Miracle-dz/UniFAR-FTUs huggingface dataset:
Preparation of Probiotic Apple Juice by Lactic Acid Fermentation

Fermentation of apple juice was done for 72 hrs by lactic acid bacteria (Lactobacillus plantarum and Streptococcus thermophilus) and physico-chemical characteristics of fermented apple juices were recorded at 0. 24, 48 and 72 hrs intervals. On the basis of highest lactic acid bacterial counts, rate of fermentation (°B/24hr), acidity, sugar utilization percentage, retention of ascorbic acid and total phenols, antioxidant activity and antimicrobial activity against pathogenic bacteria such as E. coli and S. aureus, while lowest pH, coliform, yeast and mold counts, the best treatments L. plantarum 107cfu/ ml for apple fermented apple juice was selected for storage study viz. During fermentation both vitamin C and total phenols declined, while, the antioxidant activity, antimicrobial activity, viable cell counts and lactic acid bacteria counts were increased. As the antimicrobial activity increased, the counts of coliform, yeast and mold declined. During storage of selected treatment of fermented apple juice for four weeks at 4°C retained physico-chemical parameters above the value of significance. Lactic acid bacteria remained viable in prescribed number (4.76-6.00 × 106 cfu/ml), acid and bile resistance, imparted antimicrobial activity and antioxidant activity to the apple juices during storage and thus, could be called as probiotics juices. Based on the sensory evaluation (visual colour and flavours) of fermented apple juice, it was concluded that lactic acid fermentation did not influence the desirable characteristics of apple juices. So the probiotic juices were acceptable. Identification of lactic acid bacteria by biochemical test concluded that the bacteria were L. plantarum in apple juices which were inoculated in juices for fermentation, after storage apple juice were suitable for lactic acid fermentation to produce a probiotic beverage. So, this juice can serve as healthy beverage for vegetarians and lactose allergic consumers.
The power of 3D fractal dimensions for comparative shape and structural complexity analyses of irregularly shaped organisms

The increasing interest in 3D morphological approaches for addressing evolutionary and ecological questions has driven the need for reliable, efficient, and easily accessible methods for shape quantification and complexity characterization. This applies in particular to irregularly shaped organisms, such as stony corals, which are challenging to study using traditional morphometric analyses. A potential approach to assess shape and spatial complexity of 3D documented organisms are 3D fractal dimension analyses that combine information from various spatial scales, thus enabling a holistic shape quantification. Therefore, the latest 3D scanning technology and fractal dimension analyses were used to test the performance of this novel combination of methods for quantifying inter‐ and intraspecific differences in shape and spatial complexity of highly irregularly shaped organisms. As model taxa, six widespread species of stony corals were used, belonging to the genera Acropora, Pocillopora and Porites. First, high‐resolution shape models of coral colonies were generated using 3D structured light scanning. Then the univariate fractal dimension D and the multivariate multiscale fractal dimension as well as two traditional univariate morphological measures (surface–volume ratio and rugosity) were calculated. Finally all parameters were tested for significant interspecific and intraspecific differences, and the discriminative power of the two fractal dimension and the two traditional measures were assessed. The results show that 3D shape analyses based on fractal dimensions can be used to quantify both inter‐ and intraspecific variations in irregularly shaped organisms such as corals. Compared to traditional methods, fractal dimensions performed at least as good at the interspecific level and considerably better at the intraspecific level. This study demonstrates that 3D fractal dimension analyses are an efficient and easily applicable method for shape quantification and complexity characterization of irregularly shaped organisms, such as stony corals. Given the specific properties of fractal dimensions, they may either serve as an alternative complexity measure or as an additional characteristic for studying irregularly shaped organisms. Ultimately, fractal dimensions may provide a more integrative understanding of morphological variation within an ecological and evolutionary context, and could open up new opportunities for semi‐automatic or automatic species determination based on 3D morphological images.
New reports of dactylogyridean species (Monogenea) for CentralEurope

Report of six dactylogyridean parasite species and five hosts for four Dactylogyrus species from the gills of cyprinid fish in Central Europe are decribed. Two species, D. alatus forma major and D. dulkeiti, have not previously been recorded in the Czech Republic; four species, D. inexpectatus, D. ramulosus, D. squameus and Thaparocleidus magnus were found as new records in Central Europe. New host records include Abramis ballerus for D. auriculatus, Aspius aspius for D. ramulosus, Rutilus pigus for D. rarissimus, Pseudorasbora parva and Leuciscus idus for D. vistulae.
Amplification-free, CRISPR-Cas9 Targeted Enrichment and SMRT Sequencing of Repeat-Expansion Disease Causative Genomic Regions

Targeted sequencing has proven to be an economical means of obtaining sequence information for one or more defined regions of a larger genome. However, most target enrichment methods require amplification. Some genomic regions, such as those with extreme GC content and repetitive sequences, are recalcitrant to faithful amplification. Yet, many human genetic disorders are caused by repeat expansions, including difficult to sequence tandem repeats. We have developed a novel, amplification-free enrichment technique that employs the CRISPR-Cas9 system for specific targeting multiple genomic loci. This method, in conjunction with long reads generated through Single Molecule, Real-Time (SMRT) sequencing and unbiased coverage, enables enrichment and sequencing of complex genomic regions that cannot be investigated with other technologies. Using human genomic DNA samples, we demonstrate successful targeting of causative loci for Huntington’s disease (HTT; CAG repeat), Fragile X syndrome (FMR1; CGG repeat), amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (C9orf72; GGGGCC repeat), and spinocerebellar ataxia type 10 (SCA10) (ATXN10; variable ATTCT repeat). The method, amenable to multiplexing across multiple genomic loci, uses an amplification-free approach that facilitates the isolation of hundreds of individual on-target molecules in a single SMRT Cell and accurate sequencing through long repeat stretches, regardless of extreme GC percent or sequence complexity content. Our novel targeted sequencing method opens new doors to genomic analyses independent of PCR amplification that will facilitate the study of repeat expansion disorders.
Standardizing transdifferentiation of rabbit bone marrow mesenchymal stem cells to corneal lineage by simulating corneo-limbal cues

Corneal pathologies due to limbal stem cell deficiency or trauma is a common occurrence with high incidence in the modern era. Absence of native limbal stem cells in these cases can even result in blindness unless treated. Identifying alternate autologous stem cells with potential to replace limbal stem cells, gain its significance especially in cases of bilateral limbal damage. Here we look at the suitability of proposing bone marrow derived mesenchymal stem cells as an alternate to limbal stem cells. This work had made use of the corneo – limbal cues for trans differentiating these mesodermal cells to corneal epithelial lineage. Mesenchymal stem cells were isolated from rabbit bone marrow and the culture conditions were optimized. Characterized mesenchymal stem cells were transdifferentiated by simulating limbal niche using extracellular matrix and limbal fibroblast conditioned medium. The differentiation to corneal lineage was evaluated by analyzing the expression of mesenchymal (ABCG2, CD29) and corneal epithelial (CK3/12) markers. Cells cultured in the presence of conditioned medium alone and with conditioned medium/ extracellular matrix showed the expression of CK3/12. CK3/12 expressing cells in these cultures were increasing, with a concomitant decrease in stem cell marker expression. Trans differentiating mesenchymal stem cells to corneal epithelial like cells will provide a useful, autologous source of adult stem cells in therapeutic approaches for patients suffering from bilateral limbal stem cell deficiency. Correspondence to: T.V Kumary, Scientist –G, Tissue Culture Lab, Biomedical Technology Wing, Sree Chitra Thirunal Institute for Medical Sciences and Technology, Poojappura, Trivandrum, Kerala, India, Tel: +91 471 2520271; Fax: +91 471 2341814; E-mail: tvkumary@yahoo.com; tvkumari@sctimst.ac. in
Biology and Bionomics of Zig Zag Beetle Cheilomenes sexmaculatus Fabricius (Coleoptera: Coccinellidae)

1 Department of Agricultural Entomology, C.P. College of Agriculture, S.D. Agricultural University, Sardarkrushinagar, Gujarat – 385506, India 2 Department of Agricultural Entomology, Date palm Research Station, S.D. Agricultural University, Mundra, Kachchh, Gujarat – 370421, India 3 Department of Vegetable Science, College of Horticulture, S.D. Agricultural University, Jagudan, Gujarat – 382710, India *Corresponding author
PEMBUATAN YOGURT SUSU SAPI DENGAN PEMANIS STEVIA SEBAGAI SUMBER KALSIUM UNTUK MENCEGAH OSTEOPOROSIS

Telah dilakukan pembuatan yogurt dengan penambahan pemanis alami daun stevia. Stevia (Stevia rebaudiana Bertoni ) termasuk family Asteraceae, daun kering mempunyai kemanisan 30 kali sukrosa dan tidak menghasilkan kalori. Yogurt sebagai produk olahan susu yang difermentasi mempunyai kandunagn gizi lebih baik dari susu dan merupakan sumber Ca yang bisa dikonsumsi untuk memenuhi kebutuhan tubuh agar terhindar dari osteoporosis. Tujuan pembuatan yogurt adalah mempelajari produksi yogurt berbahan dasar susu sapi yang difermentasi dan menambah pemanis sukrosa dan daun stevia. Rancangan acak lengkap dua variabel dengan tiga kali ulangan telah diterapkan dengan perlakuan perbandingan jumlah sukrosa, kombinasi sukrosa + daun stevia kering, dan stevia yang ditambahkan masing-masing 4:0, 1:1, 1:2, 1:3, dan 0:4. Hasilnya menunjukkan bahwa dari berbagai perlakuan tersebut semakin banyak daun stevia yang ditambahkan pada yogurt semakin banyak Ca yang diperoleh. Kadar Ca yang didapat masing-masing adalah 30,57mg, 39,33mg, 45,43mg, 58,00mg, dan 76,30mg.
DEPRESI SILANG DALAM BIJI DAN SEMAI Melaleuca alternifolia

Tea tree (Melaleuca alternifolia) is known as an essential oil producer. This species is commercially important as a source of essential oil especially in Australia. To improve its oil quality, research on artificial pollination between plus trees were carried out. The information about self-incompatibility and inbreeding depression due to self-pollination should be ascertained to support the pollination success. This study was aimed at examining the self-incompatibility of tea tree by conducting controlled self-pollination and cross-pollination. Controlled cross and self-pollination were carried out at a seedling seed orchard of tea tree, using four mother trees as experimental samples. Natural self-pollination was undertaken by bagging nopened flowers, without emasculation and counting the number of capsule set. Open pollination was used as a control treatment, of which the number of unopened flowers and the number of capsule set were counted. Observations revealed that no capsule was found from controlled self pollination (with the index self-incompatibility = 0), even though natural self-pollination produced low number of capsules (with the index self-incompatibility = 0.24). Therefore, it can be assumed that high level of self-incompatibility was took place in tea tree. Inbreeding depression also existed in this species, revealed by the decreased number of capsul set, lower seed germination rate of self-pollinated seeds than cross pollinated seeds. The slower growth of self-pollinated seedlings than cross pollinated seedlings in the nursery also indicated that inbreeding depression occured.
Cell autonomous and cell non-autonomous effects of mosaic Mecp2 expression on layer V pyramidal cell morphology in a mouse model of Rett Syndrome

Supervisory Committee Dr. Kerry R. Delaney, Co-supervisor (Department of Biology) Dr. Patrick Nahirney, Co-supervisor (Department of Biology) Dr. Perry L. Howard, Departmental Member (Department of Biology) Rett Syndrome (RTT) is a neurodevelopmental disorder primarily caused by mutations in the X-linked gene methyl-CpG-binding protein 2 (MECP2). The mosaic brain environment in heterozygous (MECP2) females consists of both MeCP2-wildtype (MeCP2+) and Mecp2-mutant (MeCP2-) neurons. To separate possible cell autonomous and cell non-autonomous effects three-dimensional morphological analysis was performed on individually genotyped layer V pyramidal neurons in the primary motor cortex of heterozygous (Mecp2) and wild-type (Mecp2) mature female mice (>8 months old) from the Mecp2 line. Mecp2 neurons and Mecp2+ were found to be indistinguishable while Mecp2neurons have significantly reduced basal dendritic length (p<0.05), predominantly in the region 70-130 μm from the cell body, culminating in a total reduction of 15%. Mecp2neurons have three (17%) fewer total branch points, lost specifically at the second and third branch orders. Thus the reduced total dendritic length in Mecp2neurons is a result of fewer higher-order branches. Soma and nuclear areas of 30 Mecp2 female mice (5-21 months) with X chromosome inactivation (XCI) ratios ranging from 12% to 56% were analyzed. On average Mecp2somata and nuclei were 15% and 13% smaller than Mecp2+ neurons respectively. The variation observed in the soma and nuclear sizes of Mecp2neurons was not due to age, but was found to be correlated with the XCI ratio. Animals with a balanced XCI ratio (approximately 50% Mecp2-) were found to have Mecp2neurons with a less severe cellular phenotype (1117% smaller than Mecp2+). Animals with a highly skewed XCI ratio favouring expression of the wild-type allele (less than 30% Mecp2-) were found to have a more severe Mecp2cellular phenotype (17-22% smaller than Mecp2+). These data support indicate that mutations in Mecp2 exert both cell autonomous and cell nonautonomous effects on neuronal morphology.
Physiological changes during overwintering of the Eastern oyster Crassostrea virginica (Gmelin, 1791)

This study aims at better understanding of the physiological changes that occur during the winter months in Eastern oysters (Crassostrea virginica) living at their northernmost distributional limit (48°N). It was conducted in northeastern New Brunswick, Canada (47°49′N, 64°46′W). Oysters were held in Vexar bags on the bottom of a bay and collected before (December) and during (January–April) the ice-cover period. Winter mortality was <5%. A significant decrease in the concentration of lipids stored in the digestive gland (from 42.0 to 22.5 mg/g wet tissue) indicated that the animals had access to oxygen, probably through minimal shell openings. Proteins were also used, although less heavily (decrease from 68.0 to 59.1 mg/g wet tissue), leading to an accumulation of ammonia in the intrapallial fluid (up to 0.83 μM), which is modest considering the length of time the animals lived as almost closed systems. In contrast, carbohydrates appear to play a minor role in winter energetics. Low pH values of intrapallial fluid were noted in late winter (c. 7.0) as compared with those measured at the onset of winter and in spring (c. 7.7). The animals used more energy substrates in late than in early winter, which might be partly related to the necessity to intensify detoxification mechanisms as toxic metabolites accumulate. Despite the fact that oysters do not filter-feed at temperatures <0 °C, the mass of the digestive gland increased by a factor of 1.5 during early winter, presumably as the result of nutrient transfer from other tissues. The ability of C. virginica to use energy-rich substrates and to minimize the accumulation of catabolic byproducts could partly explain the ability of the species to survive prolonged subzero conditions.
Effect of Cover Crops, and the Management Thereof, on the Weed Spectrum in a Drip-irrigated Vineyard: 1. Weeds Growing During Winter and From Grapevine Bud Break to Grapevine Berry Set

A five-year trial (2009 to 2013) was executed in a drip-irrigated full-bearing seven-year-old Shiraz/101-14 Mgt vineyard established on a sandy to sandy clay loam soil at Blaauwklippen Farm (33°58’S, 18°50’E) near Stellenbosch, South Africa. Fourteen treatments, consisting of two management practices applied to five cover crop species, as well as winter-growing weeds (no cover crop) and winter-growing weeds (no cover crop) with nematicide applied in the vine row, were applied. The effect of the five cover crop species, either controlled chemically (CC) or mechanically (MC) during grapevine bud break, on the weed spectrum was determined at the end of winter and during grapevine berry set. Total suppression of Lolium species (ryegrass) was achieved with Avena sativa cv. Pallinup (oats) (CC) and Eruca sativa cv. Nemat (Nemat) (CC) after three years. A grass-specific herbicide applied at the end of May 2012 terminated the dominance of ryegrass and facilitated the dominance of Erodium moschatum (musk heron’s bill). Sowing the cover crops as late as 2013-05-23 prevented ryegrass from regaining its dominance. After five winters, ryegrass was totally eradicated from oats (CC), oats (MC), Sinapus alba cv. Braco (white mustard) (CC) and Nemat (CC). Musk heron’s bill was totally suppressed in all treatments during berry set within two seasons and ryegrass in all the CC treatments by 2011. This probably facilitated the dominance of Digitaria sanguinalis (crab fingergrass).
Paxillus involutus Forms an Ectomycorrhizal Symbiosis and Enhances Survival of PtCOMT-modified Betula pendula in vitro

Abstract The ability of the PtCOMT (caffeate/5-hydroxyferulate O-methyltransferase from Populus tremuloides L.) - modified Betula pendula Roth. lines to form symbiosis with an ectomycorrhizal (ECM) fungus Paxillus involutus Batsch Fr. was studied in vitro. Lignin precursor gene PtCOMT was introduced into two B. pendula clones under the control of the cauliflower mosaic virus 35S promoter or the promoter of the sunflower polyubiquitin gene UbB1. Of the four transgenic lines, one 35SPtCOMT line (23) had a decreased syringyl/guaiacyl (S/G) ratio of root lignin, and two UbB1-PtCOMT lines (110 and 130) retarded root growth compared to the control clone. Both control clones and all transgenic lines were able to form ECMs with P. involutus, but the transgenic lines differed from the controls in the characteristics of the ECMs. The number of lateral roots covered with fungal hyphae and/or development of a Hartig net (HN) were reduced in line 23 with a decreased S/G ratio, and in lines 110 and 130 with slower root formation and changed root morphology, respectively. However, line 23 benefited more from the inoculation in lateral root formation than the control, and in lines 110 and 130 the percentage of viable plants increased most due to inoculation. The results show that B. pendula plants genetically transformed with the lignin gene PtCOMT could form mycorrhizal symbiosis regardless of changes in either the root S/G ratio or development. The benefits of the symbiosis were variable even in the closed in vitro system, and dependent on the clone or transgenic line and the ECM fungal symbiont.
REMOVING NEURAL CORRELATIONS IMPROVES POPULATION SENSITIVITY IN MT/MST IN RESPONSE TO RANDOM DOT STIMULI

The effect of temporal correlations in the activity of sensory neurons remains a subject of debate, with some studies suggesting that correlations may be detrimental to population coding (by reducing the amount of information that can be extracted) or may actually enhance population coding. The study of neuronal responses to random-dot motion patterns has provided the some of the most valuable insights into how the activity of neurons is related to perception. However, it is currently unknown how changes in the strength of motion signals, through the reduction of coherence of random dot patterns, affects correlated activity and population decoding. To address this question, we recorded neuronal populations in the middle temporal (MT) and medial superior temporal (MST) areas of anaesthetized marmosets with electrode arrays, while varying the coherence of random dot patterns. We used the spike rates of simultaneously recorded neurons to decode the direction of motion at each level of coherence using linear classifiers. We found that reducing motion coherence increased neuronal correlations, yet the correlation structure was conserved. We also found that removing correlations with trial shuffling generally improved population decoding performance and ignoring correlations generally impaired decoding performance. Finally, we showed that decoders trained at 100% coherence have similar performance to decoders optimized for each level of coherence, demonstrating that the optimal linear readout is independent of coherence. These results have implications for how information is encoded by populations of neurons, as well as how they may be decoded by downstream areas in decision making tasks. population activity recorded concurrently on the same set of trials to fully account for the information in a neuronal population. In this study, we addressed the effects of correlations on population decoding in MT using random dot motion. Pearson’s correlation coefficient of the trial by trial spike counts for each level of motion coherence. For each iteration of the decoding cross validation procedure, we calculated r SC and then averaged across all iterations to obtain the final estimate of r SC .
Immune Regulatory Network in Cervical Cancer Development: The Expanding Role of Innate Immunity Mechanisms

There is increasing evidence of a pivotal regulatory role of innate immune mechanisms in tumor-immune interplay. Among these diverse mechanisms, tumor-derived nucleic acids’ sensing has recently emerged as one of the fundamental pathways linking innate and adaptive immunity, with DNA-sensor STING being the crucial member of this pathway. Another clear trend is understanding the striking diversity of innate and innate- like immune cell populations implicated in suppression or promotion of tumor growth. Papillomavirus-associated cervical cancer appears to represent a complex network of antiviral and antitumor innate immune mechanisms, whose regulation can be signifi cantly influenced by developing neoplasia. In this chapter, we address new data on the problem of regulation of innate and acquired immunity in cervical cancer patients published in the past 2 years. To support the idea of multilevelness and diversity of changes in the innate arm of immunity, we also report our findings about (a) the expression of endogenous immune sensor STING in neoplastic tissue and peripheral blood lympho- cytes, (b) altered frequencies of circulating natural killer and natural killer-like cell populations, as well as regulatory T lymphocytes from patients with precancerous or early cancerous lesions. Revisiting this problem may provide new insights into therapeutic options for cervical cancer.