Convolutional Neural Network-Driven Impedance Flow Cytometry for Accurate Bacterial Differentiation.

Impedance flow cytometry (IFC) has been demonstrated to be an efficient tool for label-free bacterial investigation to obtain the electrical properties in real time. However, the accurate differentiation of different species of bacteria by IFC technology remains a challenge owing to the insignificant differences in data. Here, we developed a convolutional neural networks (ConvNet) deep learning approach to enhance the accuracy and efficiency of the IFC toward distinguishing various species of bacteria. First, more than 1 million sets of impedance data (comprising 42 characteristic features for each set) of various groups of bacteria were trained by the ConvNet model. To improve the efficiency for data analysis, the Spearman correlation coefficient and the mean decrease accuracy of the random forest algorithm were introduced to eliminate feature interaction and extract the opacity of impedance related to the bacterial wall and membrane structure as the predominant features in bacterial differentiation. Moreover, the 25 optimized features were selected with differentiation accuracies of >96% for three groups of bacteria (bacilli, cocci, and vibrio) and >95% for two species of bacilli (Escherichia coli and Salmonella enteritidis), compared to machine learning algorithms (complex tree, linear discriminant, and K-nearest neighbor algorithms) with a maximum accuracy of 76.4%. Furthermore, bacterial differentiation was achieved on spiked samples of different species with different mixing ratios. The proposed ConvNet deep learning-assisted data analysis method of IFC exhibits advantages in analyzing a huge number of data sets with capacity for extracting predominant features within multicomponent information and will bring about progress and advances in the fields of both biosensing and data analysis.

Multi-U-Net: Residual Module under Multisensory Field and Attention Mechanism Based Optimized U-Net for VHR Image Semantic Segmentation.

As the acquisition of very high resolution (VHR) images becomes easier, the complex characteristics of VHR images pose new challenges to traditional machine learning semantic segmentation methods. As an excellent convolutional neural network (CNN) structure, U-Net does not require manual intervention, and its high-precision features are widely used in image interpretation. However, as an end-to-end fully convolutional network, U-Net has not explored enough information from the full scale, and there is still room for improvement. In this study, we constructed an effective network module: residual module under a multisensory field (RMMF) to extract multiscale features of target and an attention mechanism to optimize feature information. RMMF uses parallel convolutional layers to learn features of different scales in the network and adds shortcut connections between stacked layers to construct residual blocks, combining low-level detailed information with high-level semantic information. RMMF is universal and extensible. The convolutional layer in the U-Net network is replaced with RMMF to improve the network structure. Additionally, the multiscale convolutional network was tested using RMMF on the Gaofen-2 data set and Potsdam data sets. Experiments show that compared to other technologies, this method has better performance in airborne and spaceborne images.

Using MODIS data to analyse the ecosystem water use efficiency spatial-temporal variations across Central Asia from 2000 to 2014.

It is important to understand the carbon-water cycle, which accurately reflects the temporal and spatial variabilities in ecosystem water use efficiency (WUE). In this study, the Mann-Kendall (MK) test was used to study the variabilities in the spatial patterns of the gross primary production (GPP), evapotranspiration and WUE across Central Asia [the Xinjiang Uyghur Autonomous Region (XJ) in China (CHN), Kazakhstan (KAZ), Turkmenistan (TKM), Uzbekistan (UZB), Kyrgyzstan (KGZ), and Tajikistan (TJK)] from 2000 to 2014. We compared the change results by country, land cover type, population density, and human influence. In addition, the results of GPP, evapotranspiration (ET), and WUE parameter tests were combined and classified to analyse the causes of the changes in WUE. The results showed that (1) the time series of GPP, ET and WUE exhibited no significant changes. The spatial distribution of the WUE exhibited significant increases in the northern part of KAZ, the Ili Valley and the alpine region in KGZ and exhibited decreases in south Xinjiang and the irrigated area of UZB. (2) The main land cover types that exhibited changes in WUE were farmlands and grasslands, and areas with a medium population density exhibited large WUE changes. (3) The increased WUE resulted from an increased GPP and decreased ET. The increased GPP was because of increased precipitation and the Green for Grain Project, and the decreased ET was due to the response of vegetation to drought stress; the decreased WUE was mainly caused by changes in the crops planted and unreasonable water use practices in the irrigated agricultural areas in Central Asia. This study, which is based on the variabilities in WUE spatial patterns, should provide a theoretical basis for ecosystems in arid land areas.

Assessing the Response of Ecosystem Water Use Efficiency to Drought During and after Drought Events across Central Asia.

The frequency and intensity of drought are expected to increase worldwide in the future. However, it is still unclear how ecosystems respond to drought. Ecosystem water use efficiency (WUE) is an essential ecological index used to measure the global carbon-water cycles, and is defined as the carbon absorbed per unit of water lost by the ecosystem. In this study, we applied gross primary productivity (GPP), evapotranspiration (ET), land surface temperature (LST), and normalized difference vegetation index (NDVI) data to calculate the WUE and drought index (temperature vegetation dryness index (TVDI)), all of which were retrieved from moderate resolution imaging spectroradiometer (MODIS) data. We compared the mean WUE across different vegetation types, drought classifications, and countries. The temporal and spatial changes in WUE and drought were analyzed. The correlation between drought and WUE was calculated and compared across different vegetation types, and the differences in WUE between drought and post-drought periods were compared. The results showed that (1) ecosystems with a low (high) productivity had a high (low) WUE, and the mean ecosystem WUE of Central Asia showed vast differences across various drought levels, countries, and vegetation types. (2) The WUE in Central Asia exhibited an increasing trend from 2000 to 2014, and Central Asia experienced both drought (from 2000 to 2010) and post-drought (from 2011 to 2014) periods. (3) The WUE showed a negative correlation with drought during the drought period, and an obvious drought legacy effect was found, in which severe drought affected the ecosystem WUE over the following two years, while a positive correlation between WUE and drought was found in the post-drought period. (4) A significant increase in ecosystem WUE was found after drought, which revealed that arid ecosystems exhibit high resilience to drought stress. Our results can provide a specific reference for understanding how ecosystems will respond to climate change.

Hierarchical assembly of gold nanorod stripe patterns for sensing and cells alignment.

Hierarchical assemblies of nanomaterial superstructures with controlled orientation affords a multitude of novel properties of plasmonics and broad applications. Yet constructing multi-functional superstructures with nanoparticles positioned in desired locations remains challenging. Herein, gold nanorods (GNRs) assembled in stripe patterns with controlled orientation and structures in millimeter scale for versatile application have been achieved. Applications of patterned GNRs in sensing enhancement and engineering mammalian cells alignment are investigated experimentally. The performance of patterned GNRs in surface enhanced Raman scattering (SERS) and electrical sensing are found in orientational dependence. The SERS signals of vertically arranged GNR arrays exhibit double the folder intensity than those horizontally arranged. In contrast, the horizontally arranged GNRs exhibit twice as much electrical conductivity. The system is further explored to pattern mammalian cells. For the first time, we reveal the nanostructured topography of GNR confined cells to a specific region, and direct the adhesion and extension of living cells, which opens up broad applications in tissue engineering and biosensing.

Soil Moisture Retrival Based on Sentinel-1 Imagery under Sparse Vegetation Coverage.

Soil moisture is an important aspect of heat transfer process and energy exchange between land-atmosphere systems, and it is a key link to the surface and groundwater circulation and land carbon cycles. In this study, according to the characteristics of the study area, an advanced integral equation model was used for numerical simulation analysis to establish a database of surface microwave scattering characteristics under sparse vegetation cover. Thus, a soil moisture retrieval model suitable for arid area was constructed. The results were as follows: (1) The response of the backscattering coefficient to soil moisture and associated surface roughness is significantly and logarithmically correlated under different incidence angles and polarization modes, and, a database of microwave scattering characteristics of arid soil surface under sparse vegetation cover was established. (2) According to the Sentinel-1 radar system parameters, a model for retrieving spatial distribution information of soil moisture was constructed; the soil moisture content information was extracted, and the results were consistent with the spatial distribution characteristics of soil moisture in the same period in the research area. (3) For the 0⁻10 cm surface soil moisture, the correlation coefficient between the simulated value and the measured value reached 0.8488, which means that the developed retrieval model has applicability to derive surface soil moisture in the oasis region of arid regions. This study can provide method for real-time and large-scale detection of soil moisture content in arid areas.

Flexible Film Bulk Acoustic Wave Filters toward Radiofrequency Wireless Communication.

This paper presents a flexible radiofrequency filter with a central frequency of 2.4 GHz based on film bulk acoustic wave resonators (FBARs). The flexible filter consists of five air-gap type FBARs, each comprised of an aluminum nitride piezoelectric thin film sandwiched between two thin-film electrodes. By transfer printing the inorganic film structure from a silicon wafer to an ultrathin polyimide substrate, high electrical performance and mechanical flexibility are achieved. The filter has a peak insertion loss of -1.14 dB, a 3 dB bandwidth of 107 MHz, and a temperature coefficient of frequency of -27 ppm °C-1 . The passband and roll-off characteristics of the flexible filter are comparable with silicon-based commercial products. No electrical performance degradation and mechanical failure occur under bending tests with a bending radius of 2.5 mm or after 100 bending cycles. The flexible FBAR filters are believed to be promising candidates for future flexible wireless communication systems.

The first complete genomic characterization of an Amur virus isolate from China.

Amur virus (AMRV) is a member of the genus Hantavirus in the family Bunyaviridae. In this study, we determined for the first time the complete genome sequence of the AMRV H8205 strain, which was isolated from a patient with hemorrhagic fever with renal syndrome (HFRS) in China. The complete nucleotide sequence of the S segment of AMRV H8205 is 1699 nt long, with a 5' noncoding region (5'NC) of 36 nt, followed by a coding sequence of 1290 nt and a 3'NC of 373 nt. The complete sequence of the M segment is 3615 nt long, with a 5'NC of 40 nt, followed by a coding sequence of 3408 nt and a 3'NC of 167 nt. The complete sequence of the L segment is 6536 nt long, with a 5'NC of 37 nt, followed by a coding sequence of 6453 nt and a 3'NC of 40 nt. The major open reading frame (ORF) of each of the three segments (S, nt 37-1326; M, nt 41-3445; L, nt 38-6490) has a coding capacity of 430 aa, 1135 aa, 2151 aa, respectively. Phylogenetic analysis of the nucleotide sequences using the NJ method indicated that H8205 virus, together with the Amur strains isolated from Far-Eastern Russia and Korea, forms a well-supported lineage. Our results will provide insights into the genetic diversity of hantaviruses (HNTV).

Identification of dust aerosols, their sources, and the effect of soil moisture in Central Asia.

Dust aerosols in Central Asia are an important factor in global climate change and attribution studies. Identifying the source of dust in Central Asia is crucial for understanding the ecological environment and climate, locally and globally. In this study, daily dust aerosol data were calculated and extracted for Central Asia from 2003 to 2018. The multi-year trends of dust aerosols were analyzed, dust sources were identified, the characteristics of dust aerosols in dust sources were analyzed, and the influence of soil moisture on sand initiation was explored. The results show that there are distinct seasonal characteristics in the spatial distribution of dust aerosols in Central Asia. The proportion of the area in the zone of high dust aerosols was the greatest in spring. Nearly half of the dust aerosol areas exhibited an increasing trend. A high incidence of dust sources was mainly distributed in the southern Xinjiang region. The trend of change in the dust area first increased and then decreased. With the increase in soil moisture under different wind speed conditions, the aerosols from dust sources all showed an exponentially decreasing trend, and the increase in soil moisture led to an increase in the wind speed threshold of sand initiation. This study provides basic data support for the study of dust aerosols, identifies dust sources, and provides a basis for studying the radiative forcing and climate effects of dust aerosols in Central Asia.

Pinch-off droplet generator using microscale gigahertz acoustics.

The generation and dispensing of microdroplets is a vital process in various fields such as biomedicine, medical diagnosis and chemistry. However, most methods still require the structures of nozzles or microchannels to assist droplet generation, which leads to limitations on system flexibility and restrictions on the size range of the generated droplets. In this paper, we propose a nozzle-free acoustic-based method for generating droplets using a gigahertz (GHz) bulk acoustic wave (BAW). Unlike most of the acoustofluidic approaches, the proposed method produces the droplet by pinching-off the liquid column generated by the acoustic body force at the oil-water interface. Benefitting from the focused acoustic energy and small footprint of the device, four orders of magnitude (ranging from 2 µm to 1800 µm) of droplet size could be produced by controlling the working time and power of the device. We also demonstrated cell encapsulation in the droplet and a high cell viability was achieved. The proposed acoustic-based droplet generation method exhibits capacity for generating droplets with a wide size range, versatility toward different viscosities, as well as biocompatibility for handling viable samples, which shows potential in miniaturization and scalability.

Dual-functional gold nanorods micro pattern guiding cell alignment and cellular microenvironment monitoring.

Surface topography has become a powerful tool to control cell behaviors, however, it's still difficult to monitor cellular microenvironment changes during topography-induced cell responses. Here, a dual-functional platform integrating cell alignment with extracellular pH (pHe) measurement is proposed. The platform is fabricated by assembling gold nanorods (AuNRs) into micro pattern via wettability difference interface method, which provides topographical cues and surface-enhanced Raman scattering (SERS) effect for cell alignment and biochemical detection respectively. Results demonstrate that contact guidance and cell morphology changes are achieved by the AuNRs micro pattern, and pHe are also obtained by the changes of SERS spectra during cell alignment, where the pHe near cytoplasm is lower than nucleus, revealing the heterogeneity of extracellular microenvironment. Moreover, a correlation between lower extracellular pH and higher cell migration ability is revealed, and AuNRs micro pattern can differentiate cells with different migration ability, which may be an inheritable character during cell division. Furthermore, mesenchymal stem cells response dramatically to AuNRs micro pattern, showing different morphology and increased pHe level, offering the potential of impacting stem cell differentiation. This approach provides a new idea for the research of cell regulation and response mechanism.

A self-contained acoustofluidic platform for biomarker detection.

Self-contained microfluidic platforms with on-chip integration of flow control units, microreactors, (bio)sensors, etc. are ideal systems for point-of-care (POC) testing. However, current approaches such as micropumps and microvalves, increase the cost and the control system, and it is rather difficult to integrate into a single chip. Herein, we demonstrated a versatile acoustofluidic platform actuated by a Lamb wave resonator (LWR) array, in which pumping, mixing, fluidic switching, and particle trapping are all achieved on a single chip. The high-speed microscale acoustic streaming triggered by the LWR in the confined microchannel can be utilized to realize a flow resistor and switch. Variable unidirectional pumping was realized by regulating the relative position of the LWR in various custom-designed microfluidic structures and adoption of different geometric parameters for the microchannel. In addition, to realize quantitative biomarker detection, the on-chip flow resistor, micropump, micromixer and particle trapper were also integrated with a CMOS photo sensor and electronic driver circuit, resulting in an automated handheld microfluidic system with no moving parts. Finally, the acoustofluidic platform was tested for prostate-specific antigen (PSA) sensing, which demonstrates the biocompatibility and applied potency of this proposed self-contained system in POC biomedical applications.

Virulence of H5N1 virus in mice attenuates after in vitro serial passages.

The virulence of A/Vietnam/1194/2004 (VN1194) in mice attenuated after serial passages in MDCK cells and chicken embryos, because the enriched large-plaque variants of the virus had significantly reduced virulence. In contrast, the small-plaque variants of the virus and the variants isolated from the brain of mice that were infected with the parental virus VN1194 had much higher virulence in mice. The virulence attenuation of serially propagated virus may be caused by the reduced neurotropism in mice. Our whole genome sequence analysis revealed substitutions of a total of two amino acids in PB1, three in PB2, two in PA common for virulence attenuated variants, all or part of which may be correlated with the virulence attenuation and reduced neurotropism of the serially propagated VN1194 in mice. Our study indicates that serial passages of VN1194 in vitro lead to adaptation and selection of variants that have markedly decreased virulence and neurotropism, which emphasizes the importance of direct analysis of original or less propagated virus samples.

Mixing during Trapping Enabled a Continuous-Flow Microfluidic Smartphone Immunoassay Using Acoustic Streaming.

Smartphone-enabled microfluidic chemiluminescence immunoassay is a promising portable system for point-of-care (POC) biosensing applications. However, due to the rather faint emitted light in such a limited sample volume, it is still difficult to reach the clinically accepted range when the smartphone serves as a standalone detector. Besides, the multiple separation and washing steps during sample preparation hinder the immunoassay's applications for POC usage. Herein, we proposed a novel acoustic streaming tweezers-enabled microfluidic immunoassay, where the probe particles' purification, reaction, and sensing were simply achieved on the same chip at continuous-flow conditions. The dedicatedly designed high-speed microscale vortexes not only enable dynamic trapping and washing of the probe particles on-demand but also enhance the capture efficiency of the heterogeneous particle-based immunoassay through active mixing during trapping. The enriched probe particles and enhanced biomarker capture capability increase the local chemiluminescent light intensity and enable direct capture of the immunobinding signal by a regular smartphone camera. The system was tested for prostate-specific antigen (PSA) sensing both in buffer and serum, where a limit of detection of 0.2 ng/mL and a large dynamic response range from 0.3 to 10 ng/mL using only 10 µL of sample were achieved in a total assay time of less than 15 min. With the advantages of on-chip integration of sample preparation and detection and high sensing performance, the developed POC platform could be applied for many on-site diagnosis applications.

Smartphone-enabled Dynamic Chemiluminescence Biomarker Quantitation Using Acoustic Tweezers Approach.

Quantitation of protein biomarker featured with portability, rapidity, high sensitivity is critical for the point-of-care testing (POCT) application. Herein, a novel smartphone-enabled microfluidic chemiluminescence platform for the quantitation of prostate specific antigen (PSA) was proposed based on acoustic tweezers approach. The primary antibodies labeled polystyrene microparticles (Ab1-PSs), target samples, the horseradish peroxidase labeled secondary antibodies (Ab2-HRP) were injected into the microfluidics simultaneously. Under the actuation of Lamb Wave Resonator (LWR), they were dynamically trapped and concentrated in the acoustic streaming; meanwhile, the biomolecular binding was enhanced. After the injection of chemiluminescent substrate, the concentrated immuno-particles catalyzed hydrogen peroxide (H2O2) reaction so that the emitted blue light was directly captured by smartphone. Besides, the flow rate and the applied power of LWR were optimized for the signal amplification. The chemiluminescence immunoassay exhibited a dynamic linear range from 0.5 ng/mL to 10 ng/mL with a limit of detection of 0.1 ng/mL in PBS buffer. The portable immunosensor will be utilized for the quantitation of PSA in serum samples to demonstrate the clinical significance.Clinical Relevance-The smartphone-enabled detection platform realizes the quantitation of biomarker within 10 min, which reveals a valuable potential tool for the early diagnosis of various diseases, even in resource-limited regions.

Characterization and application of monoclonal antibodies specific to West Nile virus envelope protein.

Recent epidemics of West Nile virus (WNV) around the world have been associated with significant rates of mortality and morbidity in humans. To develop standard WNV diagnostic tools that can differentiate WNV from Japanese encephalitis virus (JEV), four monoclonal antibodies (MAbs) specific to WNV envelope (E) protein were produced and characterized by isotyping, reactivity with denatured and native antigens, affinity assay, immunofluorescence assay (IFA), and epitope competition, as well as cross-reactivity with JEV. Two of the MAbs (6A11 and 4B3) showed stronger reactivity with E protein than the others (2F5 and 6H7) in Western blot analysis. 4B3 could bind with denatured antigen, as well as native antigens in indirect ELISA, flow cytometry analysis, and IFA; whereas 2F5 showed highest affinity with native antigen. 4B3 and 2F5 were therefore used to establish an antigen capture-ELISA (AC-ELISA) detection system. The sensitivity of this AC-ELISA was 3.95 TCID(50)/0.1 ml for WNV-infected cell culture supernatant. Notably, these MAbs showed no cross-reactivity with JEV, which suggests that they are useful for further development of highly sensitive, easy handling, and less time-consuming detection kits/tools in WNV surveillance in areas where JEV is epidemic.

Simultaneously subtyping of all influenza A viruses using DNA microarrays.

Rapid diagnosis of novel emerging subtypes of influenza viruses is vital for effective global influenza surveillance. To this end, a novel microarray based surveillance was developed for subtyping all influenza A viruses on one chip. Using reference strains of different influenza subtypes and samples from different areas, the results show that all the subtypes of the influenza A virus could be identified simultaneously on this microchip with high sensitivity. There was no cross-hybridization reaction with other viruses, indicating that the microarray is specific for influenza A viruses. Such a diagnostic microarray will undoubtedly be useful for identifying novel influenza A virus subtypes.

Complete genome sequences of the SARS-CoV: the BJ Group (Isolates BJ01-BJ04).

Beijing has been one of the epicenters attacked most severely by the SARS-CoV (severe acute respiratory syndrome-associated coronavirus) since the first patient was diagnosed in one of the city's hospitals. We now report complete genome sequences of the BJ Group, including four isolates (Isolates BJ01, BJ02, BJ03, and BJ04) of the SARS-CoV. It is remarkable that all members of the BJ Group share a common haplotype, consisting of seven loci that differentiate the group from other isolates published to date. Among 42 substitutions uniquely identified from the BJ group, 32 are non-synonymous changes at the amino acid level. Rooted phylogenetic trees, proposed on the basis of haplotypes and other sequence variations of SARS-CoV isolates from Canada, USA, Singapore, and China, gave rise to different paradigms but positioned the BJ Group, together with the newly discovered GD01 (GD-Ins29) in the same clade, followed by the H-U Group (from Hong Kong to USA) and the H-T Group (from Hong Kong to Toronto), leaving the SP Group (Singapore) more distant. This result appears to suggest a possible transmission path from Guangdong to Beijing/Hong Kong, then to other countries and regions.

A complete sequence and comparative analysis of a SARS-associated virus (Isolate BJ01).

The genome sequence of the Severe Acute Respiratory Syndrome (SARS)-associated virus provides essential information for the identification of pathogen(s), exploration of etiology and evolution, interpretation of transmission and pathogenesis, development of diagnostics, prevention by future vaccination, and treatment by developing new drugs. We report the complete genome sequence and comparative analysis of an isolate (BJ01) of the coronavirus that has been recognized as a pathogen for SARS. The genome is 29725 nt in size and has 11 ORFs (Open Reading Frames). It is composed of a stable region encoding an RNA-dependent RNA polymerase (composed of 2 ORFs) and a variable region representing 4 CDSs (coding sequences) for viral structural genes (the S, E, M, N proteins) and 5 PUPs (putative uncharacterized proteins). Its gene order is identical to that of other known coronaviruses. The sequence alignment with all known RNA viruses places this virus as a member in the family of Coronaviridae. Thirty putative substitutions have been identified by comparative analysis of the 5 SARS-associated virus genome sequences in GenBank. Fifteen of them lead to possible amino acid changes (non-synonymous mutations) in the proteins. Three amino acid changes, with predicted alteration of physical and chemical features, have been detected in the S protein that is postulated to be involved in the immunoreactions between the virus and its host. Two amino acid changes have been detected in the M protein, which could be related to viral envelope formation. Phylogenetic analysis suggests the possibility of non-human origin of the SARS-associated viruses but provides no evidence that they are man-made. Further efforts should focus on identifying the etiology of the SARS-associated virus and ruling out conclusively the existence of other possible SARS-related pathogen(s).