The discrimination between autoimmune glial fibrillary acidic protein astrocytopathy and tuberculous meningitis.

OBJECTIVE: The differential diagnosis between autoimmune glial fibrillary acidic protein astrocytopathy (AGFAPA) mimicking tuberculous meningitis and tuberculous meningitis (TBM) remains challenging in clinical practice. This study aims to identify the clinical, laboratory parameters, and clinical score systems that may be helpful in differentiating AGFAPA from TBM. METHOD: Overall 22 AGFAPA patients who were initially misdiagnosed as TBM (AGFAPA-TBM) and 30 confirmed TBM patients were included. The clinical, laboratory, imaging parameters, Thwaites systems, and Lancet consensus scoring systems (LCSS) of all patients were reviewed. Logistic regression was employed to establish a diagnostic formula to differentiate AGFAPA-TBM from TBM. The receiver operating characteristic (ROC) curve was applied to determine the best diagnostic critical point of the formula. RESULTS: Urinary retention was more frequent in AGFAPA-TBM patients (72.7% vs 33.3%, p = 0.012). A significantly lower ratio of T-SPOT. TB was noted in AGFAPA-TBM patients (9.1% vs 82.1%, p < 0.001). We found the LCSS was able to differentiate AGFAPA-TBM from TBM (AUC value 0.918, 95% CI=0.897-0.924). Furthermore, we set up a new scoring system with three variables: urinary retention, T-SPOT. TB, and cerebral imaging criteria in LCSS. The proposed diagnostic score ranges from -8 to 2, and a score of ≥ 0 was suggestive of AGFAPA-TBM (AUC value 0.938, 95% CI=0.878-0.951). CONCLUSIONS: This study is the first to evaluate the Thwaites system and LCSS in AGFAPA-TBM and TBM. We provide an alternative diagnostic formula to differentiate AGFAPA-TBM from TBM and suggest testing for GFAP antibodies to avoid misdiagnosis when this scoring system meets AGFAPA-TBM.

Identification and Localisation Algorithm for Sugarcane Stem Nodes by Combining YOLOv3 and Traditional Methods of Computer Vision.

Sugarcane stem node identification is the core technology required for the intelligence and mechanization of the sugarcane industry. However, detecting stem nodes quickly and accurately is still a significant challenge. In this paper, in order to solve this problem, a new algorithm combining YOLOv3 and traditional methods of computer vision is proposed, which can improve the identification rate during automated cutting. First, the input image is preprocessed, during which affine transformation is used to correct the posture of the sugarcane and a rotation matrix is established to obtain the region of interest of the sugarcane. Then, a dataset is built to train the YOLOv3 network model and the position of the stem nodes is initially determined using the YOLOv3 model. Finally, the position of the stem nodes is further located accurately. In this step, a new gradient operator is proposed to extract the edge of the image after YOLOv3 recognition. Then, a local threshold determination method is proposed, which is used to binarize the image after edge extraction. Finally, a localization algorithm for stem nodes is designed to accurately determine the number and location of the stem nodes. The experimental results show that the precision rate, recall rate, and harmonic mean of the stem node recognition algorithm in this paper are 99.68%, 100%, and 99.84%, respectively. Compared to the YOLOv3 network, the precision rate and the harmonic mean are improved by 2.28% and 1.13%, respectively. Compared to other methods introduced in this paper, this algorithm has the highest recognition rate.

A Cross-Sectional Nationwide Study on Accessibility and Availability of Neonatal care Resources in Hospitals of China: Current Situation, Mortality and Regional Differences: Neonatal Care Resources and Newborn Mortality in China.

BACKGROUND: To investigate the current situation of neonatal care resources (NCR), newborn mortality rates (NMR), regional differences and existing challenges in China. METHODS: By using a self-designed questionnaire form and the cross-sectional method, we conducted a survey of all hospitals equipped with neonatal facilities in China from March 2019 to March 2020 with respect to the level and nature of these hospitals, the number of newborn beds and NICU beds, the number of neonatal pediatricians, and the development of therapeutic techniques. The data about the newborn births and deaths were retrieved from the annual statistics of the health commissions of the related provinces, autonomous regions and municipalities. FINDING: Included in this nationwide survey were 3,020 hospitals from all 22 provinces, 5 autonomous regions and 4 municipalities directly under the Central Government of Mainland China, with a 100% response rate. They included 1,183 (39.2%) level-3 (L3) hospitals, 1629 (53.9%) L-2 hospitals and 208 (6.9%) L-1 hospitals. Geographically, 848 (31.4%) hospitals were distributed in Central China, 983 (32.5%) hospitals in East China, and 1,089 (36.1%) in West China. The 3,020 included hospitals were altogether equipped with 75,679 newborn beds, with a median of 20 (2-350) beds, of which 2,286 hospitals (75.7%) were equipped with neonatal intensive care units (NICU), totaling 28,076 NICU beds with a median of 5 (1-160) beds. There were altogether 27,698 neonatal pediatricians in these hospitals, with an overall doctor-bed ratio of 0.366. There were 48.18 newborn beds and 17.87 NICU beds per 10,000 new births in China. In East, Central and West China, the number of neonatal beds, NICU beds, neonatal pediatricians, and attending pediatricians or pediatricians with higher professional titles per 10,000 newborns was 42.57, 48.64 and 55.67; 17.07, 18.66 and 18.17; 16.26, 16.51 and 20.81; and 10.69, 10.81 and 11.29, respectively. However, when the population and area are taken into consideration and according to the health resources density index (HRDI), the number of newborn beds, NICU beds and neonatal pediatricians in West China was significantly lower than that in Central and East China. In addition, only 10.64% of the neonatal pediatricians in West China possessed the Master or higher degrees, vs. 31.7% in East China and 20.14% in Central China. On the contrary, the number of neonatal pediatricians with a lower than Bachelor degree in West China was significantly higher than that in Central and East China (13.28% vs. 7.36% and 4.28%). Technically, the application rate of continuous positive airway pressure (CPAP) and conventional mechanical ventilation (CMV) in L-1 hospitals of West China was lower than that in Central and East China. According to the statistics in 2018, the newborn mortality rate (NMR) in West China was significantly higher than that in Central and East China. INTERPRETATION: China has already possessed relatively good resources for neonatal care and treatment, which is the primary reason for the rapid decrease in the NMR in China. However, there are still substantial regional differences. The density of health resources, the level of technical development and educational background of neonatal pediatricians in West China still lag behind those in other regions of China and need to be further improved and upgraded. FUNDING: This research work was funded by National Natural Science Foundation of China (81671504) and United Nations International Children's Emergency Fund (CHINA-UNICEF501MCH).

The roles of circRNAs in cancers: Perspectives from molecular functions.

Circular RNAs (circRNAs), characteristic of covalently closed loops generated by back-splicing, are a subclass of single-stranded RNA molecules. Owing to the circular structures, circRNAs are protected from exonuclease-induced degradation, which makes them more stable compared with linear RNAs. With the development of high-throughput sequencing technology and bioinformatics, the roles of circRNAs in a variety of physiological and pathophysiological processes have been increasingly revealed. Although the functions of most circRNAs remain largely elusive, accumulating studies have identified them as microRNA(miRNA) sponges, protein regulators, transcriptional regulators, protein templates, and so forth. In this review, we briefly describe the biogenesis of circRNAs and provide an overview on their functions in cancers, including miRNA sponges, protein regulators, transcriptional regulators, protein templates. Furthermore, we discuss the potential application of circRNAs as biomarkers and give insight into future perspectives.

Inhibition of A2B Adenosine Receptor Attenuates Intestinal Injury in a Rat Model of Necrotizing Enterocolitis.

Necrotizing enterocolitis (NEC) is a lethal gastrointestinal tract disease that occurs in premature infants. Adenosine receptor A2B (A2BR) regulates the inflammation cytokine secretion and immune cell infiltration in the colonic pathophysiology conditions. In the present study, we aim to determine the roles of A2BR in the development of NEC. A NEC rat model was established and treated with A2BR agonist-BAY60-6583 or A2BR antagonist-PSB1115. Animals in the control group were free from any interventions. Our results showed that the inhibition of A2BR PSB1115 improved intestinal injury and inflammation in newborn NEC rats. The expression levels of caspase-3 and the ratio of apoptotic cells were upregulated in NEC rats, and these indices were downregulated after treating with PSB1115 but further upregulated by BAY60-6583. Meanwhile, a similar trend was also witnessed in the changes of MPO activities and proinflammatory cytokines including IL-6, IFN-γ, and TNF-α. However, the anti-inflammatory cytokine IL-10 in the NECP group was significantly higher than that in the NEC and NECB groups (p < 0.05, respectively). Moreover, the expression of Ki67 was significantly increased in the NECP group as compared with those of the NEC and the NECB groups (p < 0.05, respectively). Collectively, our study suggested that the inhibition of A2BR attenuates NEC in the neonatal rat, at least partially through the modulation of inflammation and the induction of epithelial cell proliferation.

Monolithic integration of GaN-based phototransistors and light-emitting diodes.

Monolithic integration of GaN-based phototransistors and light-emitting diodes (LEDs) is reported. Starting with an LED epitaxial wafer, selective Si diffusion was performed to produce an n-p-i-n structure for the phototransistor. A traditional AlGaN bulk electron-blocking layer (EBL) can block electron injection from an emitter to a collector, thereby hindering the photocurrent amplification process. We used an LED wafer with a superlattice EBL; blocking can be removed under a bias of approximately 7 V and above. External quantum efficiencies of more than 100% and 600% at approximately 380 nm and 330 nm, respectively, were achieved at room temperature and a bias of 11 V, corresponding to responsivities of 0.31 and 1.6 A/W, respectively, significantly higher than commercially available ultraviolet (UV) detectors. Furthermore, we demonstrated an integrated operation of the device. UV light was detected using a phototransistor that sent signals to drive an integrated LED as an indicator.

E-Jet 3D-Printed Scaffolds as Sustained Multi-Drug Delivery Vehicles in Breast Cancer Therapy.

PURPOSE: Combination chemotherapy is gradually receiving more attention because of its potential synergistic effect and reduced drug doses in clinical application. However, how to precisely control drug release dose and time using vehicles remains a challenge. This work developed an efficient drug delivery system to combat breast cancer, which can enhance drug effects despite reducing its concentration. METHODS: Controlled-release poly-lactic-co-glycolic acid (PLGA) scaffolds were fabricated by E-jet 3D printing to deliver doxorubicin (DOX) and cisplatin (CDDP) simultaneously. RESULTS: This drug delivery system allowed the use of a reduced drug dosage resulting in a better effect on the human breast cancer cell apoptosis and inhibiting tumor growth, compared with the effect of each drug and the two drugs administrated without PLGA scaffolds. Our study suggested that DOX-CDDP-PLGA scaffolds could efficiently destroy MDA-MB-231 cells and restrain tumor growth. CONCLUSIONS: The 3D printed PLGA scaffolds with their time-programmed drug release might be useful as a new multi-drug delivery vehicle in cancer therapy, which has a potential advantage in a long term tumor cure and prevention of tumor recurrence.

Engineering Deep Representations for Modeling Aesthetic Perception.

Many aesthetic models in multimedia and computer vision suffer from two shortcomings: 1) the low descriptiveness and interpretability 1 of the hand-crafted aesthetic criteria (i.e., fail to indicate region-level aesthetics) and 2) the difficulty of engineering aesthetic features adaptively and automatically toward different image sets. To remedy these problems, we develop a deep architecture to learn aesthetically relevant visual attributes from Flickr, 2 which are localized by multiple textual attributes in a weakly supervised setting. More specifically, using a bag-of-words representation of the frequent Flickr image tags, a sparsity-constrained subspace algorithm discovers a compact set of textual attributes (i.e., each textual attribute is a sparse and linear representation of those frequent image tags) for each Flickr image. Then, a weakly supervised learning algorithm projects the textual attributes at image-level to the highly-responsive image patches. These patches indicate where humans look at appealing regions with respect to each textual attribute, which are employed to learn the visual attributes. Psychological and anatomical studies have demonstrated that humans perceive visual concepts in a hierarchical way. Therefore, we normalize these patches and further feed them into a five-layer convolutional neural network to mimic the hierarchy of human perceiving the visual attributes. We apply the learned deep features onto applications like image retargeting, aesthetics ranking, and retrieval. Both subjective and objective experimental results thoroughly demonstrate the superiority of our approach.1 In this paper, "describing" and "interpretability" means the ability of seeking region-level representation of each mined textual attribute, i.e., a sparse and linear representation of those frequent image tags. 2 https://www.flickr.com/.

Camera-Assisted Video Saliency Prediction and Its Applications.

Video saliency prediction is an indispensable yet challenging technique which can facilitate various applications, such as video surveillance, autonomous driving, and realistic rendering. Based on the popularity of embedded cameras, we in this paper predict region-level saliency from videos by leveraging human gaze locations recorded using a camera, (e.g., those equipped on an iMAC and laptop PC). Our proposed camera-assisted mechanism improves saliency prediction by discovering human attended regions inside a video clip. It is orthogonal to the current saliency models, i.e., any existing video/image saliency model can be boosted by our mechanism. First of all, the spatial-and temporal-level visual features are exploited collaboratively for calculating an initial saliency map. We notice that the current saliency models are not sufficiently adaptable to the variations in lighting, different view angles, and complicated backgrounds. Therefore, assisted by a camera tracking human gaze movements, a non-negative matrix factorization algorithm is designed to accurately localize the semantically/visually salient video regions perceived by humans. Finally, the learned human gaze locations as well as the initial saliency map are integrated to optimize video saliency calculation. Empirical results thoroughly demonstrated that: 1) our approach achieves the state-of-the-art video saliency prediction accuracy by outperforming 11 mainstream algorithms considerably and 2) our method can conveniently and successfully enhance video retargeting, quality estimation, and summarization.

Quantitative Whole Genome Sequencing of Circulating Tumor Cells Enables Personalized Combination Therapy of Metastatic Cancer.

Much effort has been dedicated to developing circulating tumor cells (CTC) as a noninvasive cancer biopsy, but with limited success as yet. In this study, we combine a method for isolation of highly pure CTCs using immunomagnetic enrichment/fluorescence-activated cell sorting with advanced whole genome sequencing (WGS), based on long fragment read technology, to illustrate the utility of an accurate, comprehensive, phased, and quantitative genomic analysis platform for CTCs. Whole genomes of 34 CTCs from a patient with metastatic breast cancer were analyzed as 3,072 barcoded subgenomic compartments of long DNA. WGS resulted in a read coverage of 23× per cell and an ensemble call rate of >95%. These barcoded reads enabled accurate detection of somatic mutations present in as few as 12% of CTCs. We found in CTCs a total of 2,766 somatic single-nucleotide variants and 543 indels and multi-base substitutions, 23 of which altered amino acid sequences. Another 16,961 somatic single nucleotide variant and 8,408 indels and multi-base substitutions, 77 of which were nonsynonymous, were detected with varying degrees of prevalence across the 34 CTCs. On the basis of our whole genome data of mutations found in all CTCs, we identified driver mutations and the tissue of origin of these cells, suggesting personalized combination therapies beyond the scope of most gene panels. Taken together, our results show how advanced WGS of CTCs can lead to high-resolution analyses of cancers that can reliably guide personalized therapy. Cancer Res; 77(16); 4530-41. ©2017 AACR.

An Optical Fiber Lateral Displacement Measurement Method and Experiments Based on Reflective Grating Panel.

An optical fiber sensing method based on a reflective grating panel is demonstrated for lateral displacement measurement. The reflective panel is a homemade grating with a periodic variation of its refractive index, which is used to modulate the reflected light intensity. The system structure and operation principle are illustrated in detail. The intensity calculation and simulation of the optical path are carried out to theoretically analyze the measurement performance. A distinctive fiber optic grating ruler with a special fiber optic measuring probe and reflective grating panel is set up. Experiments with different grating pitches are conducted, and long-distance measurements are executed to accomplish the functions of counting optical signals, subdivision, and discerning direction. Experimental results show that the proposed measurement method can be used to detect lateral displacement, especially for applications in working environments with high temperatures.

The Development of a Dual-Warhead Impact System for Dynamic Linearity Measurement of a High-g Micro-Electro-Mechanical-Systems (MEMS) Accelerometer.

Despite its extreme significance, dynamic linearity measurement for high-g accelerometers has not been discussed experimentally in previous research. In this study, we developed a novel method using a dual-warhead Hopkinson bar to measure the dynamic linearity of a high-g acceleration sensor with a laser interference impact experiment. First, we theoretically determined that dynamic linearity is a performance indicator that can be used to assess the quality merits of high-g accelerometers and is the basis of the frequency response. We also found that the dynamic linearity of the dual-warhead Hopkinson bar without an accelerometer is 2.5% experimentally. Further, we verify that dynamic linearity of the accelerometer is 3.88% after calibrating the Hopkinson bar with the accelerometer. The results confirm the reliability and feasibility of measuring dynamic linearity for high-g accelerometers using this method.

[A case report of endoscopic assisted unilateral infraorbital nerve decompression].

Patients of infraorbital nerve injury often appear in the sensory abnormalities of corresponding position, such as numbness or pain. We present a case with numbness of the left cheek because of the injury. The patient were treated by endoscopic assisted on the left infraorbital nerve decompression through the approach of the canine fossa. The symptom shows improvement after the operation. The patient feels numbness significantly ease on 4 months after the operation.

Erratum: SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler.

[This corrects the article DOI: 10.1186/2047-217X-1-18.].

[Association study of CNR1, GAD1 and BDNF polymorphisms with male heroin dependence in the Dai population in Yunnan].

In order to analyze the association of CNR1(Cannabinoid receptor 1), GAD1(Glutamate decarboxylase 1), and BDNF(Brain-derived neurotrophic factor) polymorphisms with male heroin dependence in the Dai population in Yunnan Province, an eight-SNP co-amplification protocol was established to genotype on the SNaPshot platform. A case-control study was performed with 8 SNPs from CNR1, GAD1, and BDNF genes in 165 heroin-dependent males and 170 healthy males of the Dai population. Statistical analyses were conducted with SPSS17.0, Haploview4.2, PHASE2.1, and MDR software. We found that: (1) the genotype frequency of rs13306221 was significant in the case group (P<0.025); (2) the A allelic frequency of rs6265 was significantly higher in the case group; (3) the haplotypes of T-A-C, C-C-C, C-C-T, and T-C-C based on rs1978340-rs3791878-rs11542313 and haplotype A-G based on rs6265-rs13306221 were significant (P<0.05); (4) the haplotype frequencies of T-A-C, C-C-T, and A-G were significantly higher in the case group. These results indicate that the linkage between rs1978340 and rs3791878 in GAD1 has a strong association with heroin dependence. Furthermore, polymorphisms in CNR1 (rs1049353), GAD1 (rs1978340 and rs11542313), and BDNF (rs6265 and rs13306221) were associated with heroin dependence in the Yunnan Dai population, and individuals with the rs6265 A allele were more likely to be heroin dependent.

[Analysis of null alleles for 17 Y chromosome-short tandem repeat loci in infertile males].

OBJECTIVE: To investigate the characteristics of null allele for 17 Y-chromosomal short tandem repeats (Y-STR) loci in a group of infertile males. METHODS: Two hundred thirty six infertile males featuring non-obstructive azoospermia and severe oligozoospermia were analyzed with an AmpFISTR ((R)) Yfiler (TM) kit. Deletions of azoospermia factor (AZF) fragments were confirmed with Y chromosome sequence-tagged sites (STSs) analysis using modified multiplex PCR. RESULTS: The overall prevalence of AZF microdeletions was 16.95% (40/236). In the non-obstructive azoospermia group, 13 cases had AZFc deletion, 6 cases had AZFb+c deletion, 2 cases had AZFa deletion, 1 case had AZFb deletion. In the severe oligozoospermia group, 17 cases had AZFc deletion and 1 had AZFb deletion. No AZFa+b+c deletion was detected. Forty cases showed null alleles by scanning of the 17 STR loci. Deletions of DYS438, DYS439, DYS437, DYS389I and DYS389II were found in the 2 cases with AZFa deletion. In patients with AZFb deletion, DYS392 and DYS385a/b were found deleted. Deletions of DYS448 were detected in all of the 30 cases with AZFc deletion. Deletions of DYS392, DYS385a/b, and DYS448 were found in 6 cases with AZFb+c deletion. CONCLUSION: Deletions of the Y chromosome AZF regions are associated with azoospermia and severe oligozoospermia. Null allele due to complete absence of AZFa, AZFb and AZFc regions may lead to misinterpretation in the sexual assault cases. Revealing the locus heterogeneity in male infertility population can enrich the Y-STR database and facilitate interpretation STR data in forensic DNA testing.

COPE: an accurate k-mer-based pair-end reads connection tool to facilitate genome assembly.

MOTIVATION: The boost of next-generation sequencing technologies provides us with an unprecedented opportunity for elucidating genetic mysteries, yet the short-read length hinders us from better assembling the genome from scratch. New protocols now exist that can generate overlapping pair-end reads. By joining the 3' ends of each read pair, one is able to construct longer reads for assembling. However, effectively joining two overlapped pair-end reads remains a challenging task. RESULT: In this article, we present an efficient tool called Connecting Overlapped Pair-End (COPE) reads, to connect overlapping pair-end reads using k-mer frequencies. We evaluated our tool on 30× simulated pair-end reads from Arabidopsis thaliana with 1% base error. COPE connected over 99% of reads with 98.8% accuracy, which is, respectively, 10 and 2% higher than the recently published tool FLASH. When COPE is applied to real reads for genome assembly, the resulting contigs are found to have fewer errors and give a 14-fold improvement in the N50 measurement when compared with the contigs produced using unconnected reads. AVAILABILITY AND IMPLEMENTATION: COPE is implemented in C++ and is freely available as open-source code at ftp://ftp.genomics.org.cn/pub/cope. CONTACT: twlam@cs.hku.hk or luoruibang@genomics.org.cn

pIRS: Profile-based Illumina pair-end reads simulator.

MOTIVATION: The next-generation high-throughput sequencing technologies, especially from Illumina, have been widely used in re-sequencing and de novo assembly studies. However, there is no existing software that can simulate Illumina reads with real error and quality distributions and coverage bias yet, which is very useful in relevant software development and study designing of sequencing projects. RESULTS: We provide a software package, pIRS (profile-based Illumina pair-end reads simulator), which simulates Illumina reads with empirical Base-Calling and GC%-depth profiles trained from real re-sequencing data. The error and quality distributions as well as coverage bias patterns of simulated reads using pIRS fit the properties of real sequencing data better than existing simulators. In addition, pIRS also comes with a tool to simulate the heterozygous diploid genomes. AVAILABILITY: pIRS is written in C++ and Perl, and is freely available at ftp://ftp.genomics.org.cn/pub/pIRS/.

Comparison of the two major classes of assembly algorithms: overlap-layout-consensus and de-bruijn-graph.

Since the completion of the cucumber and panda genome projects using Illumina sequencing in 2009, the global scientific community has had to pay much more attention to this new cost-effective approach to generate the draft sequence of large genomes. To allow new users to more easily understand the assembly algorithms and the optimum software packages for their projects, we make a detailed comparison of the two major classes of assembly algorithms: overlap-layout-consensus and de-bruijn-graph, from how they match the Lander-Waterman model, to the required sequencing depth and reads length. We also discuss the computational efficiency of each class of algorithm, the influence of repeats and heterozygosity and points of note in the subsequent scaffold linkage and gap closure steps. We hope this review can help further promote the application of second-generation de novo sequencing, as well as aid the future development of assembly algorithms.

SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler.

BACKGROUND: There is a rapidly increasing amount of de novo genome assembly using next-generation sequencing (NGS) short reads; however, several big challenges remain to be overcome in order for this to be efficient and accurate. SOAPdenovo has been successfully applied to assemble many published genomes, but it still needs improvement in continuity, accuracy and coverage, especially in repeat regions. FINDINGS: To overcome these challenges, we have developed its successor, SOAPdenovo2, which has the advantage of a new algorithm design that reduces memory consumption in graph construction, resolves more repeat regions in contig assembly, increases coverage and length in scaffold construction, improves gap closing, and optimizes for large genome. CONCLUSIONS: Benchmark using the Assemblathon1 and GAGE datasets showed that SOAPdenovo2 greatly surpasses its predecessor SOAPdenovo and is competitive to other assemblers on both assembly length and accuracy. We also provide an updated assembly version of the 2008 Asian (YH) genome using SOAPdenovo2. Here, the contig and scaffold N50 of the YH genome were ~20.9 kbp and ~22 Mbp, respectively, which is 3-fold and 50-fold longer than the first published version. The genome coverage increased from 81.16% to 93.91%, and memory consumption was ~2/3 lower during the point of largest memory consumption.