An efficient parallelization technique for high throughput FFT-ASIPs

Fast Fourier Transformation (FFT) and it's inverse (IFFT) are used in Orthogonal Frequency Division Multiplexing (OFDM) systems for data (de)modulation. The transformations are the kernel tasks in an OFDM implementation, and are the most processing-intensive ones. Recent trends in the electronic consumer market require OFDM implementations to be flexible, making a trade-off between area, energy-efficiency, flexibility and timing a necessity. This has spurred the development of Application-Specific Instruction-Set Processors (ASIPs) for FFT processing. Parallelization is an architectural parameter that significantly influence design goals. This paper presents an analysis of the efficiency of parallelization techniques for an FFT-ASIP. It is shown that existing techniques are inefficient for high throughput applications such as Ultra Wideband (UWB), because of memory bottlenecks. Therefore, an interleaved execution technique which exploits temporal parallelism is proposed. With this technique, it is possible to meet the throughput requirement of UWB (409.6 Msamples/s) with only 4 non-trivial butterfly units for an ASIP that runs at 400MHz. © 2006 IEEE

Response of seeds and pollen of Onobrychis viciifolia and Onobrychis oxyodonta var. armena to NaCl stress

Sainfoin (Onobrychis viciifolia Scop.) is an important forage legume crop with 52 species adapted to dry and poor soils in Turkey, but little is known about the effects of salinity on germination and seedling growth in arid and semiarid regions suffering from salinity problem. The seeds and pollen of two species of sainfoin O. viciifolia and O. oxyodonta var. armena (Syn: O. armena) were exposed to 0, 5, 10, 20 and 30 dS m-1 of NaCl under in vivo and in vitro conditions and evaluated for germination under salt stress by comparing germination percentage, mean germination time, root and shoot length, fresh and dry seedling weight and dry matter. Increased salinity levels generally resulted in decrease in all traits except time to germination, dry seedling weight and dry matter, which increased at high salinity levels. O. viciifolia seeds germinated and grew more rapidly compared to O. armena seeds under NaCl stress. No decrease in germination and seedling growth up to 10 dS m-1 was recorded. On the other hand, there was a clear difference for germination and seedling growth between in vivo and in vitro conditions. Lower values were obtained from in vitro experiments; suggesting that mineral salts, sucrose and agar may have resulted in higher osmotic potential inhibiting germination and seedling growth of species compared in vivo conditions. Decrease in pollen germination with increasing salinities was very sharp, indicating that pollen germination had higher sensitive to salinity. But, pollen grains of O. armena germinated rapidly compared to O. viciifolia. The results emphasize that in vivo experiments could be used for screening of NaCl tolerance in sainfoin cultivars without expensive chemicals and sophisticated equipments, but pollen germination is more appropriate for its wild relatives

Risk Factors Associated with Adverse Fetal Outcomes in Pregnancies Affected by Coronavirus Disease 2019 (COVID-19): A Secondary Analysis of the WAPM study on COVID-19

To evaluate the strength of association between maternal and pregnancy characteristics and the risk of adverse perinatal outcomes in pregnancies with laboratory confirmed COVID-19. Secondary analysis of a multinational, cohort study on all consecutive pregnant women with laboratory-confirmed COVID-19 from February 1, 2020 to April 30, 2020 from 73 centers from 22 different countries. A confirmed case of COVID-19 was defined as a positive result on real-time reverse-transcriptase-polymerase-chain-reaction (RT-PCR) assay of nasal and pharyngeal swab specimens. The primary outcome was a composite adverse fetal outcome, defined as the presence of either abortion (pregnancy loss before 22 weeks of gestations), stillbirth (intrauterine fetal death after 22 weeks of gestation), neonatal death (death of a live-born infant within the first 28 days of life), and perinatal death (either stillbirth or neonatal death). Logistic regression analysis was performed to evaluate parameters independently associated with the primary outcome. Logistic regression was reported as odds ratio (OR) with 95% confidence interval (CI). Mean gestational age at diagnosis was 30.6\ub19.5 weeks, with 8.0% of women being diagnosed in the first, 22.2% in the second and 69.8% in the third trimester of pregnancy. There were six miscarriage (2.3%), six intrauterine device (IUD) (2.3) and 5 (2.0%) neonatal deaths, with an overall rate of perinatal death of 4.2% (11/265), thus resulting into 17 cases experiencing and 226 not experiencing composite adverse fetal outcome. Neither stillbirths nor neonatal deaths had congenital anomalies found at antenatal or postnatal evaluation. Furthermore, none of the cases experiencing IUD had signs of impending demise at arterial or venous Doppler. Neonatal deaths were all considered as prematurity-related adverse events. Of the 250 live-born neonates, one (0.4%) was found positive at RT-PCR pharyngeal swabs performed after delivery. The mother was tested positive during the third trimester of pregnancy. The newborn was asymptomatic and had negative RT-PCR test after 14 days of life. At logistic regression analysis, gestational age at diagnosis (OR: 0.85, 95% CI 0.8-0.9 per week increase; p<0.001), birthweight (OR: 1.17, 95% CI 1.09-1.12.7 per 100 g decrease; p=0.012) and maternal ventilatory support, including either need for oxygen or CPAP (OR: 4.12, 95% CI 2.3-7.9; p=0.001) were independently associated with composite adverse fetal outcome. Early gestational age at infection, maternal ventilatory supports and low birthweight are the main determinants of adverse perinatal outcomes in fetuses with maternal COVID-19 infection. Conversely, the risk of vertical transmission seems negligible

High Accuracy Mutation Detection in Leukemia on a Selected Panel of Cancer Genes

<div><p>With the advent of whole-genome and whole-exome sequencing, high-quality catalogs of recurrently mutated cancer genes are becoming available for many cancer types. Increasing access to sequencing technology, including bench-top sequencers, provide the opportunity to re-sequence a limited set of cancer genes across a patient cohort with limited processing time. Here, we re-sequenced a set of cancer genes in T-cell acute lymphoblastic leukemia (T-ALL) using Nimblegen sequence capture coupled with Roche/454 technology. First, we investigated how a maximal sensitivity and specificity of mutation detection can be achieved through a benchmark study. We tested nine combinations of different mapping and variant-calling methods, varied the variant calling parameters, and compared the predicted mutations with a large independent validation set obtained by capillary re-sequencing. We found that the combination of two mapping algorithms, namely <em>BWA-SW</em> and <em>SSAHA2</em>, coupled with the variant calling algorithm <em>Atlas-SNP2</em> yields the highest sensitivity (95%) and the highest specificity (93%). Next, we applied this analysis pipeline to identify mutations in a set of 58 cancer genes, in a panel of 18 T-ALL cell lines and 15 T-ALL patient samples. We confirmed mutations in known T-ALL drivers, including PHF6, NF1, FBXW7, NOTCH1, KRAS, NRAS, PIK3CA, and PTEN. Interestingly, we also found mutations in several cancer genes that had not been linked to T-ALL before, including JAK3. Finally, we re-sequenced a small set of 39 candidate genes and identified recurrent mutations in TET1, SPRY3 and SPRY4. In conclusion, we established an optimized analysis pipeline for Roche/454 data that can be applied to accurately detect gene mutations in cancer, which led to the identification of several new candidate T-ALL driver mutations.</p> </div

Patient empowerment in long-term conditions: development and preliminary testing of a new measure

BACKGROUND: Patient empowerment is viewed by policy makers and health care practitioners as a mechanism to help patients with long-term conditions better manage their health and achieve better outcomes. However, assessing the role of empowerment is dependent on effective measures of empowerment. Although many measures of empowerment exist, no measure has been developed specifically for patients with long-term conditions in the primary care setting. This study presents preliminary data on the development and validation of such a measure. METHODS: We conducted two empirical studies. Study one was an interview study to understand empowerment from the perspective of patients living with long-term conditions. Qualitative analysis identified dimensions of empowerment, and the qualitative data were used to generate items relating to these dimensions. Study two was a cross-sectional postal study involving patients with different types of long-term conditions recruited from general practices. The survey was conducted to test and validate our new measure of empowerment. Factor analysis and regression were performed to test scale structure, internal consistency and construct validity. RESULTS: Sixteen predominately elderly patients with different types of long-term conditions described empowerment in terms of 5 dimensions (identity, knowledge and understanding, personal control, personal decision-making, and enabling other patients). One hundred and ninety seven survey responses were received from mainly older white females, with relatively low levels of formal education, with the majority retired from paid work. Almost half of the sample reported cardiovascular, joint or diabetes long-term conditions. Factor analysis identified a three factor solution (positive attitude and sense of control, knowledge and confidence in decision making and enabling others), although the structure lacked clarity. A total empowerment score across all items showed acceptable levels of internal consistency and relationships with other measures were generally supportive of its construct validity. CONCLUSION: Initial analyses suggest that the new empowerment measure meets basic psychometric criteria. Reasons concerning the failure to confirm the hypothesized factor structure are discussed alongside further developments of the scale