A novel co-amplification system for simultaneous amplification of 23 Y-STR and identification of spermatozoa.

In alleged sexual assault cases, identification of the presence of spermatozoa at the crime scene, or on items of eventual significance, or associated with the body of the victim, is integral to the forensic investigation to support or refute the proposition that sexual act has occurred. A 3-plex MSRE-PCR (methylation-sensitive restriction enzyme-PCR) system has been developed previously to identify spermatozoa based on the presence or absence of DNA methylation. This assay showed that 0.1 ng of DNA from a semen extract was sufficient to identify the presence of spermatozoa even when there was excessively more DNA isolated from vaginal fluid than DNA from a semen extract (80 ng/0.1 ng) or a mix of the menstrual blood/semen DNA (5 ng/0.1 ng). In this study, we combine spermatozoa detection with co-amplification of 23 Y-STR loci. We perform standard validation steps to present a novel test that saves time and uses the same sample for both DNA typing and spermatozoa detection in the same reaction. The combined assay can identify Y-STR and spermatozoa simultaneously using just 0.1 ng semen DNA, even in the presence of 5 ng of DNA from a female (male/female:1/50). No other body fluid tested, such as saliva, gave a result for the presence of spermatozoa. A total of 9 non-probative forensic samples from 7 sexual assault cases were tested by this co-amplification system. In all cases, the same sperm-positive data were obtained, concordant with our previous study analyzed by only 3-plex MSRE-PCR, and the Y-STR results were also consistent with that analyzed by only PowerPlex® Y23 kit. The co-amplification will be beneficial for the limited samples in many criminal cases.

Oriented Vehicle Detection in Aerial Images Based on YOLOv4.

CNN-based object detectors have achieved great success in recent years. The available detectors adopted horizontal bounding boxes to locate various objects. However, in some unique scenarios, objects such as buildings and vehicles in aerial images may be densely arranged and have apparent orientations. Therefore, some approaches extend the horizontal bounding box to the oriented bounding box to better extract objects, usually carried out by directly regressing the angle or corners. However, this suffers from the discontinuous boundary problem caused by angular periodicity or corner order. In this paper, we propose a simple but efficient oriented object detector based on YOLOv4 architecture. We regress the offset of an object's front point instead of its angle or corners to avoid the above mentioned problems. In addition, we introduce the intersection over union (IoU) correction factor to make the training process more stable. The experimental results on two public datasets, DOTA and HRSC2016, demonstrate that the proposed method significantly outperforms other methods in terms of detection speed while maintaining high accuracy. In DOTA, our proposed method achieved the highest mAP for the classes with prominent front-side appearances, such as small vehicles, large vehicles, and ships. The highly efficient architecture of YOLOv4 increases more than 25% detection speed compared to the other approaches.

Identification of spermatozoa using a novel 3-plex MSRE-PCR assay for forensic examination of sexual assaults.

Identification of semen and then spermatozoa is essential to verify that sexual activity has occurred in alleged cases of sexual assault. Microscopic examination commonly used for spermatozoa identification is however time-consuming and can often lead to false-negative results for samples with deformed and, or, limited number of spermatozoa. To address this limitation, we report on a novel 3-plex MSRE-PCR (methylation-sensitive restriction enzyme-PCR) assay to specifically identify spermatozoa. This assay is comprised of 3 markers: a digestive control marker (DC), sperm-specific marker (SP), and Y chromosome marker (SRY). A total of 214 samples from 10 body fluids or tissues were analyzed. Specificity testing showed that all the normal semen samples were unambiguously identified as being sperm-positive, and no other body fluid (or tissues) showed a sperm-specific signal in the electropherogram. Testing for sensitivity showed that 0.1 ng of DNA from a semen extract was sufficient to identify the presence of spermatozoa by this assay. Mixture analyses illustrated the sensitivity of the assay when the vaginal/semen DNA ratio (80/0.1) was under 800 or the menstrual blood/semen DNA ratio (5/0.1) was under 50, the trace amounts (approximately 0.1 ng) of DNA from semen can still be identified by this 3-plex MSRE-PCR assay. This assay was also applied to the identification of 31 non-probative forensic samples from 18 sexual assault cases. The case studies showed that the 3-plex MSRE-PCR assay was an improvement in the sensitivity of spermatozoa detection.

Fusion of Environmental Sensing on PM2.5 and Deep Learning on Vehicle Detecting for Acquiring Roadside PM2.5 Concentration Increments.

Traffic emission is one of the major contributors to urban PM2.5, an important environmental health hazard. Estimating roadside PM2.5 concentration increments (above background levels) due to vehicles would assist in understanding pedestrians' actual exposures. This work combines PM2.5 sensing and vehicle detecting to acquire roadside PM2.5 concentration increments due to vehicles. An automatic traffic analysis system (YOLOv3-tiny-3l) was applied to simultaneously detect and track vehicles with deep learning and traditional optical flow techniques, respectively, from governmental cameras that have low resolutions of only 352 × 240 pixels. Evaluation with 20% of the 2439 manually labeled images from 23 cameras showed that this system has 87% and 84% of the precision and recall rates, respectively, for five types of vehicles, namely, sedan, motorcycle, bus, truck, and trailer. By fusing the research-grade observations from PM2.5 sensors installed at two roadside locations with vehicle counts from the nearby governmental cameras analyzed by YOLOv3-tiny-3l, roadside PM2.5 concentration increments due to on-road sedans were estimated to be 0.0027-0.0050 µg/m3. This practical and low-cost method can be further applied in other countries to assess the impacts of vehicles on roadside PM2.5 concentrations.

The detection and identification of saliva in forensic samples by RT-LAMP.

We report on a novel method for saliva identification by reverse transcription-loop-mediated isothermal amplification (RT-LAMP). In our previous report, real-time RT-LAMP was used for blood identification by using HBB detection as a model but in this advanced study, this method was refined for the identification of the more challenging body fluid of saliva. Expression of the18S rRNA gene was used as the internal control and the Statherin (STATH) gene as the saliva-specific marker. A turbidimeter was used for real-time detection of the RT-LAMP products, and confirmation was obtained that the real products were generated using: agarose gel electrophoresis, calcein fluorescence detection and/or enzymatic digestion. The specificity of the test was performed using 42 samples including 7 different body fluids, and the expression of STATH was only observed in all the saliva samples (6) with a threshold time of 39.4 ± 2.9 min. Sensitivity testing showed that RT-LAMP products for STATH were stably detected when the RNA template was not less than 6.25 ng. When the primer concentrations for STATH were two times that of 18S rRNA, saliva could be identified in the body fluid mixtures even at a ratio (saliva:semen) of 1:3 (without loop primer)/1:5 (with loop primer). A multiplex RT-LAMP was established to simultaneously amplify the 18S rRNA and STATH genes, and applied to the identification of saliva on ten non-probative cigarette butts. A positive result for saliva was obtained from all ten butts, even for those that returned a negative or ambiguous result using the amylase test. A direct RT-LAMP test is also reported where the RNA extraction step was omitted to speed the collection of data and all tests using either the simplex or multiplex RT-LAMP resulted in a positive response if saliva was present. Our data provide a simple and effective means to detect the presence of saliva.

A novel application of real-time RT-LAMP for body fluid identification: using HBB detection as the model.

We report on a novel application of real-time reverse transcription-loop-mediated isothermal amplification (real-time RT-LAMP) to identify the presence of a specific body fluid using blood as a proof-of-concept model. By comparison with recently developed methods of body fluid identification, the RT-LAMP assay is rapid and requires only one simple heating-block maintained at a single temperature, circumventing the need for dedicated equipment. RNA was extracted from different body fluids (blood, semen, saliva, menstrual blood, sweat, and urine) for use in real-time RT-LAMP reaction. The 18S rRNA locus was used as the internal control and hemoglobin beta (HBB) as the blood-specific marker. Reverse transcription and LAMP reaction were performed in the same tube using a turbidimeter for real-time monitoring the reaction products within a threshold of 60 min. HBB LAMP products were only detected in blood and not in any of the other body fluid, but products from the 18S rRNA gene were detected in all the tested body fluids as expected. The limit of detection was a minimum of 10(-5) ng total RNA for detection of both 18S rRNA and HBB. Augmenting the detection of RT-LAMP products was performed by separation of the products using gel electrophoresis and collecting the fluorescence of calcein. The data collected indicated complete concordance with the body fluid tested regardless of the method of detection used. This is the first application of real-time RT-LAMP to detect body fluid specific RNA and indicates the use of this method in forensic biology.

Characterization of the vehicle emissions in the Greater Taipei Area through vision-based traffic analysis system and its impacts on urban air quality.

In recent years, many surveillance cameras have been installed in the Greater Taipei Area, Taiwan; traffic data obtained from these surveillance cameras could be useful for the development of roadway-based emissions inventories. In this study, web-based traffic information covering the Greater Taipei Area was obtained using a vision-based traffic analysis system. Web-based traffic data were normalized and applied to the Community Multiscale Air Quality (CMAQ) model to study the impact of vehicle emissions on air quality in the Greater Taipei Area. According to an analysis of the obtained traffic data, sedans were the most common vehicles in the Greater Taipei Area, followed by motorcycles. Moderate traffic conditions with an average speed of 30-50 km/h were most prominent during weekdays, whereas traffic flow with an average speed of 50-70 km/h was most common during weekends. The proportion of traffic flows in free-flow conditions (>70 km/h) was higher on weekends than on weekdays. Two peaks of traffic flow were observed during the morning and afternoon peak hours on weekdays. On the weekends, this morning peak was not observed, and the variation in vehicle numbers was lower than on weekdays. The simulation results suggested that the addition of real-time traffic data improved the CMAQ model's performance, especially for the carbon monoxide (CO) and fine particulate matter (PM2.5) concentrations. According to sensitivity tests for total and vehicle emissions in the Greater Taipei Area, vehicle emissions contributed to >90% of CO, 80% of nitrogen oxides (NOx), and approximately 50% of PM2.5 in the downtown areas of Taipei. The vehicle emissions contribution was affected by both vehicle emissions and meteorological conditions. The connection between the surveillance camera data, vehicle emissions, and regional air quality models in this study can also be used to explore the impact of special events (e.g., long weekends and COVID-19 lockdowns) on air quality.

Analysis of nondegraded and degraded DNA mixtures of close relatives using massively parallel sequencing.

Identification of the minor contributor in DNA mixture of close relatives remains a dilemma in forensic genetics. Massively parallel sequencing (MPS) can analyze multiple short tandem repeats (STRs) and single nucleotide polymorphism (SNPs) concurrently and detect non-overlapping alleles of the minor contributors in DNA mixtures. A commercial kit for MPS of 59 identity informative STRs (iiSTRs) and 94 autosomal identity-informative SNPs (iiSNPs) was used to analyzed 34 nondegraded and 33 highly degraded two-person artificial DNA mixtures of close relatives with various minor to major ratios (1:9, 1:19, 1:29, 1:39, 1:79, 1:99). EuroForMix software was used to determine the minor contributors in the mixtures based on the likelihood ratios calculated from the MPS data, and relMix software was used to perform kinship analysis of the contributors. The STRs and SNPs of the 34 nondegraded and 33 degraded DNA mixtures were genotyped using MPS. Using EuroForMix based on the genotypes of autosomal iiSTRs and autosomal iiSNPs, 82.4% (28/34) and 54.5% (18/33) of minor donors could be accurately assigned for the nondegraded and degraded DNA mixtures, respectively. The relMix software correctly inferred the relationship between contributors in 97.1% (33/34) of nondegraded mixtures and in 97.0% (32/33) of degraded mixtures. In conclusion, combined EuroForMix and MPS data of STRs and SNPs can assist in the assignment of minor donors in nondegraded DNA mixtures of close relatives, and relMix can be used to infer relationship among contributors.

Novel identification of biofluids using a multiplex methylation sensitive restriction enzyme-PCR system.

The identification of a specific body fluid encountered in a forensic investigation can give crucial information. This identification can be aided by methylation profiles based on selected markers specific to a range of biofluids. In this study, the open database of Infinium HumanMethylation450 BeadChip was searched for markers specific for semen, vaginal fluids, saliva, venous blood and menstrual blood. A total of 8 biofluid-specific methylated markers and 2 control markers were combined into a 10-plex methylation sensitive restriction enzyme-PCR (MSRE-PCR) system. Based upon the analysis of 100 DNA samples from these 5 biofluid types, unambiguous results were obtained to identify the body fluid from which it originated. Validation studies of the developed 10-plex MSRE-PCR included sensitivity, reproducibility and mixed body fluids. Co-amplification of the established MSRE-PCR system and the microsatellite loci in AmpFlSTR® MiniFiler™ PCR Amplification Kit was performed to generate both the methylation profile for biofluid type and the miniSTR profile. This allowed human identification and the identification of the body fluid type to be performed in a single reaction. The results of this study displayed the applicability of this 10-plex MSRE-PCR system in forensic science.

Ultrasonic cardiac output monitor provides accurate measurement of cardiac output in recipients after liver transplantation.

BACKGROUND: The ultrasonic cardiac output monitor (USCOM; USCOM Pty. Ltd., Sydney, NSW, Australia) has been accepted as a noninvasive device for measuring cardiac function in various clinical conditions. The present study aimed at comparing the accuracy of this device with that of the thermodilution technique in recipients in the early postoperative period after liver transplantation. METHODS: Fifteen mechanically ventilated patients were studied on the first postoperative day after liver transplantation. We compared the left-sided and right-sided cardiac output (CO) determined by USCOM with that obtained from the thermodilution technique with a pulmonary artery catheter every 8 hours in the intensive care unit. Each patient received a total of four paired measurements. Bland-Altman analysis was used for bias and precision testing. The CO measured by USCOM and the thermodilution method were considered interchangeable if the limits of agreement lay within +/- 1 L per minute or 20% of the mean CO. RESULTS: Forty-eight paired left-sided CO measurements were obtained from 12 patients. Three patients were excluded due to unacceptable signals. Comparison of these two techniques revealed a bias of 0.13 L per minute and limits of agreement at -0.65 L and 0.92 L per minute. Fifty-six paired right-sided CO measurements were obtained from 14 patients with one patient excluded due to an unobtainable optimal signal. A bias of 0.11 L per minute with limits of agreement at -0.51 L and 0.72 L per minute were found for these two techniques. CONCLUSION: This is the first study to evaluate the accuracy of USCOM in the post-liver transplant setting. This device is accurate in measuring CO in liver transplant recipients postoperatively. Possible risks of arrhythmia, infection and pulmonary artery rupture can be avoided because of its noninvasive nature. USCOM should be considered as an alternative in hemodynamic monitoring after liver transplantation.