MVC: an integrated mitochondrial variant caller for forensics

ABSTRACT

Mitochondrial DNA (mtDNA) sequencing is a valuable forensics tool in determining the source of DNA obtained from degraded, damaged or small biological samples. However, despite the recent advances in Massively Parallel Sequencing (MPS), the analysis of mtDNA has remained challenging: alignments can be misleading and may result in incorrect variant calls, and contamination from nuclear DNA from small samples may obscure true variants. In this article, we discuss an integrated approach to solving these issues in a new mito variant caller that integrates various sources of knowledge about mtDNA, including phylotree, EMPOP and NUMTs statistics, and that avoids many of the pitfalls of standard algorithms. The knowledge is integrated into the alignment algorithm itself to distinguish true variant calls from NUMT contamination and sequencing artefacts.     

Evaluation of three MALDI‐TOF mass spectrometry libraries for the identification of filamentous fungi in three clinical microbiology laboratories in Manitoba,Canada

Matrix‐assisted laser desorption ionisation‐time of flight mass spectrometry (MALDI ‐TOF MS ) is commonly used by clinical microbiology laboratories to identify bacterial pathogens and yeasts, but not for the identification of moulds. Recent progress in extraction protocols and the composition of comparative libraries support potential application of MALDI ‐TOF MS for mould identification in clinical microbiology laboratories. We evaluated the performance of the Bruker Microflex? MALDI ‐TOF MS instrument (Billerica, MA , USA ) to identify clinical isolates and reference strains of moulds using 3 libraries, the Bruker mould library, the National Institutes of Health (NIH ) library and the Mass Spectrometry Identification (MSI ) online library, and compared those results to conventional (morphological) and molecular (18S/ITS ; gold standard) identification methods. All 3 libraries demonstrated greater accuracy in genus identification (≥94.9%) than conventional methods (86.4%). MALDI ‐TOF MS identified 73.3% of isolates to species level compared to only 31.7% by conventional methods. The MSI library demonstrated the highest rate of species‐level identification (72.0%) compared to NIH (19.5%) and Bruker (13.6%) libraries. Greater than 20% of moulds remained unidentified to species level by all 3 MALDI ‐TOF MS libraries primarily because of library limitations or imperfect spectra. The overall identification rate of each MALDI ‐TOF MS library depended on the number of species and the number of spectra representing each species in the library.     

Leiomyosarcomas and most malignant fibrous histiocytomas share very similar comparative genomic hybridization imbalances: an analysis of a series of 27 leiomyosarcomas

Twenty-seven tumor samples with a diagnosis of leiomyosarcomas (LMS) were characterized by comparative genomic hybridization. The results were compared with immunohistochemical analysis of the smooth muscle profile of the tumors and expression of the RB1 gene protein. The comparative genomic hybridization profiles suggested that 7 of the 27 tumors might have been misclassified. High levels of DNA amplification were detected in 20 different small regions and recurrently involved bands 1p34, q21, 12q13-15, 17p, and 22q. Most recurrent simple gains were noted at sites such as 1p3, 1q21, 15q12-15, 16p, 17p and 17q, 19, 20q, 22q, and Xp. Significant losses of chromosome 13 were detected in 19 of the 27 tumors with a putative common region of loss in bands 13q14-21. Losses of chromosomes 1q, 2p and 2q, 4q, 9p, 10p and 10q, 11p and 11q23, and 16q were also highly recurrent. A comparative analysis between the most frequent genomic imbalances observed in this study of LMS and the genomic imbalances observed in a large proportion of malignant fibrous histiocytomas (MFH) from a previous study demonstrated that both types of tumors had similar recurrent imbalances. Although MFH were once thought to be a separate member of the soft tissue sarcoma family, our observations support the hypothesis that MFH are a morphologic modulation in the tumoral progression of other sarcomas, particularly LMS.     

The First 2 Years of Activity of a Specialized Organ Procurement Center: Report of an Innovative Approach to Improve Organ Donation

The number of patients requiring organ transplants continues to outgrow the number of organs donated each year. In an attempt to improve the organ donation process and increase the number of organs available, we created a specialized multidisciplinary team within a specialized organ procurement center (OPC) with dedicated intensive care unit (ICU) beds and operating rooms. The OPC was staffed with ICU nurses, operating room nurses, organ donor management ICU physicians, and multidisciplinary staff. All organ donors within a designated geographic area were transferred to and managed within the OPC. During the first 2 years of operation, 126 patients were referred to the OPC. The OPC was in use for a total of 3527 h and involved 253 health workers. We retrieved 173 kidneys, 95 lungs, 68 livers, 37 hearts, and 13 pancreases for a total of 386 organs offered for transplantation. This translates to a total of 124.6 persons transplanted per million population, which compares most favorably to recently published numbers in developed countries. The OPC clearly demonstrates potential to increase the number of deceased donor organs available for transplant. Further studies are warranted to better understand the exact influence of the different components of the OPC on organ procurement.     

Intranasal fentanyl and inhaled nitrous oxide for fracture reduction: The FAN observational study

Introduction

Procedural sedation and analgesia (PSA) are frequently used for fracture reduction in pediatric emergency departments (ED). Combining intranasal (IN) fentanyl with inhalation of nitrous oxide (N₂O) allow for short recovery time and obviates painful and time-consuming IV access insertions.

Prenatal alcohol exposure and cortisol activity in 19-month-old toddlers: an investigation of the moderating effects of sex and testosterone

Rationale  

Early exposure to stress and teratogenic substances have an impact on brain structures involved in cognition and mental health. While moderate-to-high levels of prenatal alcohol exposure (PAE) have repeatedly been associated with long-term neurodevelopmental deficits, no consensus has yet been reached on the detrimental effects of low-to-moderate PAE on the children’s functioning, including the limbic–hypothalamic–pituitary–adrenal axis.     

Contribution of microCT structural imaging to preclinical evaluation of hepatocellular carcinoma chemotherapeutics on orthotopic graft in ACI rats

Animal experimentation is a prerequisite for preclinical evaluation of treatments such as chemotherapy. It's strictly regulated with the purpose of reducing the number of experimental animal as well as their pain. Small animal imaging should provide a painless longitudinal follow up of tumor progression on a single animal. The aim of the study is to validate small animal imaging by microscanner (μscan) in longitudinal follow up of a hepatocellular carcinoma (HCC) and to demonstrate its interest for in vivo evaluation of tumor response to different therapeutics. An HCC model achieved by orthotopic graft of the MH3924A cell line in ACI rats was followed using a Imtek/Siemens microscanner (μscan) with contrast agents (Fenestra^® LC/VC). The procedures giving the optimal enhancement of the liver as well as a reliable determination of tumor volumes by μscan were validated. Three protocols for therapeutic assessment through μscan longitudinal follow up were performed. Each consisted in three groups testing a chemotherapy (gemcitabine, gemcitabine-oxaliplatine or sorafenib) versus two control groups (placebo and doxorubicine). Comparison was done on tumor volumes, median and actual survivals. There was a significant correlation between tumor volumes measured by μscan and autopsy. Treatment by sorafenib, at the contrary of gemcitabine alone or with oxaliplatine, resulted in a significant reduction in tumor volumes and prolongation of actuarial survival. These results are consistent with available clinical data for these diverse therapeutics. In conclusion, small animal imaging with μscan is a non-invasive, reliable, and reproducible method for preclinical evaluation of antitumor agents.     

Prevalence and characterization of extended-spectrum β-lactamase- and AmpC β-lactamase-producing Escherichia coli: results of the CANWARD 2007-2009 study

The national prevalence of extended-spectrum β-lactamase (ESBL)-producing (2007: 3.4%, 2008: 4.9%, 2009: 4.3%) and AmpC β-lactamase (AmpC)-producing (2007: 0.8%, 2008: 3.2%, 2009: 2.7%) Escherichia coli in Canadian hospitals have fluctuated from 2007 to 2009. Rates of co-resistance to non-lactam agents are elevated, and multidrug-resistant (MDR) phenotype were observed among E. coli strains producing ESBLs (83.3% MDR) and AmpCs (31.0%). The majority (>98%) of isolates remained susceptible to colistin, tigecycline, amikacin, and the carbapenems. CMY-2 encoding gene was detected in 52.9% of AmpC-producing strains, while bla(CTX-M-15) (65.2%) was the predominant ESBL genotype. A total of 50.3% of ESBL-producing E. coli and 21.4% of AmpC producers belonged to the ST131 clone. In conclusion, ESBL- and AmpC-producing E. coli are established in Canadian hospitals; and although the prevalence rates of these isolates remain low, they are often MDR and associated with the ST131 clone.     

Navigating the challenges of prison research with women

Despite the healthcare needs of an increasing number of incarcerated women in the United States, few researchers access this underserved population. The authors provide practical information to help novice researchers navigate potential institutional challenges including obtaining institutional review board approval, gaining entry, complying with rules and regulations, recruiting and retaining participants, and collecting data.