STR typing of human telogen hairs – a new approach

A new approach to short tandem repeat (STR) typing of DNA extracted from telogen shed hairs is presented. Newly designed primer pairs with annealing positions close to the repeat units of the STR loci HUMFES, HUMTH01 and HUMTPOX were used for amplification. The typing results were compared to those obtained by the commonly used primer pairs by means of success rates. The primer pairs capable of producing very short amplicons (<106 bp with HUMFES, <86 bp with HUMTH01 and <87 bp with HUMTPOX) described in this study significantly increased the success rates when typing telogen hairs. Received: 31 January 2000 / Accepted: 12 June 2000     

Biomechanical compensation mechanisms during stair climbing – The effect of leg length inequalities

BackgroundStair climbing is a complex and demanding daily activity with increased physical loads. Therefore, analyzing stair climbing abilities is a frequently used diagnostic tool. Leg length inequalities (LLIs) are a common condition in the population, with individual consequences like lower back pain, scoliosis, and osteoarthritis. Despite its high prevalence, the necessary treatment, for mild LLIs, is still controversial. Previously, the focus was to analyze the effects of LLIs during static standing and walking. To create a holistic view on the dynamic effects of LLIs, and since climbing stairs produces a similar biomechanical imbalance as LLIs, the compensation mechanics during stair climbing are of special interest.Research questionWhat are the biomechanical compensation mechanisms of (simulated) LLIs during ascending and descending stairs?MethodsThirty-five healthy participants were measured with the inertial measurement system MyoMotion during stair climbing with simulated LLIs of 0–3 cm. The maximum estimated lower limb joint angles of the long and short leg were analyzed with statistically repeated measurement models.ResultsThe long leg showed significantly increased hip and knee flexion, while the short leg showed decreased hip and knee flexion, decreased dorsiflexion, and significantly increased plantarflexion. Different mechanisms were found in the case of 1 cm LLI when compared to greater LLIs. In the former, increased hip and knee flexion in the short leg accompanied by increased dorsiflexion in the long leg was observed. In the latter, the dorsiflexion of the long leg was reduced.SignificanceExcept for the reduced dorsiflexion of the long leg (LLI >1 cm), during stair climbing compared compensation mechanisms as during walking were presented, with the long leg functionally shortened and the short leg lengthened. Although the feet were already on different levels, during stair climbing with the step-over-step technique, significant compensation mechanisms were found as a consequence of LLIs.     

Recuperation of slow walking in de novo Parkinson’s disease is more closely associated with increased cadence,rather than with expanded stride length

IntroductionGait characteristics in the early stages of Parkinson’s disease (PD) have been less investigated so far. Moreover, the levodopa effect on gait in early PD remains to be further elucidated. We prospectively designed the study to examine gait dynamics and effect of dopaminergic treatment in patients with de novo PD.MethodsSpatiotemporal parameters were measured in healthy controls and drug naïve patients with PD, using computerized analysis with GAITRite system during usual gait. In PD group, motor symptoms and gait parameters were examined in both drug naive and levodopa 100 mg trial conditions.ResultsTwenty four de novo PD patients and 27 healthy controls (matched for age, sex, and height) were selected for the study. Compared with the controls, patients with de novo PD showed the decrease in stride length, in both Med-OFF and Med-ON conditions. Notably, drug naïve patients with PD demonstrated slow walking velocity, whereas those with levodopa administration exhibited the increase of cadence by shortening stride time, which resulted in the improvement of gait speed. In addition, the stride length (gait hypokinesia) correlated with postural instability and gait difficulty subscore, but not with tremor, rigidity, bradykinesia, or total motor score.ConclusionAs a compensatory mechanism of slow walking, we found that the increment in cadence (frequency) is more important than the increment in stride length (amplitude) in gait dynamics in de novo PD. Additionally, the results may indicate that gait hypokinesia in PD could be regarded as one of axial symptoms.     

Expanded CODIS STR allele frequencies – Evidence for the irrelevance of race-based DNA databases

The US Federal Bureau of Investigation’s (FBI) core Combined DNA Index System (CODIS) short tandem repeat (STR) panel is required for the calculations of random match probabilities (RMPs) in forensic DNA analysis. Current practice dictates that RMPs should be generated across appropriate reference STR allele frequency databases, including African American, Asian, Caucasian, Hispanic, and Native American, when the suspect’s race is unknown. Should the suspect declare their race, a specific reference database that pertains to that designation is used. This practice is based on the presumption that racial population group is relevant for calculating conservative RMPs that favor the defendant. The core CODIS panel has been expanded to 20 STRs, however, the relationship between RMP and race has not been re-evaluated.Genetic structure analyses and Bayesian-based population assignment of expanded CODIS profiles from one race-neutral and five race-specific reference databases revealed that STR data could not distinguish races as distinct biological clusters. For instance, while the average race-specific RMPs for Hispanic or Caucasian profiles were almost equally-conservative when calculated from either population's reference database, the Hispanic profiles closely affined with the Native American population. Race-neutral RMPs computed with a correction factor (θ) of 0.03 favor the defendant as much as race-specific RMPs based on a θ of 0.01. Insufficient genetic differentiation observed among the US racial populations as well as inconsequential differences between race-specific and race-neutral RMPs undermine the value of using “race” in the context of forensic DNA analysis and support the argument that forensic databases should be race-neutral.     

Six is enough? Comparison of diffusion parameters measured using six or more diffusion‐encoding gradient directions with deterministic tractography

Diffusion tensor imaging tractography is commonly used to quantify white matter tracts in the human brain via parameters such as fractional anisotropy and mean diffusivity. Simulation studies recommend the use of more than six directions for robust parameter estimates; however, no study has examined the impact of the number of gradient directions on deterministic tractography-derived diffusion parameters in human brain. Here, for 10 major white matter tracts in 11 healthy volunteers at 1.5 T, six-direction diffusion tensor imaging data were compared to 30- or 60-direction data, keeping scan time and number of b = 0 images constant within each test. Mean diffusivity was systematically lower for six-direction protocols (20/40 comparisons); six-direction data had higher fractional anisotropy in the superior longitudinal fasciculus and smaller tract volume for the genu of the corpus callosum. In general, parameter differences due to the number of directions were smaller than those from intersubject variation or signal-to-noise ratio. Despite some absolute differences, standard deviations were significantly different for only one of 160 comparisons. Thus, six-direction data provide diffusion measures with comparable robustness to 30- or 60-direction data and yield appropriate parameter values for most white matter tracts, although there are clear advantages in acquiring higher angular resolution data.     

Stature estimation from sternum length using computed tomography–volume rendering technique images of western Chinese

The objective of the present investigation was to generate linear regression models for stature estimation on the basis of sternum length derived from computed tomography–volume rendering technique (CT–VRT) images for Western Chinese. The study sample comprised 288 individuals of Western Chinese, including 124 females and 164 males, with documented ages between 19 and 78 years, and was randomly divided into two subgroups. The linear regression analysis for the calibration sample data yielded the following formulae: male stature (cm) = 137.28 + 1.99*combined length of manubrium and mesosternum and female stature (cm) = 111.59 + 3.51* combined length of manubrium and mesosternum. Pearson's correlation coefficients for the regression models were r = 0.459 and r = 0.541 for the male and female formulae, respectively. The standard errors of the estimate (SEE) were 4.76 cm for the male equation and 6.73 cm for the female equation. The 95% confidence intervals of the predicted values encompassed the correct stature of all specimen in the validation sample. The regression equations derived from the sternum length in the present study can be used for stature estimation and the length of the sternum is a reliable predictor of stature in Chinese when better predictors of stature like the long bones are not available, and the CT–VRT method may be a practical method for stature estimation.     

Genetic polymorphism investigation of the Chinese Yi minority using PowerPlex® Y23 STR amplification system

International Journal of Legal Medicine - Twenty-three Y-STR loci (DYS576, DYS389I, DYS389 II, DYS448, DYS19, DYS391, DYS481, DYS549, DYS533, DYS438, DYS437, DYS570, DYS635, DYS390, DYS439, DYS392,...     

Evaluation of forensic genetic parameters of 12 STR loci in the Korean population using the InvestigatorⓇ HDplex kit

We genotyped and calculated the forensic parameters of 10 non-CODIS loci and 2 CODIS loci of 990 Korean individuals using the Investigator^Ⓡ HDplex kit. No significant deviations from Hardy–Weinberg equilibrium (after Bonferroni correction for multiple testing) or genetic linkage disequilibrium were observed. The calculated matching probability and power of discrimination ranged from 0.0080 to 0.2014, and 0.7986 to 0.9920, respectively. We conclude that the markers of the kit are highly informative corroborative tools for forensic DNA analysis.

     

Who is who? Identification of livestock predators using forensic genetic approaches

Molecular identifications of salivary DNA are increasingly applied in wildlife forensic investigations, and are successfully used to identify unknown livestock predators, or elucidate cases of large carnivore attacks to humans. In Europe most of livestock predations are attributed to wolves (Canis lupus), thought free-ranging dogs are sometime the responsible, and false predations are declared by breeders to obtain compensations. In this study we analyzed 33 salivary DNA samples collected from the carcasses of 13 sheep and a horse presumably predated by wolves in seven farms in central Italy. Reliable individual genotypes were determined in 18 samples (corresponding to samples from nine sheep and the horse) using 12 unlinked autosomal microsatellites, mtDNA control-region sequences, a male-specific ZFX/ZFY restriction-site and four Y-linked microsatellites. Results indicate that eight animals were killed by five wolves (a male and four different females), the ninth by a female dog while the horse was post-mortem consumed by a male dog. The genotype of one female wolf matched with the genetic profile of a female wolf that was non-invasively sampled 4 years before in the same area near livestock predation remains. Genetic identifications always supported the results of veterinary reports. These findings show that salivary DNA genotyping, together with detailed veterinary field and necropsy reports, provides evidence which helps to correctly identify species, gender and individual genetic profiles of livestock predators, thus contributing to clarify attack dynamics and to evaluate the impact of wolf predations on husbandry.     

Sexual dimorphism of sternum using computed tomography – volume rendering technique images of Western Chinese

Previous studies have revealed that the sternum can provide a method for assessing sex in diverse population groups. In the current study, sternal measurements were recorded from three-dimensional multidetector-computed tomographic images of 255 individuals (112 females and 143 males) in Western China. Results demonstrated that the difference between male and female mean values for all linear dimensions and manubrium index was highly significant. The stepwise analysis of four linear sterna dimensions and manubrium index, in which the sternum index, total length and manubrium width were selected, yielded a sex classification accuracy rate of 81.6% and a sex bias of 2.6%. Furthermore, multivariate discriminant function equations incorporating dimensions of the manubrium and individual sternal dimensions, such as the total length of the sternum and the sternum body, may also be of value in the estimation of sex. The results of the present study with osteometric equations provide an effective method for assessing sex in Western Chinese, particularly in situations where the pelvis or bones of the extremities are not preserved, and the CT-VRT may be a practical method for estimation of sexual dimorphism.     

Classifying neck pain status using scalar and functional biomechanical variables – development of a method using functional data boosting

BackgroundIndividuals with neck pain have different movement and muscular activation (collectively termed as biomechanical variables) patterns compared to healthy individuals. Incorporating biomechanical variables as covariates into prognostic models is challenging due to the high dimensionality of the data.Research questionWhat is the classification performance of neck pain status of a statistical model which uses both scalar and functional biomechanical covariates?MethodsMotion capture with electromyography assessment on the sternocleidomastoid, splenius cervicis, erector spinae, was performed on 21 healthy and 26 individuals with neck pain during walking over three gait conditions (rectilinear, curvilinear clockwise (CW) and counterclockwise (CCW)). After removing highly collinear variables, 94 covariates across the three conditions were used to classify neck pain status using functional data boosting (FDboost).ResultsTwo functional covariates trunk lateral flexion angle during CCW gait, and trunk flexion angle during CW gait; and a scalar covariate, hip jerk index during CCW gait were selected. The model achieved an estimated AUC of 80.8 %. For hip jerk index, an increase in hip jerk index by one unit increased the log odds of being in the neck pain group by 0.37. A 1° increase in trunk lateral flexion angle throughout gait alone reduced the probability of being in the neck pain group from 0.5 to 0.15. A 1° increase in trunk flexion angle throughout gait alone increased the probability of being in the neck pain group from 0.5 to 0.9.SignificanceInterpreting the physiological significance of the extracted covariates, with other biomechanical variables, suggests that individuals with neck pain performed curvilinear walking using a stiffer strategy, compared to controls; and this increased the risk of being in the neck pain group. FDboost can produce clinically interpretable models with complex high dimensional data and could be used in future prognostic modelling studies in neck pain research.     

Who is more accurate in the diagnosis of neck of femur fractures, radiologists or orthopaedic trainees?

Objective

Our study aims to compare the sensitivity and specificity between orthopaedic trainees and radiologists in diagnosing occult hip fractures from pelvic radiographs.

Methods

All patients undergoing computed tomography (CT) of the hip for a suspected occult hip fracture at our two centres between November 1, 2010 and October 31, 2011 were retrospectively identified. Two orthopaedic trainees (RJ and ED) independently reviewed the initial radiographs, and if both agreed a fracture was present this was recorded. The reports from the radiologist of the initial radiograph and subsequent CT were recorded, with the CT report used as the standard of reference for comparison of performance.

Results

239 CTs were performed for suspected neck of femur fractures during the study period, compared to only 20 in 2006–07, reflecting a 1,095 % increase. The interpretation of radiographs by the orthopaedic trainees showed a sensitivity of 55.4 % and specificity of 96.6 %. In comparison, the radiologists had a sensitivity of 60.7 % and specificity of 92.9 %; this difference was shown not to be statistically significant. Radiologists and orthopaedic trainees agreed when interpreting the majority of radiographs with a Kappa co-efficient of 0.77 (a statistical measure of inter-rater agreement). In 20 of the 174 cases (11.5 %) where the radiologist and orthopaedic trainees agreed no fracture was present, the subsequent CT revealed a fracture.

Conclusion

Orthopaedic trainees and radiologists have similar accuracy at interpreting pelvic radiographs for suspected hip fractures, so the trainee’s opinion can be relied upon. If uncertainty exists, then either the orthopaedic trainee or radiologist should request further imaging urgently as we believe this will expedite diagnosis and treatment of hip fractures, and ensure judicious use of CT.     

Weapon identification using antemortem CT with 3D reconstruction,is it always possible? – A report in a case of facial blunt and sharp injuries using an ashtray

An interesting case of homicide involving the use of a heavy glass ashtray is described. The victim, a 81-years-old woman, has survived for few days and died in hospital. The external examination of the victim showed extensive blunt and sharp facial injuries and defense injuries on both the hands. The autopsy examination showed numerous tears on the face, as well as multiple fractures of the facial bones. Computer tomography scan, with 3D reconstruction, performed in hospital before death, was used to identify the weapon used for the crime. In recent years new diagnostics tools such as computer tomography has been widely used, especially in cases involving sharp and blunt forces. Computer tomography has proven to be very valuable in analyzing fractures of the cranial teca for forensic purpose, in particular antemortem computer tomography with 3D reconstruction is becoming an important tool in the process of weapon identification, thanks to the possibility to identify and make comparison between the shape of the object used to commit the crime, the injury and the objects found during the investigations. No previous reports on the use of this technique, for the weapon identification process, in cases of isolated facial fractures were described. We report a case in which, despite the correct use of this technique, it was not possible for the forensic pathologist to identify the weapon used to commit the crime. Authors wants to highlight the limits encountered in the use of computer tomography with 3D reconstruction as a tool for weapon identification when facial fractures occurred.     

Genetic data of 22 autosomal STR loci in Khyber-Pakhtunkhwa,Balochistan and Gilgit Baltistan population of Pakistan using PowerPlex® fusion system

In this study we have provided forensic genetic data of 22 autosomal STRs for Pakhtun, Balochi and Balti population of Pakistan in total of 601 samples. Among these loci, Penta E was found the most discriminatory in all groups and allele 15 was observed most frequent at D22S1045 in Balti whereas in other two populations allele 8 was more common at TPOX. The combined power of discrimination, combined power of exclusion and the combined matching probability was calculated as 0.999999999999999999999999998385, 0.999999988089728 and 1.615 × 10^-27 respectively. Based on population differentiation test, significant differences were observed when compared with other populations however, phylogenetic analysis revealed close genetic associations among Pakistani Populations.     

Extended population genetic analysis of 12 X-STRs – Exemplified using a Norwegian population sample

The use of X-chromosomal markers to resolve questions of relatedness has experienced a significant increase during the last years in forensic genetics. Perhaps primarily due to the emergence of commercial kits, but equally important due to an increased awareness of the utility of those markers. The X-chromosomal inheritance pattern entails that some cases, for instance paternal half-sisters, can potentially be resolved using a few X-chromosomal markers alone. For the statistical assessment in kinship cases it is of importance to have relevant population frequency data. In the present study 631 unrelated males from a Norwegian population sample are analyzed. The resulting haplotypes are compared to previously studied population samples and a deeper analysis of the linkage disequilibrium (LD) structure is conducted. We demonstrate that the power to detect LD will be low when few males, say below 300, are analyzed. We use entropy to describe the degree of LD between multiallelic loci and describe how this measure varies between different studied populations. Large population frequency databases have been recommended when using X-chromosomal markers, and we show that by combining reference databases from genetically similar populations, more precise haplotype frequency estimates can be obtained for rare haplotypes which improves the statistical assessment of the weight of evidence. In addition, we promote the use of simulations to assess the utility of STR markers in contrast to standard forensic parameters. Specifically we perform extensive simulations on cases where X-chromosomal markers are important and illustrate how the results can be used to infer the information gained from these markers.     

Second-generation sequencing of forensic STRs using the Ion Torrent™ HID STR 10-plex and the Ion PGM™

Second-generation sequencing (SGS) using Roche/454 and Illumina platforms has proved capable of sequencing the majority of the key forensic genetic STR systems. Given that Roche has announced that the 454 platforms will no longer be supported from 2015, focus should now be shifted to competing SGS platforms, such as the MiSeq (Illumina) and the Ion Personal Genome Machine (Ion PGM™; Thermo Fisher). There are currently several challenges faced with amplicon-based SGS STR typing in forensic genetics, including current lengths of amplicons for CE-typing and lack of uniform data analysis between laboratories.Thermo Fisher has designed a human identification (HID) short tandem repeat (STR) 10-plex panel including amelogenin, CSF1PO, D16S539, D3S1358, D5S818, D7S820, D8S1179, TH01, TPOX and vWA, where the primers have been designed specifically for the purpose of SGS and the data analysis is supported by Ion Torrent™ software. Hence, the combination of the STR 10-plex and the Ion PGM™ represents the first fully integrated SGS STR typing solution from PCR to data analysis.In this study, four experiments were performed to evaluate the alpha-version of the STR 10-plex: (1) typing of control samples; (2) analysis of sensitivity; (3) typing of mixtures; and (4) typing of biological crime case samples. Full profiles and concordant results between replicate SGS runs and CE-typing were observed for all control samples. Full profiles were seen with DNA input down to 50 pg, with the exception of a single locus drop-out in one of the 100 pg dilutions. Mixtures were easily deconvoluted down to 20:1, although alleles from the minor contributor had to be identified manually as some signals were not called by the Ion Torrent™ software. Interestingly, full profiles were obtained for all biological samples from real crime and identification cases, in which only partial profiles were obtained with PCR-CE assays. In conclusion, the Ion Torrent™ HID STR 10-plex panel offers an all-in-one solution from amplification of STRs and amelogenin, and sequencing to data analysis.     

Reduction of MRI acoustic noise achieved by manipulation of scan parameters – A study using veterinary MR sequences

Sound pressure levels were measured within an MR scan room for a range of sequences employed in veterinary brain scanning, using a test phantom in an extremity coil. Variation of TR and TE, and use of a quieter gradient mode (‘whisper’ mode) were evaluated to determine their effect on sound pressure levels (SPLs). Use of a human head coil and a human brain sequence was also evaluated. Significant differences in SPL were achieved for T2, T1, T2* gradient echo and VIBE sequences by varying TR or TE, or by selecting the ‘whisper’ gradient mode. An appreciable reduction was achieved for the FLAIR sequence. Noise levels were not affected when a head coil was used in place of an extremity coil. Due to sequence parameters employed, veterinary patients and anaesthetists may be exposed to higher sound levels than those experienced in human MR examinations. The techniques described are particularly valuable in small animal MR scanning where ear protection is not routinely provided for the patient.