Finding genomic differences from whole-genome assemblies using SyRI

Genomic differences can range from single nucleotide differences (SNPs) to large complex structural rearrangements. Current methods typically can annotate sequence differences like SNPs and large indels accurately but do not unravel the full complexity of structural rearrangements that include inversions, translocations, and duplications. Structural rearrangements involve changes in location, orientation, or copy-number between highly similar sequences and have been reported to be associated with several biological differences between organisms. However, they are still scantly studied with sequencing technologies as it is still challenging to identify them accurately. Here I present SyRI, a novel computational method for genome-wide identification of structural differences using the pairwise comparison of whole-genome chromosome-level assemblies. SyRI uses a unique approach where it first identifies all syntenic (structurally conserved) regions between two genomes. Since all non-syntenic regions are structural rearrangements by definition, this transforms the difficult problem of rearrangement identification to a comparatively easier problem of rearrangement classification. SyRI analyses the location, orientation, and copy-number of alignments between rearranged regions and selects alignments that best represent the putative rearrangements and result in the highest total alignment score between the genomes. Next, SyRI searches for sequence differences that are distinguished for residing in syntenic or rearranged regions. This distinction is important, as rearranged regions (and sequence differences within them) do not follow Mendelian Law of Segregation and are therefore inherited differently compared to syntenic regions. Using SyRI, I successfully identified rearrangements in human, A. thaliana, yeast, fruit fly, and maize genomes. Further, I also experimentally validated 92% (108/117) of the predicted translocations in A. thaliana using a genetic approach

Disaster Relief Workers: Health Issues

Introduction: Disaster is defined as any occurrence that causes damage, ecological disruption, loss of human life or deterioration of health and health services on a scale sufficient to warrant an extraordinary response from outside the affected community or area. Internationally, major disasters occur frequently, but for one country, they are unusual events. It causes severe health damage to that country. In this scenario, our rescue teams/ relief workers risk their own lives to save the life of others. Methods: The concerned topic was searched on internet in different databases with abstract or full free text available in English in previous five years. Results: This group is more vulnerable than general population to various accidents even death in relief process and also health problems such as post traumatic stress disorder, mental health risks, heat disorder, radiation exposure, respiratory problems, skin and mucous membrane problems, digestive problems, eye irritation and fatigue etc. In developed countries, their problems are dealt with great zeal, but unfortunately, in our country, we fail to address the health issue of these workers in spite of having the most important role in disaster management by providing physical and rehabilitative services to survivors. It has been proven that work output of these workers is enhanced if their health issues are taken care of properly. Discussion: We want to acknowledge the health concerns of rescue teams with possible solutions

ASHA Workers and Adolescent Health: An Explorative Study

Introduction: Adolescents constitute around 1.2 billion population of the world. Despite the fact that adolescents represent almost one quarter of the Indian population, their health needs are poorly understood and ill served. ASHAs being front line workers may play a significant role in addressing adolescence health issues at community level.Objective: To assess awareness and practices of ASHA workers regarding adolescent health issues.Materials and Methods: A cross-sectional study conducted among 1650 ASHA workers in Sonepat District of Haryana who had gathered for a training session on adolescent health. Before the session, a questionnaire in local language was distributed to assess their understanding about adolescent health issues. Data was analyzed using SPSS software (version 17). Results were presented in simple proportions and means (+SD).Results: Mean age (+SD) of ASHAs was 38.74 + 8.7 years. Maximum 1178 (71.4%) belonged to age group of 25-45 years. 1582 (95.9%) ASHAs were aware that adolescence age group was constituted by 10-19 years. 435 (26.4%) knew of anemia, 368 (22.3%) knew of vaginal discharge, 292 (17.7%) knew of menstrual problems as common problem in adolescence age group. 1297 (78.6%) reported condoms, 58 (3.5%) tubectomy, 139 (8.4%) oral pills as contraceptive methods for adolescence.Conclusion: ASHA workers should be trained adequately about adolescence health issues so that continuum of care under RMNCHA plus can be achieved. Training should provide complete knowledge about the same

E-waste - Management Practices in India

With the usage of electrical and electronic equipment (EEE) on the rise, the amountof electrical and electronic waste (e-waste) produced each day is equally growingenormously around the globe. Recycling of valuable elements contained in e-wastesuch as copper and gold has become a source of income mostly in the informalsector of developing or emerging industrialized countries. However, primitiverecycling techniques such as burning cables for retaining the inherent copper exposeboth adult and child workers as well as their families to a range of hazardoussubstances.1 By definition, e-waste or “waste electrical and electronic products” is aterm used to cover all items of electrical and electronic equipment (EEE) and itsparts that have been discarded by its owner as waste without the intent of reuse.2Such wastes encompass wide range of electrical and electronic devices such ascomputers, handheld cellular phones, personal stereos, including large householdappliances such as refrigerators, air conditioners, etc.3 E-waste consists hazardousand non-hazardous waste. It consists of ferrous and non-ferrous metals, plastics,glass, wood and plywood, printed circuit boards, concrete, ceramics, rubber andother items. Iron and steel constitute about 50% of the-waste, followed by plastics(21%), non-ferrous metals (13%) and other constituents. Non-ferrous metals consistof metals like copper, aluminum and precious metals like silver, gold, platinum,palladium and so on. The presence of elements like lead, mercury, arsenic,cadmium, selenium, hexavalent chromium, and flame retardants beyond thresholdquantities make e-waste toxic (Table 1).4 Rapid product innovation, miniaturizationand replacement, especially for information and communication technology (ICT)products and consumer equipment, are fueling the increase of e-waste and resultingin immediate and long-term concern5 because of unregulated accumulation,improper collection and treatment approaches that can lead to majorenvironmental problems endangering human health

Configurable and Scalable Turbo Decoder for 4G Wireless Receivers

The increasing requirements of high data rates and quality of service (QoS) in fourth-generation (4G) wireless communication require the implementation of practical capacity approaching codes. In this chapter, the application of Turbo coding schemes that have recently been adopted in the IEEE 802.16e WiMax standard and 3GPP Long Term Evolution (LTE) standard are reviewed. In order to process several 4G wireless standards with a common hardware module, a reconfigurable and scalable Turbo decoder architecture is presented. A parallel Turbo decoding scheme with scalable parallelism tailored to the target throughput is applied to support high data rates in 4G applications. High-level decoding parallelism is achieved by employing contention-free interleavers. A multi-banked memory structure and routing network among memories and MAP decoders are designed to operate at full speed with parallel interleavers. A new on-line address generation technique is introduced to support multiple Turbo interleaving patterns, which avoids the interleaver address memory that is typically necessary in the traditional designs. Design trade-offs in terms of area and power efficiency are analyzed for different parallelism and clock frequency goals

Configurable and Scalable High Throughput Turbo Decoder Architecture for Multiple 4GWireless Standards

In this paper, we propose a novel multi-code turbo decoder architecture for 4G wireless systems. To support various 4G standards, a configurable multi-mode MAP (maximum a posteriori) decoder is designed for both binary and duo-binary turbo codes with small resource overhead (less than 10%) compared to the single-mode architecture. To achieve high data rates in 4G, we present a parallel turbo decoder architecture with scalable parallelism tailored to the given throughput requirements. High-level parallelism is achieved by employing contention-free interleavers. Multi-banked memory structure and routing network among memories and MAP decoders are designed to operate at full speed with parallel interleavers. We designed a very low-complexity recursive on-line address generator supporting multiple interleaving patterns, which avoids the interleaver address memory. Design trade-offs in terms of area and power efficiency are explored to find the optimal architectures. A 711 Mbps data rate is feasible with 32 Radix-4 MAP decoders running at 200 MHz clock rate.Texas Instruments Incorporate