Digital holographic measurement of electron temperature and density of laser-produced plasmas with an ultrashort laser pulse.

Holography, which can provide the information of phase as well as amplitude of a laser probe, could be a powerful method to diagnose the electron density and temperature of a plasma simultaneously. In this paper, digital holography with an ultrashort laser pulse is applied to diagnose laser-produced aluminum plasmas. Detailed analyses show that the reconstruction of the wave amplitude could be profoundly affected by the difference between the phase and group velocity of the ultrashort laser pulse in the plasma, which makes it a challenge to accurately reconstruct the amplitude in the case when ultrashort laser pulses are utilized for high-temporal resolution of holography.

Sequencing-induced artefacts in NGS STR data.

Significant progress has been made in recent years in the development of techniques for Next Generation Sequencing (NGS), or Massively Parallel Sequencing (MPS), of forensically relevant short tandem repeat (STR) loci. However, as these technologies are investigated and adopted by forensic laboratories, new challenges unfold that require further scrutiny. In the analysis of DNA profiles generated using the MiSeq FGx sequencing system, we have observed noise sequences with relatively high readcounts that are challenging to distinguish from genuine alleles. These high read count noise sequences appear as allele sequences with one or a few substituted bases compared to a known allele sequence within the profile. An examination of ForenSeq DNA Signature Prep Kit STR noise sequences revealed that the substituted base of a parent allele can align to the same position on the sequence across noise sequences. This suggests that these substitution events occur at specific positions within the amplicon, resulting in multiple noise reads with substitutions at the same position. Mapping of the noise events onto the original raw read positions revealed a high number of events, or "noise spikes", occurring at specific positions within a given sequencing run. These noise spikes affected reads across the entire run, agnostic of locus or sample, while the position, occurrence, and amplitude of the spikes differed across runs. The majority of noise sequences with high read counts in a DNA profile were generated from base changes at these spike positions, and could be classified as "noise spike artefacts". In this paper we present evidence of the noise spike artefacts and their genesis during the sequencing process in the sequencing-by-synthesis (SBS) cycles, as well as the methods developed to detect them. The information and methods will assist laboratories with detecting noise spikes in MiSeq FGx sequencing runs, differentiating authentic allele sequences from noise spike artefacts, and developing protocols for analyst review and handling of MiSeq FGx data.

Estimation of population specific values of theta for sequence-based STR profiles.

We describe the estimation of θ (theta) values from autosomal STR sequencing data for five metapopulations. The data were compiled from 20 publications and included 39 datasets comprising a total of 7005 samples. The estimates are suitable for use within the calculation of match probabilities in forensic casework. We also have constructed a phylogenetic tree using this data that aligns with our understanding of human evolution.

Which are the vital factors of mobile personal health records applications that promote continued usage? A perspective on technology fit and social capital.

Introduction: With the widespread use of mobile devices and the rapid development of mobile networks, connecting mobile personal health record (mPHR) apps to wearable devices to collect personal health data for analysis and community activities has become a trend for health promotion. Therefore, the present study aims to explore the vital factors that impact the sustained usage of mPHR apps. Objective: In this study, we identified social lock-in as a major research gap in the current era of social media and the Internet. Therefore, to explore the effects of mPHR apps on continued app usage intention, we combined technology fit (individual-technology, synchronicity-technology, and task-technology fit) and social capital (structural, relational, and cognitive capital) to develop a novel study model. Methods: The purpose of this research is to investigate the willingness to participate in the mPHR apps. It collected 565 valid users' responses through the online questionnaire with a structural equation modeling approach. Results: That technology and social lock-in significantly affected the willingness of users to continue using mPHR apps (ß = 0.38, P < 0.001) and that the effects of social lock-in (ß = 0.38, P < 0.001) were more pronounced than those of technology lock-in (ß = 0.22, P < 0.001). Conclusions: The technology and social lock-in generated by technology fit and social capital had positive effects on continued app usage and the effects of both types of lock-in on continued app usage varied among different participant groups.

The role and advantage of traditional Chinese medicine in the prevention and treatment of COVID-19.

The global coronavirus disease 2019 (COVID-19) pandemic has had a massive impact on global social and economic development and human health. By combining traditional Chinese medicine (TCM) with modern medicine, the Chinese government has protected public health by supporting all phases of COVID-19 prevention and treatment, including community prevention, clinical treatment, control of disease progression, and promotion of recovery. Modern medicine focuses on viruses, while TCM focuses on differential diagnosis of patterns associated with viral infection of the body and recommends the use of TCM decoctions for differential treatment. This differential diagnosis and treatment approach, with its profoundly empirical nature and holistic view, endows TCM with an accessibility advantage and high application value for dealing with COVID-19. Here, we summarize the advantage of and evidence for TCM use in COVID-19 prevention and treatment to draw attention to the scientific value and accessibility advantage of TCM and to promote the use of TCM in response to public health emergencies. Please cite this article as: Huang M, Liu YY, Xiong K, Yang FW, Jin XY, Wang ZQ, Zhang JH, Zhang BL. The role and advantage of traditional Chinese medicine in the prevention and treatment of COVID-19. J Integr Med. 2023; 21(5): 407-412.

Developmental validation of STRmix™ NGS, a probabilistic genotyping tool for the interpretation of autosomal STRs from forensic profiles generated using NGS.

We describe the developmental validation of the probabilistic genotyping software - STRmix™ NGS - developed for the interpretation of forensic DNA profiles containing autosomal STRs generated using next generation sequencing (NGS) also known as massively parallel sequencing (MPS) technologies. Developmental validation was carried out in accordance with the Scientific Working Group on DNA Analysis Methods (SWGDAM) Guidelines for the Validation of Probabilistic Genotyping Systems and the International Society for Forensic Genetics (ISFG) recommendations and included sensitivity and specificity testing, accuracy, precision, and the interpretation of case-types samples. The results of developmental validation demonstrate the appropriateness of the software for the interpretation of profiles developed using NGS technology.

Forensic STR allele extraction using a machine learning paradigm.

We present a machine learning approach to short tandem repeat (STR) sequence detection and extraction from massively parallel sequencing data called Fragsifier. Using this approach, STRs are detected on each read by first locating the longest repeat stretches followed by locus prediction using k-mers in a machine learning sequence model. This is followed by reference flanking sequence alignment to determine precise STR boundaries. We show that Fragsifier produces genotypes that are concordant with profiles obtained using capillary electrophoresis (CE), and also compared the results with that of STRait Razor and the ForenSeq UAS. The data pre-processing and training of the sequence classifier is readily scripted, allowing the analyst to experiment with different thresholds, datasets and loci of interest, and different machine learning models.

A review of bioinformatic methods for forensic DNA analyses.

Short tandem repeats, single nucleotide polymorphisms, and whole mitochondrial analyses are three classes of markers which will play an important role in the future of forensic DNA typing. The arrival of massively parallel sequencing platforms in forensic science reveals new information such as insights into the complexity and variability of the markers that were previously unseen, along with amounts of data too immense for analyses by manual means. Along with the sequencing chemistries employed, bioinformatic methods are required to process and interpret this new and extensive data. As more is learnt about the use of these new technologies for forensic applications, development and standardization of efficient, favourable tools for each stage of data processing is being carried out, and faster, more accurate methods that improve on the original approaches have been developed. As forensic laboratories search for the optimal pipeline of tools, sequencer manufacturers have incorporated pipelines into sequencer software to make analyses convenient. This review explores the current state of bioinformatic methods and tools used for the analyses of forensic markers sequenced on the massively parallel sequencing (MPS) platforms currently most widely used.

Impurity channels of the long-lived Mossbauer effect.

Recent reports have suggested that the nuclear resonant absorption of a long-lived Mossbauer state e.g., (93m)Nb is mediated by an entangled photon pair (biphoton) rather than by a single photon. Multipolar nuclear excitation in crystals of a single isotope with a natural abundance of 100% spreads in a region containing billions of identical nuclei. As a consequence of the delocalisation, additional decay channels via the impurities, the crystal defects, and the sample boundary, give rise to a density- and temperature-dependent decay. In this letter we report our discovery of impurity channels, the intensity of which is proportional to the square of the (93m)Nb density.

Detection of phylogenetically distinct Puumala-like viruses from red-grey vole Clethrionomys rufocanus in China.

In order to investigate whether Puumala virus (PUUV) or PUUV-like virus is present in China, Clethrionomys rufocanus and C. rutilus were captured in the Jilin province during the spring and autumn of 2002-2003 for detection of PUUV viral RNA by RT-PCR and confirmation of PUUV-positive antigens by an immunofluorescence assay. PUUV-positive RNA was identified in six out of 121 C. rufocanus but not in any of the 41 C. rutilus. Complete S and partial M sequences (nt 1,316-1,598 and 2,687-3,089) were amplified by RT-PCR directly from some of the antigen positive lung tissues and subjected to nucleic acid sequencing. It was found that the Chinese PUUV-like viruses were related most closely with the PUUV strains with 77.7-81.7% identity at the nucleotide level and 91.7-97% identity at the amino acid level for S segment, and with 77-78.8% identity at the nucleotide level and 91.5-92.6% identity at the amino acid level for the partial M segment (nt 1,316-1,598). Genetic analysis indicated that the Chinese PUUV-like viruses shared the highest level of identity with the viruses which circulate in C. rufocanus in the Far East region of Russia with 85.1-87.4% identity at the nucleotide level and 95.9% identity at the amino acid level for the partial M segment (nt 2,687-3,089), respectively. Phylogenetic analysis revealed that the Chinese PUUV-like viruses are distinct from those identified from Japan, South Korea, Europe or Russia. These results indicate that PUUV-like virus is present in China in addition to Hantaan, Seoul and Dabieshan viruses.

Isolation and characterization of hantavirus carried by Apodemus peninsulae in Jilin, China.

To provide a better understanding of hantavirus epidemiology in China, Korean field mice (Apodemus peninsulae) and striped field mice (Apodemus agrarius) were captured in Jilin province, China, where haemorrhagic fever with renal syndrome (HFRS) is endemic. Hantavirus antigens were detected in eight of the 130 A. peninsulae individuals and in four of the 193 A. agrarius individuals by using an immunofluorescence assay. Partial S and M segments were amplified from all of the antigen-positive samples. Furthermore, two hantaviruses (CJAp89 and CJAp93) were isolated successfully in cell culture and the entire S and M segments were amplified from one of them (CJAp93). Phylogenetic analysis of these sequences (partial or complete) showed that hantaviruses carried by A. peninsulae and A. agrarius form two distinct lineages, although viruses carried by A. peninsulae are similar to those isolated previously from A. agrarius in China and from HFRS patients in Russia. However, the viruses detected in A. peninsulae in China are genetically different from those detected in A. peninsulae in other countries. These data suggest that A. peninsulae is also a natural host for HTNV in north-eastern China.