Exploring the Femtosecond Filamentation Threshold in Liquid Media Using a Mach-Zehnder Interferometer.

We experimentally studied the supercontinuum induced by femtosecond filamentation in different liquid media. Using a Mach-Zehnder interferometer, we determined the relative filamentation thresholds (Pth) of these media. Research has shown that the value of the filamentation threshold is greater than that of Pcr (critical power for self-focusing), which can mainly be attributed to the strong dispersion effect. Changing the focal length of the focusing lens affects filamentation dynamics, thereby affecting the measured results regarding the filamentation threshold. With shorter focal lengths, the linear focusing (i.e., geometrical focusing) regime dominates, and the measured values of Pth for different liquid media are almost the same; as the focal length becomes larger, self-focusing starts to play a role, making the values of Pth for different media different from each other. This study presents an efficient method for investigating the femtosecond filamentation phenomenon in liquid media, helpful to provide further insights into the physical mechanism of supercontinuum generation via femtosecond filamentation in liquid media.

Prevalence of multiple human papillomavirus infections and association with cervical lesions among outpatients in Fujian, China: A cross-sectional study.

Multiple human papillomavirus (HPV) infections are common, but their impact on cervical lesions remains controversial. A total of 6225 female patients who underwent colposcopies/conization following abnormal cervical cancer screening results were included in the study. The final pathological diagnosis was determined by the most severe pathological grade among the cervical biopsy, endocervical curettage, and conization. Univariate and multivariate logistic regression analyses were used to investigate the association between multiple HPV infections and cervical lesions, adjusting for age, HPV genotype, gravidity and parity. In total, 33.3% (n = 2076) of the study population was infected with multiple HPV genotypes. Multiple HPV infections were more prevalent in patients younger than 25 years and older than 55 years, with the rate of multiple HPV infections at 52.8% and 44.3%, respectively. HPV16\52\18\58 are the most common HPV genotypes and usually appear as a single infection. Compared to single HR-HPV infection, multiple HR-HPV infections do not increase the risk of HSIL+, while single HR-HPV coinfected with LR-HPV seems to reduce the risk of HSIL+ (odds ratio = 0.515, confidence interval: 0.370-0.719, p < 0.001). Multiple HR-HPV infections cannot be risk-stratified for triage of HR-HPV-positive women.

Calculation of high-order harmonic generation of atoms and molecules by combining time series prediction and neural networks.

High-order harmonic generation (HHG) from the interaction of ultra-intense laser pulses with atoms is an important tabletop short-wave coherent light source. Accurate quantum simulations of it present large computational difficulties due to multi-electron multidimensional effects. In this paper, the time-dependent response of hydrogen atoms is calculated using a time-series prediction scheme, the HHG spectrum is reconstructed very accurately. The accuracy of the forecasting is further improved by using a neural network scheme. This scheme is also applied to the simulation of the harmonic emission on multi-electron systems, and the applicability of the scheme is confirmed by the harmonic calculation of complex systems. This method is expected to simulate the nonlinear dynamic process of multi-electron atoms and molecules irradiated by intense laser pulses quickly and accurately.

Improvement of LIBS signal stability for NaCl solution using femtosecond laser-induced water film.

This paper studies the analysis of Na element concentration in NaCl aqueous solution using laser-induced breakdown spectroscopy (LIBS). The NaCl solution is transformed to a thin water film. The water film can provide a stable liquid surface, and overcome the disadvantage that laser focusing position cannot be fixed due to liquid level fluctuation (when nanosecond laser is used as the excitation light source, there is serious liquid splash phenomenon, which affects the signal stability). And, femtosecond pulse laser is used to excite the water film to produce the plasma, avoiding liquid splashing. The measured emission lines are Na (I) at 589.0 nm and 589.6 nm. The calibration curves of sodium are plotted by measuring different concentrations of NaCl solution. The linear correlation coefficients of Na (I) lines at 589.0 nm and 589.6 nm are 0.9928 and 0.9914, respectively. In addition, the relative standard deviation is also calculated; its range is from 1.5% to 4.5%. The results indicate that the combination of femtosecond laser and water film can significantly improve the signal stability for liquid analysis in LIBS.

Tracing the Coherent Manipulation of Rotational Dynamics by Shaped Femtosecond Pulse-Induced Two-Dimensional Rotational Coherent Spectrum.

The temporal delayed orthogonal pulse pairs generated by the phase shaping technique are used to study the coherent control of the rotational wave packet dynamics in air. By continuously changing the intrapulse delay of the pump pulse, we measured the corresponding revival signals and obtained a two-dimensional rotational coherent spectrum (2D RCS). An additive property of the rotational dynamics is observed from the revival signals. Moreover, combining with the coherent control model, we find that the 2D RCS can be used to demonstrate the control over the underlying Raman rotational excitation. A beat frequency-dependent oscillation of each rotational transition is obtained. The transition process is revealed from the Fourier transformation about the pump delay. The scheme of this work can be used for further control and detection of the rotational wave packet and can be extended to other molecular dynamic researches.

Association study between genetic variants and the risk of schizophrenia in the Chinese population based on GWAS-implicated 6p21.3-23.1 human genome region: a case-control study.

BACKGROUND: Schizophrenia is a polygenic disease; however, the specific risk genetic variants of schizophrenia are still largely unknown. Single nucleotide polymorphism (SNP) is important genetic factor for the susceptibility of schizophrenia. Investigating individual candidate gene contributing to disease risk remains important. METHODS: In a case-control study, five SNPs located in 6p21.3-p23.1 including rs2021722 in human leukocyte antigen (HLA) locus and rs107822, rs383711, rs439205 and rs421446 within the upstream of microRNA-219a-1 were genotyped in 454 schizophrenia patients and 445 healthy controls to investigate the possible association between the loci and schizophrenia in a Han Chinese population. RESULTS: Our results showed significant associations between the rs2021722 and schizophrenia in allele (A vs. G: adjusted OR = 1.661, 95%CI = 1.196-2.308), co-dominant (AG vs. GG: OR = 1.760, 95%CI = 1.234-2.510) and dominant genetic model (AG + AA vs. GG: OR = 1.756, 95%CI = 1.237-2.492), respectively. Haplotype analysis showed that TGGT and CAAC were protective factor for schizophrenia compared with TAAC haplotype (OR = 0.324, 95% CI = 0.157-0.672; OR = 0.423, 95% CI = 0.199-0.900). CONCLUSIONS: These findings indicate that rs2021722 in HLA locus might be involved in pathogenesis of schizophrenia and that genotypes AG and allele A of the locus are risk factors for schizophrenia in the Han Chinese population, confirming the association between immune system and schizophrenia.

Spectral resolved study of filamentation effect on the nonlinear absorption in carbon disulfide.

A Z-scan system using spectrometers as detectors is established to investigate nonlinear absorption and white light continuum separately, in which absorption coefficient that is coincident with previous work was obtained. After Z-scan experiments, spot photographs were captured to further study the spatial properties of filaments in CS2, and we obtained similar space between dual filaments with previous work. Using the experimental setup, we find that plasma generation is the main effect impacting the nonlinear absorption and refraction process, and this impact can be eliminated in the case of CS2. Therefore, effect of filamentation can be neglected for CS2. Though it is easy to generate filaments in CS2 at relatively low intensity, fitting the Z-scan curve with three-photon model at 800 nm for CS2 is reasonable. In addition, the thickness of sample can affect extracted absorption coefficient of CS2 by affecting the length of filamentation.

Ultrafast carrier dynamics of carbon nanodots in different pH environments.

Ultrafast carrier relaxation dynamics in fluorescent carbon nanodots is investigated by femtosecond transient absorption spectra at different pH environments so as to understand the mechanism of fluorescence for the first time. Utilizing multi-wavelength global analysis to fit the measured signal via a sequential model, four different relaxation channels are found, which are attributed to electron-electron scattering and surface state trapping, optical phonon scattering, acoustic phonon scattering and electron-hole recombination respectively. The results reveal that the surface states are mainly composed of different oxygen-containing functional groups (epoxy, carbonyl and carboxyl) and carbon atoms on the edge of the carbon backbone and can effectively trap a large number of photo-excited electrons. The deprotonation of carboxyl groups at high pH will change the distribution of π electron cloud density between the carbon backbone and surface states and consequently, compared with the excited electrons in the acidic and neutral environments, those in the alkaline environment can be more easily trapped by the surface within 1 ps, thereby giving rise to stronger fluorescence emission.

Optical emission generated from silicon under dual-wavelength femtosecond double-pulse laser irradiation.

In femtosecond double-pulse laser-induced breakdown spectroscopy, collinear double-pulse performance is investigated experimentally using various laser wavelength combinations of 800 nm and 400 nm Ti: sapphire lasers. The induced plasma emission line collected by BK7 lenses is the Si (I) at 390.55 nm. The double-pulse time separation ranges from -300 ps to 300 ps. The line intensity is dependent on the time separation of the dual-wavelength femtosecond double-pulse, and its behavior is unlike that of single-wavelength femtosecond double-pulses. Optical emission intensity can be enhanced by selecting appropriate time separation between sub-pulses. This result is particularly advantageous in the context of femtosecond laser-induced breakdown spectroscopy.

Influence of ambient pressure on the ablation hole in femtosecond laser drilling Cu.

The holes were drilled by femtosecond laser pulse (800 nm, 100 fs) on Cu sheets at different ambient pressures. The pressure range was from 1 Pa to atmospheric pressure. The number of pulses to drill through the target, the stable photodiode signal, and the hole diameter were obtained as functions of ambient pressure. The morphology of the hole was observed by a scanning electron microscope (SEM). The result showed that the ambient pressure had significant influence on the morphology of the hole.

The Impacts of Cellulose on Volatile Fatty Acid Production and the Microbial Community in Anaerobic Fermentation of Sludge at High and Medium Temperatures.

During large-scale sewage treatment, a large amount of excessive sludge is produced, which will cause serious pollution in the environment. In recent years, anaerobic digestion technology has been widely promoted because it can achieve better sludge reduction, and the products and byproducts after anaerobic digestion can be fully utilized as resources. In this study, cellulose was added as the co-fermentation substrate during the fermentation process at 30 ℃ and 50 ℃ to enhance the production of VFAs. The result indicated that cellulose could significantly increase the yield of VFAs in both 30 ℃ and 50 ℃. Meanwhile, COD and reducing sugar generation in the fermentation process were also measure. Analysis of the microbial community structure at the class and genus levels revealed that the proportion of several genus closely related with cellulose degradation such as Cellvibrio, Fibrobacter, and Sporocytophaga were significantly increased with the addition of cellulose. Co-fermentation was recognized as an economic and environmental friendly strategy for sludge and other solid waste treatment. The analysis of the effect of cellulose as a substrate on the production of VFAs at high and medium temperatures is highly important for exploring ways to increase the production of VFAs in anaerobic fermentation.

Conjugated molecularly imprinted polymers based on covalent organic frameworks: Fluorescent sensing platform for specific capture of urea and elimination of ethyl carbamate.

This study described the preparation of an azide covalent organic framework-embedded molecularly imprinted polymers (COFs(azide)@MIPs) platform for urea adsorption and indirect ethyl carbamate (EC) removal from Chinese yellow rice wine (Huangjiu). By modifying the pore surface of COFs using the copper-catalyzed azide-alkyne cycloaddition (CuAAC) reaction, COFs(azide) with a high fluorescence quantum yield and particular recognition ability were inventively produced. In order to selectively trap urea, the COFs(azide) were encased in an imprinted shell layer via imprinting technology. With a detection limit (LOD) of 0.016 µg L-1 (R2 = 0.9874), the COFs(azides)@MIPs demonstrated a good linear relationship with urea in the linear range of 0-5 µg L-1. Using real Huangjiu samples, the spiking recovery trials showed the viability of this sensing platform with recoveries ranging from 88.44 % to 109.26 % and an RSD of less than 3.40 %. The Huangjiu processing model system achieved 38.93 % EC reduction by COFs(azides)@MIPs. This research will open up new avenues for the treatment of health problems associated with fermented alcoholic beverages, particularly Huangjiu, while also capturing and removing hazards coming from food.

RNA quality score evaluation: A preliminary study of RNA integrity number (RIN) and RNA integrity and quality number (RNA IQ).

In the past several years, with the in-depth development of RNA-related research, exploring the application of transcriptome and corresponding RNA biomarkers has become one of the research hotspots in the field of forensic science. High-quality RNA is essential for successful downstream workflows, especially in the steps of screening biomarkers by microarray or RNA sequencing (RNA-seq). Thus, accurately evaluating the quality of RNA samples is a critical step in obtaining meaningful expression data. The RNA integrity number (RIN) generated from the Agilent Bioanalyzer system has been widely used for RNA quality control in the past two decades. Recently, Thermo Fisher Scientific launched a ratiometric fluorescence-based method to quickly check whether an RNA sample has degraded, and the results are presented as RNA integrity and quality number (RNA IQ). Both quality score systems determine RNA quality using a numerical system based on a scale of 1-10, with 1 denoting significantly degraded specimens and 10 representing high-quality, intact RNA samples. In this preliminary study, we evaluated the consistency, reproducibility and linearity of two quality scores in RNA quality determination by analyzing heat- and RNase- artificially degraded samples. Meanwhile, the expression levels of three microRNAs (hsa-let-7 g-5p, hsa-miR-93-5p and hsa-miR-191-5p) in intact and severely degraded RNA samples were estimated by TaqMan-qPCR and droplet digital PCR. Overall, both quality scores showed good repeatability and reproducibility in their respective tests. In the samples subjected to thermal degradation, RIN showed a trend corresponding to heating time, while RNA IQ value showed almost no change on the time gradient. However, in RNase A mediated degradation, RNA IQ value observed better linearity. Furthermore, the expression levels of three microRNAs in the severely degraded samples did not show significant changes compared to the intact RNA samples. RNA degradation is a very complex and highly variable process, which is difficult to comprehensively evaluate through any one index and cannot directly compare these two parameters. Nevertheless, combined with previous research results and the expression levels of three microRNAs in this study, analyzing RNA biomarkers with stable regions or small sizes in challenged samples may be a conservative and reliable approach.

Forensic characteristics and genetic structure of the Chinese Tibetan population revealed by 38 X-chromosomal InDel loci.

With the increasing importance of X-chromosome (Chr-X) genotyping in kinship identification, the exploitation of X chromosome genetic marker multiplex kits is increasing. The Human X-InDels amplification kit is a novel developed system which contained 38 X-chromosomal Insertion/deletion markers (X-InDels) and Amelogenin. Herein, we investigated the genetic diversity of the 38 X-InDels in the Tibetan ethnic minority (n = 792) from seven regions and evaluated the application potential of this novel panel. The rs16368 was the least variable locus, whereas the most polymorphic locus was the rs59605609 in Tibetan population. We confirmed three linkage groups with the haplotype diversities ranged from 0.5032 to 0.5976. The overall combined power of discrimination (PD) in males and females were 0.999999999582066 and 0.999999999999993, respectively. And the overall combined mean exclusion chance (MEC) values were not lower than 0.999125526990159. In addition, we explored the genetic relationships among the Tibetans in seven different regions via series of population comparison analyses, finding that the genetic relationship between the Ngari Tibetan and Chamdo Tibetan was the farthest, which was consistent with geographical distribution.

Distant organ metastasis patterns and prognosis of cervical adenocarcinoma: a population-based retrospective study.

Background: Adenocarcinoma is a common histological subtype of cervical cancer, accounting for 10-15% of all cases. The prognosis of cervical adenocarcinoma with distant organ metastases remains unclear. Therefore, our study aimed to investigate the patterns and prognosis of distant organ metastasis in cervical adenocarcinoma. Methods: We obtained data from the Surveillance, Epidemiology, and End Results (SEER) database spanning from 2010 to 2019. Cox regression, Kaplan-Meier, and log-rank analyses were conducted. Results: We observed that adenocarcinoma (AC) of the cervix primarily metastasizes to single organs, with a rate of 73.3%. The lungs are the most common organs of metastasis, followed by the liver and bones. Patients with bone metastases have a median survival period of 12 months, which is slightly longer compared to metastasis in other organs. Distant organ metastasis, age, positive lymph nodes, higher AJCC stages, larger tumor diameter, and higher cell grades are related to poor prognosis (p < 0.001). Furthermore, we have observed that surgical intervention, radiotherapy, and chemotherapy can potentially provide benefits for patients with distant organ metastases. Conclusion: Metastasis is an independent prognostic factor for cervical adenocarcinoma patients. Surgery, radiotherapy, and chemotherapy can provide an overall survival advantage for patients with distant organ metastases.

A proof-of-principle study: The potential application of MiniHap biomarkers in ancestry inference based on the QNome nanopore sequencing.

Haplotyped SNPs convey forensic-related information, and microhaplotypes (MHs), as the most representative of this kind of marker, have proved the potential value for human forensics. In recent years, nanopore sequencing technology has developed rapidly, with its outstanding ability to sequence long continuous DNA fragments and obtain phase information, making the detection of longer haplotype marker possible. In this proof-of-principle study, we proposed a new type of forensic marker, MiniHap, based on five or more SNPs within a molecular distance less than 800 bp, and investigated the haplotype data of 56 selected MiniHaps in five Chinese populations using the QNome nanopore sequencing. The sequencing performance, allele (haplotype) frequencies, forensic parameters, effective number of alleles (Ae), and informativeness (In) were subsequently calculated. In addition, we performed principal component analysis (PCA), phylogenetic tree, and structure analysis to investigate the population genetic relationships and ancestry components among the five investigated populations and 26 worldwide populations. MiniHap-04 exhibited remarkable forensic efficacy, with 148 haplotypes reported and the Ae was 66.9268. In addition, the power of discrimination (PD) was 0.9934, the probability of exclusion (PE) was 0.9898, and the In value was 0.7893. Of the 56 loci, 85.71% had PD values above 0.85, 66.07% had PE values above 0.54, 67.86% had Ae values over 7.0%, and 55.36% were with In values above 0.2 across all samples, indicating that most of the MiniHaps are suitable for individual identification, paternity testing, mixture deconvolution, and ancestry inference. Moreover, the results of PCA, phylogenetic tree and structure analysis demonstrated that this MiniHap panel had the competency in continental population ancestry inference, but the differentiation within intracontinental/linguistically restricted subpopulations was not ideal. Such findings suggested that the QNome device for MiniHap detection was feasible and this novel marker has the potential in ancestry inference. Yet, the establishment of a more comprehensive database with sufficient reference population data remains necessary to screen more suitable MiniHaps.

CmVCall: An automated and adjustable nanopore analysis pipeline for heteroplasmy detection of the control region in human mitochondrial genome.

Genetic associations between human mitochondrial DNA (mtDNA) heteroplasmy and mitochondrial diseases, aging, and cancer have been elaborated, contributing a lot to the further understanding of mtDNA polymorphic spectrum in anthropology, population, and forensic genetics. In the past decade, heteroplasmy detection using Sanger sequencing and next generation sequencing (NGS) was hampered by the former's inefficiency and the latter's inherent bias due to amplification and mapping of short reads, respectively. Nanopore sequencing stands out for its ability to yield long contiguous segments of DNA, providing a new insight into heterogeneity authentication. In addition to MinION from Oxford Nanopore Technologies, an alternative nanopore sequencer QNome (Qitan Technology) has also been applied to various biological research and the forensic applicability of this platform has been proved recently. In this study, we evaluated the performance of four commonly used variant callers in the heterogeneity authentication of the control region of human mtDNA based on simulations of different ratios generated by mixing QNome nanopore sequencing reads of two synthetic sequences. Then, an open-source and python-based nanopore analytics pipeline, CmVCall was developed and incorporated multiple programs including reads filtering, removal of nuclear mitochondrial sequences (NUMTs), alignment, optional 'Correction' mode, and heterogeneity identification. CmVCall can achieve high precision, accuracy, and recall of 100%, 99.9%, and 92.3% with a 5% heteroplasmy level in 'Correction' mode. Moreover, blood, saliva, and hair shaft samples from monozygotic (MZ) twins were used for heterogeneity evaluation and comparison with the NGS data. Results of MZ twin samples showed that CmVCall could identify more point heteroplasmy sites, revealing significant levels of inter- and intra-individual mtDNA polymorphism. In conclusion, we believe that this analysis pipeline will lay a solid foundation for the development of a comprehensive nanopore analysis pipeline targeting the whole mitochondrial genome.

Massively parallel sequencing of 74 microhaplotypes and forensic characteristics in three Chinese Sino-Tibetan populations.

Microhaplotype (MH), as an emerging type of forensic genetic marker in recent years, has the potential to support multiple forensic applications, especially for mixture deconvolution and biogeographic ancestry inference. Herein, we investigated the genotype data of 74 MHs included in a novel MH panel, the Ion AmpliSeq MH-74 Plex Microhaplotype Research Panel, in three Chinese Sino-Tibetan populations (Han, Tibetan, and Yi) using the Ion Torrent semiconductor sequencing. The sequencing performance, allele frequencies, effective number of alleles (Ae), informativeness (In), and forensic parameters were subsequently estimated and calculated. In addition, principal component analysis (PCA) and structure analysis were performed to explore the population relationships among the three populations and the ancestry component distribution. Overall, this novel MH panel is robust and reliable, and has an excellent sequencing performance. The Ae values ranged from 1.0126 to 7.0855 across all samples, and 75.68 % of MHs had Ae values >2.0000. Allele frequencies at some loci varied considerably among the three studied populations, and the mean In value was 0.0195. Moreover, the genetic affinity between Tibetans and Yis was closer than that between Tibetans and Hans. The aforementioned results suggest that the Ion AmpliSeq MH-74 Plex Microhaplotype Research Panel is highly polymorphic in three investigated populations and could be used as an effective tool for human forensics. Although these 74 MHs have demonstrated the competency in continental population stratification, a higher resolution for distinguishing intracontinental subpopulations and a more comprehensive database with sufficient reference population data still remain to be accomplished.

Exploring rare differences in mitochondrial genome between MZ twins using Ion Torrent semiconductor sequencing.

Monozygotic (MZ) twins are considered to be genetically identical in that they have the same genomic DNA sequences in theory, and thus cannot be differentiated using forensic standard STR-based DNA profiling. However, a recent study employed deep sequencing to explore extremely rare mutations in the nuclear genome and reported that the mutation analysis could be applied to differentiate between MZ twins. Compared with the nuclear genome, the mitochondrial DNA (mtDNA) exhibits higher mutation rates due to fewer DNA repair mechanisms in the mitochondrial genome (mtGenome) and the lack of proofreading capability of the mtDNA polymerase. In a previous study, we used Illumina ultra-deep sequencing to describe point heteroplasmy (PHP) and nucleotide variant of the mtGenomes in venous blood samples of MZ twins. In the present study, we characterized minor differences of the mtGenomes in three tissue samples from seven sets of MZ twins using Ion Torrent semiconductor sequencing (Thermo Fisher Ion S5 XL system) and commercialized mtGenome sequencing kit (Precision ID mtDNA Whole Genome Panel). PHP was observed in blood samples from one set of MZ twins and in saliva samples from two sets of twins, but it presented in hair shaft samples from all seven sets of MZ twins. Overall, the coding region of the mtGenome exhibits more PHPs than the control region. The results of this study have further attested the competence of mtGenome sequencing in differentiating between MZ twins, and that among the three kinds of samples tested, hair shaft is more likely to accumulate minor differences in the mtGenomes of MZ twins.

Association between serum lactate dehydrogenase and lymph node metastasis in cervical cancer.

The aim of the present study was to evaluate the association between serum lactate dehydrogenase (LDH) and the risk of lymph node metastasis (LNM) in the International Federation of Gynecology and Obstetrics (FIGO) 2009 cervical cancer (CC) stages IB1-IIA2. All patient medical records with FIGO 2009 stage IB1-IIA2 CC between January 2012 and January 2022 were analyzed retrospectively. The association between serum LDH and LNM was assessed using uni- and multivariate logistic regression analyses, subgroup analyses and P-splines. The present study included 586 patients, 91 (15.5%) of whom had LNM. Patients with an elevated LDH level were more likely to have a deep stromal invasion, lymph-vascular space invasion, LNM and to be of an older age. Multivariate logistic regression revealed a significant association between LNM and LDH levels. After adjusting for age, FIGO stage, tumor markers and risk factors according to the Sedlis criteria, patients in the highest LDH quartile had an increased risk of LNM compared with those in the lowest LDH quartile (odds ratio, 3.5; 95% CI, 1.57-7.81). Furthermore, P-spline regression revealed a dependence of LNM on LDH. The predictive value of LDH level remained significant in the subgroup analysis. The present study suggested that a higher LDH level was independently associated with CC and LNM, and that LDH level may serve as a potential tumor marker and treatment-related indicator.