal candidiasis (Oropharyngeal Candidiasis) is an opportunistic disease resulting from weakness of immune system caused by chemotherapy to Leukemia patients. Candida albicans yeast is the causative agent of this infection. There are many types of antifungals used to treat this fungal infection depending on the degree or type of candidiasis; but noted in recent days, increasing resistance to antifungals. This study included isolation and identification of Candida from oral cavity of ten leukemia patients who suffered from oral candidiasis in three hospitals in Sana’a city. Samples were collected by swabbing the lesional tissues in the oral cavity and cultured on Sabroud’s Dextrose Agar SDA. Six of the oral swabs gave noticeable growth on this medium, while 4 of them didn’t give any growth. Morphological and biochemical tests done to the six isolates confirmed that all were Candida albicans. These isolates were tested for antifungal susceptibility test. Antifungal agents used in this test were Miconazole 50µg, Fluconazole 25µg, and Nystatin 100µg. Results showed that Miconazole was the most efficient antifungal against all tested isolates, while Nystain and Fluconazle showed various inhibitory effects among tested isolates. Some isolates were resistant, while others were susceptible. Due to resistance development of some Candida isolates to antifungal agents, Cinnamon was examined for its ability to inhibit the growth of this yeast. Cinnamon aqueous and ethanolic extracts were prepared by using bioshaker. Antimicrobial activity of cinnamon extracts were screened by using agar disk diffusion technique ADD, and tested C.albicans inoculums were prepared by bioassay plate method. The results showed that cinnamon aqueous extract 100% concentration could slightly inhibit the growth of some isolates. By contrast cinnamon ethanolic extract could effectively inhibit the growth of all tested C.albicans isolates. The Minimum Inhibitory Concentration MIC of ethanolic extract was varied among C.albicans isolates.