Bayesian mixture modelling for glass refractive index measurement.

Glass is a common type of physical evidence in forensic science. Broken glass recovered from a suspect may have similar physical characteristics to glass collected at a crime scene and therefore can be used as evidence. Statistical treatment of this evidence involves computing a measure of the weight of evidence. This may be done in a Bayesian framework that incorporates information from the circumstances of the crime. One of the most crucial quantities in this calculation is the assessment of the relative rarity of the characteristics of the glass, essentially the probability distribution used to model the physical characteristics of recovered glass. Typical characteristics used in casework are the elemental composition of glass and the refractive index measurement. There is a considerable body of scientific literature devoted to the modelling of this information. For example a kernel density estimation has been used to model the background population of glass based on the refractive index measurement and a multivariate Gaussian finite mixture model has been used to model the elemental composition of glass. In this paper, we present an alternative approach, the Dirichlet Process Mixture Model, to model the glass refractive index measurement in a Bayesian methodology. A key advantage is that using this method allows us to model the probability density distribution of refractive index measurements in a more flexible way.

Cutting through the fat: a retrospective analysis of clinical outcomes, cost, and quality of life with the addition of panniculectomy to ventral hernia repair in overweight patients.

BACKGROUND: Due to the increased prevalence of overweight patients with ventral hernia, abdominal wall reconstruction combining ventral hernia repair (VHR) with panniculectomy (VHR-PAN) in overweight patients is increasingly considered. We present a retrospective comparison between VHR-PAN and VHR alone in overweight patients by examining costs, clinical outcomes, and quality of life (QoL). METHODS: Patients with body mass index (BMI) > 25.0 kg/m2 underwent VHR-PAN or VHR alone between September 2015 and May 2017 with a single surgeon and were matched into cohorts by BMI and age (n = 24 in each cohort). QoL was assessed using the Hernia-related Quality of Life Survey (HerQLes). Cost was assessed using billing data. Statistical analyses were performed using Fisher's exact tests, Mann-Whitney U tests, and regression modeling. RESULTS: Hernia defect size (p = 0.127), operative time (p = 0.140), mesh placement (p = 0.357), and recurrence rates (p = 0.156) did not vary significantly between cohorts at average follow up of one year. 60% of patients completed QoL surveys, with 61% net improvement in VHR-PAN postoperatively (p = 0.042) vs 36% in VHR alone (p = 0.054). Mean total hospitalization costs were higher for VHR alone (p = 0.019). Regression modeling showed no significant independent contribution of procedure performed due to differences in cost, wound complications, or hernia recurrence. CONCLUSIONS: At mean follow up of 2 years, VHR-PAN patients reported a comparable increase in QoL to those who received VHR alone without significantly different cost and complication rates. Concurrent VHR-PAN may therefore be a safe approach for overweight patients presenting with hernia and excess abdominal skin.

RNA/DNA co-analysis from human skin and contact traces--results of a sixth collaborative EDNAP exercise.

The European DNA profiling group (EDNAP) organized a sixth collaborative exercise on RNA/DNA co-analysis for body fluid/tissue identification and STR profiling. The task was to identify skin samples/contact traces using specific RNA biomarkers and test three housekeeping genes for their suitability as reference genes. Eight stains, a skin RNA dilution series and, optionally, bona fide or mock casework samples of human or non-human origin were analyzed by 22 participating laboratories using RNA extraction or RNA/DNA co-extraction methods. Two sets of previously described skin-specific markers were used: skin1 pentaplex (LCE1C, LCE1D, LCE2D, IL1F7 and CCL27) and skin2 triplex (LOR, KRT9 and CDSN) in conjunction with a housekeeping gene, HKG, triplex (B2M, UBC and UCE). The laboratories used different chemistries and instrumentation. All laboratories were able to successfully isolate and detect mRNA in contact traces (e.g., human skin, palm-, hand- and fingerprints, clothing, car interiors, computer accessories and electronic devices). The simultaneous extraction of RNA and DNA provides an opportunity for positive identification of the tissue source of origin by mRNA profiling as well as a simultaneous identification of the body fluid donor by STR profiling. The skin markers LCE1C and LOR and the housekeeping gene marker B2M were detected in the majority of contact traces. Detection of the other markers was inconsistent, possibly due to the low amounts and/or poor quality of the genetic material present in shed skin cells. The results of this and the previous collaborative RNA exercises support RNA profiling as a reliable body fluid/tissue identification method that can easily be combined with current STR typing technology.

Association of low numbers of CD206-positive cells with loss of ICC in the gastric body of patients with diabetic gastroparesis.

BACKGROUND: There is increasing evidence for specific cellular changes in the stomach of patients with diabetic (DG) and idiopathic (IG) gastroparesis. The most significant findings are loss of interstitial cells of Cajal (ICC), neuronal abnormalities, and an immune cellular infiltrate. Studies done in diabetic mice have shown a cytoprotective effect of CD206+ M2 macrophages. To quantify overall immune cellular infiltrate, identify macrophage populations, and quantify CD206+ and iNOS+ cells. To investigate associations between cellular phenotypes and ICC. METHODS: Full thickness gastric body biopsies were obtained from non-diabetic controls (C), diabetic controls (DC), DG, and IG patients. Sections were labeled for CD45, CD206, Kit, iNOS, and putative human macrophage markers (HAM56, CD68, and EMR1). Immunoreactive cells were quantified from the circular muscle layer. KEY RESULTS: Significantly fewer ICC were detected in DG and IG tissues, but there were no differences in the numbers of cells immunoreactive for other markers between patient groups. There was a significant correlation between the number of CD206+ cells and ICC in DG and DC patients, but not in C and IG and a significant correlation between iNOS+ cells and ICC in the DC group, but not the other groups. CD68 and HAM56 reliably labeled the same cell populations, but EMR1 labeled other cell types. CONCLUSIONS & INFERENCES: Depletion of ICC and correlation with changes in CD206+ cell numbers in DC and DG patients suggests that in humans, like mice, CD206+ macrophages may play a cytoprotective role in diabetes. These findings may lead to novel therapeutic options, targeting alternatively activated macrophages.

Exploring the recovery and detection of messenger RNA and DNA from enhanced fingermarks in blood.

Often in the examination of bloodstained fingermarks discussion occurs around whether to prioritise the fingerprint evidence or focus on the biological evidence. Collecting a sample for genetic profiling may result in the loss of ridge detail that could have been used for fingerprint comparison. Fingermark enhancement and recovery methods along with sample collection methods could also compromise downstream genetic analysis. Previous forensic casework has highlighted circumstances where, after enhancement had been performed, it would have been extremely valuable to both identify the body fluid and generate a DNA profile from the same sample. We enhanced depletion series of fingermarks made in blood, using single treatments consisting of aqueous amido black, methanol-based amido black, acid yellow and leucocrystal violet, and exposure to long wave UV light. We then extracted the DNA and RNA for profiling, to assess the recovery and detection of genetic material from the enhanced fingermarks. We have shown that genetic profiling of bloodstained fingermarks can be successful after chemical enhancement; however it may still be necessary to prioritise evidence types in certain circumstances. From our results it appears that even with visible bloodstained fingermarks, leucocrystal violet can reduce the effectiveness of subsequent messenger RNA profiling. Aqueous amido black and acid yellow also have adverse effects on messenger RNA profiling of depleted fingermarks with low levels of cellular material. These results help with forensic decision-making by expanding knowledge of the extent of the detrimental effects of blood-enhancement reagents on both DNA profiling and body fluid identification using messenger RNA profiling.

RNA/DNA co-analysis from human menstrual blood and vaginal secretion stains: results of a fourth and fifth collaborative EDNAP exercise.

The European DNA Profiling Group (EDNAP) organized a fourth and fifth collaborative exercise on RNA/DNA co-analysis for body fluid identification and STR profiling. The task was to identify dried menstrual blood and vaginal secretion stains using specific RNA biomarkers, and additionally test 3 housekeeping genes for their suitability as reference genes. Six menstrual blood and six vaginal secretion stains, two dilution series (1/4-1/64 pieces of a menstrual blood/vaginal swab) and, optionally, bona fide or mock casework samples of human or non-human origin were analyzed by 24 participating laboratories, using RNA extraction or RNA/DNA co-extraction methods. Two novel menstrual blood mRNA multiplexes were used: MMP triplex (MMP7, MMP10, MMP11) and MB triplex (MSX1, LEFTY2, SFRP4) in conjunction with a housekeeping gene triplex (B2M, UBC, UCE). Two novel mRNA multiplexes and a HBD1 singleplex were used for the identification of vaginal secretion: Vag triplex (MYOZ1, CYP2B7P1 and MUC4) and a Lactobacillus-specific Lacto triplex (Ljen, Lcris, Lgas). The laboratories used different chemistries and instrumentation and all were able to successfully isolate and detect mRNA in dried stains. The simultaneous extraction of RNA and DNA allowed for positive identification of the tissue/fluid source of origin by mRNA profiling as well as a simultaneous identification of the body fluid donor by STR profiling, also from old and compromised casework samples. The results of this and the previous collaborative RNA exercises support RNA profiling as a reliable body fluid identification method that can easily be combined with current STR typing technology.

Differentiation of drug and non-drug Cannabis using a single nucleotide polymorphism (SNP) assay.

Cannabis sativa is both an illegal drug and a legitimate crop. The differentiation of illegal drug Cannabis from non-drug forms of Cannabis is relevant in the context of the growth of fibre and seed oil varieties of Cannabis for commercial purposes. This differentiation is currently determined based on the levels of tetrahydrocannabinol (THC) in adult plants. DNA based methods have the potential to assay Cannabis material unsuitable for analysis using conventional means including seeds, pollen and severely degraded material. The purpose of this research was to develop a single nucleotide polymorphism (SNP) assay for the differentiation of "drug" and "non-drug"Cannabis plants. An assay was developed based on four polymorphisms within a 399 bp fragment of the tetrahydrocannabinolic acid (THCA) synthase gene, utilising the snapshot multiplex kit. This SNP assay was tested on 94 Cannabis plants, which included 10 blind samples, and was able to differentiate between "drug" and "non-drug"Cannabis in all cases, while also differentiating between Cannabis and other species. Non-drug plants were found to be homozygous at the four sites assayed while drug Cannabis plants were either homozygous or heterozygous.

An easily automated, closed-tube forensic DNA extraction procedure using a thermostable proteinase.

Most standard procedures for extracting DNA from forensic substrates involve manipulations that expose the sample to potential contamination and which reduce yields. Furthermore, most methods require centrifugation and/or solvent extraction steps that render them difficult to automate. We describe a simple closed-tube DNA extraction procedure using a proteinase from the thermophilic Bacillus species EA1 that produces good DNA yields from a wide range of forensic substrates. The reaction is controlled by a temperature shift regime programmed into a thermal cycler and so eliminates the need for solvent extraction or column purification. The new method is ideally suited to forensic samples where exposure to extraneous contaminating DNA must be avoided. In addition, The simplicity of the procedure makes it suitable for automation.

Allele frequencies for the four major sub-populations of New Zealand at three STR loci--HUMTH01, HUMTPOX and CSF1PO.

Allele frequencies for the three STR loci included in the GenePrint CTT multiplex system (HUMTH01, HUMTPOX, HUMCSF1PO) have been determined for the four major sub-populations of New Zealand.

Allele frequencies for the four major sub-populations of New Zealand at the 10 AMPFlSTR SGM Plus loci.

Allele frequencies for the 10 STR loci included in the AMPFlSTR SGM Plus multiplex system have been determined for the four major sub-populations of New Zealand.

The fallacy of independence testing and the use of the product rule.

Use of the product rule which implies the assumption of within and between locus independence, is still common, particularly in the United States of America. Whilst it may be considered by some to be an acceptable approximation it is not logical to suggest that independence testing somehow "validates" its use. This paper discusses the nature of this fallacy.

The New Zealand DNA databank: its development and significance as a crime solving tool.

The New Zealand DNA Databank was established following the introduction of legislation in August 1996. Using the Second Generation Multiplex (SGM), DNA profiles from over 13,000 convicted offenders and volunteer donors have been completed to the National DNA Database. Since June 1998, DNA profiles from over 1,400 unsolved crimes have been entered onto the Crime Sample Database. Of all unsolved crimes analysed, 33% are linked to individuals and 21% are linked to other unsolved crimes. Several high profile types of case including homicides, sexual offenses and burglaries are amongst those regularly solved.

Neoadjuvant chemotherapy, radical resection with intraoperative radiation therapy (IORT): improved treatment for gastric adenocarcinoma.

BACKGROUND: Adenocarcinoma of the stomach and gastroesophageal junction results in substantial morbidity, locoregional recurrence, and death. Surgical procedures, even with adjuvant therapy, have not significantly improved survival. This study evaluated the toxicity, response rate, locoregional control, and survival of patients with locally advanced gastric cancer that was treated with neoadjuvant multimodality therapy. METHODS: Patients with stage IIIA or early stage IV gastric adenocarcinoma received neoadjuvant 5-fluorouracil, Leucovorin, Adriamycin, and Cisplatin and underwent gastrectomy or esophagogastrectomy with intraoperative radiotherapy (IORT; 1000 cGY) to the gastric bed and postoperative radiation therapy. RESULTS: Nine of 15 patients (60%) with transmural extension and/or nodal metastases received IORT. There were 2 pathologically complete responses at the primary site. Eleven of 15 patients (73%) had tumor in perigastric lymph nodes; however, 9 of 15 patients (60%) had mucin-filled nodes without tumor cells. Neoadjuvant treatment did not increase operative morbidity rates. Ten of 15 patients (67%) remain free of disease (median, 27 months; range, 6-60 months). Five patients died 13 to 41 months (median, 17 months) after diagnosis. CONCLUSIONS: Neoadjuvant multimodality therapy with neoadjuvant 5-fluorouracil, Leucovorin, Adriamycin, and Cisplatin, radical resection with IORT, and postoperative radiation therapy is safe, can downstage tumors, provides improved locoregional control, and appears to cause significant tumor regression that may result in long-term survival or cure.

The calculation of DNA match probabilities in mixed race populations.

A coherent method is offered to estimate likelihood ratios for DNA match probabilities from mixed racial populations that avoids the approach of reporting separate estimates for each race. The method is demonstrated for some cases involving profiles derived from several individuals and incorporates a correction for 'subpopulation' effects.

An improved method for STR analysis of bloodstained denim.

Indigo dye is used to dye denim and other fabrics. It is now accepted that if this is co-extracted with the DNA, it may inhibit PCR amplification. A simple, improved method is described for the extraction of DNA from bloodstained denim for PCR amplification and short tandem repeat (STR) analysis. The DNA was extracted by constructing a blotting system using capillary action to draw a saline solution through the denim. The transferred material was collected onto nylon membranes and these were processed by chelex extraction. A variety of coloured denim substrates and other heavily dyed fabrics, including case work samples were used. In all cases the DNA was extracted, amplified and typed correctly.

Faculty and resident opinions regarding the role of morbidity and mortality conference.

BACKGROUND: The role of the surgical morbidity and mortality (M&M) conference as a forum for examination of surgical failure may remain unclear. This paper reports the results of a national survey of surgical faculty and trainees regarding the role and effectiveness of the M&M conference. METHODS: Based on focus groups and pilot studies from multiple institutions in one geographic area, a questionnaire addressing critical issues in attitudes toward the M&M conference was sent to 1,100 randomly chosen subjects nationwide: 500 residents and 600 staff. The survey includes individual and institutional demographic information, 15 statements answered using a Likert scale, and 2 open-ended questions. RESULTS: Faculty response rate was 501 of 600 (83%) and resident response rate was 166 of 500 (33%). Responses were generally positive in both groups, with staff showing small but significantly more positive attitudes than residents. A higher proportion of residents characterize the M&M conference as too defensive. CONCLUSION: The M&M conference is fulfilling its potential as a teaching tool but there may be room for improvement as residents view the experience slightly less positively than faculty. This questionnaire provides a perspective of expectations for the M&M conference, allowing educators to optimize its effectiveness.

Hypothyroidism decreases the ATP sensitivity of KATP channels from rat heart.

The effects of thyroid status on the properties of ATP-sensitive potassium channels were investigated. Single-channel recordings were made using excised inside-out membrane patches from enzymatically dissociated ventricular myocytes from hearts of control and thyroidectomized rats and each group was studied with and without administration of thyroid hormone. In patches excised from hypothyroid myocytes the IC50 for ATP inhibition of KATP channels was 110 micro m. This value was 3-fold higher than the IC50 in control myocytes (43 micro m). Treatment of hypothyroid rats to restore physiological levels of thyroid hormone (tri-iodothyronine, T3), resulted in a return to normal ATP-sensitivity (IC50 = 46 micro M). In patches from animals rendered hyperthyroid, the IC50 for ATP was 50 micro M and this value was not significantly different from the control. There was no difference in the cooperativity of ATP-binding (Hill coefficient, nH) among control (nH = 2.2), hypothyroid (nH = 2.1), T3-treated (nH = 2.0) and hyperthyroid groups (nH = 2.4). The unitary conductance was unchanged and there was no apparent change in intraburst kinetics between examples of single KATP channels from control and hypothyroid rats. Action potentials recorded in myocytes from hypothyroid rats were significantly shortened by 50 micro M levcromakalim, a KATP channel opener (P < 0.001) but unchanged in control myocytes.We conclude that hypothyroidism significantly decreased the ATP-sensitivity of KATP channels, whereas the induction of hyperthyroid conditions did not alter the ATP-sensitivity of these channels. Thus, hypothyroidism is likely to have important physiological consequences under circumstances in which KATP channels are activated, such as during ischemia.