IPv6 is the response to the shortage of IPv4 addresses. It was defined almost twenty years ago by the IETF as a replacement of IPv4, and little by little, it is becoming more preponderant as the ...Internet protocol. The growth of Internet has led to the development of high performance networks. On one hand, Ethernet has evolved significantly and today it is common to find 10 Gigabit Ethernet networks in LANs. On the other hand, another approach for high performance networking is based on RDMA (Remote Direct Memory Access) which offers innovative features such as kernel bypass, zero copy, offload of splitting and assembly of messages in packets to the CAs (Channel Adapters), etc. InfiniBand is currently the most popular technology that implements RDMA. It uses verbs instead of sockets and a big effort of the community is required to port TCP/IP software to InfiniBand, to take advantage of its benefits. Meanwhile, IPoIB (IP over InfiniBand) is a protocol that has been proposed and permits the execution of socket-based applications on top of InfiniBand, without any change, at the expense of performance. In this paper, we make a performance evaluation of IPv6 and IPv4 over 10 Gigabit Ethernet and IPoIB. Our results show that 10 Gigabit Ethernet has a better throughput than IPoIB, especially for small and medium payload sizes. However, as the payload size increases, the advantage of 10 Gigabit Ethernet is reduced in comparison to IPoIB/FDR. With respect to latency, IPoIB did much better than 10 Gigabit Ethernet. Finally, our research also indicates that in a controlled environment, IPv4 has a better performance than IPv6.
Prostate cancer (PCa) is the most common diagnosed cancer and is the third cause of cancer mortality in men in the USA. Andrographolide, a diterpenoid lactone isolated from Andrographis paniculata, ...has shown to possess anticarcinogenic activity in a variety of cancer cells. In this study, we examined the efficacy of Andrographolide in PCa using
and
models. Androgen-independent (PC3) and androgen-dependent (22RV1) cell lines were treated with Andrographolide to determine the effect in cell motility, cell proliferation and apoptosis. Andrographolide decreased PCa cell migration, decreased invasion, and increased cell apoptosis
. Tumor growth was evaluated using an orthotopic xenograft model in which the prostates of SCID mice were injected with 22RV1, and mice were treated three times per week with Andrographolide 10 mg/kg. Andrographolide decreased tumor volume, MMP11 expression and blood vessels formation
. Gene expression analysis identified cellular compromise, cell cycle, and "DNA recombination, replication and repair" as the major molecular and cellular functions altered in tumors treated with Andrographolide. Within DNA repair genes we confirmed increased expression of genes involved in DNA double strand break repair. Consistent with this observation we detected increased γH2AX in Andrographolide treated tumors and in cells in culture. Taken together, these data suggest that Andrographolide inhibits PCa by promoting DNA damage.
Species delimitation is a major quest in biology and is essential for adequate management of the organismal diversity. A challenging example comprises the fish species of red snappers in the Western ...Atlantic. Red snappers have been traditionally recognized as two separate species based on morphology: Lutjanus campechanus (northern red snapper) and L. purpureus (southern red snapper). Recent genetic studies using mitochondrial markers, however, failed to delineate these nominal species, leading to the current lumping of the northern and southern populations into a single species (L. campechanus). This decision carries broad implications for conservation and management as red snappers have been commercially over-exploited across the Western Atlantic and are currently listed as vulnerable. To address this conflict, we examine genome-wide data collected throughout the range of the two species. Population genomics, phylogenetic and coalescent analyses favour the existence of two independent evolutionary lineages, a result that confirms the morphology-based delimitation scenario in agreement with conventional taxonomy. Despite finding evidence of introgression in geographically neighbouring populations in northern South America, our genomic analyses strongly support isolation and differentiation of these species, suggesting that the northern and southern red snappers should be treated as distinct taxonomic entities.
The khmer package is a freely available software library for working efficiently with fixed length DNA words, or k-mers. khmer provides implementations of a probabilistic k-mer counting data ...structure, a compressible De Bruijn graph representation, De Bruijn graph partitioning, and digital normalization. khmer is implemented in C++ and Python, and is freely available under the BSD license at
https://github.com/dib-lab/khmer/.
To examine the trajectory of fatigue experienced by 26 Puerto Rican (PR) men over the course of External Beam Radiation Therapy (EBRT) and to assess gene expression changes from baseline to midpoint ...of EBRT using microarray technology. Design/Research Approach- Prospective exploratory and comparative design study. Setting- RT facility located in San Juan, PR. Sample/Participants-26 PR men with non-metastatic prostate cancer.
Participants completed 2 paper forms: demographics and the Spanish version of the 13-item FACT-fatigue at baseline, midpoint, and end of EBRT. Wholeblood samples were collected at baseline and at midpoint of EBRT. Descriptive data was analyzed using t-test, Wilcoxon, and Friedman test for repeated measures. Gene expression data was analyzed using the LIMMA package in R; the functional network analysis was conducted using Ingenuity Pathway analysis. Main Research Variable-Fatigue scores, gene expression.
Subjects were of ages 52-81 with fatigue scores that remained unchanged during EBRT (baseline=42.38, SD=9.34; midpoint=42.11, SD=8.93, endpoint=43.04, SD=8.62). Three hundred seventy-three genes (130-up regulated and 243-down regulated) were differentially expressed from baseline to mid-point of EBRT (FDR<0.01). The top distinct canonical pathways of the differentially expressed probesets (p<0.0001) were: "Phospholipase C Signaling," "Role of NFAT in Regulation of the Immune Response," and "Gαq Signaling."
While fatigue did not worsen over the course of EBRT for this sample as a group, there was variability in fatigue across the sample. It is possible that the over expression of the SESN3 gene, known to suppress oxidative damage, may have contributed to the attenuation of fatigue in this clinical population.
MicroRNAs (miRNAs) are a class of small noncoding RNAs that bind to 3'-untranslated (UTR) regions of target messenger RNAs to regulate protein synthesis. Reports have suggested that a set of specific ...miRNAs may be used as diagnostic and/or prognostic markers for astrocytoma grading. However, there are few studies of the specific miRNAs differentially expressed in each astrocytoma grade. MiRNA-containing total RNA was isolated from archived formalin-fixed, paraffin-embedded (FFPE) samples from WHO grade II-IV astrocytoma patients. The RNA was labeled and hybridized to Affymetrix miRNA 2.0 arrays. Statistical analysis identified several miRNAs differentially expressed in each astrocytoma grade. In particular, miR-27a, miR-210, and miR-1225-5p expression levels were able to differentiate grade IV from grade II and III astrocytomas as confirmed by real-time PCR. Kaplan-Meier survival analysis showed that disease progression occurred faster for Glioblastoma Multiforme (GBM) patients with a lower miR-27a expression level. Transfection of CRL-1690 GBM human cancer cells with a miR-27a oligonucleotide inhibitor followed by Real-time PCR identified six potential miR-27a target genes. Furthermore, the miR-27a oligonucleotide inhibitor induced CRL-1690 cell apoptosis. Taken together, our results provide additional miRNA signatures for distinguishing GBM from lower astrocytoma grades and suggest miR-27a as a prognostic and therapeutic target for GBM.
Representation of Hispanics, and in particular Hispanic women, is notoriously low in computer science programs in higher education and in the tech industry. The engagement of undergraduate students ...in research, often and early in their path towards degree completion, has been championed as one of the principal reforms necessary to increase the number of capable professionals in Science, Technology, Engineering, and Mathematics (STEM). The benefits attributed to undergraduate research experiences have been reported to disproportionately benefit individuals from groups that have been historically underrepresented in STEM. The Interdisciplinary and Quantitative Biology Research Experience for Undergraduates (IQ-Bio-REU) summer program was created to engage ten (10) underrepresented undergraduate students in authentic research experiences in emerging fields of biology which integrate quantitative and computational approaches to projects ranging from molecular biosciences to bioinformatics to ecology to bridge the digital and data divide for underrepresented Hispanics and women in computing. Our poster speaks to our observations of our students, faculty, and trainers after participating in our NSF funded summer REU at a Hispanic Serving Institution in a predominantly Hispanic, low socio-economic neighborhood in Puerto Rico.
Microarrays allow researchers to simultaneously measure the expression of thousands of genes. They give invaluable insight into the transcriptional state of biological systems, and can be important ...in understanding physiological as well as diseased conditions. However, the analysis of data from many thousands of genes, from only a few replications is very difficult. We have devised a novel method of correcting errors in microarray experiments, that also clusters genes into groups, and categorizes their measurements into coarse divisions, suitable for discrete techniques for reverse engineering. These techniques are based on finite fields and algebraic coding theory. We test these new techniques on a data set obtained from behavioral training experiments on rats, and identify two novel genes that may be involved in learning and memory. We extend this method to work with “probe level” microarray data, where each gene is represented by multiple probes. We have applied the error correction procedure to two data sets, one Affymetrix, one NimbleGen, having either 14 (Affymetrix) or approximately 10 (NimbleNen) probes per gene, derived from an odor avoidance experiment on Drosophila. The experiment is designed to validate analysis procedures by examining the degree of concordance the procedures produce across the data sets. For this data we devise a method to measure the concordance quantitatively. We have developed a technique based on mutual information to compare results obtained across the two data sets. Our results show that our error correction techniques result in a greater amount of shared information between data sets than traditional approaches based on averaging of probes and gene expression levels across repetitions. We show how our results can be extended to sets with finer gradations in expression values, and present the analysis of the Drosophila data discretized to 5 separate expression values. Finally, we present some future applications, such as using finite fields to encode expression values, allowing us to use the algebraic properties of finite fields to perform reverse engineering of gene regulatory networks.
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