Explore variation of salivary bacteria across time and geolocations.

Saliva is an informative body fluid that can be found at various crime scenes, and the salivary bacterial community has been revealed it is a potential auxiliary target for forensic identification. However, the variation of salivary bacterial community composition across time and geolocation needs to be explored. The study was designed to be carried out during the winter vacation that was across about 50 days and eight geographic locations. The high throughput sequencing was performed with the V3-V4 region of the16S rRNA gene to explore salivary bacterial community composition. An overall slight fluctuation of the salivary bacteria was observed, which primarily occurred in the relative abundance of the salivary bacterial taxa. The results of principal coordinate analysis and hierarchical clustering showed samples were clustered by the individuals. All individuals could be correctly identified with the random forest model. In summation, although the relative abundance of salivary bacteria varied across the changes of time and geolocation, the individualized characteristic of salivary bacteria remained steady, which is beneficial for the salivary bacterial application in personal identification.

Large fragment Sanger sequencing identifies the newly encountered variant that caused null alleles in parentage testing.

Short tandem repeat (STR) is regarded as a crucial tool for personal identification as well as parentage testing. Thus, genotyping errors of STRs could have negative effects on the reliability of forensic identification. A null allele at the combined DNA index system (CODIS) core loci D2S1338 was found in a father-daughter pair with the AGCU Expressmarker 22 kit which was a commonly used commercial kit during our daily laboratory work. This null allele caused the father and daughter to not conform to the laws of inheritance, thus potentially generating erroneous conclusions that excluded parentage. To figure out the reason for this phenomenon, re-amplification with new primers and then large fragment Sanger sequencing was conducted. We found a G to G/T variation at the position which is fifty-nine bases away from the 3' end of the core repeat in both samples. This probably could be considered a novel variant at the primer binding region which had not been reported that resulted in the emergence of the null allele. We also found that there was more than one single-nucleotide polymorphism (SNP) with minor allele frequency (MAF) greater than 0.1 in the upstream and downstream sequences of D2S1338. When designing primers for amplification of D2S1338, the possible adverse results of these SNPs should be taken into account and avoided.

Characterization of loss of chromosome Y in peripheral blood cells in male Han Chinese patients with schizophrenia.

BACKGROUND: Schizophrenia (SCZ) has a global prevalence of 1% and increases the risk of mortality, reducing life expectancy. There is growing evidence that the risk of this disorder is higher in males than in females and it tends to develop in early adulthood. The Y chromosome is thought to be involved in biological processes other than sex determination and spermatogenesis. Studies have shown that loss of chromosome Y (LOY) in peripheral blood cells is associated with a variety of diseases (including cancer) and increased all-cause mortality. An analysis of the relationship between LOY and schizophrenia is warranted. METHODS: A total of 442 Chinese males (271 patients with schizophrenia vs. 171 controls) were included in this study. The copy numbers of the Y and X chromosomes were detected by positive droplets targeting the amelogenin gene (AMEL) on the Y chromosome and X chromosome (AMELY and AMELX, respectively), using droplet digital PCR (ddPCR). The LOY percentage was defined as the difference between the concentration of AMELX and the concentration of AMELY divided by the concentration of AMELX, denoted as (X - Y)/X. RESULTS: In the Han Chinese population, the LOY percentage was higher in the schizophrenia group than in the control group (p < 0.05), although there was no significant difference in the presence of LOY between the two groups. A strong correlation was found between the average of the disease duration and the average of the LOY percentage (R2 = 0.506, p = 0.032). The logistic regression analysis implied that the risk of LOY increases by 0.058 and 0.057 per year according to age at onset and duration of disease, respectively (ponset = 0.013, pduration = 0.017). CONCLUSIONS: In the Han Chinese population, the LOY percentage of the disease group was significantly different from that of the control group. The age of onset and duration of schizophrenia might be risk factors for LOY in peripheral blood cells. A larger sample size and expanded clinical information are needed for more in-depth and specific analyses.

Developmental validation of the Microreader Group Y Direct ID System: A novel six-dye typing system with 54 Y-chromosomal loci for forensic application.

Y-chromosome, as a gender-determined biological marker, is inherited only between fathers and sons. The Y-chromosome short tandem repeats (Y-STRs) play an essential role in paternity lineage tracing as well as sexual assault cases. The Microreader Group Y Direct ID System as a six-dye multiplex amplification kit, including 53 Y-STR and one Y-Indel locus, would improve performance and aid in obtaining more information through a greater number of loci with high polymorphism. In the present study, to verify the accuracy and efficiency of the kit, developmental validation was conducted by investigating sensitivity, species specificity, PCR inhibition, male-male and male-female mixtures, and reproducibility. The kit was tested using 311 male samples from Han and Qiang populations in Sichuan Province. The results showed that this kit had fairly high power for forensic discrimination (Han: haplotype diversity [HD] = 1, Qiang: HD = 0.999944). Additionally, 44 confirmed father-son pairs were also genotyped, among which 69 distinct haplotypes could be obtained. These father-son pairs cannot be distinguished by commonly used Y-STR panels, indicating that adding these extra Y-STRs to a single panel can achieve better discrimination performance. Collectively, the Microreader Group Y Direct ID System is robust and informative for forensic applications.

Assess the diversity of gut microbiota among healthy adults for forensic application.

BACKGROUND: Human gut microbiota is individually unique that hints the microbiota in fecal traces left in the crime scene could act as a potential biomarker for forensic personal identification. Next-generation DNA sequencing and bioinformatic analysis of fecal samples are revolutionizing our insights into gut microbial communities. While the formation of the gut microbiota is known to be multifactorial, it is unclear whether these characteristics can be applied to forensic applications. Therefore, the gut microbiota of healthy adults with different traits was investigated in this study. RESULTS: Based on the STAMP analysis of each study group, the difference in gut microbiota composition of male and female subjects was observed. The male group was characterized by taxa in the phylum Proteobacteria, while the female group was described by Synergistetes phylum. The gut bacterial community assembly mechanism was mainly affected by the deterministic process. In addition, gut microbiota composition showed meaningful discrimination in each of the BMI groups. At the phylum level, in male subjects, increased representative phyla were Patescibacteria (p < 0.05) in the underweight group and Bacteroidetes (p < 0.05) in the normal-weight group, while in the female group, the significantly different phyla were Bacteroidetes, Firmicutes, and Actinobacteria. At the genus level, 44 unique genera were found to be significantly distinct across BMI study groups. By Fisher's Linear Discriminant Analysis, ninety-four point four percent (94.4%) of original BMI grouped subjects were correctly classified. The linear regression analysis model showed an accuracy of seventy-four percent (74%) in predicting body type. CONCLUSION: In conclusion, subjects with different individual characters have specific gut microbiota, and can be discriminated by bioinformatics methods, suggesting it is promising to apply gut microbiota to forensic personal identification.

Developmental validation of the Microreader™ RM-Y ID System: a new rapidly mutating Y-STR 17-plex system for forensic application.

Y-chromosomal short tandem repeats (Y-STRs) are widely applied to evolutionary, genealogical, and kinship analyses of male linages in forensic studies, but these low to midrange mutated Y-STRs typically fail to separate related males from the same paternal lineage. Recently, rapidly mutating Y-STRs (RM Y-STRs) have been demonstrated to improve the differentiation of male relatives and individuals. The Microreader™ RM-Y ID System is a new RM Y-STR kit that is capable of simultaneously amplifying 17 RM Y-STRs. Herein, to verify the efficiency and accuracy of the Microreader™ RM-Y ID System, developmental validation was conducted, including PCR-based studies, sensitivity, stability, species specificity, mixture, stutter percentage, and precision studies. Full profiles could be obtained when the hematin concentration was 250 µM, humic acid concentration was 1500 ng/µl, and tannic acid concentration was 200 ng/µl. Full profiles of the mixture of males/males could be detected up to a ratio of 19:1, and full profiles of females/males could always be detected even at ratios up to 24,000:1. Moreover, the forensic characteristics of 250 DNA-confirmed father-son pairs were analysed. The results showed that these 17 RM Y-STRs had high power for forensic discrimination (HD = 1) in the Chinese Han population, and the mutation rates were in the range of 4 × 10-3 (95% CI 1.00 × 10-4 to 2.21 × 10-2, DYS464) to 8.8 × 10-2 (95% CI 5.60 × 10-2 to 1.30 × 10-1, DYF399S1), indicating that the kit was effective for RM Y-STR studies and absolute individualisation of interrelated male individuals.

Research Progress on the Application of Human Oral Microbiome in Forensic Individual Identification.

The oral cavity is the second largest microbial bank in humans after the intestinal canal, colonizing a large number of microorganisms including viruses, bacteria, archaea, fungi and protozoa. The great number of microbial cells, good DNA stability, and individual has a unique microbial community, these characteristics make the human microbiome expected to become a new biomarker for forensic individual identification. This article describes the characteristics of human oral microorganisms and microbial molecular markers in detail, analyzes the potential application value of microorganisms in forensic individual identification, and reviews the research progress of human oral microorganisms in forensic individual identification.

Paternal genetic structure of Kyrgyz ethnic group in China revealed by high-resolution Y-chromosome STRs and SNPs.

Kyrgyz ethnic group is one of the nomads in China, with the majority in Xinjiang and a small part of them living in Heilongjiang province. Historically, they have went through five migrations westward due to the wars. The name "Kyrgyz" means 40 tribes, originating from the primary groups of Kyrgyz. However, it is a largely understudied population, especially from the Y chromosome. In this study, we used a previously validated high-resolution Y-chromosome single nucleotide polymorphisms (Y-SNPs) and short tandem repeats (Y-STRs) system to study Kyrgyz ethnic group. A total of 314 male samples of Kyrgyz ethnic group were genotyped by 173 Y-SNPs and 27 Y-STRs. After data analysis, the results unveiled that Kyrgyz ethnic group was a population with high percentage of both haplogroup C2a1a3a1d∼-F10091 (91/134) and R1a1a1b2a2-Z2124 (109/134), which has never been reported. This implied that Kyrgyz ethnic group might have gone through bottleneck effects twice, with these two main lineages left. Mismatch analysis indicated that the biggest mismatch number in haplogroup C2a1a3a1d∼-F10091 was 10, while that of haplogroup R1a1a1b2a2-Z2124 was 20. This huge difference reflected the different substructure in two lineages, suggesting that haplogroup C2a1a3a1d∼-F10091 might have the least admixture compared to the other two lineages. After admixture modelling with other datasets, the conclusion could be drawn that Kyrgyz ethnic group had great genetic affinity with Punjabi from Lahore, Pakistan, which supported that Kyrgyz ethnic group in China was close to central Asian.

MicroRNA-196b promotes gastric cancer progression by targeting ECRG4.

Gastric cancer is one of the most common malignant tumors. MicroRNA-196b (miR-196b) has been demonstrated to play important roles in human cancers. However, its functions in gastric cancer progression were still largely unknown. In this study, the expression of miR-196b was determined by quantitative real-time PCR. Esophageal cancer-related gene 4 (ECRG4) level was examined by western blot assay and immunohistochemistry staining assay. Cell proliferation was evaluated by Cell Counting Kit-8 (CCK-8) assay and colony formation assay. Cell migration and invasion were analyzed by transwell assay. The association between miR-196b and ECRG4 was analyzed by dual-luciferase reporter assay. The functional role of miR-196b in vivo was analyzed by murine xenograft assay. As a result, we found the expression of miR-196b was elevated and the protein expression of ECRG4 was reduced in gastric cancer tissues and cells. MiR-196b inhibition suppressed gastric cancer cell proliferation, migration and invasion. ECRG4 was a target of miR-196b and its protein expression was negatively regulated by miR-196b. Moreover, ECRG4 overexpression showed similar effects with miR-196b inhibition on the malignant behaviors of GC cells and ECRG4 knockdown reversed the effects of miR-196b inhibition on gastric cancer cell proliferation, migration and invasion. In addition, miR-196b inhibition suppressed tumor volume and weight in vivo. In conclusion, downregulation of miR-196b inhibited gastric cancer progression by modulating ECRG4 expression, indicating that miR-196b might be a potential therapeutic target for gastric cancer.

Bioconversion of steviol glycosides into steviol by Microbacterium barkeri.

The strain which degraded steviol glycosides to steviol (STE) was screened and isolated from soil samples. A phylogenetic tree was constructed and used to determine the taxonomic status of the strain. 16S rDNA sequence was ultimately used to identify the strain as Microbacterium barkeri XJ. The transformation product was detected and identified as STE by HPLC/LC-MS/IR analysis. The bioconversion rate of 1% (v/v) steviol glycosides (stevioside, rebaudioside A, rebaudioside C) into STE in basic medium were 100% within 24 h, 84 h and 144 h, respectively. The results indicated XJ was more effective than mixed flora in the bioconversion of steviol glycosides to STE.

Genetic diversity and phylogenetic analysis of 29 Y-STR loci in the Tibetan population from Sichuan Province, Southwest China.

Y-Chromosomal short tandem repeat polymorphisms (Y-STRs) are widely applied in human forensic cases and population genetic studies. There is a lack of information about the Sichuan Tibetan population in the Y-STR Haplotype Reference Database (YHRD, https://yhrd.org, release 59). In this study, 502 unrelated male individuals residing in the Sichuan Province were recruited and genotyped at 29 Y-STR loci. A total of 479 haplotypes were observed, 460 (96.03%) of which were unique. The haplotype diversity (HD) and discrimination capacity (DC) for the Sichuan Tibetan population were 0.9998 and 0.9542, respectively. To reveal the genetic diversities and relationships between the Chinese Sichuan Tibetan and 29 other previously reported populations, forensic parameter analysis, multi-dimensional scaling, and phylogenetic reconstruction were performed. The results showed that the Sichuan Tibetan population was relatively isolated from other populations, suggesting that genetic proximity is in line with geographical boundaries.

Validation of the AGCU Expressmarker 16 + 22Y Kit: a new multiplex for forensic application.

Genotyping by targeting short tandem repeats (STRs) has been widely used in forensic applications. However, most commercial kits detect autosomal STRs or Y-STRs alone, which waste both time and opportunity. The AGCU Expressmarker 16 + 22Y Kit includes 16 autosomal and 22 Y-chromosomal STR loci and is designed for the forensic science field and obtaining quicker results. Here, we conducted the validation study according to Scientific Working Group on DNA Analysis Methods (SWGDAM) guidelines. Validation of PCR-based studies, species specificity, sensitivity, DNA mixture studies, inhibitors, precision, and sizing accuracy were performed. Furthermore, this system was also tested in 346 random male samples from Han, Hui, Tibetan, and Zhuang populations in China, showing its high power for forensic discrimination in the Chinese population. In addition, this system was able to deal with AMELY deletion cases, which can correctly identify sex in forensic criminal investigations. Our results suggested that the AGCU Expressmarker 16 + 22Y Kit is a useful tool for rapid criminal investigation.

Phase unwrapping in optical metrology via denoised and convolutional segmentation networks.

The interferometry technique is commonly used to obtain the phase information of an object in optical metrology. The obtained wrapped phase is subject to a 2π ambiguity. To remove the ambiguity and obtain the correct phase, phase unwrapping is essential. Conventional phase unwrapping approaches are time-consuming and noise sensitive. To address those issues, we propose a new approach, where we transfer the task of phase unwrapping into a multi-class classification problem and introduce an efficient segmentation network to identify classes. Moreover, a noise-to-noise denoised network is integrated to preprocess noisy wrapped phase. We have demonstrated the proposed method with simulated data and in a real interferometric system.

Paraspinal Muscle Segmentation Based on Deep Neural Network.

The accurate segmentation of the paraspinal muscle in Magnetic Resonance (MR) images is a critical step in the automated analysis of lumbar diseases such as chronic low back pain, disc herniation and lumbar spinal stenosis. However, the automatic segmentation of multifidus and erector spinae has not yet been achieved due to three unusual challenges: (1) the muscle boundary is unclear; (2) the gray histogram distribution of the target overlaps with the background; (3) the intra- and inter-patient shape is variable. We propose to tackle the problem of the automatic segmentation of paravertebral muscles using a deformed U-net consisting of two main modules: the residual module and the feature pyramid attention (FPA) module. The residual module can directly return the gradient while preserving the details of the image to make the model easier to train. The FPA module fuses different scales of context information and provides useful salient features for high-level feature maps. In this paper, 120 cases were used for experiments, which were provided and labeled by the spine surgery department of Shengjing Hospital of China Medical University. The experimental results show that the model can achieve higher predictive capability. The dice coefficient of the multifidus is as high as 0.949, and the Hausdorff distance is 4.62 mm. The dice coefficient of the erector spinae is 0.913 and the Hausdorff distance is 7.89 mm. The work of this paper will contribute to the development of an automatic measurement system for paraspinal muscles, which is of great significance for the treatment of spinal diseases.

Siamese Tracking from Single Point Initialization.

Recently, we have been concerned with locating and tracking vehicles in aerial videos. Vehicles in aerial videos usually have small sizes due to use of cameras from a remote distance. However, most of the current methods use a fixed bounding box region as the input of tracking. For the purpose of target locating and tracking in our system, detecting the contour of the target is utilized and can help with improving the accuracy of target tracking, because a shape-adaptive template segmented by object contour contains the most useful information and the least background for object tracking. In this paper, we propose a new start-up of tracking by clicking on the target, and implement the whole tracking process by modifying and combining a contour detection network and a fully convolutional Siamese tracking network. The experimental results show that our algorithm has significantly improved tracking accuracy compared to the state-of-the-art regarding vehicle images in both OTB100 and DARPA datasets. We propose utilizing our method in real time tracking and guidance systems.

Sparse representation-based demosaicing method for microgrid polarimeter imagery.

To address the key image interpolation issue in microgrid polarimeters, we propose a machine learning model based on sparse representation. The sparsity and non-local self-similarity priors are used as regularization terms to enhance the stability of an interpolation model. Moreover, to make the best of the correlation among different polarization orientations, patches of different polarization channels are joined to learn adaptive sub-dictionary. Synthetic and real images are used to evaluate the interpolated performance. The experimental results demonstrate that our proposed method achieves state-of-the-art results in terms of quantitative measures and visual quality.

Learning a convolutional demosaicing network for microgrid polarimeter imagery.

We propose a polarization demosaicing convolutional neural network to address the image demosaicing issue, the last unsolved issue in microgrid polarimeters. This network learns an end-to-end mapping between the mosaic images and full-resolution ones. Skip connections and customized loss function are used to boost the performance. Experimental results show that our proposed network outperforms other state-of-the-art methods by a large margin in terms of quantitative measures and visual quality.

Genetic diversity and phylogenetic study of the Chinese Gelao ethnic minority via 23 Y-STR loci.

Haplotype diversity for 23 Y chromosomal short tandem repeat (Y-STR) loci included in the PowerPlex® Y23 System was analyzed in the Chinese Gelao minority group of 234 unrelated males living in Daozhen Gelao-Miao Autonomous County in Guizhou Province, southwest China. A total of 216 different haplotypes were detected, of which 199 haplotypes were unique. The overall haplotype diversity (HD) and discrimination capacity (DC) were 0.9996 and 0.9231, respectively. The gene diversity (GD) ranged from 0.4159 (DYS438) to 0.9650 (DYS385a/b). The haplotype frequencies varied from 0.0043 to 0.0128. The population data presented here showed high genetic polymorphism and extraordinary discriminatory power in the studied population. Population difference was observed between the Chinese Gelao ethnicity and 42 populations out of overall 59 neighboring populations in Asia region. Both multidimensional scaling (MDS) and the phylogenetic tree demonstrated that the genetic structure affinity and differentiation with Chinese Gelao ethnicity were identified in those populations geographically adjacent (Hunan Han) and distant (Chinese Tibetan), respectively. In conclusion, our study enriched the Chinese ethnic genetic information and could be used as a powerful tool in forensic genetics for male testing, paternal lineage analysis, and Gelao ethnic population evolutionary studies.

Sky Detection in Hazy Image.

Sky detection plays an essential role in various computer vision applications. Most existing sky detection approaches, being trained on ideal dataset, may lose efficacy when facing unfavorable conditions like the effects of weather and lighting conditions. In this paper, a novel algorithm for sky detection in hazy images is proposed from the perspective of probing the density of haze. We address the problem by an image segmentation and a region-level classification. To characterize the sky of hazy scenes, we unprecedentedly introduce several haze-relevant features that reflect the perceptual hazy density and the scene depth. Based on these features, the sky is separated by two imbalance SVM classifiers and a similarity measurement. Moreover, a sky dataset (named HazySky) with 500 annotated hazy images is built for model training and performance evaluation. To evaluate the performance of our method, we conducted extensive experiments both on our HazySky dataset and the SkyFinder dataset. The results demonstrate that our method performs better on the detection accuracy than previous methods, not only under hazy scenes, but also under other weather conditions.

Effect of incorporation of natural chemicals in water ice-glazing on freshness and shelf-life of Pacific saury (Cololabis saira) during -18 °C frozen storage.

BACKGROUND: Microbial spoilage and lipid oxidation are two major factors causing freshness deterioration of Pacific saury (Cololabis saira) during frozen storage. To provide a remedy, the effects of several natural chemicals incorporated alone or in combination in traditional water ice-glazing on the freshness and shelf-life of Pacific saury during frozen storage at -18 °C were investigated. Pacific sauries were subjected to individual quick freezing followed immediately by dipping into cold tap water (control) or solutions containing nisin, chitosan, phytic acid (single-factor experiment) or their combinations ((L9 (34 ) orthogonal experiment) for 10 s at 1 °C and then packaged in polypropylene bags before frozen storage at -18 °C. The storage duration tested was up to 12 months. RESULTS: All ice-glazing treatments with individual chemicals could significantly (P < 0.05) inhibit the accumulation of thiobarbituric acid-reactive substances (TBARS), total volatile basic nitrogen (TVB-N) and histamine as well as the increase in bacterial total viable count (TVC) compared with controls, while the combination treatments gave even better effects. The L9 (34 ) orthogonal experiment showed that the optimal combination was A2 B1 C2 (i.e. 0.5 g L-1 nisin, 5 g L-1 chitosan and 0.2 g L-1 phytic acid). The TBARS, TVB-N, histamine and TVC values in A2 B1 C2 -treated samples remained far below the maximum acceptable limit for good-freshness fish after 12 months of frozen storage at -18 °C. CONCLUSION: The incorporation of natural chemicals tested herein in ice-glazing could inhibit microbial spoilage and lipid oxidation and therefore maintain the freshness of Pacific saury during frozen storage. Under the optimal conditions, the shelf-life of Pacific saury could be extended up to 12 months at -18 °C. The study indicated that the combination treatment with natural chemicals could be commercially utilized to maintain the freshness and prolong the shelf-life of Pacific saury. © 2017 Society of Chemical Industry.