Full-Duplex Spectrum Sharing in Cooperative Single Carrier Systems

We propose cyclic prefix single carrier full-duplex transmission in amplify-and-forward cooperative spectrum sharing networks to achieve multipath diversity and full-duplex spectral efficiency. Integrating full-duplex transmission into cooperative spectrum sharing systems results in two intrinsic problems: 1) the residual loop interference occurs between the transmit and the receive antennas at the secondary relays and 2) the primary users simultaneously suffer interference from the secondary source (SS) and the secondary relays (SRs). Thus, examining the effects of residual loop interference under peak interference power constraint at the primary users and maximum transmit power constraints at the SS and the SRs is a particularly challenging problem in frequency selective fading channels. To do so, we derive and quantitatively compare the lower bounds on the outage probability and the corresponding asymptotic outage probability for max–min relay selection, partial relay selection, and maximum interference relay selection policies in frequency selective fading channels. To facilitate comparison, we provide the corresponding analysis for half-duplex. Our results show two complementary regions, named as the signal-to-noise ratio (SNR) dominant region and the residual loop interference dominant region, where the multipath diversity and spatial diversity can be achievable only in the SNR dominant region, however the diversity gain collapses to zero in the residual loop interference dominant region.

Cholecystectomy by single incision laparoscopic surgery (SILS): early experience and technique standardization

Single Incision Laparoscopic Surgery (SILS) is a recent surgical technique, first described in the 1990s. Its aim is to optimize the esthetic result offered by laparoscopy by minimizing the number of abdominal incisions. Various preliminary studies have been carried out on the application of SILS, especially in cholecystectomy and appendectomy. This study evaluates the preliminary results of cholecystectomy by SILS (SILS™ Port) conducted between October 2009 and February 2011 on 21 patients (4 men and 17 women) with a mean age of 49.9 years and a mean Body Mass Index (BMI) of 22.8. All patients were treated by the same team, which had previously undergone six months’ simulator training. There were two main selection criteria, both evaluated intraoperatively: absence of adhesions and of significant inflammatory sequelae from previous cholecystitis; and suitable distance between gallbladder and SILS access port. Conversion to traditional laparoscopy was necessary in just two cases, while an accessory trocar was introduced in another two cases. Conversion to open surgery was not necessary in any case. One case of SILS cholecystectomy was complicated by postoperative bile leakage, which was treated conservatively, as the fistula had a low output. The mean duration of hospitalization was 3.6 days. This preliminary experience led us to conclude that SILS is safe and highly satisfactory in the postoperative phase, thanks to the reduced need for painkillers and the improved esthetic result.

Laparoscopic approach in abdominal emergencies: a 5-year experience at a single center

Background. Laparoscopy is ever more common in both elective and emergency surgery. In fact, in abdominal emergencies it enables the resolution of preoperative diagnostic doubts as well as treatment of the underlying disease. We present a retrospective study of the results of a 5-year experience at a single center. Patients and methods. Between September 2006 and August 2011, 961 patients were treated via laparoscopy, including 486 emergency cases (15 gastroduodenal perforation; 165 acute cholecystitis; 255 acute appendicitis; 15 pelvic inflammatory disease and non-specific abdominal pain [NSAP]; 36 small bowel obstruction). All procedures were conducted by a team trained in laparoscopic surgery. Results. The conversion rate was 22/486 patients (4.53%). A definitive laparoscopic diagnosis was possible in over 96% of cases, and definitive treatment via laparoscopy was possible in most of these. Conclusions Our own experience confirms the literature evidence that laparoscopy is a valid option in the surgical treatment of abdominal emergencies. In any case, it must be performed by a dedicated and highly experienced team. Correct patient selection is also important, to enable the most suitable approach for each given situation.

Incidental cancer in patients surgically treated for benign thyroid disease. Our experience at a single institution

Increased incidence of incidental cancer in patients operated for benign thyroid disease has been reported. We report our experience about incidental thyroid cancer (ITC) in order to better characterize this nosologic entity. Between 2001 and 2009 a total of 568 patients underwent surgery for benign thyroid disease. Patients with preoperative cytology undetermined or positive for malignancy were excluded. The most frequent indication for surgery was multinodular or diffuse nontoxic goiter. We performed total thyroidectomy in 499 cases and emithyroidectomy in 69 cases. Final histology revealed ITC in 53 patients (9.3%): 44 had papillary carcinoma (20 classic variant and 24 follicular variant), 4 follicular carcinoma, 4 medullary carcinoma and 1 primitive thyroid paraganglioma. The preoperative diagnosis was multinodular or diffuse goiter in 45 cases of ITC and uninodular goiter in 8 cases. We performed total thyroidectomy in 46 case, emithyroidectomy in 4 patients with past history of lobectomy, emithyroidectomy in 3 patients with following radicalization and central neck dissection. In 14 patients the tumor was multifocal and in 12 of these patients the tumor foci were bilateral. The lesion was a microcarcinoma in 34 cases. Mean diameter of the ITC was 1.14 cm. We retrospectively reconsidered the results of preoperative ultrasound examinations in relation to the exact position of the tumor in the specimens and we found a statistically significant association between echogenicity and papillary histotype. Twenty-six patients were followed up at our Hospital. The mean follow-up period was 38.2 months. A relapse was observed in 3/26 patients. Incidental thyroid cancer in patients operated for benign disease has its own surgical and oncological relevance. A correct preoperative assessment, with a careful selection of nodules for fine-needle aspiration cytology on the basis of ultrasound pattern, could better address the choice of surgical procedure. The non irrelevant incidence of incidental thyroid cancer, the eventuality of multifocality and bilaterality and the possible occurrence of relapse, support that total thyroidectomy without residuum is a valuable option for treating benign thyroid conditions such as multinodular goitre. When an incidental cancer is diagnosed after emithyroidectomy, a radicalization with central neck dissection could be considered. We suggest that natural history of papillary microtumors and the correct surgical approach for these lesions could be better defined with a more extensive use of “Porto proposal” criteria. Incidental thyroid cancer, Papillary microcarcinoma, Papillary microtumors, Total thyroidectomy.

Domestication and the storage starch biosynthesis pathway: Signatures of selection from a whole sorghum genome sequencing strategy

Next-generation sequencing of complete genomes has given researchers unprecedented levels of information to study the multifaceted evolutionary changes that have shaped elite plant germplasm. In conjunction with population genetic analytical techniques and detailed online databases, we can more accurately capture the effects of domestication on entire biological pathways of agronomic importance. In this study, we explore the genetic diversity and signatures of selection in all predicted gene models of the storage starch synthesis pathway of Sorghum bicolor, utilizing a diversity panel containing lines categorized as either ‘Landraces’ or ‘Wild and Weedy’ genotypes. Amongst a total of 114 genes involved in starch synthesis, 71 had at least a single signal of purifying selection and 62 a signal of balancing selection and others a mix of both. This included key genes such as STARCH PHOSPHORYLASE 2 (SbPHO2, under balancing selection), PULLULANASE (SbPUL, under balancing selection) and ADP-glucose pyrophosphorylases (SHRUNKEN2, SbSH2 under purifying selection). Effectively, many genes within the primary starch synthesis pathway had a clear reduction in nucleotide diversity between the Landraces and wild and weedy lines indicating that the ancestral effects of domestication are still clearly identifiable. There was evidence of the positional rate variation within the well-characterized primary starch synthesis pathway of sorghum, particularly in the Landraces, whereby low evolutionary rates upstream and high rates downstream in the metabolic pathway were expected. This observation did not extend to the wild and weedy lines or the minor starch synthesis pathways.

Domestication and the storage starch biosynthesis pathway: signatures of selection from a whole sorghum genome sequencing strategy

Next-generation sequencing of complete genomes has given researchers unprecedented levels of information to study the multifaceted evolutionary changes that have shaped elite plant germplasm. In conjunction with population genetic analytical techniques and detailed online databases, we can more accurately capture the effects of domestication on entire biological pathways of agronomic importance. In this study, we explore the genetic diversity and signatures of selection in all predicted gene models of the storage starch synthesis pathway of Sorghum bicolor, utilizing a diversity panel containing lines categorized as either ‘Landraces’ or ‘Wild and Weedy’ genotypes. Amongst a total of 114 genes involved in starch synthesis, 71 had at least a single signal of purifying selection and 62 a signal of balancing selection and others a mix of both. This included key genes such as STARCH PHOSPHORYLASE 2 (SbPHO2, under balancing selection), PULLULANASE (SbPUL, under balancing selection) and ADP-glucose pyrophosphorylases (SHRUNKEN2, SbSH2 under purifying selection). Effectively, many genes within the primary starch synthesis pathway had a clear reduction in nucleotide diversity between the Landraces and wild and weedy lines indicating that the ancestral effects of domestication are still clearly identifiable. There was evidence of the positional rate variation within the well-characterized primary starch synthesis pathway of sorghum, particularly in the Landraces, whereby low evolutionary rates upstream and high rates downstream in the metabolic pathway were expected. This observation did not extend to the wild and weedy lines or the minor starch synthesis pathways.

Development of single nucleotide polymorphism (SNP) markers from the mango (Mangifera indica) transcriptome for mapping and estimation of genetic diversity

The development of molecular markers for genomic studies in Mangifera indica (mango) will allow marker-assisted selection and identification of genetically diverse germplasm, greatly aiding mango breeding programs. We report here our identification of thousands of unambiguous molecular markers that can be easily assayed across genotypes of the species. With origin centered in Southeast Asia, mangos are grown throughout the tropics and subtropics as a nutritious fruit that exhibits remarkable intraspecific phenotypic diversity. With the goal of building a high density genetic map, we have undertaken discovery of sequence variation in expressed genes across a broad range of mango cultivars. A transcriptome sequence reference was built de novo from extensive sequencing and assembly of RNA from cultivar 'Tommy Atkins'. Single nucleotide polymorphisms (SNPs) in protein coding transcripts were determined from alignment of RNA reads from 24 mango cultivars of diverse origins: 'Amin Abrahimpur' (India), 'Aroemanis' (Indonesia), 'Burma' (Burma), 'CAC' (Hawaii), 'Duncan' (Florida), 'Edward' (Florida), 'Everbearing' (Florida), 'Gary' (Florida), 'Hodson' (Florida), 'Itamaraca' (Brazil), 'Jakarata' (Florida), 'Long' (Jamaica), 'M. Casturi Purple' (Borneo), 'Malindi' (Kenya), 'Mulgoba' (India), 'Neelum' (India), 'Peach' (unknown), 'Prieto' (Cuba), 'Sandersha' (India), 'Tete Nene' (Puerto Rico), 'Thai Everbearing' (Thailand), 'Toledo' (Cuba), 'Tommy Atkins' (Florida) and 'Turpentine' (West Indies). SNPs in a selected subset of protein coding transcripts are currently being converted into Fluidigm assays for genotyping of mapping populations and germplasm collections. Using an alternate approach, SNPs (144) discovered by sequencing of candidate genes in 'Kensington Pride' have already been converted and used for genotyping.

Nested Rollout Policy Adaptation for optimizing vehicle selection in complex VRPs

The goal of Vehicle Routing Problems (VRP) and their variations is to transport a set of orders with the minimum number of vehicles at least cost. Most approaches are designed to solve specific problem variations independently, whereas in real world applications, different constraints are handled concurrently. This research extends solutions obtained for the traveling salesman problem with time windows to a much wider class of route planning problems in logistics. The work describes a novel approach that:  supports a heterogeneous fleet of vehicles  dynamically reduces the number of vehicles  respects individual capacity restrictions  satisfies pickup and delivery constraints  takes Hamiltonian paths (rather than cycles) The proposed approach uses Monte-Carlo Tree Search and in particular Nested Rollout Policy Adaptation. For the evaluation of the work, real data from the industry was obtained and tested and the results are reported.

A Fuzzy Decision Strategy for Topic Identification and Dynamic Selection of Language Models

International audience

Genetic analysis of the flowering date and number of petals in rose

International audience

Metastability and dynamics of stem cells: from direct observations to inference at the single cell level

Organismal development, homeostasis, and pathology are rooted in inherently probabilistic events. From gene expression to cellular differentiation, rates and likelihoods shape the form and function of biology. Processes ranging from growth to cancer homeostasis to reprogramming of stem cells all require transitions between distinct phenotypic states, and these occur at defined rates. Therefore, measuring the fidelity and dynamics with which such transitions occur is central to understanding natural biological phenomena and is critical for therapeutic interventions.

While these processes may produce robust population-level behaviors, decisions are made by individual cells. In certain circumstances, these minuscule computing units effectively roll dice to determine their fate. And while the 'omics' era has provided vast amounts of data on what these populations are doing en masse, the behaviors of the underlying units of these processes get washed out in averages.

Therefore, in order to understand the behavior of a sample of cells, it is critical to reveal how its underlying components, or mixture of cells in distinct states, each contribute to the overall phenotype. As such, we must first define what states exist in the population, determine what controls the stability of these states, and measure in high dimensionality the dynamics with which these cells transition between states.

To address a specific example of this general problem, we investigate the heterogeneity and dynamics of mouse embryonic stem cells (mESCs). While a number of reports have identified particular genes in ES cells that switch between 'high' and 'low' metastable expression states in culture, it remains unclear how levels of many of these regulators combine to form states in transcriptional space. Using a method called single molecule mRNA fluorescent in situ hybridization (smFISH), we quantitatively measure and fit distributions of core pluripotency regulators in single cells, identifying a wide range of variabilities between genes, but each explained by a simple model of bursty transcription. From this data, we also observed that strongly bimodal genes appear to be co-expressed, effectively limiting the occupancy of transcriptional space to two primary states across genes studied here. However, these states also appear punctuated by the conditional expression of the most highly variable genes, potentially defining smaller substates of pluripotency.

Having defined the transcriptional states, we next asked what might control their stability or persistence. Surprisingly, we found that DNA methylation, a mark normally associated with irreversible developmental progression, was itself differentially regulated between these two primary states. Furthermore, both acute or chronic inhibition of DNA methyltransferase activity led to reduced heterogeneity among the population, suggesting that metastability can be modulated by this strong epigenetic mark.

Finally, because understanding the dynamics of state transitions is fundamental to a variety of biological problems, we sought to develop a high-throughput method for the identification of cellular trajectories without the need for cell-line engineering. We achieved this by combining cell-lineage information gathered from time-lapse microscopy with endpoint smFISH for measurements of final expression states. Applying a simple mathematical framework to these lineage-tree associated expression states enables the inference of dynamic transitions. We apply our novel approach in order to infer temporal sequences of events, quantitative switching rates, and network topology among a set of ESC states.

Taken together, we identify distinct expression states in ES cells, gain fundamental insight into how a strong epigenetic modifier enforces the stability of these states, and develop and apply a new method for the identification of cellular trajectories using scalable in situ readouts of cellular state.

Evaluating Karner Blue Butterfly (Lycaeides Melissa Samuelis Nabokov) Habitat Selection in the State of Wisconsin, USA

The federally endangered Karner blue butterfly (Lycaeides melissa samuelis Nabokov) persists in rare oak/pine grassland communities spanning across the Great Lakes region, relying on host plant wild blue lupine (Lupinus perennis). Conservation efforts since 1992 have led to the development of several programs that restore and monitor habitat. This study aims to evaluate Karner blue habitat selection in the state of Wisconsin and develop high-resolution tools for use in conservation efforts. Spatial predictive models developed during this study accurately predicted potential habitat across state properties based on soils and canopy cover, and identified ~51-100% of Karner blue occurrences based on lupine and shrub/tree cover, and focal nectar plant abundance. When evaluated relative to American bison (Bison bison), Karner blues and lupine were more likely to occur in areas of low disturbance, but aggregated where bison were recently present in areas of moderate/high disturbance. Lupine C:N ratio increased relative to cover of shrubs/trees and focal nectar plant abundance and decreased relative to cover of groundlitter. Karner blue density increased with lupine C:N ratio, decreased with nitrogen content, and was not related to phenolic levels. We strongly suggest that areas of different soil textures must be managed differently and that maintenance techniques should generate a mix of shrubs/tree cover (10-45%), groundlitter cover (~10-40%), >5% cover of lupine, and establish an abundance of focal nectar plants. This study provides unique tools for use in conservation and should aid in focusing management efforts and recovery of this species.

Genetic Structure of the Florida Key Tree Cactus, Pilosocereus robinii, using Restriction Site associated DNA (RAD) markers

Rare plant conservation efforts must utilize current genetic methods to ensure the evolutionary potential of populations is preserved. One such effort involves the Key Tree Cactus, Pilosocereus robinii, which is an endangered columnar cactus native to the Florida Keys. The populations have precipitously declined over the past decade because of habitat loss and increasing soil salinity from rising sea levels and storm surge. Next-generation DNA sequencing was used to assess the genetic structure of the populations. Twenty individuals representative of both wild and extirpated cacti were chosen for Restriction Site Associated DNA (RAD) analysis. Samples processed using the HindIII and NotIII restriction enzymes produced 82,382,440 high quality reads used for genetic mapping, from which 5,265 Single Nucleotide Polymorphisms (SNPs) were discovered. The analysis revealed that the Keys’ populations are closely related with little population differentiation. In addition, the populations display evidence of inbreeding and low genetic diversity.

A single nucleotide polymorphism in NEUROD1 is associated with production traits in nelore beef cattle.

Feed efficiency and carcass characteristics are late-measured traits. The detection of molecular markers associated with them can help breeding programs to select animals early in life, and to predict breeding values with high accuracy. The objective of this study was to identify polymorphisms in the functional and positional candidate gene NEUROD1 (neurogenic differentiation 1), and investigate their associations with production traits in reference families of Nelore cattle. A total of 585 steers were used, from 34 sires chosen to represent the variability of this breed. By sequencing 14 animals with extreme residual feed intake (RFI) values, seven single nucleotide polymorphisms (SNPs) in NEUROD1 were identified. The investigation of marker effects on the target traits RFI, backfat thickness (BFT), ribeye area (REA), average body weight (ABW), and metabolic body weight (MBW) was performed with a mixed model using the restricted maximum likelihood method. SNP1062, which changes cytosine for guanine, had no significant association with RFI or REA. However, we found an additive effect on ABW (P ≤ 0.05) and MBW (P ≤ 0.05), with an estimated allele substitution effect of -1.59 and -0.93 kg0.75, respectively. A dominant effect of this SNP for BFT was also found (P ≤ 0.010). Our results are the first that identify NEUROD1 as a candidate that affects BFT, ABW, and MBW. Once confirmed, the inclusion of this SNP in dense panels may improve the accuracy of genomic selection for these traits in Nelore beef cattle as this SNP is not currently represented on SNP chips.