The battle of the SNPs

This month’s Genome Watch highlights new perspectives on polygenic adaptation and its consequences for fitness in microbial populations

A Polygon Model for Wireless Sensor Network Deployment with Directional Sensing Areas

The modeling of the sensing area of a sensor node is essential for the deployment algorithm of wireless sensor networks (WSNs). In this paper, a polygon model is proposed for the sensor node with directional sensing area. In addition, a WSN deployment algorithm is presented with topology control and scoring mechanisms to maintain network connectivity and improve sensing coverage rate. To evaluate the proposed polygon model and WSN deployment algorithm, a simulation is conducted. The simulation results show that the proposed polygon model outperforms the existed disk model and circular sector model in terms of the maximum sensing coverage rate

Transmission of acute infectious illness among cases of Kawasaki disease and their household members

Background/purposeKawasaki disease (KD) is a disease of unknown cause and the causative agent is most likely to be infectious in nature. To investigate the household transmission pattern of infectious illness and etiology, we thus initiated a prospective case and household study.MethodsWe enrolled KD cases and their household members from February 2004 to September 2008. The KD cases and their household members accepted questionnaire-based interviews of the contact history, signs of infection, and symptoms to check whether clusters of infectious illness occurred.ResultsA total of 142 KD cases and 561 household members were enrolled. Among the 142 KD cases, 136 cases (96%) were typical KD, and six (4%) were atypical KD. Of the 561 household members, 17% were siblings, 46% were parents, 18% were grandparents, and the others were cousins or babysitters. Prior to the onset of their KD illness, 66% (94/142) KD cases had contact with ill household members. On the same day of the onset of KD cases' illness, 4% (6/142) KD cases had household members with illness. After KD cases' disease onset, 70% (100/142) KD cases had at least one other family member with illness. Overall, 61% (343/561) of all the household members had acute infectious illness during KD cases' acute stage, and 92% (130/142) of the families had clusters of infectious illness.ConclusionA total of 66% KD cases had positive contact with ill household members prior to their disease onset and 92% of families had clusters of infectious illness, so KD is strongly associated with infections

The Complete Mitochondrial Genome Sequence of the Planthopper, Sivaloka damnosus

The complete mitochondrial genome (mitogenome) sequence was determined from the plant hopper, Sivaloka damnosus Chow and Lu (Hemiptera: Issidae), a representative of the insect family Issidae. The genome is a circular molecule of 15,287 bp with a total A+T content of 76.5%. The gene content, order, and structure are identical to that in Drosophila melanogaster, which is considered ancestral for insects. All 13 protein-coding genes of the S. damnosus mitogenome have a putative inframe ATR methionine or ATT isoleucine codons as start signals. The usual termination codons (TAA and TAG) were found in 11 protein-coding genes. However, atp6, and nad4 have incomplete termination codons. All tRNAs show stable canonical clover-leaf structures similar to other insect mitochondrial tRNAs, except for tRNASer(AGN), which has a reduced DHU arm. The A+T-rich region or putative control region includes two extensive repeat regions. The first repeat region is composed of two sets of complicated repeat units, and these repetitive sequences are arranged alternately; the second contains ten 20 bp tandemly repetitive sequences. In the phylogenetic analyses based on protein-coding genes, Cicadomorpha is a sister to Fulgoromorpha+Sternorrhyncha, and Heteroptera is a sister to all other Hemiptera

Extremely long quasiparticle spin lifetimes in superconducting aluminium using MgO tunnel spin injectors

There has been an intense search in recent years for long-lived spin-polarized carriers for spintronic and quantum-computing devices. Here we report that spin polarized quasi-particles in superconducting aluminum layers have surprisingly long spin-lifetimes, nearly a million times longer than in their normal state. The lifetime is determined from the suppression of the aluminum's superconductivity resulting from the accumulation of spin polarized carriers in the aluminum layer using tunnel spin injectors. A Hanle effect, observed in the presence of small in-plane orthogonal fields, is shown to be quantitatively consistent with the presence of long-lived spin polarized quasi-particles. Our experiments show that the superconducting state can be significantly modified by small electric currents, much smaller than the critical current, which is potentially useful for devices involving superconducting qubits

Nanostructured luminescently labeled nucleic acids

Important and emerging trends at the interface of luminescence, nucleic acids and nanotechnology are: (i) the conventional luminescence labeling of nucleic acid nanostructures (e.g. DNA tetrahedron); (ii) the labeling of bulk nucleic acids (e.g. single‐stranded DNA, double‐stranded DNA) with nanostructured luminescent labels (e.g. copper nanoclusters); and (iii) the labeling of nucleic acid nanostructures (e.g. origami DNA) with nanostructured luminescent labels (e.g. silver nanoclusters). This review surveys recent advances in these three different approaches to the generation of nanostructured luminescently labeled nucleic acids, and includes both direct and indirect labeling methods

Reversible Modulation of Spontaneous Emission by Strain in Silicon Nanowires

We computationally study the effect of uniaxial strain in modulating the spontaneous emission of photons in silicon nanowires. Our main finding is that a one to two orders of magnitude change in spontaneous emission time occurs due to two distinct mechanisms: (A) Change in wave function symmetry, where within the direct bandgap regime, strain changes the symmetry of wave functions, which in turn leads to a large change of optical dipole matrix element. (B) Direct to indirect bandgap transition which makes the spontaneous photon emission to be of a slow second order process mediated by phonons. This feature uniquely occurs in silicon nanowires while in bulk silicon there is no change of optical properties under any reasonable amount of strain. These results promise new applications of silicon nanowires as optoelectronic devices including a mechanism for lasing. Our results are verifiable using existing experimental techniques of applying strain to nanowires

Presentations of patients of poisoning and predictors of poisoning-related fatality: Findings from a hospital-based prospective study

<p>Abstract</p> <p>Background</p> <p>Poisoning is a significant public health problem worldwide and is one of the most common reasons for visiting emergency departments (EDs), but factors that help to predict overall poisoning-related fatality have rarely been elucidated. Using 1512 subjects from a hospital-based study, we sought to describe the demographic and clinical characteristics of poisoning patients and to identify predictors for poisoning-related fatality.</p> <p>Methods</p> <p>Between January 2001 and December 2002 we prospectively recruited poisoning patients through the EDs of two medical centers in southwest Taiwan. Interviews were conducted with patients within 24 hours after admission to collect relevant information. We made comparisons between survival and fatality cases, and used logistic regressions to identify predictors of fatality.</p> <p>Results</p> <p>A total of 1512 poisoning cases were recorded at the EDs during the study period, corresponding to an average of 4.2 poisonings per 1000 ED visits. These cases involved 828 women and 684 men with a mean age of 38.8 years, although most patients were between 19 and 50 years old (66.8%), and 29.4% were 19 to 30 years. Drugs were the dominant poisoning agents involved (49.9%), followed by pesticides (14.5%). Of the 1512 patients, 63 fatalities (4.2%) occurred. Paraquat exposure was associated with an extremely high fatality rate (72.1%). The significant predictors for fatality included age over 61 years, insufficient respiration, shock status, abnormal heart rate, abnormal body temperature, suicidal intent and paraquat exposure.</p> <p>Conclusion</p> <p>In addition to well-recognized risk factors for fatality in clinical settings, such as old age and abnormal vital signs, we found that suicidal intent and ingestion of paraquat were significant predictors of poisoning-related fatality. Identification of these predictors may help risk stratification and the development of preventive interventions.</p

Results of the Photometric LSST Astronomical Time-series Classification Challenge (PLAsTiCC)

Next-generation surveys like the Legacy Survey of Space and Time (LSST) on the Vera C. Rubin Observatory (Rubin) will generate orders of magnitude more discoveries of transients and variable stars than previous surveys. To prepare for this data deluge, we developed the Photometric LSST Astronomical Time-series Classification Challenge (PLAsTiCC), a competition that aimed to catalyze the development of robust classifiers under LSST-like conditions of a nonrepresentative training set for a large photometric test set of imbalanced classes. Over 1000 teams participated in PLAsTiCC, which was hosted in the Kaggle data science competition platform between 2018 September 28 and 2018 December 17, ultimately identifying three winners in 2019 February. Participants produced classifiers employing a diverse set of machine-learning techniques including hybrid combinations and ensemble averages of a range of approaches, among them boosted decision trees, neural networks, and multilayer perceptrons. The strong performance of the top three classifiers on Type Ia supernovae and kilonovae represent a major improvement over the current state of the art within astronomy. This paper summarizes the most promising methods and evaluates their results in detail, highlighting future directions both for classifier development and simulation needs for a next-generation PLAsTiCC data set

High-Level Expression of Notch1 Increased the Risk of Metastasis in T1 Stage Clear Cell Renal Cell Carcinoma

Background: Although metastasis of clear cell renal cell carcinoma (ccRCC) is basically observed in late stage tumors, T1 stage metastasis of ccRCC can also be found with no definite molecular cause resulting inappropriate selection of surgery method and poor prognosis. Notch signaling is a conserved, widely expressed signal pathway that mediates various cellular processes in normal development and tumorigenesis. This study aims to explore the potential role and mechanism of Notch signaling in the metastasis of T1 stage ccRCC. Methodology/Principal Findings: The expression of Notch1 and Jagged1 were analyzed in tumor tissues and matched normal adjacent tissues obtained from 51 ccRCC patients. Compared to non-tumor tissues, Notch1 and Jagged1 expression was significantly elevated both in mRNA and protein levels in tumors. Tissue samples of localized and metastatic tumors were divided into three groups based on their tumor stages and the relative mRNA expression of Notch1 and Jagged1 were analyzed. Compared to localized tumors, Notch1 expression was significantly elevated in metastatic tumors in T1 stage while Jagged1 expression was not statistically different between localized and metastatic tumors of all stages. The average size of metastatic tumors was significantly larger than localized tumors in T1 stage ccRCC and the elevated expression of Notch1 was significantly positive correlated with the tumor diameter. The functional significance of Notch signaling was studied by transfection of 786-O, Caki-1 and HKC cell lines with full-length expression plasmids of Notch1 and Jagged1