MSI-CIEC: MSI Cyberinfrastructure Empowerment Coalition and the TeraGrid

Paper written as a collaboration of the following institutions and presented at the 2006 TeraGrid Conference, Indianapolis, IN June 12-16: 1. University of Houston Downtown 2. NAFEO: National Association for Equal Opportunity in Higher Education 3. SDSC: San Diego Supercomputer Center 4. Indiana University, Computer Science Department 5. AIHEC: The American Indiana Highter Education Consortium 6. HACU: Hispanic Association of Colleges and Universitie

Network structure and rapid HIV transmission among people who inject drugs: A simulation-based analysis

As HIV incidence among people who inject drugs grows in the context of an escalating drug overdose epidemic in North America, investigating how network structure may affect vulnerability to rapid HIV transmission is necessary for preventing outbreaks. We compared the characteristics of the observed contact tracing network from the 2015 outbreak in rural Indiana with 1000 networks generated by an agent-based network model with approximately the same number of individuals (n = 420) and ties between them (n = 913). We introduced an initial HIV infection into the simulated networks and compared the subsequent epidemic behavior (e.g., cumulative HIV infections over 5 years). The model was able to produce networks with largely comparable characteristics and total numbers of incident HIV infections. Although the model was unable to produce networks with comparable cohesiveness (where the observed network had a transitivity value 35.7 standard deviations from the mean of the simulated networks), the structural variability of the simulated networks allowed for investigation into their potential facilitation of HIV transmission. These findings emphasize the need for continued development of injection network simulation studies in tandem with empirical data collection to further investigate how network characteristics played a role in this and future outbreaks

The effect of seasoning with herbs on the nutritional, safety and sensory properties of reduced-sodium fermented Cobrançosa cv. table olives

This study aimed at evaluating the effectiveness of seasoning Cobrancosa table olives in a brine with aromatic ingredients, in order to mask the bitter taste given by KCl when added to reduced-sodium fermentation brines. Olives were fermented in two different salt combinations: Brine A, containing 8% NaCl and, Brine B, a reduced-sodium brine, containing 4% NaCl + 4% KCl. After the fermentation the olives were immersed in seasoning brines with NaCl (2%) and the aromatic herbs (thyme, oregano and calamintha), garlic and lemon. At the end of the fermentation and two weeks after seasoning, the physicochemical, nutritional, organoleptic, and microbiological parameters, were determined. The olives fermented in the reduced-sodium brines had half the sodium concentration, higher potassium and calcium content, a lower caloric level, but were considered, by a sensorial panel, more bitter than olives fermented in NaCl brine. Seasoned table olives, previously fermented in Brine A and Brine B, had no significant differences in the amounts of protein (1.23% or 1.11%), carbohydrates (1.0% or 0.66%), fat (20.0% or 20.5%) and dietary fiber (3.4% or 3.6%). Regarding mineral contents, the sodium-reduced fermented olives, presented one third of sodium, seven times more potassium and three times more calcium than the traditional olives fermented in 8% NaCl. Additionally, according to the panelists' evaluation, seasoning the olives fermented in 4% NaCl + 4% KCl, resulted in a decrease in bitterness and an improvement in the overall evaluation and flavor. Escherichia coli and Salmonella were not found in the olives produced.info:eu-repo/semantics/publishedVersio

Disrupting Hypoxia-Induced Bicarbonate Transport Acidifies Tumor Cells and Suppresses Tumor Growth

Tumor hypoxia is associated clinically with therapeutic resistance and poor patient outcomes. One feature of tumor hypoxia is activated expression of carbonic anhydrase IX (CA9), a regulator of pH and tumor growth. In this study, we investigated the hypothesis that impeding the reuptake of bicarbonate produced extracellularly by CA9 could exacerbate the intracellular acidity produced by hypoxic conditions, perhaps compromising cell growth and viability as a result. In 8 of 10 cancer cell lines, we found that hypoxia induced the expression of at least one bicarbonate transporter. The most robust and frequent inductions were of the sodium-driven bicarbonate transporters SLC4A4 and SLC4A9, which rely upon both HIF1α and HIF2α activity for their expression. In cancer cell spheroids, SLC4A4 or SLC4A9 disruption by either genetic or pharmaceutical approaches acidified intracellular pH and reduced cell growth. Furthermore, treatment of spheroids with S0859, a small-molecule inhibitor of sodium-driven bicarbonate transporters, increased apoptosis in the cell lines tested. Finally, RNAi-mediated attenuation of SLC4A9 increased apoptosis in MDA-MB-231 breast cancer spheroids and dramatically reduced growth of MDA-MB-231 breast tumors or U87 gliomas in murine xenografts. Our findings suggest that disrupting pH homeostasis by blocking bicarbonate import might broadly relieve the common resistance of hypoxic tumors to anticancer therapy

Cellular location and activity of Escherichia coli RecG proteins shed light on the function of its structurally unresolved C-terminus

RecG is a DNA translocase encoded by most species of bacteria. The Escherichia coli protein targets branched DNA substrates and drives the unwinding and rewinding of DNA strands. Its ability to remodel replication forks and to genetically interact with PriA protein have led to the idea that it plays an important role in securing faithful genome duplication. Here we report that RecG co-localises with sites of DNA replication and identify conserved arginine and tryptophan residues near its C-terminus that are needed for this localisation. We establish that the extreme C-terminus, which is not resolved in the crystal structure, is vital for DNA unwinding but not for DNA binding. Substituting an alanine for a highly conserved tyrosine near the very end results in a substantial reduction in the ability to unwind replication fork and Holliday junction structures but has no effect on substrate affinity. Deleting or substituting the terminal alanine causes an even greater reduction in unwinding activity, which is somewhat surprising as this residue is not uniformly present in closely related RecG proteins. More significantly, the extreme C-terminal mutations have little effect on localisation. Mutations that do prevent localisation result in only a slight reduction in the capacity for DNA repair. © 2014 The Author(s)

Pomegranate peel as a natural antioxidant enhanced reproductive performance and milk yield of female rabbits

This study was designed to investigate the effects of dietary pomegranate peel (PP; 9.61% crude protein and 13.1% crude fibre) on reproductive performance and milk yield of heat-stressed rabbit does. Forty-eight V-line rabbit does with average initial live body weight of 3.59±0.11 kg (2nd parity; 9 mo old) were divided into 4 treatment  roups (12 does per group). The first group was fed diet free of PP. The second, third and fourth groups were fed diets containing 0.75, 1.5 and 3.0% PP, respectively, included in substitution of clover hay from the basal diet. Feed of the 4 groups was free of added antioxidants. The studied traits were: kindling rate, gestation period, litter size, litter weight, kit weight at both birth and weaning (28 d of lactation) for the last 3 parameters, pre-weaning mortality and milk yield. Range of temperatures and relative humidity during the experimental period in the rabbitry varied between 27.5-33.5°C and 64-76%, respectively. The inclusion of PP quadratically affected litter size at birth (P<0.001) and weaning (P<0.01), as well as milk yield (P<0.001). However, it tended to reduce the kit milk intake in most lactation periods (P=0.078), leading to a linear reduction in individual kit weight at weaning (P=0.060). In conclusion, supplementations of PP in the diet of does during summer season in Egypt can improve their productivity.Zeweil, H.; Elgindy, Y. (2016). Pomegranate peel as a natural antioxidant enhanced reproductive performance and milk yield of female rabbits. World Rabbit Science. 24(3):207-212. doi:10.4995/wrs.2016.4025.SWORD207212243Abdel-Azeem A.S., Abdel-Azim A.M., Darwish A.A., Omar E.M. 2007. Litter traits in four pure breeds of rabbits and their crosses under prevailing environmental conditions of Egypt. In Proc.: 5th International Conference on Rabbit Production in Hot Climate, 4-7 December, Hurghada, Egypt. 39-51.Al-Sobayil K.A., Al-Homidan A.H., Khalil M.K., Mehaia M.A. 2005. Heritabilities and genetic analysis of milk yield and components in crossing project of Saudi rabbits with Spanish V-line. Livest. Res. Rural Dev., 17: 1-13.AOAC. 2000. Official Methods of Analysis. 17th ed. Association of Official Analytical Chemists. Washington DC.Ayyat M.S., Marai I.F.M., El-Sayiad Gh.A. 1995. Genetic and nongenetic factors affecting milk production and pre-weaning litter traits of New Zealand White does under Egyptian conditions. World Rabbit Sci., 3: 119-124.Debier, C., Pottier, J., Goffe, C., & Larondelle, Y. (2005). Present knowledge and unexpected behaviours of vitamins A and E in colostrum and milk. Livestock Production Science, 98(1-2), 135-147. doi:10.1016/j.livprodsci.2005.10.008Di Meo C., Gazaneo M., Racca C., Bovera F., Piccolo G., Nizza A. 2004. Effect of Birth Weight and Litter Size on Productive Performance of Rabbits. Asian-Aust. J. Anim. Sci., 17: 1158- 1161.El-Fouly H.A., Boady A.M.A., Radwan A.A., Kamar G.A. R. 1977. Seasonal variation of some reproductive traits of Bouscat and Giza White rabbits. Egypt. J. Anim. Prod., 17: 9-19.Fadila, M.E., Hekal A.M. 2015. Effect of early heat exposure on some physiological and histological changes in the liver and kidney of rabbits before weaning. Egypt. Poult. Sci., 35: 149-Gonzalez R.R., Kluger M.J., Hardy J.D. 1971. Partitional calorimetery of the New Zealand White rabbit temperature 5-35°C. J. App. Physiol. 31: 728-734.Hahn J., Gabler G. 1971. Fertility in rabbit does with reference to individual arid seasonal variations. Zuchtungskunde, 4: 456.Liebler D. 1992. Peroxyl radical trapping reactions of α-tocopherol in biomimetic systems. In: Packer L., Fuchs J. (ed). Vitamin E in Health and Disease Marcel Dekker, New York, USA, 85-97.Marai I.F.M., Alnaimy A.A., Habeeb M. 1994. Thermoregulation in rabbits. Rabbits production in hot climates. In Proc.: 1st International Conf. 6-8 September. Cairo, Egypt.NRC. 1977. National Research Council: Nutrient Requirements of Rabbits. 2nd Revised Edition, National Academy of Sci., Washington, DC. USA.Schwarz, K. R. L., Pires, P. R. L., Adona, P. R., Câmara de Bem, T. H., & Leal, C. L. V. (2008). Influence of nitric oxide during maturation on bovine oocyte meiosis and embryo development in vitro. Reproduction, Fertility and Development, 20(4), 529. doi:10.1071/rd07209Singleton, V.L., Rossi J.A. 1965. Colorimetry of total phenolics with phosphomolybdic-phosphotungstic acid reagents. Am. J. Enol. Viticult.,16: 144-58.Sunil Kumar B.V., Kumar A., Kataria M. 2011. Effect of heat stress in tropical livestock and different strategies for its amelioration. J. Stress Physiol. Biochem., 7: 45-54.Szendrő Z.S., Pàlos J., Radnai I., Biró-Németh E., Romvàri R. 1996. Effect of litter size and birth weight on the mortality and weight gain of suckling and growing rabbits. In: Proc.: 6th World Rabbit Congress, 9-12 July, 1996. Toulouse, France. 2: 365-369

A genome-wide association study identifies protein quantitative trait loci (pQTLs)

There is considerable evidence that human genetic variation influences gene expression. Genome-wide studies have revealed that mRNA levels are associated with genetic variation in or close to the gene coding for those mRNA transcripts - cis effects, and elsewhere in the genome - trans effects. The role of genetic variation in determining protein levels has not been systematically assessed. Using a genome-wide association approach we show that common genetic variation influences levels of clinically relevant proteins in human serum and plasma. We evaluated the role of 496,032 polymorphisms on levels of 42 proteins measured in 1200 fasting individuals from the population based InCHIANTI study. Proteins included insulin, several interleukins, adipokines, chemokines, and liver function markers that are implicated in many common diseases including metabolic, inflammatory, and infectious conditions. We identified eight Cis effects, including variants in or near the IL6R (p = 1.8×10 -57), CCL4L1 (p = 3.9×10-21), IL18 (p = 6.8×10-13), LPA (p = 4.4×10-10), GGT1 (p = 1.5×10-7), SHBG (p = 3.1×10-7), CRP (p = 6.4×10-6) and IL1RN (p = 7.3×10-6) genes, all associated with their respective protein products with effect sizes ranging from 0.19 to 0.69 standard deviations per allele. Mechanisms implicated include altered rates of cleavage of bound to unbound soluble receptor (IL6R), altered secretion rates of different sized proteins (LPA), variation in gene copy number (CCL4L1) and altered transcription (GGT1). We identified one novel trans effect that was an association between ABO blood group and tumour necrosis factor alpha (TNF-alpha) levels (p = 6.8×10-40), but this finding was not present when TNF-alpha was measured using a different assay , or in a second study, suggesting an assay-specific association. Our results show that protein levels share some of the features of the genetics of gene expression. These include the presence of strong genetic effects in cis locations. The identification of protein quantitative trait loci (pQTLs) may be a powerful complementary method of improving our understanding of disease pathways. © 2008 Melzer et al

Purifying Selection in Deeply Conserved Human Enhancers Is More Consistent than in Coding Sequences

(c) 2014 De Silva et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited

Enzymatic pre-treatment of microalgae cells for enhanced extraction of proteins

Crude proteins and pigments were extracted from different microalgae strains, both marine and freshwater. The effectiveness of enzymatic pre-treatment prior to protein extraction was evaluated and compared to conventional techniques, including ultrasonication and high-pressure water extraction. Enzymatic pre-treatment was chosen as it could be carried out at mild shear conditions and does not subject the proteins to high temperatures, as with the ultrasonication approach. Using enzymatic pre-treatment, the extracted proteins yields of all tested microalgae strains were approximately 0.7 mg per mg of dry cell weight. These values were comparable to those achieved using a commercial lytic kit. Ultrasonication was not very effective for proteins extraction from Chlorella sp., and the extracted proteins yields did not exceed 0.4 mg per mg of dry cell weight. For other strains, similar yields were achieved by both treatment methods. The time-course effect of enzymatic incubation on the proteins extraction efficiency was more evident using laccase compared to lysozyme, which suggested that the former enzyme has a slower rate of cell disruption. The crude extracted proteins were fractionated using an ion exchange resin and were analyzed by the electrophoresis technique. They were further tested for their antioxidant activity, the highest of which was about 60% from Nannochloropsis sp. The total phenolic contents in the selected strains were also determined, with Chlorella sp. showing the highest content reaching 17 mg/g. Lysozyme was also found to enhance the extraction of pigments, with Chlorella sp. showing the highest pigments contents of 16.02, 4.59 and 5.22 mg/g of chlorophyll a, chlorophyll b and total carotenoids, respectively

From Bengali to English: sequential bilingualism of a second-generation British Bangladeshi

The paper discusses sequential language acquisition of the researcher's daughter Safa who transformed from a monolingual Bengali speaker to an almost monolingual English speaker in a few months after moving to the UK. Safa was born in Bangladesh and was a monolingual Bengali speaker until she was three years and nine months when the family moved to the UK. Unlike most research on sequential bilingualism, Safa's transition from Bengali to English went through a period of an invented language, which she developed and used for a few months. Safa then underwent language shift as Bengali became her passive language. Safa's loss of fluency in Bengali was mainly due to the absence of Bengali linguistic environment, because her family lived outside the community. Safa's mother's indifference to Bangladeshi ethnicity and her parents’ positive attitude towards Britishness meant that her decline in Bengali did not cause them much concern. Despite the lack of proficiency in Bengali, Safa still retains a strong ethnic Bangladeshi identity. Tabors and Snow’s four-stage developmental process of sequential second-language acquisition has been applied to find the similarities and differences in Safa's case, while language maintenance and shift theories have contributed to the analysis of the process of her language shift