Collaborative development of the Arrowsmith two node search interface designed for laboratory investigators

Arrowsmith is a unique computer-assisted strategy designed to assist investigators in detecting biologically-relevant connections between two disparate sets of articles in Medline. This paper describes how an inter-institutional consortium of neuroscientists used the UIC Arrowsmith web interface http://arrowsmith.psych.uic.edu in their daily work and guided the development, refinement and expansion of the system into a suite of tools intended for use by the wider scientific community.     

Effects of valproic acid, a histone deacetylase inhibitor, on improvement of locomotor function in rat spinal cord injury based on epigenetic science

Background: The primary phase of traumatic spinal cord injury (SCI) starts by a complex local inflammatory reaction such as secretion of pro-inflammatory cytokines from microglia and injured cells that substantially contribute to exacerbating pathogenic events in secondary phase. Valproic acid (VPA) is a histone deacetylase inhibitor. Acetylation of histones is critical to cellular inflammatory and repair processes. Methods: In this study, rats were randomly assigned to five experimental groups (laminectomy, untreated, and three VPA-treated groups). For SCI, severe contusion was used. In treated groups, VPA was administered intraperitoneally at doses of 100, 200 and 400 mg/kg daily three hours after injury for 7 days. To compare locomotor improvement among experimental groups, behavioral assessments were performed by the Basso, Beattie and Bresnahan (BBB) rating scale. The expression of neurotrophins was evaluated by RT-PCR and real-time PCR. Results: VPA administration increased regional brain-derived neurotrophic factor and glial cell-derived neurotrophic factor mRNA levels. Local inflammation and the expression of the lysosomal marker ED1 by activated macrophages/microglial cells were reduced by VPA and immunoreactivity of acetylated histone and microtubule-associated protein were increased. Conclusion: The results showed a reduction in the development of secondary damage in rat spinal cord trauma with an improvement in the open field test (BBB scale) with rapid recovery.Key Words: Inflammation, Epigenetics, Valproic acid (VPA)     

Effect of Delayed Icing on the Microbiological,Chemical, and Sensory Properties of Caspian Sea Golden Grey Mullet (Liza aurata)

Research has shown that fresh fish is an extremely perishable food as compared to other food commodities. In this study, quality deterioration during storage of golden grey mullet (GGM) iced for 0, 6, and 12 h after landing was monitored. Microbiological indices (total viable count, TVC; psychrophilic counts, PTC; lactic acid bacteria, LAB; and Enterobacteriaceae counts, EBC), chemical parameters (pH; total volatile basic nitrogen, TVB-N; peroxide value, PV; thiobarbituric acid, TBA; and free fatty acids, FFA) values increased over the preicing duration. Delayed icing did not lead to significant increases (p > 0.05) in TVC, PTC, LAB, and EBC throughout the period of storage. All chemical indices increased during storage (p < 0.05). This study showed that sensorial analysis of GGM correlated well with microbiological analysis. Results of this study based on the microbiological and raw fish sensorial data indicated that the shelf life of GGM stored in ice immediately after catch was approximately 10–11 days, while the 6- and 12-h delays in icing shortened the shelf life to approximately 6–7 and 2–3 days, respectively.     

Comparative study of dietary soy phytoestrogens genistein and equol effects on growth parameters and ovarian development in farmed female beluga sturgeon,Huso huso

Oocyte maturation in fish is a hormonally regulated process. In the light of long-term oocyte maturation in beluga, the aim of this research was to study the estrogenic effects of different concentrations of soy dietary genistein (GE) and equol (EQ) on the growth performance and ovary development in farmed female Huso huso. Fish were fed with concentrations 0 (control), 0.2, 0.4, 0.8 and 1.6 g of EQ and GE per kg of isoproteic (CP 45 %) and isoenergetic (19.5 MJ/kg) diets during a year. Blood samples and ovary biopsies were collected from each fish seasonally. The main results of the present experimentation are that growth performance was not affected significantly both in GE and EQ (P > 0.05). EQ at concentration 0.4 g/kg had more estrogenic effects than other concentrations of EQ and GE in beluga so that 64 % of fish were matured sexually. Some reproductive indices such as oocyte diameter, testosterone (T) and 17β-estradiol (E₂) increased significantly at EQ 0.4 g/kg at the end of experiment (P < 0.05), while 17α-hydroxy progesterone level (17α-OHP) showed no significant changes at all concentrations. Biochemical indices such as calcium, phosphorous and cholesterol increased at GE concentrations, but decreased at EQ concentrations similarly at the end of experiment. There was a negative relationship between plasma phosphorous and alkaline phosphatase enzyme levels. Based on results, EQ at concentration 0.4 g/kg improved oocyte development more than the other concentrations of GE and EQ, and therefore, it can be used as an additive to diets for inducing ovary development in this species.     

Responses of Anise Medicinal Plant Species in Terms of Essential Oil Contents and Concentrations to Different Planting Times and Various Nitrogen Fertilizer Sources under Semi-Arid Climatic Conditions

Essential oil content and concentration of anise plant planted in different times under various sources of nitrogen was evaluated in this study. The experiment was conducted in a split plot based on a randomized complete block (RCB) design (different sources of fertilizer as the main plot and planting dates as subplots) with three replications in the Agricultural Research Station at Ferdowsi University of Mashhad in 2015–2016. Treatments included: planting times (sub plot factor): (27^th of October, 27^th of November, 1^st of March, 10^th of March, and 8^th of April) and nutritional sources (main plot factor): (Cow Manure, Chemical Fertilizer, and mixture of Cow Manure + Chemical Fertilizer). The results showed that the anise plant essential oil qualitative characteristics were significantly influenced by treatments. Also, interaction between the fertilizer treatments and planting dates on the essential oil content and concentration of the plants were significant. The highest percentage of plant essential oil (3.71%) was found in the cow manure treatment, and the lowest percentage of essential oil (2.95%) was obtained in the chemical fertilizer. The highest essential oil yield (16.09 kg/ha) was found in the mixed treatment of the cow manure and the chemical fertilizer, and the chemical fertilizer treatment had the lowest rate of essential oil yield (11.41 kg/ha). The highest percentages of the plant oil (14.31%) and the plant oil yield (77.46 kg/ha) were found in the integrated treatment of the cow manure and the chemical fertilizers. The lowest amounts of the plant oil (12.19%) and the plant oil yield (41.28 kg/ha) were found in the chemical fertilizer. According to the percentage and the yield of the essential oil, the best planting time and fertilizer treatment was the one on 10th of March and using integrated cow manure and chemical fertilizer.     

Polycyclic Aromatic Hydrocarbons in Seawater, Sediment, and Rock Oyster Saccostrea cucullata from the Northern Part of the Persian Gulf (Bushehr Province)

The concentration of polycyclic aromatic hydrocarbons (PAHs) was determined in seawater, sediment, and Rock oyster Saccostrea cucullata collected from four sampling sites in the inter-tidal areas of Bushehr province. The total concentrations of 14 PAHs varied from 1.5 to 3.6 ng/L in seawater, 41.7 to 227.5 ng/g dry weight in surface sediment, and 126 to 226.1 ng/g dry weight in oyster tissue. In comparing PAH concentrations among the three matrices in Bushehr province, data showed that the pattern of individual PAHs in seawater, oyster, and sediment were different. The oysters tended to accumulate the lower molecular weight and the more water-soluble PAHs. Sediment samples were distinguished from the sea water and oyster samples by the presence of high molecular weight PAHs, especially six-ring PAHs. Three- and four-ring PAHs were the most abundant compounds among the 14 PAHs investigated in surface seawater, sediment, and oyster samples. As expected, differences in octanol/water partition coefficient among individual PAHs and the greater persistence of the higher molecular weight PAHs contributed to the accumulation patterns in oyster and sediment. The results of the study suggested that the main sources of PAHs in the seawater and sediment in the region were mixed pyrolitic and petrogenic inputs.     

Pulp and paper from kenaf bast fibers

Samples of kenaf (Hibiscus cannabinus) grown in Malaysia were examined to determine the kraft pulp and papermaking properties of their bast (or bark) fibers. Using kraft pulping process showed that bast fibers were relatively easy to cook resulting good pulp yields in the range of 45–51%. The bast pulp produced sheets with great density, tear index and dry zero-span breaking length. Kenaf bast fiber is considered promising for production of high-grade printing, writing and specialty papers.     

Common carotid intima-media thickness in patients with late rheumatoid arthritis; what is the role of gender?

This study aimed to evaluate color Doppler sonographic findings in carotid arteries in RA patients under pharmacological treatments and to compare them with normal population. Forty nine patients with late RA and 48 healthy age and sex-matched controls were recruited. The two groups were matched for other known risk factors of atherosclerosis including serum lipid abnormalities, smoking status, diabetes mellitus and hypertension. High resolution B-mode color Doppler ultrasound with a 7 MHZ transducer was used for measuring the Common Carotid Intima-Medial Thickness (CCIMT) in both sides in all subjects. Presence of atherosclerotic plaque was also investigated. The mean left and maximum CCIMT was significantly higher in the case group (0.72 vs. 0.62 mm for the left artery; p < 0.01; 0.72 vs. 0.64 mm for the maximum reading; p = 0.01). No atherosclerotic plaque was found in common carotid arteries. There were 3 (6.1), 7 (14.3) and 9 (18.4%) plaques in left internal carotid artery, right carotid bulb and left carotid bulb in the case group, respectively with no atherosclerotic plaques in the controls (p = 0.24, 0.01 and < 0.001, respectively). Comparing the findings by gender in the case group with the controls, the mentioned significant differences were only between the male patients and the controls. The process of atherosclerosis in RA patients is similar to that in normal population. However, it is apparently accelerated and more advanced in these patients.