Low-Latency and Energy-Efficient Data Preservation Mechanism in Low-Duty-Cycle Sensor Networks.

Similar to traditional wireless sensor networks (WSN), the nodes only have limited memory and energy in low-duty-cycle sensor networks (LDC-WSN). However, different from WSN, the nodes in LDC-WSN often sleep most of their time to preserve their energies. The sleeping feature causes serious data transmission delay. However, each source node that has sensed data needs to quickly disseminate its data to other nodes in the network for redundant storage. Otherwise, data would be lost due to its source node possibly being destroyed by outer forces in a harsh environment. The quick dissemination requirement produces a contradiction with the sleeping delay in the network. How to quickly disseminate all the source data to all the nodes with limited memory in the network for effective preservation is a challenging issue. In this paper, a low-latency and energy-efficient data preservation mechanism in LDC-WSN is proposed. The mechanism is totally distributed. The data can be disseminated to the network with low latency by using a revised probabilistic broadcasting mechanism, and then stored by the nodes with LT (Luby Transform) codes, which are a famous rateless erasure code. After the process of data dissemination and storage completes, some nodes may die due to being destroyed by outer forces. If a mobile sink enters the network at any time and from any place to collect the data, it can recover all of the source data by visiting a small portion of survived nodes in the network. Theoretical analyses and simulation results show that our mechanism outperforms existing mechanisms in the performances of data dissemination delay and energy efficiency.

Association of Gene Mutations with Response to Arsenic-Containing Compound Qinghuang Powder () in Patients with Myelodysplastic Syndromes.

OBJECTIVES: To investigate the relationship between gene mutations and response to Compound Qinghuang Powder (, CQHP) in patients with myelodysplastic syndrome (MDS). METHODS: Forty-three MDS patients were genotyped by ultra-deep targeted sequencing and the clinical data of patients were collected and the relationship between them was analyzed. RESULTS: Up to 41.86% of patients harbored genet mutations, in most cases with more than one mutation. The most common mutations were in SF3B1, U2AF1, ASXL1, and DNMT3A. After treatment with CQHP, about 88.00% of patients no longer required blood transfusion, or needed half of prior transfusions. CONCLUSIONS: CQHP is an effective treatment for patients with MDS, especially those with gene mutations in SF3B1, DNMT3A, U2AF1, and/or ASXL1.

High resolution global chromosomal aberrations from spontaneous miscarriages revealed by low coverage whole genome sequencing.

OBJECTIVE: Chromosome aberrations are generally considered as one of the most substantial causative factors contributing to spontaneous miscarriages. Cytogenetic analyses like G-banded karyotype and chromosomal microarray analyses are often performed to further investigate the chromosome status of a miscarried fetus. STUDY DESIGN: Here, we describe a novel method, AnnoCNV, to detect DNA copy number variations (CNVs) using low coverage whole genome sequencing (WGS). We investigated the overall frequency of chromosomal abnormalities in 149 miscarriage specimens using AnnoCNV. RESULTS: Among 149 fetal miscarriage samples, more than two fifths of them (42.95%, 64) carried at least one chromosomal abnormality, and a subset (40) was identified as autosomal trisomy which account for 26.84% of all samples. We have also developed a robust algorithm in AnnoCNV, which is able to differentiate specifically karyotype 69,XXY from sex chromosomal aneuploidy 45,X, and to identify 45,X/46,XX mosaicism. Lastly, across the whole genome AnnoCNV identifies CNVs, which are associated with both reported symptoms and unknown clinical conditions. CONCLUSION: This cost-effective strategy reveals genome wide discovery of chromosome aberrations at higher resolution, which are consistent with parallel investigation conducted by SNP based assay.

Xist-dependent imprinted X inactivation and the early developmental consequences of its failure.

The long noncoding RNA Xist is expressed from only the paternal X chromosome in mouse preimplantation female embryos and mediates transcriptional silencing of that chromosome. In females, absence of Xist leads to postimplantation lethality. Here, through single-cell RNA sequencing of early preimplantation mouse embryos, we found that the initiation of imprinted X-chromosome inactivation absolutely requires Xist. Lack of paternal Xist leads to genome-wide transcriptional misregulation in the early blastocyst and to failure to activate the extraembryonic pathway that is essential for postimplantation development. We also demonstrate that the expression dynamics of X-linked genes depends on the strain and parent of origin as well as on the location along the X chromosome, particularly at the first 'entry' sites of Xist. This study demonstrates that dosage-compensation failure has an effect as early as the blastocyst stage and reveals genetic and epigenetic contributions to orchestrating transcriptional silencing of the X chromosome during early embryogenesis.

Statistical Approach to Decreasing the Error Rate of Noninvasive Prenatal Aneuploid Detection caused by Maternal Copy Number Variation.

Analyses of cell-free fetal DNA (cff-DNA) from maternal plasma using massively parallel sequencing enable the noninvasive detection of feto-placental chromosome aneuploidy; this technique has been widely used in clinics worldwide. Noninvasive prenatal tests (NIPT) based on cff-DNA have achieved very high accuracy; however, they suffer from maternal copy-number variations (CNV) that may cause false positives and false negatives. In this study, we developed an algorithm to exclude the effect of maternal CNV and refined the Z-score that is used to determine fetal aneuploidy. The simulation results showed that the algorithm is robust against variations of fetal concentration and maternal CNV size. We also introduced a method based on the discrepancy between feto-placental concentrations to help reduce the false-positive ratio. A total of 6615 pregnant women were enrolled in a prospective study to validate the accuracy of our method. All 106 fetuses with T21, 20 with T18, and three with T13 were tested using our method, with sensitivity of 100% and specificity of 99.97%. In the results, two cases with maternal duplications in chromosome 21, which were falsely predicted as T21 by the previous NIPT method, were correctly classified as normal by our algorithm, which demonstrated the effectiveness of our approach.

Biodiversity and population dynamics of microorganisms in a full-scale membrane bioreactor for municipal wastewater treatment.

The total, ammonia-oxidizing, and denitrifying Bacteria in a full-scale membrane bioreactor (MBR) were evaluated monthly for over one year. Microbial communities were analyzed by denaturing gradient gel electrophoresis (DGGE) and clone library analysis of the 16S rRNA and ammonia monooxygenase (amoA) and nitrous oxide reductase (nosZ) genes. The community fingerprints obtained were compared to those from a conventional activated sludge (CAS) process running in parallel treating the same domestic wastewater. Distinct DGGE profiles for all three molecular markers were observed between the two treatment systems, indicating the selection of specific bacterial populations by the contrasting environmental and operational conditions. Comparative 16S rRNA sequencing indicated a diverse bacterial community in the MBR, with phylotypes from the α- and ß-Proteobacteria and Bacteroidetes dominating the gene library. The vast majority of sequences retrieved were not closely related to classified organisms or displayed relatively low levels of similarity with any known 16S rRNA gene sequences and thus represent organisms that constitute new taxa. Similarly, the majority of the recovered nosZ sequences were novel and only moderately related to known denitrifiers from the α- and ß-Proteobacteria. In contrast, analysis of the amoA gene showed a remarkably simple ammonia-oxidizing community with the detected members almost exclusively affiliated with the Nitrosomonas oligotropha lineage. Major shifts in total bacteria and denitrifying community were detected and these were associated with change in the external carbon added for denitrification enhancement. In spite of this, the MBR was able to maintain a stable process performance during that period. These results significantly expand our knowledge of the biodiversity and population dynamics of microorganisms in MBRs for wastewater treatment.