A novel 193-plex MPS panel integrating STRs and SNPs highlights the application value of forensic genetics in individual identification and paternity testing.

Massively parallel sequencing (MPS) has emerged as a promising technology for targeting multiple genetic loci simultaneously in forensic genetics. Here, a novel 193-plex panel was designed to target 28 A-STRs, 41 Y-STRs, 21 X-STRs, 3 sex-identified loci, and 100 A-SNPs by employing a single-end 400 bp sequencing strategy on the MGISEQ-2000™ platform. In the present study, a series of validations and sequencing of 1642 population samples were performed to evaluate the overall performance of the MPS-based panel and its practicality in forensic application according to the SWGDAM guidelines. In general, the 193-plex markers in our panel showed good performance in terms of species specificity, stability, and repeatability. Compared to commercial kits, this panel achieved 100% concordance for standard gDNA and 99.87% concordance for 14,560 population genotypes. Moreover, this panel detected 100% of the loci from 0.5 ng of DNA template and all unique alleles at a 1:4 DNA mixture ratio (0.2 ng minor contributor), and the applicability of the proposed approach for tracing and degrading DNA was further supported by case samples. In addition, several forensic parameters of STRs and SNPs were calculated in a population study. High CPE and CPD values greater than 0.9999999 were clearly demonstrated and these results could be useful references for the application of this panel in individual identification and paternity testing. Overall, this 193-plex MPS panel has been shown to be a reliable, repeatable, robust, inexpensive, and powerful tool sufficient for forensic practice.

Surface hydroxylation process of YAG crystal in aqueous solution.

Surface hydroxylation is the basis for material removal in chemical mechanical polishing (CMP) of monocrystalline silicon, diamond, and YAG crystals. Existing studies use experimental observations to investigate surface hydroxylation, but lack in-depth understanding of the hydroxylation process. In this paper, for the first time to the best of our knowledge, we analyze the surface hydroxylation process of YAG crystals in an aqueous solution using first-principle calculations. The presence of surface hydroxylation was verified by X-ray photoelectron spectroscopy (XPS) and thermogravimetric mass spectrometry (TGA-MS) detections. This study complements the existing research on the material removal mechanism of the CMP process of YAG crystals and provides theoretical support for the future improvement of the CMP technology.

Development and validation of a custom panel including 114 InDels using massively parallel sequencing for forensic application.

Insertion/deletion polymorphisms (InDels) have particular characteristics, such as a relatively low mutation rate, small amplicon size, and no stutter artifacts when genotyped via the capillary electrophoresis platform. It would be an important complementary tool for individual identification and certain kinship analyses. At present, massively parallel sequencing (MPS) has shown excellent application value in forensic studies. Therefore, in this study, we developed a custom MPS InDel panel that contains 114 InDels [77 autosomal InDels (A-InDels), 32 X-chromosomal InDels (X-InDels), and 5 Y-chromosomal InDels) based on previous studies. To assess this panel's performance, several validation experiments were performed, including sensitivity, inhibitor, degraded DNA testing, species specificity, concordance, repeatability, case-type samples, and population studies. The results showed that the lowest DNA input was 0.25 ng. All genotypes were obtained in the presence of 80 ng/µL humic acid, 2000 µmol/L calcium, 3000 µmol/L EDTA and indigo. In degraded DNA testing, 90% of loci could be detected for 16-day-old formalin-fixed hearts. In addition, this panel has good species specificity. The values of combined power of discrimination and the combined power of exclusion for 77 A-InDels were 1-3.9951 × 10-32 and 1-4.2956 × 10-7 , respectively. The combined mean exclusion chance for 32 X-InDels was 0.99999 in trios and 0.99904 in duos. The validation results indicate that this newly developed MPS multiplex system is a robust tool for forensic applications.

Integrating the salivary microbiome in the forensic toolkit by 16S rRNA gene: potential application in body fluid identification and biogeographic inference.

Saliva is a common body fluid with significant forensic value used to investigate criminal cases such as murder and assault. In the past, saliva identification often relied on the α-amylase test; however, this method has low specificity and is prone to false positives. Accordingly, forensic researchers have been working to find new specific molecular markers to refine the current saliva identification approach. At present, research on immunological methods, mRNA, microRNA, circRNA, and DNA methylation is still in the exploratory stage, and the application of these markers still has various limitations. It has been established that salivary microorganisms exhibit good specificity and stability. In this study, 16S rDNA sequencing technology was used to sequence the V3-V4 hypervariable regions in saliva samples from five regions to reveal the role of regional location on the heterogeneity in microbial profile information in saliva. Although the relative abundance of salivary flora was affected to a certain extent by geographical factors, the salivary flora of each sample was still dominated by Streptococcus, Neisseria, and Rothia. In addition, the microbial community in the saliva samples in this study was significantly different from that in the vaginal secretions, semen, and skin samples reported in our previous studies. Accordingly, saliva can be distinguished from the other three body fluids and tissues. Moreover, we established a prediction model based on the random forest algorithm that could distinguish saliva between different regions at the genus level even though the model has a certain probability of misjudgment which needs more in-depth research. Overall, the microbial community information in saliva stains might have prospects for potential application in body fluid identification and biogeographic inference.

Measuring the impact of an exogenous factor: An exponential smoothing model of the response of shipping to COVID-19.

Following the outbreak of the COVID-19 pandemic, various lockdown strategies restrained global economic growth bringing a significant decline in maritime transportation. However, the previous studies have not adequately recognized the specific impacts of COVID-19 on maritime transportation. In this study, a series of analyses of the Baltic Dry Index (BDI), the China Coastal Bulk Freight Index (CCBFI) and of container throughputs with and without the impact of COVID-19 were carried out to assess changing trends in dry bulk and container transportation. The results show that global dry bulk transportation was largely affected by lockdown policies in the second month during COVID-19, and BDI presented a year-on-year decrease of approximately 35.5% from 2019 to 2020. The CCBFI showed an upward trend in the second month during COVID-19, one month ahead of the BDI. The container throughputs at Shanghai Port, the Ports of Hong Kong, the Ports of Singapore and the Ports of Los Angeles from 2019 to 2020 presented the largest year-on-year drops of approximately 19.6%, 7.1%, 10.6% and 30.9%, respectively. In addition, the authors developed exponential smoothing models of BDI, CCBFI, and container transportation, and calculated the percentage prediction error between the observed and predicted values to examine the impact of exogenous effects on the shipping industry due to the outbreak of COVID-19. The results are consistent with the conclusions obtained from the comparison of BDI, CCBFI, and container transportation during the same period in 2020 and 2019. Finally, on the basis of the findings, smart shipping and special support policies are proposed to reduce the negative impacts of COVID-19.

Single-Pore versus Dual-Pore Bipyridine-Based Covalent-Organic Frameworks: An Insight into the Heterogeneous Catalytic Activity for Selective CH Functionalization.

Exponential growth in the field of covalent-organic frameworks (COFs) is emanating from the direct correlation between designing principles and desired properties. The comparison of catalytic activity between single-pore and dual-pore COFs is of importance to establish structure-function relationship. Herein, the synthesis of imine-linked dual-pore [(BPyDC)]x % -ETTA COFs (x = 0%, 25%, 50%, 75%, 100%) with controllable bipyridine content is fulfilled by three-component condensation of 4,4',4″,4'″-(ethene-1,1,2,2-tetrayl)tetraaniline (ETTA), 4,4'-biphenyldialdehyde, and 2,2'-bipyridyl-5,5'-dialdehyde in different stoichiometric ratio. The strong coordination of bipyridine moieties of [(BPyDC)]x % -ETTA COFs with palladium imparts efficient catalytic active sites for selective functionalization of sp2 CH bond to CX (X = Br, Cl) or CO bonds in good yield. To broaden the scope of regioselective CH functionalization, a wide range of electronically and sterically substituted substrates under optimized catalytic condition are investigated. A comparison of the catalytic activity of palladium decorated dual-pore frameworks with single-pore imine-linked Pd(II) @ Py-2,2'-BPyDC framework  is undertaken. The finding of this work provides a sporadic example of chelation-assisted CH functionalization and disclosed an in-depth comparison of the relationship between superior catalytic activity and core properties of rationally designed imine linked frameworks.

Efficient Electron Transfer from Electron-Sponge Polyoxometalate to Single-Metal Site Metal-Organic Frameworks for Highly Selective Electroreduction of Carbon Dioxide.

In this work, by combining the superiority of polyoxometalates (POMs) and catalytic single-metal site Co of metalloporphyrin, a series of mixed-valence POM-based metal-organic frameworks (MOFs) composites is synthesized by a post-modification method. The electron-transfer property of POM@PCN-222(Co) composite is significantly enhanced owing to the directional electron-transfer from POM to single-metal site Co in PCN-222(Co). In particular, H-POM@PCN-222(Co) gives a high Faradaic efficiency of 96.2% for electroreduction of CO2 into CO and good stability over 10 h. DFT calculations confirm that the directional electron transfer, which accelerates the multi-electron transfer from the electrode to active single-metal site Co, enriches the electron density of the Co center, and ultimately reduces the energy of the rate-determining step, thus increasing the catalytic activity of CO2 reduction reaction (CO2 RR). This work therefore suggests some new insight for the design of efficient electrocatalysts for CO2 RR.

Combined application of multiple autosomal and Y-chromosomal STR loci in solving a homicide case in 2009.

In 2009, a violent murder occurred. Two victims, a 47-year-old mother and her 21-year-old daughter, were murdered at home. After importing the 20 autosomal STR loci and 27 Y-STR loci into a database, no hit had been found. In 2019, a person with a prior criminal record was matched in the national forensic Y-STR database. When increasing the number of detected Y-STR loci to 60, all loci of the bloodstain donor at the crime and the suspect were still found to be identical. With the combined calculation of multiple autosomal STR and kinship index, we were able to identify the perpetrator as a previously unknown illegitimate child of a large family and solved the case.

Genetic diversity of 17 autosomal STR loci in Meizhou Hakka population.

The genetic polymorphism of 17 autosomal short tandem repeat (STR) loci included in the PowerPlex® 18D System was evaluated from 638 unrelated healthy Han individuals of Meizhou in Guangdong Province, Southern China. The values of combined power of discrimination (CPD) and the combined probability of exclusion (CPE) were observed as 0.999999999999999 and 0.999999933. Penta E showed the highest values of polymorphism information content (0.9073), expected heterozygosity (0.9147), and observed heterozygosity (0.9373), whereas TPOX showed the lowest (0.5373, 0.6035, and 0.6082). Furthermore, both of the PCA plot and neighbor-joining phylogenetic tree showed that the Meizhou Hakka population has a relatively close genetic relationship with the Guangdong Han population. The results showed that most of these 17 autosomal STR loci were highly informative and can be effective for forensic individual identification and paternity testing in Meizhou Hakka population.

Exploration of the microbiome community for saliva, skin, and a mixture of both from a population living in Guangdong.

The identification of biological traces provides vital evidence in forensic reconstruction at crime scenes, especially in sexual offences. Compared with traditional presumptive or confirmatory methods, the microbiome-based method has been proven to be of great value in body fluid identification. Mixture of body fluids or tissue is common in sexual assault cases; thus, it is essential to determine the sources of mixed samples. In this study, 60 samples consisting of skin, saliva, and a mixed model of saliva deposited on facial skin were collected from a population living in Guangdong. Through 16s rDNA high-throughput sequencing, we identified the predominant microbes in saliva samples, viz., Haemophilus parainfluenzae T3T1, Neisseria flava, Gemella haemolysans, Prevotella melaninogenica, and Actinomyces odontolyticus; in skin samples, Cutibacterium acnes and Corynebacterium tuberculostearicum were the predominant species. The microbial composition of the same body fluid or tissue is similar in different individuals. However, among different body fluids or tissue, the composition of microflora in saliva is more stable than that on skin. Additionally, the microbial community in the mixed model of saliva deposited on facial skin from the same and different individuals was clearly determined by the constituent fluids or tissue, apart from the differences among the donors. Overall, the microbiome-based method may have good potential as a tool for identifying single and mixed body fluid or tissue.

Signatures of vaginal microbiota by 16S rRNA gene: potential bio-geographical application in Chinese Han from three regions of China.

The human microbiome is expected to be a new and promising tool for classification of human epithelial materials. Vaginal fluids are one of the most common biological samples in forensic sexual assault cases, and its identification is crucial to accurately determine the nature of the case. With the development of molecular biology technologies, the concept of vaginal microflora in different physiological states, ethnic groups, and geography is constantly improved. In this study, we conducted high-throughput sequencing of the V3-V4 hypervariable regions of the 16S rRNA gene in vaginal samples from Henan, Guangdong, and Xinjiang populations, in an attempt to reveal more information about the vaginal microflora in different regions. The results showed that the bio-geographical factors might affect the relative abundance of some vaginal microflora, but there was no significant difference in the composition of dominant bacteria in the vagina, which was mainly composed of Lactobacillus and Gardnerella. However, prediction models based on the random forest algorithm suggested that we might be able to distinguish vaginal fluids from populations of different regions according to the species-level OTUs in low abundance. It is promising that microbiome-based methods could provide more personal information when being attempted to trace the origin of body fluids.

Internal stress and deformation analysis of ultra-thin plate-shaped optical parts in thinning process.

During the thinning process of plate-shaped optical parts (PSOP), the release of internal stress would cause the deformation of ultra-thin PSOP, which deteriorates the processed surface figure. The stress-release-induced deformation is hard to be predicted and controlled due to the difficulty in measuring the tiny internal stress in ultra-thin PSOP. In this paper, an analytical model is established to depict the variation of internal stress and deformation during the thinning process. It can be used to calculate the initial internal stress distribution along the thickness according to the deformation and the residual thickness of the sample. Meanwhile, the model can predict the residual stress distribution and deformation in the whole thinning process. The prediction results obtained from the proposed model agree well with the experimental results, and the prediction error is less than 13%. The presented model has great significance for the analysis of the tiny internal stress and then guide the process of making ultra-thin PSOP.

Food withdrawal alters the gut microbiota and metabolome in mice.

Food withdrawal as a health-enhancing measure has beneficial effects on aging, disease prevention, and treatment. However, the cellular and molecular mechanisms involving gut microbial changes and metabolic consequences resulting from food withdrawal have yet to be elucidated. In this study, we subjected lean and obese mice to a dietary intervention that consisted of a 4-d complete food withdrawal and an 8-d 50% food withdrawal, and we studied changes in cecal microbiome and host serum metabolome. The abundance of potentially pathogenic Proteobacteria was decreased and Akkermansia muciniphila was elevated by food withdrawal in mice fed a high-fat diet (HFD). Meanwhile, food withdrawal decreased the abundance of metabolites in branched chain amino acid, lipid, and free fatty acid metabolisms in host serum, more so in HFD mice than in normal mice. Microbial predicted function also showed that food withdrawal decreased the abundance of microbes associated with predicted diseases in the HFD group but not in the normal chow group. Correlation between the microbiome data and metabolomics data revealed a strong association between gut microbial and host metabolic changes in response to food withdrawal. In summary, our results showed that food withdrawal was safer and more metabolically beneficial to HFD-induced obese mice than to normal lean mice, and the beneficial effects were primarily derived from the changes in gut microbiota, which were closely associated with the host metabolome.-Zheng, X., Zhou, K., Zhang, Y., Han, X., Zhao, A., Liu, J., Qu, C., Ge, K., Huang, F., Hernandez, B., Yu, H., Panee, J., Chen, T., Jia, W., Jia, W. Food withdrawal alters the gut microbiota and metabolome in mice.

Sequencing and functional annotation of the whole genome of the filamentous fungus Aspergillus westerdijkiae.

BACKGROUND: Aspergillus westerdijkiae produces ochratoxin A (OTA) in Aspergillus section Circumdati. It is responsible for the contamination of agricultural crops, fruits, and food commodities, as its secondary metabolite OTA poses a potential threat to animals and humans. As a member of the filamentous fungi family, its capacity for enzymatic catalysis and secondary metabolite production is valuable in industrial production and medicine. To understand the genetic factors underlying its pathogenicity, enzymatic degradation, and secondary metabolism, we analysed the whole genome of A. westerdijkiae and compared it with eight other sequenced Aspergillus species. RESULTS: We sequenced the complete genome of A. westerdijkiae and assembled approximately 36 Mb of its genomic DNA, in which we identified 10,861 putative protein-coding genes. We constructed a phylogenetic tree of A. westerdijkiae and eight other sequenced Aspergillus species and found that the sister group of A. westerdijkiae was the A. oryzae - A. flavus clade. By searching the associated databases, we identified 716 cytochrome P450 enzymes, 633 carbohydrate-active enzymes, and 377 proteases. By combining comparative analysis with Kyoto Encyclopaedia of Genes and Genomes (KEGG), Conserved Domains Database (CDD), and Pfam annotations, we predicted 228 potential carbohydrate-active enzymes related to plant polysaccharide degradation (PPD). We found a large number of secondary biosynthetic gene clusters, which suggested that A. westerdijkiae had a remarkable capacity to produce secondary metabolites. Furthermore, we obtained two more reliable and integrated gene sequences containing the reported portions of OTA biosynthesis and identified their respective secondary metabolite clusters. We also systematically annotated these two hybrid t1pks-nrps gene clusters involved in OTA biosynthesis. These two clusters were separate in the genome, and one of them encoded a couple of GH3 and AA3 enzyme genes involved in sucrose and glucose metabolism. CONCLUSIONS: The genomic information obtained in this study is valuable for understanding the life cycle and pathogenicity of A. westerdijkiae. We identified numerous enzyme genes that are potentially involved in host invasion and pathogenicity, and we provided a preliminary prediction for each putative secondary metabolite (SM) gene cluster. In particular, for the OTA-related SM gene clusters, we delivered their components with domain and pathway annotations. This study sets the stage for experimental verification of the biosynthetic and regulatory mechanisms of OTA and for the discovery of new secondary metabolites.

Pre-pregnancy BMI, gestational weight gain and postpartum weight retention: a meta-analysis of observational studies.

OBJECTIVE: To determine the association of gestational weight gain (GWG) or pre-pregnancy BMI with postpartum weight retention (PPWR). DESIGN: Meta-analysis. SETTING: PubMed, Cochrane Controlled Trials Register, EMBASE, Science Citation Index Expanded, Current Contents Connects and Biosis Previews were used to search articles. SUBJECTS: Publications that described the influence of pre-pregnancy BMI or GWG on PPWR. RESULTS: Seventeen studies that satisfied the eligibility criteria were included in the analyses. Women with inadequate and excessive GWG had significantly lower mean PPWR of -2·14 kg (95 % CI -2·43, -1·85 kg) and higher PPWR of 3·21 kg (95 % CI 2·79, 3·62 kg), respectively, than women with adequate GWG. When postpartum time spans were stratified into 1-3 months, 3-6 months, 6-12 months, 12-36 months and ≥15 years, the association between inadequate GWG and PPWR faded over time and became insignificant (-1·42 kg; 95 % CI -3·08, 0·24 kg) after ≥15 years. However, PPWR in women with excess GWG exhibited a U-shaped trend; that is, a decline during the early postpartum time span (year 1) and then an increase in the following period. Meta-analysis of qualitative studies showed a significant relationship between excessive GWG and higher PPWR risk (OR=2·08; 95 % CI 1·60, 2·70). Moreover, meta-analysis of pre-pregnancy BMI on PPWR indicated that mean PPWR decreased with increasing BMI group. CONCLUSIONS: These findings suggest that GWG, rather than pre-pregnancy BMI, determines the shorter- or longer-term PPWR.

A Gradient-Guided Evolutionary Neural Architecture Search.

Neural architecture search (NAS) is a popular method that can automatically design deep neural network structures. However, designing a neural network using NAS is computationally expensive. This article proposes a gradient-guided evolutionary NAS (GENAS) to design convolutional neural networks (CNNs) for image classification. GENAS is a hybrid algorithm that combines evolutionary global and local search operators to evolve a population of subnets sampled from a supernet. Each candidate architecture is encoded as a table describing which operations are associated with the edges between nodes signifying feature maps. Besides, evolutionary optimization uses novel crossover and mutation operators to manipulate the subnets using the proposed tabular encoding. Every n generations, the candidate architectures undergo a local search inspired by differentiable NAS. GENAS is designed to overcome the limitations of both evolutionary and gradient descent NAS. This algorithmic structure enables the performance assessment of the candidate architecture without retraining, thus limiting the NAS calculation time. Furthermore, subnet individuals are decoupled during evaluation to prevent strong coupling of operations in the supernet. The experimental results indicate that the searched structures achieve test errors of 2.45%, 16.86%, and 23.9% on CIFAR-10/100/ImageNet datasets and it costs only 0.26 GPU days on a graphic card. GENAS can effectively expedite the training and evaluation processes and obtain high-performance network structures.

Microcrystalline cellulose grafted hyperbranched polyester with roll comb structure for synergistic toughening and strengthening of microbial PHBV/bio-based polyester elastomer composites.

The brittle feature of poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV) is the major challenge that strongly restricts its application at present. Successfully synthesized bio-based engineering polyester elastomers (BEPE) were combined with PHBV to create entirely bio-composites with the intention of toughening PHBV. Herein, the 2,2-Bis(hydroxymethyl)-propionic acid (DMPA) was grafted onto microcrystalline cellulose (MCC) and then further transformed into hyperbranched polyester structure via polycondensation. The modified MCC, named MCHBP, had plenty of terminal hydroxyl groups, which get dispersed between PHBV and BEPE. Besides, a large number of terminal hydroxyl groups of MCHBP can interact with the carbonyl groups of PHBV or BEPE in a wide range of hydrogen bonds, and subsequently increase the adhesion and stress transfer between the PHBV and BEPE. The tensile toughness and the elongation at break of the PHBV/BEPE composites with 0.5phr MCHBP were improved by 559.7 % and 221.8 % in comparison to those of PHBV/BEPE composites. Results also showed that MCHBP can play a heterogeneous nucleation effect on the crystallization of PHBV. Therefore, this research can address the current issue of biopolymers' weak mechanical qualities and may have uses in food packaging.

Tailoring compatibility and toughness of microbial poly(3-hydroxybutyrate-co-3-hydroxyvalerate)/bio-based polyester elastomer blends by epoxy-terminated hyperbranched polyester.

Poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV) is a type of promising bio-based thermoplastic for food packaging but find restricted industrial applications due to its brittleness and poor processability that is caused by its large spherulite sizes. In this study, for the purpose of toughening PHBV, bio-based engineering polyester elastomers (BEPE) were synthesized and blended with PHBV to prepare fully bio-based blends. In order to improve the compatibility and toughness of the BEPE/PHBV blends, epoxy-terminated hyperbranched polyesters (EHBP) were synthesized, which could be homogeneously dispersed into the PHBV/BEPE blends and improve the compatibility between the two phases of the matrix. The results showed that compared to those of the PHBV/BEPE blends, the elongation at break, impact strength and tensile toughness of the PHBV/BEPE blends with 3.0phr EHBP were enhanced by 134.2 %, 76.8 %, and 123.5 %, respectively. The crystallization study demonstrated the crystallization rate of PHBV/BEPE blends decreased due to the addition of EHBP. The reasons lied in that the addition of EHBP leads to chemical cross-linking between PHBV and BEPE. Meanwhile, the formation of hydrogen bonding, co-crystallization and chain entanglement increased the adhesion between PHBV and BEΡE, which generated the superior toughness of the blends.

Influence of handrail height and knee joint support on sit-to-stand movement.

Handrail height and knee joint support both significantly influence sit-to-stand (STS) movement. However, research on the associations between handrail height, knee joint support, and their cumulative effect on STS kinematics and changes in plantar pressure distribution during STS under different handrail heights and knee joint support is still unclear. The main objective of this study was to examine the influence of handrail height and knee joint support on the kinematics and the distribution of plantar pressure in healthy adults during STS. Twenty-six healthy adult subjects aged 23 to 58 years participated in this experiment. The subjects carried out STS movement experiments under 7 conditions: 6 experimental conditions of 3 different heights of handrail, with and without knee joint support, and 1 control condition of standing up naturally. The motions of the markers were recorded using cameras operating at 60 Hz, and total movement time, the percentage of movement time of each phase, trunk tilt angle, joint angle, plantar pressure, and the time from hindfoot to forefoot peak pressure were analyzed and compared. Handrail height significantly influences the percentage of movement time at phase I (P = .015) and the maximum trunk tilt angle (P < .05), knee joint support significantly influences the maximum trunk tilt angle and ankle angle (P = .033), and handrail height and knee joint support have an interaction on the time from hindfoot to forefoot peak pressure (P < .001). Subjects' STS performance was improved with the use of assistant devices but showed particular improvement under the condition of with knee joint support when the handrail height was middle handrail.