Miracle-dz/UniFAR-FTUs huggingface dataset:
The effect of probiotics as a starter culture for producing yogurt

Background: Many comprising studies showed that probiotics can manifest antimicrobial activity. Due to positive health effects of probiotics, they have been added in a fermentation of various foods to increase the nutrient content and to improve the quality of the foods. Furthermore, probiotics are used as a starter culture for several fermented foods like a yogurt. Probiotics may contain strains that are capable of initiating fermentation of the foods, however, a safety of the foods is not certain. Therefore, the study is done to analyze use of probiotics as a starter culture for a yogurt. Methods: The study was designed to analyze the pH pattern of three different yogurt groups (control, commercial starter culture, and probiotics). Each group had three samples that were made using Dairyland 2% milk and corresponding cultures. The control group samples were not inoculated with any culture. The commercial starter culture group samples were inoculated with Yogourtmet Freeze-Dried Starter and the probiotics group samples were inoculated with probiotic capsule, Jamieson 10 Billion Probiotic. The samples were incubated for 7 hours and every 45 minutes the pH was measured using Hanna Professional Portable Yogurt pH Meter. Results: The statistical analysis of the pH measurement showed significant different between the control groups and other two groups. The control group samples pH decreased a bit, but it was not enough to turn the samples to a yogurt. The pH pattern of the commercial group samples showed rapid decrease in pH after 180 minutes and the average pH of the last reading was 4.10. The pH of the probiotics group samples decreased linearly, and the average pH of the last reading was 4.58. Conclusions: The commercial starter culture and the probiotics group samples initiated fermentation and enough acidification occurred to decrease the pH below 4.6. With 7 hours of incubation period, the probiotics group samples just met the pH that makes the yogurt safe to consume. Therefore, the use of the probiotics as a starter culture for producing yogurt can be suggested with adequate incubation period.
Image-based Cell Phenotyping Using Deep Learning

The ability to phenotype cells is fundamentally important in biological research and medicine. Current methods rely primarily on fluorescence labeling of specific markers. However, there are many situations where this approach is unavailable or undesirable. Machine learning has been used for image cytometry but has been limited by cell agglomeration and it is unclear if this approach can reliably phenotype cells indistinguishable to the human eye. Here, we show disaggregated single cells can be phenotyped with a high degree of accuracy using low-resolution bright-field and non-specific fluorescence images of the nucleus, cytoplasm, and cytoskeleton. Specifically, we trained a convolutional neural network using automatically segmented images of cells from eight standard cancer cell-lines. These cells could be identified with an average classification accuracy of 94.6%, tested using separately acquired images. Our results demonstrate the potential to develop an “electronic eye” to phenotype cells directly from microscopy images indistinguishable to the human eye.
Structures of three MORN repeat proteins and a re-evaluation of the proposed lipid-binding properties of MORN repeats

MORN (membrane occupation and recognition nexus) repeat proteins have a wide taxonomic distribution, being found in both prokaryotes and eukaryotes. Despite this ubiquity, they remain poorly characterised at both a structural and a functional level compared to other common repeat motifs such as leucine-rich repeats, armadillo repeats, WD40 repeats, and ankyrin repeats. In functional terms, they are often assumed to be lipid-binding modules that mediate membrane targeting, but direct evidence for this role is actually lacking. This putative activity was addressed by focusing on a protein composed solely of MORN repeats - Trypanosoma brucei MORN1. No evidence for binding to membranes or lipid vesicles by TbMORN1 either in vivo or in vitro could be obtained. TbMORN1 did interact with individual phospholipids, but it remains unclear if this was physiological or an artefact. High- and low-resolution structures of the MORN1 protein from Trypanosoma brucei and homologous proteins from the parasites Toxoplasma gondii and Plasmodium falciparum were obtained using a combination of macromolecular crystallography, small-angle X-ray scattering, and electron microscopy. The structures indicated that MORN repeats can mediate homotypic interactions, and can function as both dimerisation and oligomerisation devices.
Rainforest fungal endophytes for the bio-enhancement of banana toward Fusarium oxysporum f. sp. cubense Tropical Race 4

Abstract As a safe alternative to fungicides, 155 endophytic fungi from 20 selected plants from Mt. Apo rainforest, Davao, Philippines were tested for their activity on Fusarium oxysporum f. sp. cubense Tropical Race 4 (FocTR4) causing Fusarium wilt of banana. Maximum inhibition percentage of more than 75% against FocTR4 was observed using antagonistic method from FusariumCGP150, PenicilliumCGP116, TrichodermaCGP106, PestalotiopsisCGP117 and SchizophyllumCGP119. Amylase, cellulase and protease were produced by the five fungal endophytes. Only PestalotiopsisCGP117 did not produce chitinase while the rest were positive. FusariumCGP150, PestalotiopsisCGP117, PenicilliumCGP116 and SchizophyllumCGP119 showed lipase activity and only SchizophyllumCGP119 produced laccase. SchizophyllumCGP119, TrichodermaCGP106, PestalotiopsisCGP117 and PenicilliumCGP116 significantly (p = 0.05) reduced Fusarium wilt in both GCTCV 219 and Gran Naine when used as protectant. Only SchizophyllumCGP119 showed eradicative ability against FocTR4 in GCTCV 219 but ineffective in Gran Naine. SchizophyllumCGP119 was found the most promising isolate whose identity was confirmed through DNA sequencing as Schizophyllum commune.
Frontiers in Gastroenterology

There have been a number of exciting advancements and changes in the gastroenterology field over the last few years. A new mesalamine formulation, balsalazide disodium, is now available for the treatment of ulcerative colitis (UC). Balsalazide may be utilized as first line therapy for patients with UC, or patients who are intolerant to other mesalamine preparations. In the area of irritable bowel syndrome, alosetron was removed from the market after reports that it was associated with severe constipation and death, although a causal relationship could not be established. Published data examines the risk of certain medications and the development of reflux disease and esophageal adenocarcinoma. Also, new proton pump inhibitors (PPIs) are available, esomeprazole, as well as alternate methods of administration for others. The first intravenous PPI, pantoprazole, is available in the United States, although currently there is a paucity of data regarding its efficacy. Peptic ulcer disease is also discussed, including Helicobacter pylori resistance, nonsteroidal anti-inflammatory drugs, and the treatment of bleeding ulcers. With pegylated interferon, progress in the treatment of hepatitis C offers promise for many patients. This review will highlight many recent changes in gastroenterology an offer a perspective on how disease management has changed.
Regenerative capacity in Drosophila imaginal discs is controlled by damage-responsive, maturity-silenced enhancers

Like tissues of many organisms, Drosophila imaginal discs lose the ability to regenerate as they mature. This loss of regenerative capacity coincides with reduced damage-responsive expression of multiple genes needed for regeneration. Our previous work showed that two such genes, wg and Wnt6, are regulated by a single damage-responsive enhancer, which becomes progressively inactivated via Polycomb-mediated silencing as discs mature. Here we explore the generality of this mechanism, and identify numerous damage-responsive, maturity-silenced (DRMS) enhancers, some near genes known to be required for regeneration such as Mmp1, as well as near genes that we now show are needed for regeneration. Using a novel GAL4-independent tissue ablation system we characterize two DRMS-associated genes, apontic (apt), which curtails regeneration and CG9752/asperous (aspr), which promotes it. This mechanism of suppressing regeneration by silencing damage-responsive enhancers at multiple loci can be partially overcome by reducing activity of the chromatin regulator extra sex combs (esc).
Case report Free-floating thrombus in the inferior caval vein and the right atrium

The diagnosis of free-floating thrombus in the right atrium is still met very rarely and there are no unambiguous recommendations for the way of management with such patients. We present the case of a 65-year-old patient with suspicion of thrombus in the inferior caval vein and the right atrium, who was admitted to the Department of Cardiac Surgery with the symptoms of palpitation, atypical chest pain and easy fatigue. We also discuss the most suitable management with this condition.
Genome duplication in Leishmania major relies on DNA replication outside S phase

Once every cell cycle, DNA replication takes place to allow cells to duplicate their genome and segregate the two resulting copies into offspring cells. In eukaryotes, the number of DNA replication initiation loci, termed origins, is proportional to chromosome size. However, previous studies have suggested that in Leishmania, a group of single-celled eukaryotic parasites, DNA replication starts from just a single origin per chromosome, which is predicted to be insufficient to secure complete genome duplication within S phase. Here, we show that the paucity of origins activated in early S phase is balanced by DNA synthesis activity outside S phase. Simultaneous recruitment of acetylated histone H3 (AcH3), modified base J and the kinetochore factor KKT1 is exclusively found at the origins used in early S phase, while subtelomeric DNA replication can only be linked to AcH3 and displays persistent activity through the cell cycle, including in G2/M and G1 phases. We also show that subtelomeric DNA replication, unlike replication from the previously mapped origins, is sensitive to hydroxyurea and dependent on subunits of the 9-1-1 complex. Our work indicates that Leishmania genome transmission relies on an unconventional DNA replication programme, which may have implications for genome stability in this important parasite.
Patterns of genetic diversity and population structure of the clonal herb, Potentilla fragarioides var. sprengeliana (Rosaceae) in Korea

The genetic diversity and population structure of Potentilla fragarioides var sprengeliana (Rosaceae) in Korea were investigated using genetic variation at 22 allozyme loci. The percent of polymorphic loci within the enzymes was 59.1%. The genetic diversity at the species level and at the population level was high (H_(es)=0.210; H_(ep)=0.199, respectively), whereas the extent of the population divergence was relatively low (G_(ST)=0.074). F_(IS), a measure of the deviation from random mating within the 19 populations, was 0.331. An indirect estimate of the number of migrants per generation (N_(m)=3.15) indicates that gene flow is high among Korean populations of the species. In addition, analysis of fixation indices revealed a slight heterozygote deficiency in some populations and at some loci. The mean genetic identity between populations was 0.985.
Reproducibility warning: The curious case of polyethylene glycol 6000 and spheroid cell culture

In this study we report about the reproducibility of three-dimensional cell culture of floating cell spheroids on PEG6000 treated cell culture dishes. Three-dimensional tumour spheroids or organoids present an interesting test platform for nanoparticulated drug delivery or nanoparticle toxicity. We tested the reproducibility of spheroid formation induced by the PEG coated surface. Interestingly we found that the results were different in a reproducible manner depending on the distributors of PEG6000. Despite the nearly identical physicochemical properties of PEG6000 (MALDI-MS, NMR, FTIR, Triple SEC) with only minor differences, we observed only for one PEG6000 a highly reproducible formation of spheroids with different cell lines such as HT-29, HeLa, Caco2, and PANC-1. The surface coating with the different PEG6000 was studied by AFM. The surface coating as well as the physicochemical characterization showed only small differences in mass and hydrodynamic radius between the different PEGs. A direct coating of the cells with PEG from two distributors indicate that the spheroid formation in due to direct interaction of the polymer with the cell rather than by interaction of cells with the coated surface. The experiments point out that for biological entities, such as cells or tissues, even very small differences such as impurities or batch-to-batch variations in the purchased product can have a very strong impact.
A neural circuit basis for context-modulation of individual locomotor behavior

Defying the cliche that biological variation arises from differences in nature or nurture, genetically identical animals reared in the same environment exhibit striking differences in their behaviors. Innate behaviors can be surprisingly flexible, for example by exhibiting context-dependence. The intersection of behavioral individuality and context-dependence is largely unexplored, particularly at the neural circuit level. Here, we show that individual flies’ tendencies to turn left or right (locomotor handedness) changes when ambient illumination changes. This change is itself a stable individual behavioral characteristic. Silencing output neurons of the central complex (a premotor area that mediates goal-directed navigation) blocks this change. These neurons respond to light with idiosyncratic changes to their baseline calcium levels, and idiosyncratic morphological variation in their presynaptic arbors correlates with idiosyncratic sensory-context-specific turn biases. These findings provide a circuit mechanism by which individual locomotor biases arise and are modulated by sensory context.
The phenomenon of cavitation in grapevine... unravelling implicated mechanisms.

Cavitation is a physiological dysfunction that takes place in the xylem of water stressed plants. It leads to a loss of hydraulic conductance (kL) as the vessels are filled with air. This impacts water supply, water potential (ΨL) and canopy hydration. Stomatal clossure is an effective response upon diminishing momentary or seasonal foliar hydraulic contents. Depending on each type of plant, stomata may close preventing catastrophic cavitations. This research intended to understand how stomatal control acts upon cavitation events in two contrasting grapevine varieties, Syrah and Grenache. A mechanistic was developed model based on the water and vapour fluxes, kL, stomata conductance (gs), and the vulnerability to cavitation of the xylematic tissue. The theoretical model explains how plants respond to drought and avoid catastrophic cavitation. Water stressed grapevines couple their gs with their kL in order to avoid embolism. It is not stomatal closure, by istself, the controlling mechanism. Grapevines under mild water stress, do not need to completely close their stomata in order to avoid cavitation, therefore, photosynthesis is not completely impeded, and the cost in terms of carbon assimilation is less than expected for other species.
Engineering Students Learn ABET Professional Skills: A Comparative Study of Project-Based-Learning (PBL) versus Traditional Students

This paper presents preliminary findings of a study that investigated the learning experiences of students who enrolled in two programs: a project -based learning (PBL) and a traditional engineering curriculum. The PBL students do not take classes; 100 percent of their learning is done in the context of industry projects to develop graduates with integrated technical and professional knowledge and competencies. The traditional curriculum involves classroom instruction, homework, and assessments. Using a qualitative research approach, the current study focused on students that completed two years of a n ew PBL program in a Midwest university, and compared their learning experiences to students that are graduating from a traditional program at a different university. Initial results suggest positive outcomes are more pronounced for students associated with PBL as compared with students in traditional engine ering curriculum, with regard to both Accreditation Board of Engineering and Technology (ABET) professional skills, outcomes, and future employment. For example, one immediate highlight of the PBL program is that a majority of PBL students ranked their program (i.e. instruct ors and project format) positively, and were more “encouraged” to work in teams to complete tasks for real clients in industry. The results of this study will provide insights into PBL as a mode l of learning engineering in the context of design and practice to support engineering programs aiming to establish project-based learning as well as academia in general.
Effects of climate change on pup growth and survival in a cooperative mammal, the meerkat

Breeding systems in which group members help to raise the offspring of co‐members are associated with arid, unpredictable environments. Cooperative rearing may mitigate the effects of adverse environmental conditions on pup growth and survival. However, few studies have explored the relationship between environmental variation and breeding success, and the role of helpers. Here, we show that reductions in the growth and survival of meerkat (Suricata suricatta) pups have been associated with increases in daily maximum air temperatures (Tₘₐₓ) in the southern Kalahari over the last 20 years. On days when Tₘₐₓ was high, meerkat pups gained less body mass than on cooler days. Reductions in the diurnal body mass gain (ΔMb) of pups on hotter days were not a consequence of reductions in the frequency with which pups were fed by adults as feeding rate increased with Tₘₐₓ, suggesting that the reductions in ΔMb by pups on hot days reflected a decrease in water content of the food items or an increased water and energy cost of thermoregulation. Reductions in pup ΔMb on hot days were smaller in larger groups, in which helper‐to‐pup ratios were relatively high. As increases in air temperature are predicted with climate change, further reductions in meerkat pup growth and survival seem inevitable. A free Plain Language Summary can be found within the Supporting Information of this article.
Effect of Ethephon on ripening and postharvest quality of mango

The experiment was conducted at the laboratory of Postharvest Technology Division, BARI to evaluate the effect of postharvest application of 6 concentrations (0, 250, 500, 750, 1000 & 10000 ppm) of ethephon on ripening and postharvest qualityof mango (cv. Langra) fruits harvested at mature green stage on 3rdweek of June in 2011 and 2012. The treated fruits were assessed for physiological changes such as ripening %, weight loss (%), biochemical aspects such as TSS (0Brix), titratable acidity (%), reducing sugar (%), total sugar (%), ascorbic acid content (mg/100g), total carotenoids (μg/100g), carbon di oxide production (ml/g fruit) and residual level of the applied ethephon during storage period. The observations were recorded at 2 days interval during 6 days storage at ambient condition (23±2°C with 80±5% RH). Complete yellow color (full ripe) was developed on the fruits treated with 500-1000 ppm ethephon at 4 days of storage while yellowish green and greenish yellow color was developed on 250 ppm treated and control fruits, respectively, and 10000 ppm ethephon treated fruits overripened at this period. At 6 days of storage, 250 ppm ethephon treated fruits got ripen and 500-1000 ppm ethephon treated fruits overripened whereas 10000 ppm treated fruits got rotten and control one was still unripe. Irrespective of ethephon treatments, weight loss of fruits, TSS, reducing sugar, total sugar, carbon di oxide production and total carotenoid showed increasing trends upto 6 days whereas titratable acidity, ascorbic acid and residue level of ethephon showed decreasing trends in both years. At 4 days of storage, 750-1000 ppm ethephon dipped fruits induced uniform attractive yellow color while untreated control fruits remained yellowish greenish (unripe) even after 6 days of storage. At 6 days of storage TSS, reducing sugar, toatal sugar, ascorbic acid and total carotenoid content were found maximum in 750-1000 ppm treated fruits compared to 250-500 ppm treated fruits. The residue level of ethephon in mango fruits treated with ethephon concentrations (250-1000 ppm) at 6 days of storage was found below 2 ppm (0.1 1ppm-0.54 ppm), which is safe for human consumption. Therefore, mangoes ripened by using ethephon @ 750-1000 ppm can be consumed safely without any health risk. Bangladesh J. Agril. Res. 44(3): 453-467, September 2019
Spatial variability in pollen and resource limitation for fruit production of two species in interior Alaska: Vaccinium uliginosum and V. vitis-idaea

Many recent studies assessing fruit productivity of plants in the boreal forest focus on interannual variability across a forested region, rather than on environmental variability within the forest. Frequency and severity of wildfires in the boreal forest affect soil moisture, canopy, and community structure at the landscape level, all of which may influence overall fruit production at a site directly (through resource availability) or indirectly (through impacts on pollinators). We evaluated how fruit production in two boreal shrubs, Vaccinium uliginosum (blueberry) and V. vitis-idaea (lingonberry), was explained by factors associated with resource availability (such as canopy cover and soil conditions) and pollen limitation (such as floral resources for pollinators and pollen deposition) across boreal forest sites of Interior Alaska. We classified our study sites into upland and lowland sites, which differed in elevation, soil moisture (lower in upland sites), and active layer (deeper in upland sites). We found that resource and pollen limitation differed between the two species and between uplands and lowlands. Lingonberry was more pollen limited than blueberry, and plants in lowland sites were more pollen limited relative to other sites while plants in upland sites were relatively more resource limited. Additionally, canopy cover had a significant negative effect in upland sites on a ramet’s investment in reproductive tissues and leaves versus structural growth, but little effect in lowland sites. These results point to importance of including pollinator abundance as well as resource availability in predictions for changes in berry abundance.