Optimal Code Set Selection and Security Issues in Spectral Phase-Encoded Time Spreading (SPECTS) OCDMA Systems

In this paper, we perform a thorough analysis of a spectral phase-encoded time spreading optical code division multiple access (SPECTS-OCDMA) system based on Walsh-Hadamard (W-H) codes aiming not only at finding optimal code-set selections but also at assessing its loss of security due to crosstalk. We prove that an inadequate choice of codes can make the crosstalk between active users to become large enough so as to cause the data from the user of interest to be detected by other user. The proposed algorithm for code optimization targets code sets that produce minimum bit error rate (BER) among all codes for a specific number of simultaneous users. This methodology allows us to find optimal code sets for any OCDMA system, regardless the code family used and the number of active users. This procedure is crucial for circumventing the unexpected lack of security due to crosstalk. We also show that a SPECTS-OCDMA system based on W-H 32(64) fundamentally limits the number of simultaneous users to 4(8) with no security violation due to crosstalk. More importantly, we prove that only a small fraction of the available code sets is actually immune to crosstalk with acceptable BER (<10(-9)) i.e., approximately 0.5% for W-H 32 with four simultaneous users, and about 1 x 10(-4)% for W-H 64 with eight simultaneous users.

Hydrothermal pretreatment of sugarcane bagasse using response surface methodology improves digestibility and ethanol production by SSF

Sugarcane bagasse was characterized as a feedstock for the production of ethanol using hydrothermal pretreatment. Reaction temperature and time were varied between 160 and 200A degrees C and 5-20 min, respectively, using a response surface experimental design. The liquid fraction was analyzed for soluble carbohydrates and furan aldehydes. The solid fraction was analyzed for structural carbohydrates and Klason lignin. Pretreatment conditions were evaluated based on enzymatic extraction of glucose and xylose and conversion to ethanol using a simultaneous saccharification and fermentation scheme. SSF experiments were conducted with the washed pretreated biomass. The severity of the pretreatment should be sufficient to drive enzymatic digestion and ethanol yields, however, sugars losses and especially sugar conversion into furans needs to be minimized. As expected, furfural production increased with pretreatment severity and specifically xylose release. However, provided that the severity was kept below a general severity factor of 4.0, production of furfural was below an inhibitory concentration and carbohydrate contents were preserved in the pretreated whole hydrolysate. There were significant interactions between time and temperature for all the responses except cellulose digestion. The models were highly predictive for cellulose digestibility (R (2) = 0.8861) and for ethanol production (R (2) = 0.9581), but less so for xylose extraction. Both cellulose digestion and ethanol production increased with severity, however, high levels of furfural generated under more severe pretreatment conditions favor lower severity pretreatments. The optimal pretreatment condition that gave the highest conversion yield of ethanol, while minimizing furfural production, was judged to be 190A degrees C and 17.2 min. The whole hydrolysate was also converted to ethanol using SSF. To reduce the concentration of inhibitors, the liquid fraction was conditioned prior to fermentation by removing inhibitory chemicals using the fungus Coniochaeta ligniaria.

ISOLATION AND CHARACTERISTICS OF EIGHT NOVEL POLYMORPHIC MICROSATELLITE LOCI IN LIPPIA ALBA (VERBENACEAE)

Premise of the study: A set of eight microsatellite (simple sequence repeat [SSR]) markers for Lippia alba, an important medicinal and cosmetic plant, was developed to aid studies of genetic diversity and to define efficient strategies for breeding programs. Methods and Results: Using a (CT)(8)- and (GT)(8)-enriched library, a total of 11 SSR loci were developed and optimized in L. alba. Of the 11 loci, eight were found to be polymorphic after screening 61 accessions from two populations. The parameters used to characterize loci were expected heterozygosity (H-e) and number of alleles. A total of 44 alleles were identified, with an average of 5.5 alleles per loci, which were moderately to highly informative according to H-e. Conclusions: These new SSR markers have potential for informing genetic diversity, allele mining, and mapping studies and will be used to generate information for breeding programs of L. alba

Alkaline sulfite/anthraquinone pretreatment followed by disk refining of Pinus radiata and Pinus caribaea wood chips for biochemical ethanol production

BACKGROUND: Alkaline sulfite/anthraquinone (ASA) cooking of Pinus radiata and Pinus caribaea wood chips followed by disk refining was used as a pretreatment for the production of low lignified and high fibrillated pulps. The pulps produced with different delignification degrees and refined at different energy inputs (250, 750 and 1600 Wh) were saccharified with cellulases and fermented to ethanol with Saccharomyces cerevisiae using separated hydrolysis and fermentation (SHF) or semi-simultaneous saccharification and fermentation (SSSF) processes. RESULTS: Delignification of ASA pulps was between 25% and 50%, with low glucans losses. Pulp yield was from 70 to 78% for pulps of P. radiata and 60% for the pulp of P. caribaea. Pulps obtained after refining were evaluated in assays of enzymatic hydrolysis. Glucans-to-glucose conversion varied from 20 to 70%, depending on the degree of delignification and fibrillation of the pulps. The best ASA pulp of P. radiata was used in SHF and SSSF experiments of ethanol production. Such experiments produced maximum ethanol concentration of 20 g L-1, which represented roughly90% of glucose conversion and an estimated amount of 260 L ethanol ton(-1) wood. P. caribaea pulp also presented good performance in the enzymatic hydrolysis and fermentation but, due to the low amount of cellulose present, only 140 L ethanol would be obtained from each ton of wood. CONCLUSION: ASA cooking followed by disk refining was shown to be an efficient pretreatment process, which generated a low lignified and high-fibrillated substrate that allowed the production of ethanol from the softwoods with high conversion yields. (C) 2012 Society of Chemical Industry

Toll-like Receptor 2 Knockout Mice Showed Increased Periapical Lesion Size and Osteoclast Number

Introduction: The aim of this study was to characterize the formation and progression of experimentally induced periapical lesions in TLR2 knockout (TLR2 KO) mice. Methods: Periapical lesions were induced in molars of 28 wild type (WT) and 27 TLR2 KO mice. After 7, 21, and 42 days, the animals were euthanized, and the mandibles were subjected to histotechnical processing. Hematoxylin-eosin-stained sections were examined under conventional light microscopy for the description of pulpal, apical, and periapical features and under fluorescence microscopy for the determination of the periapical lesion size. The subsequent sections were evaluated by tartrate resistant acid phosphatase histoenzymology (osteoclasts), Brown and Brenn staining (bacteria), and immunohistochemistry (RANK, RANKL, and OPG). Data were analyzed by the Mann-Whitney U and Kruskal-Wallis tests (alpha = 0.05), Results: The WT group showed significant differences (P < .05) in the periapical lesion size and the osteoclast number between 7 and 42 days and between 21 and 42 days. In the TLR2 KO group, significant differences (P < .05) in the periapical lesion size and the osteoclast number were found between 7 days and the other periods. There was a significant difference (P < .05) between the 2 types of animal regarding the periapical lesion size, which was larger in the TLR2 KO animals. No significant differences (P > .05) were found between WT and TLR2 KO mice related to the pulpal, apical, and periapical features; bacteria localization; and immunohistochemical results (except for RANK expression). Conclusions: TLR2 KO animals developed larger periapical lesions with a greater number of osteoclasts, indicating the important role of this receptor in the host's immune and inflammatory response to root canal and periradicular infection. (J Endod 2012;38:803-813)

ESMO Consensus Guidelines for management of patients with colon and rectal cancer. A personalized approach to clinical decision making

Colorectal cancer (CRC) is the most common tumour type in both sexes combined in Western countries. Although screening programmes including the implementation of faecal occult blood test and colonoscopy might be able to reduce mortality by removing precursor lesions and by making diagnosis at an earlier stage, the burden of disease and mortality is still high. Improvement of diagnostic and treatment options increased staging accuracy, functional outcome for early stages as well as survival. Although high quality surgery is still the mainstay of curative treatment, the management of CRC must be a multi-modal approach performed by an experienced multi-disciplinary expert team. Optimal choice of the individual treatment modality according to disease localization and extent, tumour biology and patient factors is able to maintain quality of life, enables long-term survival and even cure in selected patients by a combination of chemotherapy and surgery. Treatment decisions must be based on the available evidence, which has been the basis for this consensus conference-based guideline delivering a clear proposal for diagnostic and treatment measures in each stage of rectal and colon cancer and the individual clinical situations. This ESMO guideline is recommended to be used as the basis for treatment and management decisions.

Evaluation of CA-125 and soluble CD-23 in patients with pelvic endometriosis: a case-control study

Objective: To evaluate serum concentrations of CA-125 and soluble CD-23 and to correlate them with clinical symptoms, localization and stage of pelvic endometriosis and histological classification of the disease. Methods: Blood samples were collected from 44 women with endometriosis and 58 without endometriosis, during the first three days (1st sample) and during the 7th, 8th and 9th day (2nd sample) of the menstrual cycle. Measurements of CA-125 and soluble CD-23 were performed by ELISA. Mann-Whitney U test was used for age, pain evaluations (visual analog scale) and biomarkers concentrations. Results: Serum levels Of CA-125 were higher in endometriosis patients when compared to the control group during both periods of the menstrual cycle evaluated in the study. This marker was also elevated in women with chronic pelvic pain, deep dyspareunia (2nd sample), dysmenorrhea (both samples) and painful defecation during the menstrual flow (2nd sample). CA-125 concentration was higher in advanced stages of the disease in both samples and also in women with ovarian endometrioma. Concerning CD-23, no statistically significant differences were observed between groups. Conclusion: The concentrations of CA-125 were higher in patients with endometriosis than in patients without the disease. No significantly differences were observed for soluble CD-23 levels between groups.

How far can we go in simplifying biomonitoring assessments? An integrated analysis of taxonomic surrogacy, taxonomic sufficiency and numerical resolution in a megadiverse region

The need for biodiversity conservation is increasing at a rate much faster than the acquisition of knowledge of biodiversity, such as descriptions of new species and mapping species distributions. As global changes are winning the race against the acquisition of knowledge, many researchers resort to the use of surrogate groups to aid in conservation decisions. Reductions in taxonomic and numerical resolution are also desirable, because they could allow more rapid the acquisition of knowledge while requiring less effort, if little important information is lost. In this study, we evaluated the congruence among 22 taxonomic groups sampled in a tropical forest in the Amazon basin. Our aim was to evaluate if any of these groups could be used as surrogates for the others in monitoring programs. We also evaluated if the taxonomic or numerical resolution of possible surrogates could be reduced without greatly reducing the overall congruence. Congruence among plant groups was high, whereas the congruence among most animal groups was very low, except for anurans in which congruence values were only slightly lower than for plants. Liana (Bignoniaceae) was the group with highest congruence, even using genera presence-absence data. The congruence among groups was related to environmental factors, specifically the clay and phosphorous contents of soil. Several groups showed strong spatial clumping, but this was unrelated to the congruence among groups. The high degree of congruence of lianas with the other groups suggests that it may be a reasonable surrogate group, mainly for the other plant groups analyzed, if soil data are not available. Although lianas are difficult to count and identify, the number of studies on the ecology of lianas is increasing. Most of these studies have concluded that lianas are increasing in abundance in tropical forests. In addition to the high congruence, lianas are worth monitoring in their own right because they are sensitive to global warming and the increasing frequency and severity of droughts in tropical regions. Our findings suggest that the use of data on surrogate groups with relatively low taxonomic and numerical resolutions can be a reliable shortcut for biodiversity assessments, especially in megadiverse areas with high rates of habitat conversion, where the lack of biodiversity knowledge is pervasive. (c) 2012 Elsevier Ltd. All rights reserved.

Xylella fastidiosa comparative genomic database is an information resource to explore the annotation, genomic features, and biology of different strains

The Xylella fastidiosa comparative genomic database is a scientific resource with the aim to provide a user-friendly interface for accessing high-quality manually curated genomic annotation and comparative sequence analysis, as well as for identifying and mapping prophage-like elements, a marked feature of Xylella genomes. Here we describe a database and tools for exploring the biology of this important plant pathogen. The hallmarks of this database are the high quality genomic annotation, the functional and comparative genomic analysis and the identification and mapping of prophage-like elements. It is available from web site http://www.xylella.lncc.br.

Rates of description of Phytoseiidae mite species (Acari: Mesostigmata): space, time and body size variations

This study aims to analyse the degree of completeness of world inventory of the mite family Phytoseiidae and the factors that might determine the process of species description. The world data set includes 2,122 valid species described from 1839 to 2010. Species accumulation curves were analysed. The effect of localisation (latitude ranges) and body size on the species description patterns over space and time was assessed. A low proportion of species seems remain to be described, but this trend could be explained by a critical reduction in the number of specialists dedicated to the study of those mites. In addition, this trend refers to the areas where phytoseiids have been well studied around the world, and it may change considerably if the study of these mites would be intensified in some areas. The number of newly described species is lower near the tropics, and their body size is also smaller. Differences in body size were noted between the three sub-families of Phytoseiidae, the highest mean body lengths of adult females being observed for Amblyseiinae, the most diverse family. In the future, collections would have certainly to take into consideration such conclusions for instance in using more adequate optical equipment especially for field collections. The decrease in the number of phytoseiid mite described was confirmed and the factors that could explain such a trend are discussed. Information for improving further inventories is provided and discussed, especially in relation to sampling localization and study methods.

Unraveling the structure of sugarcane bagasse after soaking in concentrated aqueous ammonia (SCAA) and ethanol production by Scheffersomyces (Pichia) stipitis

Abstract Background Fuel ethanol production from sustainable and largely abundant agro-residues such as sugarcane bagasse (SB) provides long term, geopolitical and strategic benefits. Pretreatment of SB is an inevitable process for improved saccharification of cell wall carbohydrates. Recently, ammonium hydroxide-based pretreatment technologies have gained significance as an effective and economical pretreatment strategy. We hypothesized that soaking in concentrated aqueous ammonia-mediated thermochemical pretreatment (SCAA) would overcome the native recalcitrance of SB by enhancing cellulase accessibility of the embedded holocellulosic microfibrils. Results In this study, we designed an experiment considering response surface methodology (Taguchi method, L8 orthogonal array) to optimize sugar recovery from ammonia pretreated sugarcane bagasse (SB) by using the method of soaking in concentrated aqueous ammonia (SCAA-SB). Three independent variables: ammonia concentration, temperature and time, were selected at two levels with center point. The ammonia pretreated bagasse (SCAA-SB) was enzymatically hydrolysed by commercial enzymes (Celluclast 1.5 L and Novozym 188) using 15 FPU/g dry biomass and 17.5 Units of β-glucosidase/g dry biomass at 50°C, 150 rpm for 96 h. A maximum of 28.43 g/l reducing sugars corresponding to 0.57 g sugars/g pretreated bagasse was obtained from the SCAA-SB derived using a 20% v/v ammonia solution, at 70°C for 24 h after enzymatic hydrolysis. Among the tested parameters, pretreatment time showed the maximum influence (p value, 0.053282) while ammonia concentration showed the least influence (p value, 0.612552) on sugar recovery. The changes in the ultra-structure and crystallinity of native SCAA-SB and enzymatically hydrolysed SB were observed by scanning electron microscopy (SEM), x-ray diffraction (XRD) and solid-state 13C nuclear magnetic resonance (NMR) spectroscopy. The enzymatic hydrolysates and solid SCAA-SB were subjected to ethanol fermentation under separate hydrolysis and fermentation (SHF) and simultaneous saccharification and fermentation (SSF) by Scheffersomyces (Pichia) stipitis NRRL Y-7124 respectively. Higher ethanol production (10.31 g/l and yield, 0.387 g/g) was obtained through SSF than SHF (3.83 g/l and yield, 0.289 g/g). Conclusions SCAA treatment showed marked lignin removal from SB thus improving the accessibility of cellulases towards holocellulose substrate as evidenced by efficient sugar release. The ultrastructure of SB after SCAA and enzymatic hydrolysis of holocellulose provided insights of the degradation process at the molecular level.

The intronic long noncoding RNA ANRASSF1 recruits PRC2 to the RASSF1A promoter, reducing the expression of RASSF1A and increasing cell proliferation

The down-regulation of the tumor-suppressor gene RASSF1A has been shown to increase cell proliferation in several tumors. RASSF1A expression is regulated through epigenetic events involving the polycomb repressive complex 2 (PRC2); however, the molecular mechanisms modulating the recruitment of this epigenetic modifier to the RASSF1 locus remain largely unknown. Here, we identify and characterize ANRASSF1, an endogenous unspliced long noncoding RNA (lncRNA) that is transcribed from the opposite strand on the RASSF1 gene locus in several cell lines and tissues and binds PRC2. ANRASSF1 is transcribed through RNA polymerase II and is 5'-capped and polyadenylated; it exhibits nuclear localization and has a shorter half-life compared with other lncRNAs that bind PRC2. ANRASSF1 endogenous expression is higher in breast and prostate tumor cell lines compared with non-tumor, and an opposite pattern is observed for RASSF1A. ANRASSF1 ectopic overexpression reduces RASSF1A abundance and increases the proliferation of HeLa cells, whereas ANRASSF1 silencing causes the opposite effects. These changes in ANRASSF1 levels do not affect the RASSF1C isoform abundance. ANRASSF1 overexpression causes a marked increase in both PRC2 occupancy and histone H3K27me3 repressive marks, specifically at the RASSF1A promoter region. No effect of ANRASSF1 overexpression was detected on PRC2 occupancy and histone H3K27me3 at the promoter regions of RASSF1C and the four other neighboring genes, including two well-characterized tumor suppressor genes. Additionally, we demonstrated that ANRASSF1 forms an RNA/DNA hybrid and recruits PRC2 to the RASSF1A promoter. Together, these results demonstrate a novel mechanism of epigenetic repression of the RASSF1A tumor suppressor gene involving antisense unspliced lncRNA, in which ANRASSF1 selectively represses the expression of the RASSF1 isoform overlapping the antisense transcript in a location-specific manner. In a broader perspective, our findings suggest that other non-characterized unspliced intronic lncRNAs transcribed in the human genome might contribute to a location-specific epigenetic modulation of genes.

Submandibular glands and the regulation of gastric proliferation and TGFα distribution during rat postnatal development

Rodent gastric mucosa grows and differentiates during suckling-weaning transition. Among the molecules in rat milk, EGF and TGFβ are important peptides in the control of cell proliferation, and together with TGFα, they are also produced by submandibular glands. We aimed to determine the effect of saliva and milk on epithelial cell proliferation in the stomach of rat pups. We also examined the distribution of TGFα in the gastric mucosa after sialoadenectomy (SIALO) and fasting in order to determine whether this growth factor is affected by the deprivation of molecules derived from saliva and milk. SIALO was performed at 14 days and fasting was induced 3 days later. Cell proliferation was evaluated through metaphasic index and TGFα was detected by immunohistochemistry. We observed that whereas SIALO did not alter cell division, since the metaphasic index (MI) was unchanged, fasting stimulated cell proliferation (P < 0.05). After SIALO and fasting, MI was reduced when compared to the fasted group (P < 0.05). We found that TGFα is distributed along gastric gland and SIALO did not interfere in the localization and number of immunolabeled cells, but fasting increased their density when compared to the control (P < 0.05). The association of SIALO and fasting reduced TGFα immunostaining (P < 0.05). Therefore, during fasting, high MI was parallel to increased TGFα in gastric epithelium, but interestingly, this effect was found only in the presence of submandibular glands. We suggest that during suckling, peptides derived from saliva and milk are important to regulate gastric growth.

Uptake of oxLDL and IL-10 production by macrophages requires PAFR and CD36 recruitment into the same lipid rafts

Macrophage interaction with oxidized low-density lipoprotein (oxLDL) leads to its differentiation into foam cells and cytokine production, contributing to atherosclerosis development. In a previous study, we showed that CD36 and the receptor for platelet-activating factor (PAFR) are required for oxLDL to activate gene transcription for cytokines and CD36. Here, we investigated the localization and physical interaction of CD36 and PAFR in macrophages stimulated with oxLDL. We found that blocking CD36 or PAFR decreases oxLDL uptake and IL-10 production. OxLDL induces IL-10 mRNA expression only in HEK293T expressing both receptors (PAFR and CD36). OxLDL does not induce IL-12 production. The lipid rafts disruption by treatment with βCD reduces the oxLDL uptake and IL-10 production. OxLDL induces co-immunoprecipitation of PAFR and CD36 with the constitutive raft protein flotillin-1, and colocalization with the lipid raft-marker GM1-ganglioside. Finally, we found colocalization of PAFR and CD36 in macrophages from human atherosclerotic plaques. Our results show that oxLDL induces the recruitment of PAFR and CD36 into the same lipid rafts, which is important for oxLDL uptake and IL-10 production. This study provided new insights into how oxLDL interact with macrophages and contributing to atherosclerosis development.

ScPdZn and ScPtZn with YAlGe type structure: group-subgroup relation and 45Sc solid state NMR spectroscopy

The intermetallic compounds ScPdZn and ScPtZn were prepared from the elements by high-frequency melting in sealed tantalum ampoules. Both structures were refined from single crystal X-ray diffractometer data: YAlGe type, Cmcm, a = 429.53(8), b = 907.7(1), c = 527.86(1) pm, wR2 = 0.0375, 231 F2 values, for ScPdZn and a = 425.3(1), b = 918.4(2), c = 523.3(1) pm, wR2 = 0.0399, 213 F2 values for ScPtZn with 14 variables per refinement. The structures are orthorhombically distorted variants of the AlB2 type. The scandium and palladium (platinum atoms) build up ordered networks Sc3Pd3 and Sc3Pt3 (boron networks) which are slightly shifted with respect to each other. These networks are penetrated by chains of zinc atoms (262 pm in ScPtZn) which correspond to the aluminum positions, i.e. Zn(ScPd) and Zn(ScPt). The corresponding group-subgroup scheme and the differences in chemical bonding with respect to other AlB2-derived REPdZn and REPtZn compounds are discussed. 45Sc solid state NMR spectra confirm the single crystallographic scandium sites. From electronic band structure calculations the two compounds are found metallic with free electron like behavior at the Fermi level. A larger cohesive energy for ScPtZn suggests a more strongly bonded intermetallic than ScPdZn. Electron localization and overlap population analyses identify the largest bonding for scandium with the transition metal (Pd, Pt).