Miracle-dz/UniFAR-FTUs huggingface dataset:
Mix & Match: Phenotypic coexistence as a key facilitator of solid tumour invasion

Invasion of healthy tissue is a defining feature of malignant tumours. Traditionally, invasion is thought to be driven by cells that have acquired all the necessary traits to overcome the range of biological and physical defences employed by the body. However, in light of the ever-increasing evidence for geno- and phenotypic intra-tumour heterogeneity an alternative hypothesis presents itself: Could invasion be driven by a collection of cells with distinct traits that together facilitate the invasion process? In this paper, we use a mathematical model to assess the feasibility of this hypothesis in the context of acid-mediated invasion. We assume tumour expansion is obstructed by stroma which inhibits growth, and extra-cellular matrix (ECM) which blocks cancer cell movement. Further, we assume that there are two types of cancer cells: i) a glycolytic phenotype which produces acid that kills stromal cells, and ii) a matrix-degrading phenotype that locally remodels the ECM. We extend the Gatenby-Gawlinski reaction-diffusion model to derive a system of five coupled reaction-diffusion equations to describe the resulting invasion process. We characterise the spatially homogeneous steady states and carry out a simulation study in one spatial dimension to determine how the tumour develops as we vary the strength of competition between the two phenotypes. We find that overall tumour growth is most extensive when both cell types can stably coexist, since this allows the cells to locally mix and benefit most from the combination of traits. In contrast, when inter-species competition exceeds intra-species competition the populations spatially separate and invasion arrests either: i) rapidly (matrix-degraders dominate), or ii) slowly (acid-producers dominate). Overall, our work demonstrates that the spatial and ecological relationship between a heterogeneous population of tumour cells is a key factor in determining their ability to cooperate. Specifically, we predict that tumours in which different phenotypes coexist stably are more invasive than tumours in which phenotypes are spatially separated.
Detection of Human Salivary Amylase Level Deposited on Fruits with First Bite Mark

Background: Human body fluids are vital for criminological examinations. The recovery, conservation, and investigation of body fluids or its stains are critical in measurable forensic cases. The amylase testing is being utilized as a possible test to locate the crime scene saliva stains for more than three decades. This investigation was intended to decide the human salivary amylase accumulated on fruit after the first bite where the level of salivary amylase was concluded by Radial Gel Diffusion method. Methods: Three sorts of organic fruits (apple, peach, and apricot) and 20 people (10 male and 10 female) were chosen for this investigation. The specimens were assembled from bite mark area following time intervals 0 hours, 12 hours, 24 hours, 36 hours and 48 hours. Results: Experimental outcomes demonstrated that the diameter of amylase activity in male specimens was more noteworthy than female. Apples, as well as apricot pit samples, indicated amylase activity till 48 hours; however, the specimens collected from peach demonstrated amylase activity until 12 hours, after first bite mark. Conclusion: This study demonstrated that salivary amylase testing might be valuable for DNA evidence, where DNA investigations for every case might be restricted because of cost issues. Keywords: Amylase; Saliva; Investigation; Bite mark; Preservation
Clinostat Rotation Affects Metabolite Transportation and Increases Organic Acid Production by Aspergillus carbonarius, as Revealed by Differential Metabolomic Analysis

Fungi are ubiquitous in nature and have the ability to corrode various materials by producing metabolites. Research on how the space station environment, especially microgravity, affects fungal metabolism is helpful to understand the role of fungi in the space station. This work provides insights into the mechanisms involved in the metabolism of the corrosive fungus Aspergillus carbonarius under simulated microgravity conditions. Our findings have significance not only for preventing material corrosion but also for ensuring food safety, especially in the space environment. ABSTRACT Contamination by fungi may pose a threat to the long-term operation of the International Space Station because fungi produce organic acids that corrode equipment and mycotoxins that harm human health. Microgravity is an unavoidable and special condition in the space station. However, the influence of microgravity on fungal metabolism has not been well studied. Clinostat rotation is widely used to simulate the microgravity condition in studies carried out on Earth. Here, we used metabolomics differential analysis to study the influence of clinostat rotation on the accumulation of organic acids and related biosynthetic pathways in ochratoxin A (OTA)-producing Aspergillus carbonarius. As a result, clinostat rotation did not affect fungal cell growth or colony appearance but significantly increased the accumulation of organic acids, particularly isocitric acid, citric acid, and oxalic acid, and OTA both inside cells and in the medium, as well as resulted in a much higher level of accumulation of some products inside than outside cells, indicating that the transport of these metabolites from the cell to the medium was inhibited. This finding corresponded to the change in the fatty acid composition of cell membranes and the reduced thickness of the cell walls and cell membranes. Amino acid and energy metabolic pathways, particularly the tricarboxylic acid cycle, were influenced the most during clinostat rotation compared to the effects of normal gravity on these pathways. IMPORTANCE Fungi are ubiquitous in nature and have the ability to corrode various materials by producing metabolites. Research on how the space station environment, especially microgravity, affects fungal metabolism is helpful to understand the role of fungi in the space station. This work provides insights into the mechanisms involved in the metabolism of the corrosive fungus Aspergillus carbonarius under simulated microgravity conditions. Our findings have significance not only for preventing material corrosion but also for ensuring food safety, especially in the space environment.
Some relevant quality indicators of red wine from three grapes cultivars - a minireview.

In the last years studies point out the fact that the red wine is one of the most consumed beverages over the world. Appreciation of quality in food products is a complex process and is often based on multi-dimensional facets, whose measurement requires clearly validated scales. Factors that influence the overall perception of wines in terms of quality are: geographical origin – ground type, climate, grape variety and authenticity. One of the most important indicator of the red wine is polyphenolic compounds, such as flavonoids, anthocyanins and tannins present in large quantities in wine, especially in red wines; their composition in wine being influenced by the varieties, the vintage and the wineries. The aim of the present work is to make a short review about three types of wines: Cabernet Sauvignon, Merlot and Feteasca neagra quality attributes in order to establish the relationship of the intrinsic characteristics of each individual product and the extrinsic attributes and to adapt the scale to each considered product.
Eukaryotic plankton community stability across reef environments in Bocas del Toro Archipelago (Panamá)

Variation in light and temperature can influence the genetic diversity and structure of marine plankton communities. While open ocean plankton communities receive much scientific attention, little is known about how environmental variation affects tropical coral reef plankton communities. Here, we characterize eukaryotic plankton communities on coral reefs across the Bocas del Toro Archipelago in Panamá. Temperature loggers were deployed for one year and mid-day light levels were measured to quantify environmental differences across reef zones at four inner and four outer reef sites: Inner: Punta Donato, Smithsonian Tropical Research Institute (STRI) Point, Cristobal, Punta Laurel and Outer: Drago Mar, Bastimentos North, Bastimentos South, and Popa Island. Triplicate vertical plankton tows were collected mid-day and high-throughput 18S ribosomal DNA metabarcoding was leveraged to investigate the relationship between eukaryotic plankton community structure and reef zones. Plankton communities from STRI Point were additionally characterized in the morning (∼08:00), mid-day (∼12:00), and evening (∼16:00) to quantify diel variation within a single site. We found that inshore reefs experienced higher average seawater temperatures, while offshore sites offered higher light levels, presumably associated with reduced water turbidity on reefs further from shore. However, these significant reef zone-specific environmental differences did not correlate with overall plankton community differences or changes in plankton genetic diversity. Instead, we found that time of day within a site and diel vertical migration played structuring roles within these plankton communities, and therefore conclude that the time of community sampling is an important consideration for future studies. Overall, plankton communities in the Bocas del Toro Archipelago appear relatively well mixed across space; however, follow-up studies focusing on more intensive sampling efforts across space and time coupled with techniques that can detect more subtle genetic differences between and within communities will more fully capture plankton dynamics in this region.
Fabrication and in-vitro Investigation of PCL- (PVA/Collagen)Hybrid Nanofiber as Anti-Inflammatory GTR Membrane.

Background- GTR utilized in recovering procedures that result in inflammation interfering with the bone regeneration. Here an Ibu loaded nano-hybrid GTR membrane was developed as a scaffold with localized drug delivery. Material & Methods- PCL and a blend of PVA/Col were electrospun. Ibu was loaded once in the PCL context and once in the PVA/Col portion. The drug release behavior, Morphological, mechanical and physicochemical properties of fibers was investigated. Results- The heliacal structure consistists of 256nm porous pores. The controlled release of Ibu was obtained from both PCL and PVA/Col membranes. Kinetic model study indicated the following of zero-order and Higuchi models. Conclusion- The membranes indicated proper physicochemical properties and appropriate biodegradation rate as a potential GTR membrane.
Population structure and linkage disequilibrium in a large collection ofFusarium oxysporumstrains analysed through iPBS markers

In the current study, 160 pathogenic strains of Fusarium oxysporum collected from tomato, eggplant and pepper were studied. Eighteen inter‐primer binding site (iPBS)‐retrotransposon primers were used, and these primers generated 205 scorable polymorphic bands. The number of polymorphic bands per primer varied between 9 and 19, with a mean of 11 bands per primer. The highest polymorphism information content (PIC) value was determined as 0.27, and the lowest was 0.05. The unweighted pair‐group method with arithmetic averages (UPGMA) dendrogram including a heat map revealed that the 160 pathogenic strains of F. oxysporum were divided into two main clusters. The first cluster mainly included F. oxysporum f. sp. capsici (FOC) and F. oxysporum f. sp. melongenae (FOMG) isolates. The second cluster mainly comprised F. oxysporum f. sp. lycopersici (FOL) and F. oxysporum f. sp. radicis lycopersici (FORL) isolates. The highest percentage of loci in significant linkage disequilibrium (LD) was detected for FOL, whereas the lowest level of LD was found for FOC, and 95.2%, 99.4%, 99.1% and 97.4% of the relative kinship estimates were less than 0.4 for FOL, FOMG, FORL and FOC, respectively. LD differences were detected among formae speciales, and LD was higher in FOL as compare to FOC species. The findings of this study confirm that iPBS‐retrotransposon markers are highly polymorphic at the intraspecific level in Fusarium spp.
PROGNOSIS IN CHILDREN WITH OTITIS MEDIA WITH EFFUSION

The public health significance of this study is to provide researchers and clinicians interested in the study and treatment of Otitis Media with effusion (OME) with a better understanding of the associations between covariates and antibiotic treatment with the resolution of OME, which in turn will inform the decision-to-treat process. In a secondary analysis of the data from a series of three efficacy trials, we focus on the roles of laterality (unilateral vs. bilateral disease) and sidedness (right vs. left ear) as prognostic factors. The D&A trial compared the efficacy of decongestant and antihistamine (D/A) to placebo, the ABI trial was similar but compared amoxicillin (with and without to D/A) to placebo, and the ABII trial compared the efficacy of 2 promising antibiotics to amoxicillin. Each trial assessed subjects for OME at baseline, 2 weeks, and 4 weeks.The prevalence of OME at each time point was described by laterality and sidedness. McNemar's test showed no evidence that left and right ears differ with respect to prevalence rates at 2 or 4 weeks (OR = 1.106 and OR = 0.858, respectively). Transition matrices of changes in OME status from 0 to 2 weeks and 2 to 4 weeks described the dependence of prior effusion status on a subject's current OME status. Multinomial regression was used to assess baseline covariates associated with prevalence and transitions of effusion status at each time point. We identified statistically significant prognostic factors of OME, including duration of effusion. Our analyses showed no differences in either prevalence of OME or in transitions of effusion status attributable to sidedness. A Chi Square Goodness-of-Fit test at each timepoint rejected the hypothesis of independence, p < 0.001. An ear-level GEE analysis demonstrated that effusion status of a contralateral ear was a significant predictor of effusion in the other ear (OR = 1.44, p < 0.001). There was no significant effect of sidedness (p = 0.86) and bilateral disease does not resolve at the rate predicted by unilateral resolution. This reanalysis using correlated data methods augments the initial findings by further examining sidedness and documenting transitions over time.
Rapid diagnosis of neonatal sepsis by PCR for detection of 16S rRNA gene, while blood culture and PCR results were similar in E.coli-predominant EOS cases

Purpose To determine the bacteriological pattern and antibiotic susceptibility of bacterial isolates causing neonatal sepsis in Qena University Hospitals and compare polymerase chain reaction (PCR) and blood culture results in a trial for rapid diagnosis. Patients and methods Blood samples from 75 clinically suspected cases of neonatal sepsis were subjected to identification of bacteria and determination of their antibiotic sensitivity through blood culture, and rapid detection of 16S rRNA and the uidA gene (to confirm the presence of E. coli) by PCR from extracted bacterial DNA. Results Most patients were preterm (64%) and low birth weight (LBW) (68%). In total, 42.7% presented with early onset sepsis (EOS). LBW was significantly associated with EOS (P-value=0.03). Although the blood culture and PCR results were similar in EOS, the PCR results were significantly higher than those of blood culture in detecting bacteria (85.3% vs 68%, respectively, P-value=0.001). Blood culture showed 100% specificity. The most common pathogen was E. coli (86.2%) in EOS and Staphylococcus spp. (45.5%) in late-onset sepsis (LOS) (P-value=0.001 and 0.02, respectively). The most effective antibiotics against Gram-negative bacteria were ofloxacin, ciprofloxacin, imipenem, and amikacin, while vancomycin, oxacillin, and imipenem were the most effective antibiotics against Gram-positive bacteria. Conclusion EOS was mainly caused by E. coli, while LOS was mainly caused by Staphylococcus spp. The 16S rRNA PCR showed higher sensitivity with rapid and accurate diagnosis. Blood culture is the most suitable method for antimicrobial sensitivity testing.
Excessive assimilation of ammonium by plastidic glutamine synthetase is a major cause of ammonium toxicity in Arabidopsis thaliana

Plants use nitrate and ammonium in the soil as their main nitrogen sources. Recently, ammonium has attracted attention due to evidence suggesting that, in C3 species, an elevated CO2 environment inhibits nitrate assimilation. However, high concentrations of ammonium as the sole nitrogen source for plants causes impaired growth, i.e. ammonium toxicity. Although ammonium toxicity has been studied for a long time, the primary cause remains to be elucidated. Here, we show that ammonium assimilation in plastids rather than ammonium accumulation is a primary cause for toxicity. Our genetic screen of ammonium-tolerant Arabidopsis lines with enhanced shoot growth identified plastidic GLUTAMINE SYNTHETASE 2 (GLN2) as the causal gene. Our reciprocal grafting of wild-type and GLN2 or GLN1;2-deficient lines suggested that shoot GLN2 activity results in ammonium toxicity, whilst root GLN1;2 activity prevents it. With exposure to toxic levels of ammonium, the shoot GLN2 reaction produced an abundance of protons within cells, thereby elevating shoot acidity and stimulating expression of acidic stress-responsive genes. Application of an alkaline ammonia solution to the toxic ammonium medium efficiently alleviated the ammonium toxicity with a concomitant reduction in shoot acidity. Consequently, we conclude that a primary cause of ammonium toxicity is acidic stress in the shoot. This fundamental insight provides a framework for enhanced understanding of ammonium toxicity in plants.
A survey of bolus tube feeding prevalence and practice in adult patients requiring home enteral tube feeding

Abstract Anecdotal evidence suggests the use of bolus tube feeding is increasing in the long-term home enteral tube feed (HETF) patients. A cross-sectional survey to assess the prevalence of bolus tube feeding and to characterise these patients was undertaken. Dietitians from ten centres across the UK collected data on all adult HETF patients on the dietetic caseload receiving bolus tube feeding (n 604, 60 % male, age 58 years). Demographic data, reasons for tube and bolus feeding, tube and equipment types, feeding method and patients’ complete tube feeding regimens were recorded. Over a third of patients receiving HETF used bolus feeding (37 %). Patients were long-term tube fed (4·1 years tube feeding, 3·5 years bolus tube feeding), living at home (71 %) and sedentary (70 %). The majority were head and neck cancer patients (22 %) who were significantly more active (79 %) and lived at home (97 %), while those with cerebral palsy (12 %) were typically younger (age 31 years) but sedentary (94 %). Most patients used bolus feeding as their sole feeding method (46 %), because it was quick and easy to use, as a top-up to oral diet or to mimic mealtimes. Importantly, oral nutritional supplements (ONS) were used for bolus feeding in 85 % of patients, with 51 % of these being compact-style ONS (2·4 kcal (10·0 kJ)/ml, 125 ml). This survey shows that bolus tube feeding is common among UK HETF patients, is used by a wide variety of patient groups and can be adapted to meet the needs of a variety of patients, clinical conditions, nutritional requirements and lifestyles.
Brd4 Is Required for Granule Cell Progenitor Proliferation

of a dissertation at the University of Miami. Dissertation supervised by Professor Nagi G. Ayad No. of pages in text. (96) Bromodomain and extraterminal domain proteins are epigenetic reader proteins that recognize and bind acetylated histones to facilitate gene transcription. Because of their influence on transcription of genes involved in proliferation and differentiation, small molecule bromodomain inhibitors have entered clinical trials for various indications including several types of cancer. However, our understanding of bromodomain protein function is incomplete, as we do not completely understand their role in vertebrate development. We are investigating the role of the BET protein, Brd4, in cerebellar granule cell progenitor proliferation and cell cycle exit. Dysregulation of cerebellar granule cell progenitor proliferation leads to medulloblastoma, the most common pediatric brain tumor; therefore, understanding the role of Brd4 in granule cell progenitor proliferation is critical. Granule cell progenitor proliferation is dependent on the sonic hedgehog signaling pathway. Our laboratory has used time series expression modeling to identify differential expression of sonic hedgehog pathway genes during granule cell progenitor cell cycle exit and found that expression of the sonic hedgehog activator, Gli1, was dependent on Brd4 phosphorylation. As Brd4 phosphorylation is required for its activity and Gli1 expression, we hypothesized that Brd4 plays a fundamental role in granule cell progenitor proliferation during cerebellar development. Therefore, to specifically examine the role of Brd4 in granule cell progenitor proliferation, we generated a conditional Brd4 knockout mouse line using the Tg (Atoh1-Cre) driver, to limit Brd4 deletion in the cerebellum to granule cell progenitor. Upon verifying Brd4 loss in the granule cell lineage, we determined that granule cell progenitors lacking Brd4 proliferated less, had reduced expression of sonic hedgehog activator genes, and were no longer responsive to sonic hedgehog stimulation. Brd4 loss in in the granule cell lineage diminished overall cerebellum size and led to persistent morphological deficits in the Purkinje cell layer. Adult mice lacking Brd4 in the granule cell lineage displayed behavioral problems including ataxia symptoms and motor and coordination difficulties. Brd4 appears to play a critical role in granule cell progenitor proliferation and leads to lasting problems when depleted in early postnatal development.
Exopolysaccharides of bacterial endophytes from medicinal plant of forest origin show antibacterial and biosurfactant properties

Forests are a dynamic entity harboring different life forms and ecological niches inside them. Medicinal plants form an important component of benefits we derive from forests and has been part of traditional medicine since ages. Recently, endophytes from such medicinal plants have gained attention owing to discovery of numerous bioactive compounds secreted by them and its diverse biotechnological applications. We aimed to isolate bioactive compounds from bacterial endophytes derived from medicinal plants of forest origin. We searched forest region of Haryana for a medicinal plant (Withania sominfera) having significance in traditional Indian medicine-Ayurveda. We isolated and identified bacterial endophytes from this medicinal plant and found an isolate producing exopolysaccharides. The production of exopolysaccharides was optimized and checked for presence of anti-bacterial and biosurfactant properties. We could find many isolates from the stem and leaf explants from W. somnifera plant. A distinct colony which was identified as Bacillus subtilis from stem explant was found to produce exopolysaccharides in liquid culture. This exopolysaccharide was found to have antibacterial activity against pathogenic E. coli and S. typhimurium strains. This exopolysaccharide also showed biosurfactant properties. We isolated and identified a bacterial endophyte from wild medicinal plant. This isolate was found to produce exopolysaccharide which had antibacterial and biosurfactant properties. This isolate has clear medicinal values and might be of use to industry both for production and bioremediation purposes.