Comparative gene finding in chicken indicates that we are closing in on the set of multi-exonic widely-expressed human genes

The recent availability of the chicken genome sequence poses the question of whether there are human protein-coding genes conserved in chicken that are currently not included in the human gene catalog. Here, we show, using comparative gene finding followed by experimental verification of exon pairs by RT–PCR, that the addition to the multi-exonic subset of this catalog could be as little as 0.2%, suggesting that we may be closing in on the human gene set. Our protocol, however, has two shortcomings: (i) the bioinformatic screening of the predicted genes, applied to filter out false positives, cannot handle intronless genes; and (ii) the experimental verification could fail to identify expression at a specific developmental time. This highlights the importance of developing methods that could provide a reliable estimate of the number of these two types of genes.

Analysis of the multi-copy gene family FAM90A as a copy number variant in different ethnic backgrounds

Copy number variants contribute extensively to inter-individual genomic differences, but little is known about their inter-population variability and diversity. In a previous study (Bosch et al., 2007; 16:2572-2582), we reported that the primate-specific gene family FAM90A, which accounts for as many as 25 members in the human reference assembly, has expanded the number of FAM90A clusters across the hominoid lineage. Here we examined the copy number variability of FAM90A genes in 260 HapMap samples of European, African, and Asian ancestry, and showed significant inter-population differences (p<0.0001). Based on the recent study of Stranger et al. (2007; 315:848-853), we also explored the correlation between copy number variability and expression levels of the FAM90A gene family. Despite the high genomic variability, we found a low correlation between FAM90A copy number and expression levels, which could be due to the action of independent trans-acting factors. Our results show that FAM90A is highly variable in copy number between individuals and between populations. However, this variability has little impact on gene expression levels, thus highlighting the importance of genomic variability for genes located in regions containing segmental duplications.

Is the PHY layer dead?

This article originates from a panel with the above title, held at IEEE VTC Spring 2009, in which the authors took part. The enthusiastic response it received prompted us to discuss for a wider audience whether research at the physical layer (PHY) is still relevant to the field of wireless communications. Using cellular systems as the axis of our exposition, we exemplify areas where PHY research has indeed hit a performance wall and where any improvements are expected to be marginal. We then discuss whether the research directions taken in the past have always been the right choice and how lessons learned could influence future policy decisions. Several of the raised issues are subsequently discussed in greater details, e.g., the growing divergence between academia and industry. With this argumentation at hand, we identify areas that are either under-developed or likely to be of impact in coming years - hence corroborating the relevance and importance of PHY research.

Capacity-achieving input covariance for single-user multi-antenna channels

We characterize the capacity-achieving input covariance for multi-antenna channels known instantaneously at the receiver and in distribution at the transmitter. Our characterization, valid for arbitrary numbers of antennas, encompasses both the eigenvectors and the eigenvalues. The eigenvectors are found for zero-mean channels with arbitrary fading profiles and a wide range of correlation and keyhole structures. For the eigenvalues, in turn, we present necessary and sufficient conditions as well as an iterative algorithm that exhibits remarkable properties: universal applicability, robustness and rapid convergence. In addition, we identify channel structures for which an isotropic input achieves capacity.

Comprehensive evaluation of the IEEE 802.15.4 MAC layer performance with retransmissions

Supported by IEEE 802.15.4 standardization activities, embedded networks have been gaining popularity in recent years. The focus of this paper is to quantify the behavior of key networking metrics of IEEE 802.15.4 beacon-enabled nodes under typical operating conditions, with the inclusion of packet retransmissions. We corrected and extended previous analyses by scrutinizing the assumptions on which the prevalent Markovian modeling is generally based. By means of a comparative study, we singled out which of the assumptions impact each of the performance metrics (throughput, delay, power consumption, collision probability, and packet-discard probability). In particular, we showed that - unlike what is usually assumed - the probability that a node senses the channel busy is not constant for all the stages of the backoff procedure and that these differences have a noticeable impact on backoff delay, packet-discard probability, and power consumption. Similarly, we showed that - again contrary to common assumption - the probability of obtaining transmission access to the channel depends on the number of nodes that is simultaneously sensing it. We evidenced that ignoring this dependence has a significant impact on the calculated values of throughput and collision probability. Circumventing these and other assumptions, we rigorously characterize, through a semianalytical approach, the key metrics in a beacon-enabled IEEE 802.15.4 system with retransmissions.

On the Segregation of Genetically Modified, Conventional, and Organic Products in European Agriculture: A Multi-market Equilibrium Analysis, October 2005

Evaluating the possible benefits of the introduction of genetically modified (GM) crops must address the issue of consumer resistance as well as the complex regulation that has ensued. In the European Union (EU) this regulation envisions the “co-existence” of GM food with conventional and quality-enhanced products, mandates the labelling and traceability of GM products, and allows only a stringent adventitious presence of GM content in other products. All these elements are brought together within a partial equilibrium model of the EU agricultural food sector. The model comprises conventional, GM and organic food. Demand is modelled in a novel fashion, whereby organic and conventional products are treated as horizontally differentiated but GM products are vertically differentiated (weakly inferior) relative to conventional ones. Supply accounts explicitly for the land constraint at the sector level and for the need for additional resources to produce organic food. Model calibration and simulation allow insights into the qualitative and quantitative effects of the large-scale introduction of GM products in the EU market. We find that the introduction of GM food reduces overall EU welfare, mostly because of the associated need for costly segregation of non-GM products, but the producers of quality-enhanced products actually benefit.

Immigration and contested nation-building : explaining the political salience of immigration in multi-national societies

Multi-national societies present a complex setting for the politics of immigration, as migration’s linguistic, economic and cultural effects may coincide with existing contestation over nationhood between sub-units and the central state. Empirically, though, political actors only sometimes, and in some places, explicitly connect the politics of immigration to the stakes of multi-level politics. With reference to Canada, Belgium and the United Kingdom, this paper examines the conditions under which political leaders link immigration to ongoing debate about governance in multi-national societies. The paper argues that the distribution of policy competencies in the multi-level system is less important for shaping immigration and integration politics than is the perceived impact (positive or negative) on the sub-unit’s societal culture or its power relationship with the center. Immigration and integration are more often politicized where center and sub-unit hold divergent views on migration and its place in national identity.

A double layer model of the gas bubble/water interface

Zeta potential is a physico-chemical parameter of particular importance to describe sorption of contaminants at the surface of gas bubbles. Nevertheless, the interpretation of electrophoretic mobilities of gas bubbles is complex. This is due to the specific behavior of the gas at interface and to the excess of electrical charge at interface, which is responsible for surface conductivity. We developed a surface complexation model based on the presence of negative surface sites because the balance of accepting and donating hydrogen bonds is broken at interface. By considering protons adsorbed on these sites followed by a diffuse layer, the electrical potential at the head-end of the diffuse layer is computed and considered to be equal to the zeta potential. The predicted zeta potential values are in very good agreement with the experimental data of H-2 bubbles for a broad range of pH and NaCl concentrations. This implies that the shear plane is located at the head-end of the diffuse layer, contradicting the assumption of the presence of a stagnant diffuse layer at the gas/water interface. Our model also successfully predicts the surface tension of air bubbles in a KCl solution. (c) 2012 Elsevier Inc. All rights reserved.

Feasibility of replacing multiple ADSL connections with Multi-Dwelling Access

This final project was made for the Broadband/Implementation department of TeliaSonera Finland. The question to be examined is if the operator should replace multiple ADSL connections implemented over a leased line with Multi-Dwelling access based on an Ethernet/Optical Fibre access network. The project starts with describing the technology related to these access network solu-tions and presents the technology that is used in TeliaSonera Finland's access network. It continues from the technology to describe the problem with some of the ADSL implemen-tations of TeliaSonera. The problem is the implementations done over a leased line that can cost TeliaSonera over years as much as a possible investment to extend network when there is several lines leased to the same building. The project proposes a Multi-Dwelling access as a solution to this problem and defines the circumstances when to use it. After a satisfactory solution has found the project takes a view how implementation of the solution might alter the network and a new problem is found. When used commonly to replace need of ADSL implementation Multi-Dwelling access would significantly increase optical cable congestion near operators POP. As a final deed this project also proposes a technical change to existing way to implement multi-dwelling access with EPON technology.

Metastatic tumors to the colon and rectum: a multi-institutional study.

Context.-Unlike the small bowel, the colorectal mucosa is seldom the site of metastatic disease. Objective.-To determine the incidence of truly colorectal metastases, and subsequent clinicopathologic findings, in a substantial colorectal cancer population collected from 7 European centers. Design.-During the last decade, 10 365 patients were identified as having colorectal malignant tumors, other than systemic diseases. Data collected included patient demographics, clinical symptoms, treatment, the presence of metastases in other sites, disease-free interval, follow-up, and overall survival. All secondary tumors resulting from direct invasion from malignant tumors of the contiguous organs were excluded, as well as those resulting from lymph node metastases or peritoneal seeding. Results.-Only 35 patients were included (10 men) with a median age of 59 years. They presented with obstruction, bleeding, abdominal pain, or perforation. The leading source of metastases was the breast, followed by melanoma. Metastases were synchronous in 3 cases. The mean disease-free interval for the remaining cases was 6.61 years. Surgical resection was performed in 28 cases. Follow-up was available for 26 patients; all had died, with a mean survival time of 10.67 months (range, 1-41 months). Conclusions.-Colorectal metastases are exceptional (0.338%) with the breast as a leading source of metastases; they still represent a late stage of disease and reflect a poor prognosis. Therefore, the pathologist should be alert for the possibility of secondary tumors when studying large bowel biopsies. Any therapy is usually palliative, but our results suggest that prolonged survival after surgery and complementary therapy can be obtained in some patients.

Assessment of volumetric bone mineral density of the femoral neck in postmenopausal women with and without vertebral fractures using quantitative multi-slice CT.

OBJECTIVE: To demonstrate the validity and reliability of volumetric quantitative computed tomography (vQCT) with multi-slice computed tomography (MSCT) and dual energy X-ray absorptiometry (DXA) for hip bone mineral density (BMD) measurements, and to compare the differences between the two techniques in discriminating postmenopausal women with osteoporosis-related vertebral fractures from those without. METHODS: Ninety subjects were enrolled and divided into three groups based on the BMD values of the lumbar spine and/or the femoral neck by DXA. Groups 1 and 2 consisted of postmenopausal women with BMD changes <-2SD, with and without radiographically confirmed vertebral fracture (n=11 and 33, respectively). Group 3 comprised normal controls with BMD changes > or =-1SD (n=46). Post-MSCT (GE, LightSpeed16) scan reconstructed images of the abdominal-pelvic region, 1.25 mm thick per slice, were processed by OsteoCAD software to calculate the following parameters: volumetric BMD values of trabecular bone (TRAB), cortical bone (CORT), and integral bone (INTGL) of the left femoral neck, femoral neck axis length (NAL), and minimum cross-section area (mCSA). DXA BMD measurements of the lumbar spine (AP-SPINE) and the left femoral neck (NECK) also were performed for each subject. RESULTS: The values of all seven parameters were significantly lower in subjects of Groups 1 and 2 than in normal postmenopausal women (P<0.05, respectively). Comparing Groups 1 and 2, 3D-TRAB and 3D-INTGL were significantly lower in postmenopausal women with vertebral fracture(s) [(109.8+/-9.61) and (243.3+/-33.0) mg/cm3, respectively] than in those without [(148.9+/-7.47) and (285.4+/-17.8) mg/cm(3), respectively] (P<0.05, respectively), but no significant differences were evident in AP-SPINE or NECK BMD. CONCLUSION: the femoral neck-derived volumetric BMD parameters using vQCT appeared better than the DXA-derived ones in discriminating osteoporotic postmenopausal women with vertebral fractures from those without. vQCT might be useful to evaluate the effect of osteoporotic vertebral fracture status on changes in bone mass in the femoral neck.

Spirituality and religion in outpatients with schizophrenia: A multi-site comparative study of Switzerland, Canada, and the United States

Objective: To assess the importance of spirituality and religious coping among outpatients with a DSM-IV diagnosis of schizophrenia or schizoaffective disorder living in three countries. Method: A total of 276 outpatients (92 from Geneva, Switzerland, 121 from Trois-Rivières, Canada, and 63 from Durham, North Carolina), aged 18-65, were administered a semi-structured interview on the role of spirituality and religiousness in their lives and to cope with their illness. Results: Religion is important for outpatients in each of the three country sites, and religious involvement is higher than in the general population. Religion was helpful (i.e., provided a positive sense of self and positive coping with the illness) among 87% of the participants and harmful (a source of despair and suffering) among 13%. Helpful religion was associated with better social, clinical and psychological status. The opposite was observed for the harmful aspects of religion. In addition, religion sometimes conflicted with psychiatric treatment. Conclusions: These results indicate that outpatients with schizophrenia or schizoaffective disorder often use spirituality and religion to cope with their illness, basically positively, yet sometimes negatively. These results underscore the importance of clinicians taking into account the spiritual and religious lives of patients with schizophrenia.

Greenstick fractures of the middle third of the forearm. A prospective multi-centre study.

BACKGROUND: Greenstick fractures suffered during growth have a high risk for refracture and posttraumatic deformity, particularly at the forearm diaphysis. The use of a preemptive completion of the fracture by manipulation of the concave cortex is controversial and data supporting this approach are few. AIM: Aim of this study was to determine the factors which predispose to refracture and deformities, and to define therapeutic strategies. METHODS: We prospectively gathered clinical and radiographic data over a period of one year on greenstick fractures of the middle third of the forearm in children as part of a multi-centre study. Endpoint was a follow-up visit at one year. Radiographic deformity, state of consolidation at resumption of physical activities and refracture rate were analysed statistically (ANOVA, Student's t-test and Pearson's chi-square test) with regard to patient age, gender, fracture type, therapy and time in plaster. RESULTS: We collected the data of 103 patients (63 boys, 40 girls), average age 6.6 years (1.3-14.5 years), the vast majority of whom had a combined greenstick fracture of the radius and ulna. 6.7% of the patients sustained a refracture within 49 days (29-76) after plaster removal. They were significantly older (p=0.017) with a significantly higher incidence of manual completion of the fracture with radiographic signs of partial consolidation (p=0.025). Residual deformities were significantly smaller after completion of the fracture compared to reduction without completion (p=0.019) or plaster fixation alone (p<0.005). CONCLUSIONS: Completion of a greenstick fracture does not prevent refracture. Nevertheless, it diminishes the extent of secondary deformities in cases where the primary angulation exceeds the remodelling capacity. Prevention of refracture should include a routine radiographic follow-up 4-6 weeks after injury with continuation of plaster fixation in cases of partial consolidation.