Miracle-dz/UniFAR-FTUs huggingface dataset:
Green tea polyphenol induces significant cell death in human lung cancer cells

Purpose: To investigate the dose–response relationship of green tea polyphenol in an animal model of lung cancer. Methods: The effects of epigallocatechin-3-gallate (EGCG) on the inhibition of xenograft tumor growth, the accumulation of 8-hydroxy-2'-deoxyguanosine (8-OHdG), and apoptosis based on 3-(4,5- dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay were evaluated in non-small cell lung cancer (NSCLC) cell lines, namely, H1155, H661, and A427 (a human lung carcinoma-derived cell line). The dose-dependent effects of EGCG on H1155 xenograft tumor growth, as well as the levels of EGCG in plasma and tissue, were also determined in male nude mice. Results: EGCG inhibited the growth of NSCLC-derived cell lines (H1155) over a 45-day period. There was a significant reduction (57 %) in tumor weight in EGCG-fed (0.5 %) animals compared with the control group (p < 0.05). Linear regression analysis revealed a dose-dependent reduction in tumor size. MTT assay results revealed inhibition of H1155 cell growth (25 %, p < 0.05) after 24 h treatment with EGCG. The addition of superoxide dismutase (5 U/mL) and catalase (30 U/mL) reduced the inhibitory effect of EGCG. Mice administered 30 mg/kg EGCG via intraperitoneal injection exhibited the least amount of oxidative stress. Conclusion: The results demonstrate the concentration-dependent inhibitory effects of EGCG on lung cancer cells, including H1155 cells, both in vitro and in vivo . The induction of reactive oxygen species, oxidative DNA damage, and apoptosis were evident following EGCG treatment. Keywords: Green tea, Lung cancer, Catechins, Epigallocatechin-3-gallate, Oxidative stress, Oxidative DNA damage
DEPTH-DEPENDENCY OF THE AGAROPHYTE RED ALGA Gracilaria corticata J. AGARDH FOR AGAR YIELD AND QUALITY DURING ITS GROWING SEASON

The impacts of two depth ranges on the rhodophyte Gracilaria corticata for agar yield and quality were determined during its growing season (December to March) at intertidal waters. Average 4-month agar at 2-3 m and 5-6 m were 34 ± 0.04% and 42 ± 0.05%, respectively. The lowest (30 ±2.89%) and highest (51 ±4.16%) agar yields, respectively, were estimated in December at 2-3 m and in January at 5-6 m. At 2-3 m, the 4-month averages were not significantly different (P>0.05). G. corticata from a depth of 2-3 m yielded the strongest (30.64 ±1.49 g cm − 2 ) agar gel in December, and the alga sampled at 5-6 m in January revealed the lowest agar strength (7.94 ±0.38 g cm − 2 ). Agar lightness (L) ranged from lowest ( 59.6 ±3.85) at 2-3 m in December to greatest (86.8 ±3.11) at 5-6 m in February. Agar yellowish factor (a) was highest (11.6 ±3.21) at 2-3 m in December and lowest (4.8 ±1.64) at 5-6 m in February. Agar reddish factor (b) was highest (48 ±2.24) in March and lowest (38.8 ±1.30) in December at a depth of 2-3 m. G. corticata growing at relatively deeper intertidal zone yields more quality agar , and December and late winter are the best times to obtain a more rigid and enhanced agar gel.
Anticancer, Antimicrobial and Antioxidant Activities of the Essential Oils of Some Aromatic Medicinal Plants (Pulicaria inuloides-Asteraceae)

Purpose: To determine the anticancer, antimicrobial and antioxidant activities of Pulicaria inuloides essential oil (PiEO). Methods: 3-(4, 5-dimethylthiazol- 2-yl)-2, 5-diphenyltetrazolium bromide (MTT) was used to assess cytotoxic activity. Steam distillation of the aerial parts of P. inuloides was performed using a Clevenger apparatus. Antioxidant activities were determined by using 2, 2-diphenyl-1,1-picrylhydrazyl (DPPH). Disc diffusion and microtiter broth microdilution assays were employed to determine antimicrobial activity. Results: PiEO inhibited six tested strains of Listeria with minimum inhibitory concentrations of 5.49 μg/mL against L. monocytogenes, L. innocua, and L. ivanovii; 6.24 μg/mL against L. welshimeri, and L. grayi; and 11.55 μg/mL against L. seeligeri. PiEO also possessed more efficient free radical scavenging activities than butylated hydroxytoluene (BHT). PiEO possessed significant anticancer properties, indicated by growth inhibition and changes in the morphological structure of MCF-7 cancer cells treated with PiEO.
Comparative Study of the Nutritional Composition of Oyster Mushrooms Cultivated in Bangladesh

The nutritional composition of six species of oyster mushrooms such as Pleurotus sajor-caju, P. ostreatus, P. florida, P. cystidiosus, P. highking 51 and P. geestaranus was determined. The protein content was found highest in P. sajor-caju (24.5g/100g of dry weight) followed by P. ostreatus, P. highking 51, P. florida, P. geestaranus and P. cystidiosus. The highest lipid content was found in P. cystidiosus (5.5g/100g dry sample) followed by P. highking 51, P. sajor-caju, P. florida, P. geestaranus and P. ostreatus. The carbohydrate content was found highest in P. geestaranus (45.9g/100g dry sample) followed by P. cystidiosus, P. florida, P. ostreatus, P. sajor-caju and P. highking 51. The fiber content was found highest in P. highking 51 (30.3 g/100g dry sample) followed by P. ostreatus, P. florida, P. geestaranus, P. sajor-caju and P. cystidiosus. The total ash content was found highest in P. florida (8.3 g/100g dry sample) followed by P. sajor-caju, P. ostreatus, P. cystidiosus, P. highking 51 and P. geestaranus. Following these data the highest metabolizable energy was found in P. cystidiosus (262.8 kcal/100g dry sample) followed by P. sajor-caju (254.1 kcal/100g), P. geestaranus (252.7 kcal/100g), P. florida (250.1 kcal/100g), P. highking 51(249.7 kcal/100g) and P. ostreatus (242.6 kcal/100g). The moisture content of fresh oyster mushrooms was found 85-88%.
A Critical Review of Gene Marker Selection Methods and Cell Count Inference Tools

Seasonal influenza virus is a threat for human being. Understanding dynamical change of immune response induced by influenza infection could benefit diagnosis and drug development, using transcriptome analysis. But transcriptomic data is often complicated by the changing cell makeup of the tissue during disease. It’s difficult to distinguish between gene regulations and cell proliferation or migration. Therefore inference of the change in cell counts is necessary, and computational models for cell count inference are introduced in this thesis. Besides, in most models related to prediction of cell quantities, gene marker selection is used as the first step. Thus computational methodology concerning gene marker selection for cell count inference is also reviewed. Different gene marker selection methods are applied to a common dataset to evaluate their behaviors. The uniqueness and expression intensity are the key properties for evaluation of obtained markers. As for predicting cell enrichment, principles of three kinds of schemes are explained. Computational algorithms named CTen and CIBERSORT are introduced as examples of them. Estimation behaviors of these tools are tested by a microarray dataset. Analysis of the estimations shows that they may provide good estimation but are not suitable for careful study of complex problems, e.g. dynamical samples.
Action of proteases of the nematophagous fungi Pochonia chlamydosporia on Ascaris suum eggs of collared peccary (Pecari tajacu)

Among the parasites of domestic and wild swine, Ascaris suum stands out; a nematode that can lead to growth retardation and reduction in weight gain due to its action, especially in young animals. The objective of this study was to test the ovicidal action of proteases from Pochonia chlamydosporia (VC4) on A. suum eggs in an assay with Petri dishes. The fungus P. chlamydosporia (VC4) was grown in Erlenmeyers flasks with 50 ml of liquid minimal media supplemented with 0.2% gelatin for production of enzymes. In the present assay, 500 eggs were poured into Petri dishes of 4.5 cm in diameter and 5 ml of VC4 proteases were added in each Petri dish and incubated at 26°C in the dark for 14 days. After this period, the number of embryonated and destroyed A. suum eggs present in each plate from treated and control groups was counted. Significant difference (p <0.01) was found between the number of eggs from treated group compared to the control group. At the end of the experiment, the proteases of P. chlamydosporia (VC4) demonstrated efficacy in reducing embryonated eggs on the plates of the treated group (78.7%) compared to the control group (83.7%). The results presented in this study demonstrate that proteases of P. chlamydosporia (VC4) were effective in the destruction of A. suum eggs and therefore could be used as biological control of this nematode. Key words: Nematophagous fungi, Pochonia chlamydosporia, protease, Pecari tajacu, Ascaris suum.
Study of viscosity and thermal conductivity effects on condensation characteristics of some new alternative refrigerant mixtures

In this paper, a numerical study of the impact of the transport properties on the condensation characteristics of certain refrigerant mixtures is presented. New correlations have been developed to calculate the thermal conductivity and viscosity of some alternative refrigerant mixtures such as R‐507, R‐404A, R‐407C, and R‐410A. In addition, new improved condensation correlations have been developed and presented for predicting the heat transfer coefficient and pressure drop.
Effect of pre-sowing treatments on seed germination and initial seedling growth performance of Canarium resiniferum: A native threatened tree of Bangladesh

Canarium resiniferum is an economically and aesthetically important native threatened tree species of Bangladesh. In natural condition 78.5 - 98.7% seeds do not germinate due to seed predation. A study was conducted in the Seed Research Laboratory and nursery of Institute of Forestry and Environmental Sciences Chittagong University, Bangladesh in 2013 to find out appropriate pre-sowing treatment for maximizing germination and initial seedling growth. Eleven pre-sowing treatments were provided in both the seeds sown in polybags and seeds sown in propagator house. Results revealed that, germination started at first (after 20 days of seed sown) in seeds immersed in cold water for 24 hours and germination completed within 38 days. Significantly higher (p<0.05) germination percentage (33%), germination energy (16.7%), plant percent (33%) and germination value (0.4) was found with seeds immersed in cold water for 24 hours. Seedling height measured at three, four and five months after the seed germination in case of seeds treated by immersion in cold water for 24 hours was also greater than others. Therefore, pre-sowing treatment by immersion in cold water for 24 hours was more effective in germination and production of quality vigor seedling of Dhup ( C. resiniferum ).
The contribution of specific class I and II histone deacetylases in the development of anxietyrelated behavior in a mouse model of prenatal immune challenge

Several lines of evidence demonstrated that maternal infection during gestation might be an environmental risk factor for offspring to develop mood and anxiety disorders later in life. Previous experiments revealed that anxiety-related behavior, observed after prenatal immune challenge, is associated with increased histone deacetylase (HDAC) activity in adult female mice. Based on these findings, this study aims to investigate which class I and II HDAC isotypes might be involved in the development of the long-lasting consequences of prenatal immune challenge. Therefore, pregnant C57BL/6JRccHsd inbred mice were intravenously injected with poly I:C (5 mg/kg bodyweight) at gestational day (GD) 17 to mimic a viral infection. Brains from adult offspring were homogenized and used for western blotting to analyse the relative protein levels of HDAC1, 2, 3, 4, 5 and 6. Due to a lack of signal in HDAC1, HDAC3 and HDAC5, an irregular signal in HDAC2, and a weak signal in HDAC4 and HDAC6, the quality of the western blots was insufficient for protein quantification. Therefore, no subsequent comparison could be made between mice exposed to prenatal poly I:C and PBS in the current study.
Suppression of Meiotic and Mitotic Cell Divisions in Nile tilapia, Oreochromis niloticus L., and Induction of Triploids and Two Types of Gynogenetic Diploids

Studies were conducted to interfere with the normal functioning of spindle apparatus during meiotic and mitotic cell divisions in Nile tilapia, Oreochromis niloticus L. , eggs using both temperature and hydrostatic pressure shock treatments, therefore, leading to the induction of triploids and two types of gynogenetic (meiotic and mitotic) diploids.
Correlation of Protein and Oil Contents with Five Agronomic Characters of Maize (Zea mays L.) After Three Cycles of Reciprocal Recurrent Selection

A correlation analysis study was conducted with eight varieties of maize (Zea mays L.): Nsukka High Quality-Yellow Early (NHQ-YE); Nsukka High Quality-White Early (NHQ-WE); Nsukka High Quality-Yellow Late (NHQ-YL); Nsukka High Quality-White Late (NHQ-WL); Nsukka Quality Maize-Yellow Early (NQM-YE); Nsukka Quality Maize-Yellow Late (NQM-YL); Nsukka Maize-Yellow Early (NM-YE) and Nsukka Maize-Yellow Late (NM-YL); developed after three cycles of reciprocal recurrent selection, to find out the association of increasing protein and oil contents with five agronomic characters. The result showed that the 100-kernel weight and kernel density which predict yield components and days to 50 percent silking which predicts the maturity time of maize plants were independently associated with protein and oil contents in all the source varieties. This indicates that, these chemical constituents of maize can be increased or decreased and selected for without adversely affecting the five agronomic characters.
Identification of biomarkers for the management of human prostate cancer

A critical problem in the clinical management of prostate cancer is that it shows high intra- and inter-tumoural heterogeneity. As a result, accurate prediction of individual cancer behaviour is not achievable at the time of diagnosis, leading to substantial overtreatment. It remains an enigma that, in contrast to other cancers, no molecular biomarkers which define robust subtypes of prostate cancer with distinct clinical outcomes have been discovered. In the first part of this study, using data from exon microarrays, we developed a novel method that can identify transcriptional alterations within genes. The alterations might be the result of chromosomal rearrangements, such as translocations, and deletions, or of other abnormalities, such as read-through transcription and alternative transcriptional initiation sites. Using data from two independent datasets we identify several candidate alterations that are constantly correlated with the biochemical failure or that are linked to the development of metastasis. In the second part of the study we illustrate the application of an unsupervised Bayesian procedure, which identifies a subtype of the disease in five prostate cancer transcriptome datasets. Cancers assigned to this subtype (designated DESNT cancers) are characterized by low expression of a core set of 45 genes. For the four datasets with linked PSA failure data following prostatectomy, patients with DESNT cancer exhibited poor outcome relative to other patients (p = 2.65 ・ 10−5, p = 4.28 ・ 10−5, p = 2.98 ・ 10−8 and p = 1.22 ・ 10−3). The DESNT cancers are not linked with the presence of any particular class of genetic mutation, including ETS gene status. However, the methylation analysis reveals a possible role of epigenetic changes in the generation of the DESNT subtype. Our results demonstrate the existence of a novel poor prognosis category of human prostate cancer and will assist in the targeting of therapy, helping avoid treatment-associated morbidity in men with indolent disease.
Exotic Germplasm Introgression Effects on Agronomic Traits and Fiber Properties of Upland Cotton

ii Acknowledgements . iv List of Tables . viii List of Illustrations . x List of Abbreviations . xi Chapter 1 Literature Review . 1 Chapter 2 Effect of Exotic Germplasm on Agronomic Traits . 35 2.1 Abstract . 35 2.2 Materials and Methods . 37 2.2.1 Field experiment . 38 2.2.2 Data collection . 39 2.2.3 Statistical methods . 42 2.3 Results and Discussion . 48 2.3. 1 Day to first flower . 48 2.3. 2 Boll plant -1 . 50 2.3. 3 Boll size . 51 2.3. 4 Seeds boll -1 . 53 2.3. 5 Lint seed -1 . 55 2.3. 6 Seed cotton yield . 56 2.3. 7 Lint percentage . 58
Potential of sites in northern Cuba for developing an industry of the native mangrove oyster (Crassostrea rhizophorae)

Mangrove oysters ( Crassostrea rhizophorae ) were collected and raised for seven months at four sites (Punta Pargo, Jorobado, Canete, and Enfermeria) around Bahia Sagua La Grande on the north coast of Cuba, to determine which site offered the best conditions for cultivation of this commercially important species. Monthly measurements of oyster height were taken on 30 oysters randomly collected from each study site. Only oysters raised at Punta Pargo and Enfermeria reached the mean commercial size (>40 mm) within the study period; these oysters were significantly larger than oysters raised at Canete and Jorobado. No significant differences in survival between the sites were observed. Punta Pargo and Enfermeria showed the best potential for oyster farming in the Bahia de Sagua area. Despite human impact on runoff caused by damming of the adjacent river, water quality remains acceptable for oyster cultivation. With proper stock management and production of selected fast-growing oysters in hatcheries, oyster farming can become an important aquaculture industry in Cuba.
Phytochemicals and antioxidant activity in the kenaf plant ( Hibiscus cannabinus L.)

This is an Open-Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Chemical compounds from four different tissues of the kenaf plant (Hibiscus cannabinus), a valuable medicinal crop originating from Africa, were examined to determine its potential for use as a new drug material. Leaves, bark, flowers, and seeds were harvested to identify phytochemical compounds and measure antioxidant activities. Gas chromatography mass spectrometry analyses identified 22 different phytocompounds in hexane extracts of the different parts of the kenaf plant. The most abundant volatile compounds were E-phytol (32.4%), linolenic acid (47.3%), trisiloxane-1,1,1,5,5,5-hexamethyl3,3-bis[(trimethylsilyl)oxy] (16.4%), and linoleic acid (46.4%) in leaves, bark, flowers, and seeds, respectively. Ultra-high performance liquid chromatography identified the major compounds in the different parts of the kenaf plant as kaemperitrin, caffeic acid, myricetin glycoside, and p-hydroxybenzoic acid in leaves, bark, flowers, and seeds, respectively. Water extracts of flowers, leaves, and seeds exhibited the greatest DPPH radical scavenging activity and SOD activity. Our analyses suggest that water is the optimal solvent, as it extracted the greatest quantity of functional compounds with the highest levels of antioxidant activity. These results provide valuable information for the development of environmentally friendly natural products for the pharmaceutical industry.
TRANSCRIPTIONAL REGULATION OF SPECIALIZED METABOLITES IN ARABIDOPSIS THALIANA AND CATHARANTHUS ROSEUS

OF DISSERTATION TRANSCRIPTIONAL REGULATION OF SPECIALIZED METABOLITES IN ARABIDOPSIS THALIANA AND CATHARANTHUS ROSEUS For millennia humans have utilized plant specialized metabolites for health benefits, fragrances, poisons, spices, and medicine. Valued metabolites are often produced in small quantities and may command high prices. Understanding when and how the plant synthesizes these compounds is important for improving their production. Phytohormone signaling cascades, such as jasmonate (JA) activate or repress transcription factors (TF) controlling expression of metabolite biosynthetic genes. TFs regulating specialized metabolite biosynthetic genes can be manipulated to engineer plants with increased metabolite production. WRKY transcription factor are known components of both JA signaling cascades and regulation of specialized metabolism. The presence of WRKY binding sites in promoters of several terpene indole alkaloids suggested their involvement in regulating biosynthesis of these compounds. A phylogenetic analysis was used to compare Arabidopsis and Catharanthus WRKY TFs families. Gene expression analysis identified WRKY TFs induced by JA in both Arabidopsis and Catharanthus, providing candidates for future characterization. WRKY TFs suggest a possible conserved regulatory network of TFs downstream of JA signaling cascades. The origin and conservation of JA signaling in plants remain ambiguous. Identification of the first algal TIFY factor helped determine when JA signaling appeared. The charophyte, Klebsormidium flaccidum does not possess genes encoding key green-plant JA signaling components, including CORONATINE INSENSTIVE1, JASMONATE-ZIM DOMAIN, NOVEL INTERACTOR OF JAZ, and the JAZ-interacting bHLH factors, yet their orthologs are present in the moss. A molecular clock analysis dated the evolution of JA signaling evolution to during the early Ediacaran to late Cambrian periods 628 to 491 million years ago – a time corresponding to rapid diversification of animal predators. The plant Mediator complex is a core component of gene expression. Conservation of the MED25 subunit in plants, and its known involvement in JA signaling implicates this factor in regulation of specialized metabolism. MED25 is involved in anthocyanin accumulation, but how it functions remains unknown. Characterization of MED25 in Arabidopsis revealed it interacts with the transcription factor GL3 as well as the JAZ1 repressor. Importantly, the interaction of JAZ1 with MED25 reveals a new mechanism by which JAZ proteins regulate gene expression, improving our understanding of JA signaling.
Neuronal thresholds and correlations in the peripheral vestibular system during rotation discrimination

Neuronal and behavioral thresholds were measured simultaneously as trained male macaques performed a yaw rotation discrimination task in darkness. When corrected to account for variations in neuronal direction preferences, neurons in the vestibular nuclei and semicircular canal afferents had discrimination thresholds that were only two-fold smaller than behavioral thresholds. There was no significant trial-by-trial correlation between neuronal activity and perceptual decisions, despite the presence of significant pair-wise noise correlations. The lack of choice-related activity during rotation discrimination contrasts with the robust correlations observed previously between brainstem neurons and choices during translation perception. These results suggest task-dependent differences in subcortical processing of vestibular signals, as well as how signals related to perceptual decisions may propagate back to early stages of sensory processing. SIGNIFICANCE STATEMENT This is the first ever simultaneous recordings of neural and behavioral thresholds during rotation discrimination. Its importance lies on the fact that the vestibular system provides an excellent model to probe origins of perception because directional selectivity signals are similar at many levels of processing, from afferents to cortex. The findings of similar neuronal and behavioral discrimination thresholds, significant inter-neuronal correlations, but lack of correlations between behavior and neuronal activity of both afferents and central brainstem neurons are intriguing and suggest task-dependent organization of early sensory areas.