Miracle-dz/UniFAR-FTUs huggingface dataset:
Multielectrode platform for measuring oxygenation status in multicellular tumor spheroids

14 Chapter 1: Introduction to Cancer Tumor Microenvironment, Multicellular Tumor Spheroid Models, MEMS, oxygen sensing and Measurement Techniques for Interrogation of Tissue Hypoxia. 16 1.1 Tumor microenvironment. 17 1.2 Multicellular tumor spheroids models . 25 1.3 Oxygen measurement . 26 1.4 Micro-Electro-Mechanical-Systems based electrochemical sensing . 28 1.5 Measurements of oxygen inside tumor tissues and models . 29 1.6 References . 32 Chapter 2: Measuring Oxygenation Status in Multicellular Tumor Spheroid Models with a Microelectrode Array.40 2.1 Abstract . 41 2.2 Introduction . 42 2.3 Experimental . 44 4 2.4 Measurement approach . 51 2.5 Results . 55 2.6 Discussion . 58 2.7 Conclusions . 64 2.8 References . 66 Chapter 3: Modeling of oxygen concentration as a function of the rate of consumption inside multicellular tumor spheroid.80 3.1 Abstract . 81 3.2 Introduction . 81 3.3 Experimental . 83 3.4 Theory . 83 3.5 Results and Discussion . 86 3.6 Conclusions . 90 3.7 References . 92 Chapter 4: Differential pulse voltammetry versus continuous scanning.100 4.1 Abstract . 101 4.2 Introduction . 102 4.3 Experimental . 105 4.4 Theoretical considerations . 108
TOWARDS COORDINATED INTERNATIONAL SUPPORT OF CORE DATA RESOURCES FOR THE LIFE SCIENCES

On November 18-19, 2016, the Human Frontier Science Program Organization (HFSPO) hosted a meeting of senior managers of key data resources and leaders of several major funding organizations to discuss the challenges associated with sustaining biological and biomedical (i.e., life sciences) data resources and associated infrastructure. A strong consensus emerged from the group that core data resources for the life sciences should be supported through a coordinated international effort(s) that better ensure long-term sustainability and that appropriately align funding with scientific impact. Ideally, funding for such data resources should allow for access at no charge, as is presently the usual (and preferred) mechanism. Below, the rationale for this vision is described, and some important considerations for developing a new international funding model to support core data resources for the life sciences are presented.
Complete chloroplast genome sequences of two species of Chloris grass, Chloris truncata Sw. and Chloris virgata R.Br

Abstract Chloris truncata (windmill grass) and Chloris virgata (feathertop Rhodes grass) are both weedy grass species that have developed resistance to glyphosate in Australia. This paper describes the complete chloroplast genomes of these two species generated by high throughput shotgun sequencing. The chloroplast genome of C. truncata is 135,584 bp and C. virgata is 134,561 bp; both have a GC content of 38%. The gene content and order followed the conserved pattern observed across the subfamily Chloridoideae.
Phytochemical characteristics and free radical scavenging activity of ethanolic extract of Termitomyces microcarpus R. Heim

Human beings like most organisms have defence and repair systems to fight against oxidative stress but at times these become inadequate to provide complete protection and here lies the need for antioxidant supplements. The present article focuses on the antioxidative activity of ethanolic extract of the mushroom Termitomyces microcarpus. A series of in-vitro assays were conducted with chelation of 50 % ferrous ion with only 0.14 mg/ml concentration, reducing power having 50% inhibition capacity at 1.65 mg/ml. Whereas DPPH and SOD assay gave EC50 values at 1.98 mg/ml and 0.295 mg/ml concentration respectively. Even presence of phytochemicals were recorded in the order of total phenol> total flavonoids> ascorbic acid> β carotene> lycopene. Hence, it can be suggested that ethanolic extract of Termitomyces microcarpus can be used as a good medicinal entity.
Celomic cells of the marine fireworm Hermodice carunculata (Annelida, Polychaeta)

Department of Life Sciences, University of Modena and Reggio Emilia, Modena, ItalyWe have examined the morphological and functional characteristics of the celomic cells in the marine fireworm Hermodice carunculata. The cells differ in morphology, in relation to the presence of cytoplasmic granules, adhere to the glass, phagocytize zymosan A particles and contain ACTH-like molecules. We suggest the presence of only one cell type in the worm celomic fluid, i.e., the immunocyte described in other invertebrates.
Studies on İdentification of the Drought Tolerant Genes of Wheat

Bread wheat (Triticum aestivum L .), is known as the base food staple resource. With increasing the human population, new methods and approaches are needed to gain wheat cultivars with advanced characteristics. Nowadays, the problem is to produce high quality and yielding cultivars. Breeding of tolerant cultivars against biotic and abiotic stresses is desired.Drought stress, appears as water loss from the plant during the definite time, which is higher than the absorbed water by plant from the environment. Drought stress is expected to increase as the most important stress factor in the future due to the climate changes which is being evident from now. Lower cell growth would lead to the deficit in cell wall synthesis and thereby, to the unexpanded leaves and lowering the photosynthetic assimilates. Under drought stress, seed germination potential declines, and chlorophyll and protein synthesis, photosynthesis, and respiration is negatively affected.In winter wheat, resistance against drought stress is controlled by complex morphologic and physiologic mechanisms. In the recent century, despite of using classic breeding methods and gaining the high quality yielding cultivars, desirable tolerance towards environmental abiotic and biotic stresses mainly disease and pests, has not been achieved. In this study, some mechanisms of drought tolerance in wheat were considered.
CHANGED C-REACTIVE PROTEIN AND SERUM AMYLOID-A LEVELS IN BLOOD SERUM, ADIPOSE TISSUE AND LIVER OF OBESITY INDUCED RATS

C-reactive protein (CRP) and serum amyloid A (SAA) are acute-phase proteins. These proteins are synthesized predominantly by liver during the acute-phase of inflammation. Recent studies have demonstrated that CRP and SAA are synthesized and secreted by adipose tissue as well, and increase in the mass of adipose tissue during obesity leads to elevated CRP and SAA levels in blood serum. A model of animal obesity was created using high-fat diet. Sixty, eight-weeks-old male Wistar rats were randomly divided into two groups – 1) control group fed with standard rodent food and 2) experimental group fed with a high-fat diet. They were subjected on these regiments for fourteen weeks. Blood serum, liver and adipose tissue specimens were obtained from each animal at the end of the experimental period. The CRP and SAA concentrations were quantified by ELISA method. Higher blood CRP and SAA concentration and lower liver CRP and SAA levels were found for the group of obese animals compared to the control group. The concentration of SAA in adipose tissue was significantly higher in obese compared with the lean animals. No significant difference was found for the levels of CRP in adipose tissues obtained from the two experimental groups. No correlations exist between CRP and SAA levels in blood circulation, liver and adipose tissue. The changes in the
Utilization of agro-food industry by-products in the finishing of culled dairy cows

This study evaluated the effect of finishing strategies with different agro-industrial byproducts on meat quality of culled dairy cows. Culled dairy cows (n = 32) were kept individually and allotted to one of four treatments. A control group (C) was slaughtered immediately after culling-off. All others were subjected to a finishing period of 12 weeks. A forage group was fed with ad lib corn silage (F). Additionally there were a high-energy group (6 kg/day of cassava pulp + ad lib corn silage; F+) and a low-energy group (6 kg/day of crude rice bran + ad lib corn silage; F-) both based on by-products. The longissimus dorsi muscle was excised 24 h post-mortem and stored at –20 °C prior to analysis. There were no significant effects of finishing treatment on meat color of all groups. Drip, thawing and cooking losses were not statistically different between groups. The meat of C had significantly higher percentage of protein and tended to have more moisture than the other groups. Meat of the group F+ had the highest contents of fat and cholesterol. There was no significant effect by treatment on Warner-Bratzler shear force although shear force tended to be lowest with F+. The meat’s contents of soluble and insoluble collagen were not significantly different among treatment groups.
Zero to one: normal derived human ER+ cells in culture-proliferating

Cell culture technology is used to model structural and functional properties of human organs under normal and pathological conditions “in a dish”. The most obvious reason to culture human breast-derived cells is our fundamental desire to understand and ultimately treat breast cancer. Highly reproducible serum-free formulations for long-term propagation of normal human breast epithelial cells have existed for more than three decades and have served to complement the insight gained from a vast number of established breast cancer cell lines. The unspoken dichotomy in the experimental approach, however, has lied in the puzzling fact that normal-derived cells show a more myoepithelial expression profile, while breast cancer cells show more of a luminal profile making these difficult to compare experimentally. Moreover, normal estrogen receptor positive (ER+) luminal cells, thought to be equivalents to the most frequent form of human breast cancer, the ER+ subtype, completely fail to grow under standard culture conditions. One might choose to ignore this fact since breast homeostasis relies on a stem cell hierarchy and stem cells reside in the myoepithelial compartment which, if given the right conditions, can differentiate into ER+ luminal cells. The problem with this is that myoepithelial cells in culture, for unknown reasons, fail to behave like myoepithelial cells in vivo. This review summarizes some of the progress that has been made in the field with regard to the ER+ luminal breast epithelial lineage, especially within a human context, and its relevance to human breast cancer.
Comparative account of energy reserves in four co-occurring mosquito species in Kolkata, India (Diptera: Culicidae)

Abstract Energy reserves in mosquitoes are an indicator of fitness, linking larval effort in resource acquisition with adult survival and fecundity. In other words, life history strategies and disease transmission potential can be related to the amount of energy reserves. The energy reserves of four mosquitoes – Aedes aegypti, Aedes albopictus, Armigeres subalbatus and Culex quinquefasciatus (Diptera: Culicidae) – were calculated to justify species-specific differences in their life history strategies. Following repeated sampling of pupae from the respective larval habitats, the glycogen, sugar and lipid contents of individual mosquitoes were assessed and corroborated with pupal weight and adult wing length. Discriminant function analysis was used to acquire an initial reflection of the differences of the parameters among the sex and species of the mosquitoes considered in the study. Using logistic regression and ANOVA, the effects of species and sex as contributors to variations in energy reserves could be established. The results indicated that for all the mosquitoes, sex-specific differences were prominent with reference to the energy reserves. Species-specific differences in energy reserves reflect differences in resource acquisition and assimilation in the tissues, and thus the differences in the life history strategies of these four species.
Gene nucleotide composition accurately predicts expression and is linked to topological chromatin domains

Gene expression is orchestrated by distinct regulatory regions (e.g. promoters, enhancers, UTRs) to ensure a wide variety of cell types and functions. A challenge is to identify which regulatory regions are active, what are their associated features and how they work together in each cell type. Several approaches have tackled this problem by modeling gene expression based on epigenetic marks (e.g. ChIP-seq, methylation, DNase hypersensitivity), with the ultimate goal of identifying driving genomic regions and mutations that are clinically relevant in particular in precision medicine. However, these models rely on experimental data, which are limited to specific samples (even often to cell lines) and cannot be generated for all regulators and all patients. In addition, we show here that, although these approaches are accurate in predicting gene expression, their biological interpretation can be misleading. Finally these methods are not designed to capture potential regulation instructions present at the sequence level, before the binding of regulators or the opening of the chromatin. We develop here a method for predicting mRNA levels based solely on sequence features collected from distinct regulatory regions, which is as accurate as methods based on experimental data. Our approach confirms the importance of nucleotide composition in predicting gene expression and ranks regulatory regions according to their contribution. It also unveils strong influence of gene body sequence, in particular introns. We further provide evidence that the contribution of nucleotide content can be linked to co-regulations associated with genome 3D architecture and to associations of genes within topologically associated domains.
Ethanolic Extract of Bauhinia forficata: Metabolic Effects in Diabetic and Normoglycemic Rats

Aim: Bauhinia forficata (BF) is used in folk medicine to reduce glycemia in diabetes. We evaluated the glucose hepatic metabolism (ex vivo) and the hypoglycemic effects (in vivo) of an ethanolic extract of BF leaves (BFEE) in normoglycemic and streptozotocin (STZ)-induced diabetic rats. Methods: The livers of rats were perfused with BFEE (40 mg L-1) and glucose metabolism under fed or fasting conditions (l-glutamine as the substrate) was analyzed. Additionally, rats were divided into 4 groups for oral treatment: vehicle-treated nondiabetic rats; BFEE-treated (300 mg kg-1) non-diabetic rats; vehicletreated diabetic rats; and BFEE-treated (300 mg kg-1) diabetic rats. Glycemia was measured acutely and after 7 days of treatment; plasma biochemistry, hepatic glycogen contents, and hepatic and pancreatic histology were evaluated after this period. Results: Liver infusion of BFEE in fed and fasted diabetic rats reduced glucose and lactate production, respectively; however, BFEE did not affect glycemia or hepatic glycogen levels. Plasma transaminases increased in diabetic animals receiving the extract. The STZ model reduced by nearly half the number of Langerhans’ islets in comparison to non-diabetic animals, however no pancreatic difference was observed between diabetic animals treated with extract and diabetic animals treated with vehicle. Conclusions: BFEE interferes with hepatic glycolysis, glucogenesis, and lactate production from l-glutamine. Thus the BFEE effects depend of the alimentary state. However, it did not suppress hyperglycemia in diabetic rats.
Quantitative Changes of the Carboxylesterase Associated with Pyrethroid Susceptibility in Spodoptera litura (Lepidoptera: Noctuidae)

Carboxylesterase-mediated insecticide resistance was studied in Spodoptera litura Fab with three different populations from Varanasi, Delhi and Sonepat. The level of susceptibility to pyrethroid insecticides (cypermethrin and bifenthrin), activity of carboxylesterase (CarE) and amino acid substitutions in esterase gene of each population were investigated. Insecticide bioassay revealed that Sonepat and Delhi populations of S. litura were 2.2- and 2.1-fold resistant to cypermethrin and bifenthrin, respectively. Delhi and Sonepat populations had elevated activity of enzyme level of 26.47±0.21 and 28.02±0.05, respectively. The Varanasi population (10.09 ± 0.10 μmol/min/mg of protein) exhibited lowest CarE activity. The CarE gene of 500 bp fragment that encodes 167 amino acid residues was characterised in all populations. Cluster analysis of gene sequences revealed that all three populations were 92 to 95% identity and were closely related to other Spodoptera spp. Among the 167 amino acid residues, 27 were identical in all Spodoptera species and seven substitutions were observed. Sequence alignment confirmed no substitution at conserved position and one semiconserved substitution. In the characterised region, the substitution W224S which is responsible for CarE activity reduction in insecticide resistant Culex pipiens was not observed in any of the Spodoptera populations. A strong positive relation (r = 0.99) was observed between the CarE activity and determined LC50. Thus, elevated CarE activity in Delhi and Sonepat field populations was attributed to pyrethroid resistance. Metabolic detoxification mainly appears to be due to overproduction of CarE enzyme in respective populations and not because of amino acid residue changes.
The effect of fan use and folic acid supplementation on thermal and cardiovascular strain in healthy aged humans during heat exposure

Attenuated heat loss and altered cardiovascular adjustments during heat stress are considered important contributing factors to the increased prevalence of death in aged individuals during heat waves. Interventions aimed at reducing thermal and cardiovascular strain during heat stress in the aged are lacking. We therefore examined if fan use (by improving sweat evaporation) or folic acid supplementation (by improving cutaneous vasodilation) can mitigate thermal and cardiovascular strain during heat exposure, as well as modify the limit of thermal compensability in healthy aged humans. Six healthy older individuals (69 ± 3 y, 166 ± 12 cm, 72 ± 16 kg, 2 males/4 females) rested in a thermal chamber at a temperature of 42°C and a relative humidity initially maintained at 30%. After a 30 min baseline period, relative humidity was increased in 2% steps every 5 min until a relative humidity of 70% was reached (100 min). The protocol was performed with no intervention (CON), with a fan that provided ~4 m/s of air velocity (FAN), and following 6 weeks of folic acid supplementation (FOLIC). Esophageal (Tes) and mean skin (Tsk) temperatures, local forearm cutaneous vascular conductance (laser‐Doppler, CVC), forearm vascular conductance (Doppler ultrasound, FVC), local sweat rate (ventilated capsule), heart rate and blood pressure were measured throughout. At 70% relative humidity, fan use and folic acid supplementation both increased CVC relative to control (CON: 1.34 ± 0.24 vs. FAN: 1.95 ± 0.39 vs. FOLIC: 1.81 ± 0.35 units/mmHg, P≤0.05). However, this did not translate into different FVC responses (CON: 4.86 ± 1.95 vs. FAN: 5.08 ± 1.91 vs. FOLIC: 4.41 ± 1.78 mL/min/mmHg, P>0.05). Fan use also increased local sweat rate (0.84 ± 0.27 mg/min/cm2) relative to CON (0.60 ± 0.26 mg/min/cm2, P≤0.05), whereas FOLIC had no effect (0.62 ± 0.21 mg/min/cm2, P=0.64). Relative to CON (Tes: 37.62 ± 0.29°C, Tsk: 38.41 ± 0.25°C), esophageal and mean skin temperatures were greater during FAN (Tes: 37.94 ± 0.63°C, Tsk: 38.97 ± 0.55°C, P≤0.05) but not FOLIC (Tes: 37.58 ± 0.21°C, Tsk: 38.28 ± 0.25°C, P>0.05). In contrast, heart rate and blood pressure were similar during all conditions (both P>0.05). The critical humidity at which an inflection in esophageal temperature was observed did not differ between conditions (CON: 63 ± 2 vs. FAN: 64 ± 5 vs. FOLIC: 63 ± 4%, P=0.64). Under the conditions employed, fan use results in greater esophageal and mean skin temperatures during extreme heat exposure in healthy aged individuals while folic acid supplementation has no effect. Furthermore, neither intervention reduced cardiovascular strain nor did they modify the limit of thermal compensability.
Mob stocking effects on herbage nutritive value, herbage accumulation, and plant species composition

Mob stocking is a variation of rotational stocking known for restricting a large number of animals to a small area before being moved to new grass after a few hours. This method allows a long (90-day) recovery period but was hypothesized to diminish the nutritional value of herbage relative to continuous and rotational stocking with lesser stocking density at similar stocking rates. This thesis summarizes two studies conducted in Blacksburg and Raphine, and in Steeles Tavern, VA, respectively, at a single beef cattle stocking rate of 12 animal unit months per hectare live body weight. The objectives were to: (1) compare the yield and nutritional value of herbage in pastures managed with three stocking methods, termed “mob”, “rotational”, and “continuous” stocking; (2) compare the abundance of seeded clover species among the stocking methods; and (3) estimate the nutritional value of herbage that is consumed by beef cattle during ʻmobʼ stocking using extrusa sampled from esophageally-cannulated animals. Analysis of standing herbage during two years produced several important findings. Although standing herbage mass was significantly greater in mob stocked pastures at Blacksburg and Raphine, aboveground net primary productivity in 2014 did not differ significantly among mob, rotational, and continuous stocking at any of the project locations. Herbage nutritive value did not differ significantly among stocking methods over two years at Blacksburg and Raphine; however, herbage from mob stocked pastures at Steeles Tavern contained significantly greater concentrations of crude protein in September and October relative to herbage from continuousand rotationally-stocked pastures at those times. Differences in herbage mass likely contributed
Spatial ecology of the tansy beetle (Chrysolina graminis)

In Britain, the tansy beetle Chrysolina graminis is restricted to the banks of the River Ouse around York where it is monophagous on tansy Tanacetum vulgare foliage. After suffering a major decline in England over the last century, effort is now being directed towards the species' conservation. This research aims to infonn these conservation measures by investigating the beetles' spatial ecology. T. vulgare grows in clusters of patches along the Ouse. Beetles are more often found on larger patches that are less isolated from other occupied patches but patch quality apparently plays no role in determining their local distribution. Many regions of bank with seemingly suitable tansy networks were discovered and successful translocations to some of these suggest that this can be an important conservation tool. Beetle movement behaviour was examined at small scales. No abilities to detect tansy from a distance were evident in either adults or larvae, but both reduce their movement rates when on tansy and speed up when in the inter-patch matrix. Modelling of adult movements yielded accurate predictions of daily movement distances and inter-patch movement rates on local landscape scales and revealed the important role of patch-edge boundaries in restricting movements. Using multi-patch mark-recapture, dispersal was shown to be female-biased, spatially-localised and directed towards large patches. A dispersal model was developed and fitted to these data, which revealed the significance of the rare longdistance events and showed that beetle dispersal is not seasonal, but is driven by changes in the landscape structure induced by tansy patch growth, flooding and the mowing of patches. Microsatellite and allozyme markers were developed for C. gramlnlS. Using microsatellites, significant genetic structure and isolation-by-distance relationships were uncovered. Populations appeared to diverge when further apart than the beetle's dispersal range and there was evidence that the river is a barrier to dispersal.