A DNA typing panel of 201 genetic markers for degraded samples: development and validation.

With the increasing number of complex forensic cases in recent years, it's more important to combine the different types of genetic markers such as short tandem repeats (STRs), single nucleotide polymorphisms (SNPs), insertion/deletion polymorphisms (InDels), and microhaplotypes (MHs) to provide more genetic information. In this study, we selected totally 201 genetic markers, including 24 autosomes STRs (A-STRs), 24 Y chromosome STRs (Y-STRs), 110 A-SNPs, 24 Y-SNPs, 9 A-InDels, 1 Y-InDel, 8 MHs, and Amelogenin to establish the HID_AM Panel v1.0, a Next-Generation Sequencing (NGS) detection system. According to the validation guidelines of the Scientific Working Group on DNA Analysis Methods (SWGDAM), the repeatability, accuracy, sensitivity, suitability for degraded samples, species specificity, and inhibitor resistance of this system were assessed. The typing results on 48 STRs and Amelogenin of this system were completely consistent with those obtained using capillary electrophoresis. This system accurately detected 79 SNPs as parallelly confirmed by a FGx sequencer with the ForenSeq™ DNA Signature Prep Kit. Complete allele typing results could be obtained with a DNA input of no less than 200 pg. The detection success rate of this system was significantly higher than that of the GlobalFiler™ kit when the degradation index of mock degraded sample was greater than 15.87. When the concentration of hematin in the amplification system was ≤40 µmol/L, indigo blue was ≤2 mmol/L, or humic acid was ≤15 ng/µL, amplification was not significantly inhibited. The system barely amplified the DNA extract from duck, mouse, cow, rabbit, and chick. The detection rate of STRs on routine samples of this panel is 99.74%, while all the SNPs, InDels, and MHs were successfully detected. In summary, we setup a NGS individual typing panel including 201 genetic markers with the high accuracy, sensitivity, species specificity, and inhibitors resistance, which is applicable for individual identification of degraded samples.

Genetic identification of human remains from the Korean War.

The genetic identification of skeletal remains from Chinese People's Volunteers (CPVs) of the Korean War has been challenging because of the degraded DNA samples and the lack of living close relatives. This study established a workflow for identifying CPVs by combining Y-chromosome short tandem repeats (Y-STRs), mitochondrial DNA (mtDNA) hypervariable regions I and II, autosomal STRs (aSTRs), and identity-informative SNPs (iiSNPs). A total of 20 skeletal remains of CPVs and 46 samples from their alleged relatives were collected. The success rate of DNA extraction from human remains was 100%. Based on Y-STRs, six remains shared the same male lineages with their alleged relatives. Meanwhile, mtDNA genotyping supports two remains sharing the same maternal lineages with their alleged relatives. Likelihood ratios (LRs) were further obtained from 27 aSTRs and 94 iiSNPs or 1936 iiSNPs to confirm their relationship. All joint pedigree LRs were >100. Finally, six remains were successfully identified. This pilot study for the systematic genetic identification of CPVs from the Korean War can be applied for the large-scale identification of CPVs in the future.

Ternary Dry Powder Agglomerate Inhalation Formulation of Melatonin With Air Jet Mixing to Improve In Vitro And In Vivo Performance.

An improved agglomerate formulation with melatonin and fine lactose for dry powder inhalation using Turbuhaler® was developed. Co-grinding lactose with 1 % magnesium stearate prior to air jet mixing served as a key factor to improve the in vitro aerosolization and in vivo efficacy. Elevated mixing pressure facilitated the dispersion and homogenization of the cohesive mixture for even distribution of agglomerate size after spheroidization and subsequent higher emitted dose with lower variation. Magnesium stearate was employed as a tertiary component to adjust the interparticle force for better aerosolization. At optimized mixing pressure, co-grinding lactose with magnesium stearate before jet mixing displayed further improvement of fine particle fraction to 71.6 ± 3.1 %. The superior fine particle deposition efficiency contributed to rapid onset of action and a high bioavailability of 67.0 % after intratracheal administration to rats. Overall, an inhalable melatonin dry powder formulation exhibiting good aerosol property and lung deposition with clinical translation potential was developed.

Rapid genotyping of 32 insertion/deletion panel for human identification using fluorogenic probes-based multiplex real-time PCR.

BACKGROUND: Insertion and deletion (InDel) polymorphisms have considerable potential in the field of forensic genetics because of their low mutation rate and small amplicons. At present, InDel polymorphisms detection based on the technique of capillary electrophoresis is the main technique used in forensic DNA laboratory. However, this method is complicated and time-consuming, and is not suitable for rapid on-site paternity and personal identification. Next-generation sequencing analysis of InDels polymorphisms requires expensive instruments, large upfront reagent and supply costs, computational requirements and complex bioinformatics, increased the time to obtain results. Thus, there is an urgent need to establish a method to provide reliable, rapid, sensitive and economical genotyping for InDels. METHOD: A rapid InDels (32 InDels) panel was established using fluorogenic probes-based multiplex real-time PCR with microfluidic test cartridge and portable real-time PCR instrument. Then, we performed several validation studies including concordance, accuracy, sensitivity, stability, species specificity. RESULTS: It showed that the complete genotypes could be obtained from ≥100 pg of input DNA and from a series of challenging samples with high accuracy and specificity within 90 min. CONCLUSION: This method provides a rapid and cost-effective solution for InDels genotyping and personal identification in portable format.

Improving Inhalation Performance with Particle Agglomeration via Combining Mechanical Dry Coating and Ultrasonic Vibration.

Agglomerate formulations for dry powder inhalation (DPI) formed with fine particles are versatile means for the highly efficient delivery of budesonide. However, uncontrolled agglomeration induces high deposition in the upper airway, causing local side effects due to high mechanical strength, worse deagglomeration, and poor fine-particle delivery. In the present study, fine lactose was mechanically dry-coated prior to particle agglomeration, and the agglomerates were then spheroidized via ultrasonic vibration to improve their aerosol performance. The results showed that the agglomerate produced with the surface-enriched hydrophobic magnesium stearate and ultrasonic vibration demonstrated improved aerosolization properties, benefiting from their lower mechanical strength, less interactive cohesive force, and improved fine powder dispersion behavior. After dispersion utilizing a Turbuhaler® with a pharmaceutical cascade impactor test, a fine particle fraction (FPF) of 71.1 ± 1.3% and an artificial throat deposition of 19.3 ± 0.4% were achieved, suggesting the potential to improve the therapeutic outcomes of budesonide with less localized infections of the mouth and pharynx.

Analysis of risk factors for the development of cognitive dysfunction in patients with cerebral small vessel disease and the construction of a predictive model.

Background: Cognitive dysfunction in cerebral small vessel disease (CSVD) is a common cause of vascular dementia. The purpose of this study was to find independent risk factors for the development of cognitive dysfunction in patients with CSVD and establish a risk prediction model, in order to provide a reference for clinical diagnosis and treatment of such patients. Methods: In this study, clinical data of patients with CSVD admitted to the Department of Neurology in Gansu Provincial Hospital from December 2019 to December 2021 were collected, and 159 patients were finally included after strict screening according to the inclusion and exclusion criteria. There were 43 patients with normal function and 116 patients with cerebral small vessel disease cognitive impairment (CSVDCI). The logistic multivariable regression model was used to screen out the independent risk factors of cognitive dysfunction in patients with CSVD, and the nomogram of cognitive dysfunction in patients with CSVD was constructed based on the results of the logistic multivariable regression analysis. Finally, the accuracy of the prediction model was evaluated by C-index, calibration curve, receiver operating characteristic (ROC) curve, and decision curve analysis (DCA). Results: The results of multivariable logistic regression analysis showed that hypertension (OR = 2.683, 95% CI 1.119-6.432, P = 0.027), homocysteine (Hcy) (OR = 1.083, 95% CI 1.026-1.143, P = 0.004), total CSVD MRI Score (OR = 1.593, 95% CI 1.025-2.475, P = 0.039) and years of schooling (OR = 0.883, 95% CI 0.798-0.978, P = 0.017) were independent risk factors for the development of cognitive dysfunction in patients with CSVD. The C-index of this prediction model was 0.806 (95% CI 0.735-0.877), and the calibration curve, ROC curve, and DCA curve all showed good predictive power in the nomogram. Conclusions: The nomogram constructed in this study has high accuracy and clinical utility in predicting the occurrence of cognitive dysfunction in patients with CSVD. For patients with CSVD with the above risk factors, active clinical intervention and prevention are required during clinical consultation and disease management to avoid cognitive impairment as much as possible.

Complex kinship analysis with a combination of STRs, SNPs, and indels.

Complex kinship analysis has been widely applied in disaster victim identification and criminal investigations. A larger number of genetic markers is required to improve the discrimination power of the system in complex kinship analysis compared to that in paternity testing, as distant relatives share fewer genetic segments. Genetic markers, including short tandem repeats (STRs), single-nucleotide polymorphisms (SNPs), and insertions-deletions (indels), play complementary roles in kinship analysis. Few studies have systematically analyzed the system discrimination power of a new combination of different types of genetic markers before using these markers in practice. Here, we tested the ability of a set of 56 STRs available in commercial panels on complex kinship analysis. We next introduced a combination marker set of STRs, indels, and SNPs and evaluated the system discrimination power of 72 indels + 52 SNPs to improve the weight of 56 STRs. Statistical analysis of complex kinship within third-degree kinship testing was performed to compare 56 STRs or 72 indels + 52 SNPs alone. True samples were assessed, including 99 full siblings, 112 uncle/aunt-nephew/niece, 43 grandfather/grandmother-grandson/granddaughter, 63 first cousins, and 5931 unrelated pairs. Simulation was also performed using 10,000 pairs of relatives and 10,000 unrelated individuals. The effectiveness of the three marker sets in kinship testing was ranked as follows: 56 STRs + 72 indels + 52 SNPs > 56 STRs > 72 indels + 52 SNPs. All three marker sets were powerful in first-degree kinship testing; 56 STRs and 56 STRs + 72 indels + 52 SNPs could distinguish most second-degree relatives from unrelated pairs. However, only a portion of third-degree relatives was correctly determined from unrelated individuals using 56 STRs + 72 indels + 52 SNPs. In relationship testing, 56 STRs and 56 STRs + 72 indels + 52 SNPs were powerful enough to distinguish first-degree relatives from second-degree or third-degree relatives. Our results provide a strategy and guidance applicable in forensic practice for complex kinship analysis by combining STRs, SNPs, and indels.

Genetic polymorphisms of 66 InDel loci in the Chinese Han population.

Insertion/deletion polymorphism (InDel) genetic markers refer to insertion or deletion of DNA fragments into genomic DNA, which have advantages in the identification of degraded samples. In this study, we independently screened 66 highly polymorphic InDel markers from the dbSNP database to establish a multiplex PCR system for forensic DNA identification using next-generation sequencing system (66-plex InDels). We assessed the population genetic data among 251 Chinese Han population using this system and evaluated their potential forensic application. The results showed that all 66 InDel loci conformed to the Hardy-Weinberg equilibrium (P>0.000 758), and all the pairwise InDel loci were in linkage equilibrium after Bonferroni correction. The mean observed heterozygosity (Ho) was 0.482, the mean expected heterozygosity (He) was 0.483,the mean discrimination power (DP) was 0.612, the mean polymorphism information content (PIC) was 0.365, the total discrimination power (TDP) reached 0.999 999 999 999 999 999 999 999 999 428 18. The cumulative power of exclusion for 66 InDel loci was 0.999 739 in duo cases (CPEduo) and was 0.999 999 999 417 in trios cases (CPEtrio). The results show that the 66 InDel loci have high genetic polymorphisms in the Chinese Han population and can be used independently for forensic DNA identification and paternity testing.

Design and Analysis of a Pneumatic Spring Testing System for Precision Manufacturing.

The vibration isolation effect of the pneumatic spring determines the precision of the manufacturing. In this paper, in order to detect the performance of a pneumatic spring, a multi frequency band testing system with different payload is designed and developed. First, the pneumatic spring structure is analyzed, and the stiffness of the pneumatic spring is obtained based on the ideal gas model, Kelvin-Voigt model, and finite element method. Then, to verify the reliability of the system, a dynamic model of the vibration platform is established. Through an analysis of the simulation using the Simulink environment, critical parameters are determined, and the effective conditions of the vibration isolation are obtained. Based on the results from the simulation and experiment, the transmission rate is around 20% under 40 Hz vibration, and 12% under 100 Hz vibration. The pneumatic spring proves to be effective under vibrations beyond 7 H. This achievement will become an important basis for future research concerning precision manufacturing.

Pairwise kinship testing with a combination of STR and SNP loci.

Individual commercially available kits exhibit limited discrimination power in full-sibling and second-degree kinship analysis, and therefore they are commonly combined with other kits to obtain more loci and a higher efficacy. However, few studies have systematically evaluated the discrimination power of combined loci. In this study, we combined the ForenSeq™ DNA Signature kit (containing 27 short tandem repeats [STRs] + 91 single nucleotide polymorphisms [SNPs]) with the AGCU NC 21 + 1 PCR amplification kit (containing 21 STRs) to obtain a non-overlapping set of 40 STR and 91 SNP markers. The discrimination power was evaluated for 74 full-sibling pairs, 114 uncle/aunt-nephew/niece pairs and 93 grandparent-grandson/granddaughter pairs. The results show that the efficacy of the 40 STR + 91 SNP combination is higher than the efficacy of either 27 STRs + 91 SNPs or 40 STRs alone. Both the sensitivity and specificity of the 40 STR + 91 SNP marker set achieved 100 % in full-sibling testing, with strong power to distinguish second-degree relatives from unrelated pairs. The 40 STR + 91 SNP set could also distinguish most full-sibling relatives from second-degree relatives but was insufficient to distinguish relatives who belong to the same autosomal kinship class. Our results suggest that ignoring linkage can lead to incorrect likelihood ratios for both related and unrelated pairs, while mutation had a relatively lower effect on the likelihood ratios. Moreover, linkage and mutation had a higher impact on full-sibling testing than on second-degree kinship testing. The discrimination power of the 40 STR and 91 SNP marker set could be strengthened by adding an additional relative.

Evaluation of the performance of Illumina's ForenSeq™ system on serially degraded samples.

The use of next generation sequencing is increasing in the field of forensic genomics. This study assesses the performance of Illumina's MiSeq FGx System in the recovery of forensic genomic sequencing information from degraded and low-template DNA. The analysis involved a sensitivity study where a range of 1 ng to 5 pg of 2800M DNA was utilized. DNA was artificially and systematically degraded by incubating 2800 M DNA at 98°C for 10, 20, 30, 40, 50, 60, 70, 120 and 180 min (resulting in degradation index values ranging from 0.837 to 232.247). The results revealed the detected allele call frequencies were greater than 80% when the DNA input was > = 50 pg or the degradation index was lower than 72.28. The allele balance was lower than 0.6 when the samples were heated for more than 120 min or the input quantity was less than 25 pg. Our data also indicated that the stutter type and ratio depend on the specific locus, while the sequencing run was the most significant factor in noise occurrence. The results of this study will help laboratories to develop workflows for the analysis of challenging samples using the ForenSeq FGx system.

A Simple and Efficient Method of Extracting DNA from Aged Bones and Teeth.

DNA is often difficult to extract from old bones and teeth due to low levels of DNA and high levels of degradation. This study established a simple yet efficient method for extracting DNA from 20 aged bones and teeth (approximately 60 years old). Based on the concentration and STR typing results, the new method of DNA extraction (OM) developed in this study was compared with the PrepFiler™ BTA Forensic DNA Extraction Kit (BM). The total amount of DNA extracted using the OM method was not significantly different from that extracted using the commercial kit (p > 0.05). However, the number of STR loci detected was significantly higher in the samples processed using the OM method than using the BM method (p < 0.05). This study aimed to establish a DNA extraction method for aged bones and teeth to improve the detection rate of STR typing and reduce costs compared to the BM technique.

The Schizosaccharomyces pombe PPR protein Ppr10 associates with a novel protein Mpa1 and acts as a mitochondrial translational activator.

The pentatricopeptide repeat (PPR) proteins characterized by tandem repeats of a degenerate 35-amino-acid motif function in all aspects of organellar RNA metabolism, many of which are essential for organellar gene expression. In this study, we report the characterization of a fission yeast Schizosaccharomyces pombe PPR protein, Ppr10 and a novel Ppr10-associated protein, designated Mpa1. The ppr10 deletion mutant exhibits growth defects in respiratory media, and is dramatically impaired for viability during the late-stationary phase. Deletion of ppr10 affects the accumulation of specific mitochondrial mRNAs. Furthermore, deletion of ppr10 severely impairs mitochondrial protein synthesis, suggesting that Ppr10 plays a general role in mitochondrial protein synthesis. Ppr10 interacts with Mpa1 in vivo and in vitro and the two proteins colocalize in the mitochondrial matrix. The ppr10 and mpa1 deletion mutants exhibit very similar phenotypes. One of Mpa1's functions is to maintain the normal protein level of Ppr10 protein by protecting it from degradation by the mitochondrial matrix protease Lon1. Our findings suggest that Ppr10 functions as a general mitochondrial translational activator, likely through interaction with mitochondrial mRNAs and mitochondrial translation initiation factor Mti2, and that Ppr10 requires Mpa1 association for stability and function.

Tiliroside, the major component of Agrimonia pilosa Ledeb ethanol extract, inhibits MAPK/JNK/p38-mediated inflammation in lipopolysaccharide-activated RAW 264.7 macrophages.

In the present study, the in vivo anti-inflammatory activity of Agrimonia pilosa Ledeb (AP) ethanol extract was confirmed in experimental animal models, including xylene-induced ear edema in mice and carrageenan-induced paw edema in rats. Tiliroside, the major component of AP extract, was isolated and purified by high-performance liquid chromatography. The anti-inflammatory mechanism of tiliroside was then examined using lipopolysaccharide (LPS)-activated RAW 264.7 macrophage cells. An MTT assay was used to determine cytotoxicity and a Griess assay was used to determine nitric oxide (NO) production. Concentration levels of tumor necrosis factor-α (TNF-α) and interleukin-6 (IL-6) were determined by enzyme-linked immunosorbent assay. Protein expression levels of inducible nitric oxide synthase (iNOS), cyclooxygenase-2 (COX-2), phosphorylated (p)-extracellular signal-regulated kinase (ERK) 1/2, p-c-Jun N-terminal kinases (JNK), p-p38 and inhibitor of κB-α were detected by western blot analysis. AP ethanol extract was revealed to inhibit xylene-induced ear edema in mice and carrageenan-induced paw edema in rats. Tiliroside significantly suppressed the overproduction of NO (P<0.01), but revealed no notable inhibition of the release of TNF-α and IL-6. In addition, tiliroside significantly downregulated the elevated expression levels of iNOS and COX-2 induced by LPS (P<0.01). The phosphorylation of JNK and p38 proteins were also significantly inhibited (P<0.01), however, tiliroside exhibited no obvious inhibition on the phosphorylation of ERK 1/2 and the degradation of IκB-α protein. In conclusion, the anti-inflammatory molecular mechanism of tiliroside may involve the downregulation of iNOS and COX-2 protein expression levels, and the inactivation of mitogen-activated protein kinase (MAPK)/JNK, in addition to the MAPK/p38 signaling pathway.

Inhibition of lipopolysaccharide-induced iNOS and COX-2 expression by indole alkaloid, 3-(hydroxymethyl)-6,7-dihydroindolo[2,3-a]quinolizin-(12H)-one, via NF-κB inactivation in RAW 264.7 macrophages.

3-(Hydroxymethyl)-6,7-dihydroindolo[2,3-a]quinolizin-(12H)-one is a bioactive indole alkaloid isolated from Nauclea officinalis, a plant species which is used as a traditional Chinese medicine. We investigated the anti-inflammatory properties of 3-(hydroxymethyl)-6,7-dihydroindolo[2,3-a]quinolizin-(12H)-one in RAW 264.7 murine macrophages. The results indicated that it inhibited the overproduction of NO and the release of TNF-α. Furthermore, this compound inhibited the expression of iNOS and COX-2 proteins, the enzymatic activity of iNOS, and the translocation of NF-κB to the nucleus induced by LPS. Therefore, we suggested that the effect of 3-(hydroxymethyl)-6,7-dihydroindolo[2,3-a]quinolizin-(12H)-one-mediated inhibition of the expression of LPS-induced iNOS and COX-2 genes is due to the suppression of NF-κB activation in the transcriptional level.

Factors predictive of prognosis after esophagectomy for squamous cell cancer.

OBJECTIVE: To evaluate the prognosis after esophagectomy for squamous cell carcinoma of the thoracic esophagus and its prognostic factors. METHODS: Six hundred five patients with primary squamous cell carcinoma of the thoracic esophagus who underwent curative esophagectomy between June 1997 and June 1998 were collected from 3 medical centers. Among them, 26 patients died from the operation and 26 patients did not complete adjuvant treatment owing to toxicity. Univariate and multivariate analysis was performed to identify prognostic factors for survival. The effect of adjuvant treatment on survival was also evaluated. RESULTS: The 1-, 3-, 5-, and 10-year overall survivals of 605 patients were 90%, 65%, 36%, and 8%, respectively. Multivariate analysis identified the following as independent prognostic factors: number of lymph node metastases (P < .001), histologic differentiation (P < .001), tumor location (P = .002), depth of invasion (P = .020), and vascular invasion (P = .023). CONCLUSIONS: Several pathologic characteristics of the primary tumor are correlated with the outcome of esophagectomy for squamous carcinoma of the thoracic esophagus. Patients with fewer than 2 metastatic nodes after curative esophagectomy have a better prognosis than those with multiple involved nodes (>2). To stratify patients appropriately for prognosis, it is necessary to refine the current 6th edition TNM staging system.

[Diagnosis and treatment for postoperative lobar torsion].

OBJECTIVE: To analyze retrospectively 8 cases of postoperative lobar torsion after thoracotomy. METHODS: 8 cases of postoperative lobar torsion were collected (5 men and 3 women; median age, 55.0 +/- 7.7 years), including lobectomy 4 (left upper lobe of lung 2, right upper lobe of lung 2), esophageal carcinosectomy 2, resection of schwannoma in the right upper mediastinum 1, and descending aorta replacement 1. RESULTS: The postoperative lobar torsions were right middle lobe 2, right upper lobe 1, left upper lobe 3, left lower lobe 1, left lung 1. The median peak temperature was 38.4 degrees C (range, 37.8 - 40.2 degrees C) and the median white blood cell count was 10.6 x 10(9) cells/L (range, 9.3 - 14.9 x 10(9) cell/L) during the first 48 hours postoperatively. Postoperative radiographs demonstrated pulmonary infiltrates and volume loss in 6 patients and complete opacification in 2 patients. The diagnosis of lobar torsion was made a median of 4 days (range, 2 - 14 days) after the initial operation; 6 patients underwent resection of lung and recovered; 2 had the injured lobe or lung rotated and died. Complications after reoperation included respiratory failure in 2 patients, atrial arrhythmia in 2 patients. Median hospitalization was 24 days and range from 10 to 56 days. CONCLUSIONS: The mobilization of hilus of lung or residual pulmonary atelectasis is the main mechanism of the lobar torsion after thoracotomy. Lobar torsion represents a difficult diagnostic dilemma in the early postoperative period after thoracotomy. Exploratory thoracotomy must be performed without delay. The injured parenchyma should be sacrificed unless the diagnosis is obtained very early. When the injured lobe or lung is rotated back into normal position, simultaneous endotracheal suction is very important to prevent aspiration of fluid from the obstructed part of the bronchial tree to the uninvolved segments and dangerous postoperative hypoxia.