Presence of virus neutralizing antibodies in cerebral spinal fluid correlates with non-lethal rabies in dogs.

BACKGROUND: Rabies is traditionally considered a uniformly fatal disease after onset of clinical manifestations. However, increasing evidence indicates that non-lethal infection as well as recovery from flaccid paralysis and encephalitis occurs in laboratory animals as well as humans. METHODOLOGY/PRINCIPAL FINDINGS: Non-lethal rabies infection in dogs experimentally infected with wild type dog rabies virus (RABV, wt DRV-Mexico) correlates with the presence of high level of virus neutralizing antibodies (VNA) in the cerebral spinal fluid (CSF) and mild immune cell accumulation in the central nervous system (CNS). By contrast, dogs that succumbed to rabies showed only little or no VNA in the serum or in the CSF and severe inflammation in the CNS. Dogs vaccinated with a rabies vaccine showed no clinical signs of rabies and survived challenge with a lethal dose of wild-type DRV. VNA was detected in the serum, but not in the CSF of immunized dogs. Thus the presence of VNA is critical for inhibiting virus spread within the CNS and eventually clearing the virus from the CNS. CONCLUSIONS/SIGNIFICANCE: Non-lethal infection with wt RABV correlates with the presence of VNA in the CNS. Therefore production of VNA within the CNS or invasion of VNA from the periphery into the CNS via compromised blood-brain barrier is important for clearing the virus infection from CNS, thereby preventing an otherwise lethal rabies virus infection

Benchmarking of eight recurrent neural network variants for breath phase and adventitious sound detection on a self-developed open-access lung sound database-HF_Lung_V1

A reliable, remote, and continuous real-time respiratory sound monitor with automated respiratory sound analysis ability is urgently required in many clinical scenarios-such as in monitoring disease progression of coronavirus disease 2019-to replace conventional auscultation with a handheld stethoscope. However, a robust computerized respiratory sound analysis algorithm has not yet been validated in practical applications. In this study, we developed a lung sound database (HF_Lung_V1) comprising 9,765 audio files of lung sounds (duration of 15 s each), 34,095 inhalation labels, 18,349 exhalation labels, 13,883 continuous adventitious sound (CAS) labels (comprising 8,457 wheeze labels, 686 stridor labels, and 4,740 rhonchi labels), and 15,606 discontinuous adventitious sound labels (all crackles). We conducted benchmark tests for long short-term memory (LSTM), gated recurrent unit (GRU), bidirectional LSTM (BiLSTM), bidirectional GRU (BiGRU), convolutional neural network (CNN)-LSTM, CNN-GRU, CNN-BiLSTM, and CNN-BiGRU models for breath phase detection and adventitious sound detection. We also conducted a performance comparison between the LSTM-based and GRU-based models, between unidirectional and bidirectional models, and between models with and without a CNN. The results revealed that these models exhibited adequate performance in lung sound analysis. The GRU-based models outperformed, in terms of F1 scores and areas under the receiver operating characteristic curves, the LSTM-based models in most of the defined tasks. Furthermore, all bidirectional models outperformed their unidirectional counterparts. Finally, the addition of a CNN improved the accuracy of lung sound analysis, especially in the CAS detection tasks.Comment: 48 pages, 8 figures. To be submitte

Robust estimation of bacterial cell count from optical density

Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts

Disabled-2 small interfering RNA modulates cellular adhesive function and MAPK activity during megakaryocytic differentiation of K562 cells

AbstractPrevious studies have shown that Disabled-2 (DAB2) is up-regulated during megakaryocytic differentiation of human K562 cells. To delineate the consequences of DAB2 induction, a DNA vector-based small interfering RNA (siRNA) was designed to intervene in DAB2 expression. We found that DAB2 siRNA specifically inhibited DAB2 induction, resulting in the modulation of cell–cell adhesion and mitogen-activated protein kinase (MAPK) phosphorylation. The morphological changes and β3 integrin expression associated with megakaryocytic differentiation were not affected. Since the MAPK pathway has been shown to involve DAB2 induction [Tseng et al., Biochem. Biophys. Res. Commun. 285 (2001) 129–135], our results suggest a reciprocal regulation between DAB2 and MAPK in the differentiation of K562 cells. In addition, we have demonstrated for the first time that DAB2 siRNA is a valuable tool for unveiling the biological consequences of DAB2 expression

Design of books inventory with RFID antenna in library management system

A 915 MHz printed radio-frequency-identification (RFID) antennas with the characteristics of good gain and omnidirectional beam wave is constructed and evaluated in this study. The objective is to find out their best reading rates for providing effective wireless communications among RFID antenna during the library book inventory process. And an optimal library inventory system which is based on electromagnetic identification (EMID) technology is proposed, which is constructed to find the optimal tag location for a book, test the tag readability for bookshelves, and connect a couple of multi-layer bookshelves with multiplexers and updat the tag reading status in the database of the computer terminal. The fabricated antenna reader and the proposed system are embedded into different locations of bookshelves and tested at the library of Cheng Shiu University in Taiwan. According to the experimental results, the designed prototype of the antenna reader has the characteristics of the directional radiation pattern, good gain, simple shape, low cost and is easy to be integrated into the bookshelf. And the designed library inventory system can authenticate the location of a book automatically. They can benefit administrating librarians with the capabilities of decreasing the library inventory processing time and reducing the possibility of the books being misplaced

Design of books inventory with RFID antenna in library management system

A 915 MHz printed radio-frequency-identification (RFID) antennas with the characteristics of good gain and omnidirectional beam wave is constructed and evaluated in this study. The objective is to find out their best reading rates for providing effective wireless communications among RFID antenna during the library book inventory process. And an optimal library inventory system which is based on electromagnetic identification (EMID) technology is proposed, which is constructed to find the optimal tag location for a book, test the tag readability for bookshelves, and connect a couple of multi-layer bookshelves with multiplexers and updat the tag reading status in the database of the computer terminal. The fabricated antenna reader and the proposed system are embedded into different locations of bookshelves and tested at the library of Cheng Shiu University in Taiwan. According to the experimental results, the designed prototype of the antenna reader has the characteristics of the directional radiation pattern, good gain, simple shape, low cost and is easy to be integrated into the bookshelf. And the designed library inventory system can authenticate the location of a book automatically. They can benefit administrating librarians with the capabilities of decreasing the library inventory processing time and reducing the possibility of the books being misplaced

Self-Organized Cognitive Sensor Networks: Distributed Channel Assignment for Pervasive Sensing

We study the channel assignment strategy in multichannel wireless sensor networks (WSNs) where macrocells and sensor nodes are overlaid. The WSNs dynamically access the licensed spectrum owned by the macrocells to provide pervasive sensing services. We formulate the channel assignment problem as a potential game which has at least one pure strategy Nash equilibrium (NE). To achieve the NE, we propose a stochastic learning-based algorithm which does not require the information of other players’ actions and the time-varying channel. Cluster heads as players in the game act as self-organized learning automata and adjust assignment strategies based on their own action-reward history. The convergence property of the proposed algorithm toward pure strategy NE points is shown theoretically and verified numerically. Simulation results demonstrate that the learning algorithm yields a 26% sensor node capacity improvement as compared to the random selection, and incurs less than 10% capacity loss compared to the exhaustive search

Local Packing Density Is the Main Structural Determinant of the Rate of Protein Sequence Evolution at Site Level

Functional and biophysical constraints result in site-dependent patterns of protein sequence variability. It is commonly assumed that the key structural determinant of site-specific rates of evolution is the Relative Solvent Accessibility (RSA). However, a recent study found that amino acid substitution rates correlate better with two Local Packing Density (LPD) measures, the Weighted Contact Number (WCN) and the Contact Number (CN), than with RSA. This work aims at a more thorough assessment. To this end, in addition to substitution rates, we considered four other sequence variability scores, four measures of solvent accessibility (SA), and other CN measures. We compared all properties for each protein of a structurally and functionally diverse representative dataset of monomeric enzymes. We show that the best sequence variability measures take into account phylogenetic tree topology. More importantly, we show that both LPD measures (WCN and CN) correlate better than all of the SA measures, regardless of the sequence variability score used. Moreover, the independent contribution of the best LPD measure is approximately four times larger than that of the best SA measure. This study strongly supports the conclusion that a site’s packing density rather than its solvent accessibility is the main structural determinant of its rate of evolution